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Fragment-based Drug Discovery Literature to May 2007 © IOTA Pharmaceuticals Ltd |
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Title |
Abstract |
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Abad-Zapatero C, Metz JT. |
Drug Discov Today. 2005 Apr 1;10(7):464-9. No abstract available. |
Successful drug discovery involves the optimization of many variables, such as compound potency, selectivity and solubility. Drug development is an arduous process, beginning with lead selection and continuing through to preclinical testing in animal models. Efficient navigation through these steps should be facilitated by reducing the number of variables. |
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Adrian FJ, Ding Q, Sim T, Velentza A, Sloan C, Liu Y, Zhang G, Hur W, Ding S, Manley P, Mestan J, Fabbro D, Gray NS. |
Nat Chem Biol. 2006 Feb;2(2):95-102. Epub 2006 Jan 15. |
Allosteric inhibitors of Bcr-abl-dependent cell proliferation. |
Chronic myelogenous leukemia (CML) is a myeloproliferative disorder characterized at the molecular level by the expression of Bcr-abl, a 210-kDa fusion protein with deregulated tyrosine kinase activity. Encouraged by the clinical validation of Bcr-abl as the target for the treatment of CML by imatinib, we sought to identify pharmacological agents that could target this kinase by a distinct mechanism. We report the discovery of a new class of Bcr-abl inhibitors using an unbiased differential cytotoxicity screen of a combinatorial kinase-directed heterocycle library. Compounds in this class (exemplified by GNF-2) show exclusive antiproliferative activity toward Bcr-abl-transformed cells, with potencies similar to imatinib, while showing no inhibition of the kinase activity of full-length or catalytic domain of c-abl. We propose that this new class of compounds inhibits Bcr-abl kinase activity through an allosteric non-ATP competitive mechanism. |
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Andrews MJ, Kontopidis G, McInnes C, Plater A, Innes L, Cowan A, Jewsbury P, Fischer PM. |
Chembiochem. 2006 Dec;7(12):1909-15. |
REPLACE: a strategy for iterative design of cyclin-binding groove inhibitors. |
We describe a drug-design strategy termed REPLACE (REplacement with Partial Ligand Alternatives through Computational Enrichment) in which nonpeptidic surrogates for specific determinants of known peptide ligands are identified in silico by using a core peptide-bound protein structure as a design anchor. In the REPLACE application example, we present the effective replacement of two critical binding motifs in a lead protein-protein interaction inhibitor pentapeptide with more druglike phenyltriazole and diphenyl ether groups. These were identified through docking of fragment libraries into the volume of the cyclin-binding groove of CDK2/cyclin A vacated through truncation of the inhibitor peptide-binding determinants. Proof of concept for this strategy was obtained through the generation of potent peptide-small-molecule hybrids and by the confirmation of inhibitor-binding modes in X-ray crystal structures. This method therefore allows nonpeptide fragments to be identified without the requirement for a high-sensitivity binding assay and should be generally applicable in replacing amino acids as individual residues or groups in peptide inhibitors to generate pharmaceutically acceptable lead molecules. |
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Aronov AM, Bemis GW. |
Proteins. 2004 Oct 1;57(1):36-50. |
We present a novel method for stepwise scaffold assembly that integrates fragment-by-fragment ligand design approaches with high-throughput virtual library screening (COREGEN). As an extension of our earlier studies of common features present in drug molecules, we investigate the hypothesis that most pharmaceutically interesting ligands can be expressed in terms of the ring-linker frameworks that comprise them. Analysis of 119 published kinase inhibitors from at least 18 different targets illustrates that a basis set of 4 rings and 8 linkers is sufficient to describe approximately 90% of ring and linker occurrences, respectively. A similar result was derived from a larger set of approximately 40,000 kinase inhibitors from curated patents. A method for ring-linker-based assembly of scaffold libraries that uses experimental information to guide the placement of anchor fragments is validated using a set of reported kinase inhibitors of Bcr-Abl, Cdk2, and Src. In every case, the predominant structural motif of reported ligand cores is reproduced and variations are suggested. To underscore generality of this approach, a novel scaffold for a cyclooxygenase-2 (COX-2) selective ligand is proposed. |
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Babaoglu K, Shoichet BK. |
Nat Chem Biol. 2006 Dec;2(12):720-3. Epub 2006 Oct 29. |
Fragment-based screens test multiple low-molecular weight molecules for binding to a target. Fragments often bind with low affinities but typically have better ligand efficiencies (DeltaG(bind)/heavy atom count) than traditional screening hits. This efficiency, combined with accompanying atomic-resolution structures, has made fragments popular starting points for drug discovery programs. Fragment-based design adopts a constructive strategy: affinity is enhanced either by cycles of functional-group addition or by joining two independent fragments together. The final inhibitor is expected to adopt the same geometry as the original fragment hit. Here we consider whether the inverse, deconstructive logic also applies--can one always parse a higher-affinity inhibitor into fragments that recapitulate the binding geometry of the larger molecule? Cocrystal structures of fragments deconstructed from a known beta-lactamase inhibitor suggest that this is not always the case. |
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Bailey D, Zanders E, Dean P. |
Pharmacogenomics J. 2001;1(1):38-47. |
Site-specific molecular design and its relevance to pharmacogenomics and chemical biology. |
The emergence of the new discipline of pharmacogenomics reflects the growing convergence of chemical and genomic space. The massive information-driven growth in both computational chemistry and structural biology is leading to unprecedented opportunities in both chemical and biological design. In this paper we relate current opinion in structural biology to recent developments in computational drug design. Sequence information now permits protein structure prediction and, together with experimental protein structure determination, a complete database of ligand-binding sites and protein-protein interactions can be assembled. When aligned with site exploration and virtual screening, this information provides a foundation for structure-based pharmacogenomics. In association with chemical genomics, structure-based design will allow major new insights into a compound's biological and pharmaceutical properties. |
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Bailey D, Zanders E, Dean P. |
Nat Biotechnol. 2001 Mar;19(3):207-9. No abstract available. |
[No abstract] |
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Barakat MT, Dean PM. |
J Comput Aided Mol Des. 1995 Oct;9(5):457-62. |
The fragment placement method has been successfully extended to the problem of envelope-directed design. The atom assignment paradigm was based on molecular similarity between two molecular structures. A composite supersurface is defined to form the surface onto which the molecular fields are projected. The assignment process is then determined by using molecular similarity in the objective function to be optimized. In principle, this procedure is closely similar to that outlined in the previous paper for site-directed design. The rationale has been extensively tested on two benzodiazepine antagonists believed to bind to the same site. |
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Barakat MT, Dean PM. |
J Comput Aided Mol Des. 1995 Oct;9(5):448-56. |
Three previous papers in this series have outlined an optimization method for atom assignment in drug design using fragment placement. In this paper the procedure is rigorously tested on a selection of five ligand-protein co-crystals. The algorithm is presented with the molecular graph of the ligand, and the electrostatic/hydrophobic potential of the site, with the aim of creating a placement on the molecular graph which is as electrostatically complementary or hydrophobically similar to the site as possible. Various designer options were tested, including, where appropriate, hydrogen bonding and a restricted number of halogens. In most cases, the placement obtained was at least as good as the native ligand, if not significantly better. |
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Barakat MT, Dean PM. |
J Comput Aided Mol Des. 1995 Aug;9(4):359-72. |
Atom assignment onto 3D molecular graphs is a combinatoric problem in discrete space. If atoms are to be placed efficiently on molecular graphs produced in drug binding sites, the assignment must be optimized. An algorithm, based on simulated annealing, is presented for efficient optimization of fragment placement. Extensive tests of the method have been performed on five ligands taken from the Protein Data Bank. The algorithm is presented with the ligand graph and the electrostatic potential as input. Self placement of molecular fragments was monitored as an objective test. A hydrogen-bond option was also included, to enable the user to highlight specific needs. The algorithm performed well in the optimization, with successful replications. In some cases, a modification was necessary to reduce the tendency to give multiple halogenated structures. This optimization procedure should prove useful for automated de novo drug design. |
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Barakat MT, Dean PM. |
J Comput Aided Mol Des. 1995 Aug;9(4):351-8. |
If atom assignment onto 3D molecular graphs is to be optimized, an efficient scheme for placement must be developed. The strategy adopted in this paper is to analyze the molecular graphs in terms of cyclical and non-cyclical nodes; the latter are further divided into terminal and non-terminal nodes. Molecular fragments, from a fragments database, are described in a similar way. A canonical numbering scheme for the fragments and the local subgraph of the molecular graph enables fragments to be placed efficiently onto the molecular graph. Further optimization is achieved by placing similar fragments into bins using a hashing scheme based on the canonical numbering. The graph perception algorithm is illustrated in detail. |
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Barakat MT, Dean PM. |
J Comput Aided Mol Des. 1995 Aug;9(4):341-50. |
This paper is the first of a series which examines the problems of atom assignment in automated de novo drug design. In subsequent papers, a combinatoric optimization method for fragment placement onto 3D molecular graphs is provided. Molecules are built from molecular graphs by placing fragments onto the graph. Here we examine the transferability of atomic residual charge, by fragment placement, with respect to the electrostatic potential. This transferability has been tested on 478 molecular structures extracted from the Cambridge Structural Database. The correlation found between the electrostatic potential computed from composite fragments and that computed for the whole molecule was encouraging, except for extended conjugated systems. |
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Baurin N, Aboul-Ela F, Barril X, Davis B, Drysdale M, Dymock B, Finch H, Fromont C, Richardson C, Simmonite H, Hubbard RE. |
J Chem Inf Comput Sci. 2004 Nov-Dec;44(6):2157-66. |
We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites. |
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Baurin N, Baker R, Richardson C, Chen I, Foloppe N, Potter A, Jordan A, Roughley S, Parratt M, Greaney P, Morley D, Hubbard RE. |
J Chem Inf Comput Sci. 2004 Mar-Apr;44(2):643-51. |
We have implemented five drug-like filters, based on 1D and 2D molecular descriptors, and applied them to characterize the drug-like properties of commercially available chemical compounds. In addition to previously published filters (Lipinski and Veber), we implemented a filter for medicinal chemistry tractability based on lists of chemical features drawn up by a panel of medicinal chemists. A filter based on the modeling of aqueous solubility (>1 microM) was derived in-house, as well as another based on the modeling of Caco-2 passive membrane permeability (>10 nm/s). A library of 2.7 million compounds was collated from the 23 compound suppliers and analyzed with these filters, highlighting a tendency toward highly lipophilic compounds. The library contains 1.6 M unique structures, of which 37% (607,223) passed all five drug-like filters. None of the 23 suppliers provides all the members of the drug-like subset, emphasizing the benefit of considering compounds from various compound suppliers as a source of diversity for drug discovery. |
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Baurin N, Mozziconacci JC, Arnoult E, Chavatte P, Marot C, Morin-Allory L. |
J Chem Inf Comput Sci. 2004 Jan-Feb;44(1):276-85. |
Using classification (SOM, LVQ, Binary, Decision Tree) and regression algorithms (PLS, BRANN, k-NN, Linear), this paper details the building of eight 2D-QSAR models from a 266 COX-2 inhibitor training set. The predictive performances of these eight models were subsequently compared using an 88 COX-2 inhibitor test set. Each ligand is described by 52 2D descriptors expressed as van der Waals Surface Areas (P_VSA) and its COX-2 binding IC50. One of our best predictive models is the neural network model (BRANN), which is able to select a subset, from the 88 ligand test set, that contains 94% COX-2 active inhibitors (pIC50>7.5) and detects 71% of all the actives. We then introduce a QSAR consensus prediction protocol that is shown to be more predictive than any single QSAR model: our C3 consensus approach is able to select a subset from the 88 ligand test set that contains 94% active inhibitors and 83% of all the actives. The 2D QSAR consensus protocol was finally applied to the high-throughput virtual screening of the NCI database, containing 193,477 organic compounds. |
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Baurin N, Vangrevelinghe E, Morin-Allory L, Merour JY, Renard P, Payard M, Guillaumet G, Marot C. |
J Med Chem. 2000 Mar 23;43(6):1109-22. |
Displaying an unprecedented structural diversity, 119 I(2) ligands, and their pK(i) values, were collected and submitted to a comparative molecular fields analysis (CoMFA) study. They were discerned into three structural subsets (A, B, C), to explore the I(2) 3D-QSARs from finite structural systems (A, B, C) to more complex ones (AB, AC, BC, ABC). In addition, various key steps of the CoMFA methology were explored. The applied method used two pharmacophore templates and seven molecular field combinations (electrostatic, lipophilic, steric), as well as eight alignment methods (two point-by-point and six similarity-based variations). That way, 644 CoMFA models were obtained and further selected according to their predictive ability through two filters. The first filter was mainly based on the q(2), which internally evaluates the predictive ability from the training set. For the second filter, the predictive ability was externally evaluated through the prediction of test sets. Finally, one model was extracted from the whole data as the best. Indeed, it combines three features of upmost importance for the further design of ligands endowed with high I(2) affinity: structural diversity (n = 73), robustness (N = 9, r(2) = 0.96, s = 0. 28, F = 148), and a great fully assessed predictive ability (q(2) = 0.50, r(2)(test set) = 0.81, n(test set) = 46). On the basis of structural data and CoMFA isocontours, some elements of the I(2) tridimensional pharmacophore are also suggested. |
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Bender A, Mussa HY, Glen RC. |
J Biomol Screen. 2005 Oct;10(7):658-66. Epub 2005 Sep 16. |
A fragment-based similarity searching method, MOLPRINT 2D, was employed for virtual screening of Escherichia coli dihydrofolate reductase inhibitors. Using the original training set of 50,000 compounds, only marginal enrichment factors (between 1 and 3) could be achieved on the test library. The active structures contained in the training and test libraries represented different types of "chemistry", that is, different substructural features associated with activity. Training and test sets were pooled in a 2nd step and randomly split into training and test of equal size, with the objective of smoothing out the different chemical characteristics of both libraries. In a 10-fold cross-validation study on the new training and test sets, typically 10-fold enrichment could be found in the first 96 positions, 4-fold enrichment in the first 384 positions, and 3-fold enrichment in the first 1536 positions, corresponding to 6, 10, and 28 hits, respectively (out of a total of 307; activity defined as average residual activity of less than 80%). The conclusions are 2-fold. On one hand, the exact fragment-matching similarity searching method employed here is not capable of finding completely novel hit structures. On the other hand, this study emphasizes the requirement for a comparable distribution of chemical features of the training and test sets. MOLPRINT 2D is freely downloadable from http://www.cheminformatics.org. |
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Blume A, Angulo J, Biet T, Peters H, Benie AJ, Palcic M, Peters T. |
J Biol Chem. 2006 Oct 27;281(43):32728-40. Epub 2006 Aug 21. |
Saturation transfer difference NMR experiments on human blood group B alpha-(1,3)-galactosyltransferase (GTB) for the first time provide a comprehensive set of binding epitopes of donor substrate analogs in relation to the natural donor UDP-Gal. This study revealed that the enzyme binds several UDP-activated sugars, including UDP-Glc, UDP-GlcNAc, and UDP-GalNAc. In all cases, UDP is the dominant binding epitope. To identify the minimum requirements for specific binding, a detailed analysis utilizing a fragment-based approach was employed. The binding of donor substrate to GTB is essentially controlled by the base as a "molecular anchor." Uracil represents the smallest fragment that is recognized, whereas CDP, AMP, and GDP do not exhibit any significant binding affinity for the enzyme. The ribose and beta-phosphate moieties increase the affinity of the ligands, whereas the pyranose sugar apparently weakens the binding, although this part of the molecule controls the specificity of the enzyme. Accordingly, UDP represents the best binder. The binding affinities of UDP-Gal, UDP-Glc, and UMP are about the same, but lower than that of UDP. Furthermore, we observed that beta-D-galactose and alpha-D-galactose bind weakly to GTB. Whereas beta-D-galactose binds to the acceptor and donor sites, it is suggested that alpha-D-galactose occupies a third hitherto unknown binding pocket. Finally, our experiments revealed that modulation of enzymatic activity by metal ions critically depends on the total enzyme concentration, raising the question as to which of the bivalent metal cations Mg(2+) and Mn(2+) is more relevant under physiological conditions. |
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Blume A, Benie AJ, Stolz F, Schmidt RR, Reutter W, Hinderlich S, Peters T. |
J Biol Chem. 2004 Dec 31;279(53):55715-21. Epub 2004 Oct 21. |
The bifunctional enzyme UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase is the key enzyme for the biosynthesis of sialic acids. As terminal components of glycoconjugates, sialic acids are associated with a variety of pathological processes such as inflammation and cancer. For the first time, this study reveals characteristics of the interaction of the epimerase site of the enzyme with its natural substrate, UDP-N-acetylglucosamine (UDP-GlcNAc) and derivatives thereof at atomic resolution. Saturation transfer difference NMR experiments were crucial in obtaining ligand binding epitopes and to rank ligands according to their binding affinities. Employing a fragment based approach, it was possible to assign the major component of substrate recognition to the UDP moiety. In particular, the binding epitopes of the uridine moieties of UMP, UDP, UDP-GalNAc, and UDP-GlcNAc are rather similar, suggesting that the binding mode of the UDP moiety is the same in all cases. In contrast, the hexopyranose units of UDP-GlcNAc and UDP-GalNAc display small differences reflecting the inability of the enzyme to process UDP-GalNAc. Surprisingly, saturation transfer difference NMR titrations show that UDP has the largest binding affinity to the epimerase site and that at least one phosphate group is required for binding. Consequently, this study provides important new data for rational drug design. |
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Blundell TL, Sibanda BL, Montalvao RW, Brewerton S, Chelliah V, Worth CL, Harmer NJ, Davies O, Burke D. |
Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29;361(1467):413-23. Review. |
Impressive progress in genome sequencing, protein expression and high-throughput crystallography and NMR has radically transformed the opportunities to use protein three-dimensional structures to accelerate drug discovery, but the quantity and complexity of the data have ensured a central place for informatics. Structural biology and bioinformatics have assisted in lead optimization and target identification where they have well established roles; they can now contribute to lead discovery, exploiting high-throughput methods of structure determination that provide powerful approaches to screening of fragment binding. |
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Braisted AC, Oslob JD, Delano WL, Hyde J, McDowell RS, Waal N, Yu C, Arkin MR, Raimundo BC. |
J Am Chem Soc. 2003 Apr 2;125(13):3714-5. No abstract available. |
Discovery of a potent small molecule IL-2 inhibitor through fragment assembly. |
Using a site-directed fragment discovery method called tethering, we have identified a 60 nM small molecule antagonist of a cytokine/receptor interaction (IL-2/IL2R) with cell-based activity. Starting with a low micromolar hit, we employed a combination of tethering, structural biology, and computational analysis to design a focused set of 20 compounds. Eight of these compounds were at least 5-fold more active than the original hit. One of these compounds showed a 50-fold enhancement and represents the highest affinity inhibitor reported against this protein-protein target class. This method of coupling selected fragments with a low micromolar hit shows great potential for generating high-affinity lead compounds. |
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Capdeville R, Buchdunger E, Zimmermann J, Matter A. |
Nat Rev Drug Discov. 2002 Jul;1(7):493-502. Review. |
Glivec (STI571, imatinib), a rationally developed, targeted anticancer drug. |
In the early 1980s, it became apparent that the work of pioneers such as Robert Weinberg, Mariano Barbacid and many others in identifying cancer-causing genes in humans was opening the door to a new era in anticancer research. Motivated by this, and by dissatisfaction with the limited efficacy and tolerability of available anticancer modalities, a drug discovery programme was initiated with the aim of rationally developing targeted anticancer therapies. Here, we describe how this programme led to the discovery and continuing development of Glivec (Gleevec in the United States), the first selective tyrosine-kinase inhibitor to be approved for the treatment of a cancer. |
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Card GL, Blasdel L, England BP, Zhang C, Suzuki Y, Gillette S, Fong D, Ibrahim PN, Artis DR, Bollag G, Milburn MV, Kim SH, Schlessinger J, Zhang KY. |
Nat Biotechnol. 2005 Feb;23(2):201-7. Epub 2005 Jan 30. |
Cyclic nucleotide phosphodiesterases (PDEs) comprise a large family of enzymes that regulate a variety of cellular processes. We describe a family of potent PDE4 inhibitors discovered using an efficient method for scaffold-based drug design. This method involves an iterative approach starting with low-affinity screening of compounds followed by high-throughput cocrystallography to reveal the molecular basis underlying the activity of the newly identified compounds. Through detailed structural analysis of the interaction of the initially discovered pyrazole carboxylic ester scaffold with PDE4D using X-ray crystallography, we identified three sites of chemical substitution and designed small selective libraries of scaffold derivatives with modifications at these sites. A 4,000-fold increase in the potency of this PDE4 inhibitor was achieved after only two rounds of chemical synthesis and the structural analysis of seven pyrazole derivatives bound to PDE4B or PDE4D, revealing the robustness of this approach for identifying new inhibitors that can be further developed into drug candidates. |
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Carr RA, Congreve M, Murray CW, Rees DC. |
Drug Discov Today. 2005 Jul 15;10(14):987-92. Review. |
Fragment-based lead discovery (also referred to as needles, shapes, binding elements, seed templates or scaffolds) is a new lead discovery approach in which much lower molecular weight (120-250 Da) compounds are screened relative to HTS campaigns. Fragment-based hits are typically weak inhibitors (10 microM-mM), and therefore need to be screened at higher concentration using very sensitive biophysical detection techniques such as protein crystallography and NMR as the primary screening techniques, rather than bioassays. Compared with HTS hits, these fragments are simpler, less functionalized compounds with correspondingly lower affinity. However, fragment hits typically possess high 'ligand efficiency' (binding affinity per heavy atom) and so are highly suitable for optimization into clinical candidates with good drug-like properties. |
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Carter TA, Wodicka LM, Shah NP, Velasco AM, Fabian MA, Treiber DK, Milanov ZV, Atteridge CE, Biggs WH 3rd, Edeen PT, Floyd M, Ford JM, Grotzfeld RM, Herrgard S, Insko DE, Mehta SA, Patel HK, Pao W, Sawyers CL, Varmus H, Zarrinkar PP, Lockhart DJ. |
Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):11011-6. Epub 2005 Jul 26. |
Inhibition of drug-resistant mutants of ABL, KIT, and EGF receptor kinases. |
To realize the full potential of targeted protein kinase inhibitors for the treatment of cancer, it is important to address the emergence of drug resistance in treated patients. Mutant forms of BCR-ABL, KIT, and the EGF receptor (EGFR) have been found that confer resistance to the drugs imatinib, gefitinib, and erlotinib. The mutations weaken or prevent drug binding, and interestingly, one of the most common sites of mutation in all three kinases is a highly conserved "gatekeeper" threonine residue near the kinase active site. We have identified existing clinical compounds that bind and inhibit drug-resistant mutant variants of ABL, KIT, and EGFR. We found that the Aurora kinase inhibitor VX-680 and the p38 inhibitor BIRB-796 inhibit the imatinib- and BMS-354825-resistant ABL(T315I) kinase. The KIT/FLT3 inhibitor SU-11248 potently inhibits the imatinib-resistant KIT(V559D/T670I) kinase, consistent with the clinical efficacy of SU-11248 against imatinib-resistant gastrointestinal tumors, and the EGFR inhibitors EKB-569 and CI-1033, but not GW-572016 and ZD-6474, potently inhibit the gefitinib- and erlotinib-resistant EGFR(L858R/T790M) kinase. EKB-569 and CI-1033 are already in clinical trials, and our results suggest that they should be considered for testing in the treatment of gefitinib/erlotinib-resistant non-small cell lung cancer. The results highlight the strategy of screening existing clinical compounds against newly identified drug-resistant mutant variants to find compounds that may serve as starting points for the development of next-generation drugs, or that could be used directly to treat patients that have acquired resistance to first-generation targeted therapy. |
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Caskey CT. |
Annu Rev Med. 2007;58:1-16. Review. |
Despite advancements in genetics, chemistry, and protein engineering, recent years have seen fewer approvals of new drugs, increases in development costs, and high-profile drug withdrawals. This article focuses on technologic methods for improving drug development efficiency. These technologies include high-content cell screening, expression profiling, mass spectroscopy, mouse models of disease, and a post-launch screening program that enables investigations of adverse drug effects. Implementation of these new technologies promises to improve performance in drug development and safety. |
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Chau PL, Dean PM. |
J Comput Aided Mol Des. 1994 Oct;8(5):527-44. |
Electrostatic complementarity between proteins and ligands. 2. Ligand moieties. |
Drug design strategies consider factors governing intermolecular interactions to build up putative ligands. In many strategies, the ligand is constructed using fragments which are placed in the site sequentially. The optimization is then performed with each fragment. We would like to examine if this optimization strategy could generate ligands with optimal electrostatic interactions. The electrostatic complementarities between constituent moieties and the receptor site have been calculated. The whole-ligand complementarity does not appear to be the mathematical mean of the individual complementarities, nor have we found a simple relationship between the moiety and whole-ligand complementarities. The results demonstrate clearly that, using a simple model, it is very difficult to predict the electrostatic potential complementarity of the whole ligand from the complementarities of its constituent chemical moieties. This means that ligand design strategies must optimize the electrostatic complementarity globally, and not moiety by moiety. |
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Chau PL, Dean PM. |
J Comput Aided Mol Des. 1992 Aug;6(4):407-26. |
Department of Pharmacology,
University of Cambridge, U.K. |
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Chau PL, Dean PM. |
J Comput Aided Mol Des. 1992 Aug;6(4):397-406. |
In this paper a database of small frequently occurring molecular fragments is used for the determination of fragment bond lengths from the Cambridge Structural Database. A large number of bond types are described that have not been reported previously. |
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Chau PL, Dean PM. |
J Comput Aided Mol Des. 1992 Aug;6(4):385-96. |
If a method is to be developed to assemble putative ligand structures in site-directed drug design, from molecular graphs generated in the site, then basic building blocks are needed. Structure assembly is a combinatoric process that needs to be optimised if it is to be tractable. What has to be determined is whether small molecular fragments can have transferable properties from one molecule to another. In this paper we determine all possible combinations of 3-, 4- and 5-atom aliphatic fragments from a small set of atoms H, C, N, O, F or Cl. The frequency of occurrence of these candidate fragments is searched for in the Cambridge Structural Database. A similar analysis is performed on charged fragments. A more restricted search is carried out for P and S and aromatic structures. A basic set of fragments can be derived that have a significant frequency in known crystal structures. The transferability of fragment properties is discussed in subsequent papers. |
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Chavatte P, Yous S, Marot C, Baurin N, Lesieur D. |
J Med Chem. 2001 Sep 27;44(20):3223-30. |
The three-dimensional quantitative structure-activity relationship (3D-QSAR) approach using comparative molecular field analysis (CoMFA) was applied to an extensive series of 305 varied diarylheterocyclic derivatives known as COX-2 selective inhibitors. X-ray crystal structure of COX-2 bound with SC-558, a selective COX-2 inhibitor, was used to derive the putative bioactive conformation of these inhibitors. Five statistically significant models were obtained from the randomly constituted training sets (229 compounds) and subsequently validated with the corresponding test sets (76 compounds). The best predictive model (n = 229, q(2) = 0.714, N = 8, r(2) = 0.905, s = 0.291, F = 261.545) was selected for further comparison of the CoMFA contour maps obtained for steric, electrostatic, and lipophilic fields with the enzyme structure. The high level of compatibility with the COX-2 enzyme topology shows the great accuracy of this model that can predict inhibitory activities for a wide range of compounds and offers important structural insight into designing novel antiinflammatory drugs prior to their synthesis. |
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Cherry M, Williams DH. |
Curr Med Chem. 2004 Mar;11(6):663-73. Review. |
Recent years have seen an explosion in the number of publicly available x-ray crystal structures of protein kinases. These structures have provided a wealth of information on the regulatory mechanisms, conformational plasticity and drugability of this important family of enzymes. Drawing upon structural information, new insights into the development of protein kinase inhibitors are discussed including de-novo design, molecular templates for ATP competitive inhibitors and alternative mechanisms of inhibition. The highly conserved nature of the ATP binding site is of central concern to drug development and the concept of a selectivity profile has arisen with structure-based design emerging as a key tool for addressing the challenges of specificity. In addition, protein-ligand complexes, where the enzyme is in an inactive conformation, signify an alternate approach to protein kinase inhibition. The belief that an inactive kinase presents a less conserved target is reviewed using observations on the structural changes occurring during protein kinase regulation. |
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Choong IC, Lew W, Lee D, Pham P, Burdett MT, Lam JW, Wiesmann C, Luong TN, Fahr B, DeLano WL, McDowell RS, Allen DA, Erlanson DA, Gordon EM, O'Brien T. |
J Med Chem. 2002 Nov 7;45(23):5005-22. |
The design, synthesis, and in vitro activities of a series of potent and selective small-molecule inhibitors of caspase-3 are described. From extended tethering, a salicylic acid fragment was identified as having binding affinity for the S(4) pocket of caspase-3. X-ray crystallography and molecular modeling of the initial tethering hit resulted in the synthesis of 4, which reversibly inhibited caspase-3 with a K(i) = 40 nM. Further optimization led to the identification of a series of potent and selective inhibitors with K(i) values in the 20-50 nM range. One of the most potent compounds in this series, 66b, inhibited caspase-3 with a K(i) = 20 nM and selectivity of 8-500-fold for caspase-3 vs a panel of seven caspases (1, 2, and 4-8). A high-resolution X-ray cocrystal structure of 4 and 66b supports the predicted binding modes of our compounds with caspase-3. |
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Ciulli A, Lobley CM, Tuck KL, Smith AG, Blundell TL, Abell C. |
Acta Crystallogr D Biol Crystallogr. 2007 Feb;63(Pt 2):171-8. Epub 2007 Jan 16. |
The crystal structure of Escherichia coli ketopantoate reductase in complex with 2'-monophosphoadenosine 5'-diphosphoribose, a fragment of NADP+ that lacks the nicotinamide ring, is reported. The ligand is bound at the enzyme active site in the opposite orientation to that observed for NADP+, with the adenine ring occupying the lipophilic nicotinamide pocket. Isothermal titration calorimetry with R31A and N98A mutants of the enzyme is used to show that the unusual ;reversed binding mode' observed in the crystal is triggered by changes in the protonation of binding groups at low pH. This research has important implications for fragment-based approaches to drug design, namely that the crystallization conditions and the chemical modification of ligands can have unexpected effects on the binding modes. |
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Ciulli A, Williams G, Smith AG, Blundell TL, Abell C. |
J Med Chem. 2006 Aug 10;49(16):4992-5000. |
Mapping interactions at protein-ligand binding sites is an important aspect of understanding many biological reactions and a key part of drug design. In this paper, we have used a fragment-based approach to probe "hot spots" at the cofactor-binding site of a model dehydrogenase, Escherichia coli ketopantoate reductase. Our strategy involved the breaking down of NADPH (Kd = 300 nM) into smaller fragments and the biophysical characterization of their binding using WaterLOGSY NMR spectroscopy, isothermal titration calorimetry (ITC), and inhibition studies. The weak binding affinities of fragments were measured by direct ITC titrations under low c value conditions. The 2'-phosphate and the reduced nicotinamide groups were found to contribute a large part of the binding energy. A combination of ITC and site-directed mutagenesis enabled us to locate the fragments at separate hot spots on opposite ends of the cofactor-binding site. This study has identified structural determinants for cofactor recognition that represent a blueprint for future inhibitor design. |
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Clark LA, Boriack-Sjodin PA, Eldredge J, Fitch C, Friedman B, Hanf KJ, Jarpe M, Liparoto SF, Li Y, Lugovskoy A, Miller S, Rushe M, Sherman W, Simon K, Van Vlijmen H. |
Protein Sci. 2006 May;15(5):949-60. Epub 2006 Apr 5. |
Improving the affinity of a high-affinity protein-protein interaction is a challenging problem that has practical applications in the development of therapeutic biomolecules. We used a combination of structure-based computational methods to optimize the binding affinity of an antibody fragment to the I-domain of the integrin VLA1. Despite the already high affinity of the antibody (Kd approximately 7 nM) and the moderate resolution (2.8 A) of the starting crystal structure, the affinity was increased by an order of magnitude primarily through a decrease in the dissociation rate. We determined the crystal structure of a high-affinity quadruple mutant complex at 2.2 A. The structure shows that the design makes the predicted contacts. Structural evidence and mutagenesis experiments that probe a hydrogen bond network illustrate the importance of satisfying hydrogen bonding requirements while seeking higher-affinity mutations. The large and diverse set of interface mutations allowed refinement of the mutant binding affinity prediction protocol and improvement of the single-mutant success rate. Our results indicate that structure-based computational design can be successfully applied to further improve the binding of high-affinity antibodies. |
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Clark M, Guarnieri F, Shkurko I, Wiseman J. |
J Chem Inf Model. 2006 Jan-Feb;46(1):231-42. |
Grand canonical Monte Carlo simulation of ligand-protein binding. |
A new application of the grand canonical thermodynamics ensemble to compute ligand-protein binding is described. The described method is sufficiently rapid that it is practical to compute ligand-protein binding free energies for a large number of poses over the entire protein surface, thus identifying multiple putative ligand binding sites. In addition, the method computes binding free energies for a large number of poses. The method is demonstrated by the simulation of two protein-ligand systems, thermolysin and T4 lysozyme, for which there is extensive thermodynamic and crystallographic data for the binding of small, rigid ligands. These low-molecular-weight ligands correspond to the molecular fragments used in computational fragment-based drug design. The simulations correctly identified the experimental binding poses and rank ordered the affinities of ligands in each of these systems. |
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Coles M, Heller M, Kessler H. |
Drug Discov Today. 2003 Sep 1;8(17):803-10. Review. |
NMR-based ligand screening is now an established field in its own right. In recent years, advances in both methodology and hardware have broadened its range of applications and pushed back practical limitations, leading to the growing importance of NMR screening as a tool in industrial drug research. An overview of new screening methods and applications is presented here, and ways in which NMR-screening is being used in cooperation with other screening techniques are discussed. |
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Congreve M, Aharony D, Albert J, Callaghan O, Campbell J, Carr RA, Chessari G, Cowan S, Edwards PD, Frederickson M, McMenamin R, Murray CW, Patel S, Wallis N. |
J Med Chem. 2007 Mar 22;50(6):1124-32. Epub 2007 Feb 22. |
Fragment-based lead discovery has been successfully applied to the aspartyl protease enzyme beta-secretase (BACE-1). Fragment hits that contained an aminopyridine motif binding to the two catalytic aspartic acid residues in the active site of the enzyme were the chemical starting points. Structure-based design approaches have led to identification of low micromolar lead compounds that retain these interactions and additionally occupy adjacent hydrophobic pockets of the active site. These leads form two subseries, for which compounds 4 (IC50 = 25 microM) and 6c (IC50 = 24 microM) are representative. In the latter series, further optimization has led to 8a (IC50 = 690 nM). |
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Congreve M, Carr R, Murray C, Jhoti H. |
Drug Discov Today. 2003 Oct 1;8(19):876-7. No abstract available. |
Recent literature has addressed the properties of small molecules that are required to produce good lead compounds. Lipinski's Rule of Five, as discussed recently in Drug Discovery Today, provided the original framework for the development of orally bioavailable drug candidates. These rules have been enhanced by others, such as Veber and co-workers, who discovered that the number of rotatable bonds (NROT) is an important parameter, a maximum of seven seeming to be optimal for oral bioavailability. Literature also indicates that polar surface area (PSA) is another key property; passively absorbed molecules with a PSA of 110–140 Å2 are thought to have low oral bioavailabilities. Recently, the term ‘lead-like’ was introduced for molecules identified from HTS campaigns that were suitable for optimization and that have properties relatively ‘scaled-down’ in comparison to the Lipinski values. The body of literature is addressing the issues facing compounds that are discovered by screening of drug-size compound libraries. A novel, alternative approach has recently emerged and is referred to as ‘fragment-based’ discovery. Using this approach, the hits identified generally obey a ‘Rule of Three’ and this could be a useful rule for the construction of fragment libraries for lead generation. |
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Dalvit C, Ardini E, Flocco M, Fogliatto GP, Mongelli N, Veronesi M. |
J Am Chem Soc. 2003 Nov 26;125(47):14620-5. |
A general NMR method for rapid, efficient, and reliable biochemical screening. |
High-throughput screening is usually the method of drug-lead discovery. It is now well accepted that, for a functional assay, quality is more important than quantity. The ligand-based or protein-based NMR screening methodologies for detecting compounds binding to the macromolecular target of interest are now well established. A novel and sensitive NMR method for rapid, efficient, and reliable biochemical screening is presented. The method named 3-FABS (three fluorine atoms for biochemical screening) requires the labeling of the substrate with a CF(3) moiety and utilizes (19)F NMR spectroscopy for the detection of the starting and enzymatically modified substrates. The method allows for high-quality screening of large compound or natural product extract collections and for measuring their IC(50) values. Applications of this technique to the screening of inhibitors of the Ser/Thr kinase AKT1 and the protease trypsin are presented. In addition, an interesting application of 3-FABS to functional genomics is also presented. |
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Dalvit C, Ardini E, Fogliatto GP, Mongelli N, Veronesi M. |
Drug Discov Today. 2004 Jul 15;9(14):595-602. Review. |
An NMR method called 3-FABS has extended the capabilities of NMR, enabling rapid, efficient and reliable high-throughput functional screening for the identification of inhibitors and for measuring their 50% mean inhibition concentration (IC(50)) with accuracy. The substrate is tagged with a CF(3) moiety and (19)F NMR spectroscopy is used for the detection of the substrate and product components. We provide comprehensive insight into 3-FABS, a discussion of its strength and weakness when compared with other HTS techniques and a presentation of some of its applications to the screening of different enzymes and to multiple screening. |
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Dalvit C, Fagerness PE, Hadden DT, Sarver RW, Stockman BJ. |
J Am Chem Soc. 2003 Jun 25;125(25):7696-703. |
Competition ligand-based NMR screening experiments have recently been introduced to overcome most of the problems associated with traditional ligand-based NMR screening. Molecules with marginal solubility and high affinity for a given target can be easily identified in a high-throughput manner by screening chemical mixtures against the target in the presence of a weak- to medium-affinity ligand of known binding constant. While the original competition-based approaches utilized (1)H detection, significant advantages are obtained using (19)F detection. The absence of spectral overlap permits the screening of large chemical mixtures and allows for automated analysis of the spectra, even in the presence of protonated buffers, solvents, and detergents. The large chemical shift anisotropy of fluorine and the significant exchange contribution allow for the selection of a weak-affinity spy molecule, thus resulting in a lower binding affinity threshold for the identified NMR hits. The method, labeled FAXS (fluorine chemical shift anisotropy and exchange for screening) is rapid and requires only a limited amount of protein and, therefore, compares favorably with the other established non-NMR techniques used in high-throughput screening. Herein the theoretical aspects of this powerful (19)F-based approach are presented and discussed in detail. The experimental conditions together with the detection limits and binding constant measurements are investigated using human serum albumin as the target. |
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Dalvit C, Fagerness PE, Hadden DT, Sarver RW, Stockman BJ. |
J Am Chem Soc. 2003 Jun 25;125(25):7696-703. |
Competition ligand-based NMR screening experiments have recently been introduced to overcome most of the problems associated with traditional ligand-based NMR screening. Molecules with marginal solubility and high affinity for a given target can be easily identified in a high-throughput manner by screening chemical mixtures against the target in the presence of a weak- to medium-affinity ligand of known binding constant. While the original competition-based approaches utilized (1)H detection, significant advantages are obtained using (19)F detection. The absence of spectral overlap permits the screening of large chemical mixtures and allows for automated analysis of the spectra, even in the presence of protonated buffers, solvents, and detergents. The large chemical shift anisotropy of fluorine and the significant exchange contribution allow for the selection of a weak-affinity spy molecule, thus resulting in a lower binding affinity threshold for the identified NMR hits. The method, labeled FAXS (fluorine chemical shift anisotropy and exchange for screening) is rapid and requires only a limited amount of protein and, therefore, compares favorably with the other established non-NMR techniques used in high-throughput screening. Herein the theoretical aspects of this powerful (19)F-based approach are presented and discussed in detail. The experimental conditions together with the detection limits and binding constant measurements are investigated using human serum albumin as the target. |
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Dalvit C, Flocco M, Knapp S, Mostardini M, Perego R, Stockman BJ, Veronesi M, Varasi M. |
J Am Chem Soc. 2002 Jul 3;124(26):7702-9. |
High-throughput NMR-based screening with competition binding experiments. |
The Achilles heel of ligand-based NMR screening methods is their failure to detect high-affinity ligands and molecules that bind covalently to the receptor. We have developed a novel approach for performing high-throughput screening with NMR spectroscopy that overcomes this limitation. The method also permits detection of potential high-affinity molecules that are only marginally soluble, thus significantly enlarging the diversity of compounds amenable to NMR screening. The techniques developed utilize transverse and/or selective longitudinal relaxation parameters in combination with competition binding experiments. Mathematical expressions are derived for proper setup of the NMR experiments and for extracting an approximate value of the binding constant for the identified ligand from a single-point measurement. With this approach it is possible to screen thousands of compounds in a short period of time against protein or DNA and RNA fragments. The methodology can also be applied for screening plant and fungi extracts. |
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Dalvit C, Flocco M, Stockman BJ, Veronesi M. |
Comb Chem High Throughput Screen. 2002 Dec;5(8):645-50. Review. |
Many lead molecules that have high affinity for a therapeutic target in vitro exhibit a reduced efficacy in vivo. Drug binding to human serum albumin is a major contributor to this reduction in potency, and many drug discovery programs expand significant resources preparing compounds that have decreased albumin binding. As rational and structure-based approaches have already been demonstrated to design compounds that have reduced affinity for albumin, the ability to rapidly and accurately assess protein binding will be valuable in lead optimization. This review will summarize some of the NMR-based efforts towards developing universal, rapid, accurate, and site-specific assays for estimating protein binding. |
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Dalvit C, Flocco M, Veronesi M, Stockman BJ. |
Comb Chem High Throughput Screen. 2002 Dec;5(8):605-11. |
High-throughput ligand-based NMR screening with competition binding experiments is extended to (19)F detection. Fluorine is a favorable nucleus for these experiments because of the significant contribution of the Chemical Shift Anisotropy (CSA) to the (19)F transverse relaxation of the ligand signal when bound to a macromolecular target. A low to moderate affinity ligand containing a fluorine atom is used as a reference molecule for the detection and characterization of new ligands. Titration NMR experiments with the selected reference compound are performed for finding the optimal set-up conditions for HTS and for deriving the binding constants of the identified NMR hits. Rapid HTS of large chemical mixtures and plant or fungi extracts against the receptor of interest is possible due to the high sensitivity of the (19)F nucleus and the absence of overlap with the signals of the mixtures to be screened. Finally, a novel approach for HTS using a reference molecule in combination with a control molecule is presented. |
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Dalvit C, Flocco M, Veronesi M, Stockman BJ. |
Comb Chem High Throughput Screen. 2002 Dec;5(8):605-11. |
High-throughput ligand-based NMR screening with competition binding experiments is extended to (19)F detection. Fluorine is a favorable nucleus for these experiments because of the significant contribution of the Chemical Shift Anisotropy (CSA) to the (19)F transverse relaxation of the ligand signal when bound to a macromolecular target. A low to moderate affinity ligand containing a fluorine atom is used as a reference molecule for the detection and characterization of new ligands. Titration NMR experiments with the selected reference compound are performed for finding the optimal set-up conditions for HTS and for deriving the binding constants of the identified NMR hits. Rapid HTS of large chemical mixtures and plant or fungi extracts against the receptor of interest is possible due to the high sensitivity of the (19)F nucleus and the absence of overlap with the signals of the mixtures to be screened. Finally, a novel approach for HTS using a reference molecule in combination with a control molecule is presented. |
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Dalvit C, Hadden DT, Sarver RW, Ho AM, Stockman BJ. |
Comb Chem High Throughput Screen. 2003 Aug;6(5):445-53. Review. |
High-throughput ligand-based proton NMR screening performed in the presence of a spy molecule and a control molecule is a valuable tool for identifying drug leads. A limitation of the technique is represented by the severe overlap encountered in the screening of large chemical mixtures. An approach for overcoming this overlap problem is the use of multi-selective R(1) filtered and COSY or TOCSY experiments. Application of this methodology to compounds binding to the Sudlow site I of human serum albumin is presented. The screening is performed by simply monitoring the intensity of two signals. The precise measurement of the relative intensity of the two resonances permits determination of the binding constant of the NMR-hit. For a simple competition binding mechanism, the rapidly-derived NMR binding constants are in good agreement with the values derived from full-titration ITC and fluorescence spectroscopy measurements. |
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Dalvit C, Mongelli N, Papeo G, Giordano P, Veronesi M, Moskau D, Kummerle R. |
J Am Chem Soc. 2005 Sep 28;127(38):13380-5. |
NMR-based binding and functional screening performed with FAXS (fluorine chemical shift anisotropy and exchange for screening) and 3-FABS (three fluorine atoms for biochemical screening) represents a potential alternative approach to high-throughput screening for the identification of novel potential drug candidates. The major limitation of this method in its current status is its intrinsic low sensitivity that limits the number of tested compounds. One approach for overcoming this problem is the use of a cryogenically cooled (19)F probe that reduces the thermal noise in the receiver circuitry. Sensitivity improvement in the two screening techniques achieved with the novel cryogenic (19)F probe technology permits an increased throughput, detection of weaker binders and inhibitors (relevant in a fragment-based lead discovery program), detection of slow binders, and reduction in protein and substrate consumption. These aspects are analyzed with theoretical simulations and experimental quantitative performance evaluation. Application of 3-FABS combined with the cryogenic (19)F probe technology to rapid screening at very low enzyme concentrations and the current detection limits reached with this approach are also presented. |
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Davies TG, Verdonk ML, Graham B, Saalau-Bethell S, Hamlett CC, McHardy T, Collins I, Garrett MD, Workman P, Woodhead SJ, Jhoti H, Barford D. |
J Mol Biol. 2007 Mar 30;367(3):882-94. Epub 2007 Jan 9. |
A structural comparison of inhibitor binding to PKB, PKA and PKA-PKB chimera. |
Although the crystal structure of the anti-cancer target protein kinase B (PKBbeta/Akt-2) has been useful in guiding inhibitor design, the closely related kinase PKA has generally been used as a structural mimic due to its facile crystallization with a range of ligands. The use of PKB-inhibitor crystallography would bring important benefits, including a more rigorous understanding of factors dictating PKA/PKB selectivity, and the opportunity to validate the utility of PKA-based surrogates. We present a "back-soaking" method for obtaining PKBbeta-ligand crystal structures, and provide a structural comparison of inhibitor binding to PKB, PKA, and PKA-PKB chimera. One inhibitor presented here exhibits no PKB/PKA selectivity, and the compound adopts a similar binding mode in all three systems. By contrast, the PKB-selective inhibitor A-443654 adopts a conformation in PKB and PKA-PKB that differs from that with PKA. We provide a structural explanation for this difference, and highlight the ability of PKA-PKB to mimic the true PKB binding mode in this case. |
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Dean PM, Wakelin LP. |
Philos Trans R Soc Lond B Biol Sci. 1979 Dec 7;287(1025):571-604. No abstract available. |
[No abstract] |
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Dean PM, Zanders ED, Bailey DS. |
Trends Biotechnol. 2001 Aug;19(8):288-92. |
The demands on drug discovery organizations have increased dramatically in recent years, partly because of the need to identify novel targets that are both relevant to disease and chemically tractable. This is leading to an industrial approach to traditional biology and chemistry, inspired in part by the revolution in genomics. The purpose of this article is to highlight the flow of investigation from gene sequence of potential therapeutic targets, through mRNA and protein expression, to protein structure and drug design. To deal with this scale of activity, many commercial and public organizations have been established and some of the key players will be listed in this article. |
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Degen J, Rarey M. |
ChemMedChem. 2006 Aug;1(8):854-68. |
FlexNovo: structure-based searching in large fragment spaces. |
We present a new molecular design program, FlexNovo, for structure-based searching within large fragment spaces following a sequential growth strategy. The fragment spaces consist of several thousands of chemical fragments and a corresponding set of rules that specify how the fragments can be connected. FlexNovo is based on the FlexX molecular docking software and makes use of its incremental construction algorithm and the underlying chemical models. Interaction energies are calculated by using standard scoring functions. Several placement geometry, physicochemical property (drug-likeness), and diversity filter criteria are directly integrated into the "build-up" process. FlexNovo has been used to design potential inhibitors for four targets of pharmaceutical interest (dihydrofolate reductase, cyclin-dependant kinase 2, cyclooxygenase-2, and the estrogen receptor). We have carried out calculations using different diversity parameters for each of these targets and generated solution sets containing up to 50 molecules. The compounds obtained show that FlexNovo is able to generate a diverse set of reasonable molecules with drug-like properties. The results, including an automated similarity analysis with the Feature Tree program, indicate that FlexNovo often reproduces structural motifs as well as the corresponding binding modes seen in known active structures. |
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Dickopf S, Frank M, Junker HD, Maier S, Metz G, Ottleben H, Rau H, Schellhaas N, Schmidt K, Sekul R, Vanier C, Vetter D, Czech J, Lorenz M, Matter H, Schudok M, Schreuder H, Will DW, Nestler HP. |
Anal Biochem. 2004 Dec 1;335(1):50-7. |
Custom chemical microarray production and affinity fingerprinting for the S1 pocket of factor VIIa. |
The goal of this study was to explore the applicability of surface plasmon resonance (SPR)-based fragment screening to identify compounds that bind to factor VIIa (FVIIa). Based on pharmacophore models virtual screening approaches, we selected fragments anticipated to have a reasonable chance of binding to the S1-binding pocket of FVIIa and immobilized these compounds on microarrays. In affinity fingerprinting experiments, a number of compounds were identified to be specifically interacting with FVIIa and shown to fall into four structural classes. The results demonstrate that the chemical microarray technology platform using SPR detection generates unique chemobiological information that is useful for de novo discovery and lead development and allows the detection of weak interactions with ligands of low molecular weight. |
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Diercks T, Coles M, Kessler H. |
Curr Opin Chem Biol. 2001 Jun;5(3):285-91. Review. |
NMR, already some 50 years old, has long been an invaluable analytical method in industry for verification of chemical synthesis and compound characterisation. The range of molecular information accessible through NMR, however, offers a far larger horizon of applications. Of these, ligand screening by NMR has emerged as a very promising new method in drug discovery. Its unmatched screening sensitivity, combined with the abundance of available information on the structure and nature of molecular binding, justifies the growing interest in this dynamically expanding NMR application. |
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Disingrini T, Muth M, Dallanoce C, Barocelli E, Bertoni S, Kellershohn K, Mohr K, De Amici M, Holzgrabe U. |
J Med Chem. 2006 Jan 12;49(1):366-72. |
A novel series of muscarinic receptor ligands of the hexamethonio-type was prepared which contained, on one side, the phthalimidopropane or 1,8-naphthalimido-2,2-dimethylpropane moiety typical for subtype selective allosteric antagonists and, on the other, the acetylenic fragment typical for the nonselective orthosteric muscarinic agonists oxotremorine, oxotremorine-M, and related muscarinic agonists. Binding experiments in M(2) receptors using [(3)H]N-methylscopolamine as an orthosteric probe proved an allosteric action of both groups of hybrids, 7a-10a and 8b-10b. The difference in activity between a-group and b-group hybrids corresponded with the activity difference between the allosteric parent compounds. In M(1)-M(3) muscarinic isolated organ preparations, most of the hybrids behaved as subtype selective antagonists. [(35)S]GTPgammaS binding assays using human M(2) receptors overexpressed in CHO cells revealed that a weak intrinsic efficacy was preserved in 8b-10b. Thus, attaching muscarinic allosteric antagonist moieties to orthosteric muscarinic agonists may lead to hybrid compounds in which functions of both components are mixed. |
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Donald A, McHardy T, Rowlands MG, Hunter LJ, Davies TG, Berdini V, Boyle RG, Aherne GW, Garrett MD, Collins I. |
J Med Chem. 2007 May 17;50(10):2289-92. Epub 2007 Apr 24. |
Rapid Evolution of 6-Phenylpurine Inhibitors of Protein Kinase B through Structure-Based Design. |
6-Phenylpurines were identified as novel, ATP-competitive inhibitors of protein kinase B (PKB/Akt) from a fragment-based screen and were rapidly progressed to potent compounds using iterative protein-ligand crystallography with a PKA-PKB chimeric protein. An elaborated lead compound showed cell growth inhibition and effects on cellular signaling pathways characteristic of PKB inhibition. |
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Eggeling C, Brand L, Ullmann D, Jager S. |
Drug Discov Today. 2003 Jul 15;8(14):632-41. Review. |
Highly sensitive fluorescence detection technology currently available for HTS. |
Homogeneous fluorescence methods are providing an important tool for HTS technologies. A wide range of different techniques have been established on the market, with read-outs ranging from total fluorescence intensity to statistical analysis of fluorescence fluctuations for biochemical assays or fluorescence imaging techniques for cellular systems. Each method has its own advantages and limitations, which have to be accounted for when designing a specific assay. Here, recently developed fluorescence techniques and some of their applications, with a particular focus on sensitivity, are summarized and their principles are presented. |
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Erlanson DA, Hansen SK. |
Curr Opin Chem Biol. 2004 Aug;8(4):399-406. Review. |
Making drugs on proteins: site-directed ligand discovery for fragment-based lead assembly. |
Rapid progress in genomics and proteomics has provided a wealth of new targets for the pharmaceutical industry, even as many older targets still remain challenging for small-molecule drug discovery. Fragment-based lead discovery, in which leads are built progressively by expanding or combining small fragments, is a rapidly growing field that offers potential advantages over traditional lead-discovery processes. However, identifying and assembling the fragments themselves can be challenging. Here, we review the concept of site-directed ligand discovery, in which a covalent bond is used to stabilize the interaction between a low-affinity fragment and a target protein. We also describe how this technique can facilitate fragment-based lead discovery and help overcome some of the limitations of traditional screening methods. |
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Erlanson DA, McDowell RS, O'Brien T. |
J Med Chem. 2004 Jul 1;47(14):3463-82. Review. No abstract available. |
[No abstract] |
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Erlanson DA, Wells JA, Braisted AC. |
Annu Rev Biophys Biomol Struct. 2004;33:199-223. Review. |
The genomics revolution has provided a deluge of new targets for drug discovery. To facilitate the drug discovery process, many researchers are turning to fragment-based approaches to find lead molecules more efficiently. One such method, Tethering1, allows for the identification of small-molecule fragments that bind to specific regions of a protein target. These fragments can then be elaborated, combined with other molecules, or combined with one another to provide high-affinity drug leads. In this review we describe the background and theory behind Tethering and discuss its use in identifying novel inhibitors for protein targets including interleukin-2 (IL-2), thymidylate synthase (TS), protein tyrosine phosphatase 1B (PTP-1B), and caspases. |
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Erlanson DA. |
Curr Opin Biotechnol. 2006 Dec;17(6):643-52. Epub 2006 Nov 3. Review. |
Fragment-based lead discovery constructs drug leads from small molecular fragments. In theory, this is a highly efficient method for drug discovery, and the technique has become enormously popular in the past few years. In this review, I describe how a variety of approaches in fragment-based lead discovery--including NMR, X-ray crystallography, mass spectrometry, functional screening, and in silico screening--have produced drug leads. Although the examples show that the technique can reliably generate potent molecules, there is still much work to be done to maintain the efficiency of molecules' binding affinities as fragments are linked, expanded, and otherwise improved. |
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Estrada E, Uriarte E, Molina E, Simon-Manso Y, Milne GW. |
J Chem Inf Model. 2006 Nov-Dec;46(6):2709-24. |
An integrated in silico analysis of drug-binding to human serum albumin. |
Approaches such as quantitative structure-activity relationships (QSAR) and molecular modeling are integrated with the study of complex networks to understand drug binding to human serum albumin (HSA). A robust QSAR model using the topological substructural molecular descriptors/design (TOPS-MODE) approach has been derived and shows good predictability and interpretability in terms of structural contribution to drug binding to HSA. A perfect agreement exists between the group/fragment contributions found by TOPS-MODE and the specific interactions of drugs with HSA. These results indicate a preponderant contribution of hydrophobic regions of drugs to the specific binding to drug-binding sites 1 and 2 in HSA and specific roles of polar groups which anchor drugs to HSA binding sites. The occurrence of fragments contributing to drug binding to HSA can be represented by complex networks. The fragment-to-fragment complex network displays "small-world" and "scale-free" characteristics and in this way is similar to other complex networks including biological, social, and technological networks. A small number of fragments appear very frequently in most drugs. These molecular "empathic" fragments are good candidates for guiding future drug discovery research. |
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Fabian MA, Biggs WH 3rd, Treiber DK, Atteridge CE, Azimioara MD, Benedetti MG, Carter TA, Ciceri P, Edeen PT, Floyd M, Ford JM, Galvin M, Gerlach JL, Grotzfeld RM, Herrgard S, Insko DE, Insko MA, Lai AG, Lelias JM, Mehta SA, Milanov ZV, Velasco AM, Wodicka LM, Patel HK, Zarrinkar PP, Lockhart DJ. |
Nat Biotechnol. 2005 Mar;23(3):329-36. Epub 2005 Feb 13. |
A small molecule-kinase interaction map for clinical kinase inhibitors. |
Kinase inhibitors show great promise as a new class of therapeutics. Here we describe an efficient way to determine kinase inhibitor specificity by measuring binding of small molecules to the ATP site of kinases. We have profiled 20 kinase inhibitors, including 16 that are approved drugs or in clinical development, against a panel of 119 protein kinases. We find that specificity varies widely and is not strongly correlated with chemical structure or the identity of the intended target. Many novel interactions were identified, including tight binding of the p38 inhibitor BIRB-796 to an imatinib-resistant variant of the ABL kinase, and binding of imatinib to the SRC-family kinase LCK. We also show that mutations in the epidermal growth factor receptor (EGFR) found in gefitinib-responsive patients do not affect the binding affinity of gefitinib or erlotinib. Our results represent a systematic small molecule-protein interaction map for clinical compounds across a large number of related proteins. |
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Fattori D. |
Drug Discov Today. 2004 Mar 1;9(5):229-38. Review. |
Molecular recognition: the fragment approach in lead generation. |
The successful practice of medicinal chemistry is crucially dependent on the principles of molecular recognition: the first and "fundamental" requirement for a drug is to bind to its target; specificity, or at least selectivity, of binding is also a must. Subsequent optimization steps to develop a lead compound into a drug are a complex mixture of processes that are not yet fully understood or predictable. Fortunately, criteria exist to discard leads that would be intractable for optimization. The concepts of non-lead-likeness and lead-likeness, in respect to drug-likeness and non-drug-likeness, have prompted a rich discussion in the recent medicinal chemistry literature. The fragment approach is an emerging philosophy in the process of lead compound discovery. The basic interactions responsible for binding affinity are defined from the "protein interactions world" and key structural fragments are combined according to the criteria of three-dimensional diversity to find new leads. New techniques in screening are used for the detection of the weaker interactions of fragments with their targets that might be undetectable in classical biological assays. |
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Fattorusso R, Jung D, Crowell KJ, Forino M, Pellecchia M. |
J Med Chem. 2005 Mar 10;48(5):1649-56. |
In this paper, we report a simple structure-based iterative optimizations (SUBITO) strategy to identify and optimize new protein ligands and inhibitors. The approach is based on a combination of NMR-based screening and computational docking methods and enabled the identification of novel chemical leads among hundreds of thousands of commercially available compounds by screening only a few hundred compounds from a scaffold library followed by iterative screening steps where only few dozen compounds are tested. As an application, we report on the discovery of a novel class of non-peptide reversible caspase inhibitors, with IC(50) values in the low micromolar range. |
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Fauman EB, Hopkins AL, Groom CR. |
Methods Biochem Anal. 2003;44:477-97. Review. No abstract available. |
[No abstract] |
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Fechner U, Schneider G. |
J Chem Inf Model. 2006 Mar-Apr;46(2):699-707. |
Flux (1): a virtual synthesis scheme for fragment-based de novo design. |
It is demonstrated that the fragmentation of druglike molecules by applying simplistic pseudo-retrosynthesis results in a stock of chemically meaningful building blocks for de novo molecule generation. A stochastic search algorithm in conjunction with ligand-based similarity scoring (Flux: fragment-based ligand builder reaxions) facilitated the generation of new molecules using a single known reference compound as a template. This molecule assembly method is applicable in the absence of receptor-structure information. In a case study, we used imantinib (Gleevec) and a Factor Xa inhibitor as the reference structures. The algorithm succeeded in redesigning the templates from scratch and suggested several alternative molecular structures. The resulting designed molecules were chemically reasonable and contained essential substructure motifs. A comparison of molecular descriptors suggests that holographic descriptors might be advantageous over binary fingerprints for ligand-based de novo design. |
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Fernandes C, Oliveira C, Gano L, Bourkoula A, Pirmettis I, Santos I. |
Bioorg Med Chem. 2007 Jun 15;15(12):3974-80. Epub 2007 Apr 10. |
In our search for the development of novel SPECT radioligands for EGFR positive tumours, new potentially irreversible tyrosine kinase (TK) inhibitors are being explored. The radioiodination of N-{4-[(3-chloro-4-fluorophenyl) amino]quinazoline-6-yl}-3-bromopropionamide, a novel EGFR-TK inhibitor synthesised in our laboratory, was accomplished via halogen exchange. Purification by RP-HPLC gave [(125)I]-N-{4-[(3-chloro-4-fluorophenyl)amino]quinazoline-6-yl}-3-iodopropionamide with a radiochemical purity higher than 95% and a high specific activity. In vitro studies indicate that both iodinated quinazoline and its bromo precursor inhibit A431 cell growth and also possess higher potency than the parent quinazoline to inhibit the EGFR autophosphorylation. In vivo stability studies suggest metabolization of the radioiodinated quinazoline indicating a short biological half-life. The in vitro results point out that these quinazoline derivatives could be promising candidates for SPECT imaging of EGFR positive tumours provided that they are selectively modified in order to achieve better in vivo radiochemical stability. |
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Fielding L. |
Curr Top Med Chem. 2003;3(1):39-53. Review. |
NMR methods for the determination of protein-ligand dissociation constants. |
This article is a review with 83 references of the application of NMR to the measurement of the dissociation constants of protein-ligand complexes. After briefly discussing some general concepts of molecular stability, the text turns to consider which NMR parameters are reporters of complex formation. The available data treatments required to translate observed NMR effects into quantitative measurements of the stability of the complex in the form of the dissociation constant (KD) are introduced. Linearisation methods and curve fitting methods are explained in detail and are illustrated with examples drawn from recent reports of protein-small molecule interactions. Throughout the text examples of the commonly observed NMR parameters , 1 / T1 and 1 / T2 are drawn from biological studies of 1H, 31P, 19F 15N (and other nuclei). The advantages of NMR diffusion experiments as a measure of KD are considered. Some less frequently used NMR approaches, some new ideas and some non-general methods are grouped together in a miscellaneous section. The major sources of errors in the determination of KD are identified. This allows recommendations for optimal experimental set up. Options for dealing with strong binding are reviewed. Finally, the implications of abstracting KD data from high throughput screening experiments are considered and several different approaches to generate this data are discussed. |
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Forino M, Johnson S, Wong TY, Rozanov DV, Savinov AY, Li W, Fattorusso R, Becattini B, Orry AJ, Jung D, Abagyan RA, Smith JW, Alibek K, Liddington RC, Strongin AY, Pellecchia M. |
Proc Natl Acad Sci U S A. 2005 Jul 5;102(27):9499-504. Epub 2005 Jun 27. |
We describe here the fragment-based design of potent DNA gyrase inhibitors. Using the tools of virtual screening and NMR spectroscopy we identified the binding of two low-molecular weight fragments (2-aminobenzimidazole and indolin-2-one) to the 24kDa N-terminal fragment of DNA gyrase B. Further in silico optimization of indolin-2-one led to the discovery of potent DNA gyrase inhibitors. |
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Freeman GA, Andrews Iii CW 3rd, Hopkins AL, Lowell GS, Schaller LT, Cowan JR, Gonzales SS, Koszalka GW, Hazen RJ, Boone LR, Ferris RG, Creech KL, Roberts GB, Short SA, Weaver K, Reynolds DJ, Milton J, Ren J, Stuart DI, Stammers DK, Chan JH. |
J Med Chem. 2004 Nov 18;47(24):5923-36. |
HIV-1 nonnucleoside reverse transcriptase inhibitors (NNRTIs) are part of the combination therapy currently used to treat HIV infection. The features of a new NNRTI drug for HIV treatment must include selective potent activity against both wild-type virus as well as against mutant virus that have been selected by use of current antiretroviral treatment regimens. Based on analogy with known HIV-1 NNRTI inhibitors and modeling studies utilizing the X-ray crystal structure of inhibitors bound in the HIV-1 RT, a series of substituted 2-quinolones was synthesized and evaluated as HIV-1 inhibitors. |
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Gill A. |
Mini Rev Med Chem. 2004 Mar;4(3):301-11. Review. |
New lead generation strategies for protein kinase inhibitors - fragment based screening approaches. |
The protein kinase superfamily represents both an enormous opportunity and a unique challenge for drug discovery. Protein kinases play central roles in the cellular economy and it is well known that a large number of diseases involve aberrant protein kinase activity. This review discusses how fragment based screening strategies, such as virtual screening, NMR and high-throughput X-ray crystallography are being employed to identify new chemo-types to produce the next generation of protein kinase inhibitors. |
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Gill AL, Frederickson M, Cleasby A, Woodhead SJ, Carr MG, Woodhead AJ, Walker MT, Congreve MS, Devine LA, Tisi D, O'Reilly M, Seavers LC, Davis DJ, Curry J, Anthony R, Padova A, Murray CW, Carr RA, Jhoti H. |
J Med Chem. 2005 Jan 27;48(2):414-26. |
Identification of novel p38alpha MAP kinase inhibitors using fragment-based lead generation. |
We describe the structure-guided optimization of the molecular fragments 2-amino-3-benzyloxypyridine 1 (IC(50) 1.3 mM) and 3-(2-(4-pyridyl)ethyl)indole 2 (IC(50) 35 microM) identified using X-ray crystallographic screening of p38alpha MAP kinase. Using two separate case studies, the article focuses on the key compounds synthesized, the structure-activity relationships and the binding mode observations made during this optimization process, resulting in two potent lead series that demonstrate significant increases in activity. We describe the process of compound elaboration either through the growing out from fragments into adjacent pockets or through the conjoining of overlapping fragments and demonstrate that we have exploited the mobile conserved activation loop, consisting in part of Asp168-Phe169-Gly170 (DFG), to generate significant improvements in potency and kinase selectivity. |
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Gosalia DN, Salisbury CM, Maly DJ, Ellman JA, Diamond SL. |
Proteomics. 2005 Apr;5(5):1292-8. |
Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays. |
A novel microarray-based proteolytic profiling assay enabled the rapid determination of protease substrate specificities with minimal sample and enzyme usage. A 722-member library of fluorogenic protease substrates of the general format Ac-Ala-X-X-(Arg/Lys)-coumarin was synthesized and microarrayed, along with fluorescent calibration standards, in glycerol nanodroplets on microscope slides. The arrays were then activated by deposition of an aerosolized enzyme solution, followed by incubation and fluorometric scanning. The specificities of human blood serine proteases (human thrombin, factor Xa, plasmin, and urokinase plasminogen activator) were examined. The arrays provided complete maps of protease specificity for all of the substrates tested and allowed for detection of cooperative interactions between substrate subsites. The arrays were further utilized to explore the conservation of thrombin specificity across species by comparing the proteolytic fingerprints of human, bovine, and salmon thrombin. These enzymes share nearly identical specificity profiles despite approximately 390 million years of divergent evolution. Fluorogenic substrate microarrays provide a rapid way to determine protease substrate specificity information that can be used for the design of selective inhibitors and substrates, the study of evolutionary divergence, and potentially, for diagnostic applications. |
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Groom CR, Hopkins AL. |
Drug Discov Today. 2002 Aug 1;7(15):801-2. No abstract available. |
Current reviews of research directed towards protein kinases present an optimistic view of the field. In a recent issue of Drug Discovery Today, Scapin discusses how structure-based drug design has been applied to great effect against several protein kinases. Other encouragement is drawn from the approval of Gleevec™ (Novartis; http://www.novartis.com) for the treatment of chronic myeloid leukemia and the potential to assay lead compounds for selectivity against an ever-growing panel of protein kinases. Although it would be churlish to detract from some great achievements in this field, one cannot escape the observation that drugs targeting protein kinases are still rare. This leads one to question whether the current optimism is well founded, given that protein kinase programs account for approximately a fifth of the current research programs in many large pharmaceutical companies and that protein kinases comprise the largest gene family coded for by the human genome that has proven tractable to inhibition by small-molecule therapeutics. |
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Hajduk PJ, Greer J. |
Nat Rev Drug Discov. 2007 Mar;6(3):211-9. Epub 2007 Feb 9. |
A decade of fragment-based drug design: strategic advances and lessons learned. |
Since the early 1990s, several technological and scientific advances - such as combinatorial chemistry, high-throughput screening and the sequencing of the human genome - have been heralded as remedies to the problems facing the pharmaceutical industry. The use of these technologies in some form is now well established at most pharmaceutical companies; however, the return on investment in terms of marketed products has not met expectations. Fragment-based drug design is another tool for drug discovery that has emerged in the past decade. Here, we describe the development and evolution of fragment-based drug design, analyse the role that this approach can have in combination with other discovery technologies and highlight the impact that fragment-based methods have made in progressing new medicines into the clinic. |
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Hajduk PJ. |
J Med Chem. 2006 Nov 30;49(24):6972-6. |
Much has been discussed about the proper physicochemical properties (e.g., molecular weight, hydrophobicity, etc.) that should be considered when utilizing fragment leads in drug design. However, little has been reported as to what emphasis, if any, should be placed on the potency of the resulting fragment leads. In this report, a retrospective analysis of 18 highly optimized inhibitors is described in which the compounds were systematically deconstructed until the minimal binding elements could be identified. An analysis of the potency changes that were observed as the leads were reduced in size indicate that a nearly linear relationship exists between molecular weight and binding affinity over the entire range of sizes and potencies represented in the dataset. On the basis of these observations, prediction maps can be constructed that enable critical and quantitative assessments of the process of lead identification and optimization. These data place well-defined limits on the ideal size and potency of fragment leads that are being considered for use in fragment-based drug design. |
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Hajduk PJ. |
Nat Chem Biol. 2006 Dec;2(12):658-9. No abstract available. |
Puzzling through fragment-based drug design. |
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Hajduk PJ. |
Mol Interv. 2006 Oct;6(5):266-72. |
It has been nearly ten years since the introduction of SAR by NMR and the advent of fragment-based drug design. During this time, we have gained a tremendous amount of knowledge about protein druggability, the limits of chemical diversity, and crafting high-affinity ligands from low molecular weight, weakly binding leads. This review will describe the concept of fragment-based drug design, discuss why it works, and illustrate the power of the approach with two case studies on the design of potent inhibitors of matrix metalloproteinases and Bcl-2 family proteins. |
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Hartshorn MJ, Murray CW, Cleasby A, Frederickson M, Tickle IJ, Jhoti H. |
J Med Chem. 2005 Jan 27;48(2):403-13. |
Fragment screening offers an alternative to traditional screening for discovering new leads in drug discovery programs. This paper describes a fragment screening methodology based on high throughput X-ray crystallography. The method is illustrated against five proteins (p38 MAP kinase, CDK2, thrombin, ribonuclease A, and PTP1B). The fragments identified have weak potency (>100 microM) but are efficient binders relative to their size and may therefore represent suitable starting points for evolution to good quality lead compounds. The examples illustrate that a range of molecular interactions (i.e., lipophilic, charge-charge, neutral hydrogen bonds) can drive fragment binding and also that fragments can induce protein movement. We believe that the method has great potential for the discovery of novel lead compounds against a range of targets, and the companion paper illustrates how lead compounds have been identified for p38 MAP kinase starting from fragments such as those described in this paper. |
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Haus-Cohen M, Assaraf YG, Binyamin L, Benhar I, Reiter Y. |
Int J Cancer. 2004 May 1;109(5):750-8. |
Inherent and acquired MDR is characterized by simultaneous resistance to diverse anticancer drugs and continues to be a major impediment in the curative chemotherapy of cancer. The MDR1 gene product, Pgp, is an ATP-driven efflux pump, which extrudes a variety of dissimilar hydrophobic cytotoxic compounds from MDR cells. Pgp overexpression results in MDR of tumor cell lines in vitro as well as of a variety of human malignancies. Thus, one major goal is to develop strategies aimed at specifically disrupting Pgp drug-efflux activity. To this end, we have developed a small recombinant antibody capable of potent reversal of MDR, by disrupting Pgp drug-efflux activity. Using a phage display approach, we isolated a small scFv recombinant antibody fragment that specifically reacts with the first extracellular loop of human Pgp. This scFv fragment binds specifically to various Pgp-overexpressing human MDR carcinoma cell lines, consequently disrupts Pgp drug-efflux function and thereby reverses the MDR phenotype. We have successfully disrupted anticancer drug-extrusion pump activity in MDR cells using a small recombinant scFv fragment. We propose that these novel small Fv-based recombinant antibody molecules may lead to the development of a new class of antibody fragment-based agents that specifically inhibit Pgp drug extrusion. Hence, these small recombinant antibody fragments may be applied in combination chemotherapy to overcome MDR in various human cancers. |
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Haystead TA. |
Curr Top Med Chem. 2006;6(11):1117-27. Review. |
Much attention has focused on the development of protein kinases as drug targets to treat a variety of human diseases including diabetes, cancer, hypertension and arthritis. To date, Gleevec is one example of a drug targeting protein that has successfully treated human cancer. Several other protein kinase inhibitors are in clinical development. However, protein kinases are in fact part of a larger collection of some 2000 distinct proteins expressed by the genome that like the protein kinases also bind purines (the purinome), either to be utilized as substrates or as co-factors in the form of NAD, NADP and co-enzyme A. The solution structures of many representative gene family members within the purinome show these proteins bind purines in a similar orientations to that observed in all protein kinases. Several non-protein kinase purine utilizing proteins are established drug targets such as HMG CoA reductase, dihydrofolate reductase, phosphodiesterase and HSP90. Searches of OMIM identifies many purine utilizing enzymes that are associated with inborn errors in metabolism. Inhibition of any one of which by a drug could lead to an undesirable side effect. The purinome is therefore somewhat of a drug discovery mixed blessing. It is a rich source of therapeutic targets, but also contains a large collection of diverse proteins whose inhibition could result in an adverse outcome. Drug discovery within the purinome should therefore encompass strategies that enable broad assessment of selectivity across the entire purinome at the earliest stages of the discovery process. In this article we review the purinome within the context of drug discovery and discuss approaches for avoiding off target binding during the discovery/lead optimization process with particular emphasis on use of proteome mining technology. |
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Hopkins AL, Groom CR, Alex A. |
Drug Discov Today. 2004 May 15;9(10):430-1. No abstract available. |
Potency is not the only consideration when selecting a lead compound for further optimization into a drug, but it does hold a powerful attraction to the medicinal chemist. |
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Hopkins AL, Groom CR. |
Ernst Schering Res Found Workshop. 2003;(42):11-7. No abstract available. |
[No abstract] |
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Hopkins AL, Groom CR. |
Nat Rev Drug Discov. 2002 Sep;1(9):727-30. |
An assessment of the number of molecular targets that represent an opportunity for therapeutic intervention is crucial to the development of post-genomic research strategies within the pharmaceutical industry. Now that we know the size of the human genome, it is interesting to consider just how many molecular targets this opportunity represents. We start from the position that we understand the properties that are required for a good drug, and therefore must be able to understand what makes a good drug target. |
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Hopkins AL, Mason JS, Overington JP. |
Curr Opin Struct Biol. 2006 Feb;16(1):127-36. Epub 2006 Jan 25. Review. |
Structure-based drug design is now used widely in modern medicinal chemistry. The application of structural biology to medicinal chemistry has heralded the "rational drug design" vision of discovering exquisitely selective ligands. However, recent advances in post-genomic biology are indicating that polypharmacology may be a necessary trait for the efficacy of many drugs, therefore questioning the "one drug, one target" assumption of current rational drug design. By combining advances in chemoinformatics and structural biology, it might be possible to rationally design the next generation of promiscuous drugs with polypharmacology. |
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Hopkins AL, Ren J, Milton J, Hazen RJ, Chan JH, Stuart DI, Stammers DK. |
J Med Chem. 2004 Nov 18;47(24):5912-22. |
We have used a structure-based approach to design a novel series of non-nucleoside inhibitors of HIV-1 RT (NNRTIs). Detailed analysis of a wide range of crystal structures of HIV-1 RT-NNRTI complexes together with data on drug resistance mutations has identified factors important for tight binding of inhibitors and resilience to mutations. Using this approach we have designed and synthesized a novel series of quinolone NNRTIs. Crystal structure analysis of four of these compounds in complexes with HIV-1 RT confirms the predicted binding modes. Members of this quinolone series retain high activity against the important resistance mutations in RT at Tyr181Cys and Leu100Ile. |
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Hou TJ, Xu XJ. |
J Chem Inf Comput Sci. 2003 May-Jun;43(3):1058-67. |
A novel method for the calculations of 1-octanol/water partition coefficient (log P) of organic molecules has been presented here. The method, SLOGP v1.0, estimates the log P values by summing the contribution of atom-weighted solvent accessible surface areas (SASA) and correction factors. Altogether 100 atom/group types were used to classify atoms with different chemical environments, and two correlation factors were used to consider the intermolecular hydrophobic interactions and intramolecular hydrogen bonds. Coefficient values for 100 atom/group and two correction factors have been derived from a training set of 1850 compounds. The parametrization procedure for different kinds of atoms was performed as follows: first, the atoms in a molecule were defined to different atom/group types based on SMARTS language, and the correction factors were determined by substructure searching; then, SASA for each atom/group type was calculated and added; finally, multivariate linear regression analysis was applied to optimize the hydrophobic parameters for different atom/group types and correction factors in order to reproduce the experimental log P. The correlation based on the training set gives a model with the correlation coefficient (r) of 0.988, the standard deviation (SD) of 0.368 log units, and the absolute unsigned mean error of 0.261. Comparison of various procedures of log P calculations for the external test set of 138 organic compounds demonstrates that our method bears very good accuracy and is comparable or even better than the fragment-based approaches. Moreover, the atom-additive approach based on SASA was compared with the simple atom-additive approach based on the number of atoms. The calculated results show that the atom-additive approach based on SASA gives better predictions than the simple atom-additive one. Due to the connection between the molecular conformation and the molecular surface areas, the atom-additive model based on SASA may be a more universal model for log P estimation especially for large molecules. |
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Howard N, Abell C, Blakemore W, Chessari G, Congreve M, Howard S, Jhoti H, Murray CW, Seavers LC, van Montfort RL. |
J Med Chem. 2006 Feb 23;49(4):1346-55. |
The screening of fragments is an alternative approach to high-throughput screening for the identification of leads for therapeutic targets. Fragment hits have been discovered using X-ray crystallographic screening of protein crystals of the serine protease enzyme thrombin. The fragment library was designed to avoid any well-precedented, strongly basic functionality. Screening hits included a novel ligand (3), which binds exclusively to the S2-S4 pocket, in addition to smaller fragments which bind to the S1 pocket. The structure of these protein-ligand complexes are presented. A chemistry strategy to link two such fragments together and to synthesize larger drug-sized compounds resulted in the efficient identification of hybrid inhibitors with nanomolar potency (e.g., 7, IC50 = 3.7 nM). These potent ligands occupy the same area of the active site as previously described peptidic inhibitors, while having very different chemical architecture. |
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Huth JR, Sun C, Sauer DR, Hajduk PJ. |
Methods Enzymol. 2005;394:549-71. |
The advent of large-scale NMR-based screening has enabled new strategies for the design of novel, potent inhibitors of therapeutic targets. In particular, fragment-based strategies, in which molecular portions of the final high-affinity ligand are experimentally identified prior to chemical synthesis, have found widespread utility. This chapter will discuss some of the practical considerations for identifying and utilizing these fragment leads in drug design, with special emphasis on some of the lessons learned from more than a decade of industry experience. |
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Huth JR, Sun C. |
Comb Chem High Throughput Screen. 2002 Dec;5(8):631-43. Review. |
Utility of NMR in lead optimization: fragment-based approaches. |
NMR has proven to be a valuable tool for identifying small molecule drug leads that serve as starting points for lead optimization programs. In addition, NMR screening can also be applied during lead optimization in order to improve the pharmacokinetic properties of a compound. In this paper we review the NMR methods that can be used for this purpose. Several examples are then summarized to demonstrate the usefulness of fragment-based approaches in optimizing the physical properties of potential drug candidates. |
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Jacoby E, Davies J, Blommers MJ. |
Curr Top Med Chem. 2003;3(1):11-23. Review. |
Design of small molecule libraries for NMR screening and other applications in drug discovery. |
There are conceptual differences between high-throughput screening (HTS) and fragment-based screening by NMR. The number of compounds in libraries for NMR screening may be significantly smaller than those used for HTS. Because one relies on a small library its design is significantly important and is the object of this article. A short introduction on fragment-based NMR screening approaches will be provided. Although there are currently very few reports describing the design of libraries of small molecules for NMR screening, aspects of the question of how to compile diverse collections of small molecular fragments useful for drug design were previously addressed for the purposes of combinatorial library design and de novo drug design. As these disciplines are highly interrelated and are applied in an interconnected manner with NMR screening within the drug discovery process, a review of combinatorial library design and especially the building block or fragment selection strategies applied for combinatorial library design and de novo design is well suited to reveal fundamental strategies and potential techniques for the design of NMR screening libraries. This section will be rounded off by a report on hands-on-experience with the design of the Novartis second-site NMR screening library and practical considerations for the design of compound mixtures. Rather than providing an exact protocol general guidelines will be indicated. |
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Jahnke W, Florsheimer A, Blommers MJ, Paris CG, Heim J, Nalin CM, Perez LB. |
Curr Top Med Chem. 2003;3(1):69-80. Review. |
One of the prime merits of NMR as a tool for lead finding in drug discovery research is its sensitivity and robustness to detect weak protein-ligand interactions. This sensitivity allows to build up ligands for a given target in a modular way, by a fragment-based approach. In this approach, two ligands are seperately identified which bind to the target protein generally weakly, but at adjacent binding sites. In a next step, they are chemically linked to produce a high-affinity ligand. This review discusses methods to detect "second-site" ligands that bind to a protein in the presence of a "first-site" ligand, and methods to elucidate structural details on the spatial orientation of both ligands, so that chemical linkage is based on a large piece of experimental information. Published examples from second-site screening and linker design are summarized, and are complemented by previously unpublished in-house examples. |
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Katritzky AR, Kuanar M, Slavov S, Dobchev DA, Fara DC, Karelson M, Acree WE Jr, Solov'ev VP, Varnek A. |
Bioorg Med Chem. 2006 Jul 15;14(14):4888-917. Epub 2006 May 11. |
Correlation of blood-brain penetration using structural descriptors. |
Experimental blood-brain partition coefficients (logBB) for a diverse set of 113 drug molecules are correlated with computed structural descriptors using CODESSA-PRO and ISIDA programs to give statistically significant QSAR models based respectively, on molecular and on fragment descriptors. The linear correlation CODESSA-PRO five-descriptor model has correlation coefficient R2=0.781 and standard deviation s2=0.123. The 'consensus model' of ISIDA gave R2=0.872 and s2=0.047. The developed models were successfully validated using the central nervous system activity data of an external test set of 40 drug molecules. |
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Kehoe JW, Maly DJ, Verdugo DE, Armstrong JI, Cook BN, Ouyang YB, Moore KL, Ellman JA, Bertozzi CR. |
Bioorg Med Chem Lett. 2002 Feb 11;12(3):329-32. |
Tyrosylprotein sulfotransferase inhibitors generated by combinatorial target-guided ligand assembly. |
Tyrosylprotein sulfotransferases (TPSTs) catalyze the sulfation of tyrosine residues within secreted and membrane-bound proteins. The modification modulates protein-protein interactions in the extracellular environment. Here we use combinatorial target-guided ligand assembly to discover the first known inhibitors of human TPST-2. |
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Keseru GM, Makara GM. |
Drug Discov Today. 2006 Aug;11(15-16):741-8. Review. |
Hit discovery technologies range from traditional high-throughput screening to affinity selection of large libraries, fragment-based techniques and computer-aided de novo design, many of which have been extensively reviewed. Development of quality leads using hit confirmation and hit-to-lead approaches present their own challenges, depending on the hit discovery method used to identify the initial hits. In this paper, we summarize common industry practices adopted to tackle hit-to-lead challenges and review how the advantages and drawbacks of different hit discovery techniques could affect the various issues hit-to-lead groups face. |
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Kuntz ID, Chen K, Sharp KA, Kollman PA. |
Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):9997-10002. |
We explore the question of what are the best ligands for macromolecular targets. A survey of experimental data on a large number of the strongest-binding ligands indicates that the free energy of binding increases with the number of nonhydrogen atoms with an initial slope of approximately -1.5 kcal/mol (1 cal = 4.18 J) per atom. For ligands that contain more than 15 nonhydrogen atoms, the free energy of binding increases very little with relative molecular mass. This nonlinearity is largely ascribed to nonthermodynamic factors. An analysis of the dominant interactions suggests that van der Waals interactions and hydrophobic effects provide a reasonable basis for understanding binding affinities across the entire set of ligands. Interesting outliers that bind unusually strongly on a per atom basis include metal ions, covalently attached ligands, and a few well known complexes such as biotin-avidin. |
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Lameijer EW, Kok JN, Back T, Ijzerman AP. |
J Chem Inf Model. 2006 Mar-Apr;46(2):553-62. |
Mining a chemical database for fragment co-occurrence: discovery of "chemical cliches". |
Nowadays millions of different compounds are known, their structures stored in electronic databases. Analysis of these data could yield valuable insights into the laws of chemistry and the habits of chemists. We have therefore explored the public database of the National Cancer Institute (>250,000 compounds) by pattern searching. We split the molecules of this database into fragments to find out which fragments exist, how frequent they are, and whether the occurrence of one fragment in a molecule is related to the occurrence of another, nonoverlapping fragment. It turns out that some fragments and combinations of fragments are so frequent that they can be called "chemical cliches". We believe that the fragment data can give insight into the chemical space explored so far by synthesis. The lists of fragments and their (co-)occurrences can help create novel chemical compounds by (i) systematically listing the most popular and therefore most easily used substituents and ring systems for synthesizing new compounds, (ii) being an easily accessible repository for rarer fragments suitable for lead compound optimization, and (iii) pointing out some of the yet unexplored parts of chemical space. |
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Landon MR, Lancia DR Jr, Yu J, Thiel SC, Vajda S. |
J Med Chem. 2007 Mar 22;50(6):1231-1240. Epub 2007 Feb 17. |
Here we apply the computational solvent mapping (CS-Map) algorithm toward the in silico identification of hot spots, that is, regions of protein binding sites that are major contributors to the binding energy and, hence, are prime targets in drug design. The CS-Map algorithm, developed for binding site characterization, moves small organic functional groups around the protein surface and determines their most energetically favorable binding positions. The utility of CS-Map algorithm toward the prediction of hot spot regions in druggable binding pockets is illustrated by three test systems: (1) renin aspartic protease, (2) a set of previously characterized druggable proteins, and (3) E. coli ketopantoate reductase. In each of the three studies, existing literature was used to verify our results. Based on our analyses, we conclude that the information provided by CS-Map can contribute substantially to the identification of hot spots, a necessary predecessor of fragment-based drug discovery efforts. |
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Lange G, Lesuisse D, Deprez P, Schoot B, Loenze P, Benard D, Marquette JP, Broto P, Sarubbi E, Mandine E. |
J Med Chem. 2003 Nov 20;46(24):5184-95. |
Results from a novel approach which uses protein crystallography for the screening of a low affinity inhibitor fragment library are analyzed by comparing the X-ray structures with bound fragments to the structures with the corresponding full length inhibitors. The screen for new phospho-tyrosine mimics binding to the SH2 domain of (pp60)src was initiated because of the limited cell penetration of phosphates. Fragments in our library typically had between 6 and 30 atoms and included compounds which had either millimolar activity in a Biacore assay or were suggested by the ab initio design program LUDI but had no measurable affinity. All identified fragments were located in the phospho-tyrosine pocket. The most promising fragments were successfully used to replace the phospho-tyrosine and resulted in novel nonpeptidic high affinity inhibitors. The significant diversity of successful fragments is reflected in the high flexibility of the phospho-tyrosine pocket. Comparison of the X-ray structures shows that the presence of the H-bond acceptors and not their relative position within the pharmacophore are essential for fragment binding and/or high affinity binding of full length inhibitors. The X-ray data show that the fragments are recognized by forming a complex H-bond network within the phospho-tyrosine pocket of SH2. No fragment structure was found in which this H-bond network was incomplete, and any uncompensated H-bond within the H-bond network leads to a significant decrease in the affinity of full length inhibitors. No correlation between affinity and fragment binding was found for these polar fragments and hence affinity-based screening would have overlooked some interesting starting points for inhibitor design. In contrast, we were unable to identify electron density for hydrophobic fragments, confirming that hydrophobic interactions are important for inhibitor affinity but of minor importance for ligand recognition. Our results suggest that a screening approach using protein crystallography is particularly useful to identify universal fragments for the conserved hydrophilic recognition sites found in target families such as SH2 domains, phosphatases, kinases, proteases, and esterases. |
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Leach AR, Hann MM, Burrows JN, Griffen EJ. |
Mol Biosyst. 2006 Sep;2(9):430-46. |
There are clearly many different philosophies associated with adapting fragment screening into mainstream Drug Discovery Lead Generation strategies. Scientists at Astex, for instance, focus entirely on strategies involving use of X-ray crystallography and NMR. However, AstraZeneca uses a number of different fragment screening strategies. One approach is to screen a 2000 compound fragment set (with close to "lead-like" complexity) at 100 microM in parallel with every HTS such that the data are obtained on the entire screening collection at 10 microM plus the extra samples at 100 microM; this provides valuable compound potency data in a concentration range that is usually unexplored. The fragments are then screen-specific "privileged structures" that can be searched for in the rest of the HTS output and other databases as well as having synthesis follow-up. A typical workflow for a fragment screen within AstraZeneca is shown below (Figure 24) and highlights the desirability (particularly when screening >100 microM) for NMR and X-ray information to validate weak hits and give information on how to optimise them. In this chapter, we have provided an introduction to the theoretical and practical issues associated with the use of fragment methods and lead-likeness. Fragment-based approaches are still in an early stage of development and are just one of many interrelated techniques that are now used to identify novel lead compounds for drug development. Fragment based screening has some advantages, but like every other drug hunting strategy will not be universally applicable. There are in particular some practical challenges associated with fragment screening that relate to the generally lower level of potency that such compounds initially possess. Considerable synthetic effort has to be applied for post-fragment screening to build the sort of potency that would be expected to be found from a traditional HTS. However, if there are no low-hanging fruit in a screening collection to be found by HTS then the use of fragment screening can help find novelty that may lead to a target not being discarded as intractable. As such, the approach offers some significant advantages by providing less complex molecules, which may have better potential for novel drug optimisation and by enabling new chemical space to be more effectively explored. Many literature examples that cover examples of fragment screening approaches are still at the "proof of concept" stage and although delivering inhibitors or ligands, may still prove to be unsuitable when further ADMET and toxicity profiling is done. The next few years should see a maturing of the area, and as our understanding of how the concepts can be best applied, there are likely to be many more examples of attractive, small molecule hits, leads and candidate drugs derived from the approaches described. |
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Lemmen C, Hiller C, Lengauer T. |
J Comput Aided Mol Des. 1998 Sep;12(5):491-502. |
If structural knowledge of a receptor under consideration is lacking, drug design approaches focus on similarity or dissimilarity analysis of putative ligands. In this context the mutual ligand superposition is of utmost importance. Methods that are rapid enough to facilitate interactive usage, that allow to process sets of conformers and that enable database screening are of special interest here. The ability to superpose molecular fragments instead of entire molecules has proven to be helpful too. The RIGFIT approach meets these requirements and has several additional advantages. In three distinct test applications, we evaluated how closely we can approximate the observed relative orientation for a set of known crystal structures, we employed RIGFIT as a fragment placement procedure, and we performed a fragment-based database screening. The run time of RIGFIT can be traded off against its accuracy. To be competitive in accuracy with another state-of-the-art alignment tool, with which we compare our method explicitly, computing times of about 6 s per superposition on a common day workstation are required. If longer run times can be afforded the accuracy increases significantly. RIGFIT is part of the flexible superposition software FLEXS which can be accessed on the WWW [http:/(/)cartan.gmd.de/FlexS]. |
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Lepre CA, Moore JM, Peng JW. |
Chem Rev. 2004 Aug;104(8):3641-76. Review. No abstract available. |
Theory and applications of NMR-based screening in pharmaceutical research. |
[No abstract] |
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Lesuisse D, Lange G, Deprez P, Benard D, Schoot B, Delettre G, Marquette JP, Broto P, Jean-Baptiste V, Bichet P, Sarubbi E, Mandine E. |
J Med Chem. 2002 Jun 6;45(12):2379-87. |
(pp60)Src is a protein involved in signal transduction and is mainly expressed in neurones, platelets, and osteoclasts. Its precise biological role was recently discovered with the KO experiments by Soriano that gave rise to no other apparent phenotype than osteopetrosis, a disease resulting in excedent bone formation. The SH2 domain of the Src family specifically recognizes a sequence of tetrapeptide featuring a phosphotyrosine and a lipophilic aminoacid at the +1 and +3 positions. Recently we engaged in the search for SH2 ligands via modular peptidomimicry of this tetrapetide. This gave rise to several families of nanomolar inhibitors; the best one incorporated a caprolactam scaffold, a biphenyl moiety, and a phosphotyrosine. However, these inhibitors still incorporated the phosphate group that confers good binding affinity to the protein. Phosphates have undesirable features for drug candidates, namely, high rate of hydrolysis of the phosphate group by phosphatases and high charge content precluding cell penetration. Therefore, while searching for optimal non-peptide ligands for Src SH2, we looked for phosphate replacements. For this, we have designed an SAR by fragment crystallography approach. The start of this work resulted from two experimental observations. First, the fact that phenyl phosphate itself displayed detectable binding affinity for Src SH2 permitted us to perform a screening of small aromatic compounds as phenyl phosphate surrogates. Second, the obtention of large Src SH2 crystals displaying a channel large enough for soaking purposes allowed structure determination of over 40 of these small aromatic compounds bound in the phosphotyrosine binding pocket. This search and the way it gave rise to low nanomolar range Src SH2 inhibitors devoid of phosphate groups will be the subject of the present paper. |
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Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. |
Adv Drug Deliv Rev. 2001 Mar 1;46(1-3):3-26. Review. |
Experimental and computational approaches to estimate solubility and permeability in discovery and development settings are described. In the discovery setting 'the rule of 5' predicts that poor absorption or permeation is more likely when there are more than 5 H-bond donors, 10 H-bond acceptors, the molecular weight (MWT) is greater than 500 and the calculated Log P (CLogP) is greater than 5 (or MlogP > 4.15). Computational methodology for the rule-based Moriguchi Log P (MLogP) calculation is described. Turbidimetric solubility measurement is described and applied to known drugs. High throughput screening (HTS) leads tend to have higher MWT and Log P and lower turbidimetric solubility than leads in the pre-HTS era. In the development setting, solubility calculations focus on exact value prediction and are difficult because of polymorphism. Recent work on linear free energy relationships and Log P approaches are critically reviewed. Useful predictions are possible in closely related analog series when coupled with experimental thermodynamic solubility measurements. |
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Liu G, Huth JR, Olejniczak ET, Mendoza R, DeVries P, Leitza S, Reilly EB, Okasinski GF, Fesik SW, von Geldern TW. |
J Med Chem. 2001 Apr 12;44(8):1202-10. |
The interaction between leukocyte function-associated antigen-1 (LFA-1) and intracellular adhesion molecule-1 (ICAM-1) has been implicated in inflammatory and immune diseases. Recently, a novel series of p-arylthio cinnamides has been described as potent antagonists of the LFA-1/ICAM-1 interaction. These compounds were found to bind to the I domain of LFA-1 using two-dimensional NMR spectroscopy of 15N-labeled LFA-1 I domain. On the basis of NOE studies between compound 1 and the I domain of LFA-1, a model of the complex was constructed. This model revealed that compound 1 does not directly inhibit ICAM-1 binding by interacting with the metal ion dependent adhesion site (MIDAS). Instead, it binds to the previously proposed I domain allosteric site (IDAS) of LFA-1 and likely modulates the activation of LFA-1 through its interaction with this regulatory site. A fragment-based NMR screening strategy was applied to identify small, more water-soluble ligands that bind to a specific region of the IDAS. When incorporated into the parent cinnamide template, the resulting analogues exhibited increased aqueous solubility and improved pharmacokinetic profiles in rats, demonstrating the power of this NMR-based screening approach for rapidly modifying high-affinity ligands. |
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Liu G, Xin Z, Pei Z, Hajduk PJ, Abad-Zapatero C, Hutchins CW, Zhao H, Lubben TH, Ballaron SJ, Haasch DL, Kaszubska W, Rondinone CM, Trevillyan JM, Jirousek MR. |
J Med Chem. 2003 Sep 25;46(20):4232-5. |
Using an NMR-based fragment screening and X-ray crystal structure-based assembly, starting with millimolar ligands for both the catalytic site and the second phosphotyrosine binding site, we have identified a small-molecule inhibitor of protein tyrosine phosphatase 1B with low micromolar inhibition constant, high selectivity (30-fold) over the highly homologous T-cell protein tyrosine phosphatase, and good cellular activity in COS-7 cells. |
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Llorens O, Perez JJ, Villar HO. |
J Med Chem. 2001 Aug 16;44(17):2793-804. |
Toward the design of chemical libraries for mass screening biased against mutagenic compounds. |
The ability to develop a chemical into a drug depends on multiple factors. Beyond potency and selectivity, ADME/PK and the toxicological profile of the compound play a significant role in its evaluation as a candidate for development. Those factors are being brought into bear earlier in the discovery process and even into the design of libraries for screening. The purpose of our study is the comparative analysis of simple physical characteristics of compounds that have been reported to be mutagens and nonmutagenic ones. The analysis of differences can lead to the development of knowledge-based biases in the libraries designed for massive screening. For each of four Salmonella strains, TA-98, TA-100, TA-1535, and TA-1537, an analysis of the statistical significance of the deviance of the averages for a number of global properties was carried out. The properties studied included parameters, such as topological indices, and bit strings representing the presence or absence of certain chemical moieties. The results suggest that mutagens display a larger number of hydrogen bond acceptor centers for most strains. Moreover, the use of bit strings points to the importance of certain molecular fragments, such a nitro groups, for the outcome of a mutagenicity study. Development of multivariate models based on global molecular properties or bit strings point to a small advantage of the latter for the prediction of mutagenicity. The benefits of the bit strings are in accord with the use of fragment-based approaches for the prediction of carcinogenicity and mutagenicity in methods described in the literature. |
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Ludwiczek ML, Baminger B, Konrat R. |
J Am Chem Soc. 2004 Feb 18;126(6):1636-7. No abstract available. |
NMR probing of protein-protein interactions using reporter ligands and affinity tags. |
[No abstract] |
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MacDonald ML, Lamerdin J, Owens S, Keon BH, Bilter GK, Shang Z, Huang Z, Yu H, Dias J, Minami T, Michnick SW, Westwick JK. |
Nat Chem Biol. 2006 Jun;2(6):329-37. Epub 2006 May 7. |
Identifying off-target effects and hidden phenotypes of drugs in human cells. |
We present a strategy for identifying off-target effects and hidden phenotypes of drugs by directly probing biochemical pathways that underlie therapeutic or toxic mechanisms in intact, living cells. High-content protein-fragment complementation assays (PCAs) were constructed with synthetic fragments of a mutant fluorescent protein ('Venus', EYFP or both), allowing us to measure spatial and temporal changes in protein complexes in response to drugs that activate or inhibit particular pathways. One hundred and seven different drugs from six therapeutic areas were screened against 49 different PCA reporters for ten cellular processes. This strategy reproduced known structure-function relationships and also predicted 'hidden,' potent antiproliferative activities for four drugs with novel mechanisms of action, including disruption of mitochondrial membrane potential. A simple algorithm identified a 25-assay panel that was highly predictive of antiproliferative activity, and the predictive power of this approach was confirmed with cross-validation tests. This study suggests a strategy for therapeutic discovery that identifies novel, unpredicted mechanisms of drug action and thereby enhances the productivity of drug-discovery research. |
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Maly DJ, Choong IC, Ellman JA. |
Proc Natl Acad Sci U S A. 2000 Mar 14;97(6):2419-24. |
A method for the rapid and efficient identification of ligands to biological targets is reported. The combinatorial method does not require structural or mechanistic information and is accomplished in four straightforward steps. (i) A set of potential binding elements is prepared wherein each molecule incorporates a common chemical linkage group. (ii) The set of potential binding elements is screened to identify all binding elements that interact even weakly with the biological target. (iii) A combinatorial library of linked binding elements is prepared whereby the binding elements are connected by the common chemical linkage groups through a set of flexible linkers. (iv) The combinatorial library is screened to identify the tightest-binding ligands. The utility of the method was demonstrated by the identification of a potent and subtype-selective small molecule inhibitor of the non-receptor tyrosine kinase c-Src (IC(50) = 64 nM). Because the method relies on connecting two distinct binding elements, the relative contributions of the two binding elements to the potency and selectivity of the inhibitor were readily determined. This information provides valuable insight into the molecular basis of inhibition. |
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Manley PW, Cowan-Jacob SW, Mestan J. |
Biochim Biophys Acta. 2005 Dec 30;1754(1-2):3-13. Epub 2005 Sep 8. Review. |
The constitutively activated Abl tyrosine kinase domain of the chimeric Bcr-Abl oncoprotein is responsible for the transformation of haematopoietic stem cells and the symptoms of chronic myeloid leukaemia (CML). Imatinib targets the tyrosine kinase activity of Bcr-Abl and is a first-line therapy for this malignancy. Although highly effective in chronic phase CML, patients who have progressed to the advanced phase of the disease frequently fail to respond to imatinib or develop resistance to therapy and relapse. This is often due to the emergence of clones expressing mutant forms of Bcr-Abl, which exhibit a decreased sensitivity towards inhibition by imatinib. Considerable progress has recently been made in understanding the structural biology of Abl and the molecular basis for resistance, facilitating the discovery and development of second generation drugs designed to combat mutant forms of Bcr-Abl. The first of these compounds to enter clinical development were BMS-354825 (BristolMyersSquibb) and AMN107 (Novartis Pharma) and, from Phase I results, both of these promise a breakthrough in the treatment of imatinib-resistant CML. Recent advances with these and other promising classes of new CML drugs are reviewed. |
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Mercier KA, Germer K, Powers R. |
Comb Chem High Throughput Screen. 2006 Aug;9(7):515-34. |
Design and characterization of a functional library for NMR screening against novel protein targets. |
In the past few years, NMR has been extensively utilized as a screening tool for drug discovery using various types of compound libraries. The designs of NMR specific chemical libraries that utilize a fragment-based approach based on drug-like characteristics have been previously reported. In this article, a new type of compound library will be described that focuses on aiding in the functional annotation of novel proteins that have been identified from various ongoing genomics efforts. The NMR functional chemical library is comprised of small molecules with known biological activity such as: co-factors, inhibitors, metabolites and substrates. This functional library was developed through an extensive manual effort of mining several databases based on known ligand interactions with protein systems. In order to increase the efficiency of screening the NMR functional library, the compounds are screened as mixtures of 3-4 compounds that avoids the need to deconvolute positive hits by maintaining a unique NMR resonance and function for each compound in the mixture. The functional library has been used in the identification of general biological function of hypothetical proteins identified from the Protein Structure Initiative. |
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Meyer B, Peters T. |
Angew Chem Int Ed Engl. 2003 Feb 24;42(8):864-90. Review. |
NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. |
Binding events of ligands to receptors are the key for an understanding of biological processes. Gaining insight into protein-protein and protein-ligand interactions in solution has recently become possible on an atomic level by new NMR spectroscopic techniques. These experiments identify binding events either by looking at the resonance signals of the ligand or the protein. Ideally, both techniques together deliver a complete picture of ligand binding to a receptor. The approaches discussed in this review allow screening of compound libraries as well as a detailed identification of the groups involved in the binding events. Also, characterization of the binding strength and kinetics is possible, competitive binding as well as allosteric effects can be identified, and it has even been possible to identify ligand binding to intact viruses and membrane-bound proteins. |
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Mooij WT, Hartshorn MJ, Tickle IJ, Sharff AJ, Verdonk ML, Jhoti H. |
ChemMedChem. 2006 Aug;1(8):827-38. |
Automated protein-ligand crystallography for structure-based drug design. |
An approach to automate protein-ligand crystallography is presented, with the aim of increasing the number of structures available to structure-based drug design. The methods we propose deal with the automatic interpretation of diffraction data for targets with known protein structures, and provide easy access to the results. Central to the system is a novel procedure that fully automates the placement of ligands into electron density maps. Automation provides an objective way to structure solution, whereas manual placement can be rather subjective, especially for data of low to medium resolution. Ligands are placed by docking into electron density, whilst taking care of protein-ligand interactions. The ligand fitting procedure has been validated on both public domain and in-house examples. Some of the latter deal with cocktails of low-molecular weight compounds, as used in fragment-based drug discovery by crystallography. For such library-screening experiments we show that the method can automatically identify which of the compounds from a cocktail is bound. |
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Moore J, Abdul-Manan N, Fejzo J, Jacobs M, Lepre C, Peng J, Xie X. |
J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):97-100. Epub 2003 Nov 28. |
In the last several years, NMR strategies in drug discovery have evolved from a primarily structural focus to a set of technologies that are non-structural in nature but that have a much greater impact on the identification and optimization of real drug leads. NMR-based screening methods, such as the SHAPES strategy, help rapidly identify good starting points for drug design in a relatively high throughput implementation. The SHAPES method uses simple NMR techniques to detect binding of a limited, but diverse library of low molecular weight, soluble compounds to a potential drug target. SHAPES library compounds are derived largely from molecular frameworks most commonly found in known therapeutic agents. The NMR experiments used in these protocols are based on the well-known NMR techniques, and may be applied to targets with no limitation on molecular weight and no requirement for isotope labeling. Following screening, SHAPES hits may be used to guide virtual screening, synthesis of combinatorial libraries, and bias the first compounds that undergo high throughput screening. Integration of the SHAPES strategy with iterative X-ray crystallographic structure determination can be very useful in deriving an initial structural pharmacophore model and achieving significant in vitro potency in a short time frame. Here, examples are provided of how the combination of NMR SHAPES screening, virtual screening, molecular modeling and X-ray crystallography has led to novel drug scaffolds in several drug discovery programs: JNK3 MAP kinase and the fatty acid binding protein, aP2. |
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Moore JM. |
Curr Opin Biotechnol. 1999 Feb;10(1):54-8. Review. |
NMR methods in drug discovery have traditionally been used to obtain structural information for drug targets or target-ligand complexes. Recently, it has been shown that NMR may be used as an alternative approach for identification of ligands that bind to protein drug targets, shifting the emphasis of many NMR laboratories towards screening and design of potential drug molecules, rather than structural characterization. |
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Moreira IS, Fernandes PA, Ramos MJ. |
J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 2006 Jun 8;110(22):10962-9. |
Alanine-scanning mutagenesis of protein-protein interfacial residues is a very important process for rational drug design. In this study, we have used the improved MM-PBSA approach that combining molecular mechanics and continuum solvent permits one to calculate the free energy differences through alanine mutation. To identify the binding determinants of the complex formed between the IgG1 (immunoglobulin-binding protein G) and protein G, we have extended the experimental alanine scanning mutagenesis study to both proteins of this complex and, therefore, to all interfacial residues of this binding complex. As a result, we present new residues that can be characterized as warm spots and, therefore, are important for complex formation. We have further increased the understanding of the functionality of this improved computational alanine-scanning mutagenesis approach testing its sensitivity to a protein-protein complex with an interface made up of residues mainly polar. In this study, we also have improved the method for the detection of an important amino acid residue that frequently constitutes a hot spot--tryptophan. |
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Morphy R, Rankovic Z. |
Drug Discov Today. 2007 Feb;12(3-4):156-60. Epub 2006 Dec 14. Review. |
Modulating multiple protein targets simultaneously can be beneficial for treating complex diseases. The redundancy that exists within biological networks means that modulating single proteins might not be sufficient to produce the desired efficacy while, at the same time, minimizing adverse effects. Designing multi-target drugs can be challenging for medicinal chemists, with current lead-discovery strategies often producing large, complex molecules with low ligand efficiency and poor oral bioavailability. Paradoxically, analyses of the relationship between the selectivity of biologically active compounds and their molecular size suggest that promiscuous compounds should typically be smaller than target-selective compounds. A fragment-based approach to multi-target drug discovery could lead to a new generation of compounds with improved physicochemical and pharmacokinetic properties. |
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Murray CW, Callaghan O, Chessari G, Cleasby A, Congreve M, Frederickson M, Hartshorn MJ, McMenamin R, Patel S, Wallis N. |
J Med Chem. 2007 Mar 22;50(6):1116-23. Epub 2007 Feb 22. |
Application of Fragment Screening by X-ray Crystallography to beta-Secretase. |
This paper describes an application of fragment screening to the aspartyl protease enzyme, beta-secretase (BACE-1), using high throughput X-ray crystallography. Three distinct chemotypes were identified by X-ray crystallography as binding to the catalytic aspartates either via an aminoheterocycle (such as 2-aminoquinoline), a piperidine, or an aliphatic hydroxyl group. The fragment hits were weak inhibitors of BACE-1 in the millimolar range but were of interest because most of them displayed relatively good ligand efficiencies. The aminoheterocycles exhibited a novel recognition motif that has not been seen before with aspartic proteases. Virtual screening around this motif identified an aminopyridine with increased potency and attractive growth points for further elaboration using structure-based drug design. The companion paper illustrates how sub-micromolar inhibitors were developed starting from this fragment. |
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Murray CW, Verdonk ML. |
J Comput Aided Mol Des. 2002 Oct;16(10):741-53. |
When a small molecule binds to a protein, it loses a significant amount of rigid body translational and rotational entropy. Estimates of the associated energy barrier vary widely in the literature yet accurate estimates are important in the interpretation of results from fragment-based drug discovery techniques. This paper describes an analysis that allows the estimation of the rigid body entropy barrier from the increase in binding affinities that results when two fragments of known affinity and known binding mode are joined together. The paper reviews the relatively rare number of examples where good quality data is available. From the analysis of this data, we estimate that the barrier to binding, due to the loss of rigid-body entropy, is 15-20 kJ/mol, i.e. around 3 orders of magnitude in affinity at 298 K. This large barrier explains why it is comparatively rare to observe multiple fragments binding to non-overlapping adjacent sites in enzymes. The barrier is also consistent with medicinal chemistry experience where small changes in the critical binding regions of ligands are often poorly tolerated by enzymes. |
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Nacro K, Bienfait B, Lee J, Han KC, Kang JH, Benzaria S, Lewin NE, Bhattacharyya DK, Blumberg PM, Marquez VE. |
J Med Chem. 2000 Mar 9;43(5):921-44. |
The design of potent protein kinase C (PK-C) ligands with low nanomolar binding affinities was accomplished by the combined use of pharmacophore- and receptor-guided approaches based on the structure of the physiological enzyme activator, diacylglycerol (DAG). Earlier use of the former approach, which was based on the structural equivalence of DAG and phorbol ester pharmacophores, identified a fixed template for the construction of a semirigid "recognition domain" that contained the three principal pharmacophores of DAG constrained into a lactone ring (DAG-lactones). In the present work, the pharmacophore-guided approach was refined to a higher level based on the X-ray structure of the C1b domain of PK-Cdelta complexed with phorbol-13-O-acetate. A systematic search that involved modifying the DAG-lactone template with a combination of linear or branched acyl and alpha-alkylidene chains, which functioned as variable hydrophobic "affinity domains", helped identify compounds that optimized hydrophobic contacts with a group of conserved hydrophobic amino acids located on the top half of the C1 domain where the phorbol binds. The hydrophilic/hydrophobic balance of the molecules was estimated by the octanol/water partition coefficients (log P) calculated according to a fragment-based approach. The presence of branched alpha-alkylidene or acyl chains was of critical importance to reach low nanomolar binding affinities for PK-C. These branched chains appear to facilitate important van der Waals contacts with hydrophobic segments of the protein and help promote the activation of PK-C through critical membrane interactions. Molecular modeling of these DAG-lactones into an empty C1b domain using the program AutoDock 2.4 suggests the existence of competing binding modes (sn-1 and sn-2) depending on which carbonyl is directly involved in binding to the protein. Inhibition of epidermal growth factor (EGF) binding, an indirect PK-C mediated response, was realized with some DAG-lactones at a dose 10-fold higher than with the standard phorbol-12, 13-dibutyrate (PDBU). Through the National Cancer Institute (NCI) 60-cell line in vitro screen, DAG-lactone 31 was identified as a very selective and potent antitumor agent. The NCI's computerized, pattern-recognition program COMPARE, which analyzes the degree of similarity of mean-graph profiles produced by the screen, corroborated our principles of drug design by matching the profile of compound 31 with that of the non-tumor-promoting antitumor phorbol ester, prostratin. The structural simplicity and the degree of potency achieved with some of the DAG-lactones described here should dispel the myth that chemical complexity and pharmacological activity go hand in hand. Even as a racemate, DAG-lactone 31 showed low namomolar binding affinity for PK-C and displayed selective antitumor activity at equivalent nanomolar levels. Our present approach should facilitate the generation of multiple libraries of structurally similar DAG-lactones to help exploit molecular diversity for PK-C and other high-affinity receptors for DAG and the phorbol esters. The success of this work suggests that substantially simpler, high-affinity structures could be identified to function as surrogates of other complex natural products. |
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Nestler HP. |
Curr Drug Discov Technol. 2005 Mar;2(1):1-12. Review. |
Combinatorial chemistry and fragment screening--two unlike siblings? |
Efficiently scouting the chemical space is one of the major challenges for lead discovery for drug development. In recent times some shifts have been made away from HTS and combinatorial chemistry to more focused approaches. Combinatorial chemistry was the starting point for the development of synthesis concepts that were intended to cover and explore the chemical space without having to prepare every individual compound. In this review, these lead finding approaches will be discussed comparing virtual and synthesized libraries. In addition we discuss the concepts and relationships of evolutionary libraries using genetic algorithms and dynamic combinatorial chemistries, as well as templated fragment ligation concepts. Taking a more abstract view of all approaches, the concepts may loop back into Combinatorial Chemistry allowing a more educated choice of building blocks and chemistries. |
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Oblak M, Grdadolnik SG, Kotnik M, Jerala R, Filipic M, Solmajer T. |
Bioorg Med Chem Lett. 2005 Dec 1;15(23):5207-10. Epub 2005 Oct 3. |
In silico fragment-based discovery of indolin-2-one analogues as potent DNA gyrase inhibitors. |
We describe here the fragment-based design of potent DNA gyrase inhibitors. Using the tools of virtual screening and NMR spectroscopy we identified the binding of two low-molecular weight fragments (2-aminobenzimidazole and indolin-2-one) to the 24kDa N-terminal fragment of DNA gyrase B. Further in silico optimization of indolin-2-one led to the discovery of potent DNA gyrase inhibitors. |
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O'Brien T, Fahr BT, Sopko MM, Lam JW, Waal ND, Raimundo BC, Purkey HE, Pham P, Romanowski MJ. |
Acta Crystallograph Sect F Struct Biol Cryst Commun. 2005 May 1;61(Pt 5):451-8. Epub 2005 Apr 9. |
Structural analysis of caspase-1 inhibitors derived from Tethering. |
Caspase-1 is a key endopeptidase responsible for the post-translational processing of the IL-1beta and IL-18 cytokines and small-molecule inhibitors that modulate the activity of this enzyme are predicted to be important therapeutic treatments for many inflammatory diseases. A fragment-assembly approach, accompanied by structural analysis, was employed to generate caspase-1 inhibitors. With the aid of Tethering with extenders (small molecules that bind to the active-site cysteine and contain a free thiol), two novel fragments that bound to the active site and made a disulfide bond with the extender were identified by mass spectrometry. Direct linking of each fragment to the extender generated submicromolar reversible inhibitors that significantly reduced secretion of IL-1beta but not IL-6 from human peripheral blood mononuclear cells. Thus, Tethering with extenders facilitated rapid identification and synthesis of caspase-1 inhibitors with cell-based activity and subsequent structural analyses provided insights into the enzyme's ability to accommodate different inhibitor-binding modes in the active site. |
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O'Hare T, Walters DK, Stoffregen EP, Jia T, Manley PW, Mestan J, Cowan-Jacob SW, Lee FY, Heinrich MC, Deininger MW, Druker BJ. |
Cancer Res. 2005 Jun 1;65(11):4500-5. |
Imatinib, a Bcr-Abl tyrosine kinase inhibitor, is a highly effective therapy for patients with chronic myelogenous leukemia (CML). Despite durable responses in most chronic phase patients, relapses have been observed and are much more prevalent in patients with advanced disease. The most common mechanism of acquired imatinib resistance has been traced to Bcr-Abl kinase domain mutations with decreased imatinib sensitivity. Thus, alternate Bcr-Abl kinase inhibitors that have activity against imatinib-resistant mutants would be useful for patients who relapse on imatinib therapy. Two such Bcr-Abl inhibitors are currently being evaluated in clinical trials: the improved potency, selective Abl inhibitor AMN107 and the highly potent dual Src/Abl inhibitor BMS-354825. In the current article, we compared imatinib, AMN107, and BMS-354825 in cellular and biochemical assays against a panel of 16 kinase domain mutants representing >90% of clinical isolates. We report that AMN107 and BMS-354825 are 20-fold and 325-fold more potent than imatinib against cells expressing wild-type Bcr-Abl and that similar improvements are maintained for all imatinib-resistant mutants tested, with the exception of T315I. Thus, both inhibitors hold promise for treating imatinib-refractory CML. |
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Oltersdorf T, Elmore SW, Shoemaker AR, Armstrong RC, Augeri DJ, Belli BA, Bruncko M, Deckwerth TL, Dinges J, Hajduk PJ, Joseph MK, Kitada S, Korsmeyer SJ, Kunzer AR, Letai A, Li C, Mitten MJ, Nettesheim DG, Ng S, Nimmer PM, O'Connor JM, Oleksijew A, Petros AM, Reed JC, Shen W, Tahir SK, Thompson CB, Tomaselli KJ, Wang B, Wendt MD, Zhang H, Fesik SW, Rosenberg SH. |
Nature. 2005 Jun 2;435(7042):677-81. Epub 2005 May 15. |
An inhibitor of Bcl-2 family proteins induces regression of solid tumours. |
Proteins in the Bcl-2 family are central regulators of programmed cell death, and members that inhibit apoptosis, such as Bcl-X(L) and Bcl-2, are overexpressed in many cancers and contribute to tumour initiation, progression and resistance to therapy. Bcl-X(L) expression correlates with chemo-resistance of tumour cell lines, and reductions in Bcl-2 increase sensitivity to anticancer drugs and enhance in vivo survival. The development of inhibitors of these proteins as potential anti-cancer therapeutics has been previously explored, but obtaining potent small-molecule inhibitors has proved difficult owing to the necessity of targeting a protein-protein interaction. Here, using nuclear magnetic resonance (NMR)-based screening, parallel synthesis and structure-based design, we have discovered ABT-737, a small-molecule inhibitor of the anti-apoptotic proteins Bcl-2, Bcl-X(L) and Bcl-w, with an affinity two to three orders of magnitude more potent than previously reported compounds. Mechanistic studies reveal that ABT-737 does not directly initiate the apoptotic process, but enhances the effects of death signals, displaying synergistic cytotoxicity with chemotherapeutics and radiation. ABT-737 exhibits single-agent-mechanism-based killing of cells from lymphoma and small-cell lung carcinoma lines, as well as primary patient-derived cells, and in animal models, ABT-737 improves survival, causes regression of established tumours, and produces cures in a high percentage of the mice. |
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Oprea TI, Davis AM, Teague SJ, Leeson PD. |
J Chem Inf Comput Sci. 2001 Sep-Oct;41(5):1308-15. |
Is there a difference between leads and drugs? A historical perspective. |
To be considered for further development, lead structures should display the following properties: (1) simple chemical features, amenable for chemistry optimization; (2) membership to an established SAR series; (3) favorable patent situation; and (4) good absorption, distribution, metabolism, and excretion (ADME) properties. There are two distinct categories of leads: those that lack any therapeutic use (i.e., "pure" leads), and those that are marketed drugs themselves but have been altered to yield novel drugs. We have previously analyzed the design of leadlike combinatorial libraries starting from 18 lead and drug pairs of structures (S. J. Teague et al. Angew. Chem., Int. Ed. Engl. 1999, 38, 3743-3748). Here, we report results based on an extended dataset of 96 lead-drug pairs, of which 62 are lead structures that are not marketed as drugs, and 75 are drugs that are not presumably used as leads. We examined the following properties: MW (molecular weight), CMR (the calculated molecular refractivity), RNG (the number of rings), RTB (the number of rotatable bonds), the number of hydrogen bond donors (HDO) and acceptors (HAC), the calculated logarithm of the n-octanol/water partition (CLogP), the calculated logarithm of the distribution coefficient at pH 7.4 (LogD(74)), the Daylight-fingerprint druglike score (DFPS), and the property and pharmacophore features score (PPFS). The following differences were observed between the medians of drugs and leads: DeltaMW = 69; DeltaCMR = 1.8; DeltaRNG = DeltaHAC =1; DeltaRTB = 2; DeltaCLogP = 0.43; DeltaLogD(74) = 0.97; DeltaHDO = 0; DeltaDFPS = 0.15; DeltaPPFS = 0.12. Lead structures exhibit, on the average, less molecular complexity (less MW, less number of rings and rotatable bonds), are less hydrophobic (lower CLogP and LogD(74)), and less druglike (lower druglike scores). These findings indicate that the process of optimizing a lead into a drug results in more complex structures. This information should be used in the design of novel combinatorial libraries that are aimed at lead discovery. |
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Overington JP, Al-Lazikani B, Hopkins AL. |
Nat Rev Drug Discov. 2006 Dec;5(12):993-6. Review. |
For the past decade, the number of molecular targets for approved drugs has been debated. Here, we reconcile apparently contradictory previous reports into a comprehensive survey, and propose a consensus number of current drug targets for all classes of approved therapeutic drugs. One striking feature is the relatively constant historical rate of target innovation (the rate at which drugs against new targets are launched); however, the rate of developing drugs against new families is significantly lower. The recent approval of drugs that target protein kinases highlights two additional trends: an emerging realization of the importance of polypharmacology, and also the power of a gene-family-led approach in generating novel and important therapies. |
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Paniagua RT, Sharpe O, Ho PP, Chan SM, Chang A, Higgins JP, Tomooka BH, Thomas FM, Song JJ, Goodman SB, Lee DM, Genovese MC, Utz PJ, Steinman L, Robinson WH. |
J Clin Invest. 2006 Oct;116(10):2633-42. Epub 2006 Sep 14. |
Selective tyrosine kinase inhibition by imatinib mesylate for the treatment of autoimmune arthritis. |
Tyrosine kinases play a central role in the activation of signal transduction pathways and cellular responses that mediate the pathogenesis of rheumatoid arthritis. Imatinib mesylate (imatinib) is a tyrosine kinase inhibitor developed to treat Bcr/Abl-expressing leukemias and subsequently found to treat c-Kit-expressing gastrointestinal stromal tumors. We demonstrate that imatinib potently prevents and treats murine collagen-induced arthritis (CIA). We further show that micromolar concentrations of imatinib abrogate multiple signal transduction pathways implicated in RA pathogenesis, including mast cell c-Kit signaling and TNF-alpha release, macrophage c-Fms activation and cytokine production, and fibroblast PDGFR signaling and proliferation. In our studies, imatinib attenuated PDGFR signaling in fibroblast-like synoviocytes (FLSs) and TNF-alpha production in synovial fluid mononuclear cells (SFMCs) derived from human RA patients. Imatinib-mediated inhibition of a spectrum of signal transduction pathways and the downstream pathogenic cellular responses may provide a powerful approach to treat RA and other inflammatory diseases. |
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Paolini GV, Shapland RH, van Hoorn WP, Mason JS, Hopkins AL. |
Nat Biotechnol. 2006 Jul;24(7):805-15. |
We present the global mapping of pharmacological space by the integration of several vast sources of medicinal chemistry structure-activity relationships (SAR) data. Our comprehensive mapping of pharmacological space enables us to identify confidently the human targets for which chemical tools and drugs have been discovered to date. The integration of SAR data from diverse sources by unique canonical chemical structure, protein sequence and disease indication enables the construction of a ligand-target matrix to explore the global relationships between chemical structure and biological targets. Using the data matrix, we are able to catalog the links between proteins in chemical space as a polypharmacology interaction network. We demonstrate that probabilistic models can be used to predict pharmacology from a large knowledge base. The relationships between proteins, chemical structures and drug-like properties provide a framework for developing a probabilistic approach to drug discovery that can be exploited to increase research productivity. |
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Papeo G, Giordano P, Brasca MG, Buzzo F, Caronni D, Ciprandi F, Mongelli N, Veronesi M, Vulpetti A, Dalvit C. |
J Am Chem Soc. 2007 May 2;129(17):5665-72. Epub 2007 Apr 7. |
Polyfluorinated amino acids for sensitive 19F NMR-based screening and kinetic measurements. |
Two novel series of polyfluorinated amino acids (PFAs) were designed and synthesized according to a very short and scalable synthetic sequence. The advantages and limitations of these moieties for screening purposes are presented and discussed. The potential applications of these PFAs were tested with their incorporation into small arginine-containing peptides that represent suitable substrates for the enzyme trypsin. The enzymatic reactions were monitored by 19F NMR spectroscopy, using the 3-FABS (three fluorine atoms for biochemical screening) technique. The high sensitivity achieved with these PFAs permits a reduction in substrate concentration required for 3-FABS. This is relevant in the utilization of 3-FABS in fragment-based screening for identification of small scaffolds that bind weakly to the receptor of interest. The large dispersion of 19F isotropic chemical shifts allows the simultaneous measurement of the efficiency of the different substrates, thus identifying the best substrate for screening purposes. Furthermore, the knowledge of KM and Kcat for the different substrates allows the identification of the structural motifs responsible for the binding affinity to the receptor and those affecting the chemical steps in enzymatic catalysis. This enables the construction of suitable pharmacophores that can be used for designing nonpeptidic inhibitors with high affinity for the enzyme or molecules that mimic the transition state. The novel PFAs can also find useful application in the FAXS (fluorine chemical shift anisotropy and exchange for screening) experiment, a 19F-based competition binding assay for the detection of molecules that inhibit the interaction between two proteins. |
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Parniak MA, Min KL, Budihas SR, Le Grice SF, Beutler JA. |
Anal Biochem. 2003 Nov 1;322(1):33-9. |
A fluorescence resonance energy transfer assay readily applicable to 96-well and 384-well microplate formats with robotic operation was developed to enable high-throughput screening for inhibitors of human immunodeficiency virus-1 (HIV-1) reverse transcriptase (RT)-associated RNase H activity, an underexplored target for antiretroviral development. The assay substrate is an 18-nucleotide 3'-fluorescein-labeled RNA annealed to a complementary 18-nucleotide 5'-Dabcyl-modified DNA. The intact duplex has an extremely low background fluorescent signal and provides up to 50-fold fluorescent signal enhancement following hydrolysis. The size and sequence of the duplex are such that HIV-1 RT-RNase H cuts the RNA strand close to the 3' end. The fluorescein-labeled ribonucleotide fragment readily dissociates from the complementary DNA at room temperature with immediate generation of a fluorescent signal. This assay is rapid, inexpensive, and robust, providing Z' factors of 0.8 and coefficients of variation of about 5%. The assay can be carried out both in real-time (continuous) and in "quench" modes; the latter requires only two addition steps with no washing and is thus suitable for robotic operation. Several chemical libraries totaling more than 106,000 compounds were screened with this assay in approximately 1 month. |
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Patterson AW, Wood WJ, Ellman JA. |
Nat Protoc. 2007;2(2):424-33. |
Substrate activity screening (SAS) is a fragment-based method for the rapid development of novel substrates and their conversion into non-peptidic inhibitors of Cys and Ser proteases. The method consists of three steps: (i) a library of N-acyl aminocoumarins with diverse, low-molecular-weight N-acyl groups is screened to identify protease substrates using a simple fluorescence-based assay; (ii) the identified N-acyl aminocoumarin substrates are optimized by rapid analog synthesis and evaluation; and (iii) the optimized substrates are converted into inhibitors by direct replacement of the aminocoumarin with known mechanism-based pharmacophores. This protocol describes a general procedure for the solid-phase synthesis of a library of N-acyl aminocoumarin substrates and the screening procedure to identify weak binding substrates. |
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Patterson AW, Wood WJ, Hornsby M, Lesley S, Spraggon G, Ellman JA. |
J Med Chem. 2006 Oct 19;49(21):6298-307. |
The substrate activity screening method, a substrate-based fragment identification and optimization method for the development of enzyme inhibitors, was previously applied to cathepsin S to obtain low nanomolar 1,4-disubstituted-1,2,3-triazole-based aldehyde inhibitors (Wood, W. J. L.; Patterson, A. W.; Tsuruoka, H.; Jain, R. K.; Ellman, J. A. J. Am. Chem. Soc. 2005, 127, 15521-15527). Replacement of the metabolically labile aldehyde pharmacophore with the nitrile pharmacophore provided inhibitors with moderate potency for cathepsin S. The inhibitors showed good selectivity over cathepsins B and L but no selectivity over cathepsin K. X-ray structures of two crystal forms (1.5 and 1.9 A) of a complex between cathepsin S and a triazole inhibitor incorporating a chloromethyl ketone pharmacophore guided the design of triazole substrates with increased cleavage efficiency and selectivity for cathepsin S over cathepsins B, L, and K. Conversion of select substrates to nitrile inhibitors yielded a low molecular weight (414 Da) and potent (15 nM) cathepsin S inhibitor that showed >1000-fold selectivity over cathepsins B, L, and K. |
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Pellecchia M, Becattini B, Crowell KJ, Fattorusso R, Forino M, Fragai M, Jung D, Mustelin T, Tautz L. |
Expert Opin Ther Targets. 2004 Dec;8(6):597-611. Review. |
NMR-based techniques in the hit identification and optimisation processes. |
In this review, the use of general NMR spectroscopy techniques to detect ligand binding and to monitor enzyme kinetics and inhibition, which appear particularly useful in hit identification and validation, is reiterated. Furthermore, the use of NMR-based strategies for lead optimisations that are based on either iterative derivatisations of an initial core structure or on linking fragments that occupy adjacent pockets in the target's binding site will also be described. Several recent examples will be reported and the use of these techniques in cases when the three dimensional structure of the target protein is known will be discussed. |
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Pellecchia M, Sem DS, Wuthrich K. |
Nat Rev Drug Discov. 2002 Mar;1(3):211-9. Review. |
NMR spectroscopy has evolved into an important technique in support of structure-based drug design. Here, we survey the principles that enable NMR to provide information on the nature of molecular interactions and, on this basis, we discuss current NMR-based strategies that can identify weak-binding compounds and aid their development into potent, drug-like inhibitors for use as lead compounds in drug discovery. |
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Peng JW, Lepre CA, Fejzo J, Abdul-Manan N, Moore JM. |
Methods Enzymol. 2001;338:202-30. Review. No abstract available. |
Nuclear magnetic resonance-based approaches for lead generation in drug discovery. |
[No abstract] |
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Pinacho Crisostomo FR, Carrillo R, Leon LG, Martin T, Padron JM, Martin VS. |
J Org Chem. 2006 Mar 17;71(6):2339-45. |
Molecular simplification in bioactive molecules: formal synthesis of (+)-muconin. |
The concept of molecular simplification as a drug design strategy to shorten synthetic routes, while keeping or enhancing the biological activity of the lead drug, has been applied to (+)-muconin, an acetogenin with remarkable cytotoxicity. A novel approach that enables the stereoselective synthesis of such a natural compound or its enantiomer from a common precursor is described. An additional advantage of the method is complete stereochemical control and the decrease in the number of chemical steps required, thus providing an enhancement of the overall yield. Antiproliferative studies against the human solid tumor cell lines showed that the aliphatic chain-THF/THP fragment of (+)-muconin has modest cytotoxic activity. The strategy opens the way to preparing novel bioactive acetogenin analogues by shorter synthetic routes. |
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Poulsen SA, Bornaghi LF. |
Bioorg Med Chem. 2006 May 15;14(10):3275-84. Epub 2006 Jan 20. |
A fragment-based drug discovery approach to the synthesis and identification of small molecule inhibitors of bovine carbonic anhydrase II (bCA II) is described. The classical bCA II recognition fragment is an aromatic sulfonamide (ArSO2NH2) moiety. This fragment was incorporated into a scaffold building block, which was subsequently derivatized by dynamic combinatorial chemistry utilizing alkene cross metathesis as the reversible reaction. Screening against bCA II was then carried out and the results allowed determination of the relative bCA II binding affinities of the cross metathesis products that contained the ArSO2NH2 fragment. A bCA II competitive binding assay validated these results with a representative number of pure compounds. The results for screening, without prior isolation of the active constituent, were in full agreement with those obtained for equilibrium dissociation constants (K(i)'s) of pure compounds. Some of these compounds exhibited K(i)'s in the low nanomolar range. Heterogeneous catalysis was shown to be very effective in this drug discovery application of dynamic combinatorial chemistry. |
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Rees DC, Congreve M, Murray CW, Carr R. |
Nat Rev Drug Discov. 2004 Aug;3(8):660-72. Review. No abstract available. |
[No abstract] |
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Rotstein SH, Murcko MA. |
J Med Chem. 1993 Jun 11;36(12):1700-10. |
GroupBuild: a fragment-based method for de novo drug design. |
A novel method for de novo drug design, GroupBuild, has been developed to suggest chemically reasonable structures which fill the active sites of enzymes. The proposed molecules provide good steric and electrostatic contact with the enzyme and exist in low-energy conformations. These structures are composed entirely of individual functional groups (also known as "building blocks" or "fragments") which the program chooses from a predefined library. User-selected enzyme seed atom(s) may be used to determine the area(s) in which structure generation begins. Alternatively, GroupBuild may begin with a predocked "inhibitor core" from which fragments are grown. For each new fragment generated by the program, several thousand candidates in a variety of locations and orientations are considered. Each of these candidates is scored based on a standard molecular mechanics potential function. The selected fragment and orientation are chosen from among the highest scoring cases. Tests of the method using HIV protease, FK506 binding protein, and human carbonic anhydrase demonstrate that structures similar to known potent inhibitors may be generated with GroupBuild. |
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Rummey C, Nordhoff S, Thiemann M, Metz G. |
Bioorg Med Chem Lett. 2006 Mar 1;16(5):1405-9. |
In silico fragment-based discovery of DPP-IV S1 pocket binders. |
Dipeptidyl peptidase IV is a clinically validated target for type-2 diabetes and belongs to a family of peptidases with a quite unique post-proline cleavage specificity. Known inhibitors contain a limited number of molecular anchors occupying the small prototypical S1 pocket. A virtual screening approach for such S1-binding fragments was carried out using FlexX docking to evaluate its potential to confirm known and find novel compounds. Several low molecular weight inhibitors exhibiting activities in the micromolar range could be identified as starting points for structure-based design. |
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Salisbury CM, Ellman JA. |
Chembiochem. 2006 Jul;7(7):1034-7. No abstract available. |
Rapid identification of potent nonpeptidic serine protease inhibitors. |
[No abstract] |
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Salvatella X, Giralt E. |
Chem Soc Rev. 2003 Nov;32(6):365-72. Review. |
Nuclear Magnetic Resonance (NMR) spectroscopy has long been a favourite tool of chemists interested in host-guest systems because it permits access to a wealth of information about the molecular recognition reaction. NMR has evolved dramatically in the last 15 years and, in parallel with the development of NMR methods for the determination of protein structure, a variety of tools aimed at detecting protein ligand interactions have been proposed and are being now used both in industrial and academic laboratories as valuable tools for structure-based drug discovery. Very recent developments have considerably increased the fraction of therapeutic targets that can be tackled by NMR and significantly reduced the amount of sample required for analysis; in this tutorial review we outline the essential NMR-based techniques and describe some examples of their implementation as part of drug discovery programmes. |
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Sanders WJ, Nienaber VL, Lerner CG, McCall JO, Merrick SM, Swanson SJ, Harlan JE, Stoll VS, Stamper GF, Betz SF, Condroski KR, Meadows RP, Severin JM, Walter KA, Magdalinos P, Jakob CG, Wagner R, Beutel BA. |
J Med Chem. 2004 Mar 25;47(7):1709-18. |
Potent inhibitors of 7,8-dihydroneopterin aldolase (DHNA; EC 4.1.2.25) have been discovered using CrystaLEAD X-ray crystallographic high-throughput screening followed by structure-directed optimization. Screening of a 10 000 compound random library provided several low affinity leads and their corresponding X-ray crystal structures bound to the enzyme. The presence of a common structural feature in each of the leads suggested a strategy for the construction of a directed library of approximately 1000 compounds that were screened for inhibitory activity in a traditional enzyme assay. Several lead compounds with IC(50) values of about 1 microM against DHNA were identified, and crystal structures of their enzyme-bound complexes were obtained by cocrystallization. Structure-directed optimization of one of the leads thus identified afforded potent inhibitors with submicromolar IC(50) values. |
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Sarver RW, Rogers JM, Stockman BJ, Epps DE, DeZwaan J, Harris MS, Baldwin ET. |
Anal Biochem. 2002 Oct 15;309(2):186-95. |
Several small molecules identified by high-throughput screening (HTS) were evaluated for their ability to bind to a nonstructural protein 3 (NS3) helicase from hepatitis C virus (HCV). Equilibrium dissociation constants (K(d)'s) of the compounds for this helicase were determined using several techniques including an assay measuring the kinetics of isothermal enzyme denaturation at several concentrations of the test molecule. Effects of two nonhydrolyzable ATP analogs on helicase denaturation were measured as controls using the isothermal denaturation (ITD) assay. Two compounds, 4-(2,4-dimethylphenyl)-2,7,8-trimethyl-4,5-quinolinediamine and 2-phenyl-N-(5-piperazin-1-ylpentyl)quinazolin-4-amine, were identified from screening that inhibited the enzyme and had low micromolar dissociation constants for NS3 helicase in the ITD assay. Low micromolar affinity of the quinolinediamine to helicase was also confirmed by nuclear magnetic resonance experiments. Unfortunately, isothermal titration calorimetry (ITC) experiments indicated that a more water-soluble analog bound to the 47/23-mer oligonucleotide helicase substrate with low micromolar affinity as did the substituted quinazolinamine. There was no further interest in these templates as helicase inhibitors due to the nonspecific binding to enzyme and substrate. A combination of physical methods was required to discern the mode of action of compounds identified by HTS and remove undesirable lead templates from further consideration. |
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Saxena R, Voight BF, Lyssenko V, Burtt NP, de Bakker PI, Chen H, Roix JJ, Kathiresan S, Hirschhorn JN, Daly MJ, Hughes TE, Groop L, Altshuler D, Almgren P, Florez JC, Meyer J, Ardlie K, Bengtsson K, Isomaa B, Lettre G, Lindblad U, Lyon HN, Melander O, Newton-Cheh C, Nilsson P, Orho-Melander M, Rastam L, Speliotes EK, Taskinen MR, Tuomi T, Guiducci C, Berglund A, Carlson J, Gianniny L, Hackett R, Hall L, Holmkvist J, Laurila E, Sjogren M, Sterner M, Surti A, Svensson M, Svensson M, Tewhey R, Blumenstiel B, Parkin M, Defelice M, Barry R, Brodeur W, Camarata J, Chia N, Fava M, Gibbons J, Handsaker B, Healy C, Nguyen K, Gates C, Sougnez C, Gage D, Nizzari M, Gabriel SB, Chirn GW, Ma Q, Parikh H, Richardson D, Ricke D, Purcell S. |
Science. 2007 Apr 26; [Epub ahead of print] |
Genome-Wide Association Analysis Identifies Loci for Type 2 Diabetes and Triglyceride Levels. |
New strategies for prevention and treatment of type 2 diabetes (T2D) require improved insight into disease etiology. We analyzed 386,731 common single nucleotide polymorphisms (SNPs) in 1,464 patients with T2D and 1,467 matched controls, each characterized for measures of glucose metabolism, lipids, obesity, and blood pressure. With collaborators (FUSION and WTCCC/UKT2D) we identify and confirm three loci associated with T2D -- in a non-coding region near CDKN2A and CDKN2B, in an intron of IGF2BP2, and an intron of CDKAL1 -- and replicate associations near HHEX and in SLC30A8 found by a recent whole genome association study. We identify and confirm association of a SNP in an intron of glucokinase regulatory protein with serum triglycerides. The discovery of associated variants in unsuspected genes and outside coding regions illustrates the ability of genome-wide association studies to provide potentially important clues into the pathogenesis of common diseases. |
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Saxty G, Woodhead SJ, Berdini V, Davies TG, Verdonk ML, Wyatt PG, Boyle RG, Barford D, Downham R, Garrett MD, Carr RA. |
J Med Chem. 2007 Apr 24; [Epub ahead of print] |
Identification of Inhibitors of Protein Kinase B Using Fragment-Based Lead Discovery. |
Using fragment-based screening techniques, 5-methyl-4-phenyl-1H-pyrazole (IC50 80 muM) was identified as a novel, low molecular weight inhibitor of protein kinase B (PKB). Herein we describe the rapid elaboration of highly potent and ligand efficient analogues using a fragment growing approach. Iterative structure-based design was supported by protein-ligand structure determinations using a PKA-PKB "chimera" and a final protein-ligand structure of a lead compound in PKBbeta itself. |
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Scapin G. |
Curr Drug Targets. 2006 Nov;7(11):1443-54. Review. |
Protein kinase inhibition: different approaches to selective inhibitor design. |
Protein kinases represent a large family of enzymes involved in regulating complex molecular machineries that control many cellular functions, from survival and proliferation to apoptosis. Abnormal protein kinase activity has been involved in a variety of pathophysiologic states, including cancer, inflammatory and autoimmune disorders, and cardiac diseases, and protein kinases have become one of the major therapeutical targets of the past 10 years. The major problem associated with ATP-competitive kinase inhibition is target specificity, since many other enzymes, kinases and not-kinases alike, utilize ATP: less specific inhibitors would be expected to exhibit undesirable toxicities that would limit their potential utility as therapeutic agents. The purpose of this review is to offer the reader an idea of the evolution of the methodologies utilized in the quest for selective kinase inhibitors, from the more traditional, screening-based methods to the newer technology of chemogenomics, proteomics and chemical genetics. |
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Schade M, Oschkinat H. |
Curr Opin Drug Discov Devel. 2005 May;8(3):365-73. Review. |
NMR fragment screening: tackling protein-protein interaction targets. |
High-throughput screening of libraries containing compounds of 'drug-like' molecular weight has frequently resulted in no or poor drug candidates, especially when screening against demanding drug targets such as protein-protein interactions. Fragment-based lead discovery and optimization has evolved as a promising solution to this problem by combining the universal adaptability of low-molecular-weight fragments with immediate structural information on fragment binding modes. This review focuses on nuclear magnetic resonance (NMR) fragment screening techniques, which provide a unique combination of medium-throughput, direct binding site information and broad applicability. The utility and exemplary data of chemical shift-detected NMR fragment screening applied to the challenging protein-protein interaction target PDZ domains are summarized. |
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Schade M. |
IDrugs. 2006 Feb;9(2):110-3. |
Nuclear magnetic resonance (NMR)-fragment-screening is a useful tool for lead identification and optimization in cases where shallow binding pockets have to be targeted, where highly selective lead structures are to be designed, and where novel, best-fit scaffolds for combinatorial library design are required. Robust and complementary protein- and ligand-detected NMR-screening methods are available for target proteins of various molecular weights and from different expression systems. The advantages of the NMR assay over other analytical techniques are high sensitivity toward loose fragment binders, comparatively high throughput and the ability to offer unique structural binding site information. |
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Schneider G, Lee ML, Stahl M, Schneider P. |
J Comput Aided Mol Des. 2000 Jul;14(5):487-94. |
De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks. |
An evolutionary algorithm was developed for fragment-based de novo design of molecules (TOPAS, TOPology-Assigning System). This stochastic method aims at generating a novel molecular structure mimicking a template structure. A set of approximately 25,000 fragment structures serves as the building block supply, which were obtained by a straightforward fragmentation procedure applied to 36,000 known drugs. Eleven reaction schemes were implemented for both fragmentation and building block assembly. This combination of drug-derived building blocks and a restricted set of reaction schemes proved to be a key for the automatic development of novel, synthetically tractable structures. In a cyclic optimization process, molecular architectures were generated from a parent structure by virtual synthesis, and the best structure of a generation was selected as the parent for the subsequent TOPAS cycle. Similarity measures were used to define 'fitness', based on 2D-structural similarity or topological pharmacophore distance between the template molecule and the variants. The concept of varying library 'diversity' during a design process was consequently implemented by using adaptive variant distributions. The efficiency of the design algorithm was demonstrated for the de novo construction of potential thrombin inhibitors mimicking peptide and non-peptide template structures. |
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Schneider G. |
Curr Med Chem. 2002 Dec;9(23):2095-101. Review. |
Recent developments in combinatorial molecular design using virtual screening methods are summarised. These include similarity-based compound clustering techniques, structure-based docking and scoring, and fragment-based de novo design. Three major trends have been identified: i) the design of small target-focused compound libraries yielding activity-enriched sets of molecules; ii) advanced prediction methods for "drug-like" molecular properties complement activity predictions in the library design process, forming a multi-dimensional objective function; iii) "cherry picking" of selected products is increasingly used in lead generation and optimisation compared to purely educt-driven library design methods aiming at maximising structural diversity. |
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Schuffenhauer A, Ruedisser S, Marzinzik AL, Jahnke W, Blommers M, Selzer P, Jacoby E. |
Curr Top Med Chem. 2005;5(8):751-62. Review. |
According to Hann's model of molecular complexity an increased probability of detection binding to a target protein can be expected when small, low complex molecular fragments are screened with high sensitivity instead of full-sized ligands with lower sensitivity. Analysis of the HTS summary data of Novartis and comparison with NMR screening results obtained on generic fragment libraries indicate this expectation to be true with hitrates of 0.001% - 0.151% observed in the identification of ligands with an IC(50) threshold in the micromolar range in an HTS setup and hitrates above or equal to 3% observed in NMR screening of fragments with an affinity threshold in the millimolar range. It is however necessary to keep in mind that the sets of target studied were not identical for both method and the experience in NMR screening is too limited for a final conclusion. The term hitrate as used here reflects only the success rate in the observation of ligand binding event. It must not be confused with the overall success rate of fragment and high throughput screening in the lead finding process, which can be entirely different, since the steps required to follow-up a ligand binding event to a lead are different for both methods. A survey of fragment-based lead discovery case studies given in the literature shows that in approximately half of the cases the initial hit fragment was discovered by screening a generic library, whereas in the other cases some knowledge about an initial ligands or the protein binding site has been used, whereas systematic virtual screening of fragment databases has been only rarely reported. As comparatively high hitrates were obtained, further consideration to optimize the generic fragment screening library were directed to the chemical tractability of the fragment. As several functional groups preferred by chemists for modification and linking of the fragments are also preferentially involved in interactions between the fragments and the target protein, a set of screening fragments was derived from chemical building blocks by masking its linker group by a chemical transformation which can be later on used in the chemical follow-up of the fragment hit. For example primary amines can be masked as acetamides. If the screening fragment is active the related building block can then be used for synthesis of a follow-up library. |
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Shuker SB, Hajduk PJ, Meadows RP, Fesik SW. |
Science. 1996 Nov 29;274(5292):1531-4. |
A nuclear magnetic resonance (NMR)-based method is described in which small organic molecules that bind to proximal subsites of a protein are identified, optimized, and linked together to produce high-affinity ligands. The approach is called "SAR by NMR" because structure-activity relationships (SAR) are obtained from NMR. With this technique, compounds with nanomolar affinities for the FK506 binding protein were rapidly discovered by tethering two ligands with micromolar affinities. The method reduces the amount of chemical synthesis and time required for the discovery of high-affinity ligands and appears particularly useful in target-directed drug research. |
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Siani MA, Skillman AG, Carreras CW, Ashley G, Kuntz ID, Santi DV. |
J Mol Graph Model. 2000 Aug-Oct;18(4-5):497-511, 539-40. |
A virtual library of macrocyclic polyketide molecules was generated and screened to identify novel, conformationally constrained potential motilin receptor agonists ("motilides"). A motilide pharmacophore model was generated from the potent 6,9-enol ether erythromycin and known derivatives from the literature. The pharmacophore for each molecular conformation was a point in a distance-volume space based on presentation of the putative binding moieties. Two methods, one fragment based method and the other reaction based, were explored for constructing the polyketide virtual library. First, a virtual library was assembled from monomeric fragments using the CHORTLES language. Second, the virtual library was assembled by the in silico application of all possible polyketide synthase enzyme reactions to generate the product library. Each library was converted to low-energy 3D conformations by distance geometry and standard minimization methods. The distance-volume metric was calculated for low-energy conformations of the members of the virtual polyketide library and screened against the enol ether pharmacophore. The goal was to identify novel macrocycles that satisfy the pharmacophore. We identified three conformationally constrained, novel polyketide series that have low-energy conformations satisfying the distance-volume constraints of the motilide pharmacophore. |
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Siegel MG, Vieth M. |
Drug Discov Today. 2007 Jan;12(1-2):71-9. Epub 2006 Nov 28. Review. |
The authors of this review have examined the complete set of marketed drugs, with regards to looking for structural similarities between drugs. By comparing the structures of all drugs, it has been established how many times one marketed drug occurred as a substructure within another marketed drug. A total of 209 from 1386 marketed drugs sized between 100 and 1500 Da (i.e. 15% of the 1386 total) are contained within other drugs, differing by one or more continuous chemical fragment, and as many as 418 drugs from the total of 1386 (i.e. 30%) contain other drugs as substructure fragments. Many smaller drugs occur in multiple larger drugs. Most of the small changes tend to retain primary indicated pharmacology, whereas larger changes more often lead to different primary pharmacology. We identify a subset of drugs that can be used in fragment-based drug discovery strategies. In addition, the analysis enhances understanding of marketed drug space from the chemical building-block perspective. |
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Sivachenko AY, Yuryev A. |
Expert Opin Ther Targets. 2007 Mar;11(3):411-21. Review. |
One of the major challenges of drug discovery today is the poor understanding of the detailed molecular mechanisms underlying both disease progression and drug action. Insufficient drug specificity and side effects are often discovered during the late stages of drug development, sometimes after the drug is released on the market. These discoveries result in a high target attrition rate, a slow drug design pipeline and high development costs. Recent advances in systems biology and pathway analysis can help make true rational design a reality through the integration of experimental observations with underlying cellular regulation and metabolic networks. It should enable the formulation of better and more informed testable hypotheses with regard to the most efficient target candidates. In this article, the authors overview the broad and heterogeneous field of molecular interaction databases and pathway analysis tools, and the challenges existing in the field. The authors describe and classify different approaches for data acquisition, storage and navigation, give a detailed description of the integrative technology behind the Pathway Studio software solution, and present a comparison with other integrative pathway analysis platforms suitable for drug discovery tasks. |
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Sonpavde G, Hutson TE. |
Expert Opin Biol Ther. 2007 Feb;7(2):233-42. |
Metastatic clear cell renal cell cancer has traditionally been treated with cytokines (interferon or interleukin-2). Improved understanding of biology has engendered novel targeted therapeutic agents that have radically altered the outlook. Vascular endothelial growth factor, the related receptor and the mTOR signal transduction pathway have particularly been exploited. Sunitinib malate, sorafenib and temsirolimus have improved clinical outcomes compared with interferon in randomized trials. Other multitargeted tyrosine kinase inhibitors (lapatinib, axatinib and pazopanib) and antiangiogenic agents (bevacizumab and lenalidomide) have also demonstrated activity in early studies. Combinations of these agents are being evaluated. The future of the therapy of renal cancer appears promising owing to the efficacy of these novel agents. Clinical trials designed to further assess these and other agents need to be vigorously supported. |
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Stockman BJ, Farley KA, Angwin DT. |
Methods Enzymol. 2001;338:230-46. Review. No abstract available. |
[No abstract] |
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Stockman BJ, Lodovice IJ, Fisher DA, McColl AS, Xie Z. |
J Biomol Screen. 2007 Mar 22; [Epub ahead of print] |
Nicotinamide adenine dinucleotide synthetase (NadE) is an essential enzyme for bacterial pathogens and is thus a promising antibacterial target. It catalyzes the conversion of nicotinic acid adenine dinucleotide to nicotinamide adenine dinucleotide. Changes in chemical shifts that occur in the nicotinic acid ring as it is converted to nicotinamide can be used for monitoring the reaction. A robust nuclear magnetic resonance-based activity assay was developed using robotically controlled reaction initiation and quenching. The single-enzyme assay has less potential for false positives compared to a coupled activity assay and is especially well suited to the high concentration of compounds in fragment screens. The assay has been used to screen fragment libraries for NadE inhibitors. |
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Sun C, Hajduk PJ. |
Curr Opin Drug Discov Devel. 2006 Jul;9(4):463-70. Review. |
Nuclear magnetic resonance in target profiling and compound file enhancement. |
Nuclear magnetic resonance (NMR) has matured as an important tool in drug discovery and development, with firm establishment of its roles in lead generation and optimization through application of NMR-based fragment screening and structure-based drug design. Besides these applications, NMR technology has expanded to make contributions both earlier and later in the drug discovery process. This review will focus on the impact of NMR in the early stages of drug discovery, in particular in characterizing the viability of targets for further discovery exercises and improving high-throughput screening through compound file-enhancement initiatives. |
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Szczepankiewicz BG, Liu G, Hajduk PJ, Abad-Zapatero C, Pei Z, Xin Z, Lubben TH, Trevillyan JM, Stashko MA, Ballaron SJ, Liang H, Huang F, Hutchins CW, Fesik SW, Jirousek MR. |
J Am Chem Soc. 2003 Apr 9;125(14):4087-96. |
Protein tyrosine phosphatase 1B (PTP1B) is an enzyme that downregulates the insulin receptor. Inhibition of PTP1B is expected to improve insulin action, and the design of small molecule PTP1B inhibitors to treat type II diabetes has received considerable attention. In this work, NMR-based screening identified a nonselective competitive inhibitor of PTP1B. A second site ligand was also identified by NMR-based screening and then linked to the catalytic site ligand by rational design. X-ray data confirmed that the inhibitor bound with the catalytic site in the native, "open" conformation. The final compound displayed excellent potency and good selectivity over many other phosphatases. The modular approach to drug design described in this work should be applicable for the design of potent and selective inhibitors of other therapeutically relevant protein tyrosine phosphatases. |
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Takahashi K, Ikura M, Habashita H, Nishizaki M, Sugiura T, Yamamoto S, Nakatani S, Ogawa K, Ohno H, Nakai H, Toda M. |
Bioorg Med Chem. 2005 Jul 15;13(14):4527-43. |
Generation of structurally new matrix metalloproteinase inhibitors was successfully carried out using an in silico technique. In order to identify the small fragment interacting with residues in the S1' pocket of MMP-1 through hydrogen bonds, we performed in silico screening using the LUDI program. As a result, acetyl-L-alanyl-(N-methyl)amide (Ac-L-Ala-NHMe) was selected to link with another fragment, hydroxamic acid that interacted with catalytic zinc. By this approach, the L-glutamic acid derivative 2b was discovered to be a new type of matrix metalloproteinase inhibitor. Further transformation to reduce its peptidic nature and improve activity yielded nonpeptidic lead compounds as inhibitors of MMP-1, -2, -3, and -9. |
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Taylor JD, Gilbert PJ, Williams MA, Pitt WR, Ladbury JE. |
Proteins. 2007 Jun 1;67(4):981-90. |
Discovery of small molecule inhibitors of protein-protein interactions is a major challenge to pharmaceutical development. Fragment-based approaches have begun to be widely adopted as an effective way of exploring chemical space on a protein surface with reduced library size. On completion of a fragment screen, the subsequent selection of appropriate "hit" molecules for development is a key decision point. Thermodynamic parameters can be used in this decision process. In this work, a fragment identification protocol based on a virtual fragment analysis and selection followed by 19F NMR screening was directed at the phosphotyrosine binding site of the Src SH2 domain. Three new ligands were identified. Isothermal titration calorimetry was used to provide thermodynamic parameters for the physiologically relevant ligand and the selected fragments. One of these fragments possesses a highly favorable enthalpic contribution to complex formation compared to other fragments and to the physiologically relevant ligand suggesting that it would make a good candidate for compound development. |
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Tsao DH, Sutherland AG, Jennings LD, Li Y, Rush TS 3rd, Alvarez JC, Ding W, Dushin EG, Dushin RG, Haney SA, Kenny CH, Malakian AK, Nilakantan R, Mosyak L. |
Bioorg Med Chem. 2006 Dec 1;14(23):7953-61. Epub 2006 Aug 17. |
ZipA is a membrane anchored protein in Escherichia coli that interacts with FtsZ, a homolog of eukaryotic tubulins, forming a septal ring structure that mediates bacterial cell division. Thus, the ZipA/FtsZ protein-protein interaction is a potential target for an antibacterial agent. We report here an NMR-based fragment screening approach which identified several hits that bind to the C-terminal region of ZipA. The screen was performed by 1H-15N HSQC experiments on a library of 825 fragments that are small, lead-like, and highly soluble. Seven hits were identified, and the binding mode of the best one was revealed in the X-ray crystal structure. Similar to the ZipA/FtsZ contacts, the driving force in the binding of the small molecule ligands to ZipA is achieved through hydrophobic interactions. Analogs of this hit were also evaluated by NMR and X-ray crystal structures of these analogs with ZipA were obtained, providing structural information to help guide the medicinal chemistry efforts. |
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Ujvary I, Gyorffy W, Lopata A. |
Acta Pharm Hung. 2003;73(3):163-9. Hungarian. |
This case study examined various structural features of the 55 bioisosteric fragments of the phenol group registered in version 2002.1 of the Bioster database. The size, calculated lipophilicity and H-bond donor or acceptor character of the fragments were found to vary on a fairly wide scale. In most cases, molecular modelling calculations indicated similarities in the electrostatic potential maps of the fragments. |
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Vajda S, Guarnieri F. |
Curr Opin Drug Discov Devel. 2006 May;9(3):354-62. Review. |
Characterization of protein-ligand interaction sites using experimental and computational methods. |
The ability to identify the sites of a protein that can bind with high affinity to small, drug-like compounds has been an important goal in drug design. Accurate prediction of druggable sites and the identification of small compounds binding in those sites have provided the input for fragment-based combinatorial approaches that allow for a more thorough exploration of the chemical space, and that have the potential to yield molecules that are more lead-like than those found using traditional high-throughput screening. Current progress in experimental and computational methods for identifying and characterizing druggable ligand binding sites on protein targets is reviewed herein, including a discussion of successful nuclear magnetic resonance, X-ray crystallography and tethering technologies. Classical geometric and energy-based computational methods are also discussed, with particular focus on two powerful technologies, that is, computational solvent mapping and grand canonical Monte Carlo simulations (as used by Locus Pharmaceuticals Inc). Both methods can be used to reliably identify druggable sites on proteins and to facilitate the design of novel, low-nanomolar-affinity ligands. |
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van Dongen M, Weigelt J, Uppenberg J, Schultz J, Wikstrom M. |
Drug Discov Today. 2002 Apr 15;7(8):471-8. Review. |
Structure-based screening represents an integrated approach for the identification and optimization of hits by the combined use of nuclear magnetic resonance (NMR) spectroscopy, homology modeling and X-ray crystallography. A general feature of the methodology is the introduction of structure-based methods (NMR, modeling and X-ray) early in the drug discovery process to optimize hits in terms of their affinities and specificities. This approach promises to deliver leads with improved physicochemical properties as compared with leads generated from a traditional HTS program. This review presents examples of structure-based screening from published and in-house drug discovery projects. |
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Verdonk ML, Hartshorn MJ. |
Curr Opin Drug Discov Devel. 2004 Jul;7(4):404-10. Review. |
Fragment-based ligand screening can be a highly effective strategy for drug discovery. In general, fragment hits interact efficiently with the target, and although the potency of these small binders is often low, their optimization into potent leads is tractable. For a hit optimization phase to take full advantage of a good quality fragment binder, we believe it is essential to obtain reliable structural data for the hits. In this review, we describe the methods used for structure-based fragment screening and fragment-to-lead optimization and discuss a number of applications from the literature. |
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Villar HO, Yan J, Hansen MR. |
Curr Opin Chem Biol. 2004 Aug;8(4):387-91. Review. |
Several recent technology-driven advances in the area of NMR have rekindled an interest in the application of the technology to problems in drug discovery and development. A unique aspect of NMR is that it has applicability in broadly different areas of the drug discovery and optimization processes. NMR techniques for screening aimed at the discovery of novel ligands or low molecular weight structures for fragment-based build up procedures are being applied commonly in the industry. Application of NMR in structure-guided drug design and metabonomics are also becoming routine. We present an overview of some of the most recent NMR developments in these areas. |
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von Korff M, Sander T. |
J Chem Inf Model. 2006 Mar-Apr;46(2):536-44. |
We describe a toxicity alerting system for uncharacterized compounds, which is based upon comprehensive tables of substructure fragments that are indicative of toxicity risk. These tables were derived computationally by analyzing the RTECS database and the World Drug Index. We provide, free of charge, a Java applet for structure drawing and toxicity risk assessment. In an independent investigation, we compared the toxicity classification performance of naive Bayesian clustering, k next neighbor classification, and support vector machines. To visualize the chemical space of both toxic and druglike molecules, we trained a large self-organizing map (SOM) with all compounds from the RTECS database and the IDDB. In summary, we found that a support vector machine performed best at classifying compounds of defined toxicity into appropriate toxicity classes. Also, SOMs performed excellently in separating toxic from nontoxic substances. Although these two methods are limited to compounds that are structurally similar to known toxic substances, our fragment-based approach extends predictions to compounds that are structurally dissimilar to compounds used in the training set. |
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Wada CK, Holms JH, Curtin ML, Dai Y, Florjancic AS, Garland RB, Guo Y, Heyman HR, Stacey JR, Steinman DH, Albert DH, Bouska JJ, Elmore IN, Goodfellow CL, Marcotte PA, Tapang P, Morgan DW, Michaelides MR, Davidsen SK. |
J Med Chem. 2002 Jan 3;45(1):219-32. |
A novel series of sulfone N-formylhydroxylamines (retrohydroxamates) have been investigated as matrix metalloproteinases (MMP) inhibitors. The substitution of the ether linkage of ABT-770 (5) with a sulfone group 13a led to a substantial increase in activity against MMP-9 but was accompanied by a loss of selectivity for inhibition of MMP-2 and -9 over MMP-1 and diminished oral exposure. Replacement of the biphenyl P1' substituent with a phenoxyphenyl group provided compounds that are highly selective for inhibition of MMP-2 and -9 over MMP-1. Optimization of the substituent adjacent to the retrohydroxamate center in this series led to the clinical candidate ABT-518 (6), a highly potent, selective, orally bioavailable MMP inhibitor that has been shown to significantly inhibit tumor growth in animal cancer models. |
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Wagener M, Lommerse JP. |
J Chem Inf Model. 2006 Mar-Apr;46(2):677-85. |
To help advance drug discovery projects, a new and validated search method is presented by which potential bioisosteric replacements can be retrieved from a database of more than 700,000 structural fragments. The heart of the search method is an optimized topological pharmacophore fingerprint which describes each fragment as a combination of attachment points, hydrogen bond donors and acceptors, hydrophobic centers, conjugated atoms, and non-hydrogen atoms. In the fingerprint the influence of the attachment point is enhanced by giving it extra weight relative to the other descriptors. The Euclidean distance has proven to be the optimum distance measure to compare the fingerprints in a database search. The performance of the pharmacophore fingerprint based search method has been validated using more than 2200 bioisosteric fragment pairs extracted in an unbiased procedure from the BIOSTER database. The true bioisosteric pairs have been compared with pairs of random fragments originating from the WDI database. Normalized by the standard deviation of the random pairs distance distributions, an excellent separation of true pairs from random pairs was obtained for R-group fragments (2.2 standard deviation units) as well as for linkers (2.6 units) and cores (2.6 units). The bioisoster search method has been implemented as an intranet application called IBIS and is now routinely used by Organon researchers. |
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Walker DP, Wishka DG, Piotrowski DW, Jia S, Reitz SC, Yates KM, Myers JK, Vetman TN, Margolis BJ, Jacobsen EJ, Acker BA, Groppi VE, Wolfe ML, Thornburgh BA, Tinholt PM, Cortes-Burgos LA, Walters RR, Hester MR, Seest EP, Dolak LA, Han F, Olson BA, Fitzgerald L, Staton BA, Raub TJ, Hajos M, Hoffmann WE, Li KS, Higdon NR, Wall TM, Hurst RS, Wong EH, Rogers BN. |
Bioorg Med Chem. 2006 Dec 15;14(24):8219-48. Epub 2006 Oct 2. |
A novel set of azabicyclic aryl amides have been identified as potent and selective agonists of the alpha7 nAChR. A two-pronged approach was taken to improve the potential hERG liability of previously disclosed alpha7 nAChR agonist, PNU-282,987, while maintaining the compound's other desirable pharmacological properties. The first approach involved further exploration of the aryl carboxylic acid fragment of PNU-282,987, while the second approach focused on modification of the azabicyclic amine portion of PNU-282,987. The best compounds from each series are characterized by rapid brain penetration, good oral bioavailability in rat, and demonstrate in vivo efficacy in a rat P50 auditory sensory gating assay. At least one analog from each series (1h, 1o, 2a, 9a, and 18a) shows an improved hERG safety profile over PNU-282,987. |
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Warner SL, Bashyam S, Vankayalapati H, Bearss DJ, Han H, Mahadevan D, Von Hoff DD, Hurley LH. |
Mol Cancer Ther. 2006 Jul;5(7):1764-73. Erratum in: Mol Cancer Ther. 2006 Dec;5(12):3312. Mahadevan, Daruka [added]. |
Aurora A and Aurora B are potential targets for anticancer drug development due to their roles in tumorigenesis and disease progression. To identify small-molecule inhibitors of the Aurora kinases, we undertook a structure-based design approach that used three-dimensional structural models of the Aurora A kinase and molecular docking simulations of chemical entities. Based on these computational methods, a new generation of inhibitors derived from quinazoline and pyrimidine-based tricyclic scaffolds were synthesized and evaluated for Aurora A kinase inhibitory activity, which led to the identification of 4-(6,7-dimethoxy-9H-1,3,9-triaza-fluoren-4-yl)-piperazine-1-carbothioic acid [4-(pyrimidin-2-ylsulfamoyl)-phenyl]-amide. The lead compound showed selectivity for the Aurora kinases when it was evaluated against a panel of diverse kinases. Additionally, the compound was evaluated in cell-based assays, showing a dose-dependent decrease in phospho-histone H3 levels and an arrest of the cell cycle in the G(2)-M fraction. Although biological effects were observed only at relatively high concentrations, this chemical series provides an excellent starting point for drug optimization and further development. |
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Widmer H, Jahnke W. |
Cell Mol Life Sci. 2004 Mar;61(5):580-99. Epub 2004 Feb 26. Review. |
Nuclear magnetic resonance (NMR) spectroscopy is a versatile biophysical technique with wide applicability in drug discovery research, particularly for the detection and characterization of molecular interactions. This review highlights in a comprehensive manner the aspects of biomolecular NMR which are most beneficial for pharmaceutical research and presents them as contributions to the different stages of a drug discovery program: target selection, assay development, lead generation and lead optimization. Emphasis is put on the concept of the particular NMR application, rather than on technical details, and on recent examples. Finally, an appendix of frequently asked questions is given. |
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Wilhelm S, Carter C, Lynch M, Lowinger T, Dumas J, Smith RA, Schwartz B, Simantov R, Kelley S. |
Nat Rev Drug Discov. 2006 Oct;5(10):835-44. Review. Erratum in: Nat Rev Drug Discov. 2007 Feb;6(2):126. |
Discovery and development of sorafenib: a multikinase inhibitor for treating cancer. |
Since the molecular revolution of the 1980s, knowledge of the aetiology of cancer has increased considerably, which has led to the discovery and development of targeted therapies tailored to inhibit cancer-specific pathways. The introduction and refinement of rapid, high-throughput screening technologies over the past decade has greatly facilitated this targeted discovery and development process. Here, we describe the discovery and continuing development of sorafenib (previously known as BAY 43-9006), the first oral multikinase inhibitor that targets Raf and affects tumour signalling and the tumour vasculature. The discovery cycle of sorafenib (Nexavar; Bayer Pharmaceuticals) - from initial screening for a lead compound to FDA approval for the treatment of advanced renal cell carcinoma in December 2005 - was completed in just 11 years, with approval being received approximately 5 years after the initiation of the first Phase I trial. |
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Williams DH, Mitchell T. |
Curr Opin Pharmacol. 2002 Oct;2(5):567-73. Review. |
Protein kinases have been identified as being implicated in many diseases, and the launch of the anti-cancer Bcr/Abl-kinase inhibitor Glivec has been a major advance in validating protein kinases as 'druggable' targets. High-resolution data exists for many classes of protein kinases and, in some cases, these structures are co-complexed with an inhibitor and/or substrate mimic. Coupled with the increasing reliability of computational predictions, structure-based design is now playing an increasingly important role in the discovery and optimisation of novel, potent and selective protein kinase inhibitors. |
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Wood WJ, Patterson AW, Tsuruoka H, Jain RK, Ellman JA. |
J Am Chem Soc. 2005 Nov 9;127(44):15521-7. |
A new fragment-based method for the rapid development of novel and distinct classes of nonpeptidic protease inhibitors, Substrate Activity Screening (SAS), is described. This method consists of three steps: (1) a library of N-acyl aminocoumarins with diverse, low molecular weight N-acyl groups is screened to identify protease substrates using a simple fluorescence-based assay, (2) the identified N-acyl aminocoumarin substrates are optimized by rapid analogue synthesis and evaluation, and (3) the optimized substrates are converted to inhibitors by direct replacement of the aminocoumarin with known mechanism-based pharmacophores. The SAS method was successfully applied to the cysteine protease cathepsin S, which is implicated in autoimmune diseases. Multiple distinct classes of nonpeptidic substrates were identified upon screening an N-acyl aminocoumarin library. Two of the nonpeptidic substrate classes were optimized to substrates with >8000-fold improvements in cleavage efficiency for each class. Select nonpeptidic substrates were then directly converted to low molecular weight, novel aldehyde inhibitors with nanomolar affinity to cathepsin S. This study demonstrates the unique characteristics and merits of this first substrate-based method for the rapid identification and optimization of weak fragments and provides the framework for the development of completely nonpeptidic inhibitors to many different proteases. |
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Workman P. |
Cancer Chemother Pharmacol. 2003 Jul;52 Suppl 1:S45-56. Epub 2003 Jun 18. Review. |
There are now unprecedented opportunities for the development of improved drugs for cancer treatment. Following on from the Human Genome Project, the Cancer Genome Project and related activities will define most of the genes in the majority of common human cancers over the next 5 years. This will provide the opportunity to develop a range of drugs targeted to the precise molecular abnormalities that drive various human cancers and opens up the possibility of personalized therapies targeted to the molecular pathology and genomics of individual patients and their malignancies. The new molecular therapies should be more effective and have less-severe side effects than cytotoxic agents. To develop the new generation of molecular cancer therapeutics as rapidly as possible, it is essential to harness the power of a range of new technologies. These include: genomic and proteomic methodologies (particularly gene expression microarrays); robotic high-throughput screening of diverse compound collections, together with in silico and fragment-based screening techniques; new structural biology methods for rational drug design (especially high-throughput X-ray crystallography and nuclear magnetic resonance); and advanced chemical technologies, including combinatorial and parallel synthesis. Two major challenges to cancer drug discovery are: (1) the ability to convert potent and selective lead compounds with activity by the desired mechanism on tumor cells in culture into agents with robust, drug-like properties, particularly in terms of pharmacokinetic and metabolic properties; and (2) the development of validated pharmacodynamic endpoints and molecular markers of drug response, ideally using noninvasive imaging technologies. The use of various new technologies will be exemplified. A major conceptual and practical issue facing the development and use of the new molecular cancer therapeutics is whether a single drug that targets one of a series of key molecular abnormalities in a particular cancer (e.g. BRAF) will be sufficient on its own to deliver clinical benefit ("house of cards" and tumor addiction models). The alternative scenario is that it will require either a combination of agents or a class of drug that has downstream effects on a range of oncogenic targets. Inhibitors of the heat-shock protein (HSP) 90 molecular chaperone are of particular interest in the latter regard, because they offer the potential of inhibiting multiple oncogenic pathways and simultaneous blockade of all six "hallmark traits" of cancer through direct interaction with a single molecular drug target. The first-in-class HSP90 inhibitor 17AAG exhibited good activity in animal models and is now showing evidence of molecular and clinical activity in ongoing clinical trials. Novel HSP90 inhibitors are also being sought. The development of HSP90 inhibitors is used to exemplify the application of new technologies in drug discovery against a novel molecular target, and in particular the need for innovative pharmacodynamic endpoints is emphasized as an essential component of hypothesis-testing clinical trials. |
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Wyss DF, Arasappan A, Senior MM, Wang YS, Beyer BM, Njoroge FG, McCoy MA. |
J Med Chem. 2004 May 6;47(10):2486-98. |
NMR-based screening of a customized fragment library identified 16 small-molecule hits that bind weakly (K(D) approximately 100 microM to 10 mM) to substrate binding sites of the NS4A-bound NS3 protease of the hepatitis C virus (HCV). Analogues for five classes of NMR hits were evaluated by a combination of NMR and biochemical data yielding SAR and, in most cases, optimized hits with improved potencies (K(D) approximately K(I) approximately 40 microM to 1 mM). NMR chemical shift perturbation data were used to establish the binding location and orientation of the active site directed scaffolds in these five analogue series. Two of these scaffolds, which bind the enzyme at the proximal S1-S3 and S2' substrate binding sites, were linked together producing competitive inhibitors of the HCV NS3 protease with potencies in the micromolar range. This example illustrates that the low molecular weight scaffolds discovered from structure-based NMR screening can be optimized with focused structure-guided chemistry to produce potent nonpeptidic small-molecule inhibitors of the HCV NS3 protease. |
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Wyss DF, McCoy MA, Senior MM. |
Curr Opin Drug Discov Devel. 2002 Jul;5(4):630-47. Review. |
NMR methods have long been used for studying molecular interactions. In the last few years, various NMR approaches have been developed to aid lead discovery. These involve different NMR screening methods to identify initial compounds, which often bind only weakly (in the micro- to millimolar range) to the drug target. Intelligent and focused follow-up strategies enable the development of these compounds into potent, submicromolar drug-like inhibitors for use as leads in drug discovery projects. NMR can be used as both a remarkably reliable screening tool and a structural tool; thus, this technique has unique opportunities for lead discovery. |
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Ye Y, Liu M, Kao JL, Marshall GR. |
Biopolymers. 2006;84(5):472-89. |
Novel trihydroxamate-containing peptides: design, synthesis, and metal coordination. |
Novel trihydroxamate-containing peptides were designed to mimic desferrioxamine (Desferal(R), DFO, a naturally occurring siderophore) but possess distinct conformational restrictions and varied lipophilicity to probe structure vs. metal coordination. The synthesis was performed via fragment condensation of hydroxamate-containing oligopeptides such as Fmoc-Leu- Psi[CON(OBz)]-Phe-Ala-Pro-OH and H-Leu-Psi[CON(OBz)]-Phe-Ala-Pro-OBu(t) (Fmoc: 9-fluor enylmethoxycarbonyl; OBz: benzyl; OBu(t): tert-butyl) either in solution or on a solid support. The metal-binding properties were studied by electrospray ionization-mass spectroscopy (ESI-MS), ultraviolet (UV)-visible spectroscopy, and (1)H nuclear magnetic resonance (NMR). Similar to the dihydroxamate analogs previously explored [Biopolymers (Peptide Science), 2003, Vol. 71, pp. 489-515], the compounds with three hydroxamates arrayed at 10-atom intervals, i.e., H-[Leu-Psi[CON(OH)]-Phe-Ala-Pro](3)-OH (P1), cyclo[Leu-Psi[CON(OH)]-Phe-Ala-Pro](3) (P2), and H-[Leu-Psi(CONOH)-Phe-Ala-Pro](2)-Leu-NHOH (P7), exhibited high affinities for intramolecular coordination with Fe(III) and Ga(III). As expected, both P1 and P2 showed higher relative Fe(III)-binding affinities than the corresponding dihydroxamate-containing peptide analogs (P11 and P12). Even though both P1 and P2 did not compete with DFO in the relative metal-binding affinity in both solution and gas phases, P1, P2, and DFO exhibited similar relative binding selectivities to 11 different metal ions including Fe(III), Fe(II), Al(III), Ga(III), In(III), Zn(II), Cu(II), Co(II), Ni(II), Gd(III), and Mn(II). Compared to the other metal ions, they had higher relative binding affinities with Fe(III), Fe(II), Al(III), Ga(III), and In(III). The decreased metal-binding affinities of P1 and P2 in comparison with DFO suggested the conformational restrictions of their backbones perturb their three hydroxamate groups from optimal hexadentate orientations for metal coordination. As detected by ESI-MS, P2 was distinguished from both P1 and DFO by solvation of its Ga(III) and Fe(III) complexes (such as acetonitrile or water), thereby stabilizing the resulting complexes in the gas phase. Noteworthy, P2 led to 69% death rate in Hela cells at a concentration of 50 microM, exhibiting higher cytotoxicity than DFO in vitro despite its much lower affinity for iron. This enhanced toxicity may simply reflect the increased lipophilicity of the cyclic trihydroxamate (P2) together with the improvements in its cell penetration, and/or subsequent intracellular molecular recognition of both side chains and hydroxamate groups. The cytotoxicity was significantly suppressed by precoordination with Ga(III) or Fe(III), suggesting a mechanism of toxicity via sequestration of essential metal ions as well as the importance of curbing the metal coordination before targeting. The potential of such siderophore-mimicking peptides in oncology needs further exploration. (c) 2006 Wiley Periodicals, Inc. |
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Zartler ER, Shapiro MJ. |
Curr Pharm Des. 2006;12(31):3963-72. Review. |
Protein NMR as a screening tool in drug discovery has become prominent within the past ten years. Advances in protein manipulation, whether by biological means (labeling) or physical means (NMR), have created a powerful method that is able to observe ligand-target interactions in solution. |
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Zartler ER, Shapiro MJ. |
Curr Opin Chem Biol. 2005 Aug;9(4):366-70. Review. |
The use of smaller molecules (fragments) in the drug discovery process has led to success in delivering novel leads for many different targets. This process is a highly integrated process, starting from library design to screening and medicinal chemistry. An overview of this process is presented with particular emphasis placed on the NMR aspect of screening. |
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Zartler ER, Yan J, Mo H, Kline AD, Shapiro MJ. |
Curr Top Med Chem. 2003;3(1):25-37. Review. |
The drug discovery process often involves the screening of compound libraries to identify drug candidates capable of binding to target macromolecules. New approaches in biological and chemical research are driving a change in the pharmaceutical industry. Recent advances in NMR spectroscopy such as affinity NMR techniques, which detect binding of a small molecule with a "receptor", have been shown to be valuable tools to perform rapid screening of compounds for biological activity. These NMR observable events include using relaxation, chemical shift perturbations, translational diffusion, and magnetization transfer. These one dimensional NMR methods increase both the throughput of screening and yield crucial data on the mode of binding. The practical utility of these techniques will be described. |
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Zhang YJ, Wang Z, Sprous D, Nabioullin R. |
Bioorg Med Chem Lett. 2006 Feb;16(3):525-8. Epub 2005 Nov 8. |
Fragment-based virtual library design and virtual screening have been conducted against malic enzyme (ME) homology model. Several scaffolds have been identified as promising motifs to target ME's NADP binding site. One small focused library has been synthesized and tested against ME. Several compounds from this library have shown sub-micromolar inhibitory activity against malic enzyme. |
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Zheng M, Yu K, Liu H, Luo X, Chen K, Zhu W, Jiang H. |
J Comput Aided Mol Des. 2006 Sep;20(9):549-66. Epub 2006 Nov 11. |
QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR. |
The recent wide spreading of the H5N1 avian influenza virus (AIV) in Asia, Europe and Africa and its ability to cause fatal infections in human has raised serious concerns about a pending global flu pandemic. Neuraminidase (NA) inhibitors are currently the only option for treatment or prophylaxis in humans infected with this strain. However, drugs currently on the market often meet with rapidly emerging resistant mutants and only have limited application as inadequate supply of synthetic material. To dig out helpful information for designing potent inhibitors with novel structures against the NA, we used automated docking, CoMFA, CoMSIA, and HQSAR methods to investigate the quantitative structure-activity relationship for 126 NA inhibitors (NIs) with great structural diversities and wide range of bioactivities against influenza A virus. Based on the binding conformations discovered via molecular docking into the crystal structure of NA, CoMFA and CoMSIA models were successfully built with the cross-validated q (2) of 0.813 and 0.771, respectively. HQSAR was also carried out as a complementary study in that HQSAR technique does not require 3D information of these compounds and could provide a detailed molecular fragment contribution to the inhibitory activity. These models also show clearly how steric, electrostatic, hydrophobicity, and individual fragments affect the potency of NA inhibitors. In addition, CoMFA and CoMSIA field distributions are found to be in well agreement with the structural characteristics of the corresponding binding sites. Therefore, the final 3D-QSAR models and the information of the inhibitor-enzyme interaction should be useful in developing novel potent NA inhibitors. |
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Zhou CC, Swaney SM, Shinabarger DL, Stockman BJ. |
Antimicrob Agents Chemother. 2002 Mar;46(3):625-9. |
1H nuclear magnetic resonance study of oxazolidinone binding to bacterial ribosomes. |
The oxazolidinones are a novel class of antibiotics that inhibit initiation of protein synthesis in bacteria. In order to investigate their novel mechanism of action, the interactions of several oxazolidinones with bacterial 70S ribosomes, 50S subunits, and 30S subunits have been characterized by (1)H nuclear magnetic resonance (NMR) line-broadening analyses and transferred nuclear Overhauser enhancement (TRNOE) experiments. PNU-177553 and PNU-100592 (eperezolid) and their corresponding enantiomers, PNU-184414 and PNU-107112, were studied. The dissociation constants were determined to be 94 +/- 44 microM and 195 +/- 40 microM for PNU-177553 and eperezolid, respectively. There was a approximately 4-fold decrease in affinity for their corresponding enantiomers. The NMR-derived dissociation constants are consistent with their antibacterial activity. PNU-177553 and eperezolid were found to bind only to the 50S subunit, with similar affinity as to the 70S ribosome, and to have no affinity for the 30S subunit. Specific binding of PNU-177553 was further confirmed in TRNOE experiments in which positive NOEs observed for the small molecule alone were changed to negative NOEs in the presence of bacterial 70S ribosomes. The observed NOEs indicated that PNU-177553 did not adopt a significantly different conformation when bound to the 70S ribosome, compared to the extended conformation that exists when free in solution. Since this is likeliest the case for each of the four compounds included in this study, the A ring C5 side chain may be positioned in the proper orientation for antibacterial activity in PNU-177553 and eperezolid but not in their inactive enantiomers. |