501
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Unexpected stereochemical tolerance for the biological activity of tyroscherin. Bioorg Med Chem 2011; 19:1708-13. [PMID: 21315614 DOI: 10.1016/j.bmc.2011.01.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 01/07/2011] [Accepted: 01/13/2011] [Indexed: 11/20/2022]
Abstract
Here we describe the concise syntheses of the 15 diastereomers and key analogs of the natural product tyroscherin. While systematic analysis of the analogs clearly demonstrated that the hydrocarbon tail is important for biological activity, structure-activity relationship studies of the complete tyroscherin diastereoarray revealed a surprisingly expansive stereochemical tolerance for the cytotoxic activity. Our results represent a departure from the tenet that biological activity is constrained to a narrow pharmacophore, and highlight the recently emerging appreciation for stereochemical flexibility in defining the essential structural elements of biologically active small molecules.
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502
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Abstract
Fragment-based design has significantly modified drug discovery strategies and paradigms in the last decade. Besides technological advances and novel therapeutic avenues, one of the most significant changes brought by this new discipline has occurred in the minds of drug designers. Fragment-based approaches have markedly impacted rational computer-aided design both in method development and in applications. The present review illustrates the importance of molecular fragments in many aspects of rational ligand design, and discusses how thinking in "fragment space" has boosted computational biology and chemistry.
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503
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Combining NMR and X-ray Crystallography in Fragment-Based Drug Discovery: Discovery of Highly Potent and Selective BACE-1 Inhibitors. Top Curr Chem (Cham) 2011; 317:83-114. [DOI: 10.1007/128_2011_183] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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504
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Abstract
The fragment-based approach is now well established as an important component of modern drug discovery. A key part in establishing its position as a viable technique has been the development of a range of biophysical methodologies with sufficient sensitivity to detect the binding of very weakly binding molecules. X-ray crystallography was one of the first techniques demonstrated to be capable of detecting such weak binding, but historically its potential for screening was under-appreciated and impractical due to its relatively low throughput. In this chapter we discuss the various benefits associated with fragment-screening by X-ray crystallography, and describe the technical developments we have implemented to allow its routine use in drug discovery. We emphasize how this approach has allowed a much greater exploitation of crystallography than has traditionally been the case within the pharmaceutical industry, with the rapid and timely provision of structural information having maximum impact on project direction.
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505
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Bourry D, Sinnaeve D, Gheysen K, Fritzinger B, Vandenborre G, Van Damme EJM, Wieruszeski JM, Lippens G, Ampe C, Martins JC. Intermolecular interaction studies using small volumes. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2011; 49:9-15. [PMID: 21162136 DOI: 10.1002/mrc.2699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 09/15/2010] [Accepted: 10/13/2010] [Indexed: 05/30/2023]
Abstract
We present the use of 1-mm room-temperature probe technology to perform intermolecular interaction studies using chemical shift perturbation methods and saturation transfer difference (STD) spectroscopy using small sample volumes. The use of a small sample volume (5-10 µl) allows for an alternative titration protocol where individual samples are prepared for each titration point, rather than the usual protocol used for a 5-mm probe setup where the ligand is added consecutively to the solution containing the protein or host of interest. This allows for considerable economy in the consumption and cost of the protein and ligand amounts required for interaction studies. For titration experiments, the use of the 1-mm setup consumes less than 10% of the ligand amount required using a 5-mm setup. This is especially significant when complex ligands that are only available in limited quantities, typically because they are obtained from natural sources or through elaborate synthesis efforts, need to be investigated. While the use of smaller volumes does increase the measuring time, we demonstrate that the use of commercial small volume probes allows the study of interactions that would otherwise be impossible to address by NMR.
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Affiliation(s)
- David Bourry
- Department of Chemistry, Ghent University, Ghent, Belgium
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506
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Abstract
Lead generation can be a very challenging phase of the drug discovery process. The two principal methods for this stage of research are blind screening and rational design. Among the rational or semirational design approaches, fragment-based drug discovery (FBDD) has emerged as a useful tool for the generation of lead structures. It is particularly powerful as a complement to high-throughput screening approaches when the latter failed to yield viable hits for further development. Engagement of medicinal chemists early in the process can accelerate the progression of FBDD efforts by incorporating drug-friendly properties in the earliest stages of the design process. Medium-chain acyl-CoA synthetase 2b and ketohexokinase are chosen as examples to illustrate the importance of close collaboration of medicinal chemists, crystallography, and modeling.
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Affiliation(s)
- James Lanter
- Medicinal Chemistry, Johnson & Johnson Pharmaceutical Research and Development, L.L.C., Spring House, Pennsylvania, USA
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507
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Abstract
Fragment-based drug discovery (FBDD) has emerged in the past decade as a powerful tool for discovering drug leads. The approach first identifies starting points: very small molecules (fragments) that are about half the size of typical drugs. These fragments are then expanded or linked together to generate drug leads. Although the origins of the technique date back some 30 years, it was only in the mid-1990s that experimental techniques became sufficiently sensitive and rapid for the concept to be become practical. Since that time, the field has exploded: FBDD has played a role in discovery of at least 18 drugs that have entered the clinic, and practitioners of FBDD can be found throughout the world in both academia and industry. Literally dozens of reviews have been published on various aspects of FBDD or on the field as a whole, as have three books (Jahnke and Erlanson, Fragment-based approaches in drug discovery, 2006; Zartler and Shapiro, Fragment-based drug discovery: a practical approach, 2008; Kuo, Fragment based drug design: tools, practical approaches, and examples, 2011). However, this chapter will assume that the reader is approaching the field with little prior knowledge. It will introduce some of the key concepts, set the stage for the chapters to follow, and demonstrate how X-ray crystallography plays a central role in fragment identification and advancement.
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508
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509
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Fragment-based screening by X-ray crystallography, MS and isothermal titration calorimetry to identify PNMT (phenylethanolamine N-methyltransferase) inhibitors. Biochem J 2010; 431:51-61. [PMID: 20642456 DOI: 10.1042/bj20100651] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
CNS (central nervous system) adrenaline (epinephrine) is implicated in a wide range of physiological and pathological conditions. PNMT (phenylethanolamine N-methyltransferase) catalyses the final step in the biosynthesis of adrenaline, the conversion of noradrenaline (norepinephrine) to adrenaline by methylation. To help elucidate the role of CNS adrenaline, and to develop potential drug leads, potent, selective and CNS-active inhibitors are required. The fragment screening approach has advantages over other lead discovery methods including high hit rates, more efficient hits and the ability to sample chemical diversity more easily. In the present study we applied fragment-based screening approaches to the enzyme PNMT. We used crystallography as the primary screen and identified 12 hits from a small commercial library of 384 drug-like fragments. The hits include nine chemicals with two fused rings and three single-ring chemical systems. Eight of the hits come from three chemical classes: benzimidazoles (a known class of PNMT inhibitor), purines and quinolines. Nine of the hits have measurable binding affinities (~5-700 μM) as determined by isothermal titration calorimetry and all nine have ligand efficiencies of 0.39 kcal/mol per heavy atom or better (1 kcal≈4.184 kJ). We synthesized five elaborated benzimidazole compounds and characterized their binding to PNMT, showing for the first time how this class of inhibitors interact with the noradrenaline-binding site. Finally, we performed a pilot study with PNMT for fragment-based screening by MS showing that this approach could be used as a fast and efficient first-pass screening method prior to characterization of binding mode and affinity of hits.
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510
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The flow synthesis of heterocycles for natural product and medicinal chemistry applications. Mol Divers 2010; 15:613-30. [PMID: 20960230 DOI: 10.1007/s11030-010-9282-1] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 09/14/2010] [Indexed: 10/18/2022]
Abstract
This article represents an overview of recent research from the Innovative Technology Centre in the field of flow chemistry which was presented at the FROST2 meeting in Budapest in October 2009. After a short introduction of this rapidly expanding field, we discuss some of our results with a main focus on the synthesis of heterocyclic compounds which we use in various natural product and medicinal chemistry programmes.
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511
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Sándor M, Kiss R, Keseru GM. Virtual fragment docking by Glide: a validation study on 190 protein-fragment complexes. J Chem Inf Model 2010; 50:1165-72. [PMID: 20459088 DOI: 10.1021/ci1000407] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The docking accuracy of Glide was evaluated using 16 different docking protocols on 190 protein-fragment complexes representing 78 targets. Standard precision docking (Glide SP) based protocols showed the best performance. The average root-mean-square deviation (rmsd) between the docked and cocrystallized poses achieved by Glide SP with pre- and postprocessing was 1.17 A, and an acceptable binding mode with rmsd < 2 A could be found in 80% of the cases. Comparison of the docking results produced by different protocols suggests that the sampling efficacy of Glide is adequate for fragment docking. The docking accuracy seems to be limited by the performance of scoring schemes, which is supported by the weak correlation between experimental binding affinities and GlideScores. Cross-docking experiments performed on 8 targets represented by 63 complexes revealed that Glide SP gave similar results to that of the computationally more intensive Glide XP. The average rmsd achieved by Glide SP with pre- and postprocessing was 2.06 A, and an acceptable binding mode with rmsd < 2 A could be found in 63% of the cases. These cross-docking results were improved significantly selecting the optimal X-ray structure for each target (average rmsd = 1.3 A, success rate = 77%), indicating the importance of enrichment studies and the use of multiple X-ray structures in virtual fragment screening.
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Affiliation(s)
- Márk Sándor
- Discovery Chemistry, Gedeon Richter plc., P.O. Box 27, H-1475 Budapest, Hungary
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512
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Woodhead AJ, Angove H, Carr MG, Chessari G, Congreve M, Coyle JE, Cosme J, Graham B, Day PJ, Downham R, Fazal L, Feltell R, Figueroa E, Frederickson M, Lewis J, McMenamin R, Murray CW, O'Brien MA, Parra L, Patel S, Phillips T, Rees DC, Rich S, Smith DM, Trewartha G, Vinkovic M, Williams B, Woolford AJA. Discovery of (2,4-dihydroxy-5-isopropylphenyl)-[5-(4-methylpiperazin-1-ylmethyl)-1,3-dihydroisoindol-2-yl]methanone (AT13387), a novel inhibitor of the molecular chaperone Hsp90 by fragment based drug design. J Med Chem 2010; 53:5956-69. [PMID: 20662534 DOI: 10.1021/jm100060b] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inhibitors of the molecular chaperone heat shock protein 90 (Hsp90) are currently generating significant interest in clinical development as potential treatments for cancer. In a preceding publication (DOI: 10.1021/jm100059d ) we describe Astex's approach to screening fragments against Hsp90 and the subsequent optimization of two hits into leads with inhibitory activities in the low nanomolar range. This paper describes the structure guided optimization of the 2,4-dihydroxybenzamide lead molecule 1 and details some of the drug discovery strategies employed in the identification of AT13387 (35), which has progressed through preclinical development and is currently being tested in man.
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513
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Webb RL, Schiering N, Sedrani R, Maibaum J. Direct Renin Inhibitors as a New Therapy for Hypertension. J Med Chem 2010; 53:7490-520. [DOI: 10.1021/jm901885s] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Randy L. Webb
- Novartis Pharmaceuticals Corp., Institutes for BioMedical Research, East Hanover, New Jersey
| | - Nikolaus Schiering
- Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Richard Sedrani
- Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Jürgen Maibaum
- Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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514
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Jahnke W, Rondeau JM, Cotesta S, Marzinzik A, Pellé X, Geiser M, Strauss A, Götte M, Bitsch F, Hemmig R, Henry C, Lehmann S, Glickman JF, Roddy TP, Stout SJ, Green JR. Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery. Nat Chem Biol 2010; 6:660-6. [DOI: 10.1038/nchembio.421] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 07/12/2010] [Indexed: 12/31/2022]
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515
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Murray CW, Blundell TL. Structural biology in fragment-based drug design. Curr Opin Struct Biol 2010; 20:497-507. [DOI: 10.1016/j.sbi.2010.04.003] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 03/26/2010] [Accepted: 04/14/2010] [Indexed: 10/19/2022]
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516
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Czarna A, Beck B, Srivastava S, Popowicz G, Wolf S, Huang Y, Bista M, Holak TA, Dömling A. Robust generation of lead compounds for protein-protein interactions by computational and MCR chemistry: p53/Hdm2 antagonists. Angew Chem Int Ed Engl 2010; 49:5352-6. [PMID: 20575124 PMCID: PMC3772515 DOI: 10.1002/anie.201001343] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anna Czarna
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Barbara Beck
- Departments of Pharmaceutical Sciences and Chemistry, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA, Fax: (+) 412-383-5298
| | - Stuti Srivastava
- Departments of Pharmaceutical Sciences and Chemistry, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA, Fax: (+) 412-383-5298
| | - Grzegorz Popowicz
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Siglinde Wolf
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Yijun Huang
- Departments of Pharmaceutical Sciences and Chemistry, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA, Fax: (+) 412-383-5298
| | - Michal Bista
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Tad A. Holak
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Alexander Dömling
- Departments of Pharmaceutical Sciences and Chemistry, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA, Fax: (+) 412-383-5298
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517
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Shelke S, Cutting B, Jiang X, Koliwer-Brandl H, Strasser D, Schwardt O, Kelm S, Ernst B. A Fragment-Based In Situ Combinatorial Approach To Identify High-Affinity Ligands for Unknown Binding Sites. Angew Chem Int Ed Engl 2010; 49:5721-5. [DOI: 10.1002/anie.200907254] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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518
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Shelke S, Cutting B, Jiang X, Koliwer-Brandl H, Strasser D, Schwardt O, Kelm S, Ernst B. A Fragment-Based In Situ Combinatorial Approach To Identify High-Affinity Ligands for Unknown Binding Sites. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907254] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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519
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Czarna A, Beck B, Srivastava S, Popowicz G, Wolf S, Huang Y, Bista M, Holak T, Dömling A. Robust Generation of Lead Compounds for Protein-Protein Interactions by Computational and MCR Chemistry: p53/Hdm2 Antagonists. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001343] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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520
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Bhat VT, Caniard AM, Luksch T, Brenk R, Campopiano DJ, Greaney MF. Nucleophilic catalysis of acylhydrazone equilibration for protein-directed dynamic covalent chemistry. Nat Chem 2010; 2:490-7. [PMID: 20489719 PMCID: PMC2913121 DOI: 10.1038/nchem.658] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 03/30/2010] [Indexed: 12/25/2022]
Abstract
Dynamic covalent chemistry uses reversible chemical reactions to set up an equilibrating network of molecules at thermodynamic equilibrium, which can adjust its composition in response to any agent capable of altering the free energy of the system. When the target is a biological macromolecule, such as a protein, the process corresponds to the protein directing the synthesis of its own best ligand. Here, we demonstrate that reversible acylhydrazone formation is an effective chemistry for biological dynamic combinatorial library formation. In the presence of aniline as a nucleophilic catalyst, dynamic combinatorial libraries equilibrate rapidly at pH 6.2, are fully reversible, and may be switched on or off by means of a change in pH. We have interfaced these hydrazone dynamic combinatorial libraries with two isozymes from the glutathione S-transferase class of enzyme, and observed divergent amplification effects, where each protein selects the best-fitting hydrazone for the hydrophobic region of its active site.
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Affiliation(s)
- Venugopal T. Bhat
- EastChem, School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Anne M. Caniard
- EastChem, School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Torsten Luksch
- College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Ruth Brenk
- College of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Dominic J. Campopiano
- EastChem, School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK
| | - Michael F. Greaney
- EastChem, School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK
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521
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522
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Galons H, Oumata N, Meijer L. Cyclin-dependent kinase inhibitors: a survey of recent patent literature. Expert Opin Ther Pat 2010; 20:377-404. [PMID: 20180621 DOI: 10.1517/13543770903524284] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
IMPORTANCE OF THE FIELD Abnormalities in protein phosphorylation by cyclin-dependent kinases (CDKs) have been observed in numerous major human diseases, which has strongly encouraged the search for pharmacological inhibitors. Almost 10 years after the first compounds entered clinical studies, numerous CDK inhibitors with differing selectivity profiles are now undergoing preclinical and clinical evaluation. Nevertheless, these intensive searches have not yet resulted in drug approvals. AREAS COVERED IN THIS REVIEW This paper reviews patent activity associated with these efforts during the 2005 - 2008 period. WHAT THE READER WILL GAIN Readers will rapidly obtain an overview of the majority of CDK inhibitor scaffolds; they will discover which companies are the main players in the field and acquire information on products that have reached the clinical phases. TAKE HOME MESSAGE In most cases, applications have been claimed in the field of cancer; however, potential applications of CDK inhibitors in other therapeutic areas are regularly reported and could herald therapeutic introduction over the next few years.
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Affiliation(s)
- Hervé Galons
- INSERM U648, Université Paris Descartes, 4 avenue de l'observatoire, 75006 Paris, France.
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523
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Whalen KL, Pankow KL, Blanke SR, Spies MA. Exploiting Enzyme Plasticity in Virtual Screening: High Efficiency Inhibitors of Glutamate Racemase. ACS Med Chem Lett 2010; 1:9-13. [PMID: 20634968 PMCID: PMC2903749 DOI: 10.1021/ml900005b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 12/09/2009] [Indexed: 11/30/2022] Open
Abstract
Glutamate racemase is an attractive antimicrobial drug target. Virtual screening using a transition-state conformation of the enzyme resulted in the discovery of several μM competitive inhibitors, dissimilar from current amino acid-like inhibitors, providing novel scaffolds for drug discovery. The most effective of these competitive inhibitors possesses a very high ligand efficiency value of -0.6 kcal/mol/heavy atom, and is effective against three distinct glutamate racemases representing two species of Bacillus. The benefits of employing the transition-state conformation of the receptor in virtual screening are discussed.
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524
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Medina JR, Grant SW, Axten JM, Miller WH, Donatelli CA, Hardwicke MA, Oleykowski CA, Liao Q, Plant R, Xiang H. Discovery of a new series of Aurora inhibitors through truncation of GSK1070916. Bioorg Med Chem Lett 2010; 20:2552-5. [DOI: 10.1016/j.bmcl.2010.02.091] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 10/19/2022]
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525
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Chan AE, Laskowski RA, Selwood DL. Chemical Fragments that Hydrogen Bond to Asp, Glu, Arg, and His Side Chains in Protein Binding Sites. J Med Chem 2010; 53:3086-94. [DOI: 10.1021/jm901696w] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A.W. Edith Chan
- Biological and Medicinal Chemistry Group, Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, U.K
| | - Roman A. Laskowski
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - David L. Selwood
- Biological and Medicinal Chemistry Group, Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, U.K
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526
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Coyne AG, Scott DE, Abell C. Drugging challenging targets using fragment-based approaches. Curr Opin Chem Biol 2010; 14:299-307. [PMID: 20223699 DOI: 10.1016/j.cbpa.2010.02.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Revised: 02/08/2010] [Accepted: 02/15/2010] [Indexed: 02/02/2023]
Abstract
Fragment-based approaches have now become firmly established in the drug discovery armoury. After notable early successes against protein kinases, the versatility and power of fragment-based approaches are increasingly being demonstrated on more diverse and difficult protein targets. This review highlights seven examples including targeting protein-protein interactions, a RNA polymerase and a DNA-binding protein. It shows how fragment-based approaches using small libraries have been successful when large HTS screens have failed. It also highlights the range of biophysical approaches being used and the interplay between experimental and in silico screens. The examples all show the iterative way in which potency is built up by synthetic elaboration of the initial fragment hits.
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Affiliation(s)
- Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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527
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Abstract
In the last decade, various target-guided synthesis (TGS) approaches have been developed in which a target protein is actively engaged in the assembly of its own bidentate ligand from a pool of smaller reactive fragments. Although TGS is relatively less explored, it demonstrates great promise to streamline drug discovery by combining screening and synthesis into a single step. Herein, we focus on the class of kinetic TGS approaches which utilize irreversible reactions to combine two reactive fragments into the inhibitory compound. These kinetic TGS applications have been successful due to the unique combination of the slow nature of the chemical reaction combining the two fragments into a single molecule and the use of reactive fragments displaying good affinities toward one of the binding sites. So far, kinetic TGS and especially in situ click chemistry, a kinetic TGS variant using the 1,3-dipolar cycloaddition of azides and alkynes, have led to the identification of highly potent inhibitors. This tutorial review focuses on kinetic TGS approaches aside from those employing the 1,3-dipolar cycloaddition of azides and alkynes, and discusses the features and advantages of these TGS approaches in detail.
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Affiliation(s)
- Xiangdong Hu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205 A, Tampa, FL 33620, USA
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528
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Moumné R, Larue V, Seijo B, Lecourt T, Micouin L, Tisné C. Tether influence on the binding properties of tRNALys3 ligands designed by a fragment-based approach. Org Biomol Chem 2010; 8:1154-9. [PMID: 20165808 DOI: 10.1039/b921232a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A small library of 1,5-triazole derivatives linking a diaminocyclopentadiol and aromatic ketones has been prepared and screened using NMR and fluorescent techniques against tRNA(Lys)(3), the HIV reverse transcription primer. The comparison of their binding properties to those of their 1,4-triazole isomers, previously discovered in a fragment-based approach, outlines the influence of the linker on affinity and binding selectivity in such an approach.
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Affiliation(s)
- Roba Moumné
- Chimie Thérapeutique, Université Paris Descartes, CNRS UMR 8638, 4 avenue de l'Observatoire, 75006, Paris, France
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529
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Leeson PD, Empfield JR. Reducing the Risk of Drug Attrition Associated with Physicochemical Properties. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2010. [DOI: 10.1016/s0065-7743(10)45024-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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530
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V. Ley S, Baumann M, R. Baxendale I, Kirschning A, Wegner J. Synthesis of Highly Substituted Nitropyrrolidines, Nitropyrrolizines and Nitropyrroles via Multicomponent-Multistep Sequences within a Flow Reactor. HETEROCYCLES 2010. [DOI: 10.3987/com-10-s(e)77] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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531
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Frearson JA, Collie IT. HTS and hit finding in academia--from chemical genomics to drug discovery. Drug Discov Today 2009; 14:1150-8. [PMID: 19793546 PMCID: PMC2814004 DOI: 10.1016/j.drudis.2009.09.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 09/09/2009] [Accepted: 09/10/2009] [Indexed: 11/19/2022]
Abstract
The liaison between academia and the pharmaceutical industry was originally served primarily through the scientific literature and limited, specific industry-academia partnerships. Some of these partnerships have resulted in drugs on the market, such as Vorinostat (Memorial Sloan-Kettering Cancer Centre and Merck) and Tenofovir (University of Leuven; Institute of Organic Chemistry and Biochemistry, Czech Republic; and GlaxoSmithKline), but the timescales from concept to clinic have, in most cases, taken many decades. We now find ourselves in a world in which the edges between these sectors are more blurred and the establishment and acceptance of high-throughput screening alongside the wider concept of 'hit discovery' in academia provides one of the key platforms required to enable this sector to contribute directly to addressing unmet medical need.
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532
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Scott DE, Dawes GJ, Ando M, Abell C, Ciulli A. A fragment-based approach to probing adenosine recognition sites by using dynamic combinatorial chemistry. Chembiochem 2009; 10:2772-9. [PMID: 19827080 PMCID: PMC4458376 DOI: 10.1002/cbic.200900537] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Indexed: 11/06/2022]
Abstract
A new strategy that combines the concepts of fragment-based drug design and dynamic combinatorial chemistry (DCC) for targeting adenosine recognition sites on enzymes is reported. We demonstrate the use of 5'-deoxy-5'-thioadenosine as a noncovalent anchor fragment in dynamic combinatorial libraries templated by Mycobacterium tuberculosis pantothenate synthetase. A benzyl disulfide derivative was identified upon library analysis by HPLC. Structural and binding studies of protein-ligand complexes by X-ray crystallography and isothermal titration calorimetry informed the subsequent optimisation of the DCC hit into a disulfide containing the novel meta-nitrobenzyl fragment that targets the pantoate binding site of pantothenate synthetase. Given the prevalence of adenosine-recognition motifs in enzymes, our results provide a proof-of-concept for using this strategy to probe adjacent pockets for a range of adenosine binding enzymes, including other related adenylate-forming ligases, kinases, and ATPases, as well as NAD(P)(H), CoA and FAD(H2) binding proteins.
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Affiliation(s)
- Duncan E. Scott
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Gwen J. Dawes
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Michiyo Ando
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Chris Abell
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
| | - Alessio Ciulli
- University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge, CB2 1EW (UK)
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533
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Hung A, Silvestre H, Wen S, Ciulli A, Blundell T, Abell C. Application of Fragment Growing and Fragment Linking to the Discovery of Inhibitors ofMycobacterium tuberculosisPantothenate Synthetase. Angew Chem Int Ed Engl 2009; 48:8452-6. [DOI: 10.1002/anie.200903821] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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534
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Hung A, Silvestre H, Wen S, Ciulli A, Blundell T, Abell C. Application of Fragment Growing and Fragment Linking to the Discovery of Inhibitors ofMycobacterium tuberculosisPantothenate Synthetase. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903821] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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535
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Biet T. Rendezvous im Magnetfeld. NMR-Spektren bei der Wirkstoffsuche. CHEM UNSERER ZEIT 2009. [DOI: 10.1002/ciuz.200900498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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536
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Smith GF. Medicinal chemistry by the numbers: the physicochemistry, thermodynamics and kinetics of modern drug design. PROGRESS IN MEDICINAL CHEMISTRY 2009; 48:1-29. [PMID: 21544956 DOI: 10.1016/s0079-6468(09)04801-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Affiliation(s)
- Graham F Smith
- Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115, USA
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