Fragment-Based Approaches in Drug Discovery and Chemical Biology
Abstract
Fragment-based approaches to finding novel small molecules that bind to proteins are now firmly established in drug discovery and chemical biology. Initially developed primarily in a few centers in the biotech and pharma industry, this methodology has now been adopted widely in both the pharmaceutical industry and academia. After the initial success with kinase targets, the versatility of this approach has now expanded to a broad range of different protein classes. Herein we describe recent fragment-based approaches to a wide range of target types, including Hsp90, β-secretase, and allosteric sites in human immunodeficiency virus protease and fanesyl pyrophosphate synthase. The role of fragment-based approaches in an academic research environment is also examined with an emphasis on neglected diseases such as tuberculosis. The development of a fragment library, the fragment screening process, and the subsequent fragment hit elaboration will be discussed using examples from the literature.
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FBLD has been mostly limited to the study of purified proteins in vitro due to the generally low affinity of fragment hits and the biophysical methods typically used for their discovery.
“However, due to the generally low affinity of fragment hits and the biophysical methods typically used for their discovery (e.g., NMR, surface plasmon resonance, isothermal calorimetry), FBLD has been mostly limited to the study of purified proteins in vitro11.”
From Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs (2019) · cites this paper as [11]
Fragment-based ligand discovery (FBLD) has emerged as a versatile approach for the discovery of atom-efficient, small-molecule binders for a wide range of proteins.
“Fragment-based ligand discovery (FBLD) has emerged as a versatile approach for the discovery of atom-efficient, small-molecule binders for a wide range of proteins10–12.”
From Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs (2019) · cites this paper as [11]
Cites
Molecular properties that influence the oral bioavailability of drug candidates
Veber, D. F., Johnson, S. R., Cheng, H.-Y., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002) · Journal of Medicinal Chemistry · doi:10.1021/jm020017n · Cited by 8,420 · see citing works
Modified Spin-Echo Method for Measuring Nuclear Relaxation Times
Meiboom, S., & Gill, D. (1958) · Review of Scientific Instruments · doi:10.1063/1.1716296 · Cited by 6,077 · see citing works
How many drug targets are there?
Overington, J. P., Al-Lazikani, B., & Hopkins, A. L. (2006) · Nature Reviews Drug Discovery · doi:10.1038/nrd2199 · Cited by 3,505 · see citing works
High-Resolution Crystal Structure of an Engineered Human β 2 -Adrenergic G Protein–Coupled Receptor
Cherezov, V., Rosenbaum, D. M., Hanson, M. A., Rasmussen, S. G. F., Thian, F. S., Kobilka, T. S., Choi, H., Kühn, P., Weis, W. I., Kobilka, B. K., et al. (2007) · Science · doi:10.1126/science.1150577 · Cited by 3,280 · see citing works
Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design
Meanwell, N. A. (2011) · Journal of Medicinal Chemistry · doi:10.1021/jm1013693 · Cited by 2,886 · see citing works
Niesen, F., Berglund, H., & Vedadi, M. (2007) · Nature Protocols · doi:10.1038/nprot.2007.321 · Cited by 2,420 · see citing works
Discovering High-Affinity Ligands for Proteins: SAR by NMR
Shuker, S. B., Hajduk, P. J., Meadows, R. P., & Fesik, S. W. (1996) · Science · doi:10.1126/science.274.5292.1531 · Cited by 2,045 · see citing works
Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma
Bollag, G. E., Hirth, P., Tsai, J. Y., Zhang, J., Ibrahim, P. N., Cho, H., Spevak, W. R., Zhang, C., Zhang, Y., Habets, G. G. M., et al. (2010) · Nature · doi:10.1038/nature09454 · Cited by 1,841 · see citing works
The 2.6 Angstrom Crystal Structure of a Human A 2A Adenosine Receptor Bound to an Antagonist
Jaakola, V., Griffith, M. T., Hanson, M. A., Cherezov, V., Chien, E. Y. T., Lane, J. R., IJzerman, A. P., & Stevens, R. C. (2008) · Science · doi:10.1126/science.1164772 · Cited by 1,786 · see citing works
Structures of the CXCR4 Chemokine GPCR with Small-Molecule and Cyclic Peptide Antagonists
Wu, B., Chien, E. Y. T., Mol, C. D., Fenalti, G., Liu, W., Katritch, V., Abagyan, R. A., Brooun, A., Wells, P. G., Bi, F. C., et al. (2010) · Science · doi:10.1126/science.1194396 · Cited by 1,785 · see citing works
Structure of a nanobody-stabilized active state of the β2 adrenoceptor
Rasmussen, S. G. F., Choi, H., Fung, J. J., Pardon, E., Casarosa, P., Chae, P. S., DeVree, B. T., Rosenbaum, D. M., Thian, F. S., Kobilka, T. S., et al. (2011) · Nature · doi:10.1038/nature09648 · Cited by 1,682 · see citing works
A ‘Rule of Three’ for fragment-based lead discovery?
Congreve, M., Carr, R. A. E., Murray, C. W., & Jhoti, H. (2003) · Drug Discovery Today · doi:10.1016/s1359-6446(03)02831-9 · Cited by 1,365 · see citing works
Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity
Tsai, J., Lee, J. T., Wang, W., Zhang, J., Cho, H., Mamo, S., Bremer, R., Gillette, S., Kong, J., Haass, N. K., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0711741105 · Cited by 1,346 · see citing works
Structure of a β1-adrenergic G-protein-coupled receptor
Warne, T., Serrano‐Vega, M. J., Baker, J. G., Moukhametzianov, R., Edwards, P. C., Henderson, R. A., Leslie, A. G. W., Tate, C. G., & Schertler, G. F. X. (2008) · Nature · doi:10.1038/nature07101 · Cited by 1,345 · see citing works
Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist
Chien, E. Y. T., Liu, W., Zhao, Q., Katritch, V., Han, G. W., Hanson, M. A., Shi, L., Newman, A. H., Javitch, J. A., Cherezov, V., et al. (2010) · Science · doi:10.1126/science.1197410 · Cited by 1,134 · see citing works
On the attribution and additivity of binding energies
Jencks, W. P. (1981) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.78.7.4046 · Cited by 914 · see citing works
The maximal affinity of ligands
Kuntz, I. D., Chen, K., Sharp, K. A., & Kollman, P. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.18.9997 · Cited by 859 · see citing works
Erlanson, D. A., McDowell, R. S., & O'Brien, T. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm040031v · Cited by 645 · see citing works
High-throughput crystallography for lead discovery in drug design
Blundell, T. L., Jhoti, H., & Abell, C. (2002) · Nature Reviews Drug Discovery · doi:10.1038/nrd706 · Cited by 529 · see citing works
Self-citationDalvit, C., Pevarello, P., Tatò, M., Veronesi, M., Vulpetti, A., & Sundström, M. (2000) · Journal of Biomolecular NMR · doi:10.1023/a:1008354229396 · Cited by 470 · see citing works
Site-directed ligand discovery
Erlanson, D. A., Braisted, A. C., Raphael, D. R., Randal, M., Stroud, R. M., Gordon, E. M., & Wells, J. A. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.17.9367 · Cited by 466 · see citing works
Fink, T., & Reymond, J. (2007) · Journal of Chemical Information and Modeling · doi:10.1021/ci600423u · Cited by 457 · see citing works
The design of drugs for HIV and HCV
Clercq, E. D. (2007) · Nature Reviews Drug Discovery · doi:10.1038/nrd2424 · Cited by 429 · see citing works
Nonleadlikeness and leadlikeness in biochemical screening
Rishton, G. M. (2003) · Drug Discovery Today · doi:10.1016/s1359644602025722 · Cited by 381 · see citing works
Hajduk, P. J., Olejniczak, E. T., & Fesik, S. W. (1997) · Journal of the American Chemical Society · doi:10.1021/ja9715962 · Cited by 372 · see citing works
Wyatt, P. G., Woodhead, A., Berdini, V., Boulstridge, J. A., Carr, M. G., Cross, D. M., Davis, D., Devine, L. A., Early, T. R., Feltell, R. E., et al. (2008) · Journal of Medicinal Chemistry · doi:10.1021/jm800382h · Cited by 346 · see citing works
Keynote review: Structural biology and drug discovery
Congreve, M., Murray, C. W., & Blundell, T. L. (2005) · Drug Discovery Today · doi:10.1016/s1359-6446(05)03484-7 · Cited by 338 · see citing works
Howard, S., Berdini, V., Boulstridge, J. A., Carr, M. G., Cross, D. M., Curry, J. E., Devine, L. A., Early, T. R., Fazal, L., Gill, A. L., et al. (2008) · Journal of Medicinal Chemistry · doi:10.1021/jm800984v · Cited by 338 · see citing works
Discovering novel ligands for macromolecules using X-ray crystallographic screening
Nienaber, V. L., Richardson, P. L., Klighofer, V., Bouska, J. J., Giranda, V. L., & Greer, J. (2000) · Nature Biotechnology · doi:10.1038/80319 · Cited by 322 · see citing works
Discovery of a Potent Inhibitor of the Antiapoptotic Protein Bcl-x L from NMR and Parallel Synthesis
Petros, A. M., Dinges, J., Augeri, D. J., Baumeister, S. A., Betebenner, D. A., Bures, M. G., Elmore, S. W., Hajduk, P. J., Joseph, M. K., Landis, S. K., et al. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm0507532 · Cited by 295 · see citing works
Ertl, P. (2002) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci0255782 · Cited by 294 · see citing works
Route to three-dimensional fragments using diversity-oriented synthesis
Hung, A. W., Ramek, A., Wang, Y., Kaya, T., Wilson, J. A., Clemons, P. A., & Young, D. W. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1015271108 · Cited by 272 · see citing works
Woodhead, A., Angove, H. C., Carr, M. G., Chessari, G., Congreve, M., Coyle, J. E., Cosme, J., Graham, B. L., Day, P. J., Downham, R., et al. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm100060b · Cited by 267 · see citing works
Nitric Oxide: Chemical Puzzles Posed by a Biological Messenger
Pfeiffer, S., Mayer, B., & Hemmens, B. (1999) · Angewandte Chemie International Edition · doi:10.1002/(sici)1521-3773(19990614)38:12 · Cited by 266 · see citing works
Applications of ESI-MS in drug discovery: interrogation of noncovalent complexes
Hofstadler, S. A., & Sannes‐Lowery, K. A. (2006) · Nature Reviews Drug Discovery · doi:10.1038/nrd2083 · Cited by 250 · see citing works
CYTOCHROME P450 ACTIVATION OF ARYLAMINES AND HETEROCYCLIC AMINES
Kim, D., & Guengerich, F. P. (2004) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.45.120403.100010 · Cited by 250 · see citing works
Edwards, P. D., Albert, J. S., Sylvester, M. A., Aharony, D., Andisik, D. W., Callaghan, O., Campbell, J. B., Carr, R. A. E., Chessari, G., Congreve, M., et al. (2007) · Journal of Medicinal Chemistry · doi:10.1021/jm070829p · Cited by 213 · see citing works
Structural biology in fragment-based drug design
Murray, C. W., & Blundell, T. L. (2010) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.04.003 · Cited by 208 · see citing works
Murray, C. W., & Verdonk, M. L. (2002) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1022446720849 · Cited by 201 · see citing works
SPR-based Fragment Screening: Advantages and Applications
Neumann, T., Junker, H.-D., Schmidt, K., & Sekul, R. (2007) · Current Topics in Medicinal Chemistry · doi:10.2174/156802607782341073 · Cited by 190 · see citing works
Chung, C., Dean, A. W., Woolven, J. M., & Bamborough, P. (2011) · Journal of Medicinal Chemistry · doi:10.1021/jm201320w · Cited by 188 · see citing works
Murray, C. W., Carr, M. G., Callaghan, O., Chessari, G., Congreve, M., Cowan, S., Coyle, J. E., Downham, R., Figueroa, E., Frederickson, M., et al. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm100059d · Cited by 186 · see citing works
Apo and Inhibitor Complex Structures of BACE (β-secretase)
Patel, S., Vuillard, L. M., Cleasby, A., Murray, C. W., & Yon, J. R. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.08.018 · Cited by 180 · see citing works
Bamborough, P., Diallo, H., Goodacre, J. D., Gordon, L. J., Lewis, A. J., Seal, J. T., Wilson, D. M., Woodrow, M. D., & Chung, C. (2011) · Journal of Medicinal Chemistry · doi:10.1021/jm201283q · Cited by 175 · see citing works
Brough, P. A., Barril, X., Borgognoni, J., Chêne, P., Davies, N. G. M., Davis, B. J., Drysdale, M. J., Dymock, B. W., Eccles, S. A., Garcı́a-Echeverrı́a, C., et al. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm900357y · Cited by 175 · see citing works
NMR-Based Discovery of Lead Inhibitors That Block DNA Binding of the Human Papillomavirus E2 Protein
Hajduk, P. J., Dinges, J., Miknis, G. F., Merlock, M., Middleton, T. R., Kempf, D. J., Egan, D. A., Walter, K. A., Robins, T. S., Shuker, S. B., et al. (1997) · Journal of Medicinal Chemistry · doi:10.1021/jm9703404 · Cited by 169 · see citing works
Fragment Screening by Surface Plasmon Resonance
Navratilova, I. H., & Hopkins, A. L. (2010) · ACS Medicinal Chemistry Letters · doi:10.1021/ml900002k · Cited by 168 · see citing works
Discovery and development of heat shock protein 90 inhibitors
Taldone, T., Sun, W., & Chiosis, G. (2008) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2008.10.087 · Cited by 162 · see citing works
A class of selective antibacterials derived from a protein kinase inhibitor pharmacophore
Miller, J. R., Dunham, S. A., Mochalkin, I., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811275106 · Cited by 159 · see citing works
Discovery of a Novel Warhead against β-Secretase through Fragment-Based Lead Generation
Geschwindner, S., Olsson, L., Albert, J. S., et al. (2007) · Journal of Medicinal Chemistry · doi:10.1021/jm070825k · Cited by 149 · see citing works
Hung, A. W., Silvestre, H. L., Wen, S., et al. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200903821 · Cited by 147 · see citing works
Application of Fragment Screening by X-ray Crystallography to β-Secretase
Murray, C. W., Callaghan, O., Chessari, G., Cleasby, A., Congreve, M., Frederickson, M., Hartshorn, M. J., McMenamin, R. L., Patel, S., & Wallis, N. G. (2007) · Journal of Medicinal Chemistry · doi:10.1021/jm0611962 · Cited by 145 · see citing works
Congreve, M., Aharony, D., Albert, J. S., Callaghan, O., Campbell, J. B., Carr, R. A. E., Chessari, G., Cowan, S., Edwards, P. D., Frederickson, M., et al. (2007) · Journal of Medicinal Chemistry · doi:10.1021/jm061197u · Cited by 144 · see citing works
Integration of fragment screening and library design
Siegal, G., Eiso, A. B., & Schultz, J. (2007) · Drug Discovery Today · doi:10.1016/j.drudis.2007.08.005 · Cited by 142 · see citing works
Eakin, A. E., Green, O., Hales, N. J., et al. (2011) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.05485-11 · Cited by 138 · see citing works
Protein Thermal Shifts to Identify Low Molecular Weight Fragments
Kranz, J. K., & Schalk‐Hihi, C. (2011) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-381274-2.00011-x · Cited by 136 · see citing works
Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors
Howard, N., Abell, C., Blakemore, W. E., Chessari, G., Congreve, M., Howard, S., Jhoti, H., Murray, C. W., Seavers, L. C. A., & van Montfort, R. L. M. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm050850v · Cited by 134 · see citing works
Self-citationDocking Performance of Fragments and Druglike Compounds
Verdonk, M. L., Giangreco, I., Hall, R. J., Korb, O., Mortenson, P. N., & Murray, C. W. (2011) · Journal of Medicinal Chemistry · doi:10.1021/jm200558u · Cited by 130 · see citing works
Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery
Jahnke, W., Rondeau, J., Cotesta, S., Marzinzik, A. L., Pellé, X., Geiser, M., Strauss, A., Götte, M., Bitsch, F., Hemmig, R., et al. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.421 · Cited by 129 · see citing works
Identifying Chelators for Metalloprotein Inhibitors Using a Fragment-Based Approach
Jacobsen, J. A., Fullagar, J. L., Miller, M. T., & Cohen, S. M. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm101266s · Cited by 129 · see citing works
Lessons for fragment library design: analysis of output from multiple screening campaigns
Chen, I., & Hubbard, R. E. (2009) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-009-9280-5 · Cited by 122 · see citing works
Zhu, Z., Sun, Z. J., Ye, Y., Voigt, J. H., Strickland, C., Smith, E. M., Cumming, J. N., Wang, L., Wong, J. K. Y., Wang, Y., et al. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm901408p · Cited by 121 · see citing works
Fragment Screening of Stabilized G-Protein-Coupled Receptors Using Biophysical Methods
Congreve, M., Rich, R. L., Myszka, D. G., et al. (2011) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-381274-2.00005-4 · Cited by 120 · see citing works
Discovery of Leukotriene A4 Hydrolase Inhibitors Using Metabolomics Biased Fragment Crystallography
Davies, D. R., Mamat, B., Magnússon, Ó. Þ., Christensen, J., Haraldsson, M. H., Mishra, R. K., Pease, B., Hansen, E., Singh, J., Zembower, D. E., et al. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm900259h · Cited by 119 · see citing works
Basse, N., Kaar, J. L., Settanni, G., Joerger, A. C., Rutherford, T. J., & Fersht, A. R. (2010) · Chemistry & Biology · doi:10.1016/j.chembiol.2009.12.011 · Cited by 117 · see citing works
Discovery and Design of Novel HSP90 Inhibitors Using Multiple Fragment‐based Design Strategies
Huth, J. R., Park, C., Petros, A. M., Kunzer, A. R., Wendt, M. D., Wang, X., Lynch, C. L., Mack, J. C., Swift, K. M., Judge, R. A., et al. (2007) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2007.00535.x · Cited by 116 · see citing works
Hung, A. W., Silvestre, H. L., Wen, S., et al. (2009) · Angewandte Chemie · doi:10.1002/ange.200903821 · Cited by 115 · see citing works
Fragment-based approaches to enzyme inhibition
Ciulli, A., & Abell, C. (2007) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2007.09.003 · Cited by 109 · see citing works
Self-citationReductive activation of nitroheterocyclic compounds
Tocher, J. H. (1997) · General Pharmacology The Vascular System · doi:10.1016/s0306-3623(96)00283-2 · Cited by 108 · see citing works
Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery
Valkov, E., Sharpe, T., Marsh, M., Greive, S., & Hyvönen, M. (2011) · Topics in Current Chemistry · doi:10.1007/128_2011_265 · Cited by 107 · see citing works
Mochalkin, I., Miller, J. R., Narasimhan, L. S., et al. (2009) · ACS Chemical Biology · doi:10.1021/cb9000102 · Cited by 107 · see citing works
Wang, Y., Strickland, C., Voigt, J. H., Kennedy, M. E., Beyer, B. M., Senior, M. M., Smith, E. M., Nechuta, T. L., Madison, V., Czarniecki, M., et al. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm901472u · Cited by 103 · see citing works
Discovery of cell-active phenyl-imidazole Pin1 inhibitors by structure-guided fragment evolution
Potter, A. J., Oldfield, V., Nunns, C. L., et al. (2010) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2010.09.063 · Cited by 97 · see citing works
Native Ms: An ‘Esi’ Way to Support Structure- and Fragment-Based Drug Discovery
Vivat, V., Atmanène, C., Zeyer, D., DORSSELAER, A. V., & Cianférani, S. (2009) · Future Medicinal Chemistry · doi:10.4155/fmc.09.141 · Cited by 87 · see citing works
Drugging challenging targets using fragment-based approaches
Coyne, A. G., Scott, D. E., & Abell, C. (2010) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2010.02.010 · Cited by 86 · see citing works
Self-citationGroup Efficiency: A Guideline for Hits‐to‐Leads Chemistry
Verdonk, M. L., & Rees, D. C. (2008) · ChemMedChem · doi:10.1002/cmdc.200800132 · Cited by 85 · see citing works
Edink, E., Rucktooa, P., Retra, K., Akdemir, A., Nahar, T. T., Zuiderveld, O. P., van Elk, R., Janssen, E., van Nierop, P., van Muijlwijk‐Koezen, J. E., et al. (2011) · Journal of the American Chemical Society · doi:10.1021/ja110571r · Cited by 80 · see citing works
Fragment-Based Drug Discovery and X-Ray Crystallography
Davies, T. G., & Hyvönen, M. (2012) · Topics in current chemistry · doi:10.1007/978-3-642-27540-1 · Cited by 77 · see citing works
Sledz, P., Silvestre, H. L., Hung, A. W., et al. (2010) · Journal of the American Chemical Society · doi:10.1021/ja100595u · Cited by 75 · see citing works
Fragment Library Screening and Lead Characterization Using SPR Biosensors
Danielson, U. H. (2009) · Current Topics in Medicinal Chemistry · doi:10.2174/156802609790102392 · Cited by 70 · see citing works
Tanaka, R., Squires, M. S., Kimura, S. H., Yokota, A., Nagao, R., Yamauchi, T., Takeuchi, M., Yao, H., Reule, M., Smyth, T., et al. (2010) · Blood · doi:10.1182/blood-2009-03-211466 · Cited by 69 · see citing works
Verlinde, C. L. M. J., Rudenko, G., & Hol, W. G. J. (1992) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf00129424 · Cited by 69 · see citing works
Fragment‐Based Screen against HIV Protease
Perryman, A. L., Zhang, Q., Soutter, H. H., Rosenfeld, R. J., McRee, D. E., Olson, A. J., Elder, J. E., & Stout, C. D. (2010) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2009.00943.x · Cited by 66 · see citing works
NMR-based screening: a powerful tool in fragment-based drug discovery
Klages, J., Coles, M. P., & Kessler, H. (2007) · The Analyst · doi:10.1039/b709658p · Cited by 62 · see citing works
The discovery of novel benzofuran-2-carboxylic acids as potent Pim-1 inhibitors
Xiang, Y., Hirth, B. H., Asmussen, G., et al. (2011) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2011.03.030 · Cited by 62 · see citing works
Fragment-based discovery of hepatitis C virus NS5b RNA polymerase inhibitors
Antonysamy, S., Aubol, B. E., Blaney, J., et al. (2008) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2008.03.056 · Cited by 60 · see citing works
A Fragment-Based Approach to Identifying Ligands for Riboswitches
Chen, L., Cressina, E., Leeper, F. J., et al. (2010) · ACS Chemical Biology · doi:10.1021/cb9003139 · Cited by 59 · see citing works
Fragment screening against the thiamine pyrophosphate riboswitchthiM
Cressina, E., Chen, L., Abell, C., et al. (2010) · Chemical Science · doi:10.1039/c0sc00406e · Cited by 58 · see citing works
Self-citationApplication of NMR Screening in Drug Discovery
Fejzo, J., Lepre, C. A., & Xie, X. (2003) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026033392796 · Cited by 56 · see citing works
Molecular model of shikimate kinase from Mycobacterium tuberculosis
de Azevedo, W. F., Canduri, F., de Oliveira, J. S., et al. (2002) · Biochemical and Biophysical Research Communications · doi:10.1016/s0006-291x(02)00632-0 · Cited by 51 · see citing works
Ligand specificity, privileged substructures and protein druggability from fragment-based screening
Barelier, S., & Krimm, I. (2011) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2011.02.020 · Cited by 49 · see citing works
A Fragment-Based Approach for the Discovery of Isoform-Specific p38α Inhibitors
Chen, J., Zhang, Z., Stebbins, J. L., et al. (2007) · ACS Chemical Biology · doi:10.1021/cb700025j · Cited by 49 · see citing works
Fragment‐based Identification of Hsp90 Inhibitors
Barker, J. J., Barker, O., Boggio, R., Chauhan, V., Cheng, R. K. Y., Corden, V., Courtney, S. M., Edwards, N., Falque, V. M., Fusar, F., et al. (2009) · ChemMedChem · doi:10.1002/cmdc.200900011 · Cited by 48 · see citing works
Drinkwater, N., Vu, H., Lovell, K. M., Criscione, K. R., Collins, B. M., Prisinzano, T. E., Poulsen, S., McLeish, M. J., Grunewald, G. L., & Martin, J. L. (2010) · Biochemical Journal · doi:10.1042/bj20100651 · Cited by 45 · see citing works
Geitmann, M., Elinder, M., Seeger, C., Brandt, P., de Esch, I. J. P., & Danielson, U. H. (2011) · Journal of Medicinal Chemistry · doi:10.1021/jm1010513 · Cited by 44 · see citing works
The Use of GPCR Structures in Drug Design
Congreve, M., Langmead, C. J., & Marshall, F. H. (2011) · Advances in pharmacology · doi:10.1016/b978-0-12-385952-5.00011-7 · Cited by 43 · see citing works
Fragment-based discovery and optimization of BACE1 inhibitors
Madden, J., Dod, J. R., Godemann, R., Kraemer, J., Smith, M., Biniszkiewicz, M., Hallett, D. J., Barker, J. J., Dyekjær, J. D., & Hesterkamp, T. (2010) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2010.06.089 · Cited by 42 · see citing works
Electron Density Guided Fragment-Based Lead Discovery of Ketohexokinase Inhibitors
Gibbs, A. C., Abad, M. C., Zhang, X., Tounge, B. A., Lewandowski, F. A., Struble, G. T., Sun, W., Sui, Z., & Kuo, L. C. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm100677s · Cited by 41 · see citing works
Structure‐Based and in silico Design of Hsp90 Inhibitors
Sgobba, M., & Rastelli, G. (2009) · ChemMedChem · doi:10.1002/cmdc.200900256 · Cited by 40 · see citing works
Fragment based discovery of a novel and selective PI3 kinase inhibitor
Hughes, S. J., Millan, D. S., Kilty, I., et al. (2011) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2011.07.117 · Cited by 39 · see citing works
Makara, G. M. (2007) · Journal of Medicinal Chemistry · doi:10.1021/jm0700316 · Cited by 32 · see citing works
Huggins, D. J., McKenzie, G. J., Robinson, D. D., Narvaez, A. J., Hardwick, B. S., Roberts-Thomson, M., Venkitaraman, A. R., Grant, G. H., & Payne, M. C. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000880 · Cited by 30 · see citing works
Structure-guided expansion of kinase fragment libraries driven by support vector machine models
Erickson, J. A., Mader, M. M., Watson, I. A., Webster, Y., Higgs, R. E., Bell, M. A., & Vieth, M. (2009) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2009.12.002 · Cited by 25 · see citing works
Validation of the SPROUT de novo design program
Law, J. M. S., Fung, D. Y. K., Zsoldos, Z., et al. (2003) · Journal of Molecular Structure THEOCHEM · doi:10.1016/j.theochem.2003.08.104 · Cited by 25 · see citing works
SERAPhiC: A Benchmark for in Silico Fragment-Based Drug Design
Favia, A. D., Bottegoni, G., Nobeli, I., et al. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci2003363 · Cited by 21 · see citing works
Abdel‐Rahman, N., Martínez-Arias, A., & Blundell, T. L. (2011) · Biochemical Society Transactions · doi:10.1042/bst0391327 · Cited by 17 · see citing works
Design of a High Fragment Efficiency Library by Molecular Graph Theory
Venhorst, J., Núñez, S., & Kruse, C. G. (2010) · ACS Medicinal Chemistry Letters · doi:10.1021/ml100163s · Cited by 14 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Proteome-wide covalent ligand discovery in native biological systems
Backus, K. M., Correia, B. E., Lum, K. M., Forli, S., Horning, B. D., González-Páez, G. E., Chatterjee, S., Lanning, B. R., Teijaro, J. R., Olson, A. J., et al. (2016) · Nature · doi:10.1038/nature18002 · Cited by 940 · see citing works
Ligand and Target Discovery by Fragment-Based Screening in Human Cells
Parker, C. G., Galmozzi, A., Wang, Y., Correia, B. E., Sasaki, K., Joslyn, C. M., Kim, A. S., Cavallaro, C. L., Lawrence, R. M., Johnson, S. R., et al. (2017) · Cell · doi:10.1016/j.cell.2016.12.029 · Cited by 439 · see citing works
Targeting protein–protein interactions as an anticancer strategy
Ivanov, A. A., Khuri, F. R., & Fu, H. (2013) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2013.04.007 · Cited by 401 · see citing works
An Activity-Guided Map of Electrophile-Cysteine Interactions in Primary Human T Cells
Vinogradova, E. V., Zhang, X., Remillard, D., Lazar, D. C., Suciu, R. M., Wang, Y., Bianco, G., Yamashita, Y., Crowley, V. M., Schafroth, M. A., et al. (2020) · Cell · doi:10.1016/j.cell.2020.07.001 · Cited by 351 · see citing works
Rapid Covalent-Probe Discovery by Electrophile-Fragment Screening
Resnick, E., Bradley, A., Gan, J., Douangamath, A., Krojer, T., Sethi, R., Geurink, P. P., Aimon, A., Amitai, G., Bellini, D., et al. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b02822 · Cited by 335 · see citing works
Oncogenic protein interfaces: small molecules, big challenges
Nero, T. L., Morton, C. J., Holien, J. K., Wielens, J., & Parker, M. W. (2014) · Nature Reviews Cancer · doi:10.1038/nrc3690 · Cited by 312 · see citing works
Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs
Wang, Y., Dix, M. M., Bianco, G., Remsberg, J. R., Lee, H.-Y., Kalocsay, M., Gygi, S. P., Forli, S., Vite, G., Lawrence, R. M., et al. (2019) · Nature Chemistry · doi:10.1038/s41557-019-0351-5 · Cited by 179 · see citing works
Chessari, G., Buck, I. M., Day, J. E. H., Day, P. J., Iqbal, A., Johnson, C. N., Lewis, E. J., Martins, V., Miller, D., Reader, M., et al. (2015) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b00706 · Cited by 90 · see citing works
High‐Throughput Kinetic Analysis for Target‐Directed Covalent Ligand Discovery
Craven, G. B., Affron, D. P., Allen, C. E., Matthies, S., Greener, J. G., Morgan, R. M. L., Tate, E. W., Armstrong, A., & Mann, D. J. (2018) · Angewandte Chemie International Edition · doi:10.1002/anie.201711825 · Cited by 73 · see citing works
Chacón Simon, S., Wang, F., Thomas, L. R., Phan, J., Zhao, B., Olejniczak, E. T., Macdonald, J. D., Shaw, J. G., Schlund, C., Payne, W., et al. (2020) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.0c00224 · Cited by 76 · see citing works
Cierpicki, T., & Grembecka, J. (2015) · Immunological Reviews · doi:10.1111/imr.12244 · Cited by 53 · see citing works
Golden, M. S., Cote, S. M., Sayeg, M., Zerbe, B. S., Villar, E. A., Beglov, D., Sazinsky, S. L., Georgiadis, R. M., Vajda, S., Kozakov, D., et al. (2013) · Journal of the American Chemical Society · doi:10.1021/ja400914z · Cited by 47 · see citing works
Artificial Intelligence and the Future of Diagnostic and Therapeutic Radiopharmaceutical Development
Ataeinia, B., & Heidari, P. (2021) · PET Clinics · doi:10.1016/j.cpet.2021.06.008 · Cited by 31 · see citing works
Fragment-based drug discovery of triazole inhibitors to block PDEδ-RAS protein-protein interaction
Chen, D., Chen, Y., Lian, F., Chen, L., Li, Y., Cao, D., Wang, X., Chen, L., Li, J., Meng, T., et al. (2019) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2018.12.018 · Cited by 31 · see citing works
- Authors
- Scott, D. E., Coyne, A. G., Hudson, S. A., & Abell, C.
- Affiliations
- University of Cambridge (GB)
- Corresponding author
- Abell, Chris
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-06-14
- Volume
- 51
- Issue
- 25
- Pages
- 4990-5003
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- OpenAlex
- W2314041260
- Cited by
- 460
- References
- 108
- Citations by year
- 2026: 18 · 2025: 16 · 2024: 24 · 2023: 22 · 2022: 24 · 2021: 28 · 2020: 33 · 2019: 39 · 2018: 39 · 2017: 45 · 2016: 46 · 2015: 40 · 2014: 38 · 2013: 43 · 2012: 5
- FWCI
- 4.66
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Biochemistry (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust (GR 080083, GR091058)
- Biotechnology and Biological Sciences Research Council (BB/I019669/1)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- fragment-based drug discovery, fragment libraries, fragment screening, protein-ligand binding, kinase inhibitors, HSP90, beta-secretase, HIV protease, allosteric site, farnesyl diphosphate synthase, tuberculosis, neglected diseases
- MeSH terms
- Humans, Peptide Fragments, Protein Binding, Crystallography, X-Ray, Small Molecule Libraries, Drug Discovery, High-Throughput Screening Assays
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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