메뉴 건너뛰기




Volumn 11, Issue 6, 2016, Pages 1693-1701

Six Biophysical Screening Methods Miss a Large Proportion of Crystallographically Discovered Fragment Hits: A Case Study

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC PROTEINASE; ENDOTHIAPEPSIN; PROTEIN BINDING; PROTEINASE INHIBITOR;

EID: 84975230932     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/acschembio.5b01034     Document Type: Article
Times cited : (87)

References (60)
  • 1
    • 84862869077 scopus 로고    scopus 로고
    • Fragment-Based Approaches in Drug Discovery and Chemical Biology
    • Scott, D. E., Coyne, A. G., Hudson, S. A., and Abell, C. (2012) Fragment-Based Approaches in Drug Discovery and Chemical Biology Biochemistry 51, 4990-5003 10.1021/bi3005126
    • (2012) Biochemistry , vol.51 , pp. 4990-5003
    • Scott, D.E.1    Coyne, A.G.2    Hudson, S.A.3    Abell, C.4
  • 2
    • 84881315859 scopus 로고    scopus 로고
    • The 'rule of three' for fragment-based drug discovery: Where are we now?
    • Jhoti, H., Williams, G., Rees, D. C., and Murray, C. W. (2013) The 'rule of three' for fragment-based drug discovery: where are we now? Nat. Rev. Drug Discovery 12, 644-645 10.1038/nrd3926-c1
    • (2013) Nat. Rev. Drug Discovery , vol.12 , pp. 644-645
    • Jhoti, H.1    Williams, G.2    Rees, D.C.3    Murray, C.W.4
  • 3
    • 84881423067 scopus 로고    scopus 로고
    • Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery
    • Silvestre, H. L., Blundell, T. L., Abell, C., and Ciulli, A. (2013) Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery Proc. Natl. Acad. Sci. U. S. A. 110, 12984-12989 10.1073/pnas.1304045110
    • (2013) Proc. Natl. Acad. Sci. U. S. A. , vol.110 , pp. 12984-12989
    • Silvestre, H.L.1    Blundell, T.L.2    Abell, C.3    Ciulli, A.4
  • 4
    • 79952429629 scopus 로고    scopus 로고
    • Experiences in Fragment-Based Lead Discovery
    • Hubbard, R. E. and Murray, J. B. (2011) Experiences in Fragment-Based Lead Discovery Methods Enzymol. 493, 509-531 10.1016/B978-0-12-381274-2.00020-0
    • (2011) Methods Enzymol. , vol.493 , pp. 509-531
    • Hubbard, R.E.1    Murray, J.B.2
  • 5
    • 84887001050 scopus 로고    scopus 로고
    • A three-stage biophysical screening cascade for fragment-based drug discovery
    • Mashalidis, E. H., Sledz, P., Lang, S., and Abell, C. (2013) A three-stage biophysical screening cascade for fragment-based drug discovery Nat. Protoc. 8, 2309-2324 10.1038/nprot.2013.130
    • (2013) Nat. Protoc. , vol.8 , pp. 2309-2324
    • Mashalidis, E.H.1    Sledz, P.2    Lang, S.3    Abell, C.4
  • 6
    • 84858140219 scopus 로고    scopus 로고
    • Fragment screening using X-ray crystallography
    • Davies, T. G. and Tickle, I. J. (2011) Fragment screening using X-ray crystallography Top. Curr. Chem. 317, 33-59 10.1007/128-2011-179
    • (2011) Top. Curr. Chem. , vol.317 , pp. 33-59
    • Davies, T.G.1    Tickle, I.J.2
  • 9
    • 0026848170 scopus 로고
    • In search of new lead compounds for trypanosomiasis drug design: A protein structure-based linked-fragment approach
    • Verlinde, C. L., Rudenko, G., and Hol, W. G. (1992) In search of new lead compounds for trypanosomiasis drug design: a protein structure-based linked-fragment approach J. Comput.-Aided Mol. Des. 6, 131-147 10.1007/BF00129424
    • (1992) J. Comput.-Aided Mol. Des. , vol.6 , pp. 131-147
    • Verlinde, C.L.1    Rudenko, G.2    Hol, W.G.3
  • 10
    • 0029836953 scopus 로고    scopus 로고
    • Discovering high-affinity ligands for proteins: SAR by NMR
    • Shuker, S. B., Hajduk, P. J., Meadows, R. P., and Fesik, S. W. (1996) Discovering high-affinity ligands for proteins: SAR by NMR Science 274, 1531-1534 10.1126/science.274.5292.1531
    • (1996) Science , vol.274 , pp. 1531-1534
    • Shuker, S.B.1    Hajduk, P.J.2    Meadows, R.P.3    Fesik, S.W.4
  • 11
    • 67649341990 scopus 로고    scopus 로고
    • From fragment to clinical candidate - A historical perspective
    • Chessari, G. and Woodhead, A. J. (2009) From fragment to clinical candidate-a historical perspective Drug Discovery Today 14, 668-675 10.1016/j.drudis.2009.04.007
    • (2009) Drug Discovery Today , vol.14 , pp. 668-675
    • Chessari, G.1    Woodhead, A.J.2
  • 13
    • 33748636243 scopus 로고    scopus 로고
    • Automated protein-ligand crystallography for structure-based drug design
    • Mooij, W. T., Hartshorn, M. J., Tickle, I. J., Sharff, A. J., Verdonk, M. L., and Jhoti, H. (2006) Automated protein-ligand crystallography for structure-based drug design ChemMedChem 1, 827-838 10.1002/cmdc.200600074
    • (2006) ChemMedChem , vol.1 , pp. 827-838
    • Mooij, W.T.1    Hartshorn, M.J.2    Tickle, I.J.3    Sharff, A.J.4    Verdonk, M.L.5    Jhoti, H.6
  • 19
    • 84924040633 scopus 로고    scopus 로고
    • Advantages of crystallographic fragment screening: Functional and mechanistic insights from a powerful platform for efficient drug discovery
    • Patel, D., Bauman, J. D., and Arnold, E. (2014) Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery Prog. Biophys. Mol. Biol. 116, 92-100 10.1016/j.pbiomolbio.2014.08.004
    • (2014) Prog. Biophys. Mol. Biol. , vol.116 , pp. 92-100
    • Patel, D.1    Bauman, J.D.2    Arnold, E.3
  • 20
    • 77955982439 scopus 로고    scopus 로고
    • Structural biology in fragment-based drug design
    • Murray, C. W. and Blundell, T. L. (2010) Structural biology in fragment-based drug design Curr. Opin. Struct. Biol. 20, 497-507 10.1016/j.sbi.2010.04.003
    • (2010) Curr. Opin. Struct. Biol. , vol.20 , pp. 497-507
    • Murray, C.W.1    Blundell, T.L.2
  • 21
    • 84874414338 scopus 로고    scopus 로고
    • Fragment-based lead discovery grows up
    • Baker, M. (2013) Fragment-based lead discovery grows up Nat. Rev. Drug Discovery 12, 5-7 10.1038/nrd3926
    • (2013) Nat. Rev. Drug Discovery , vol.12 , pp. 5-7
    • Baker, M.1
  • 24
  • 25
    • 0036218648 scopus 로고    scopus 로고
    • Aspartic proteinases in disease: A structural perspective
    • Cooper, J. B. (2002) Aspartic proteinases in disease: a structural perspective Curr. Drug Targets 3, 155-173 10.2174/1389450024605382
    • (2002) Curr. Drug Targets , vol.3 , pp. 155-173
    • Cooper, J.B.1
  • 26
    • 0022354970 scopus 로고
    • Energy calculations on aspartic proteinases: Human renin, endothiapepsin and its complex with an angiotensinogen fragment analogue, H-142
    • Hemmings, A. M., Foundling, S. I., Sibanda, B. L., Wood, S. P., Pearl, L. H., and Blundell, T. (1985) Energy calculations on aspartic proteinases: human renin, endothiapepsin and its complex with an angiotensinogen fragment analogue, H-142 Biochem. Soc. Trans. 13, 1036-1041 10.1042/bst0131036
    • (1985) Biochem. Soc. Trans. , vol.13 , pp. 1036-1041
    • Hemmings, A.M.1    Foundling, S.I.2    Sibanda, B.L.3    Wood, S.P.4    Pearl, L.H.5    Blundell, T.6
  • 27
    • 84936870389 scopus 로고    scopus 로고
    • Fragment growing exploiting dynamic combinatorial chemistry of inhibitors of the aspartic protease endothiapepsin
    • Mondal, M., Groothuis, D. E., and Hirsch, A. K. H. (2015) Fragment growing exploiting dynamic combinatorial chemistry of inhibitors of the aspartic protease endothiapepsin MedChemComm 6, 1267-1271 10.1039/C5MD00157A
    • (2015) MedChemComm , vol.6 , pp. 1267-1271
    • Mondal, M.1    Groothuis, D.E.2    Hirsch, A.K.H.3
  • 29
    • 81555228214 scopus 로고    scopus 로고
    • A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes
    • Köster, H., Craan, T., Brass, S., Herhaus, C., Zentgraf, M., Neumann, L., Heine, A., and Klebe, G. (2011) A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes J. Med. Chem. 54, 7784-7796 10.1021/jm200642w
    • (2011) J. Med. Chem. , vol.54 , pp. 7784-7796
    • Köster, H.1    Craan, T.2    Brass, S.3    Herhaus, C.4    Zentgraf, M.5    Neumann, L.6    Heine, A.7    Klebe, G.8
  • 31
    • 79960994066 scopus 로고    scopus 로고
    • Efficiency of hit generation and structural characterization in fragment-based ligand discovery
    • Larsson, A., Jansson, A., Aberg, A., and Nordlund, P. (2011) Efficiency of hit generation and structural characterization in fragment-based ligand discovery Curr. Opin. Chem. Biol. 15, 482-488 10.1016/j.cbpa.2011.06.008
    • (2011) Curr. Opin. Chem. Biol. , vol.15 , pp. 482-488
    • Larsson, A.1    Jansson, A.2    Aberg, A.3    Nordlund, P.4
  • 32
    • 77956645261 scopus 로고    scopus 로고
    • Fragment-based screening by X-ray crystallography, MS and isothermal titration calorimetry to identify PNMT (phenylethanolamine N-methyltransferase) inhibitors
    • Drinkwater, N., Vu, H., Lovell, K. M., Criscione, K. R., Collins, B. M., Prisinzano, T. E., Poulsen, S. A., McLeish, M. J., Grunewald, G. L., and Martin, J. L. (2010) Fragment-based screening by X-ray crystallography, MS and isothermal titration calorimetry to identify PNMT (phenylethanolamine N-methyltransferase) inhibitors Biochem. J. 431, 51-61 10.1042/BJ20100651
    • (2010) Biochem. J. , vol.431 , pp. 51-61
    • Drinkwater, N.1    Vu, H.2    Lovell, K.M.3    Criscione, K.R.4    Collins, B.M.5    Prisinzano, T.E.6    Poulsen, S.A.7    McLeish, M.J.8    Grunewald, G.L.9    Martin, J.L.10
  • 33
    • 79952367809 scopus 로고    scopus 로고
    • Predicting the success of fragment screening by X-ray crystallography
    • Davies, D. R., Begley, D. W., Hartley, R. C., Staker, B. L., and Stewart, L. J. (2011) Predicting the success of fragment screening by X-ray crystallography Methods Enzymol. 493, 91-114 10.1016/B978-0-12-381274-2.00004-2
    • (2011) Methods Enzymol. , vol.493 , pp. 91-114
    • Davies, D.R.1    Begley, D.W.2    Hartley, R.C.3    Staker, B.L.4    Stewart, L.J.5
  • 34
    • 0036051992 scopus 로고    scopus 로고
    • High-throughput crystallography for lead discovery in drug design
    • Blundell, T. L., Jhoti, H., and Abell, C. (2002) High-throughput crystallography for lead discovery in drug design Nat. Rev. Drug Discov 1, 45-54 10.1038/nrd706
    • (2002) Nat. Rev. Drug Discov , vol.1 , pp. 45-54
    • Blundell, T.L.1    Jhoti, H.2    Abell, C.3
  • 35
    • 79952370896 scopus 로고    scopus 로고
    • Key factors for successful generation of protein-fragment structures requirement on protein, crystals, and technology
    • Böttcher, J., Jestel, A., Kiefersauer, R., Krapp, S., Nagel, S., Steinbacher, S., and Steuber, H. (2011) Key factors for successful generation of protein-fragment structures requirement on protein, crystals, and technology Methods Enzymol. 493, 61-89 10.1016/B978-0-12-381274-2.00003-0
    • (2011) Methods Enzymol. , vol.493 , pp. 61-89
    • Böttcher, J.1    Jestel, A.2    Kiefersauer, R.3    Krapp, S.4    Nagel, S.5    Steinbacher, S.6    Steuber, H.7
  • 36
    • 84941025550 scopus 로고    scopus 로고
    • Successful generation of structural information for fragment-based drug discovery
    • Oster, L., Tapani, S., Xue, Y., and Kack, H. (2015) Successful generation of structural information for fragment-based drug discovery Drug Discovery Today 20, 1104-1111 10.1016/j.drudis.2015.04.005
    • (2015) Drug Discovery Today , vol.20 , pp. 1104-1111
    • Oster, L.1    Tapani, S.2    Xue, Y.3    Kack, H.4
  • 38
    • 84859782888 scopus 로고    scopus 로고
    • Missing Fragments: Detecting Cooperative Binding in Fragment-Based Drug Design
    • Nair, P. C., Malde, A. K., Drinkwater, N., and Mark, A. E. (2012) Missing Fragments: Detecting Cooperative Binding in Fragment-Based Drug Design ACS Med. Chem. Lett. 3, 322-326 10.1021/ml300015u
    • (2012) ACS Med. Chem. Lett. , vol.3 , pp. 322-326
    • Nair, P.C.1    Malde, A.K.2    Drinkwater, N.3    Mark, A.E.4
  • 41
    • 84921059243 scopus 로고    scopus 로고
    • Thermodynamic signatures of fragment binding: Validation of direct versus displacement ITC titrations
    • Rühmann, E., Betz, M., Fricke, M., Heine, A., Schäfer, M., and Klebe, G. (2015) Thermodynamic signatures of fragment binding: Validation of direct versus displacement ITC titrations Biochim. Biophys. Acta, Gen. Subj. 1850, 647-656 10.1016/j.bbagen.2014.12.007
    • (2015) Biochim. Biophys. Acta, Gen. Subj. , vol.1850 , pp. 647-656
    • Rühmann, E.1    Betz, M.2    Fricke, M.3    Heine, A.4    Schäfer, M.5    Klebe, G.6
  • 42
    • 84941588187 scopus 로고    scopus 로고
    • Fragment Binding Can Be Either More Enthalpy-Driven or Entropy-Driven: Crystal Structures and Residual Hydration Patterns Suggest Why
    • Rühmann, E., Betz, M., Heine, A., and Klebe, G. (2015) Fragment Binding Can Be Either More Enthalpy-Driven or Entropy-Driven: Crystal Structures and Residual Hydration Patterns Suggest Why J. Med. Chem. 58, 6960-6971 10.1021/acs.jmedchem.5b00812
    • (2015) J. Med. Chem. , vol.58 , pp. 6960-6971
    • Rühmann, E.1    Betz, M.2    Heine, A.3    Klebe, G.4
  • 45
    • 84861486823 scopus 로고    scopus 로고
    • XDSAPP: A graphical user interface for the convenient processing of diffraction data using XDS
    • Krug, M., Weiss, M. S., Heinemann, U., and Mueller, U. (2012) XDSAPP: a graphical user interface for the convenient processing of diffraction data using XDS J. Appl. Crystallogr. 45, 568-572 10.1107/S0021889812011715
    • (2012) J. Appl. Crystallogr. , vol.45 , pp. 568-572
    • Krug, M.1    Weiss, M.S.2    Heinemann, U.3    Mueller, U.4
  • 49
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • (Charles, W. and Carter, J. Ed.), Academic Press
    • Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode, In Methods in Enzymology (Charles, W. and Carter, J., Ed.), pp 307-326, Academic Press.
    • (1997) Methods in Enzymology , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 52
  • 55
    • 84975228280 scopus 로고    scopus 로고
    • The PyMOL molecular graphics system on world wide web
    • DeLano, W. L. (2002) The PyMOL molecular graphics system on world wide web, http://www.pymol.org.
    • (2002)
    • DeLano, W.L.1
  • 56
    • 79951480123 scopus 로고    scopus 로고
    • R Development Core Team. ((), R Foundation for Statistical Computing, Vienna, Austria
    • R Development Core Team. ((2010) R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria.
    • (2010) R: A Language and Environment for Statistical Computing
  • 57
    • 0034650726 scopus 로고    scopus 로고
    • Exact analysis of competition ligand binding by displacement isothermal titration calorimetry
    • Sigurskjold, B. W. (2000) Exact analysis of competition ligand binding by displacement isothermal titration calorimetry Anal. Biochem. 277, 260-266 10.1006/abio.1999.4402
    • (2000) Anal. Biochem. , vol.277 , pp. 260-266
    • Sigurskjold, B.W.1
  • 58
    • 0032144872 scopus 로고    scopus 로고
    • Low-affinity binding determined by titration calorimetry using a high-affinity coupling ligand: A thermodynamic study of ligand binding to protein tyrosine phosphatase 1B
    • Zhang, Y. L. and Zhang, Z. Y. (1998) Low-affinity binding determined by titration calorimetry using a high-affinity coupling ligand: a thermodynamic study of ligand binding to protein tyrosine phosphatase 1B Anal. Biochem. 261, 139-148 10.1006/abio.1998.2738
    • (1998) Anal. Biochem. , vol.261 , pp. 139-148
    • Zhang, Y.L.1    Zhang, Z.Y.2
  • 59
    • 84861840835 scopus 로고    scopus 로고
    • High-precision isothermal titration calorimetry with automated peak-shape analysis
    • Keller, S., Vargas, C., Zhao, H., Piszczek, G., Brautigam, C. A., and Schuck, P. (2012) High-precision isothermal titration calorimetry with automated peak-shape analysis Anal. Chem. 84, 5066-5073 10.1021/ac3007522
    • (2012) Anal. Chem. , vol.84 , pp. 5066-5073
    • Keller, S.1    Vargas, C.2    Zhao, H.3    Piszczek, G.4    Brautigam, C.A.5    Schuck, P.6
  • 60
    • 33845937672 scopus 로고    scopus 로고
    • Studying multisite binary and ternary protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: Application to adaptor protein complexes in cell signaling
    • Houtman, J. C. D., Brown, P. H., Bowden, B., Yamaguchi, H., Appella, E., Samelson, L. E., and Schuck, P. (2007) Studying multisite binary and ternary protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: Application to adaptor protein complexes in cell signaling Protein Sci. 16, 30-42 10.1110/ps.062558507
    • (2007) Protein Sci. , vol.16 , pp. 30-42
    • Houtman, J.C.D.1    Brown, P.H.2    Bowden, B.3    Yamaguchi, H.4    Appella, E.5    Samelson, L.E.6    Schuck, P.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.