메뉴 건너뛰기




Volumn 8, Issue 3, 2005, Pages 355-364

Maximizing discovery efficiency with a computationally driven fragment approach

Author keywords

Binding site predictions; Fragment; Free energy; Grand canonical ensembles; Protein flexibility; Simulated annealing

Indexed keywords

NEW DRUG;

EID: 17844391276     PISSN: 13676733     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review
Times cited : (35)

References (39)
  • 1
    • 0034677966 scopus 로고    scopus 로고
    • Drug discovery: A historical perspective
    • Drews J: Drug discovery: A historical perspective. Science (2000) 287(5640):1960-1964.
    • (2000) Science , vol.287 , Issue.5640 , pp. 1960-1964
    • Drews, J.1
  • 2
    • 17844384139 scopus 로고    scopus 로고
    • Tufts Center for the Study of Drug Development, Boston, MA, USA
    • Tufts Center for the Study of Drug Development, Boston, MA, USA. http://csdd.tufts.edu/
  • 3
    • 17844400240 scopus 로고    scopus 로고
    • Welcome, industry update and meeting overview
    • Dana Point, CA, USA
    • Burrill GS: Welcome, industry update and meeting overview. The Biotech Meeting at Laguna Niguel, Dana Point, CA, USA (2004).
    • (2004) The Biotech Meeting at Laguna Niguel
    • Burrill, G.S.1
  • 4
    • 0030039619 scopus 로고    scopus 로고
    • The art and practice of structure-based drug design: A molecular modeling perspective
    • Bohacek RD, McMartin C, Guida WD: The art and practice of structure-based drug design: A molecular modeling perspective. Med Res Rev (1996) 16(1):3-50.
    • (1996) Med Res Rev , vol.16 , Issue.1 , pp. 3-50
    • Bohacek, R.D.1    McMartin, C.2    Guida, W.D.3
  • 5
    • 0019407381 scopus 로고
    • On the attribution and additivity of binding energies
    • Jencks WP: On the attribution and additivity of binding energies. Proc Natl Acad Sci USA (1981) 78(7):4046-4050. Provides an important historical perspective on fragment-based approaches to drug discovery.
    • (1981) Proc Natl Acad Sci USA , vol.78 , Issue.7 , pp. 4046-4050
    • Jencks, W.P.1
  • 6
    • 3042689621 scopus 로고    scopus 로고
    • Fragment-based drug discovery
    • Erlanson DA, McDowell RS, O'Brien T: Fragment-based drug discovery. J Med Chem (2004) 47(14):3463-3482. A comprehensive review of fragment-based discovery approaches.
    • (2004) J Med Chem , vol.47 , Issue.14 , pp. 3463-3482
    • Erlanson, D.A.1    McDowell, R.S.2    O'Brien, T.3
  • 7
    • 0029836953 scopus 로고    scopus 로고
    • Discovering high-affinity ligands for proteins: SAR by NMR
    • Shuker SB, Hajduk PJ, Meadows RP, Fesik SW: Discovering high-affinity ligands for proteins: SAR by NMR, Science (1996) 274(5292):1531-1534.
    • (1996) Science , vol.274 , Issue.5292 , pp. 1531-1534
    • Shuker, S.B.1    Hajduk, P.J.2    Meadows, R.P.3    Fesik, S.W.4
  • 8
    • 0033213957 scopus 로고    scopus 로고
    • The SHAPES strategy: An NMR-based approach for lead generation in drug discovery
    • Fejzo J, Lepre CA, Peng JW, Bemis GW, Ajay, Murcko MA. Moore JM: The SHAPES strategy: An NMR-based approach for lead generation in drug discovery. Chem Biol (1999) 6(10):755-769.
    • (1999) Chem Biol , vol.6 , Issue.10 , pp. 755-769
    • Fejzo, J.1    Lepre, C.A.2    Peng, J.W.3    Bemis, G.W.4    Ajay5    Murcko, M.A.6    Moore, J.M.7
  • 9
    • 0038198865 scopus 로고    scopus 로고
    • High-throughput crystallography to enhance drug discovery
    • Sharff A, Jhoti H: High-throughput crystallography to enhance drug discovery. Curr Opin Chem Biol (2003) 7(3):340-345. An informative review on the status of fragment-based crystallographic methodology.
    • (2003) Curr Opin Chem Biol , vol.7 , Issue.3 , pp. 340-345
    • Sharff, A.1    Jhoti, H.2
  • 10
    • 0037325440 scopus 로고    scopus 로고
    • Astex, Structural Genomix and Syrrx. I can see clearly now: Structural biology and drug discovery
    • Mountain V: Astex, Structural Genomix and Syrrx. I can see clearly now: Structural biology and drug discovery. Chem Biol (2003) 10(2):95-98.
    • (2003) Chem Biol , vol.10 , Issue.2 , pp. 95-98
    • Mountain, V.1
  • 12
    • 0027658106 scopus 로고
    • A novel computational tool for automated structure-based drug design
    • Bohm HJ: A novel computational tool for automated structure-based drug design. J Mol Recognit (1993) 6(3):131-137.
    • (1993) J Mol Recognit , vol.6 , Issue.3 , pp. 131-137
    • Bohm, H.J.1
  • 13
    • 0026903902 scopus 로고
    • Automated site-directed drug design: The generation of a basic set of fragments to be used for automated structure assembly
    • Chau PL, Dean PM: Automated site-directed drug design: The generation of a basic set of fragments to be used for automated structure assembly. J Comput Aided Mol Des (1992) 6(4):385-396.
    • (1992) J Comput Aided Mol des , vol.6 , Issue.4 , pp. 385-396
    • Chau, P.L.1    Dean, P.M.2
  • 14
    • 0034257202 scopus 로고    scopus 로고
    • Dynamic ligand design and combinatorial optimization: Designing inhibitors to endothiapepsin
    • Stultz CM, Karplus M: Dynamic ligand design and combinatorial optimization: Designing inhibitors to endothiapepsin. Proteins (2000) 40(2):258-289.
    • (2000) Proteins , vol.40 , Issue.2 , pp. 258-289
    • Stultz, C.M.1    Karplus, M.2
  • 16
    • 0034959530 scopus 로고    scopus 로고
    • Large-scale virtual screening for discovering leads in the postgenomic era
    • Waszkowyz B, Perkins TD, Sykes RA, Li J: Large-scale virtual screening for discovering leads in the postgenomic era. IBM Systems Journal (2001) 40(2):360-376.
    • (2001) IBM Systems Journal , vol.40 , Issue.2 , pp. 360-376
    • Waszkowyz, B.1    Perkins, T.D.2    Sykes, R.A.3    Li, J.4
  • 17
    • 0037007068 scopus 로고    scopus 로고
    • Computational mapping identifies the binding sites of organic solvents on proteins
    • Dennis S, Kortvelyesi T, Vajda S: Computational mapping identifies the binding sites of organic solvents on proteins. Proc Natl Acad Sci USA (2002) 99(7):4290-4295. Seminal publication on the application of a computational-based fragment approach to identify binding sites.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.7 , pp. 4290-4295
    • Dennis, S.1    Kortvelyesi, T.2    Vajda, S.3
  • 18
  • 19
    • 13444265957 scopus 로고    scopus 로고
    • Exploring the binding site structure of the PPAR-γ ligand-binding domain by computational solvent mapping
    • Sheu S-H, Kaya T, Waxman DJ, Vajda S: Exploring the binding site structure of the PPAR-γ ligand-binding domain by computational solvent mapping. Biochemistry (2005) 44(4):1193-1209.
    • (2005) Biochemistry , vol.44 , Issue.4 , pp. 1193-1209
    • Sheu, S.-H.1    Kaya, T.2    Waxman, D.J.3    Vajda, S.4
  • 20
    • 0029812557 scopus 로고    scopus 로고
    • Simulated annealing of chemical potential: A general procedure for locating bound waters. Application to the study of the differential hydration propensities of the major and minor grooves of DNA
    • Guarnieri F, Mezei M: Simulated annealing of chemical potential: A general procedure for locating bound waters. Application to the study of the differential hydration propensities of the major and minor grooves of DNA. J Am Chem Soc (1996) 118(35):8493-8494. Describes the principles of the Locus Pharmaceuticals process and confirmatory findings.
    • (1996) J Am Chem Soc , vol.118 , Issue.35 , pp. 8493-8494
    • Guarnieri, F.1    Mezei, M.2
  • 21
    • 0002015005 scopus 로고
    • A survey of methods for searching the conformational space of small and medium-sized molecules
    • Lipkowitz K, Boyd D (Eds), VCH Publishers Inc, New York, NY, USA
    • Leach AR: A survey of methods for searching the conformational space of small and medium-sized molecules. In: Reviews in Computational Chemistry. Lipkowitz K, Boyd D (Eds), VCH Publishers Inc, New York, NY, USA (1991) 2:1-55.
    • (1991) Reviews in Computational Chemistry , vol.2 , pp. 1-55
    • Leach, A.R.1
  • 22
    • 0007793280 scopus 로고
    • Conformations of cycloheptadecane. A comparison of methods for conformational searching
    • Saunders M, Houk KN, Wu Y-D, Still WC, Lipton M, Chang G, Guida WC: Conformations of cycloheptadecane. A comparison of methods for conformational searching. J Am Chem Soc (1990) 112(4):1419-1427.
    • (1990) J Am Chem Soc , vol.112 , Issue.4 , pp. 1419-1427
    • Saunders, M.1    Houk, K.N.2    Wu, Y.-D.3    Still, W.C.4    Lipton, M.5    Chang, G.6    Guida, W.C.7
  • 23
    • 0025916872 scopus 로고
    • Functionality maps of binding sites: A multiple copy simultaneous search method
    • Miranker A, Karplus M: Functionality maps of binding sites: A multiple copy simultaneous search method. Proteins (1991) 11(1):29-34.
    • (1991) Proteins , vol.11 , Issue.1 , pp. 29-34
    • Miranker, A.1    Karplus, M.2
  • 24
    • 0032749096 scopus 로고    scopus 로고
    • MCSS functionality maps for a flexible protein
    • Stultz CM, Karplus M: MCSS functionality maps for a flexible protein. Proteins (1999) 37(4):512-529.
    • (1999) Proteins , vol.37 , Issue.4 , pp. 512-529
    • Stultz, C.M.1    Karplus, M.2
  • 25
    • 3142655877 scopus 로고    scopus 로고
    • Application of the local-bulk partitioning and competitive binding models to interpret preferential interactions of glycine betaine and urea with protein surface
    • Felitsky DJ, Record T Jr: Application of the local-bulk partitioning and competitive binding models to interpret preferential interactions of glycine betaine and urea with protein surface. Biochemistry (2004) 43(28):9276-9288.
    • (2004) Biochemistry , vol.43 , Issue.28 , pp. 9276-9288
    • Felitsky, D.J.1    Record Jr., T.2
  • 26
    • 0030970305 scopus 로고    scopus 로고
    • Simulation of protein conformational freedom as a function of pH: Constant-pH molecular dynamics using implicit titration
    • Baptista AM, Martel PJ, Petersen SB: Simulation of protein conformational freedom as a function of pH: Constant-pH molecular dynamics using implicit titration. Proteins (1997) 27(4):523-544.
    • (1997) Proteins , vol.27 , Issue.4 , pp. 523-544
    • Baptista, A.M.1    Martel, P.J.2    Petersen, S.B.3
  • 27
    • 0036955427 scopus 로고    scopus 로고
    • Current trends in lead discovery: Are we looking for the appropriate properties?
    • Oprea TI: Current trends in lead discovery: Are we looking for the appropriate properties? Mol Diversity (2002) 5(4):199-208. Provides a thought-provoking discussion on chemical approaches to lead-finding and generating.
    • (2002) Mol Diversity , vol.5 , Issue.4 , pp. 199-208
    • Oprea, T.I.1
  • 28
    • 17844369895 scopus 로고    scopus 로고
    • Generalized fragment-substructure based property prediction method
    • Clark M: Generalized fragment-substructure based property prediction method. J Chem Info Modeling (2005) 45(1):30-38. A new method in which fragment properties can be used to describe whole molecule ADMET parameters.
    • (2005) J Chem Info Modeling , vol.45 , Issue.1 , pp. 30-38
    • Clark, M.1
  • 29
    • 0142028917 scopus 로고    scopus 로고
    • Structure-activity relationships of the p38α MAP kinase inhibitor 1-(5-tert-butyl-2-p-tolyl-2H-pyrazol-3-yl)-3-[4-(2-morpholin-4-yl-ethoxy) -naphthalen-1-yl]urea (BIRB 796)
    • Regan J, Capolino A, Cirillo PF, Gilmore T, Graham AG, Mickey E, Kroe RR, Madwed J, Moriak M, Nelson R, Pargellis CA et al: Structure-activity relationships of the p38α MAP kinase inhibitor 1-(5-tert-butyl-2-p-tolyl- 2H-pyrazol-3-yl)-3-[4-(2-morpholin-4-yl-ethoxy)-naphthalen-1-yl]urea (BIRB 796). J Med Chem (2003) 46(22):4676-4686. An important publication on the properties of BIRB-796 and its interactions with the p38 allosteric site.
    • (2003) J Med Chem , vol.46 , Issue.22 , pp. 4676-4686
    • Regan, J.1    Capolino, A.2    Cirillo, P.F.3    Gilmore, T.4    Graham, A.G.5    Mickey, E.6    Kroe, R.R.7    Madwed, J.8    Moriak, M.9    Nelson, R.10    Pargellis, C.A.11
  • 31
    • 0036289349 scopus 로고    scopus 로고
    • Crystal structures of MAP kinase p38 complexed to the docking sites on its nuclear substrate MEF2A and activator MKK3b
    • Chang CI, Xu BE, Akella R, Cobb MH, Goldsmith EJ: Crystal structures of MAP kinase p38 complexed to the docking sites on its nuclear substrate MEF2A and activator MKK3b. Mol Cell (2002) 9(6):1241-1249.
    • (2002) Mol Cell , vol.9 , Issue.6 , pp. 1241-1249
    • Chang, C.I.1    Xu, B.E.2    Akella, R.3    Cobb, M.H.4    Goldsmith, E.J.5
  • 33
    • 17844394632 scopus 로고    scopus 로고
    • Crystallographic and biochemical analysis of predicted inhibitor binding on p38 MAP kinase: Evaluation of predictive ability of a novel de novo design approach
    • Keystone, CO, USA
    • Karpusas M: Crystallographic and biochemical analysis of predicted inhibitor binding on p38 MAP kinase: Evaluation of predictive ability of a novel de novo design approach. Keystone Symposia on Structural Genomics, Keystone, CO, USA (2004).
    • (2004) Keystone Symposia on Structural Genomics
    • Karpusas, M.1
  • 35
    • 0036305832 scopus 로고    scopus 로고
    • Artificial protein cavities as specific ligand-binding templates: Characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein
    • Musah RA, Jensen GM, Bunte SW, Rosenfeld RJ, Goodin DB: Artificial protein cavities as specific ligand-binding templates: Characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein. J Mol Biol (2002) 315(4):845-857.
    • (2002) J Mol Biol , vol.315 , Issue.4 , pp. 845-857
    • Musah, R.A.1    Jensen, G.M.2    Bunte, S.W.3    Rosenfeld, R.J.4    Goodin, D.B.5
  • 36
    • 1942471391 scopus 로고    scopus 로고
    • Assessing scoring functions for protein-ligand interactions
    • Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL 3rd: Assessing scoring functions for protein-ligand interactions. J Med Chem (2004) 47(12):3032-3047. An excellent review on the status and limitations of computational discovery approaches.
    • (2004) J Med Chem , vol.47 , Issue.12 , pp. 3032-3047
    • Ferrara, P.1    Gohlke, H.2    Price, D.J.3    Klebe, G.4    Brooks III, C.L.5
  • 37
    • 0029016268 scopus 로고
    • Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme
    • Morton A, Baase WA, Matthews BW: Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry (1995) 34(27):8564-8575.
    • (1995) Biochemistry , vol.34 , Issue.27 , pp. 8564-8575
    • Morton, A.1    Baase, W.A.2    Matthews, B.W.3
  • 38
    • 0344558911 scopus 로고    scopus 로고
    • An experimental approach to mapping the binding surfaces of crystalline proteins
    • Allen KN, Bellamacina CR, Ding X, Jeffery CJ, Mattos C, Petsko GA, Ringe D: An experimental approach to mapping the binding surfaces of crystalline proteins. J Phys Chem (1996) 100:2605-2611. A seminal paper describing how fragments (co-solvents) and crystallographic methods can identify protein binding sites.
    • (1996) J Phys Chem , vol.100 , pp. 2605-2611
    • Allen, K.N.1    Bellamacina, C.R.2    Ding, X.3    Jeffery, C.J.4    Mattos, C.5    Petsko, G.A.6    Ringe, D.7
  • 39
    • 0029868304 scopus 로고    scopus 로고
    • Locating and characterizing binding sites on proteins
    • Mattos C, Ringe D: Locating and characterizing binding sites on proteins. Nat Biotechnol (1996) 14(5):595-599.
    • (1996) Nat Biotechnol , vol.14 , Issue.5 , pp. 595-599
    • Mattos, C.1    Ringe, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.