Using computational techniques in fragment-based drug discovery

Methods in Enzymology

Volumn 493, Issue , 2011, Pages 137-155

  Desjarlais, Renee L ^a  

^a JOHNSON AND JOHNSON PHARMACEUTICAL RESEARCH AND DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING AFFINITY; CALIBRATION; CHEMICAL STRUCTURE; COMPUTER MODEL; COMPUTER PROGRAM; DRUG DEVELOPMENT; DRUG SYNTHESIS; FRAGMENT BASED DRUG DISCOVERY; HIGH THROUGHPUT SCREENING; HYDROGEN BOND; MOLECULAR BIOLOGY; MOLECULAR DOCKING; MOLECULAR LIBRARY; PRIORITY JOURNAL; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY;

EID: 79952374737     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381274-2.00006-6     Document Type: Chapter

References (55)

1. C. Abad-Zapatero, and J.T. Metz Ligand efficiency indices as guideposts for drug discovery Drug Discov. Today 10 2005 464 469
2. P. Andrews, D.J. Craik, and J.L. Martin Functional group contributions to drugreceptor interactions J. Med. Chem. 27 1984 1648 1657 (Pubitemid 15177908)
3. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne The Protein Data Bank Nucleic Acids Res. 28 2000 235 242 (Pubitemid 30047768)
4. H.-J. Bhm The computer program LUDI: A new simple method for the de novo design of enzyme inhibitors J. Comput. Aided Mol. Des. 6 1992 61 78
5. H.-J. Bhm, M. Boehringer, D. Bur, H. Gmuender, W. Huber, W. Klaus, D. Kostrewa, H. Kuehne, T. Luebbers, N. Meunier-Keller, and F. Mueller Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening J. Med. Chem. 43 2000 2664 2674 (Pubitemid 30463915)
6. R.A. Carr, M. Congreve, C.W. Murray, and D.C. Rees Fragment-based lead discovery: Leads by design Drug Discov. Today 10 2005 987 992 (Pubitemid 40967047)
7. A.C. Cheng, R.G. Coleman, K.T. Smyth, Q. Cao, P. Soulard, D.R. Caffrey, A.C. Salzberg, and E.S. Huang Structure-based maximal affinity model predicts small-molecule druggability Nat. Biotech. 25 2007 71 75 (Pubitemid 46087905)
8. M. Congreve, R. Carr, C. Murray, and H. Jhoti A 'Rule of Three' for fragment-based lead discovery? Drug Discov. Today 8 2003 876 877 (Pubitemid 37194496)
9. M.D. Cummings, R.L. DesJarlais, A.C. Gibbs, V. Mohan, and E.P. Jaeger Comparison of automated docking programs as virtual screening tools J. Med. Chem. 48 2005 962 976 (Pubitemid 40270442)
10. S. Datta, B.K. Biswal, and M. Vijayan The effect of stabilizing additives on the structure and hydration of proteins: A study involving tetragonal lysozyme Acta Crystallogr. D 57 2001 1614 1620 (Pubitemid 33037725)
11. J. Degen, and M. Rarey Flexnovo: Structure-based searching in large fragment spaces ChemMedChem 1 2006 854 868 (Pubitemid 44384546)
12. J.L. Durant, B.A. Leland, D.R. Henry, and J.G. Nourse Reoptimization of MDL keys for use in drug discovery J. Chem. Inf. Comput. Sci. 42 2002 1273 1280 (Pubitemid 35468313)
13. M.B. Eisen, D.C. Wiley, M. Karplus, and R.E. Hubbard HOOK: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site Proteins 19 1994 199 221 (Pubitemid 24215048)
14. D. Ekonomiuk, X.-C. Su, K. Ozawa, C. Bodenreider, S.P. Lim, G. Otting, D. Huang, and A. Caflisch Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics J. Med. Chem. 52 2009 4860 4868
15. R.A. Friesner, J.L. Banks, R.B. Murphy, T.A. Halgren, J.J. Klicic, D.T. Mainz, M.P. Repasky, E.H. Knoll, M. Shelley, J.K. Perry, D.E. Shaw, and P. Francis Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy J. Med. Chem. 47 2004 1739 1749 (Pubitemid 38380917)
16. V.J. Gillett, G. Myatt, Z. Zsoldos, and A.P. Johnson SPROUT, HIPPO and CAESA: Tools for de novo structure generation and estimation of synthetic accessibility Perspect. Drug Discov. Des. 3 1995 34 50
17. P.J. Hajduk Fragment-Based drug design: How big is too big? J. Med. Chem. 49 2006 6972 6976 (Pubitemid 44885985)
18. T.A. Halgren, R.B. Murphy, R.A. Friesner, H.S. Beard, L.L. Frye, W.T. Pollard, and J.L. Banks Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening J. Med. Chem. 47 2004 1750 1759 (Pubitemid 38380918)
19. M.M. Hann, A.R. Leach, and G. Harper Molecular Complexity and its impact on the probability of finding leads for drug discovery J. Chem. Inf. Comput. Sci. 41 2001 856 864
20. M.J. Hartshorn, C.W. Murray, A. Cleasby, M. Frederickson, I.J. Tickle, and H. Jhoti Fragment-based lead discovery using X-ray crystallography J. Med. Chem. 48 2005 403 413 (Pubitemid 40139783)
21. M. Hassan, R.D. Brown, S. Varma-O'Brien, and D. David Rogers Cheminformatics analysis and learning in a data pipelining environment Mol. Divers. 10 2007 283 299
22. A.L. Hopkins, C.R. Groom, and A. Alex Ligand efficiency: A useful metric for lead selection Drug Discov. Today 9 2004 430 431 (Pubitemid 38510559)
23. J.J. Irwin, and B.K. Shoichet ZINCA free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 45 2005 177 182 (Pubitemid 40736970)
24. A.N. Jain Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine J. Med. Chem. 46 2003 499 511 (Pubitemid 36182752)
25. G. Jones, P. Willet, R.C. Glen, A.R. Leach, and R. Taylor Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 267 1997 727 748 (Pubitemid 27170693)
26. S. Kawatka, H. Wang, R. Czerminski, and D. Joseph-McCarthy Virtual fragment screening: An exploration of various docking and scoring protocols for fragments using glide J. Comput. Aided Mol. Des. 23 2009 527 539
27. P. Kolb, and A. Caflisch Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking J. Med. Chem. 49 2006 7384 7392 (Pubitemid 44913398)
28. I.D. Kuntz, J.M. Blaney, S.J. Oatley, R. Langridge, and T.E. Ferrin A geometric approach to macromoleculeligand interactions J. Mol. Biol. 161 1982 269 288
29. I.D. Kuntz, E.C. Meng, and B.K. Shoichet Structure-based molecular design Acc. Chem. Res. 27 1994 117 123 (Pubitemid 24972237)
30. I.D. Kuntz, K. Chen, K.A. Sharp, and P.A. Kollman The maximal affinity of ligands Proc. Natl. Acad. Sci. USA 96 1999 9997 10002 (Pubitemid 29422500)
31. R. Law, O. Barker, J.J. Barker, T. Hesterkamp, R. Godemann, O. Andersen, T. Fryatt, S. Courtney, D. Hallett, and M. Whittaker The multiple roles of computational chemistry in fragment-based drug design J. Comput. Aided Mol. Des. 23 2009 459 473
32. P.D. Leeson, and B. Springthorpe The influence of drug-like concepts on decision-making in medicinal chemistry Nat. Rev. Drug Discov. 6 2007 881 890 (Pubitemid 350042396)
33. C. Lepre Fragment-based drug discovery using the SHAPES method Expert Opin. Drug Discov. 2 2007 1555 1566 (Pubitemid 350285345)
34. C.A. Lipinski, F. Lombardo, B.W. Dominy, and P.J. Feeney Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug Deliv. Rev. 46 2001 3 26 (Pubitemid 33653411)
35. Q. Liu, B. Masek, K. Smith, and J. Smith Tagged fragment method for evolutionary structure-based de novo lead generation and optimization J. Med. Chem. 50 2007 5392 5402 (Pubitemid 350057850)
36. N. Majeux, M. Scarsi, J. Apostolakis, C. Ehrhardt, and A. Caflisch Exhaustive docking of molecular fragments on protein binding sites with electrostatic solvation Proteins 37 1999 88 105 (Pubitemid 29408922)
37. N. Majeux, M. Scarsi, and A. Caflisch Efficient electrostatic solvation model for protein-fragment docking Proteins 42 2001 256 268 (Pubitemid 32047334)
38. M. McGann, H. Almond, A. Nicholls, J.A. Grant, and F. Brown Gaussian docking functions. Biopolymers 68 2003 76 90
39. A. Miranker, and M. Karplus Functionality maps of binding sites: A multiple copy simultaneous search method Proteins 11 1991 29 34
40. MOEThe Molecular Operating Environment Software available from Chemical Computing Group Inc., 1010 Sherbrooke Street West, Suite 910, Montreal, Canada H3A 2R7 http://www.chemcomp.com 2009
41. M. Orita, K. Ohno, M. Warizaya, Y. Amano, and T. Niimi Lead generation and examples: Opinion regarding how to follow up hits Methods Enzymol. 493 2011 383 422
42. M. Rarey, B. Kramer, T. Lengauer, and G.A. Klebe Fast flexible docking method using an incremental construction algorithm J. Mol. Biol. 261 1996 470 489 (Pubitemid 26335901)
43. C.R. Reynolds, B.A. Tounge, and S.D. Bembenek Ligand binding efficiency: trends, physical basis, and implications J. Med. Chem. 51 2008 2432 2438 (Pubitemid 351628504)
44. D. Rogers, and M. Hahn Extended-connectivity fingerprints J. Chem. Inf. Model. 50 2010 742 754
45. M. Sandor, R. Kiss, and G.M. Keseru Virtual fragment docking by glide: A validation study on 190 proteinfragment complexes J. Chem. Inf. Model. 50 2010 1165 1172
46. N.E. Shemetulskis, D. Weininger, C.J. Blankley, J.J. Yang, and C. Humblet Stigmata: An algorithm to determine structural commonalities in diverse datasets J. Chem. Inf. Comput. Sci. 36 1996 862 871 (Pubitemid 126581739)
47. T.T. Tanimoto 1957 IBM Internal Report, 17th Nov. IBM Corp., Armonk, New York
48. D.G. Teotico, K. Babaoglu, G.J. Rocklin, R.S. Ferreira, A.M. Giannetti, and B.K. Shoichet Docking for fragment inhibitors of AmpCβ-lactamase Proc. Natl. Acad. Sci. USA 106 2009 7455 7460
49. B.A. Tounge, and M.H. Parker Designing a diverse high-quality library for crystallography-based FBDD screening Methods Enzymol. 493 2011 1 20
50. B.A. Tounge, and C.H. Reynolds Defining privileged reagents using subsimilarity comparison J. Chem. Inf. Comput. Sci. 44 2004 1810 1815
51. D.F. Veber, S.R. Johnson, H.-Y. Cheng, B.R. Smith, K.W. Ward, and K.D. Kopple Molecular properties that influence the oral bioavailability of drug candidates J. Med. Chem. 45 2002 2615 2623 (Pubitemid 34595232)
52. C.M. Venkatachalam, X. Jiang, T. Oldfield, and M. Waldman Ligand-Fit: A novel method for the shape-directed rapid docking of ligands to protein active sites J. Mol. Graph. Model. 21 2003 289 307 (Pubitemid 35441326)
53. M.L. Verdonk, J.C. Cole, M.J. Hartshorn, C.W. Murray, and R.D. Taylor Improved proteinligand docking using GOLD Proteins 52 2003 609 623 (Pubitemid 37034158)
54. H.M. Vinkers, M.R. de Jonge, F.F.D. Daeyaert, J. Heeres, L.M.H. Koymans, J.H. van Lenthe, P.J. Lewi, H. Timmerman, K. Van Aken, and P.A.J. Janssen SYNOPSIS: Synthesize and optimize system in silico J. Med. Chem. 46 2003 2765 2773 (Pubitemid 36702544)
55. G.L. Warren, C.W. Andrews, A.-M. Capelli, B. Clarke, J. LaLonde, M.H. Lambert, M. Lindvall, N. Nevins, S.F. Semus, S. Senger, G. Tedesco, and I.D. Wall A critical assessment of docking programs and scoring functions J. Med. Chem. 49 2006 5912 5931 (Pubitemid 44484938)