Pharmacophore inference and its application to computational drug discovery

Drug Development Research

Volumn 72, Issue 1, 2011, Pages 17-25

  Wallach, Izhar ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Computer aided drug discovery; Pharmacophore modeling; Structure based drug design

Indexed keywords

DRUG BINDING SITE; DRUG DESIGN; DRUG PROTEIN BINDING; DRUG RECEPTOR BINDING; HIGH THROUGHPUT SCREENING; LIGAND BINDING; MOLECULAR INTERACTION; PHARMACOPHORE; REVIEW; VIRTUAL REALITY;

EID: 79951800136     PISSN: 02724391     EISSN: 10982299     Source Type: Journal    
DOI: 10.1002/ddr.20398     Document Type: Review

References (63)

1. Andrew Miranker MK. 1991. Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins 11:29-34.
2. Arnold JR, Burdick KW, Pegg SC, Toba S, Lamb ML, Kuntz ID. 2004. SitePrint: three-dimensional pharmacophore descriptors derived from protein binding sites for family based active site analysis classification and drug design. J Chem Inf Comput Sci 44:2190-2198.
3. Bajorath J. 2002. Integration of virtual and high-throughput screening. Nat Rev Drug Discov 1:882-894. (Pubitemid 37361583)
4. Barillari C, Marcou G, Rognan D. 2008. Hot-Spots-Guided Receptor-Based Pharmacophores (HS-Pharm): a knowledge-based approach to identify ligand-anchoring atoms in protein cavities and prioritize structure-based pharmacophores. J Chem Inf Model 48:1396-1410.
5. Barnum D, Greene J, Smellie A, Sprague P. 1996. Martinez identification of common functional configurations among molecules. J Chem Inf Model 36:563-571. (Pubitemid 126539357)
6. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The Protein Data Bank. Nucleic Acids Res 28:235-242. (Pubitemid 30047768)
7. Bleicher KH, Böhm HJ, Müller K, Alanine AI. 2003. Hit and lead generation: beyond high-throughput screening. Nat Rev Drug Discov 2:369-378. (Pubitemid 37361707)
8. Campbell SJ, Gold ND, Jackson RM, Westhead DR. 2003. Ligand binding: functional site location similarity and docking. Curr Opin Struct Biol 13:389-395. (Pubitemid 36782467)
9. Chen X, Andrew R, Tropsha A, Young SS. 1999. Automated pharmacophore identification for large chemical data sets. J Chem Inf Model 39:887-896.
10. Chen Z, Tian G, Wang Z, Jiang H, Shen J, Zhu W. 2010. Multiple pharmacophore models combined with molecular docking: a reliable way for efficiently identifying novel PDE4 inhibitors with high structural diversity. J Chem Inf Model 50:615-625.
11. Chuaqui C, Deng Z, Singh J. 2005. Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening. J Med Chem 48:121-133. (Pubitemid 40105253)
12. Congreve M, Murray CW, Blundell TL. 2005. Keynote review: structural biology and drug discovery. Drug Discov Today 10:895-907. (Pubitemid 40922788)
13. Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C. 2009. Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J Chem Inf Model 49:1455-1474.
14. Deng Z, Chuaqui C, Singh J. 2004. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J Med Chem 47:337-344. (Pubitemid 38057878)
15. Dixon S, Smondyrev A, Knoll E, Rao S, Shaw D, Friesner R. 2006. PHASE: a new engine for pharmacophore perception 3D QSAR model development and 3D database screening. 1. Methodology and preliminary results. J Comput-Aided Mol Des 20:647-671. (Pubitemid 46023928)
16. Dror O, Shulman-Peleg A, Nussinov R, Wolfson HJ. 2006. Predicting molecular interactions in silico. I. An updated guide to pharmacophore identification and its applications to drug design. Front Med Chem 3:551-584.
17. Ehrlich P. 1911. The theory and practice of chemotherapy. Fol Serol 7:697-714.
18. Gillet V, Johnson AP, Mata P, Sike S, Williams P. 1993. SPROUT: a program for structure generation. J Comput-Aided Mol Des 7:127-153.
19. Güner OF. 2002. History and evolution of the pharmacophore concept in computer-aided drug design. Curr Top Med Chem 2:1321-1332.
20. Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL. 2004. Glide: a new approach for rapid accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750-1759. (Pubitemid 38380918)
21. Hindle SA, Rarey M, Buning C, Lengauer T. 2002. Flexible docking under pharmacophore type constraints. J Comput-Aided Mol Des 16:129-149. (Pubitemid 34855039)
22. Hopkins A, Mason J, Overington J. 2006. Can we rationally design promiscuous drugs? Curr Opin Struct Biol 16:127-136.
23. Hopkins AL. 2008. Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 4:682-690.
24. Huang Q, Li L-L, Yang S-Y. 2010. PhDD: a new pharmacophore-based de novo design method of drug-like molecules combined with assessment of synthetic accessibility. J Mol Graph Model 28:775-787.
25. Inbar Y, Schneidman-Duhovny D, Dror O, Nussinov R, Wolfson HJ. 2007. Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules. In: Research in computational molecular biology. Vol 4453. Oakland, CA: Springer. p 412-429.
26. Joseph-McCarthy D, Alvarez JC. 2003. Automated generation of MCSS-derived pharmacophoric DOCK site points for searching multiconformation databases. Proteins 51:189-202. (Pubitemid 36397752)
27. Joseph-McCarthy D, Thomas BE, Belmarsh M, Moustakas D, Alvarez JC. 2003. Pharmacophore-based molecular docking to account for ligand flexibility. Proteins 51:172-188. (Pubitemid 36397751)
28. Karaman MW, Herrgard S, Treiber DK, Gallant P, Atteridge CE, Campbell BT, Chan KW, Ciceri P, Davis MI, Edeen PT, et al. 2008. A quantitative analysis of kinase inhibitor selectivity. Nat Biotechnol 26:127-132.
29. Keseru GM, Makara GM. 2006. Hit discovery and hit-to-lead approaches. Drug Discov Today 11:741-748. (Pubitemid 44038630)
30. Khedkar SA, Malde AK, Coutinho EC, Srivastava S. 2007. Pharmacophore modeling in drug discovery and development: an overview. Med Chem 3:187-197. (Pubitemid 47454883)
31. Kupas K, Ultsch A, Klebe G. 2007. Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties selectivity discrimination and putative cross-reactivity. Proteins 71:1288-1306. (Pubitemid 351564053)
32. Langer T, Hoffmann RD. 2006. Pharmacophores and pharmacophore searches. 1st ed. Palo Alto, CA: Wiley-VCH.
33. Leach AR, Gillet VJ, Lewis RA, Taylor R. 2010. Three-dimensional pharmacophore methods in drug discovery. J Med Chem 53:539-558.
34. Lerner MG, Meagher KL, Carlson HA. 2008. Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design. J Comput-Aided Mol Des 22:727-736.
35. Li H, Sutter J, Remy H. 2000. Pharmacophore perception development and use in drug design chapter HypoGen: an automated system for generating 3D predictive pharmacophore models. La Jolla, CA: International University Line. p 49-68.
36. Lin S-K. 2000. Pharmacophore perception development and use in drug design. Molecules 5:987-989.
37. Makino S, Kuntz ID. 1997. Automated flexible ligand docking method and its application for database search. J Comput Chem 18:1812-1825. (Pubitemid 127598548)
38. Martin YC. 2000. Pharmacophore perception development and use in drug design. In: DISCO: what we did right and what we missed. La Jolla, CA: International University Line. p 49-68.
39. McGregor M. 2007. A pharmacophore map of small molecule protein kinase inhibitors. J Chem Inf Model 47:2374-2382. (Pubitemid 350275102)
40. Moon JB, Howe WJ. 1991. Computer design of bioactive molecules: a method for receptor-based de novo ligand design. Proteins 11:314-328.
41. Overington JP, Al-Lazikani B, Hopkins AL. 2006. How many drug targets are there? Nat Rev Drug Discov 5:993-996.
42. Patani GA, LaVoie EJ. 1996. Bioisosterism: a rational approach in drug design. Chem Rev 96:3147-3176. (Pubitemid 126641132)
43. Podolyan Y, Karypis G. 2009. Common pharmacophore identification using frequent clique detection algorithm. J Chem Inf Model 49:13-21.
44. Puvanendrampillai D, Mitchell JBO. 2003. Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes. Bioinformatics 19:1856-1857. (Pubitemid 37220482)
45. Ramensky V, Sobol A, Zaitseva N, Rubinov A, Zosimov V. 2007. A novel approach to local similarity of protein binding sites substantially improves computational drug design results. Proteins 69:349-357.
46. Rasmussen SGF, Choi H-J, Rosenbaum DM, Kobilka TS, Thian FS, Edwards PC, Burghammer M, Ratnala VRP, Sanishvili R, Fischetti RF, et al. 2007. Crystal structure of the human BGR2 adrenergic G-protein-coupled receptor. Nature 4507168:383-387. (Pubitemid 350126755)
47. Renner S, Derksen S, Radestock S, Morchen F. 2008. Maximum common binding modes (MCBM): consensus docking scoring using multiple ligand information and interaction fingerprints. J Chem Inf Model 48:319-332. (Pubitemid 351473035)
48. Richmond NJ, Abrams CA, Wolohan PRN, Abrahamian E, Willett P, Clark RD. 2006. GALAHAD. 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D. J Comput-Aided Mol Des 20:567-587. (Pubitemid 44823892)
49. Roe DC, Kuntz ID. 1995. BUILDER v.2: improving the chemistry of a de novo design strategy. J Comput-Aided Mol Des 9:269-282.
50. Schmitt S, Kuhn D, Klebe G. 2002. A new method to detect related function among proteins independent of sequence and fold homology. J Mol Biol 323:387-406. (Pubitemid 35283699)
51. Stuart AC, Ilyin VA, Sali A. 2002. LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics 18:200-201. (Pubitemid 34145052)
52. Tschinke V, Cohen NC. 1993. The NEWLEAD program: a new method for the design of candidate structures from pharmacophoric hypotheses. J Med Chem 36:3863-3870. (Pubitemid 24006717)
53. van De Waterbeemd H, Smith DA, Beaumont K, Walker DK. 2001. Property-based design: optimization of drug absorption and pharmacokinetics. J Med Chem 44:1313-1333. (Pubitemid 32852106)
54. Vinkers HM, de Jonge MR, Daeyaert FF, Heeres J, Koymans LM, van Lenthe JH, Lewi PJ, Timmerman H, Van Aken K, Janssen PA. 2003. SYNOPSIS: SYNthesize and OPtimize System in Silico. J Med Chem 46:2765-2773. (Pubitemid 36702544)
55. Wallach I, Lilien R. 2009a. Predicting multiple ligand binding modes using self-consistent pharmacophore hypotheses. J Chem Inf Model 49:2116-2128.
56. Wallach I, Lilien R. 2009b. The protein-small-molecule database a non-redundant structural resource for the analysis of protein-ligand binding. Bioinformatics 25:615-620.
57. Wallach I, Lilien RH. 2009c. Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation. Bioinformatics 25:i296-i304.
58. Warren G, Andrews C, Capelli A-M, Clarke B, LaLonde J, Lambert M, Lindvall M, Nevins N, Semus S, Senger S, et al. 2006. A critical assessment of docking programs and scoring functions. J Med Chem 49:5912-5931. (Pubitemid 44484938)
59. Welsch ME, Snyder SA, Stockwell BR. 2010. Privileged scaffolds for library design and drug discovery. Curr Opin Chem Biol 14:347-361.
60. Wermuth CG, Ganellin CR, Lindberg P, Mitscher LA. 1998. Glossary of terms used in medicinal chemistry (IUPAC recommendations 1998). Pure Appl Chem 70:1129-1143.
61. Wolber G, Langer T. 2005. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J Chem Inf Model 45:160-169. (Pubitemid 40736968)
62. Wolfson HJ, Rigoutsos I. 1997. Geometric hashing: an overview. Comput Sci Eng IEEE 4:10-21.
63. Yang S-Y. 2010. Pharmacophore modeling and applications in drug discovery: challenges and recent advances. Drug Disc Today 15:444-450.