Comparative residue interaction analysis (CoRIA): A 3D-QSAR approach to explore the binding contributions of active site residues with ligands

Journal of Computer-Aided Molecular Design

Volumn 20, Issue 6, 2006, Pages 343-360

  Datar, Prasanna A ^a   Khedkar, Santosh A ^a   Malde, Alpeshkumar K ^a   Coutinho, Evans C ^a  

^a BOMBAY COLLEGE OF PHARMACY   (India)

Author keywords

CoRIA; COX 2; Docking; G PLS statistics; QSAR; Simulations

Indexed keywords

BINDING ENERGY; BIOACTIVITY; COMPUTATIONAL CHEMISTRY; ENZYMES; MOLECULAR GRAPHICS; MONTE CARLO METHODS; SIMULATED ANNEALING; THERMODYNAMICS; VAN DER WAALS FORCES;

ACTIVE SITE; BINDING AFFINITIES; COMPARATIVE RESIDUE INTERACTION ANALYSE; COX-2; DOCKING; G/PLS STATISTIC; INTERACTION ANALYSIS; INTERACTION ENERGIES; QSAR; SIMULATION;

LIGANDS;

LIGAND; PROSTAGLANDIN SYNTHASE INHIBITOR;

ARTICLE; BINDING SITE; CHEMISTRY; METABOLISM; MONTE CARLO METHOD; QUANTITATIVE STRUCTURE ACTIVITY RELATION; VALIDATION STUDY;

BINDING SITES; CYCLOOXYGENASE INHIBITORS; LIGANDS; MONTE CARLO METHOD; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 34548172749     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-006-9051-5     Document Type: Article

References (66)

1. Hansch C, Maloney PP, Fujita T, Muir RM (1962) Nature 194:178
2. Hansch C, Muir RM, Fujita T, Maloney PP, Geiger CF, Streich M (1963) J Am Chem Soc 85:2817
3. Hansch C, Fujita T (1964) J Am Chem Soc 86:5175
4. Cramer RD III, Patterson DE, Bunce JD (1988) J Am Chem Soc 110:5959
5. Tokarski JS, Hopfinger AJ (1994) J Med Chem 37:3639
6. Klebe G, Abraham U, Mietzner T (1994) J Med Chem 37:4130
7. Havel TF, Kuntz ID, Crippen GM (1983) Bull Math Biol 45:665
8. Doweyko AM (1988) J Med Chem 31:1396
9. Walters DE, Hinds RM (1994) J Med Chem 37:2527
10. Jain AN, Koile K, Chapman D (1994) J Med Chem 37:2315
11. Müller K (ed) (1995) Perspectives in drug discovery and design, vol 3. ESCOM Science Publishers, BV, Leiden, pp 1-20
12. Nelson LM, Malhotra D, Hopfinger AJ (1981) Comput Chem 5:19
13. Ortiz AR, Pisabarro MT, Gago F, Wade RC (1995) J Med Chem 38:2681
14. Gohlke H, Klebe G (2002) J Med Chem 45:4153
15. Vedani A, Briem H, Dobler M, Dollinger K, McMasters DR (2000) J Med Chem 43:4416
16. Vedani A, Dobler M (2002) J Med Chem 45:2139
17. Vedani A, Dobler M, Lill L (2005) J Med Chem 48:3700
18. Tokarski JS, Hopfinger AJ (1997) J Chem Info Comput Sci 37:792
19. Charifson PS (ed) (1997) Practical application of computeraided drug design, Marcel Dekker Inc., pp 355-410
20. Delphi 2.5, User Guide. Accelrys Inc., San Diego, CA, USA
21. Scott WR, Schiffer CA (2000) Structure Fold Des 8:1259
22. Charifson PS (ed) (1997) Practical application of computeraided drug design. Marcel Dekker Inc., pp 495-538
23. Knetgel RMA, Grootenhuis PDJ (1998) Perspect Drug Discov Des 9-11:99
24. Williams DH, Cox JPL, Doig AJ, Garner M, Gerhard U, Kaye PT, Lal AR, Nicholls IA, Salter J, Mitchell RC (1991) J Am Chem Soc 113:7020
25. Insight II, version 2000.3 L. Accelrys Inc., San Diego, CA, USA
26. Dauber-Osguthorpe P, Roberts VA, Osguthorpe DJ, Wolff J, Genest M, Hagler AT (1988) Proteins 4:31
27. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE (1982) J Mol Biol 161:269
28. Affinity v. 98 Molecular Modeling Program Package. Accelrys Inc. San Diego, CA, 1998
29. Cerius2 version 4.8. Accelrys Inc., San Diego CA, 1999
30. Khanna IK, Weier RM, Yu Y, Collins PW, Miyashiro JM, Koboldt CM, Veenhuizen AW, Currie JL, Seibert K, Isakson PC (1997) J Med Chem 40:1619
31. Khanna IK, Weier RM, Yu Y, Xu XD, Koszyk FJ, Collins PW, Koboldt CM, Veenhuizen AW, Perkins WE, Casler JJ, Masferrer JL, Zhang YY, Gregory SA, Seibert K, Isakson PC (1997) J Med Chem 40:1634
32. Khanna IK, Yu Y, Huff RM, Weier RM, Xu X, Koszyk FJ, Collins PW, Cogburn JN, Isakson PC, Koboldt CM, Masferrer JL, Perkins WE, Seibert K, Veenhuizen AW, Yuan J, Yang DC, Zhang YY (2000) J Med Chem 43:3168
33. Reitz DB, Li JJ, Norton MB, Reinhart EJ, Collins JT, Anderson GD, Gregory SA, Koboldt CM, Perkins WE, Seibert K, Isakson PC (1994) J Med Chem 38:3878
34. Li JJ, Anderson GD, Burton EG, Cogburn JN, Collins JT, Garland DJ, Gregory SA, Huang HC, Isakson PC, Koboldt CM, Logusch EW, Norton MB, Perkins WE, Reinhart EJ, Seibert K, Veenhuizen AW, Zhang Y, Reitz DB (1995) J Med Chem 38:4570
35. Li JJ, Norton MB, Reinhart EJ, Anderson GD, Gregory SA, Isakson PC, Koboldt CM, Masferrer JL, Perkins WE, Seibert K, Zhang Y, Zweifel BS, Reitz DB (1996) J Med Chem 39:1846
36. Penning TD, Talley JJ, Bertenshaw SR, Carter JS, Collins PW, Docter S, Graneto MJ, Lee LF, Malecha JW, Miyashiro JM, Rogers RS, Rogier DJ, Yu SS, Anderson GD, Burton EG, Cogburn JN, Gregory SA, Koboldt CM, Perkins WE, Seibert K, Veenhuizen AW, Zhang YY, Isakson PC (1997) J Med Chem 40:1347
37. Huang HC, Li JJ, Garland DJ, Chamberlain TS, Reinhart EJ, Manning RE, Seibert K, Koboldt CM, Gregory SA, Anderson GD, Veenhuizen AW, Zhang Y, Perkins WE, Burton EG, Cogburn JN, Isakson PC, Reitz DB (1996) J Med Chem 39:253
38. Talley JJ, Brown DL, Carter JS, Graneto MJ, Koboldt CM, Masferrer JL, Perkins WE, Rogers RS, Shaffer AF, Zhang YY, Zweifel BS, Seibert K (2000) J Med Chem 43:775
39. Lee LF (1996) Pat. No. WO 9624585, US
40. Song Y, Connor DT, Doubleday R, Sorenson RJ, Sercel AD, Unangst PC, Roth BD, Gilbertsen RB, Chan K, Schrier DJ, Guglietta A, Bornemeier DA, Dyer RD (1999) J Med Chem 42:1151
41. Song Y, Connor DT, Sercel AD, Sorenson RJ, Doubleday R, Unangst PC, Roth BD, Gilbertsen RB, Chan K, Schrier DJ, Guglietta A, Bornemeier DA, Dyer RD (1999) J Med Chem 42:1161
42. Kurumbail RG, Stevens AM, Gierse JK, McDonald JJ, Stegeman RA, Pak JY, Gildehaus D, Miyashiro JM, Penning TD, Seibert K, Isakson PC, Stallings WC (1996) Nature 384:644
43. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28:235
44. MS, QCPE. Creative Arts Bldg. 181, Indiana University, Bloomington, IN 47405
45. Ding HQ, Karasawa N, Goddard WA III (1992) J Chem Phys 97:4309
46. Nicholls A, Honig B (1991) J Comput Chem 12:435
47. Maple JR, Hwang M-J, Stockfisch TP, Dinur U, Waldman M, Ewig CS, Hagler AT (1994) J Comput Chem 15:162
48. Dixit SB, Bhasin R, Rajasekaran E, Jayaram B (1997) J Chem Soc Faraday Trans 93:1105
49. Waller CL, Marshall GR (1993) J Med Chem 36:2390
50. Kodithala K, Hopfinger AJ, Thompson ED, Robinson MK (2002) Toxicol Sci 66:336
51. Stanton DT, Jurs PC (1990) Anal Chem 62:2323
52. Ghose A, Crippen G (1986) J Comput Chem 7:565
53. Rogers D, Hopfinger AJ (1994) J Chem Inf Comput Sci 34:854
54. Kubinyi H. (ed) (1993) 3D QSAR in drug design: theory, methods and applications, ESCOM, Leiden, pp 523-550
55. Cerius2 4.8, User's Manual. Accelrys Inc., San Diego, CA, USA
56. Vieth M, Cummins DJ (2000) J Med Chem 43:3020
57. Ryn JV, Trummlitz G, Pairet M (2000) Curr Med Chem 7:1145
58. Shimokawa T, Kulmacz RJ, De Witt DL, Smith WL (1990) J Biol Chem 265:20073
59. Kalgutkar AS, Crews BC, Rowlinson SW, Marnett AB, Kozak KR, Remmel RP, Marnett LJ (2000) Proc Natl Acad Sci USA 97:925
60. So OY, Scarafia E, Mak AY, Callan OH, Swinney DC (1998) J Biol Chem 273:5801
61. Greig GM, Francis DA, Falgueyret JP, Ouellet M, Percival MD, Roy P, Bayly C, Mancini JA, O'Neil GP (1997) Mol Pharmacol 52:829
62. Desiraju GR, Gopalakrishnan B, Jetti RKR, Raveendra D, Sarma JARP, Subramanya HS (2000) Molecules 7:945
63. Chavatte P, Yous S, Lesieur D (2001) J Med Chem 44:3223
64. Liu H, Huang X, Shen J, Luo X, Li M, Xiong H, Chen G, Shen J, Yang Y, Jiang H, Chen K (2002) J Med Chem 45:4816
65. Datar PA, Coutinho EC (2004) J Mol Graph Model 23:239
66. Kim H-J, Chae CH, Yi KY, Park K-L, Yoo S (2004) Bioorg Med Chem 12:1629