Evaluating molecular similarity using reduced representations of the electron density

Journal of Molecular Modeling

Volumn 11, Issue 3, 2005, Pages 237-247

  Meurice, Nathalie ^a,b,c   Maggiora, Gerald M ^a   Vercauteren, Daniel P ^b  

^a UNIVERSITY OF ARIZONA   (United States)

^b UNIVERSITY OF NAMUR   (Belgium)

^c University of Arizona ^*  (United States)

Author keywords

Critical point graphs; Genetic algorithms; Molecular alignment; Molecular similarity; Peripheral benzodiazepine receptors

Indexed keywords

4' CHLORODIAZEPAM; BENZODIAZEPINE RECEPTOR; DIAZEPAM; QUINAZOLINONE DERIVATIVE; TRIAZOLOQUINAZOLINONE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; CRYSTALLOGRAPHY; DRUG RECEPTOR BINDING; ELECTRIC FIELD; GENETIC ALGORITHM; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; METHODOLOGY; MOLECULAR MODEL; PHARMACOPHORE; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; STEREOSPECIFICITY; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

BENZODIAZEPINES; ELECTRONS; HUMANS; INHIBITORY CONCENTRATION 50; MODELS, MOLECULAR; RECEPTORS, GABA; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 22144458682     PISSN: 16102940     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00894-005-0264-7     Document Type: Article

References (61)

1. N Meurice L Leherte DP Vercauteren J-J Bourguignon CG Wermuth 1997 Development of a genetic algorithm method especially designed for the comparison of molecular models: Application to the elucidation of the benzodiazepine receptor pharmacophore In: H Waterbeemd van de B Testa G Folkers (eds.) Computer-assisted lead finding and optimization. Verlag Helvetica Chimica Acta Basel 497-510
2. Meurice N, Leherte L, Vercauteren DP (1998) SAR QSAR Environ Res 8:195-232 1:CAS:528:DyaK1cXhslGhu7o%3D
3. Leherte L, Meurice N, Vercauteren DP (2000) J Chem Inf Comput Sci 40:816-832 10.1021/ci990112d
4. N Meurice GM Maggiora DP Vercauteren 2000 Study of the molecular similarity among three HIV reverse transcriptase inhibitors in order to validate GAGS, a genetic algorithm for graph similarity search In: C Gundertofte FS Jorgensen (eds) Molecular modeling and prediction of bioactivity. Kluwer New York 427-428
5. L Leherte N Meurice DP Vercauteren 2000 Applications of multiresolution analyses to electron density maps: A critical point analysis approach for the comparison of molecules In: NE Mastorakis (ed) Mathematics and computers in modern science. World Scientific and Engineering Society Danvers MA 158-164
6. DC Rohrer 1995 3D molecular similarity modeling in computational drug design In: R Carbó (ed) Molecular similarity and reactivity: From quantum to phenomenological approaches. Kluwer Amsterdam 141-161
7. Mestres J, Rohrer DC, Maggiora GM (1997) J Comput Chem 18:934-954 10.1002/(SICI)1096-987X(199705)18:7<934::AID-JCC6>3.0.CO;2-S
8. Mestres J, Rohrer DC, Maggiora GM (1997) J Mol Graph Model 15:114-121 10.1016/S1093-3263(97)00003-X
9. DC Rohrer 1998 3D molecular similarity methods: In search of a pharmacophore In: PW Codding (ed) Structure-based drug design. Kluwer Dordrecht 65-76
10. JR Blinn DC Rohrer GM Maggiora 1999 Field-based similarity forcing in energy minimization and molecular matching In: RB Altman AK Dunker L Hunter TE Klein (eds) Proceedings of the Pacific Symposium on Biocomputing '99. World Scientific Singapore 415-425
11. Mestres J, Rohrer DC, Maggiora GM (1999) J Comput Aided Mol Des 13:79-93 10.1023/A:1008098215954
12. Mestres J, Rohrer DC, Maggiora GM (2000) J Comput Aided Mol Des 14:39-51 10.1023/A:1008168228728
13. Möhler H, Okada T (1977) Science 198:849-851 918669
14. Braestrup C, Squires RF (1977) Proc Natl Acad Sci USA 74:3805-3809 1:CAS:528:DyaE1cXht1I%3D
15. Squires RF, Braestrup C (1977) Nature 266:732-734 1:CAS:528:DyaE1cXmvV2msw%3D%3D
16. Tallman JF, Thomas JW, Gallager DW (1978) Nature 274:383-385 1:CAS:528:DyaE1MXjtlOjtA%3D%3D
17. Costa E, Guidotti A, Toffano G (1978) Br J Psychiatry 133:239-248 1:CAS:528:DyaE1MXhsl2qtr4%3D
18. Haefely WE (1987) Chimia 41:389-396 1:CAS:528:DyaL1cXhsFKmsQ%3D%3D
19. Sieghart W (1992) Trends Pharmacol Sci 13:446-450 10.1016/ 0165-6147(92)90142-S
20. Jordan AD, Kordik CP, Reitz AB, Sanfilippo PJ (1996) Expert Opin Ther Patients 6:1047-1060 1:CAS:528:DyaK28XmtlSqtLw%3D
21. Schoemaker H, Boles RG, Horst WD, Yamamura HI (1983) J Pharmacol Exp Ther 225:61-69 1:CAS:528:DyaL3sXktVSisro%3D
22. Wang JKT, Taniguchi T, Spector S (1984) Mol Pharmacol 25:349-351 1:CAS:528:DyaL2cXks1Gmtrc%3D
23. Anholt RRH, Pedersen PL, De Souza EB, Snyder SH (1986) J Biol Chem 261:576-583 1:CAS:528:DyaL28XhtVagsrg%3D
24. Gavish M, Bachman I, Shoukrun R, Katz Y, Veenman L, Weisinger G, Weizman A (1999) Pharmacol Rev 51:629-650 1:CAS:528:DC%2BD3cXnslChsLo%3D
25. Bernassau JM, Reversat JL, Ferrara P, Caput D, Lefur G (1993) J Mol Graph 11:236-244 10.1016/0263-7855(93)80003-A
26. Casellas P, Galiegue S, Basile AS (2002) Neurochem Int 40:475-486 10.1016/S0197-0186(01)00118-8
27. Galiegue S, Tinel R, Casellas P (2003) Curr Med Chem 10:1563-1572 10.2174/0929867033457223
28. Anholt RRH (1986) Trends Pharmacol Sci 7:506-511 10.1016/ 0165-6147(86)90438-4
29. Farges R, Joseph-Liauzun E, Shire D, Caput D, Le Fur G, Loison G, Ferrara P (1993) FEBS Lett 335:305-308 10.1016/0014-5793(93)80407-L
30. Meurice N (2001) Part of Ph.D. thesis work. Développement d'un algorithme génétique original pour l'alignement de graphes moléculaires issus de la densité électronique-Application à l'étude comparative de composes d'intérêt pharmacologique. Laboratoire de Physico-Chimie Informatique, University of Namur, Belgium
31. J-J Bourguignon 1993 Endogenous and synthetic ligands of mitochondrial benzodiazepine receptors: Structure-affinity relationships In: E Giesen-Crouse (ed) Peripheral benzodiazepine receptors. Academic London 59-85
32. Allen FH (2002) Acta Crystallogr B 58:380-388 10.1107/S0108768102003890
33. Camerman A, Camerman N (1972) J Am Chem Soc 94:268-272 10.1021/ ja00756a047
34. Hempel A, Camerman N, Camerman A (1987) Can J Chem 65:1608-1612 1:CAS:528:DyaL1cXnsFelug%3D%3D
35. Meurice N, Norberg B, Durant F, Didier B, Bourguignon J-J, Vercauteren DP (2005) Acta Cryst C (in preparation)
36. Binamé J, Meurice N, Leherte L, Glasgow J, Fortier S, Vercauteren DP (2004) J Chem Inf Comput Sci 44:1394-1401 10.1021/ci034157x
37. SR Hall DJ du Boulay R Olthof-Hazekamp 2000 Xtal3.7 System University of Western Australia Crawley
38. CK Johnson 1977 ORCRIT-the Oak Ridge Critical point network program Chemistry Division Oak Ridge National Laboratory Oak Ridge TN
39. CK Johnson 1993 ORCRIT-the Oak Ridge Critical point network program User's guide Oak Ridge TN
40. Leherte L, Fortier S, Glasgow J, Allen FH (1994) Acta Crystallogr D 50:155-166 10.1107/S0907444993011345
41. DE Goldberg 1989 Genetic algorithms in search, optimization, and machine learning University of Alabama (ed) Addison-Wesley Reading MA
42. Cartwright HM (1993) Applications of artificial intelligence in chemistry. In: Compton RG, Davies SG, Evans J (eds) Oxford University Press, New York
43. Lucasius CB, Kateman G (1993) Chemom Intell Lab Syst 19:1-33 10.1016/ 0169-7439(93)80079-W
44. Crippen GM (1979) J Med Chem 22:988-997 10.1021/jm00194a020
45. Crippen GM (1982) Mol Pharmacol 22:11-19 1:CAS:528:DyaL38Xlt1Sgu78%3D
46. Loew GH, Nienow JR, Poulsen M (1984) Mol Pharmacol 26:19-34 1:CAS:528:DyaL2cXlt1amtbs%3D
47. Loew GH, Nienow JR, Lawson JA, Toll L, Uyeno ET (1985) Mol Pharmacol 28:17-31 1:CAS:528:DyaL2MXkvFygsLo%3D
48. Villar HO, Uyeno ET, Toll L, Polgar W, Davies MF, Loew GH (1989) Mol Pharmacol 36:589-600 1:CAS:528:DyaK3cXjtVantg%3D%3D
49. Villar HO, Davies MF, Loew GH, Maguire PA (1991) Life Sci 48:593-602 10.1016/0024-3205(91)90533-H
50. Codding PW, Muir AKS (1985) Mol Pharmacol 28:178-184 1:CAS:528:DyaL2MXltlCntbw%3D
51. Allen MS, Hagen TJ, Trudell ML, Codding PW, Skolnick P, Cook JM (1988) J Med Chem 31:1854-1861 10.1021/jm00117a029
52. Hollinshead SP, Trudell ML, Skolnick P, Cook JM (1990) J Med Chem 33:1062-1069 10.1021/jm00165a028
53. Wong G, Koehler KF, Skolnick P, Gu Z-Q, Ananthan S, Schönholzer P, Hunkeler W, Zhang W, Cook JM (1993) J Med Chem 36:1820-1830 10.1021/ jm00065a004
54. Borea PA, Gilli G, Bertolasi V, Ferretti V (1987) Mol Pharmacol 31:334-344 1:CAS:528:DyaL2sXktlalsrY%3D
55. Bertolasi V, Ferretti V, Gilli G, Borea PA (1990) J Chem Soc Perkin Trans 2:283-289
56. Tebib S, Bourguignon J-J, Wermuth CG (1987) J Comput Aided Mol Des 1:153-170 1:CAS:528:DyaL1cXjtFeitQ%3D%3D
57. Didier B (1998) Ph.D. thesis. Laboratoire de Pharmacochimie de la Communication Cellulaire, Université Louis Pasteur, Illkirch
58. Didier B, Bourguignon J-J, Personal communication
59. Anzini M, Cappelli A, Vomero S, Seeber M, Menziani MC, Langer T, Hagen B, Manzoni C, Bourguignon J-J (2001) J Med Chem 44:1134-1150 10.1021/ jm0009742
60. N Meurice GM Maggiora DP Vercauteren 2000 Study of the molecular similarity among three HIV reverse transcriptase inhibitors in order to validate GAGS, a genetic algorithm for graph similarity search In: C Gundertofte FS Jorgensen (eds) Molecular modeling and prediction of bioactivity. Kluwer New York 427-428
61. Meurice N, Vercauteren DP (2005) J Chem Inf Model (in preparation)