Hydrophobic molecular similarity from MST fractional contributions to the octanol/water partition coefficient

Journal of Computer-Aided Molecular Design

Volumn 19, Issue 6, 2005, Pages 401-419

  Muñoz Muriedas, Jordi ^a   Perspicace, Samantha ^b   Bech, Nuria ^a   Guccione, Salvatore ^b   Orozco, Modesto ^a,c   Luque, F Javier ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

^b UNIVERSITY OF CATANIA   (Italy)

^c INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

Author keywords

Continuum solvation methods; Hydrophobicity; Molecular alignment; Molecular similarity; MST model; Octanol water partition coefficient

Indexed keywords

ALCOHOLS; BIOACTIVITY; CONTINUUM MECHANICS; HYDROPHOBICITY; MOLECULES; PATTERN RECOGNITION;

COMPUTATIONAL STRATEGY; CONTINUUM MODEL; CONTINUUM SOLVATION METHOD; CONTINUUM SOLVATIONS; HYDROPHOBICS; MOLECULAR SIMILARITY; MST MODEL; OCTANOL-WATER PARTITION COEFFICIENT; SIMILARITY INDICES; WATER TRANSFERS;

FREE ENERGY;

CHOLESTEROL ACYLTRANSFERASE INHIBITOR; CYCLOOXYGENASE 2 INHIBITOR; OCTANOL; SEROTONIN 3 AGONIST; WATER;

ARTICLE; ATOM; COMPUTER AIDED DESIGN; CONTROLLED STUDY; DRUG ACTIVITY; DRUG DESIGN; DRUG STRUCTURE; HYDROPHILICITY; HYDROPHOBICITY; MATHEMATICAL COMPUTING; MOLECULAR BIOLOGY; MOLECULAR MODEL; MOLECULAR RECOGNITION; MONTE CARLO METHOD; PARTITION COEFFICIENT; PHARMACOPHORE; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; STRUCTURE ACTIVITY RELATION;

EID: 84962448558     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-005-7928-3     Document Type: Article

References (46)

1. T. Lengauler and M. Rarey (1996) Curr. Opt. Struct. Biol. 6 402 10.1016/S0959-440X(96)80061-3
2. M.A. Johnson and G.M. Maggiora (1990) Concepts and Applications of Molecular Similarity Wiley New York
3. T.R. Hagadone (1992) J. Chem. Inf. Comput. Sci. 32 51510.1021/ci00009a019
4. S.E. Jakes and P. Willett (1986) J. Mol. Graphics 4 1210.1016/ 0263-7855(86)80088-1
5. J.H. Drie Van D. Weininger and Y.C. Martin (1989) J. Comput.-Aided Mol. Design 3 22510.1007/BF01533070
6. R. Carbó-Dorca D. Robert L. Amat X. Gironés and E. Besalú (2000) Lecture Notes in Chemistry Vol 7 Springer Berlin
7. E.E. Hodgkin and W.G. Richards (1987) Int J. Quantum Chem., Quantum Biol. Symp. 14 105
8. G. Klebe T. Mietzner and F. Weber (1994) J. Comput.-Aided Mol. Design 8 75110.1007/BF00124019
9. J. Mestres D.C. Rohrer and G.M. Maggiora (1997) J. Comput. Chem. 18 93410.1002/(SICI)1096-987X(199705)18:7<934::AID-JCC6>3.0.CO;2-S
10. Cramer , R.D., III, Patterson, D.E. and Bunce, J.D., J. Am. Chem. Soc., 110 (1988) 5959.
11. K. Palm K. Luthman A.L. Ungell G. Strandlund F. Begi P. Lundahl and P. Artursson (1998) J. Med. Chem. 41 5-382 10.1021/jm980313t
12. A. Kantola H.O. Villar and G.H. Loew (1991) J. Comput. Chem. 12 68110.1002/jcc.540120605
13. R.C. Wade K.J. Clark and P.J. Goodford (1993) J. Med. Chem. 36 14010.1021/jm00053a018 8421280
14. R. Jäger S.M. Kast and J. Brickmann (2003) J. Chem. Inf. Comput. Sci. 43 23710.1021/ci025576h 12546558
15. F.W. Heiden G. Moeckel and J. Brickmann (1993) J. Comput.-Aided Mol. Design 7 50310.1007/BF00124359
16. Carrupt, P., Testa, B. and Gaillard, P., 1997 In Lipkowitz, K.B. and Boyd, D.B., (Eds.), Reviews in Computational Chemistry, Vol. 11. Wiley-VCH, New York, 1997, pp. 241-315.
17. F. Croizet M.H. Langlois J.P. Dubost P. Braquet E. Audry P. Dallet and J.C. Colleter (1990) J. Mol. Graphics 8 15310.1016/0263-7855(90)80056-L
18. J. Muñoz X. Barril B. Hernández M. Orozco and F.J. Luque (2002) J. Comput. Chem. 23 55410.1002/jcc.10055 11948582
19. C. Curutchet M. Orozco and F.J. Luque (2001) J. Comput. Chem. 22 118010.1002/jcc.1076
20. S. Miertus E. Scrocco and J. Tomasi (1981) Chem. Phys. 55 11710.1016/ 0301-0104(81)85090-2
21. F.J. Luque J.M. Bofill and M. Orozco (19950 J. Chem. Phys. 103 1018310.1063/1.469921
22. F.J. Luque X. Barril and M. Orozco (1999) J. Comput.-Aided Mol. Des. 13 13910.1023/A:1008036526741 10091120
23. Muñoz, J., Barril, X., Luque, F.J., Gelpí, J.L. and Orozco, M., In Carbó-Dorca, R., Gironés, G. and Mezey, P.G. (Eds.), Fundamentals of Molecular Similarity, Vol. 4 Kluwer, New York, 2001, pp. 143-168.
24. R. Carbó A. Leyda and M. Arnau (1980) Int. J. Quantum Chem. 17 118510.1002/qua.560170612
25. N.V. Harris C. Smith M.J. Ashton A.W. Bridge R.C. Bush E.C.J. Coffee D.I. Dron M.F. Harper D.J. Lythgoe C.G. Newton and D. Riddel (1992) J. Med. Chem. 35 438410.1021/jm00101a016 1447739
26. M.P. Giovannoni V. Dal Piaz B.-M. Kwon M.-K. Kim Y.-K. Kim L. Toma D. Barlocco F. Bernini and M. Canavesi (2001) J. Med. Chem. 44 429210.1021/ jm010807h 11708931
27. L. Toma M.P. Giovannoni V. Dal Piaz B.-M. Kwon Y.-K. Kim A. Gelain and D. Barlocco (2001) Heterocycles 57 39-46
28. Roth, B.D., Drug Disc. Today, 3 (1998) 19.
29. A. Morreale I. Iriepa and E. Gálvez (2002) Curr. Med. Chem. 9 9911860352
30. H.S. Parihar and K.S. Kirschbaum (20020 Bioorg. Med. Chem. Lett. 12 274310.1016/S0960-894X(02)00514-0 12217367
31. I.K. Khana R.M. Weier Y. Yu X.D. Xu F.J. Koszyk P.W. Collins C.M. Koboldt A.W. Veenhuizen W.E. Perkins J.J. Casler J.L. Masferrer and Y.Y. Zhang (1997) J. Med. Chem. 40 163410.1021/jm9700225 9171873
32. I.K. Khana Y. Yu R.M. Huff R.M. Weier X. Xu F.J. Koszyk P.W. Collins J.N. Cogburn P.C. Isakson C.M. Koboldt J.L. Masferrer W.E. Perkins K. Seibert A.W. Veenhuizen J. Yuan D.C. Yang and Y.Y. Zhang (2000) J. Med. Chem. 43 316810.1021/jm0000719 10956225
33. P. Mantri and D. Witiak (1994) Curr. Med. Chem. 1 328
34. M.J.S. Dewar E.G. Zoebisch E.F. Healy and J.J.P. Stewart (1995) J. Am. Chem. Soc. 107 390210.1021/ja00299a024
35. C. Curutchet A. Salichs X. Barril M. Orozco and F.J. Luque (2003) J. Comput. Chem. 24 3210.1002/jcc.10155 12483673
36. MOPAC6.0. Version locally modified by Luque, F.J. and Orozco, M. (Univ. Barcelona).
37. A. Capelli M. Anzini S. Vomero L. Canullo L. Mennuni F. Makovec E. Doucet M. Hamon M.C. Menzini P.G. Benedetti De G. Bruni G. Romero and A. Donati (1999) J. Med. Chem. 42 155610.1021/jm981112s 10229626
38. M. Modica M. Santagati S. Guccione A. Santagati F. Russo A. Cagnotto M. Goegan and T. Mennini (2001) Eur. J. Med. Chem. 36 28710.1016/ S0223-5234(01)01216-8 11337106
39. C. Colominas F.J. Luque and M. Orozco (19990 J. Comput. Chem. 7 66510.1002/(SICI)1096-987X(199905)20:7<665::AID-JCC2>3.0.CO;2-W
40. X. Barril J. Muñoz F.J. Luque and M. Orozco (2000) Phys. Chem. Chem. Phys. 2 489710.1039/b000020p
41. J.J.P. Stewart (1989) J. Comput. Chem. 10 22110.1002/jcc.540100209
42. R. Wang Y. Fu and L. Lai (1997) J. Chem. Inf. Comput. Sci. 37 61510.1021/ ci960169p
43. R. Soliva C. Almansa S.G. Kalko F.J. Luque and M. Orozco (2003) J. Med. Chem. 46 137210.1021/jm0209376 12672237
44. G.R. Desiraju B. Gopalakrishnan R.K.R. Jetti A. Nagaraju D. Raveendra J.A.R.P. Sarma M.E. Sobhia and R. Thilagavathi (2002) J. Med. Chem. 45 484710.1021/jm020198t 12383010
45. P. Chavatte S. Yous C. Marot N. Baurin and D. Lesieur (2001) J. Med. Chem. 44 322310.1021/jm0101343 11563921
46. R.G. Kurumbail A.M. Stevens J.K. Gierse J.J. McDonald R.A. Stegeman J.Y. Pak D. Didelhaus J.M. Miyashiro T.D. Penning K. Seibert P.C. Isakson and W.C. Stallings (1996) Nature 384 64410.1038/384644a0 8967954