Toward prediction of alkane/water partition coefficients

Journal of Medicinal Chemistry

Volumn 51, Issue 13, 2008, Pages 3720-3730

  Toulmin, Anita ^a   Wood, J Matthew ^a   Kenny, Peter W ^a  

^a ASTRAZENECA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALKANE; HEXADECANE; OCTANOL; WATER;

ARTICLE; CHEMICAL ANALYSIS; CHEMISTRY; ELECTRIC POTENTIAL; HYDROGEN BOND; LIPOPHILICITY; PARTITION COEFFICIENT;

EID: 46849091131     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm701549s     Document Type: Article

References (69)

1. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Delivery Rev. 1997, 23, 3-25.
2. van de Waterbeemd, H.; Smith, D. A.; Beaumont, K.; Walker, D. K. Property-based design: Optimization of drug absorption and pharmacokinetics. J. Med. Chem. 2001, 44, 1-21.
3. Avdeef, A. Physicochemical profiling (solubility, permeability and charge state). Curr. Top. Med. Chem. 2001, 1, 277-351.
4. Fujita, T.; Iwasa, J.; Hansch, C. A new substituent constant, π, derived from partition coefficients. J. Am. Chem. Soc. 1964, 86, 5175-5180.
5. Avdeef, A.; Bendels, S.; Di, L.; Faller, B.; Kansy, M.; Sugano, K.; Yamauchi, Y. Parallel artificial membrane permeability assay (PAMPA)-critical factors for better predictions of absorption. J. Pharm. Sci. 2007, 96, 2893-2909.
6. Hitchcock, S. A.; Pennington, L. D. Structure-brain exposure relationships. J. Med. Chem. 2006, 49, 7559-7583.
7. Lombardo, F.; Obach, R. S.; Shalaeva, M. Y.; Gao, F. Prediction of volume of distribution values in humans for neutral and basic drugs using physicochemical measurements and plasma protein binding data. J. Med. Chem. 2002, 45, 2867-2876.
8. Delaney, J. S. Predicting aqueous solubility from structure. Drug Discovery Today 2005, 10, 289-295.
9. Ran, Y.; Yalkowsky, S. H. Prediction of drug solubility by the general solubility equation (GSE). J. Chem. Inf. Comput. Sci. 2001, 41, 354-357.
10. Jamieson, C. M. J.; Moir, E. M.; Rankovic, Z.; Wishart, G. Medicinal chemistry of hERG optimizations: Highlights and hang-ups. J. Med. Chem. 2006, 49, 5029-5045.
11. ClogP, BioByte Corp., 201 W 4th Street, no. 204, Claremont CA 91711-4707; http://www.biobyte.com
12. Dallas, A. J.; Carr, P. W. A thermodynamic and solvatochromic investigation of the effect of water on the phase-transfer properties of octan-1-ol. J. Chem. Soc., Perkin Trans. 2 1992, 2155-2161.
13. Mayer, P. T.; Anderson, B. T. Transport across 1,9-decadiene precisely mimics the chemical selectivity of the barrier in egg Lecithin bilayers. J. Pharm. Sci. 2002, 91, 640-646.
14. Wolfenden, R. Experimental measures of amino acid hydrophobicity and the topology of transmembrane and globular proteins. J. Gen. Physiol. 2007, 129, 357-362.
15. Fujii, Y.; Sobue, K.; Tanaka, M. Solvent effect on the dimerization and hydration constant of benzoic acid. J. Chem. Soc., Faraday Trans. I 1978, 74, 1467-1476.
16. Seiler, P. Interconversion of lipophilicities from hydrocarbon/water systems into the octanol/water system. Eur. J. Med. Chem. 1974, 9, 473-479.
17. Young, R. C.; Mitchell, R. C.; Brown, T. H.; Ganellin, C. R.; Griffiths; Jones, R. M.; Rana, K. K.; Saunders, D.; Smith, I. R.; Sore, N.; Wilks, T. J. Development of a new physicochemical model for brain penetration and its application to the design of centrally acting H2 receptor histamine antagonists. J. Med. Chem. 1988, 31, 656-671.
18. Goodwin, J. T.; Conradi, R. A.; Ho, N. F. H.; Burton, P. S. Physicochemical determinants of passive membrane permeability: role of solute hydrogen-bonding potential and volume. J. Med. Chem. 2001, 44, 3721-3729.
19. Leahy, D. E.; Morris, J. J.; Taylor, P. J.; Wait, A. R. Model solvent systems for QSAR. Part 2. Fragment values (f-values) for the critical quartet. J. Chem. Soc. Perkin Trans. 2 1992, 723-731.
20. Leahy, D. E.; Morris, J. J.; Taylor, P. J.; Wait, A. R. Model solvent systems for QSAR. Part 3. An LSER analysis of the critical quartet. New light on hydrogen bond strength and directionality. J. Chem. Soc. Perkin Trans. 2 1992, 705-722.
21. Leahy, D. E.; Morris, J. J.; Taylor, P. J.; Wait, A. R. Model solvent systems for QSAR. Part IV. The Hydrogen Bond Acceptor Behaviour of Heterocycles. J. Phys. Org. Chem. 1994, 7, 743-750.
22. Riebesehl, W.; Tomlinson, E.; Gruenbauer, H. J. M. Thermodynamics of solute transfer between alkanes and water. J. Phys. Chem. 1984, 88, 4775-4779.
23. Abraham, M. H.; Grellier, P. L.; McGill, R. A. Determination of olive oil-gas and hexadecane-gas partition coefficients, and calculation of the corresponding olive oil-water and hexadecane-water partition coefficients. J. Chem. Soc., Perkin Trans. 2 1987, 797-803.
24. Abraham, M. H.; Whiting, G. S.; Fuchs, R. J.; Chambers, E. J. Thermodynamics of solute transfer from water to hexadecane. J. Chem. Soc., Perkin Trans. 2 1990, 291-300.
25. Abraham, M. H.; Chadha, H. S.; Whiting, G. S.; Mitchell, R. C. Hydrogen bonding. 32. An analysis of water-octanol and water-alkane partitioning and the AlogP parameter of Seiler. J. Pharm. Sci. 1994, 83, 1085-1100.
26. Tsai, R. S.; Fan, W.; El Tayar, N.; Carrupt, P. A; Testa, B.; Kier, L. B. Solute-water interactions in the organic phase of a biphasic system. 1. Structural influence of organic solutes on the "water-dragging" effect. J. Am. Chem. Soc. 1993, 115, 9632-9639.
27. Palm, K.; Luthman, K.; Ungell, A.-L.; Strandlund, G.; Artursson, P. Correlation of drug absorption with molecular surface properties. J. Pharm. Sci. 1996, 85, 32-39.
28. Ertl, P.; Rohde, B.; Selzer, P. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. J. Med. Chem. 2000, 43, 3714-3717.
29. Labute, P. A widely applicable set of descriptors. J. Mol. Graph. Model. 2000, 18, 464-477.
30. Abraham, M. H. Scales of solute hydrogen-bonding; their construction and application to physicochemical and biochemical processes. Chem. Soc. Rev. 1993, 22, 73-83.
31. Laurence, C.; Berthelot, M. Observations on the strength of hydrogen bonding. Perspect. Drug Discovery Des. 2000, 18, 39-60.
32. Abraham, M. H.; Duce, P. D.; Prior, D. V.; Barratt, D. G.; Morris, J. J.; Taylor, P. J. Hydrogen bonding: part 9. Solute proton donor and proton acceptor scales for use in drug design. J. Chem. Soc., Perkin Trans. 2 1998, 1355-1375.
33. Abraham, M. H.; Ibrahim, A.; Zissimos, A. M.; Zhao, Y. H.; Comer, J.; Reynolds, D. P. Application of hydrogen bonding calculations in property based drug design. Drug Discovery Today 2002, 7, 1056-1063.
34. Murray, J. S.; Politzer, P. Relationships between solute hydrogen-bond acidity/basicity and the calculated electrostatic potential. J. Chem. Res. S. 1992, 3, 110-111.
35. Murray, J. S.; Raganathan, S.; Politzer, P. Correlations between the solvent hydrogen bond acceptor parameter β and the calculated molecular electrostatic potential. J. Org. Chem. 1991, 56, 3734-3739.
36. Kenny, P. W. Prediction of hydrogen bond basicity from computed molecular electrostatic properties: Implications for comparative molecular field analysis. J. Chem. Soc., Perkin Trans. 2 1994, 199-202.
37. Perrin, D. D. Dissociation constants of organic bases in aqueous solution: Supplement 1972; Butterworths: London, 1972.
38. Szabo, A.; Ostlund, N. S. Modern Quantum Chemistry. Introduction to Advanced Electronic Structure Theory; Dover: Mineola, NY, 1996.
39. Koch, W.; Holthausen, M. C. A Chemist's Guide to Density Functional Theory; Wiley-VCH Verlag GmbH & Co.: Weinhem, 2000.
40. Avdeef, A.; Barrett, D. A.; Shaw, P. N.; Knaggs, R. D.; Davis, S. S. Octanol-, chloroform-, and propylene glycol dipelargonate-water partitioning of morphine-6-glucuronide and other related opiates. J. Med. Chem. 1996, 39, 4377-4381.
41. Kelder, J.; Grootenhuis, P. D. J.; Bayada, D. M.; Delbressine, L. P. C.; Ploemen, J.-P. Polar molecular surface as a dominating determinant for oral absorption and brain penetration of drugs. Pharm. Res. 1999, 16, 1514-1519.
42. Hansch, C.; Leo, A.; Hoekman; D. Exploring QSAR Hydrophobic, Electronic, and Steric Constants; American Chemical Society: Washington DC, 1995.
43. Zwanzig, R. W. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J. Chem. Phys. 1954, 22, 1420-1426.
44. Kenny, P. W.; Sadowski, J. Structure Modification in Chemical Databases. In Chemoinformatics in Drug Discovery; Oprea, T. I., Ed.; Wiley-VCH Verlag GmbH & Co.: Weinheim, 2005; Vol. 23, pp 271-284.
45. Leach, A. G.; Jones, H. D.; Cosgrove, D. A.; Kenny, P. W.; Ruston, L.; MacFaul, P.; Wood, J. M.; Colclough, N.; Law, B. Matched molecular pairs as a guide in the optimization of pharmaceutical properties; A study of aqueous solubility, plasma protein binding and oral exposure. J. Med. Chem. 2006, 49, 6672-6682.
46. a values of quinolones from mobility and spectroscopic data obtained by capillary electrophoresis and a diode array detector. Anal. Chim. Acta 2002, 464, 37-45.
47. Edwards, J. O.; Pearson, R. G. The Factors Determining Nucleophilic Reactivities. J. Am. Chem. Soc. 1962, 84, 16-24.
48. Wood, J. M.; Page, M. I. The mechanisms of sulfonyl transfer in strained cyclic sulfonamides. Trends Heterocycl. Chem. 2002, 8, 19-34.
49. 3. J. Chem. Soc., Perkin Trans. 2 1996, 1047-1051.
50. Jorgensen, W. L.; Pranata, J. Importance of secondary interactions in triply hydrogen bonded complexes: guanine-cytosine vs uracil-2,6- diaminopyridine. J. Am. Chem. Soc. 1990, 112, 2008-2010.
51. Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method. J. Comput. Chem. 2000, 21, 132-146.
52. Day, G. M.; Motherwell, W. D. S.; Jones, W. Beyond the Isotropic Atom Model in Crystal Structure Prediction of Rigid Molecules: Atomic Multipoles versus Point Charges. Cryst. Growth Des. 2005, 5, 1023-1033.
53. Rasmussen, T. D.; Ren, P.; Ponder, J. W.; Jensen, F. Force field modeling of conformational energies: importance of multipole moments and intramolecular polarization. Int. J. Quantum Chem. 2007, 107, 1390-1395.
54. Cheeseright, T.; Mackey, M.; Rose, S.; Vinter, A. Molecular field extrema as descriptors of biological activity: Definition and validation. J. Chem. Inf. Mod. 2006, 46, 665-676.
55. Sharp, K. Entropy-enthalpy compensation: fact or artifact? Protein Sci. 2001, 10, 661-667.
56. Dunitz, J. D. Win some, lose some: Enthalpy-entropy compensation in weak intermolecular interactions. Chem. Biol. 1995, 2, 709-712.
57. Lumry, R.; Rajender, S. Enthalpy-entropy compensation phenomena in water solutions of proteins and small molecules: A ubiquitous property of water. Biopolymers 1970, 9, 1125-1227.
58. Maple, J. R.; Cao, Y.; Damm, W.; Halgren, T. A.; Kaminski, G. A.; Zhang, L. Y.; Friesner, R. A. A polarizable force field and continuum solvation methodology for modeling of protein-ligand interactions. J. Chem. Theory Comput. 2005, 1, 694-715.
59. Xie, W.; Pu, J.; MacKerell, A. D.; Gao, J. Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. J. Chem. Theory Comput. 2007, 3, 1878-1889.
60. Patrick, G. L. An Introduction to Medicinal Chemistry, 3rd ed.; Oxford University Press: Oxford, 2005, pp 620.
61. Rang, H. P.; Dale, M. M.; Ritter, J. M. Pharmacology, 4th ed.; Churchill Livingstone: Edinburgh, 1999; pp 598.
62. Summerfield, S. G.; Stevens, A. J.; Cutler, L.; Osuna, M. D. C.; Hammond, B.; Tang, S.-P.; Hersey, A.; Spalding, D. J.; Jeffrey, P. Improving the in vitro prediction of in vivo central nervous system penetration: integrating permeability, P-glycoprotein efflux, and free fractions in blood and brain. J. Pharmacol. Exp. Ther. 2006, 316, 1282-1290.
63. Kalvass, J. C.; Maurer, T. S.; Pollack, G. M. Use of plasma and brain unbound fractions to assess the extent of brain distribution of 34 drugs: comparison of unbound concentration ratios to in vivo P-glycoprotein efflux ratios. Drug Metab. Dispos. 2007, 35, 660-666.
64. Dearden, J. C.; Bresnen, G. M. The measurement of partition coefficients. Quant. Struct. - Act. Relat. 1988, 7, 133-144.
65. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision B.05; Gaussian, Inc.: Wallingford, CT, 2004; http://www.gaussian.com.
66. Cambridge Structural Database, Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; http://www.ccd-c.cam.ac.uk/products/csd/.
67. Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 1988, 28, 31-36.
68. Property calculation engine mib v2007.04, Molinspiration; http://www.molinspiration.com.
69. JMP Version 6.0.0, SAS Institute, SAS Campus Drive, Building S, Cary, NC 27513; http://www.jmp.com.