Novel methods for the prediction of logP, Pka, and logD

Journal of Chemical Information and Computer Sciences

Volumn 42, Issue 4, 2002, Pages 796-805

  Xing, Li ^a,b   Glen, Robert C ^a,c  

^a TRIPOS INC   (United States)

^b PFIZER INC   (United States)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC CHARGES;

ACIDS; ALKALINITY; DRUG PRODUCTS; IONIZATION; PH EFFECTS;

MOLECULAR STRUCTURE;

NITROGEN; OXYGEN;

ALGORITHM; ARTICLE; BIOAVAILABILITY; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; FACTUAL DATABASE; HYDROGEN BOND; PH;

ALGORITHMS; BIOLOGICAL AVAILABILITY; COMPUTER SIMULATION; DATABASES, FACTUAL; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; MODELS, CHEMICAL; MOLECULAR STRUCTURE; NITROGEN; OXYGEN;

EID: 0036628547     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci010315d     Document Type: Article

References (33)

1. Leo, A.; Hansch, C.; Elkins, D. Partition Coefficients and Their Uses. Chem. Rev. 1971, 71, 525.
2. Linpinski, C.A.; Lombardo, F.; Dominy, B.W.; Freeny, P. Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings. Adv. Drug Deliv. Rev. 1997, 23, 3-25.
3. Winiwarter, S.; Bonham, N.M.; Ax, F.; Hallberg, F.; Hallberg, A.; Lennernas, H.; Karlen, A. Correlation of Human Jejunal Permeability (in vivo) of Drags with Experimentally and Theoretically Derived Parameters. A Multivariate Data Analysis Approach. J. Med. Chem. 1998, 41, 4939-4949.
4. Hansch, C.; Leo, A.J. Substituent constants for Correlation Analysis in Chemistry and Biology; Wiley: New York, 1979.
5. Rekker, R.F.; Mannhold, R. Calculation of Drug Lipophilicity; VCH Publishers: Weinheim, 1992.
6. Rekker, R.F.; ter Laak A.M. On the Reliability of Calculated logP-Values: Rekker, Hansch/Leo and Suzuki Approach. Quant. Struct.-Act. Relat. 1993, 12, 152-157.
7. Mannhold, R.; Rekker, R.F.; Sonntag, C.; Ter Laak, A.M.; Dross, K.; Polymeropoulos, E.E. Comparative Evaluation of the Predictive Power of Calculation Procedures for Molecular Lipophilicity. J. Pharm. Sci. 1995, 84, 1410-1419.
8. Klopman, G.; Li, J.-Y.; Wang, S.; Dimayuga, M. Computer Automated logP Calculations Based on an Extended Group Contribution Approach. J. Chem. Inf. Comput. Sci. 1994, 34, 752-781.
9. Buchwald, P.; Bodor, N. Octanol-Water Partition: Searching For Predictive Models. Curr. Med. Chem. 1998, 5, 353-380.
10. Wildman, S.A.; Crippen, G.M. Prediction of Physicochemical Parameters by Atomic Contributions. J. Chem. Inf. Comput. Sci. 1999, 39, 868-873.
11. Duprat, A.F.; Huynh, T.; Dreyfus, G. Toward a Principled Methodology for Neural Network Design and Performance Evaluation in QSAR. Application to the Prediction of logP. J. Chem. Inf. Comput. Sci. 1998, 38, 586-594.
12. Beck, B.; Breindl, A.; Clark, T. QM/NN QSPR Models with Error Estimation: Vapor Pressure and LogP. J. Chem. Inf. Comput. Sci. 2000, 40, 1046-1051.
13. Reynolds, C.H. Estimating Lipophilicity Using the GB/SA Continuum Solvation Model: A Direct Methord for Computing Partition Coefficients. J. Chem. Inf. Comput. Sci. 1995, 35, 738-742.
14. Ruelle, P. Universal Model Based on the Mobile Order and Disorder Theory for Predicting Liphphilicity and Partition Coefficients in All Mutually Immiscible Two-Phase Liquid Systems. J. Chem. Inf. Comput. Sci. 2000, 40, 681-700.
15. a Prediction for Organic Acids and Bases; Chapman and Hall: New York, 1981.
16. Tsantili-Kakoulidou, A.; Panderi, I.; Csizmadia, F.; Darvas, F. Prediction of Distribution Coefficient from Structure 2. Validation of Prolog D, au Expert System. J. Pharm. Sci. 1997, 86, 1173-1179.
17. a Values in Aqueous Solution I. Carboxylic Acids. J. Phys. Chem. A 1999, 103, 11194-11199.
18. a of Phenols, Carboxylic Acids and Alcohols from Semiempirical Quantum Chemical Methods. Chemosphere 1999, 38, 191-206.
19. a and Acid pH-Dependent Stability Estimation in Proteins: Removing Dielectric and Counterion Boundaries. Protein Sci. 1999, 8, 418-425.
20. Glen, R.C. A Fast Empirical Method for the Calculation of Molecular Polarizability. J. Computer-Aided Mol. Des. 1994, 8, 457-466.
21. Slater, J.C. Atomic Shielding Constants. Phys. Rev. 1930, 36, 57-64.
22. Sybyl is a product of Tripos; Inc., 1699 South Hanley Road, St. Louis, MO 63144; www.tripos.com.
23. CRC Handbook of Chemical and Physics, 72nd ed.; Lide, D.R., Ed.; CRC Press: Boston, 1991.
24. Pomona Medchem database (MASTERFILE); Pomona College: Claremont, CA 91711.
25. Wold, S.; Sjostrom, M. In Chemometrics: Theory and Application; Kowalski, B.R., Ed.; American Chemical Society: Washington, DC, 1977; p 243.
26. Lange's Handbook of Chemistry, 13th ed.; Dean, J.A., Ed.; McGraw-Hill: 1985; Tables 5-8.
27. Klopman, G.; Iroff, L.D. Calculation of partition coefficients by the charge density method. J. Comput. Chem. 1981, 2, 157-160.
28. Bodor, N.; Gabanyi, Z.; Wong, C.-K. A New Method for the Estimation of Partition Coefficient. J. Am. Chem. Soc. 1989, 111, 3783-3786.
29. Platts, J.A.; Abraham, M.H.; Butina, D.; Hersey, A. Estimation of Molecular Linear Free Energy Relationship Descriptors by a Group Contribution Approach. 2. Prediction of Partition Coefficeints. J. Chem. Inf. Comput. Sci. 2000, 40, 71-80.
30. Brickmann, J.; Goetze, T.; Heiden, W.; Moeckel, G.; Reiling, S.; Vollhardt, H.; Zachmann, C.-D. Interactive Visualization of Molecular Scenarios with MOLCAD/SYBYL. In Data Visualization in Molecular Science - Tools for Insight and Innovation; Bowie, J.E., Ed.; Addison-Wesley Publishing Company Inc.: Reading, MA, 1995; pp 83-97.
31. 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. Chem. Inf. Comput. Sci. 2000, 43, 3714-3717.
32. Unity is a product of Tripos, Inc., 1699 South Hanley Road, St. Louis, MO 63144; www.tripos.com.
33. Dewar, M.J.S.; Zoebisch, E.G.; Healy, E.F.; Stewart, J.J.P. AM1: A new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 1985, 103, 3902-3909.