Theoretical and Practical Aspects of Three-Dimensional Quantitative Structure-Activity Relationships

Reviews in Computational Chemistry

Volumn 11, Issue , 1997, Pages 127-182

  Oprea, Tudor I ^a,b   Waller, Chris L ^c,d  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b ASTRAZENECA R AND D   (Sweden)

^c U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^d Oncogene Science Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0031531210     PISSN: 10693599     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (151)

1. C. Hansch and A. Leo, Exploring QSAR: Fundamentals and Applications in Chemistry and Biology, American Chemical Society, Washington, DC, 1995, Vol. 1.
2. M. Stone and P. Jonathan, J. Chemometrics, 7, 455 (1993). Statistical Thinking and Technique tor QSAR and Related Studies. 1. General Theory.
3. C. Hansch, Acc. Chem. Res., 26, 147 (1993). Quantitative Structure Activity Relationships and the Unnamed Science.
4. S. N. Deming and S. L. Morgan, Experimental Design: A Chemometric Approach, 2nd ed., Elsevier, Amsterdam, 1993, pp. 25-40. Response Surfaces.
5. S. A. Kauffman, Origins of Order, Oxford University Press, New York, 1993, pp. 121-172. The Structure of Adaptive Landscapes Underlying Protein Evolution.
6. G. Weber, Protein Interactions, Chapman & Hall, New York, 1992, pp. 1-70.
7. T. P. Kenakin, Pharmacologic Analysis of Drug-Receptor Interactions, Raven Press, New York, 1987.
8. P. M. Dean, Molecular Foundations of Drug-Receptor Interactions, Cambridge University Press, Cambridge, 1987.
9. P. W. Atkins, Physical Chemistry, 4th ed., Oxford University Press, Oxford, 1990, pp. 49-52, 654-662.
10. 50) of an Enzymatic Reaction.
11. T. I. Oprea, C. L. Waller, and G. R. Marshall, in Cellular Proteolytic Systems, A. Ciechanover and A. Schwartz, Eds., Wiley-Liss, New York, 1994, pp. 183-221. Viral Proteases: Structure and Function.
12. P. Y. S. Lam, P. K. Jadhav, C. J. Eyermann, C. N. Hodge, Y. Ru, L. T. Bacheler, J. L. Meek, M. J. Otto, M. M. Rayner, Y. N. Wong, C. H. Chang, P. C. Weber, D. A. Jackson, . R. Sharpe, and S. Erickson-Viitanen, Science, 263, 380 (1994). Rational Design of Potent, Bioavailable, Nonpeptide Cyclic Ureas as HIV Protease Inhibitors.
13. L. P. Hammett, Physical Organic Chemistry, 2 ed., McGraw-Hill, New York, 1970.
14. R. W. Taft, in Steric Effects in Organic Chemistry, M. S. Newman, Ed., Wiley, New York, 1956, pp. 556-675. Separation of Polar, Steric and Resonance Effects in Reactivity.
15. C. Hansch, D. Hoekman, and A. Leo, Medchem/Biobyte QSAR Database (1996). Available from Biobyte Corp., 201 W. Fourth St., Suite #204, Claremont, CA 91711. World Wide Web address (URL) http://fox.pomona.claremont.edu/chem/qsar-db.
16. oct from Structures.
17. (b) P.-A. Carrupt, B. Testa, and P. Gaillard, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. 11, pp. 241-315. Computational Approaches to Lipophilicity: Methods and Applications.
18. C. Hansch, Drug Intell. Clin. Pharmacy, 16, 391 (1982). DHFR Inhibition. A Study in the Use of X-Ray Crystallography, Molecular Graphics, and QSAR in Drug Design.
19. C. Hansch, B. A. Hathaway, Z. R. Guo, C. D. Selassie, S. W. Dietrich, J. M. Blaney, R. Langridge, K. W. Volz, and B. T. Kaufman, J. Med. Chem., 27, 129 (1984). Crystallography, QSAR and Molecular Graphics in a Comparative Analysis of the Inhibition of DHFR from Chicken Liver and Lactobacillus casei by 4,6-Diamino-1,2-dihydro-2,2-dimethyl-1-(substituted-phenyl)-s-triazines.
20. B. A. Hathaway, Z. R. Guo, C. Hansch, T. J. Delcamp, S. S. Susten, and J. H. Freisheim, J. Med. Chem., 27, 144 (1984). Inhibition of DHFR by 4,6-Diamino-1,2-dihydro-2,2-dimethyl-1-(substituted-phenyl)-s-triazines. A QSAR Analysis.
21. C. D. Selassie, Z. X. Fang, R. L. Li, C. Hansch, T. Klein, and R. Langridge, J. Med. Chem., 29, 621 (1986). Inhibition of Chicken Liver DHFR by 5-(Substituted benzyl)-2,4-diaminopyrimidines. A QSAR and Graphics Analysis.
22. C. D. Selassie, C. D. Strong, C. Hansch, T. J. Delcamp, J. H. Freisheim, and T. A. Khwaja, Cancer Res., 46, 744 (1986). Comparison of Triazines as Inhibitors of L1210 DHFR and of L1210 Cells Sensitive and Resistant to Methotrexate.
23. R. G. Booth, C. D. Selassie, C. Hansch, and D. V. Santi, J. Med. Chem., 30, 1218 (1987). QSAR of Triazine-antifolate Inhibition of Leishmania DHFR and Cell Growth.
24. Z. Simon, A. Chiriac, S. Holban, D. Ciubotariu, and G. I. Mihalas, Minimum Steric Difference. The MTD-Method for QSAR Studies, Research Studies Press, Letchworth, 1984.
25. D. Ciuhotariu, E. Deretey, T. I. Oprea, T. Sulea, Z. Simon, L. Kurunczi, and A. Chiriac, Quant. Struct.-Act. Relat., 12, 367 (1993). Multiconformational Minimal Steric Difference. Structure-Acetylcholinesterase Hydrolysis Rates Relations for Acetic Acid Esters.
26. A. Verloop, W. Hoogenstraaten, and J. Tipker, in Drug Design, E. J. Ariens Ed., Academic Press, New York, 1976, Vol. 7, pp. 165-207. Development and Application of New Steric Substituent Parameters in Drug Design.
27. 2, Molecular Simulations, Inc., 9685 Scranton Rd., San Diego, CA 92121. Drug Discovery Workbench QSAR+ Software, Release 2.0 (1995).
28. A. J. Hopfinger, J. Med. Chem., 24, 818 (1981). Inhibition of Dihydrofolate Reductase: Structure-Activity Correlations of 2,4-Diamino-5-benzylpyrimidines Based upon Molecular Shape Analysis.
29. A. J. Hopfinger, J. Am. Chem. Soc., 102, 7196 (1981). A QSAR Investigation of Dihydrofolate Reductase Inhibition by Baker Triazines Based upon Molecular Shape Analysis.
30. J. Topliss and R. Edwards, J. Med. Chem., 22, 1238 (1979). Chance Factors in Studies of QSAR.
31. M. Clark and R. D. Cramer III, Quant. Struct.-Act. Relat., 12, 137 (1993). The Probability of Chance Correlation using PLS.
32. S. Wold, K. Esbensen, and P. Geladi, Chemometrics Intelligent Lab. Systems, 2, 37 (1987). Principal Component Analysis.
33. R. D. Cramer III, J. Am. Chem. Soc., 102, 1837 (1980). BC(DEF) Parameters. 1. The Intrinsic Dimensionality of Intermolecular Interactions in the Liquid State.
34. R. D. Cramer III, J. Am. Chem. Soc., 102, 1849 (1980). BC(DEF) Parameters. 2. An Empirical Structure-Based Scheme for Prediction of Some Physical Properties.
35. L. H. Hall and L. B. Kier, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd Eds., VCH Publishers, New York, 1991, Vol. 2, pp. 367-422. The Molecular Connectivity Chi Indexes and Kappa Shape Indexes in Structure-Property Modeling.
36. G. R. Marshall and R. D. Cramer III, Trends Pharmacol. Sci., 9, 285 (1988). Three-Dimensional Structure-Activity Relationships.
37. S. M. Green and G. R. Marshall, Trends Pharmacol. Sci., 16, 285 (1995). 3D-QSAR: A Current Perspective.
38. R. D. Cramer III, D. E. Patterson, and J. D. Bunce, J. Am. Chem. Soc., 110, 5959 (1988). Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins.
39. A. N. Jain, K. Koile, and D. Chapman, J. Med. Chem., 37, 2315 (1994). Compass: Predicting Biological Activities from Molecular Surface Properties. Performance Comparisons on a Steroid Benchmark. The automatic alignment procedure of Compass can also be implemented with CoMFA, giving results similar to Compass (U. Norinder, Sweden, personal communication to T. I. Oprea, 1997).
40. A. N. Jain, K. Koile, and D. Chapman, J. Med. Chem., 37, 2315 (1994). Compass: Predicting Biological Activities from Molecular Surface Properties. Performance Comparisons on a Steroid Benchmark. The automatic alignment procedure of Compass can also be implemented with CoMFA, giving results similar to Compass (U. Norinder, Sweden, personal communication to T. I. Oprea, 1997).
41. J. H. Van Drie, D. Weininger, and Y. C. Martin, J. Comput.-Aided Mol. Design, 3, 225 (1989). ALADDIN: An Integrated Tool for Computer-Assisted Molecular Design and Pharmacophore Recognition from Geometric, Steric and Substructure Searching of Three-Dimensional Molecular Structures.
42. (a) S. K. Kearsley and G. M. Smith, Tetrahedron Comput. Methodol., 3, 615 (1990). An Alternative Method for the Alignment of Molecular Structures: Maximizing Electrostatic and Steric Overlap.
43. (b) G. Jones, P. Willett, and R. C. Glen, J. Comput.-Aided Mol. Design, 9, 532 (1995). A Genetic Algorithm for Flexible Molecular Overlay and Pharmacophore Elucidation. This program is available via the World Wide Web at http://www.tripos.com/ gasphome.html.
44. M. S. Searle and D. H. Williams, J. Am. Chem. Soc., 114, 10690 (1992). The Cost of Conformational Order: Entropy Changes in Molecular Associations.
45. T. D. J. Perkins, J. E. J. Mills, and P. M. Dean, J. Comput.-Aided Mol. Design, 9, 479 (1995). Molecular Surface-Volume and Property Matching to Superpose Flexible Dissimilar Molecules.
46. S. Muresan, T. Sulea, D. Ciubotariu, L. Kurunczi, and Z. Simon, Quant. Struct.-Act. Relat., 15, 31 (1996). Van der Waals Intersection Envelope Volumes as a Possible Basis for Steric Interactions in CoMFA. See also Ref. 95.
47. B. Lee, Biophys. Chem., 51, 271 (1994). Enthalpy-Entropy Compensation in the Thermodynamics of Hydrophobicity.
48. G. E. Kellogg and D. J. Abraham, HINT software available from EduSoft LC, P.O. Box 1811, Ashland, VA 23005.
49. G. E. Kellogg, S. F. Semus, and D. J. Abraham, J. Comput.-Aided Mol. Design, 5, 545 (1991). HINT: A New Method of Empirical Hydrophobic Field Calculation for CoMFA.
50. P.-A. Carrupt, P. Gaillard, F. Billois, P. C. Weber, B. Testa, C. Meyer, and S. Perez, in Lipophilicity in Drug Action and Toxicology, V. Pliska, B. Testa, and H. Van de Waterbeemd, Eds., Methods and Principles in Medicinal Chemistry series, VCH Publishers, Weinheim, 1996, Vol. 4, pp. 195-217. The Molecular Lipophilicity Potential (MLP): A New Tool for log P Calculations and Docking and in Comparative Molecular Field Analysis. See also Ref. 16b.
51. Z. Simon, Rev. Roum. Chim., 37, 323 (1992). Comparative Molecular Field Analysis. Critical Comments.
52. H. Kubinyi, Ed., 3D-QSAR in Drug Design: Theory, Methods and Applications, ESCOM, Leiden, 1993. See also H. Kubinyi, G. Folkers, and Y. C. Martin, Eds., 3D-QSAR in Drug Design: Recent Advances, ESCOM (Kluwer), Leiden, 1997, in press.
53. H. Kubinyi, Ed., 3D-QSAR in Drug Design: Theory, Methods and Applications, ESCOM, Leiden, 1993. See also H. Kubinyi, G. Folkers, and Y. C. Martin, Eds., 3D-QSAR in Drug Design: Recent Advances, ESCOM (Kluwer), Leiden, 1997, in press.
54. F. Sanz, J. Giraldo, and F. Manaut, Eds., QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications, J. R. Prous, Barcelona, 1995.
55. H. Van de Waterbeemd, Ed., Chemometric Methods in Molecular Design, Methods and Principles in Medicinal Chemistry Series, VCH Publishers, Weinheim, 1995, Vol. 2.
56. R. D. Cramer III and J. D. Bunce, in QSAR in Drug Design and Toxicology, D. Hadzi and B. Jerman-Blazic, Eds., Elsevier, Amsterdam, 1987, pp. 3-12. The DYLOMMS Method: Initial Results from a Comparative Study of Approaches to 3D QSAR.
57. R. D. Cramer III, S. A. DePriest, D. E. Patterson, and P. Hecht, in 3D-QSAR in Drug Design: Theory, Methods and Applications, H. Kubinyi, Ed., ESCOM, Leiden, 1993, pp. 443-485. The Developing Practice of Comparative Molecular Field Analysis.
58. P. J. Goodford, J. Am. Chem. Soc., 28, 849 (1985). A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules.
59. M. Baroni, G. Costantino, G. Cruciani, D. Riganelli, R. Valigi, and S. Clementi, Quant. Struct.-Act. Relat., 12, 9 (1993). Generating Optimal Linear PLS Estimations (GOLPE): An Advanced Chemometric Tool for Handling 3D-QSAR Problems.
60. R. C. Wade, in 3D-QSAR in Drug Design: Theory, Methods and Applications, H. Kubinyi, Ed., ESCOM, Leiden, 1993, pp. 486-505. Molecular Interaction Fields.
61. D. Rogers and A. J. Hopfinger, J. Chem. Inf. Comput. Sci., 34, 854 (1994). Application of Genetic Function Approximation to Quantitative Structure-Activity Relationships and Quantitative Structure-Property Relationships.
62. A. Doweyko, J. Med. Chem., 31, 1396 (1988). The Hypothetical Active Site Lattice. An Approach to Modelling Active Sites from Data on Inhibitor Molecules. See also J. J. Kaminski and A. M. Doweyko, J. Med. Chem., 40, 427 (1997). Antiulcer Agents. 6. Analysis of the in Vitro Biochemical and in Vivo Gastric Antisecretory Activity of Substituted Imidazo[1,2-a]pyridines and Related Analogues Using Comparative Molecular Field Analysis and Hypothetical Active Site Lattice Methodologies.
63. A. Doweyko, J. Med. Chem., 31, 1396 (1988). The Hypothetical Active Site Lattice. An Approach to Modelling Active Sites from Data on Inhibitor Molecules. See also J. J. Kaminski and A. M. Doweyko, J. Med. Chem., 40, 427 (1997). Antiulcer Agents. 6. Analysis of the in Vitro Biochemical and in Vivo Gastric Antisecretory Activity of Substituted Imidazo[1,2-a]pyridines and Related Analogues Using Comparative Molecular Field Analysis and Hypothetical Active Site Lattice Methodologies.
64. V. E. Golender and E. R. Vorpagel, in 3D-QSAR in Drug Design: Theory, Methods and Applications, H. Kubinyi, Ed., ESCOM, Leiden, 1993, pp. 137-149. Computer-Assisted Pharmacophore Identification. V. E. Golender and A. B. Rozenblit, Logical and Combinatorial Algorithms for Drug Design. Research Studies Press, Letchworth, 1983.
65. V. E. Golender and E. R. Vorpagel, in 3D-QSAR in Drug Design: Theory, Methods and Applications, H. Kubinyi, Ed., ESCOM, Leiden, 1993, pp. 137-149. Computer-Assisted Pharmacophore Identification. V. E. Golender and A. B. Rozenblit, Logical and Combinatorial Algorithms for Drug Design. Research Studies Press, Letchworth, 1983.
66. U. Thibaut, in 3D-QSAR in Drug Design: Theory, Methods and Applications, H. Kubinyi, Ed., ESCOM, Leiden, 1993, pp. 661-696. Applications of CoMFA and Related 3D QSAR Approaches. See also references within.
67. G. Folkers, A. Merz, and D. Rognan, in 3D-QSAR in Drug Design: Theory, Methods and Applications, H. Kubinyi, Ed., ESCOM, Leiden, 1993, pp. 583-618. CoMFA: Scope and Limitations. See also references within.
68. K. H. Kim, in Molecular Similarity in Drug Design, P. M. Dean, Ed., Chapman & Hall, London, 1995, pp. 291-331. Comparative Molecular Field Analysis.
69. U. Thibaut, G. Folkers, G. Klebe, H. Kubinyi, A. Merz, and D. Rognan, in 3D-QSAR in Drug Design: Theory, Methods and Applications, H. Kubinyi, Ed., ESCOM, Leiden, 1993, pp. 711-716. Recommendations for CoMFA Studies and 3D QSAR Publications. Y. C. Martin, K.-H. Kim, and C. T. Lin, in Advances in Quantitative Structure-Property Relationships, M. Charton, Ed., JAI Press, Greenwich, CT, 1996, Vol. 1, pp. 1-52. Comparative Molecular Field Analysis: CoMFA.
70. U. Thibaut, G. Folkers, G. Klebe, H. Kubinyi, A. Merz, and D. Rognan, in 3D-QSAR in Drug Design: Theory, Methods and Applications, H. Kubinyi, Ed., ESCOM, Leiden, 1993, pp. 711-716. Recommendations for CoMFA Studies and 3D QSAR Publications. Y. C. Martin, K.-H. Kim, and C. T. Lin, in Advances in Quantitative Structure-Property Relationships, M. Charton, Ed., JAI Press, Greenwich, CT, 1996, Vol. 1, pp. 1-52. Comparative Molecular Field Analysis: CoMFA.
71. G. Greco, E. Novellino, and Y. C. Martin, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. 11, pp. 183-240. Approaches to Three-Dimensional Quantitative Structure-Activity Relationships.
72. J. W. McFarland, J. Med. Chem., 35, 2543 (1992). Comparative Molecular Field Analysis of Anticoccidial Triazines.
73. C. L. Waller and J. D. McKinney, Chem. Res. Toxicol., 8, 847 (1995). 3D-QSAR of Dioxins and Dioxin-like Compounds: Model Validation and AH Receptor Characterization.
74. T. Sulea, L. Kurunczi, T. I. Oprea, and Z. Simon, J. Comput.-Aided Mol. Design, in press (1997). MTD-ADJ: A Multiconformational Minimal Topologic Difference for Determining Bioactive Conformers Using Adjusted Biological Activities.
75. C. L. Waller, T. I. Oprea, A. Giolitti, and G. R. Marshall, J. Med. Chem., 36, 4152 (1993). 3-D QSAR of Human Immunodeficiency Virus (1) Protease Inhibitors. I. A CoMFA Study Employing Experimentally Determined Alignment Rules.
76. G. Cruciani and K. A. Watson, J. Med. Chem., 37, 2589 (1994). Comparative Molecular Field Analysis Using GRID Force-Field and GOLPE Variable Selection Methods in a Study of Inhibitors of Glycogen Phosphorylase b.
77. G. R. Marshall, C. D. Barry, H. E. Bosshard, R. A. Dammkoehler, and D. A. Dunn, in Computer-Assisted Drug Design, E. C. Olson and R. E. Christoffersen Eds., ACS Symposium Series 112, American Chemical Society, Washington DC, 1979, pp. 205-226. The Conformational Parameter in Drug Design: The Active Analog Approach.
78. G. R. Marshall, in Burger's Medicinal Chemistry and Drug Discovery, 5th ed., M. F. Wolff, Ed., Wiley, New York, 1995, Vol. 1, pp. 573-659. Molecular Modeling in Drug Design.
79. R. A. Dammkoehler, S. F. Karasek, E. F. B. Shands, and G. R. Marshall, J. Comput.-Aided Mol. Design, 3 3 (1989). Constrained Search of Conformational Hyperspace.
80. R. Dammkoehler and F. Berkley-Shands, RECEPTOR software available from Tripos Inc., 1699 S. Hanley Rd., St. Louis MO 63144.
81. SYBYL Molecular Modeling System, software available from Tripos Inc., 1699 S. Hanley Rd., St. Louis, MO 63144.
82. Y. C. Martin, M. G. Bures, E. A. Danaber, and J. DeLazzer, in Trends in QSAR and Molecular Modelling 92, C.-G. Wermuth, Ed., ESCOM, Leiden, 1993, pp. 22-27. New Strategies That Improve the Efficiency of the 3D Design of Bioactive Molecules. See also references within.
83. T. D. J. Perkins and P. M. Dean, J. Comput.-Aided Mol. Design, 7, 155 (1993). An Exploration of a Novel Strategy for Superposing Several Flexible Molecules.
84. G. Klebe and U. Abraham, J. Med. Chem., 36, 70 (1993). On the Prediction of Binding Properties of Drug Molecules by Comparative Molecular Field Analysis. See also H. Breim and I. D. Kuntz, J. Med. Chem., 39, 3401 (1996). Molecular Similarity Based on COC-Generated Fingerprints.
85. G. Klebe and U. Abraham, J. Med. Chem., 36, 70 (1993). On the Prediction of Binding Properties of Drug Molecules by Comparative Molecular Field Analysis. See also H. Breim and I. D. Kuntz, J. Med. Chem., 39, 3401 (1996). Molecular Similarity Based on COC-Generated Fingerprints.
86. T. I. Oprea, C. L. Waller, and G. R. Marshall, J. Med. Chem., 37, 2206 (1994). 3D-QSAR of Human Immunodeficiency Virus (1) Protease Inhibitors. II. Predictive Power Using Limited Exploration of Alternate Binding Modes.
87. M. Clark, R. D. Cramer III, D. M. Jones, D. E. Patterson, and P. E. Simeroth, Tetrahedron Comput. Methodol. 3, 47 (1990). Comparative Molecular Field Analysis (CoMFA). 2. Toward Its Use with 3D-Structural Databases.
88. J. A. Calder, J. A. Wyatt, D. A. Frenkel, and J. E. Casida, J. Comput.-Aided Mol. Design, 7, 45 (1993). CoMFA Validation of the Superposition of Six Classes of Compounds Which Block GABA Receptors Non-Competitively.
89. J. P. Horwitz, I. Massova, T. E. Wiese, A. J. Wozniak, T. H. Corbett, J. S. Sebolt-Leopold, D. B. Capps, and W. R. Leopold, J. Med. Chem., 36, 3511 (1993). Comparative Molecular Field Analysis of the In Vitro Growth Inhibition of L1210 and HCT-8 Cells by Some Pyrazolo-aridines.
90. J. P. Horowitz, I. Massova, T. E. Wiese, B. B. Beseler, and T. H. Corbett, J. Med. Chem., 37, 781 (1994). Comparative Molecular Field Analysis of the Antitumor Activity of 9H-Thioxanthen-9-one Derivatives Against Pancreatic Ductal Carcinoma.
91. G. Klebe, T. Mietzner, and F. Weber, J. Comput.-Aided Mol. Design, 8, 751 (1994). Different Approaches Toward an Automatic Structural Alignment of Drug Molecules: Applications to Sterol Mimics, Thrombin and Thermolysin Inhibitors.
92. J. Hinze and H. H. Jaffe, J. Am Chem. Soc., 84, 540 (1962). Electroncgativity. I. Orbital Electronegativity of Neutral Atoms.
93. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc., 107, 3902 (1985). The Development and Use of Quantum-Mechanical Molecular-Models. 76. AM1: A New General-Purpose Quantum-Mechanical Molecular Model.
94. J. J. P. Stewart, J. Comput. Chem., 10, 209 (1989). Optimization of Parameters for Semiempirical Methods. 1. Method.
95. R. S. Mulliken, J. Chem. Phys., 23, 1833 (1955). Electronic Population Analysis on LCAO-MO Molecular Wave Functions. I. R. S. Mulliken, J. Chem. Phys., 23, 1841 (1955). Electronic Population Analysis on LCAO-MO Molecular Wave Functions. II. Overlap Populations, Bond Orders and Covalent Bond Energies.
96. R. S. Mulliken, J. Chem. Phys., 23, 1833 (1955). Electronic Population Analysis on LCAO-MO Molecular Wave Functions. I. R. S. Mulliken, J. Chem. Phys., 23, 1841 (1955). Electronic Population Analysis on LCAO-MO Molecular Wave Functions. II. Overlap Populations, Bond Orders and Covalent Bond Energies.
97. S. M. Bachrach, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH, New York, 1994, Vol. 5, pp. 171-227. Population Analysis and Electron Densities from Quantum Mechanics.
98. B. H. Besler, K. M. Merz Jr., and P. A. Kollman, J. Comput. Chem., 11, 431 (1990). Atomic Charges Derived from Semiempirical Methods. P. Cieplak, W. D. Cornell, C. Bayly, and P. A. Kollman, J. Comput. Chem., 16, 1357 (1995). Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derivation for DNA, RNA and Proteins.
99. B. H. Besler, K. M. Merz Jr., and P. A. Kollman, J. Comput. Chem., 11, 431 (1990). Atomic Charges Derived from Semiempirical Methods. P. Cieplak, W. D. Cornell, C. Bayly, and P. A. Kollman, J. Comput. Chem., 16, 1357 (1995). Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derivation for DNA, RNA and Proteins.
100. J. W. Storer, D. J. Giesen, C. J. Cramer, and D. G. Truhlar, J. Comput.-Aided Mol. Design, 9, 87 (1995). Class-IV Charge Models: A New Semiempirical Approach in Quantum-Chemistry.
101. R. T. Kroemer, P. Hecht, and K. R. Liedl, J. Comput. Chem., 17, 1296 (1996). Different Electrostatic Descriptors in Comparative Molecular Field Analysis: A Comparison of Molecular Electrostatic and Coulomb Potentials.
102. C. L. Waller, B. W. Juma, L. E. Gray Jr., and W. R. Kelce, Toxicol. Appl. Pharmacol., 137, 219 (1996). Three-Dimensional Quantitative Structure-Activity Relationship Models for Androgen Receptor Ligands.
103. 2-Guided Region Selection for Comparative Molecular Field Analysis: A Simple Method to Achieve Consistent Results.
104. J. P. Jones, M. He, W. F. Trager, and A. E. Rettie, Drug Metab. Disposition, 24, 1 (1996). Three-Dimensional Quantitative Structure-Activity Relationship for Inhibitors of Cytochromc P4502C9.
105. T. Sulea, T. I. Oprea, S. Muresan, and S. L. Chan, J. Chem. Inf. Comput. Sci., in press (1997). A Different Method for Steric Field Evaluation in CoMFA Improves Model Robustness.
106. T. I. Oprea and A. E. Garcia, J. Comput.-Aided Mol. Design, 10, 186 (1996). Comparative Molecular Field Analysis of Steroid Aromatase Inhibitors.
107. G. Folkers and A. Merz., in Lipophilicity in Drug Action and Toxicology, V. Pliska, B. Testa, and H. Van de Waterbeemd, Eds., Methods and Principles in Medicinal Chemistry Series, VCH Publishers, Weinheim, 1996, Vol. 4, pp. 219-232. Hydrophobic Fields in Quantitative Structure-Activity Relationships.
108. J. P. Dubost, in Trends in QSAR and Molecular Modelling '92, C.-G. Wermuth, Ed., ESCOM, Leiden, 1993, pp. 93-100. 2D and 3D Lipophilicity Parameters in QSAR. See also Ref. 16b.
109. K. H. Kim, Quant. Struct.-Act. Relat., 12, 232 (1993). 3D-Quantitative Structure-Activity Relationships: Describing Hydrophobic Interactions Directly from 3D Structures Using a Comparative Molecular Field Analysis (CoMFA) Approach.
110. P. Goodford, Molecular Discovery User Manual, software available from Molecular Discovery Ltd., West Way House, Elms Parade, Oxford, OX2 9LL, England. GRID program, version 14, 1996.
111. K. H. Kim, G. Greco, E. Novellino, C. Silipo, and A. Vittoria, J. Comput.-Aided. Mol. Design, 7, 263 (1993). Use of the Hydrogen Bond Potential Function in a Comparative Molecular Field Analysis (CoMFA) on a Set of Benzodiazepines.
112. C. L. Waller and G. R. Marshall, J. Med. Chem., 36, 2390 (1993). 3D-QSAR of Angiotensin-Converting Enzyme and Thermolysin Inhibitors. II. A Comparison of CoMFA Models Incorporating Molecular Orbital Fields and Desolvation Free Energies Based on Active Analog and Complementary-Receptor-Field Alignment Rules.
113. C. L. Waller, M. V. Evans, and J. D. McKinney, Drug Metab. Disposition, 24, 203 (1996). Modeling the Cytochrome P450-Mediated Metabolism of Chlorinated Volatile Organic Compounds.
114. G. Klebe, U. Abraham, and I. Mietzner, J. Med. Chem., 37, 4130 (1994). Molecular Similarity Indices in a Comparative Analysis (CoMSIA) of Drug Molecules to Correlate and Predict Their Biological Activity.
115. V. N. Viswanadhan, A. K. Ghose, G. R. Revankar, and R. K. Robins, J. Chem. Inf. Comput. Sci., 29, 163 (1989). Atomic Physicochemical Parameters for Three-Dimensional Structure Directed Quantitative Structure-Activity Relationships. 4. Additional Parameters for Hydrophobic and Dispersive Interactions and Their Application for an Automated Superposition of Certain Naturally Occurring Nucleoside Antibiotics.
116. S. A. DePriest, D. Mayer, C. B. Naylor, and G. R. Marshall, J. Am. Chem. Soc., 115, 5372 (1993). 3D-QSAR of Angiotensin-Converting Enzyme and Thermolysin Inhibitors: A Comparison of CoMFA Models Based on Deduced and Experimentally Determined Active Site Geometries.
117. M. K. Gilson and K. H. Honig, Nature, 330, 84 (1987). Calculation of Electrostatic Potentials in an Enzyme Active Site.
118. A. Nicholls and B. H. Honig, J. Comput, Chem., 12, 435 (1991). A Rapid Finite Difference Algorithm, Utilizing Successive Over-Relaxation to Solve Poisson-Boltzmann Equations.
119. T. I. Oprea, R. D. Head, and G. R. Marshall, in QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications, F. Sanz, J. Giraldo, and F. Manaut, Eds., J. R. Prous, Barcelona, 1995, pp. 451-156. The Basis of Crossreactivity for a Series of Steroids Binding to a Monoclonal Antibody Against Progesterone (DB3). A Molecular Modeling and QSAR Study.
120. J. H. Arevalo, M. J. Taussig, and I. A. Wilson, Nature, 365, 859 (1993). Molecular Basis of Crossreactivity and the Limits of Antibody-Antigen Complementarity.
121. M. Stone and P. Jonathan, J. Chemometrics, 8, 1 (1994). Statistical Thinking and Technique for QSAR and Related Studies. II. Specific Methods.
122. P. Geladi and B. R. Kowalski, Anal. Chim. Acta, 185, 1 (1986). Partial Least Squares Regression: A Tutorial.
123. S. Wold, E. Johansson, and M. Cocchi, in 3D-QSAR in Drug Design: Theory, Methods and Applications, H. Kubinyi, Ed., ESCOM, Leiden, 1993, pp. 523-550. PLS - Partial Least-Squares Projections to Latent Structures.
124. a Perturbation in Triosephosphate Isomerase Using an Electrostatically Trained Neural Network (SONNIC).
125. G. Klopman, J. Am. Chem. Soc., 106, 7315 (1984). Artificial Intelligence Approach to Structure-Activity Studies. Computer Automated Structure Evaluation of Biological Activity of Organic Molecules.
126. T. I. Oprea, C. M. W. Ho, and G. R. Marshall, in Computer-Aided Molecular Design: Applications in Agrochemicals, Materials, and Pharmaceuticals, C. H. Reynolds, M. K. Holloway, and H. K. Cox, Eds., American Chemical Society, Washington, DC, 1995, pp. 64-81. De Novo Design: Ligand Construction and Prediction of Affinity.
127. T. I. Oprea, unpublished work (1996). Because CoMFA fields are derived from a three-dimensional grid placed in Cartesian space, one can empirically estimate that CoMFA models should exhibit three PLS components. A requirement for higher complexity to fit the data set may indicate that mechanisms in addition to ligand fit (e.g., transport, diffusion) are included in the target property.
128. R. D. Cramer III, J. D. Bunce, D. E. Patterson, and I. E. Frank, Quant. Struct.-Act. Relat., 7, 18 (1988). Crossvalidation, Bootstrapping, and Partial Least Squares Compared with Multiple Regression in Conventional QSAR Studies.
129. S. Weisberg, Applied Linear Regression, 2nd ed. Wiley, New York, 1985, pp. 196-239.
130. G. Cruciani, M. Baroni, S. Clementi, G. Costantino, D. Riganelli, and B. Skagerberg, J. Chemometrics, 6, 335 (1992). Predictive Ability of Regression Models. Part I: Standard Deviation of Prediction Errors (SDEP).
131. T. I. Oprea, C. L. Waller, and G. R. Marshall, Drug Design Discovery, 12, 29 (1994). 3D-QSAR of Human Immunodeficiency Virus (1) Protease Inhibitors. III. Interpretation of CoMFA Results.
132. M. Numazawa and M. Oshibe, J. Med. Chem., 37, 1312 (1994). 6-Alkyl- and 6-Arylandrost-4-ene-3,17-diones as Aromatase Inhibitors. Synthesis and Structure-Activity Relationships.
133. T. I. Oprea, L. Kurunczi, and S. Timofei, Dyes Pigm., 33, 41 (1997). QSAR Studies of Disperse Azo Dyes. Towards the Negation of the Pharmacophore Theory of Dye-Fiber Interaction?
134. D. Hoekman, MacLogP, version 1.0.3. (1995), software available from Biohyte Corp., 201 W. Fourth St., Suite #204, Claremont, CA 91711.
135. T. I. Oprea, D. Ciubotariu, T. I. Sulea, and Z. Simon, Quant. Struct.-Act. Relat., 12, 21 (1993). Comparison of the Minimal Steric Difference (MTD) and Comparative Molecular Field Analysis (CoMFA) Methods for Analysis of Binding of Steroids to Carrier Proteins.
136. C. Hansch and L. Zhang, Drug Metab. Rev., 25, 1 (1993). Quantitative Structure-Activity Relationships of Cytochrome P-450.
137. K. H. Kim, in Classical and 3D-QSAR in Agrochemistry and Toxicology, C. Hansch and T. Fujita, Eds., American Chemical Society Symposium Series 606, American Chemical Society, Washington, DC, 1995, pp. 302-317. Comparison of Classical QSAR and CoMFA: Toward Lateral Validation.
138. T. I. Oprea Abstracts of the 212th American Chemical Society National Meeting Orlando, FL, August 25-29, 1996, COMP 234. The Hypothetical World of CoMFA and Model Validation.
139. C. L. Waller, T. I. Oprea, K. Chae, H.-K. Rhee-Park, K. S. Korach, S. Laws, T. E. Wiese, W. R. Kelce, and L. H. Gray Jr., Chem. Res. Toxicol., 9, 1240 (1996). Ligand-Based Identification of Environmental Estrogens.
140. Q. Xue and E. S. Yeung, Nature, 373, 681 (1995). Differences in the Chemical Reactivity of Individual Molecules of an Enzyme. By characterizing individual molecules of lactate dehydrogenase (LDH-1), a four times difference in reactivity was observed among LDH molecules. This can be explained by different informational arrangements of the four subunits, thereby exhibiting differences in binding site accessibility.
141. R D. Cramer, R. D. Clark, D. E. Patterson, and A. M. Fergusson, J. Med. Chem., 39, 3060 (1996). Bioisosterism as a Molecular Diversity Descriptor: Steric Fields of Single "Topomeric" Conformers.
142. D. E. Patterson, R. D. Cramer, A. M. Ferguson, R. D. Clark, and L. E. Weinberger, J. Med. Chem., 39, 3049 (1996). Neighborhood Behavior: A Useful Concept for Validation of "Molecular Diversity" Descriptors.
143. A. K. Debnath, C. Hansch, K. H. Kim, and Y. C. Martin, J. Med. Chem., 36, 1007 (1993). Mechanistic Interpretation of the Genotoxicity of Nitrofurans (Antibacterial Agents) Using QSAR and CoMFA.
144. K. H. Kim, Quant. Struct.-Act. Relat., 11, 433 (1992). 3D-QSAR: Investigation of Steric Effects with Descriptors directly from 3D Structures Using a CoMFA Approach.
145. A. M. Davis, N. P. Gensmantel, E. Johansson, and D. P. Marriott, J. Med. Chem., 37, 963 (1994). The Use of the GRID Program in the 3D-QSAR Analysis of a Series of Calcium-Channel Agonists.
146. A. D. Harpalani, S. W. Snyder, B. Subramanyam, M. J. Egorin, and P. S. Callery, Cancer Res., 53, 766 (1993). Alkylamides as Inducers of Human Leukemia Cell Differentiation: A QSAR Study Using CoMFA.
147. 2 = 0.989 and SEE = 12.2 (with 5 PCs). This correlation holds true for halogens (as reflected in van der Waals volume changes), but not for organometallic compounds. The alkylamides in Ref. 137 contained only C, N, O, and H.
148. R. Douglas, in The Pharmacological Basis of Therapeutics, 8th ed., A. G. Gilman, T. W. Rall, A. S. Nies, and P. Taylor, Eds., Pergamon Press, New York, 1990, pp. 1182-1201. Antiviral Agents.
149. S. N. Deming and S. L. Morgan, in Experimental Design: A Chemometic Approach, 2nd ed., Elsevier, Amsterdam, 1993, pp. 22-274. Approximating a Region of a Multifactor Response Surface.
150. S. Clementi, G. Cruciani, M. Baroni, and G. Costantino, in 3D-QSAR in Drug Design: Theory, Methods and Applications, H. Kubinyi, ED., ESCOM, Leiden, 1993, pp. 567-582. Series Design.
151. For example, Chem-X from Chemical Design Ltd., Roundway House, Cromwell Park, Chipping Norton, Oxon, OX7 5SR, U.K. See also, D. B. Boyd, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1495, Vol. 7, pp. 303-380. Compendium of Software for Molecular Modeling.