Similarity methods in analog selection, property estimation and clustering of diverse chemicals

Arkivoc

Volumn 2006, Issue 9, 2006, Pages 157-210

  Basak, Subhash C ^a   Gute, Brian D ^a   Mills, Denise ^a  

^a UNIVERSITY OF MINNESOTA DULUTH   (United States)

Author keywords

Atom pair; kNN technique; QMSA; Similarity; Tailoring; Topological indices

Indexed keywords

EID: 33749538343     PISSN: None     EISSN: 14246376     Source Type: Journal    
DOI: None     Document Type: Article

References (97)

1. CAS Registry Number and Substance Counts, http://www.cas.org/cgi-bin/ regreport.pl (accessed Mar 2006).
2. Auer, C.M.; Zeeman, M.; Nabholz, J. V.; Clements, R. G. SAR - the U.S. regulatory perspective. SAR QSAR Environ. Res. 1994, 2, 29.
3. Goodman and Gilman's The Pharmacological Basis of Therapeutics; Goodman, A. G., Wall, T. W., Nies, A. S., Taylor, P., Eds.; Pergamon Press: New York, 1990.
4. Thornber, C. W. Isosterism and molecular modification in drug design. Chem. Soc. Rev. 1979, 5, 563.
5. Advances in Molecular Similarity. Vol. 2; Carbo-Dorca, R., Mezey, P. G., Eds.; JAI Press: Stamford, CN., 1998.
6. Johnson, M.; Maggiora, G. M. Concepts and Applications of Molecular Similarity; John Wiley & Sons, Inc.: New York, 1990.
7. Whyte, L. L. Atomism, structure and form: a report on the natural philosophy of form. In Structure in Art and Science; Kepes, G., Ed.; George Braziler, Inc.: New York, 1965; pp 20-28.
8. Basak, S. C.; Magnuson, V. R.; Niemi, G. J.; Regal, R. R. Determining structural similarity of chemicals using graph-theoretic indices. Discrete Appl. Math. 1988, 19, 17.
9. Weininger, S. J. The molecular structure conundrum: Can classical chemistry be reduced to quantum chemistry? J. Chem. Educ. 1984, 61, 939.
10. Woolley, R. G. Must a molecule have a shape? J. Am. Chem. Soc. 1978, 100, 1073.
11. Basak, S. C. Use of molecular complexity indices in predictive pharmacology and toxicology: A QSAR approach. Med. Sci. Res. 1987, 15, 605.
12. Kier, L. B.; Hall, L.H. Molecular Connectivity in Chemistry and Drug Research; Academic Press: New York, 1976.
13. Richards, W. G. Quantum Pharmacology; Butterworths: London, 1977.
14. Grossman, S. C. Chemical ordering of molecules - A graph theoretical approach to structure-property studies. Int. J. Quantum Chem. 1985, 28, 1.
15. Bunge, M. Method, Model and Matter; D. Reidel Publishing Co.: Dordrecht-Holland/Boston, 1973.
16. Sylvester, J. J. On an application of the new atomic theory to the graphical representation of the invariants and covariants of binary quantics. Amer. J. Math. 1878, 1, 64.
17. Balaban, A. T. Applications of graph theory in chemistry. J. Chem. Inf. Comput. Sci. 1985, 25, 334.
18. Basak, S. C.; Niemi, G. J.; Veith, G. D. Recent developments in the characterization of chemical structure using graph-theoretic indices. In Computational Chemical Graph Theory; Rouvray, D. H., Ed.; Nova Science Publishers, Inc.: Commack, NY, 1990; pp 235-277.
19. Johnson, M.; Basak, S.C.; Maggiora, G. A characterization of molecular similarity methods for property prediction. Mathl. Comput. Modelling 1988, 11, 630.
20. O'Brien, S. E.; Popelier, P. L. A. Quantum molecular similarity. Part 2: The relation between properties in BCP space and bond length. Can. J. Chem. 1999, 77, 28.
21. O'Brien, S. E.; Popelier, P. L. A. Quantum molecular similarity. 3. QTMS descriptors. J. Chem. Inf. Comput. Sci. 2001, 41, 764.
22. O'Brien, S. E.; Popelier, P. L. A. Quantum topological molecular similarity. Part 4. A QSAR study of cell growth inhibitory properties of substituted (E)-1-phenylbut-1-en-3-ones. J. Chem. Soc., Perkin Trans. 2002, 2, 478.
23. Popelier, P. L. A. Quantum molecular similarity. 1. BCP space. J. Phys. Chem. 1999, 103, 2883.
24. Trinajstic, N. Chemical Graph Theory, 2nd Edn.; CRC Press: Boca Raton, FL, 1992.
25. Kier, L. B.; Hall, L. H. Molecular Connectivity in Structure-Activity Analysis; Research Studies Press: Letchworth, Hertfordshire, U.K., 1986.
26. Kier, L. B.; Murray, W. J.; Randic, M.; Hall, L. H. Molecular connectivity. V. Connectivity series concept applied to diversity. J. Pharm. Sci. 1976, 65, 1226.
27. Wiener, N. Cybernetics; Wiley: New York, 1948.
28. Trinajstic, N. Chemical Graph Theory, Vols. I & II.; CRC Press: Boca Raton, Florida, 1983.
29. Shannon, C. E. A mathematical theory of communication. Bell Syst. Tech. J. 1948, 27, 379.
30. Rashevsky, N. Life, information theory and topology. Bull. Math. Biophys. 1955, 17, 229.
31. Trucco, E. On the information content of graphs: compound symbols: different states for each point. Bull. Math. Biophys. 1956, 18, 237.
32. Trucco, E. A note on the information content of graphs. Bull. Math. Biophys. 1956, 18, 129.
33. Sarkar, R.; Roy, A. B.; Sarkar, R. K. Topological information content of genetic molecules - I. Math. Biosci. 1978, 39, 299.
34. Roy, A. B.; Basak, S. C.; Harriss, D. K.; Magnuson, V. R. Neighborhood complexities and symmetry of chemical graphs and their biological applications. In Mathematical Modelling in Science and Technology; Avula, X. J. R., Kalman, R. E., Liapis, A. I., Rodin, E. Y., Eds.; Pergamon Press: Elmsford, NY, 1984; pp 745-750.
35. Magnuson, V. R.; Harriss, D. K.; Basak, S. C. Topological indices based on neighborhood symmetry: Chemical and biological applications. In Chemical Applications of Topology and Graph Theory; King, R. B., Ed.; Elsevier: New York, 1983; pp 178-191.
36. Mowshowitz, A. Entropy and the complexity of graphs: I. An index of the relative complexity of a graph. Bull. Math. Biophys. 1968, 30, 175.
37. Mowshowitz, A. Entropy and the complexity of graphs: II. The information content of digraphs and infinite graphs. Bull. Math. Biophys. 1968, 30, 225.
38. Mowshowitz, A. Entropy and the complexity of graphs: III. Graphs with prescribed information content. Bull. Math. Biophys. 1968, 30, 387.
39. Mowshowitz, A. Entropy and the complexity of graphs: IV. Entropy measures and graphical structure. Bull. Math. Biophys. 1968, 30, 533.
40. Basak, S. C.; Roy, A. B.; Ghosh, J. J. Study of the structure-function relationship of pharmacological and toxicological agents using information theory. In Proceedings of the Second International Conference on Mathematical Modelling; Avula, X. J. R., Bellman, R., Luke, Y. L., Rigler, A. K., Eds.; University of Missouri-Rolla: Rolla, Missouri, 1980; pp 851.
41. Basak, S. C.; Magnuson, V. R. Molecular topology and narcosis: A quantitative structure-activity relationship (QSAR) study of alcohols using complementary information content (CIC). Arzneim.-Forsch./Drug Res. 1983, 33, 501.
42. Bonchev, D.; Trinajstic, N. Information theory, distance matrix and molecular branching. J. Chem. Phys. 1977, 67, 4517.
43. Schreider, J.A. Equality, Resemblance, and Order; Mir Publishers: Moscow, 1975.
44. Basak, S. C.; Magnuson, V. R.; Niemi, G. J.; Regal, R. R.; Veith, G. D. Topological indices: Their nature, mutual relatedness, and applications. Mathl. Model. 1987, 8, 300.
45. Russom, C. L.; Anderson, E. B.; Greenwood, B. E.; Pilli, A. ASTER: An integration of the AQUIRE data base and the QSAR system for use in ecological risk assessments. Sci. Total Environ. 1991, 109/110, 667.
46. 4. J. Chem. Inf. Comput. Sci. 1992, 32, 233.
47. 4 using neural networks. J. Chem. Inf. Comput. Sci. 1994, 34, 1118.
48. Needham, D. E.; Wei, I. C.; Seybold, P. G. Molecular modelling of the physical properties of alkanes. J. Am. Chem. Soc. 1988, 110, 4186.
49. Mekenyan, O.; Bonchev, D.; Trinajstic, N. Chemical graph theory: Modeling the thermodynamic properties of molecules. Int. J. Quant. Chem. 1980, 18, 369.
50. Spectral Atlas of Polycyclic Aromatic Hydrocarbons, Vol. 2; Karcher, W., Ed.; Kluwer Academic: Dordrecht, The Netherlands, 1988.
51. Leo, A.; Weininger, D. CLOGP Version 3.2 User Reference Manual; Pomona College: Claremont, CA, 1984.
52. Basak, S. C. H-Bond; University of Minnesota: Duluth, MN, 1988.
53. Brooke, D. N.; Dobbs, A. J.; Williams, N. Octanol:water partition coefficients (P): Measurement, estimation and interpretation, particularly for chemicals with P > 10.5. Ecotoxicol. Environ. Safety 1986, 11, 251.
54. De Brujin, J.; Busser, F.; Seinen, W.; Hermens, J. Measuring octanol/water partition coefficients with a "slow-stirring method". Environ. Toxicol. Chem. 1989, 8, 499.
55. Basak, S. C.; Grunwald, G. D. Use of topological space and property space in selecting structural analogs. Mathl. Model. Sci. Computing 1994, 4, 464.
56. Kamlet, M. J. White Oak Laboratory, Silver Spring, MD. Personal communication, 1987.
57. AFOSR JP-8 Jet Fuel Workshop, University of Arizona, Tucson, Arizona, 2000.
58. Hansch, C.; Yoshimoto, M. Structure-activity relationships in immunochemistry. 2. Inhibition of complement by benzamidines. J. Med. Chem. 1974, 17, 1160.
59. Baker, B. R.; Cory, M. Irreversible enzyme inhibitors. CLXIV. Proteolytic enzymes. XIV. Inhibition of guinea pig complement by meta-substituted benzamidines. J. Med. Chem. 1969, 12, 1049.
60. Baker, B. R.; Cory, M. Irreversible enzyme inhibitors. CLXV. Proteolytic enzymes. XV. Inhibition of guinea pig complement by derivatives of m-phenoxypropoxybenzamidine. J. Med. Chem. 1969, 12, 1053.
61. Baker, B. R.; Cory, M. Irreversible enzyme inhibitors. 180. Irreversible inhibitors of the C'1a component of complement derived from m-(phenoxypropoxy) benzamidine and phenoxyacetamide. J. Med. Chem. 1971, 14, 119.
62. Baker, B. R.; Cory, M. Irreversible enzyme inhibitors. 186. Irreversible inhibitors of the C'1a component of complement derived from m-(phenoxypropoxy) benzamidine by bridging to a terminal sulfonyl fluoride. J. Med. Chem. 1971, 14, 805.
63. Cohen, G. M.; Mannering, G. J. Involvement of a hydrophobic site in the inhibition of the microsomal p-hydroxylation of aniline by alcohols. Mol. Pharmacol. 1973, 9, 383.
64. Hall, L.H.; Kier, L.B.; Phipps, G. Structure-activity relationship studies on the toxicities of benzene derivatives: I. An additivity model. Environ. Toxicol. Chem. 1984, 3, 355.
65. Soderman, J. V. CRC Handbook of Identified Carcinogens and Noncarcinogens: Carcinogenicity-Mutagenicity Database. Vol. 1; CRC Press: Boca Raton, FL, 1982.
66. Basak, S. C.; Bertelsen, S.; Grunwald, G. D. Use of graph theoretic parameters in risk assessment of chemicals. Toxicol. Lett. 1995, 79, 239.
67. Debnath, A. K.; Debnath, G.; Shusterman, A. J.; Hansch, C. A QSAR investigation of the role of hydrophobicity in regulating mutagenicity in the Ames test: 1. Mutagenicity of aromatic and heteroaromatic amines in Salmonella typhimurium TA98 and TA100. Environ. Mol. Mutagen. 1992, 19, 37.
68. Benigni, R.; Andreoli, C.; Giuliani, A. QSAR models for both mutagenic potency and activity: Application to nitroarenes and aromatic amines. Environ. Mol. Mutagen. 1994, 24, 208.
69. McCann, J.; Choi, E.; Yamasaki, E.; Ames, B. N. Detection of carcinogens as mutagens in the Salmonella/microsome test: Assay of 300 chemicals. Proc. Natl. Acad. Sci. 1975, 72, 5135.
70. Yamaguchi, T.; Hasegawa, R.; Hagiwara, A.; Hirose, M.; Imaida, K.; Ito, N.; Shirai, T. Results for 277 chemicals in the medium term liver carcinogenesis bioassay of rats, 1999.
71. Basak, S. C.; Grunwald, G. D.; Host, G. E.; Niemi, G. J.; Bradbury, S. P. A comparative study of molecular similarity, statistical, and neural network methods for predicting toxic modes of action of chemicals. Environ. Toxicol. Chem. 1998, 17, 1056.
72. Basak, S. C.; Gute, B. D.; Grunwald, G. D. Quantitative comparison of five molecular structure spaces in selecting analogs of chemicals. Mathl. Modelling Sci. Comput., in press.
73. Basak, S. C.; Bertelsen, S.; Grunwald, G. D. Application of graph theoretical parameters in quantifying molecular similarity and structure-activity relationships. J. Chem. Inf. Comput. Sci. 1994, 34, 270.
74. Basak, S. C.; Gute, B. D.; Grunwald, G. D. Use of graph invariants in QMSA and predictive toxicology, DIMACS Series 51. In Discrete Mathematical Chemistry; Hansen, P., Fowler, P., Zheng, M., Eds.; American Mathematical Society: Providence, RI, 2000; pp 9-24.
75. Basak, S. C.; Gute, B. D.; Grunwald, G. D. Development and application of molecular similarity methods using nonempirical parameters. Mathl. Modelling Sci. Comput., in press.
76. Basak, S. C.; Grunwald, G. D. Molecular similarity and risk assessment: analog selection and property estimation using graph invariants. SAR QSAR Environ. Res. 1994, 2, 289.
77. Basak, S. C.; Grunwald, G. D. Estimation of lipophilicity from molecular structural similarity. New J. Chem. 1995, 19, 231.
78. Basak, S. C.; Grunwald, G. D. Molecular similarity and estimation of molecular properties. J. Chem. Inf. Comput. Sci. 1995, 35, 366.
79. Basak, S. C.; Grunwald, G. D. Predicting mutagenicity of chemicals using topological and quantum chemical parameters: A similarity based study. Chemosphere 1995, 31, 2529.
80. Basak, S. C.; Grunwald, G. D. Tolerance space and molecular similarity. SAR QSAR Environ. Res. 1995, 3, 265.
81. Basak, S. C.; Gute, B. D. Characterization of molecular structures using topological indices. SAR QSAR Environ. Res. 1997, 7, 1.
82. Basak, S. C.; Gute, B. D. Use of graph theoretic parameters in predicting inhibition of microsomal hydroxylation of anilines by alcohols: a molecular similarity approach. In Proceedings of the International Congress on Hazardous Waste: Impact on Human and Ecological Health; Johnson, B. L., Xintaras, C., Andrews, J. S., Eds.; Princeton Scientific Publishing Co, Inc.: Princeton, NJ, 1997; pp 492-504.
83. Gute, B. D.; Grunwald, G. D.; Mills, D.; Basak, S. C. Molecular similarity based estimation of properties: A comparison of structure spaces and property spaces. SAR QSAR Environ. Res. 2001, 11, 363.
84. Carhart, R. E.; Smith, D. H.; Venkataraghavan, R. Atom pairs as molecular features in structure-activity studies: Definition and applications. J. Chem. Inf. Comput. Sci. 1985, 25, 64.
85. Basak, S. C.; Grunwald, G. D. APProbe; University of Minnesota: Duluth, MN, 1993.
86. SAS/STAT User's Guide, Release 6.03; SAS Institute Inc.: Cary, NC, 1988.
87. Auer, C. M.; Nabholz, J. V.; Baetcke, K. P. Mode of action and the assessment of chemical hazards in the presence of limited data: use of structure-activity relationships (SAR) under TSCA, Section 5. Environ. Health Perspect. 1990, 87, 183.
88. Basak, S. C.; Gute, B. D.; Grunwald, G. D. Characterization of the molecular similarity of chemicals using topological invariants. In Advances in Molecular Similarity, Vol. 2; Carbo-Dorca, R., Mezey, P. G., Eds.; JAI Press: Stamford, CT, 1998; pp 171-185.
89. Gute, B. D.; Basak, S. C. Molecular similarity-based estimation of properties: A comparison of three structure spaces. J. Mol. Graphics and Model. 2001, 20, 95.
90. Basak, S. C.; Gute, B. D.; Mills, D.; Hawkins, D. M. Quantitative molecular similarity methods in the property/toxicity estimation of chemicals: A comparison of arbitrary versus tailored similarity spaces. J. Mol. Struct. (THEOCHEM) 2003, 622, 121.
91. Gute, B. D.; Basak, S. C.; Mills, D.; Hawkins, D. M. Tailored similarity spaces for the prediction of physicochemical properties. Internet Electr. J. Mol. Design 2002, 1, 374.
92. Basak, S. C.; Gute, B. D.; Mills, D. Quantitative molecular similarity analysis (QMSA) methods for property estimation: A comparison of property-based, arbitrary, and tailored similarity spaces. SAR QSAR Environ. Res. 2002, 13, 727.
93. Gute, B. D.; Basak, S. C. 2006. Optimal neighbor selection in molecular similarity: Comparison of arbitrary versus tailored prediction spaces. SAR QSAR Environ. Res. 2006, 17, 37.
94. Hawkins, D.; Basak, S.; Shi, X. QSAR with few compounds and many features. J. Chem. Inf. Comput. Sci. 2001, 41, 663.
95. Basak, S. C.; Mills, D. Quantitative structure-property relationships (QSPRs) for the estimation of vapor pressure: A hierarchical approach using mathematical structural descriptors. J. Chem. Inf. Comput. Sci. 2001, 41, 692.
96. Lajiness, M. Molecular similarity-based methods for selecting compounds for screening. In Computational Chemical Graph Theory; Rouvray, D. H., Ed.; Nova Science Publishers, Inc.: Commack, NY, 1990; pp 299-316.
97. Basak, S. C.; Mills, D.; Gute, B. D.; Balaban, A. T.; Basak, K.; Grunwald, G. D. Use of mathematical structural invariants in analyzing combinatorial libraries: A case study with Psoralen derivatives. In Some Aspects of Mathematical Chemistry; Sinha, D. K., Basak, S. C., Mohanty, R. K., Basumallick, I. N., Eds.; Visva-Bharati University: Shantineketan, India, in press.