Novel Chirality Descriptors Derived from Molecular Topology

Journal of Chemical Information and Computer Sciences

Volumn 41, Issue 1, 2001, Pages 147-158

  Golbraikh, Alexander ^a   Bonchev, Danail ^b   Tropsha, Alexander ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ORGANIC COMPOUND;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; STEREOISOMERISM;

MODELS, CHEMICAL; ORGANIC CHEMICALS; STEREOISOMERISM;

EID: 0035227491     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci000082a     Document Type: Article

References (50)

1. Moran, L. A.; Scrimgeour, K. G.; Horton, H. R.; Ochs, R. S.; Rawn, J. D. Biochemistry; Neil Patterson Publishers, Prentice Hall: Englewood Cliffs, NJ, 1994.
2. Potapov, V. M. Stereochemistry; Khimia: Moscow, 1988.
3. Mislow K. Fuzzy Restrictions and Inherent Uncertainties in Chirality Studies. In Fuzzy Logic in Chemistry; Rouvray, D. H., Ed.; Academic Press: San Diego, 1997; pp 65-90.
4. Cramer, R. D., III; Patterson, D. E.; Bunce, J. D. Comparative Molecular-Field Analysis (Comfa). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
5. Marshall, G. R.; Cramer, R. D., III. 3-Dimensional Structure Activity Relationships. Trends Pharmacol. Sci. 1988, 9, 285-289.
6. SYBYL. Ligand-Based Design Manual; Tripos, Inc.: St Louis, MO, 1996.
7. Wold, S. PLS for Multivariate Linear Modeling. In Chemometrics Methods in Molecular Design; Waterbeemd, H. van de, Ed.; VCH: 1995; pp 195-218.
8. Clementi, S.; Wold, S. How to Choose the Proper Statistical Methodol. In Chemometrics Methods in Molecular Design; Waterbeemd, H. van de, Ed.; VCH: Weinheim, Germany, 1995; pp 319-338.
9. Pérez, C.; Pastor, M.; Ortiz, AR.; Gago, F. Comparative Binding Energy Analysis of HIV-1 Protease Inhibitors: Incorporation of Solvent Effects and Validation as a Powerful Tool in Receptor-Based Drug Design. J. Med. Chem. 1998, 41, 836-852.
10. 2 Guided Region Selection for Comparative Molecular Field Analysis (CoMFA): A Simple Method To Achieve Consistent Results. J. Med. Chem. 1995, 38, 1060-1066.
11. Klebe, G. Comparative Molecular Similarity Indices Analysis -CoMSIA. In 3D QSAR in Drug Design. Vol. 3. Recent Advances; Kubinyi, H., Folkers, G., Martin, Y. C., Eds.; Kluwer/ESCOM: Dodrecht, The Netherlands, 1998; pp 87-104.
12. Kubinyi, H.; Hamprecht, F. A.; Mietzner, T. Three-Dimensional Quantitative Similarity-Activity Relationships (3D QSiAR) from SEAL Similarity Matrices. J. Med. Chem. 1998, 41, 2553-2564.
13. Cho, S. J.; Serrano, M. G.; Bier, J.; Tropsha, A. Structure Based Alignment and Comparative Molecular Field Analysis of Acetylcholinesterase Inhibitors. J. Med. Chem. 1996, 39, 5064-5071.
14. Pilger, C.; Bartolucci, C.; Lamba, D.; Tropsha, A.; Fels, G. Accurate Prediction of the Bound Conformation of Galanthamine in the Active Site of Torpedo Californica Acetylcholinesterase Using Molecular Docking. J. Mol. Graphics Modell., in press.
15. Brusniak, M. Y.; Perlman, R. S.; Neve, K. A.; Wilcox, R. E. Comparative Molecular Field Analysis-Based Prediction of Drug Affinities at Recombinant D1A Dopamine Receptors. J. Med. Chem. 1996, 39, 850-859.
16. Bucholtz, E. C.; Booth, R. B.; Wyrick, S. D.; Tropsha, A. The Effect of Region Size on CoMFA Analyses. Med. Chem. Res. 1999, 9, 675-685.
17. Clementi, S. GOLPE 3.0; Multivariate Infometric Analyses (MIA): Perugia, Italy, 1995; SGI.
18. Kubinyi, H. Variable Selection In Qsar Studies. 1. An Evolutionary Algorithm Quant. Struct.-Act. Relat. 1994, 13, 285-294.
19. Kubinyi, H. Variable Selection in Qsar Studies. 2. A Highly Efficient Combination of Systematic Search and Evolution Quant. Struct.-Act. Relat. 1994, 13, 393-401.
20. Hoffman, B.; Cho, S. J.; Zheng, W.; Wyrick, S. D.; Nichols, D. E.; Mailman, R. B.; Tropsha, A. Quantitative Structure-Activity Relationship Modeling of Dopamine D-1 Antagonists Using Comparative Molecular Field Analysis, Genetic Algorithms-Partial Least-Squares, and K Nearest Neighbor Methods. J. Med. Chem. 1999, 42, 3217-3226.
21. Zheng, W.; Tropsha, A. Novel Variable Selection QSAR Approach Based on the K Nearest-Neighbor Principle. J. Chem. Inf. Comput. Sci. 2000, 40, 185-194.
22. Bures, M. G.; Martin, Y. C. Computational methods in molecular diversity and combinatorial chemistry. Curr. Opin. Chem. Biol. 1998, 2, 376-80.
23. MolconnZ. http://www.eslc.vabiotech.com/molconn/manuals/350/.
24. 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, 64-73.
25. Schultz, H. P.; Schultz, E. B.; Schultz, T. P. Topological Organic Chemistry. 9. Graph Theory and Molecular Topological Indices of Stereoisomeric Organic Compounds. J. Chem. Inf. Comput. Sci. 1995, 35, 864-870.
26. Julián-Ortiz, J. V. de; Alapont, C. de G.; Ríos-Santamarina, I.; García-Doménech, R.; Gálvez, J. Prediction of properties of chiral compounds by molecular topology. J. Mol. Graphics Modell. 1998, 16, 14-18.
27. Gutman, I.; Ruscić, B.; Trinajstić, N.; Wilcox, C. F., Jr. Graph theory and molecular orbitals. XII. Acyclic polyenes. J. Chem. Phys. 1975, 62, 3399-3405.
28. Randić, M. On Characterization on Molecular Branching. J. Am. Chem. Soc. 1975, 97, 6609-6615.
29. Kier, L. B.; Hall, L. H. Molecular Connectivity in Chemistry and Drug Research; Academic Press: New York, 1976.
30. Kier, L. B.; Hall, L. H. Molecular Connectivity in Structure-Activity Analysis; Wiley: New York, 1986.
31. Rücker, G.; Rücker, C. Counts of All Walks as Atomic and Molecular Descriptors. J. Chem. Inf. Comput. Sci. 1993, 33, 683-695.
32. Bonchev, D. Overall Connectivity and Molecular Complexity. In Topological Indices and Related Descriptors; Devillers, J., Balaban, A. T., Eds.; Gordon and Breach: Reading, U.K., 1999; pp. 361-401.
33. Bonchev, D. Novel Indices for the Topological Complexity of Molecules. SAR/QSAR Environ. Res. 1997, 7, 23-43.
34. Gálvez, J.; García-Domenech, R.; Julian-Ortiz, J. V. de; Soler, R. Topological approach to drug design. J. Chem. Inf. Comput. Sci. 1995, 35, 272-284.
35. Dinan, L.; Hormann, R. E.; Fujimoto T. An extensive ecdysteroid CoMFA. J. Comput.-Aided Mol. Des. 1999, 13 (Mar), 185-207.
36. Ecdysone: From Chemistry to Mode of Action; Koolman, J., Ed.; Thieme: Leipzig, Germany, 1989.
37. Kier, L. B. A shape index from molecular graphs. Quant. Struct.-Act. Relat. 1985, 4, 109-116.
38. Kier, L. B. Inclusion of symmetry as a shape attribute in kappa-index analysis. Quant. Struct-Act. Relat. 1987, 6, 8-12.
39. Hall, L. H.; Kier, L. B. Determination of topological equivalence in molecular graphs from the topological state. Quant. Struct.-Act. Relat 1990, 9, 115-131.
40. Hall, L. H.; Mohney, B. K.; Kier, L. B. The Electrotopological State: An Atom Index for QSAR. Quant. Struct.-Act. Relat. 1991, 10, 43-51.
41. Hall, L. H.; Mohney, B. K.; Kier, L. B. The Electrotopological State: Structure Information at the Atomic Level for Molecular Graphs. J. Chem. Inf. Comput. Sci. 1991, 31, 76-82.
42. Kier, L. B.; Hall, L. H. Molecular Structure Description: The Electrotopological State; Academic Press: New York, 1999.
43. Kellogg, G. E.; Kier, L. B.; Gaillard, P.; Hall, L. H. The E-State Fields. Applications to 3D QSAR. J. Comput.-Aided Mol. Des. 1996, 10, 513-520.
44. Kier, L. B.; Hall, L. H. A Differential Molecular Connectivity Index. Quant. Struct.-Act. Relat. 1991, 10, 134-140.
45. Petitjean, M. Applications of the Radius-Diameter Diagram to the Classification of Topological and Geometrical Shapes of Chemical Compounds. J. Chem. Inf. Comput. Sci. 1992, 32, 331-337.
46. Wiener, H. Structural Determination of Paraffin Boiling Points. J. Am. Chem. Soc. 1947, 69, 17.
47. Platt, J. R. Prediction of Isomeric Differences in Paraffin Properties. J. Phys. Chem. 1952, 56, 328.
48. Shannon, C.; Weaver, W. Mathematical theory of Communication; University of Illinois: Urbana, 1949.
49. Bonchev, D.; Mekenyan, O.; Trinajstić, N. Isomer discrimination by topological information approach. J Comput Chem 1981, 2, 127-148.
50. Mezey, P. G. Fuzzy Measures of Molecular Shape and Size. In Fuzzy Logic in Chemistry; Rouvray, D. H., Ed.; Academic Press: San Diego, 1997; pp 139-223.