Computing wiener-type indices for virtual combinatorial libraries generated from heteroatom-containing building blocks

Journal of Chemical Information and Computer Sciences

Volumn 42, Issue 1, 2002, Pages 8-22

  Ivanciuc, Ovidiu ^a   Klein, Douglas J ^a  

^a TEXAS A AND M UNIVERSITY AT GALVESTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMBINATORIAL LIBRARIES;

ALGORITHMS; CHEMICAL BONDS; DRUG PRODUCTS; MOLECULAR GRAPHICS; TOPOLOGY;

ORGANIC COMPOUNDS;

EID: 0036432336     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci010072p     Document Type: Article

References (68)

1. Gallop, M.A.; Barrett, R.W.; Dower, W.J.; Fodor, S.P.A.; Gordon, E.M. Application of Combinatorial Technologies to Drug Discovery. 1. Background and Peptide Combinatorial Libraries. J. Med. Chem. 1994, 37, 1233-1251.
2. Gordon, E.M.; Barrett, R.W.; Dower, W.J.; Fodor, S.P.A.; Gallop, M.A. Application of Combinatorial Technologies to Drag Discovery. 2. Combinatorial Organic-synthesis, Library Screening Strategies, and Future Directions. J. Med. Chem. 1994, 37, 1385-1401.
3. Fauchère, J.-L.; Boutin, J.A.; Henlin, J.-M.; Kucharczyk, N.; Ortuno, J.-C. Combinatorial Chemistry for the Generation of Molecular Diversity and the Discovery of Bioactive Leads. Chemom. Intell. Lab. Syst. 1998, 43, 43-68.
4. Drewry, D.H.; Young, S.S. Approaches to the Design of Combinatorial Libraries. Chemom. Intell. Lab. Syst. 1999, 48, 1-20.
5. Agrafiotis, D.K.; Myslik, J.C.; Salemme, F.R. Advances in Diversity Profiling and Combinatorial Series Design. Mol. Diversity 1999, 4, 1-22.
6. Beno, B.R.; Mason, J.S. The Design of Combinatorial Libraries Using Properties and 3D Pharmacophore Fingerprints. Drug Design Today 2001, 6, 251-258.
7. Sheridan, R.P.; Kearsley, S.K. Using a Genetic Algorithm to Suggest Combinatorial Libraries. J. Chem. Inf. Comput. Sci. 1995, 35, 310-320.
8. Taylor, R. Simulation Analysis of Experimental Design Strategies for Screening Random Compounds as Potential New Drugs and Agrochemicals. J. Chem. Inf. Comput. Sci. 1995, 35, 59-67.
9. Gillet, V.J.; Willett, P.; Bradshaw, J. The Effectiveness of Reactant Pools for Generating Structurally-Diverse Combinatorial Libraries. J. Chem. Inf. Comput. Sci. 1997, 37, 731-740.
10. Good, A.C.; Lewis, R.A. New Methodology for Profiling Combinatorial Libraries and Screening Sets: Cleaning Up the Design Process with HARPick. J. Med. Chem. 1997, 40, 3926-3936.
11. Pickett, S.D.; Luttmann, C.; Guerin, V.; Laoui, A.; James, E. DIVSEL and COMPLIB - Strategies for the Design and Comparison of Combinatorial Libraries Using Pharmacophoric Descriptors. J. Chem. Inf. Comput. Sci. 1998, 38, 144-150.
12. Gillet, V.J.; Willett, P.; Bradshaw, J.; Green, D.V.S. Selecting Combinatorial Libraries to Optimize Diversity and Physical Properties. J. Chem. Inf. Comput. Sci. 1999, 39, 169-177.
13. Grassy, G.; Calas, B.; Yasri, A.; Lahana, R.; Woo, J.; Iyer, S.; Kaczorek, M.; Floc'h, R.; Buelow, R. Computer-Assisted Rational Design of Immunosuppressive Compounds. Nature Biotechnol. 1998, 16, 748-752.
14. Armstrong, R.W.; Combs, A.P.; Tempest, P.A.; Brown, S.D.; Keating, T.A. Multiple-Component Condensation Strategies for Combinatorial Library Synthesis. Acc. Chem. Res. 1996, 29, 123-131.
15. Ivanciuc, O.; Balaban, A.T. The Graph Description of Chemical Structures. In Topological Indices and Related Descriptors in QSAR and QSPR; Devillers, J., Balaban, A.T., Eds.; Gordon and Breach Science Publishers: Amsterdam, 1999; pp 59-167.
16. Ivanciuc, O.; Ivanciuc, T.; Balaban, A.T. Vertex- and Edge-Weighted Molecular Graphs and Derived Structural Descriptors. In Topological Indices and Related Descriptors in QSAR and QSPR; Devillers, J., Balaban, A.T., Eds.; Gordon and Breach Science Publishers: Amsterdam, 1999; pp 169-220.
17. Ivanciuc, O.; Ivanciuc, T. Matrices and Structural Descriptors Computed from Molecular Graph Distances. In Topological Indices and Related Descriptors in QSAR and QSPR; Devillers, J., Balaban, A.T., Eds.; Gordon and Breach Science Publishers: Amsterdam, 1999; pp 221-277.
18. Wiener, H. Structural Determination of Paraffin Boiling Points. J. Am. Chem. Soc. 1947, 69, 17-20.
19. Wiener, H. Correlation of Heats of Isomerization and Differences in Heats of Vaporization of Isomers among the Paraffin Hydrocarbons. J. Am. Chem. Soc. 1947, 69, 2636-2638.
20. Randić, M. On Characterization of Molecular Branching. J. Am. Chem. Soc. 1975, 97, 6609-6615.
21. Kier, L.B.; Hall, L.H. Molecular Connectivity in Chemistry and Drug Research; Academic Press: New York, 1976.
22. Balaban, A.T. Highly Discriminating Distance-Based Topological Index. Chem. Phys. Lett. 1982, 89, 399-404.
23. Balaban, A.T. Chemical Graphs. Part 48. Topological Index J for Heteroatom-Containing Molecules Taking Into Account Periodicities of Element Properties. MATCH (Commun. Math. Chem.) 1986, 21, 115-122.
24. Plavšic, D.; Nikolić, S.; Trinajstić, N.; Mihalić, Z. On the Harary Index for the Characterization of Chemical Graphs. J. Math. Chem. 1993, 12, 235-250.
25. Ivanciuc, O.; Balaban, T.-S.; Balaban, A.T. Design of Topological Indices. Part 4. Reciprocal Distance Matrix, Related Local Vertex Invariants and Topological Indices. J. Math. Chem. 1993, 12, 309-318.
26. Pearlman, R.S.; Smith, K.M. Metric Validation and the Receptor-Relevant Subspace Concept. J. Chem. Inf. Comput. Sci. 1999, 39, 28-35.
27. Ivanciuc, O.; Taraviras, S.L.; Cabrol-Bass, D. Quasi-Orthogonal Basis Sets of Molecular Graph Descriptors as a Chemical Diversity Measure. J. Chem. Inf. Comput. Sci. 2000, 40, 126-134.
28. Taraviras, S.L.; Ivanciuc, O.; Cabrol-Bass, D. Identification of Groupings of Graph Theoretical Molecular Descriptors Using a Hybrid Cluster Analysis Approach. J. Chem. Inf. Comput. Sci. 2000, 40, 1128-1146.
29. Ajay; Walters, W.P.; Murcko, M.A. Can We Learn to Distinguish between "Drug-like" and "Nondrug-like" Molecules? J. Med. Chem. 1998, 41, 3314-3324.
30. Sadowski, J.; Kubinyi, H. A Scoring Scheme for Discriminating between Drugs and Nondrugs. J. Med. Chem. 1998, 41, 3325-3329.
31. Ghose, A.K.; Viswanadhan, V.N.; Wendoloski, J.J. A Knowledge-Based Approach in Designing Combinatorial or Medicinal Chemistry Libraries for Drug Discovery. 1. A Qualitative and Quantitative Characterization of Known Drug Databases. J. Comb. Chem. 1999, 1, 55-68.
32. Oprea, T.I. Property Distribution of Drug-related Chemical Databases. J. Comput.-Aided Mol. Design 2000, 14, 251-264.
33. Xue, L.; Bajorath, J. Molecular Descriptors for Effective Classification of Biologically Active Compounds Based on Principal Component Analysis Identified by a Genetic Algorithm. J. Chem. Inf. Comput. Sci. 2000, 40, 801-809.
34. Zheng, W.; Cho, S.J.; Tropsha, A. Rational Design of a Targeted Combinatorial Chemical Library with Opiatelike Activity. Int. J. Quantum Chem. 1998, 69, 65-75.
35. Linusson, A.; Gottfries, J.; Lindgren, F.; Wold, S. Statistical Molecular Design of Building Blocks for Combinatorial Chemistry. J. Chem. Inf. Comput. Sci. 2000, 40, 1320-1328.
36. Ajay; Bemis, G.W.; Murcko, M.A. Designing Libraries with CNS Activity. J. Med. Chem. 1999, 42, 4942-4951.
37. Oprea, T.I.; Gottfries, J. Chemography: The Art of Navigating in Chemical Space. J. Comb. Chem. 2001, 3, 157-166.
38. Shi, S.; Peng, Z.; Kostrowicki, J.; Paderes, G.; Kuki, A. Efficient Combinatorial Filtering for Desired Molecular Properties of Reaction Products. J. Mol. Graphics Modell. 2000, 18, 478-496.
39. Wildman, S.A.; Crippen, G.M. Prediction of Physicochemical Parameters by Atomic Contributions. J. Chem. Inf. Comput. Sci. 1999, 39, 868-873.
40. 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.
41. Labute, P. A Widely Applicable Set of Descriptors. J. Mol. Graph. Modell. 2000, 18, 464-477.
42. Österberg, T.; Norinder, U. Prediction of Polar Surface Area and Drug Transport Processes Using Simple Parameters and PLS Statistics. J. Chem. Inf. Comput. Sci. 2000, 40, 1408-1411.
43. Oprea, T.I. Rapid Estimation of Hydrophobicity for Virtual Combinatorial Library Analysis. SAR QSAR Environ. Res. 2001, 12, 129-141.
44. Ivanciuc, O.; Klein, D.J. Building-Block Computation of Wiener-Type Indices for the Virtual Screening of Combinatorial Libraries. Croat. Chem. Acta 2002, 75, 000-000.
45. Barysz, M.; Jashari, G.; Lall, R.S.; Srivastava, V.K.; Trinajstid, N. On the Distance Matrix of Molecules Containing Heteroatoms. In Chemical Applications of Topology and Graph Theory; King, R.B., Ed.; Elsevier: Amsterdam, 1983; pp 222-227.
46. Ivanciuc, O.; Ivanciuc, T.; Balaban A.T. Design of Topological Indices. Part 10. Parameters Based on Electronegativity and Covalent Radius for the Computation of Molecular Graph Descriptors for Heteroatom-Containing Molecules. J. Chem. Inf. Comput. Sci. 1998, 38, 395-401.
47. Ivanciuc, O.; Ivanciuc, T.; Cabrol-Bass, D.; Balaban, A.T. Comparison of Weighting Schemes for Molecular Graph Descriptors: Application in Quantitative Structure-Retention Relationship Models for Alkylphenols in Gas-Liquid Chromatography. J. Chem. Inf. Comput. Sci. 2000, 40, 732-743.
48. Ivanciuc, O. Design of Topological Indices. Part 12. Parameters for Vertex- and Edge-Weighted Molecular Graphs. Rev. Roum. Chim. 2000, 45, 289-301.
49. Ivanciuc, O. Design of Topological Indices. Part 14. Distance-Valency Matrices and Structural Descriptors for Vertex- and Edge-Weighted Molecular Graphs. Rev. Roum. Chim. 2000, 45, 587-596.
50. Nakamura, M.; Inoue, J.; Yamada, T. A Two-Step, One-Pot Synthesis of Diverse N-Pyruvoyl Amino Acid Derivatives Using the Ugi Reaction. Bioorg. Med. Chem. Lett. 2000, 10, 2807-2810.
51. Ivanciuc, O.; Balaban, A.T. Graph Theory in Chemistry. In The Encyclopedia of Computational Chemistry; Schleyer, P.v.R., Allinger, N.L., Clark, T., Gasteiger, J., Kollman, P.A., Schaefer, H.F., III, Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, U.K., 1998; pp 1169-1190.
52. Diudea, M.V.; Silaghi-Dumitrescu, I. Molecular Topology. I. Valence Group Electronegativity as a Vertex Discriminator. Rev. Roum. Chim. 1989, 34, 1175-1182.
53. Kier, L.B.; Hall, L.H. An Electrotopological-State Index for Atoms in Molecules. Pharm. Res. 1990, 7, 801-807.
54. Balaban, A.T.; Kier, L.B.; Joshi, N. Correlations Between Chemical Structure and Normal Boiling Points of Acyclic Ethers, Peroxides, Acetals, and their Sulfur Analogues. J. Chem. Inf. Comput. Sci. 1992, 32, 237-244.
55. Ivanciuc, O.; Balaban, A.T. Design of Topological Indices. Part 5. Precision and Error in Computing Graph Theoretic Invariants for Molecules Containing Heteroatoms and Multiple Bonds. MATCH (Commun. Math. Chem.) 1994, 30, 117-139.
56. Ivanciuc, O. QSAR Comparative Study of Wiener Descriptors for Weighted Molecular Graphs. J. Chem. Inf. Comput. Sci. 2000, 40, 1412-1422.
57. Balaban, A.T.; Ivanciuc, O. FORTRAN 77 Computer Program for Calculating the Topological Index J for Molecules Containing Heteroatoms. In MATH/CHEM/COMP 1988; Graovac, A., Ed.; Studies in Physical and Theoretical Chemistry; Elsevier: Amsterdam, 1989; Vol. 63, pp 193-212.
58. Hosoya, H. A Newly Proposed Quantity Characterizing the Topological Nature of Structural Isomers of Saturated Hydrocarbons. Bull. Chem. Soc. Jpn. 1971, 44, 2332-2339.
59. Klein, D.J.; Randić, M. Resistance Distance. J. Math. Chem. 1993, 12, 81-95.
60. Gutman, I.A Formula for the Wiener Number of Trees and Its Extension to Graphs Containing Cycles. Graph Theory Notes New York 1994, 27, 9-15.
61. Diudea, M.V. Cluj Matrix Invariants. J. Chem. Inf. Comput. Sci. 1997, 37, 300-305.
62. Polansky, O.E.; Bonchev, D. The Wiener Number of Graphs. I. General Theory and Changes Due to Some Graph Operations. MATCH (Commun. Math. Chem.) 1986, 21, 133-186.
63. Diudea, M.V.; Kacsó, I.E. Molecular Topology. 9. Composition Rules for Some Topological Indices. MATCH (Commun. Math. Chem.) 1991, 26, 255-269.
64. Ivanciuc, O.; Ivanciuc, T.; Klein, D.J.; Seitz, W.A.; Balaban, A.T. Wiener Index Extension by Counting Even/Odd Graph Distances. J. Chem. Inf. Comput. Sci. 2001, 41, 536-549.
65. Ivanciuc, O.; Ivanciuc, T.; Klein, D.J. Quantitative Structure-Property Relationships Generated with Optimizable Even/Odd Wiener Polynomial Descriptors. SAR QSAR Environ. Res. 2001, 12, 1-16.
66. Zhu, H.-Y.; Klein, D.J. Graph-Geometric Invariants for Molecular Structures. J. Chem. Inf. Comput. Sci. 1996, 36, 1067-1075.
67. Klein, D.J. Graph Geometry, Graph Metrics, & Wiener. MATCH (Commun. Math. Comput. Chem.) 1997, 35, 7-27.
68. Klein, D.J.; Zhu, H.-Y. Distances and Volumina for Graphs. J. Math. Chem. 1998, 23, 179-195.