Topological and Stereochemical Molecular Descriptors for Databases Useful in QSAR, Similarity/Dissimilarity and Drug Design

Abstract A review is presented on: (i) topological indices (TIs) which are numbers derived from constitutional formulas and which have continuously evolved towards higher discriminating power and better correlating ability; (ii) stereochemical descriptors, allowing structures of diastereomers and enantiomers to be encoded in computer language. Uses of these descriptors include: structure encoding and retrieval; quantitative structure-activity relationships (QSAR) and computer-assisted drug design (CADD); creation and exploration of data bases; quantitative assessment of similarity and dissimilarity.

[1]  Alexandru T. Balaban,et al.  Chemical graphs , 1979 .

[2]  Thomas E. Moock,et al.  Conformational searching in ISIS/3D databases , 1994, J. Chem. Inf. Comput. Sci..

[3]  Douglas J. Klein,et al.  Graph-Geometric Invariants for Molecular Structures , 1996, J. Chem. Inf. Comput. Sci..

[4]  Alexandru T. Balaban.  Enumeration of Isomers , 1992 .

[5]  Julian M. Ivanov,et al.  3DGEN: A system for exhaustive 3D molecular design proceeding from molecular topology , 1994, J. Chem. Inf. Comput. Sci..

[6]  Subhash C. Basak,et al.  Molecular Similarity and Estimation of Molecular Properties , 1995, J. Chem. Inf. Comput. Sci..

[7]  N. Trinajstic,et al.  Computer-aided enumeration and generation of the kekulé structures in conjugated hydrocarbons , 1982 .

[8]  Catherine Pepperrell,et al.  Three-Dimensional Chemical Similarity Searching , 1994 .

[9]  Ante Graovac,et al.  Molecular Topology, 15. 3D Distance Matrixes and Related Topological Indices , 1995, Journal of chemical information and computer sciences.

[10]  Gilles Klopman,et al.  A novel approach to the use of graph theory in structure–activity relationship studies. Application to the qualitative evaluation of mutagenicity in a series of nonfused ring aromatic compounds , 1988 .

[11]  Alexandru T. Balaban,et al.  Correlations between chemical structure and normal boiling points of halogenated alkanes C1-C4 , 1992 .

[12]  Lemont B. Kier,et al.  The electrotopological state: structure information at the atomic level for molecular graphs , 1991, J. Chem. Inf. Comput. Sci..

[13]  Lemont B. Kier,et al.  Electrotopological State Indices for Atom Types: A Novel Combination of Electronic, Topological, and Valence State Information , 1995, J. Chem. Inf. Comput. Sci..

[14]  Ekaterina Gordeeva,et al.  Traditional topological indexes vs electronic, geometrical, and combined molecular descriptors in QSAR/QSPR research , 1993, J. Chem. Inf. Comput. Sci..

[15]  Paul G. Mezey,et al.  Potential Energy Hypersurfaces , 1987 .

[16]  George W. A. Milne,et al.  National Cancer Institute Drug Information System 3D Database , 1994, J. Chem. Inf. Comput. Sci..

[17]  Subhash C. Basak,et al.  Correlation between Structure and Normal Boiling Points of Haloalkanes C1-C4 Using Neural Networks , 1994, J. Chem. Inf. Comput. Sci..

[18]  E. Feigenbaum,et al.  Applications of artificial intelligence for chemical inference. I. Number of possible organic compounds. Acyclic structures containing carbon, hydrogen, oxygen, and nitrogen , 1969 .

[19]  Gareth Jones,et al.  Pharmacophoric pattern matching in files of three-dimensional chemical structures: Comparison of conformational-searching algorithms for flexible searching , 1994, J. Chem. Inf. Comput. Sci..

[20]  Milan Randic,et al.  Molecular Topographic Indices , 1995, J. Chem. Inf. Comput. Sci..

[21]  Ovidiu Ivanciuc,et al.  Design of topological indices. Part 4. Reciprocal distance matrix, related local vertex invariants and topological indices , 1993 .

[22]  Andreas Dietz,et al.  Yet Another Representation of Molecular Structure , 1995, Journal of chemical information and computer sciences.

[23]  Alexandru T. Balaban,et al.  Chemical graphs—XII: Configurations of annulenes , 1971 .

[24]  S. Unger.  Molecular Connectivity in Structure–activity Analysis , 1987 .

[25]  Michel Petitjean,et al.  Topological statistics on a large structural file , 1990, J. Chem. Inf. Comput. Sci..

[26]  Alexandru T. Balaban.  Local versus Global (i.e. Atomic versus Molecular) Numerical Modeling of Molecular Graphs , 1994, J. Chem. Inf. Comput. Sci..

[27]  Alexandru T. Balaban,et al.  A new approach for devising local graph invariants: Derived topological indices with low degeneracy and good correlation ability , 1987 .

[28]  A. Balaban.  Highly discriminating distance-based topological index , 1982 .

[29]  Ann M. Richard,et al.  Quantitative comparison of molecular electrostatic potentials for structure‐activity studies , 1991 .

[30]  William C. Herndon,et al.  Molecular similarity concepts. 5. Analysis of steroid-protein binding constants , 1991 .

[31]  Alexandru T. Balaban,et al.  Correlations between chemical structure and normal boiling points of acyclic ethers, peroxides, acetals, and their sulfur analogs , 1992, J. Chem. Inf. Comput. Sci..

[32]  N. Trinajstic.  Chemical Graph Theory , 1992 .

[33]  M. Randic.  Characterization of molecular branching , 1975 .

[34]  N. Trinajstić,et al.  On the three-dimensional wiener number. A comment , 1990 .

[35]  Milan Randic,et al.  Distance/Distance Matrixes , 1994, J. Chem. Inf. Comput. Sci..

[36]  Lionello Pogliani.  On a Graph Theoretical Characterization of Cis/Trans Isomers , 1994, J. Chem. Inf. Comput. Sci..

[37]  A. Balaban.  Chemical applications of graph theory , 1976 .

[38]  Harry P. Schultz,et al.  Topological Organic Chemistry, 9. Graph Theory and Molecular Topological Indices of Stereoisomeric Organic Compounds , 1995, J. Chem. Inf. Comput. Sci..

[39]  H. Hosoya.  Topological Index. A Newly Proposed Quantity Characterizing the Topological Nature of Structural Isomers of Saturated Hydrocarbons , 1971 .

[40]  Paul G. Mezey,et al.  Shape Group Analysis of Molecular Similarity: Shape Similarity of Six-Membered Aromatic Ring Systems , 1995, J. Chem. Inf. Comput. Sci..

[41]  Zlatko Mihalić,et al.  The algebraic modelling of chemical structures: On the development of three-dimensional molecular descriptors , 1991 .

[42]  Ernest L. Eliel,et al.  Stereochemistry of Organic Compounds , 1962 .

[43]  F. Harary,et al.  Chemical graphs—V : Enumeration and proposed nomenclature of benzenoid cata-condensed polycyclic aromatic hydrocarbons , 1968 .

[44]  Marvin Johnson,et al.  Concepts and applications of molecular similarity , 1990 .

[45]  Alexandru T. Balaban,et al.  Topological indices based on topological distances in molecular graphs , 1983 .

[46]  Borka Jerman-Blazic,et al.  Development of 3-dimensional molecular descriptors , 1990, Comput. Chem..

[47]  Paul G. Mezey,et al.  Shape in Chemistry: An Introduction to Molecular Shape and Topology , 1993 .

[48]  A. Balaban,et al.  Unique description of chemical structures based on hierarchically ordered extended connectivities (HOC procedures). I. Algorithms for finding graph orbits and canonical numbering of atoms , 1985 .

[49]  J. Devillers.  Genetic algorithms in molecular modeling , 1996 .

[50]  N. Trinajstic,et al.  On the Harary index for the characterization of chemical graphs , 1993 .

[51]  Alexandru T. Balaban,et al.  Using real numbers as vertex invariants for third-generation topological indexes , 1992, J. Chem. Inf. Comput. Sci..

[52]  H. Wiener.  Correlation of Heats of Isomerization, and Differences in Heats of Vaporization of Isomers, Among the Paraffin Hydrocarbons , 1947 .

[53]  L. Hall,et al.  Molecular connectivity in chemistry and drug research , 1976 .

[54]  Peter Willett,et al.  Three-dimensional chemical structure handling , 1991 .

[55]  W. C. Herndon.  Graph codes and a definition of structural similarity , 1988 .

[56]  A. Balaban,et al.  New vertex invariants and topological indices of chemical graphs based on information on distances , 1991 .

[57]  Johnz Willett.  Similarity and Clustering in Chemical Information Systems , 1987 .

[58]  Peter Willett,et al.  Similarity searching in files of three-dimensional chemical structures: Comparison of fragment-based measures of shape similarity , 1994, J. Chem. Inf. Comput. Sci..

[59]  Lemont B. Kier,et al.  Molecular Similarity Based on Novel Atom-Type Electrotopological State Indices , 1995, J. Chem. Inf. Comput. Sci..

[60]  Robert P. Sheridan,et al.  Chemical Similarity Using Geometric Atom Pair Descriptors , 1996, J. Chem. Inf. Comput. Sci..

[61]  Nenad Trinajstić,et al.  In search for graph invariants of chemical interes , 1993 .

[62]  N. Trinajstic,et al.  On the three-dimensional wiener number , 1989 .

[63]  Osman F. Güner,et al.  Use of flexible queries for searching conformationally flexible molecules in databases of three-dimensional structures , 1992, J. Chem. Inf. Comput. Sci..

[64]  H. Wiener.  Structural determination of paraffin boiling points. , 1947, Journal of the American Chemical Society.

[65]  Tad Hurst,et al.  Flexible 3D searching: The directed tweak technique , 1994, J. Chem. Inf. Comput. Sci..

[66]  Robert P. Sheridan,et al.  3DSEARCH: a system for three-dimensional substructure searching , 1989, J. Chem. Inf. Comput. Sci..

[67]  Peter Willett,et al.  The Extent of the Relationship between the Graph-Theoretical and the Geometrical Shape Coefficients of Chemical Compounds , 1995, J. Chem. Inf. Comput. Sci..

[68]  Michel Petitjean,et al.  Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds , 1992, J. Chem. Inf. Comput. Sci..

[69]  Alexandru T. Balaban,et al.  Real number vertex invariants: Regressive distance sums and related topological indexes , 1993, J. Chem. Inf. Comput. Sci..

[70]  Subhash C. Basak,et al.  Application of graph theoretical parameters in quantifying molecular similarity and structure-activity relationships , 1994, J. Chem. Inf. Comput. Sci..

[71]  Robert W. Robinson,et al.  The numbers of chiral and achiral alkanes and monosubstituted alkanes , 1976 .

[72]  Alexandru T. Balaban,et al.  Molecular topology. IV. Regressive vertex degrees (new graph invariants) and derived topological indices , 1991 .

[73]  Zlatko Mihalić,et al.  A graph-theoretical approach to structure-property relationships , 1992 .

[74]  George W. A. Milne,et al.  CONCORD and CAMBRIDGE: comparison of computer generated chemical structures with x-ray crystallographic data , 1993, J. Chem. Inf. Comput. Sci..

[75]  Ernesto Estrada.  Three-Dimensional Molecular Descriptors Based on Electron Charge Density Weighted Graphs , 1995, J. Chem. Inf. Comput. Sci..

[76]  R. Cramer,et al.  Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. , 1988, Journal of the American Chemical Society.

[77]  David J. Wild,et al.  Similarity searching in files of three-dimensional chemical structures. Implementation of atom mapping on the distributed array processor DAP-610, the MasPar MP-1104, and the connection machine CM-200 , 1994, J. Chem. Inf. Comput. Sci..

[78]  Alan R. Katritzky,et al.  COMPREHENSIVE DESCRIPTORS FOR STRUCTURAL AND STATISTICAL ANALYSIS. 1 : CORRELATIONS BETWEEN STRUCTURE AND PHYSICAL PROPERTIES OF SUBSTITUTED PYRIDINES , 1996 .

[79]  Ramaswamy Nilakantan,et al.  New method for rapid characterization of molecular shapes: applications in drug design , 1993, J. Chem. Inf. Comput. Sci..

[80]  Steven H. Bertz,et al.  Linear notations and molecular graph similarity , 1987 .

[81]  Danail Bonchev,et al.  Unique description of chemical structures based on hierarchically ordered extended connectivities (HOC procedures). III. Topological, chemical, and stereochemical coding of molecular structure , 1985 .