A Similarity Search Using Molecular Topological Graphs

A molecular similarity measure has been developed using molecular topological graphs and atomic partial charges. Two kinds of topological graphs were used. One is the ordinary adjacency matrix and the other is a matrix which represents the minimum path length between two atoms of the molecule. The ordinary adjacency matrix is suitable to compare the local structures of molecules such as functional groups, and the other matrix is suitable to compare the global structures of molecules. The combination of these two matrices gave a similarity measure. This method was applied to in silico drug screening, and the results showed that it was effective as a similarity measure.

[1]  Haruki Nakamura,et al.  An Efficient in Silico Screening Method Based on the Protein-Compound Affinity Matrix and Its Application to the Design of a Focused Library for Cytochrome P450 (CYP) Ligands , 2006, J. Chem. Inf. Model..

[2]  J. Gasteiger,et al.  ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .

[3]  Y. Fukunishi,et al.  Classification of chemical compounds by protein-compound docking for use in designing a focused library. , 2006, Journal of medicinal chemistry.

[4]  Robert S. Pearlman,et al.  Metric Validation and the Receptor-Relevant Subspace Concept , 1999, J. Chem. Inf. Comput. Sci..

[5]  Ismael Zamora,et al.  Virtual Screening and Scaffold Hopping Based on GRID Molecular Interaction Fields , 2005, J. Chem. Inf. Model..

[6]  Schmid,et al.  "Scaffold-Hopping" by Topological Pharmacophore Search: A Contribution to Virtual Screening. , 1999, Angewandte Chemie.

[7]  Alexandre Varnek,et al.  Chemoinformatics approaches to virtual screening , 2008 .

[8]  E. Lindsay,et al.  Chapter 10 , 1994, Genji & Heike.

[9]  M. Kanehisa,et al.  Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. , 2003, Journal of the American Chemical Society.

[10]  Haruki Nakamura,et al.  A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening , 2006, J. Comput. Aided Mol. Des..

[11]  David M. Rocke,et al.  Predicting ligand binding to proteins by affinity fingerprinting. , 1995, Chemistry & biology.

[12]  Haruki Nakamura,et al.  Multiple target screening method for robust and accurate in silico ligand screening. , 2006, Journal of molecular graphics & modelling.

[13]  Xiaoming Wang,et al.  Chapter 7 , 2003, School Health Policy & Practice.

[14]  Hans Briem,et al.  Flexsim-R: A virtual affinity fingerprint descriptor to calculate similarities of functional groups , 2002, J. Comput. Aided Mol. Des..

[15]  Gisbert Schneider,et al.  Protein-ligand interactions from molecular recognition to drug design , 2003 .

[16]  Han van de Waterbeemd,et al.  Computer-Assisted Lead Finding and Optimization , 1997 .

[17]  Y. Fukunishi,et al.  Finding ligands for G protein-coupled receptors based on the protein-compound affinity matrix. , 2007, Journal of Molecular Graphics and Modelling.

[18]  M. Kanehisa,et al.  Heuristics for chemical compound matching. , 2003, Genome informatics. International Conference on Genome Informatics.

[19]  J. Gasteiger,et al.  Chemoinformatics: A Textbook , 2003 .

[20]  Hans Briem,et al.  Flexsim-X: A Method for the Detection of Molecules with Similar Biological Activity , 2000, J. Chem. Inf. Comput. Sci..

[21]  A. Leach.  Molecular Modelling: Principles and Applications , 1996 .

[22]  Jon Baskin.  Chapter 6 , 2003, Tom Sawyer Abroad / Tom Sawyer, Detective.

[23]  P. Beroza,et al.  Novel cyclooxygenase-1 inhibitors discovered using affinity fingerprints. , 2004, Journal of medicinal chemistry.

[24]  Y. Fukunishi,et al.  Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening. , 2005, Journal of molecular graphics & modelling.

[25]  G. Vigers,et al.  Multiple active site corrections for docking and virtual screening. , 2004, Journal of medicinal chemistry.

[26]  Xiaoming Wang,et al.  Chapter 8 , 2003, The Sermons and Liturgy of Saint James.

[27]  I. Kuntz,et al.  Molecular similarity based on DOCK-generated fingerprints. , 1996, Journal of medicinal chemistry.

[28]  Johann Gasteiger,et al.  A new model for calculating atomic charges in molecules , 1978 .

[29]  Haruki Nakamura,et al.  Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening , 2006, J. Chem. Inf. Model..

[30]  U. Lessel,et al.  In vitro and in silico affinity fingerprints: Finding similarities beyond structural classes , 2000 .