Voronoi binding site models: Calculation of binding modes and influence of drug binding data accuracy

✍ Scribed by Laurent G. Boulu; Gordon M. Crippen

• Book ID: 102878393
• Publisher: John Wiley and Sons
• Year: 1989
• Tongue: English
• Weight: 824 KB
• Volume: 10
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.540100509

✦ Synopsis

A new and accurate method for calculating the geometrically allowed modes of binding of a ligand molecule to a Voronoi site model is reported. It is shown that the feasibility of the binding of a group of atoms to a Voronoi site reduces to a simple set of linear and quadratic inequalities and quadratic equalities which can be solved by minimization of a simple function. Newton's numerical method of solution coupled to a line search proved to be successful. Moreover, we have developed efficient molecular and site data bases to discard quickly infeasible binding modes without time-consuming numerical calculation. The method is tested with a data set consisting of the binding constants for a series of biphenyls binding to prealbumin. After determination of the conformation space of the molecules and proposal of a Voronoi site geometry, the geometrically feasible modes are calculated and the energy interaction parameters determined to tit the observed binding energies to the site within experimental error ranges. We actually allowed these ranges to vary in order to study the influence of their broadness on the site geometry and found that as they increase, one can first model the receptor as a three-region site then as a single region site, but never as a two-region site.