Prediction of Protein-Ligand Binding Sites for Cisplatin and Transplatin based on Hydrogen Bonds

Abstract

Volume 8(1) 015-022 (2015)-15 J Proteomics Bioinform ISSN: 0974-276X JPB, an open access journal Abstract Platinum compounds are very important to treatment of various malignant tumors. However, prediction of platinum-binding sites is very hard to be made. Nevertheless, hydrolysis of leaving groups bounded to platinum compounds plays an important role in delivering platinum to a target molecule. Herein, a study in silico provides an understanding of the molecular surface in atomic level of three-dimensional structure of cisplatin and transplatin and their binding-sites in order to offer some insights in drug designing. The goal of this work was to implement a new approach based on geometric and physicochemical parameters to find platinum-binding sites using parallel computing algorithms for graphics processing units (GPUs). These algorithms were tested and validated by analysing platinum-binding sites in five known proteins. The results indicated that these binding sites were predicted with significant success. In our analysis HexServer and PatchDock server did not find putative binding-sites for cisplatin and transplatin as we found for the five chosen proteins. Herein, we have shown that the present method have had a better prediction of platinum-binding site than HexServer and PatchDock methods.