Journal of Proteomics & Bioinformatics
Open Access

Abstract

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

Flavio Almeida Curvelo dos Anjos and Manoel Victor Frutuoso Barrionuevo

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.