Journal d'informatique et de biologie des systèmes

Human Rab8b Protein as a Cancer Target - An In Silico Study

Abstract

Aboubakr HA, Lavanya SP, Thirupathi M, Rohini R, Sarita RP and Uma V

Testicular cancer develops in one or both of the testicles in young men. Rab8b is a member of the Rab small G protein family, participates in intracellular trafficking events at the site of the adherence junction dynamics in the testis. Overexpression of Rab8b and loss of functioning adherence junction accelerates the tumorigenesis in testis. In the present work, the computer aided high throughput virtual screening studies are applied to identify potent leads for human Rab8b protein. The homology model of Rab8b of 207 amino acid residues chain length was evaluated based on the crystal structure of an appropriate template, and reveals the presence of 6 α-helices and 6 β-strands. The energy of the generated model was minimized and the model was validated using ProSA PROCHECK and ERRAT server tools. The active site was identified using the computational binding site prediction tools like CASTp, efindsite seversand Sitemap of Schrödinger, which show that the residues (GLU33 to GLN60) are important for binding. The molecular interactions of Rab8b with its natural substrate Rabin 8, were examined by in silico protein-protein docking studies using patchDock tool, and the results were corroborated with the active site identified from the computational tools. Virtual screening studies were carried out with ligand databases using Glide docking program of Schrödinger suite. The ligands obtained from XP docking with high Glide score and Glide energy, were subjected to QikProp module to predict their ADME properties. These ligands, based on the pharmacokinetic properties, which are new entities, were considered as novel potent inhibitors in cancer therapy.