Untitled

Abstract

ABSTRACT:In this study, homology modeling and molecular docking studies were performed to explore structural features and binding mechanism of synthesized benzimidazole derivatives as ubiquitin inhibitors. A homology modeling procedure was employed to construct a 3D model of ubiquitin protein by using MODELLER9.15. For this procedure, the X-ray crystal structure of Gumby / fam105b in Complex with linear Di-ubiquitin (PDB ID: 4KSL) at 2.83 Å resolution was used as template. The predicted model was analyzed by PROCHECK. The 3D structure of predicted model shows 93.9% of amino acids in most favored region. The predicted model was used for molecular docking studies by using Autodock4.2. All the synthesized benzimidazole derivatives show good binding energy and interactions with the model. Compound one shows three interactions with Asp348, Leu297 and Tyr351.