Exploring the Binding Affinity and Molecular Interactions: A Comprehensive Study on the Molecular Docking of Benzimidazole Derivatives

Abstract

The aim of this research work was to study the comparative binding affinities of benzimidazole derivatives (2-methyl-1H-benzo[d]imidazole and 2-phenyl benzimidazole) against COX, LOX, and estrogen receptor. Benzimidazole stands as a vital heterocyclic aromatic organic molecule, playing a pivotal role in medicinal chemistry due to its essential pharmacophore and structural significance. The three-dimensional structures of COX, LOX, and the estrogen receptor were sourced from the PDB database. Concurrently, the structures of the benzimidazole derivatives, namely 2-methyl-1H-benzo[d]imidazole and 2-phenyl benzimidazole, were obtained from the PubChem database. Docking studies were conducted using the PyRx software. A total of nine modes for each receptor were generated, and 2E77 was selected as the best dock. The docking result shows that the interaction of 2-methyl-1H-benzo[d]imidazole with E77 has the highest binding energy. A total of nine modes for each receptor were generated, and 1CX2 was selected as the best dock. The docking result shows that the interaction of 2-phenyl benzimidazole with 1CX2 has the highest binding energy. The in-silico studies show that 2-phenyl benzimidazole has more binding energy with receptors as compared to 2-methyl-1H-benzo[d]imidazole.