In silico investigation of potential inhibitor molecules against caseinolytic peptidase B (ClpB) protein

Abstract

Proteins are the most versatile and intricately structured macromolecules among all biologically active systems. Molecular chaperones are distinct proteins that have evolved within cells to facilitate protein folding and prevent protein aggregation. Caseinolytic Peptidase B (ClpB) is a bacterial chaperone that utilizes the energy from adenosine triphosphate (ATP) hydrolysis to thread out protein molecules from aggregates. Computational methods are being utilized to develop new ways to discover and develop drug candidates to address the increased demand for antimicrobial agents. An in silico investigation was carried out to evaluate the inhibitory effect of Guanidine hydrochloride (GuHCl), D-Arginine and L-Arginine on ClpB protein (PDB ID:1QVR). Docking results from AutoDock Vina suggested-5.9 kcal/mol binding affinities for both D-Arginine and L-Arginine to Nucleotide Binding Domain-1 (NBD-1), respectively, and-3.5 kcal/mol affinity of GuHCl to NBD-2 of 1QVR. Molecular dynamic (MD) simulations performed with GROMACS showed that all three molecules induce conformational changes in the NBD-1, consistent with the docking findings. Trajectory data revealed a stable Root-Mean-Square Deviation (RMSD) confirming the equilibrated yet altered NDB-1 domain of the protein as supported by Solvent-Accessible Surface Area (SASA), Radius of gyration (Rg), and Root-Mean-Square Fluctuation (RMSF) data. Steeper peeks in SASA of the entire protein observed with GuHCl, L-Arginine and D-Arginine binding suggested the hydrophobic core of ClpB becoming more accessible to the surrounding aqueous environment. Cluster analysis confirmed the visible conformational changes after 100 ns of simulation. The binding of GuHCl, L-Arginine, and D-Arginine induces conformational changes in the NBD-1, resulting in the depletion of ATP turnover, which is crucial for the reactivation of protein aggregates, as suggested by previous experimental data. However, further in vitro investigations are suggested to validate these findings.