Computational assessment of guanidine and arginine isomers as inhibitors of Caseinolytic Peptidase B (ClpB): Targeting bacterial chaperones for novel antimicrobial strategies

Bacterial infections pose a significant global health threat due to their resistance to broad-spectrum antimicrobials, necessitating novel therapeutic strategies. Caseinolytic Peptidase B (ClpB), a bacterial chaperone absent in human cells, plays a crucial role in bacterial survival under stress by disaggregating protein aggregates, making it a promising antimicrobial target. This study utilized computational methods to evaluate guanidine hydrochloride (GuHCl), D-arginine, and L-arginine as potential ClpB inhibitors. Molecular docking studies using AutoDock Vina against ClpB (PDB ID: 1QVR) identified possible binding poses of the ligands. Both D-Arginine and L-Arginine showed a binding affinity of -5.9 kcal/mol to Nucleotide Binding Domain-1 (NBD-1), while GuHCl exhibited a binding affinity of -3.5 kcal/mol to Nucleotide Binding Domain-2 (NBD-2). The formation of favorable conventional hydrogen bonds between the protein and the ligands primarily contributed to the observed binding affinities in the docking results. SwissADME predicted drug-likeness and pharmacokinetics, while ProTox-II assessed toxicity. None of the ligands violated Lipinski’s rule, indicating their suitability for oral administration. In silico toxicity, predictions classified GuHCl as slightly toxic (Class IV; LD50: 350 mg/kg) and L-arginine and D-arginine as possibly harmful (Class V; LD50: 245,050 mg/kg), yet overall reflecting a favourable safety profile. Molecular dynamics (MD) simulation trajectories for 100 ns revealed stable root-mean-square deviation (RMSD) and consistent hydrogen bond formation, indicating stable ligand binding. However, solvent-accessible surface area (SASA), radius of gyration (Rg), and root-mean-square fluctuation (RMSF) analyses revealed minor alterations in the NBD-1 domain. These structural changes align with experimental findings for GuHCl, suggesting impaired ClpB activity. Binding free energy calculations using MM/PBSA confirmed favourable interactions, with all test molecules showing negative free energy values. These findings suggest that GuHCl, L-arginine, and D-arginine have potential as ClpB inhibitors, warranting further in vitro and in vivo validation for antimicrobial therapy.