A chemoinformatic-biophysics based approach to identify novel anti-virulent compounds against Pseudomonas aeruginosa disulfide-bond protein A1

Abstract

The conventional course of drug discovery is a lengthy, expensive and complex process and often experiences a high failure rate. This in-silico based study screened novel drug molecules against Pseudomonas aeruginosa disulfide-bond protein A1 (PaDsbA1; PDB ID of 4ZL7) using a variety of chemoinformatic and biophysics approaches. The structure-based virtual screening identified three antipseudomonal compounds (BDC_30129064, BDC_20699588 and BDC_25329008) that targeted PaDsbA1 enzyme with a binding energy score of −7.8 kcal/mol, −7.7 kcal/mol and −7.7 kcal/mol, respectively. The compounds revealed deep binding at the enzyme active pocket with close distance hydrogen bond interactions with Thr46, Pro55, Val58, Arg62, His88, and Asp180. The co-crystalized hexaethylene glycol revealed a binding energy of −6.02 kcal/mol. The docked compounds were further subjected to molecular dynamics simulation analysis in order to check the dynamic movements of docked complexes. The complexes reported no drastic changes during simulation time. In the simulation, stable compounds binding and docked conformation were accomplished. The docking and simulation results were validated using free binding energies calculation through molecular mechanics with generalized born surface area solvation and molecular mechanics Poisson Boltzmann surface area (MMGBSA/MMPBSA) approaches. The net binding energy estimated by MMGBSA for BDC_30129064, BDC_20699588 and BDC_25329008 was −75.07 kcal/mol, −77.87 kcal/mol and −59.1 kcal/mol, respectively while that of MMPBSA for the compounds was −72.47 kcal/mol, −78.99 kcal/mol and −60.991 kcal/mol, respectively. The physiochemical properties of the selected compounds indicated them to be physiochemically stable with good absorption, distribution, metabolism and elimination properties. From the above observations and predictions, the compounds can be recommended for further experimental validation in order to decipher their anti-virulence capacity in blocking disulfide bond formation in P. aeruginosa.

Communicated by Ramaswamy H. Sarma

Keywords:

• Pseudomonas aeruginosa
• PaDsbA1
• structural-based drug designing
• molecular docking
• molecular dynamic simulation

Additional information

Funding

The authors would like to acknowledge the Researchers Supporting Project number (RSPD2023R632), King Saud University, Riyadh, Saudi Arabia.