Integrating Multi-Domain Approach for Identification of Neo Anti-DHPS Inhibitors Against Pathogenic Stenotrophomonas maltophilia

Abstract

Background: The increasing number of resistant bacterial strains is reducing the effectiveness of antimicrobial drugs in preventing infections. It has been shown that resistant strains invade living organisms and cause a wide range of illnesses, leading to a surprisingly high death rate. Objective: The present study aimed to identify novel dihydropteroate synthase (DHPS) inhibitors from Stenotrophomonas maltophilia using structure-based computational techniques. Methodology: This in silico study used various bioinformatics and cheminformatics approaches to find new DHPS inhibitors. It began by retrieving the crystal structure via PDB ID: 7L6P, followed by energy minimization. The DHPS enzyme was virtually screened against the CHEMBL library to target S. maltophilia through enzyme inhibition. Then, absorption, distribution, metabolism, and excretion (ADME) analysis was performed to select the top hits. This process identified the top-10 hits. Additionally, imidazole (control) was used for comparative assessment. Furthermore, a 100 ns molecular dynamics simulation and post-simulation analyses were conducted. The docking results were validated through binding free energy calculations and entropy energy estimation approaches. Results: The docking results prioritized 10 compounds based on their binding scores, with a maximum threshold of −7 kcal/mol for selection. The ADME assessment shortlisted 3 out of 10 compounds: CHEMBL2322256, CHEMBL2316475, and CHEMBL2334441. These compounds satisfied Lipinski’s rule of five and were considered drug-like. The identified inhibitors demonstrated greater stability and less deviation compared to the control (imidazole). The average RMSD stayed below 2 Å, indicating overall stability without major deviations in the DHPS–ligand complexes. Post-simulation analysis assessed the stability and interaction profiles of the complexes under physiological conditions. Hydrogen bonding analysis showed the control to be more stable than the three tested complexes. Increased salt bridge interactions suggested stronger electrostatic stabilization, while less alteration of the protein’s secondary structure indicated better structural compatibility. These findings support the potential of these novel ligands as potent DHPS inhibitors. Binding energy estimates showed that CHEMBL2322256 was the most stable, with scores of −126.49 and −124.49 kcal/mol. Entropy calculations corroborated these results, indicating that CHEMBL2322256 had an estimated entropy of 8.63 kcal/mol. Conclusions: The newly identified compounds showed more promising results compared to the control. While these compounds have potential as innovative drugs, further research is needed to confirm their effectiveness as anti-DHPS agents against antibiotic resistance and S. maltophilia infections.