Molecular docking and molecular dynamics studies of natural products unravel potential inhibitors against OmpA of Acinetobacter baumannii

Abstract

Emerging antimicrobial resistance has highlighted the need to design more effective antibiotics to treat deadly bacterial infections. Acinetobacter baumannii’s outer membrane protein A (OmpA) is a critical virulence component involved in biofilm formation, immunomodulation, and antibiotic resistance, which characterizes it as a potential therapeutic target. The present study aimed to screen the natural product database (>1,00,000) to identify the potential inhibitor against OmpA. Molecular docking studies revealed that 10 compounds had good docking scores (≤ −7 kcal/mol) compared to the reported inhibitor epiestriol (-3.079). Further, these 10 compounds were subjected to ADME analysis and MMGBSA analysis. Based on MMGBSA results, we selected 5 compounds [NP-1 (MolPort-039-337-117), NP-5(MolPort-019-932-973), NP-6 (MolPort-005-948-336), NP-8(MolPort-042-673-978) and NP-9(MolPort-042-673-766)] with high binding affinity. Molecular dynamics simulation found that NP-5, NP-8, and NP-9 were stable after analysing their RMSD, RMSF, the radius of gyration, and hydrogen interactions of complexes. Our study revealed that NP-5, NP-8, and NP-9 bind perfectly with OmpA and can act as its potential inhibitors. The results of this study imply that the identified inhibitors have the potential for further investigation. Communicated by Ramaswamy H. Sarma