Cyanobacterial compound Tolyporphine K as an inhibitor of Apo-PBP (penicillin-binding protein) in A. baumannii and its ADME assessment

Abstract

Antibiotic-resistant Acinetobacter baumannii, is a common pathogen found in hospital settings and has become nosocomial due to its high infection-causing tendency amongst ICU patients. The present study explores the cyanocompoundswhich were capable to inhibit the Penicillin Binding Protein of A. baumannii through molecular docking, ADMET, and molecular dynamicssimulation strategy. A database having structural and origin details was generated for 85 bioactive compounds in MS Excel. The 3-D structures weredownloaded from the PubChem database and minimized. The receptor protein was minimized and validated for structure correctness. The database was screened against the penicillin-binding protein of A. baumannii through PyRx software. The top 5 compounds including the control molecule werefurther redocked to the receptor molecule through Autodock Vina software. The molecule pose having the highest affinity was further subjected to 100ns MD- simulation and simultaneously the in-vitro activity of the methanol extract and hexane extract was checked through agar well diffusion assay.Docking studies indicate Tolyporphine K to be a lead molecule which was further assessed through Molecular dynamics and MM/PBSA. The in-silicoresults suggested that the protein-ligand complex was found to be stable over the 100 ns trajectory with a binding free energy of -8.56 Kcalmol-1. Theligand did not induce any major structural conformation in the protein moiety and was largely stabilized by hydrophobic interactions. The bioactivityscore and ADME properties of the compounds were also calculated. The in-vitro agar well diffusion assay showed a moderate zone of inhibition of12.33mm. The results indicate that the compound Tolyporphin- K could be a potential inhibitor of penicillin-binding protein in A. baumannii. Yet furtherwork needs to be done to have a more concrete basis for the pathway of inhibition.

Communicated by Ramaswamy H. Sarma

Keywords:

• Cyano-compounds
• Tolyporphine K
• antibacterial activity
• MD simulation
• molecular docking
• Acinetobacter baumannii
• penicillin-binding protein

Acknowledgments

Authors would like to thank Amity University, Noida, for providing the facility for work.

Authors’ contribution

Conceptualization, A.C. and A.R., P.P.; writing—original draft preparation, M.G.; molecular dynamics simulation, P.G., M.G.; reviewing and editing, A.C., P.P., A.R., H.S.T., A.G.; supervision, T.J. and R.L.; project administration, T.J. All authors have read and agreed to the published version of the manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.