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Gurnani M, Chauhan A, Ranjan A, Gopi P, Ghosh A, Tuli HS, Haque S, Pandya P, Lal R, Jindal T. Cyanobacterial compound Tolyporphine K as an inhibitor of Apo-PBP (penicillin-binding protein) in A. baumannii and its ADME assessment. J Biomol Struct Dyn 2024; 42:4133-4144. [PMID: 37261797 DOI: 10.1080/07391102.2023.2218930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
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.
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Affiliation(s)
- Manisha Gurnani
- Amity Institute of Environmental Sciences, Amity University, Noida, India
| | - Abhishek Chauhan
- Amity Institute of Environment Toxicology and Safety Management, Amity University, Noida, India
| | - Anuj Ranjan
- Amity Institute of Environment Toxicology and Safety Management, Amity University, Noida, India
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University, Noida, India
| | - Arabinda Ghosh
- Department of Botany, Microbiology Division, Guwahati University, Guwahati, India
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Ambala, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Noida, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India
| | - Tanu Jindal
- Amity Institute of Environmental Sciences, Amity University, Noida, India
- Amity Institute of Environment Toxicology and Safety Management, Amity University, Noida, India
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