High throughput virtual screening and molecular dynamics simulation analysis of phytomolecules against BfmR of Acinetobacter baumannii: anti-virulent drug development campaign

Abstract

Acinetobacter baumannii is a notorious multidrug resistant bacterium responsible for several hospital acquired infections assisted by its capacity to develop biofilms. A. baumannii BfmR (RstA), a response regulator from the BfmR/S two-component signal transduction system, is the major controller of A. baumannii biofilm development and formation. As a result, BfmR represents a novel target for anti-biofilm treatment against A. baumannii. The discovery of the high-resolution crystal structure of BfmR provides a good chance for computational screening of its probable inhibitors. Therefore, in this study we aim to search new, less toxic, and natural BfmR inhibitors from 8450 phytomolecules available in the Indian Medicinal Plants, Phytochemistry and Therapeutic (IMPPAT) database by analyzing molecular docking against BfmR (PDB ID: 6BR7). Out of these 8450 phytomolecules 6742 molecules were successfully docked with BfmR with the docking score range −6.305 kcal/mol to +5.120 kcal/mol. Structure based-molecular docking (SB-MD) and ADMET (absorption, distribution, metabolism, excretion, & toxicity) profile examination revealed that Norepinephrine, Australine, Calystegine B3, 7,7 A-Diepialexine, and Alpha-Methylnoradrenaline phytocompounds strongly binds to the active site residues of BfmR. Furthermore, molecular dynamics simulation (MDS) studies for 100 ns and the binding free energy (MM/GBSA) analysis elucidated the binding mechanism of Calystegine B3, 7,7 A-Diepialexine, and Alpha-Methylnoradrenaline to BfmR. In summary, these phytocompounds seems to have the promising molecules against BfmR, and thus necessitates further verification by both in vitro and in vivo experiments.

Highlights

• BfmR plays a key role in biofilm development and exopolysaccharide (EPS) synthesis in A. baumannii.

• Computational approach to search for promising BfmR inhibitors from IMPAAT database.

• The lead phytomolecules such as Calystegine B3, 7,7 A-Diepialexine, and Alpha-Methylnoradrenaline displayed significant binding with BfmR active site.

• The outcome of BfmR binding phytomolecules has broadened the scope of hit molecules validation.

Communicated by Ramaswamy H. Sarma

Keywords:

• Acinetobacter baumannii
• multidrug-resistant
• IMPPAT database
• phytomolecules
• computational docking
• molecular simulation
• ADMET

Acknowledgement

The authors are thankful to DYPBBI (Dr. D. Y. Patil Biotechnology and Bioinformatics Institute) Dr. D. Y. Patil Vidyapeeth Tathawade, Pune, for providing the infrastructure and facilities to perform this study. The authors also acknowledge the DST-SERB, Govt. of India, New Delhi, (File Number: YSS/2015/002035) for Optimized Supercomputer facility for dynamics calculations. Mr. Kiran Bharat Lokhande acknowledges the ICMR (Indian Council of Medical Research), New Delhi, India for Senior Research Fellowship (Project ID: 2019-3458; file: ISRM/11(54)/2019). The authors also would like to acknowledge the support of Schrodinger, and the team for providing an Evaluation License to our Bioinformatics Research Laboratory. The authors acknowledge the support of the Bioinformatics Centre, Savitribai Phule Pune University, Pune, for providing the Schrodinger software for FDA drugs docking calculations.

Disclosure statement

No potential conflict of interest was reported by the authors.

Author contributions

Conceived and designed the experiments: SP; Performed the experiments: KL, SP and SM; Analyzed the data: KL, SP and SM; Wrote the manuscript: KL, SP and SM; Proofread of final version: KL, SP, NN and SKV.

Additional information

Funding

This work received funding from Dr. D. Y. Patil Vidyapeeth, Pune (DPU/421/2018).