Deployment of in-silico analysis to reveal the antibacterial profiles of Allium sativum against Aeromonas hydrophila

Abstract

The key challenges in aquaculture are the emergence of antimicrobial resistance in fish cultivation due to the frequent use of antibiotics. Over the past three decades, this led to a major threat in the persistence of multidrug-resistant bacteria. Aeromonas hydrophila is a Gram-negative bacterium, a common causative agent of motile bacterial septicemia in fisheries. Combining these two key factors of the presented narrative, the essential type II topoisomerase enzyme ‘DNA gyrase’ (encoded by the gyrA and gyrB genes) as a potential drug target in Aeromonas hydrophila was taken, retrieve its sequence from UniProtKB (Id-A0KKQ2), constructs the 3-D structure using SWISS-MODEL (in absence of the experimental structure), and performs an in-silico screening of selected drug-like compounds (25 antibacterial phytochemicals) most of which are bioactive compounds of A. sativum through molecular docking. Quercetin a derivative of A. sativum was observed as a more potent drug molecule than other studied molecules based on ligand binding energy as docking score −7.812, showed highly encouraging results, supported by a study using structural dynamics of the receptor-ligand complex for a duration of 100 ns by Molecular Dynamic Simulations and confirm binding stability with MM-GBSA calculations. This study also provides theoretical grounds for drug discovery against other pathogenic bacteria posing threats to the ecosystem. Switching to herbal products is the best way to combat the plurality of problems to avoid seen or unseen post-treatment side effects.

Communicated by Ramaswamy H. Sarma

Keywords:

• Aeromonas hydrophila
• allium sativum
• bacterial septicemia
• DNA gyrase
• molecular docking
• MD simulation
• quercetin
• Prime-MMGBSA

Acknowledgements

We would like to express our gratitude to Amity Institute of Biotechnology, Amity University, Lucknow Campus, and team Schrodinger for their support. We would also like to thank everyone who helped us, directly or indirectly. We are appreciative of the help that bioinformatics tools, software, and databases have given us.

Ethics issues

Not applicable. No ethical approval is needed.

Disclosure statement

We certify that none of our known financial or interpersonal conflicts may have seemed to have an impact on the research presented in this paper.

Authors' contributions

Mahendra Kumar Savita was concerned with the experiments’ conception and design, execution, data analysis, creation of figures and/or tables, and writing or reviewing early versions of the publication.

The experiments were created and planned by Vinay Dwivedi, who also examined the data, evaluated early versions of the manuscript, and allowed the final version.

The experiments were created and planned by Prachi Srivastava, who also wrote or evaluated earlier versions of the manuscript and conveyed her final approval.

Additional information

Funding

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