AMPing Up the Search: A Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies, and a Case Study of Its Application to Corynebacterium striatum , an Emerging Pathogen.

Autor:	Mhade S; Department of Bioinformatics, Guru Nanak Khalsa College of Arts, Science and Commerce (Autonomous), Mumbai, India., Panse S; Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, College State, PA, United States., Tendulkar G; Department of Bioinformatics, Sir Sitaram and Lady Shantabai Patkar College of Arts and Science and V P Varde College of Commerce and Economics (Autonomous), Mumbai, India., Awate R; Khoury College of Computer Sciences, Northeastern University, Boston, MA, United States., Narasimhan Y; Department of Bioinformatics, School of Chemical and Biotechnology, Shanmugha Arts, Science, Technology & Research Academy (SASTRA), Deemed to Be University, Thanjavur, India., Kadam S; Hull York Medical School, University of Hull, Hull, United Kingdom., Yennamalli RM; Department of Bioinformatics, School of Chemical and Biotechnology, Shanmugha Arts, Science, Technology & Research Academy (SASTRA), Deemed to Be University, Thanjavur, India., Kaushik KS; Department of Biotechnology, Savitribai Phule Pune University, Pune, India.
Jazyk:	angličtina
Zdroj:	Frontiers in cellular and infection microbiology [Front Cell Infect Microbiol] 2021 Dec 16; Vol. 11, pp. 803774. Date of Electronic Publication: 2021 Dec 16 (Print Publication: 2021).
DOI:	10.3389/fcimb.2021.803774
Abstrakt:	Antimicrobial peptides (AMPs) have been recognized for their ability to target processes important for biofilm formation. Given the vast array of AMPs, identifying potential anti-biofilm candidates remains a significant challenge, and prompts the need for preliminary in silico investigations prior to extensive in vitro and in vivo studies. We have developed Biofilm-AMP (B-AMP), a curated 3D structural and functional repository of AMPs relevant to biofilm studies. In its current version, B-AMP contains predicted 3D structural models of 5544 AMPs (from the DRAMP database) developed using a suite of molecular modeling tools. The repository supports a user-friendly search, using source, name, DRAMP ID, and PepID (unique to B-AMP). Further, AMPs are annotated to existing biofilm literature, consisting of a vast library of over 10,000 articles, enhancing the functional capabilities of B-AMP. To provide an example of the usability of B-AMP, we use the sortase C biofilm target of the emerging pathogen Corynebacterium striatum as a case study. For this, 100 structural AMP models from B-AMP were subject to in silico protein-peptide molecular docking against the catalytic site residues of the C. striatum sortase C protein. Based on docking scores and interacting residues, we suggest a preference scale using which candidate AMPs could be taken up for further in silico , in vitro and in vivo testing. The 3D protein-peptide interaction models and preference scale are available in B-AMP. B-AMP is a comprehensive structural and functional repository of AMPs, and will serve as a starting point for future studies exploring AMPs for biofilm studies. B-AMP is freely available to the community at https://b-amp.karishmakaushiklab.com and will be regularly updated with AMP structures, interaction models with potential biofilm targets, and annotations to biofilm literature. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2021 Mhade, Panse, Tendulkar, Awate, Narasimhan, Kadam, Yennamalli and Kaushik.)
Databáze:	MEDLINE
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