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

Shreeya Mhade; Stutee Panse; Gandhar Tendulkar; Rohit Awate; Yatindrapravanan Narasimhan; Snehal Kadam; Ragothaman M Yennamalli; Karishma S Kaushik

doi:10.3389/fcimb.2021.803774

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

Front Cell Infect Microbiol. 2021 Dec 16:11:803774. doi: 10.3389/fcimb.2021.803774. eCollection 2021.

Authors

Shreeya Mhade¹, Stutee Panse², Gandhar Tendulkar³, Rohit Awate⁴, Yatindrapravanan Narasimhan⁵, Snehal Kadam⁶, Ragothaman M Yennamalli⁵, Karishma S Kaushik⁷

Affiliations

¹ Department of Bioinformatics, Guru Nanak Khalsa College of Arts, Science and Commerce (Autonomous), Mumbai, India.
² Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, College State, PA, United States.
³ 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.
⁴ Khoury College of Computer Sciences, Northeastern University, Boston, MA, United States.
⁵ Department of Bioinformatics, School of Chemical and Biotechnology, Shanmugha Arts, Science, Technology & Research Academy (SASTRA), Deemed to Be University, Thanjavur, India.
⁶ Hull York Medical School, University of Hull, Hull, United Kingdom.
⁷ Department of Biotechnology, Savitribai Phule Pune University, Pune, India.

Abstract

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.

Keywords: antimicrobial peptides; biofilms; curated database; functional annotation; molecular docking; molecular modeling; structural repository.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Antimicrobial Peptides* / chemistry
Antimicrobial Peptides* / pharmacology
Biofilms*
Corynebacterium*
Molecular Docking Simulation

Substances

Antimicrobial Peptides

Supplementary concepts

Corynebacterium striatum