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AMPing up the Search: A Structural and Functional Repository of Antimicrobial Peptides (AMPs) for Biofilm Studies (Biofilm-AMP), and a Case Study of its Application to Corynebacterium striatum, an Emerging Pathogen
CC BY-NC-ND 4.0 · Indian J Med Paediatr Oncol 2022; 43(S 01): S1-S19
DOI: DOI: 10.1055/s-0042-1755507
Correspondence to: karishmaskaushik@unipune.ac.in
Background: Antimicrobial peptides (AMPs) have been recognized for their ability to target crucial biofilm formation processes. Identifying potential AMP candidates remains a significant challenge, necessitating preliminary in silico studies prior to in vitro and in vivo studies.
Materials and Methods: We have developed biofilm-AMP (B-AMP), a curated 3D structural repository of AMPs, focusing on AMPs relevant to biofilm studies. To demonstrate the user applicability of B-AMP, we use the sortase C biofilm target of the emerging pathogen Corynebacterium striatum as a case study.
Results: B-AMP contains predicted 3D structural models of 5544 AMPs (from the DRAMP database) generated with a suite of molecular modelling tools, with user friendly, multioption search capabilities. AMPs are annotated to existing biofilm literature, consisting of over 10,000 publications, enhancing the functional capabilities of B-AMP. For the case study, 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. We propose a preference scale based on docking scores and interacting residues to select candidate AMPs for further evaluation.
Conclusion: B-AMP (https://b-amp.karishmakaushiklab.com/) is a comprehensive structural and functional repository of AMPs, serving as a starting point for future studies on AMPs in biofilms. B-AMP will be regularly updated with AMP structures, interaction models with potential biofilm targets, and annotations to biofilm literature.
Publication History
Article published online:
22 August 2022
© 2022. Indian Society of Medical and Paediatric Oncology. This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. (https://creativecommons.org/licenses/by-nc-nd/4.0/)
Thieme Medical and Scientific Publishers Pvt. Ltd.
A-12, 2nd Floor, Sector 2, Noida-201301 UP, India
Correspondence to: karishmaskaushik@unipune.ac.in
Background: Antimicrobial peptides (AMPs) have been recognized for their ability to target crucial biofilm formation processes. Identifying potential AMP candidates remains a significant challenge, necessitating preliminary in silico studies prior to in vitro and in vivo studies.
Materials and Methods: We have developed biofilm-AMP (B-AMP), a curated 3D structural repository of AMPs, focusing on AMPs relevant to biofilm studies. To demonstrate the user applicability of B-AMP, we use the sortase C biofilm target of the emerging pathogen Corynebacterium striatum as a case study.
Results: B-AMP contains predicted 3D structural models of 5544 AMPs (from the DRAMP database) generated with a suite of molecular modelling tools, with user friendly, multioption search capabilities. AMPs are annotated to existing biofilm literature, consisting of over 10,000 publications, enhancing the functional capabilities of B-AMP. For the case study, 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. We propose a preference scale based on docking scores and interacting residues to select candidate AMPs for further evaluation.
Conclusion: B-AMP (https://b-amp.karishmakaushiklab.com/) is a comprehensive structural and functional repository of AMPs, serving as a starting point for future studies on AMPs in biofilms. B-AMP will be regularly updated with AMP structures, interaction models with potential biofilm targets, and annotations to biofilm literature.
No conflict of interest has been declared by the author(s).
Publication History
Article published online:
22 August 2022
© 2022. Indian Society of Medical and Paediatric Oncology. This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. (https://creativecommons.org/licenses/by-nc-nd/4.0/)
Thieme Medical and Scientific Publishers Pvt. Ltd.
A-12, 2nd Floor, Sector 2, Noida-201301 UP, India