PyAMPA: a high-throughput prediction and optimization tool for antimicrobial peptides

Mostra el registre complet Registre parcial de l'ítem

• dc.contributor.author Ramos Llorens, Marc
• dc.contributor.author Bello Madruga, Roberto
• dc.contributor.author Valle, Javier
• dc.contributor.author Andreu Martínez, David
• dc.contributor.author Torrent Burgas, Marc
• dc.date.accessioned 2024-09-17T06:24:28Z
• dc.date.available 2024-09-17T06:24:28Z
• dc.date.issued 2024
• dc.description.abstract The alarming rise of antibiotic-resistant bacterial infections is driving efforts to develop alternatives to conventional antibiotics. In this context, antimicrobial peptides (AMPs) have emerged as promising candidates for their ability to target a broad range of microorganisms. However, the development of AMPs with optimal potency, selectivity, and/or stability profiles remains a challenge. To address it, computational tools for predicting AMP properties and designing novel peptides have gained increasing attention. PyAMPA is a novel platform for AMP discovery. It consists of five modules, namely AMPScreen, AMPValidate, AMPSolve, AMPMutate, and AMPOptimize, that allow high-throughput proteome inspection, candidate screening, and optimization through point-mutation and genetic algorithms. The platform also offers additional tools for predicting and evaluating AMP properties, including antimicrobial and cytotoxic activity, and peptide half-life. By providing innovative and accessible inroads into AMP motifs in proteomes, PyAMPA will enable advances in AMP development and potential translation into clinically useful molecules. PyAMPA is available at: https://github.com/SysBioUAB/PyAMPA. Importance: This paper introduces PyAMPA, a new bioinformatics platform designed for the discovery and optimization of antimicrobial peptides (AMPs). It addresses the urgent need for new antimicrobials due to the rise of antibiotic-resistant infections. PyAMPA, with its five predictive modules -AMPScreen, AMPValidate, AMPSolve, AMPMutate and AMPOptimize, enables high-throughput screening of proteomes to identify potential AMP motifs and optimize them for clinical use. Its unique approach, combining prediction, design, and optimization tools, makes PyAMPA a robust solution for developing new AMP-based therapies, offering a significant advance in combatting antibiotic resistance.
• dc.description.sponsorship Grants from MCIN, Spanish Ministry of Science and Innovation (PID2020-113184RB-C22/AEI/10.13039/501100011033 to D.A. and PID2020-114627RB-I00/AEI/10.13039/501100011033 to M.T. were funded by MCIN/AEI; PDC2021-121544-I00/AEI/10.13039/501100011033 to M.T. was funded by MCIN/AEI and European Union Next GenerationEU/ PRTR). Work at UPF was also supported by La Caixa Health Foundation (grant HR17-00409 to D.A.) and by MCIN “María de Maeztu” Program for Units of Excellence in R&D (CEX2018-000792-M) to the UPF Department of Medicine and Life Sciences at (MELIS-UPF). Work at UAB was further supported by a 2022 grant from the European Society of Clinical Microbiology and Infectious Diseases (ESCMID). R.B.M. is recipient of a pre-doctoral FPI scholarship (PRE2021-097678) from the Spanish Ministerio de Ciencia e Innovación.
• dc.format.mimetype application/pdf
• dc.identifier.citation Ramos-Llorens M, Bello-Madruga R, Valle J, Andreu D, Torrent M. PyAMPA: a high-throughput prediction and optimization tool for antimicrobial peptides. mSystems. 2024 Jul 23;9(7):e0135823. DOI: 10.1128/msystems.01358-23
• dc.identifier.doi http://dx.doi.org/10.1128/msystems.01358-23
• dc.identifier.issn 2379-5077
• dc.identifier.uri http://hdl.handle.net/10230/61110
• dc.language.iso eng
• dc.publisher American Society for Microbiology
• dc.relation.ispartof mSystems. 2024 Jul 23;9(7):e0135823
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-113184RB-C22
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-114627RB-I00
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PDC2021-121544-I00
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/CEX2018-000792-M
• dc.rights © 2024 Ramos-Llorens et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/).
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Antimicrobial peptide
• dc.title PyAMPA: a high-throughput prediction and optimization tool for antimicrobial peptides
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion