Mining the heparinome for cryptic antimicrobial peptides that selectively kill Gram-negative bacteria

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• dc.contributor.author Bello Madruga, Roberto
• dc.contributor.author Sandín, Daniel
• dc.contributor.author Valle, Javier
• dc.contributor.author Gómez Borrego, Jordi
• dc.contributor.author Comas, Laura
• dc.contributor.author Larrosa, María Nieves
• dc.contributor.author González-López, Juan José
• dc.contributor.author Jiménez, María Ángeles
• dc.contributor.author Andreu Martínez, David
• dc.contributor.author Torrent Burgas, Marc
• dc.date.accessioned 2025-06-13T07:47:06Z
• dc.date.available 2025-06-13T07:47:06Z
• dc.date.issued 2025
• dc.description Data de publicació electrònica: 23-05-2025
• dc.description.abstract Glycosaminoglycan (GAG)-binding proteins regulating essential processes such as cell growth and migration are essential for cell homeostasis. As both GAGs and the lipid A disaccharide core of Gram-negative bacteria contain negatively charged disaccharide units, we hypothesized that GAG-binding proteins could also recognize LPS and enclose cryptic antibiotic motifs. Here, we report novel antimicrobial peptides (AMPs) derived from heparin-binding proteins (HBPs), with specific activity against Gram-negative bacteria and high LPS binding. We used computational tools to locate antimicrobial regions in 82% of HBPs, most of those colocalizing with putative heparin-binding sites. To validate these results, we synthesized five candidates [HBP-1-5] that showed remarkable activity against Gram-negative bacteria, as well as a strong correlation between heparin and LPS binding. Structural characterization of these AMPs shows that heparin or LPS recognition promotes a conformational arrangement that favors binding. Among all analogs, HBP-5 displayed the highest affinity for both heparin and LPS, with antimicrobial activities against Gram-negative bacteria at the nanomolar range. These results suggest that GAG-binding proteins are involved in LPS recognition, which allows them to act also as antimicrobial proteins. Some of the peptides reported here, particularly HBP-5, constitute a new class of AMPs with specific activity against Gram-negative bacteria.
• dc.description.sponsorship Financial support from the Spanish Ministry of Economy and Innovation (PDC2021-121544-I00 funded by MCIN/AEI/10.13039/501100011033 and European Union Next Generation EU/ PRTR to MT; project PID2020-114627RB-I00 funded by MCIN/AEI/10.13039/501100011033 to MT; PID2020-112821GB-I00 funded by MCIN/AEI/10.13039/501100011033 to MAJ and PID2020-113184RB-C22 to DA), the Departament de Recerca i Universitats de la Generalitat de Catalunya (2023PROD00021 to MT), and from La Caixa Banking Foundation (HR17-00409, to DA). This work has been co-financed by the Spanish Ministry of Science and Innovation with funds from the European Union Next Generation EU, from the Recovery, Transformation and Resilience Plan (PRTR-C17.I1), European Society of Clinical Microbiology and Infectious Diseases (ESCMID) ESCMID2022 and from the Autonomous Community of Catalonia within the framework of the Biotechnology Plan Applied to Health. Work at UPF was funded by the MCI María de Maeztu network of Units of Excellence. NMR experiments were performed in the “Manuel Rico” NMR laboratory (LMR) of the Spanish National Research Council (CSIC), a node of the Spanish Large-Scale National Facility (ICTS R-LRB). DS and RBM are recipients of pre-doctoral a FPI scholarship (PRE2018-083243 and PRE2021-097678, respectively) from the Spanish Ministry of Science and Innovation.
• dc.format.mimetype application/pdf
• dc.identifier.citation Bello-Madruga R, Sandín D, Valle J, Gómez J, Comas L, Larrosa MN, et al. Mining the heparinome for cryptic antimicrobial peptides that selectively kill Gram-negative bacteria. Mol Syst Biol. 2025 May 23. DOI: 10.1038/s44320-025-00120-6
• dc.identifier.doi http://dx.doi.org/10.1038/s44320-025-00120-6
• dc.identifier.issn 1744-4292
• dc.identifier.uri http://hdl.handle.net/10230/70682
• dc.language.iso eng
• dc.publisher EMBO Press
• dc.relation.ispartof Mol Syst Biol. 2025 May 23
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PDC2021-121544-I00
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-114627RB-I00
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-112821GB-I00
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-113184RB-C22
• dc.rights © 2025 The Author(s). Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Antimicrobial peptide
• dc.subject.keyword Glycosaminoglycans
• dc.subject.keyword Heparin
• dc.subject.keyword Heparin-binding protein
• dc.subject.keyword Lipopolysaccharide
• dc.title Mining the heparinome for cryptic antimicrobial peptides that selectively kill Gram-negative bacteria
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion