https://doi.org/10.4081/jbr.2025.13130
Bioinformatics exploration of identified garlic-derived antimicrobial peptides: a food-based approach to quorum sensing inhibition in foodborne pathogens
Submitted: September 20, 2024
Accepted: December 31, 2024
Published: January 22, 2025
Accepted: December 31, 2024
Abstract Views: 4778
PDF: 690
Supplementary Materials: 684
Supplementary Materials: 684
Publisher's note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.
Authors
The growing frequency of antibiotic-resistant microorganisms requires novel antimicrobial methods. Quorum Sensing (QS), a bacterial communication system, is critical for controlling virulence factors and biofilm development, contributing to many foodborne bacteria' pathogenicity. Garlic, a natural substance, is a widely consumed plant with antimicrobial properties and antibacterial capabilities, although its peptide components are poorly unknown. This study evaluated garlic-derived peptides' ability to inhibit QS in foodborne bacteria. Two garlic-derived peptides, including VS-9 and F3-3-c, undergo bioinformatics research to determine their structural features, bioactivity, physicochemical parameters, and potential interactions with target modeled proteins of LasR QS from Pseudomonas aeruginosa, Biofilm-associated surface protein (Baps) from Staphylococcus aureus, and sortase A (SrtA) from Staphylococcus aureus. VS-9 has the most favorable structure properties, which could be essential for its inhibitory activity against LasR, Baps, and SrtA proteins. We have modeled, characterized, and docked garlic-derived peptides to assess their antimicrobial properties. Even though VS-9 showed more anti QS activity than F3-3-c, more research is needed to fully understand their mechanisms of action and maximize their therapeutic potential.
Papenfort K, Bassler BL. Quorum sensing signal–response systems in Gram-negative bacteria. Nat Rev Microbiol 2016; 14:576–88.
DOI: https://doi.org/10.1038/nrmicro.2016.89
Sahoo A, Swain SS, Behera A, et al. Antimicrobial peptides derived from insects offer a novel therapeutic option to combat biofilm. Rev Front Microbiol 2021;12:661195.
DOI: https://doi.org/10.3389/fmicb.2021.661195
Rutherford ST, Bassler BL. Bacterial quorum sensing: its role in virulence and possibilities for its control. Cold Spring Harb Perspect Med 2012;2:a012427.
DOI: https://doi.org/10.1101/cshperspect.a012427
Bronesky D, Wu Z, Marzi S, et al P. Staphylococcus aureus RNAIII and Its regulon link quorum sensing, stress responses, metabolic adaptation, and regulation of virulence gene expression. Annu Rev Microbiol 2016;70:299–6.
DOI: https://doi.org/10.1146/annurev-micro-102215-095708
Kessler E, Safrin M, Olson JC, Ohman DE. Secreted LasA of Pseudomonas aeruginosa is a staphylolytic protease. J Biol Chem 1993;268:7503–8.
DOI: https://doi.org/10.1016/S0021-9258(18)53203-8
Bolken TC, Franke CA, Jones KF, et al. Inactivation of the srtA gene in Streptococcus gordonii inhibits cell wall anchoring of surface proteins and decreases in vitro and in vivo adhesion. Infect Immun 2001;69:75–80.
DOI: https://doi.org/10.1128/IAI.69.1.75-80.2001
Pallen MJ, Lam AC, Antonio M, Dunbar K. An embarrassment of sortases - a richness of substrates? Trends Microbiol 2001;9:97–2.
DOI: https://doi.org/10.1016/S0966-842X(01)01956-4
Cossart P, Jonquières R. Sortase, a universal target for therapeutic agents against gram-positive bacteria? Proc Natl Acad Sci USA 2000;97:5013–5.
DOI: https://doi.org/10.1073/pnas.97.10.5013
JamunaBai A, Rai VR. Bacterial quorum sensing and food industry. Compr Rev Food SciF 2011;10:183–93.
DOI: https://doi.org/10.1111/j.1541-4337.2011.00150.x
Bridier A, Sanchez-Vizuete P, Guilbaud M, et al. Biofilm-associated persis tence of food-borne pathogens. Food Microbiol 2015;45:167–78.
DOI: https://doi.org/10.1016/j.fm.2014.04.015
Parker CT, Sperandio V. Cell-to-cell signalling during pathogenesis. Cell Microbiol 2009;11:363–69.
DOI: https://doi.org/10.1111/j.1462-5822.2008.01272.x
Ma J, Cheng X, Xu Z, et al. Structural mechanism for modulation of functional amyloid and biofilm formation by Staphylococcal Bap protein switch. EMBO J 2021;40:e107500.
DOI: https://doi.org/10.15252/embj.2020107500
Mulder KC, Lima LA, Miranda VJ, et al. Current scenario of peptide-based drugs: the key roles of cationic antitumor and antiviral peptides. Front Microbiol 2013;4:321.
DOI: https://doi.org/10.3389/fmicb.2013.00321
Nassimi Z, Taheri P, Kong X, et al. The antimicrobial peptide AsR416 can inhibit the growth, sclerotium formation and virulence of Rhizoctonia solani AG1-IA. Eur J Plant Pathol 2021;160:469–85.
DOI: https://doi.org/10.1007/s10658-021-02257-0
Melo MN, Ferre R, Castanho MARB. Antimicrobial peptides: linking partition, activity and high membrane-bound concentrations. Nat Rev Microbiol 2009;7:245–50.
DOI: https://doi.org/10.1038/nrmicro2095
Izadpanah A, Gallo RL. Antimicrobial peptides. J Am Acad Dermatol 2005;52:381–90.
DOI: https://doi.org/10.1016/j.jaad.2004.08.026
Lombardi L, Falanga A, Del Genio V, Galdiero S. A new hope: self-assembling peptides with antimicrobial activity. Pharmaceutics. Pharmaceutics 2019;11:66.
DOI: https://doi.org/10.3390/pharmaceutics11040166
Vlase L, Parvu M, Parvu E.A, Toiu A. Chemical constituents of three Allium species from Romania. Molecules 2013;18:114–27.
DOI: https://doi.org/10.3390/molecules18010114
Amagase H, Petesch BL, Matsuura H, et al. Intake of Garlic and its bioactive components. J Nutr 2001;31:955S-62S.
DOI: https://doi.org/10.1093/jn/131.3.955S
Sasi M, Kumar S, Kumar M, et al. Garlic (Allium sativum L.) bioactives and its role in alleviating oral pathologies. Antioxidants 2021;10:11.
DOI: https://doi.org/10.3390/antiox10111847
Kodera Y, Ushijima M, Amano H, et al. Chemical and biological properties of s-1-propenyl-l-cysteine in aged garlic extract. Molecules 2017;22:1–18.
DOI: https://doi.org/10.3390/molecules22040570
Yu X, Lim CYX, Dong B, Hadinoto K. Development of magnetic solid phase extraction platform for the purification of bioactive γ-glutamyl peptides from garlic (Allium sativum). LWT 2020 1;127:109410.
DOI: https://doi.org/10.1016/j.lwt.2020.109410
Ejike CECC, Collins SA, Balasuriya N, et al. Prospects of microalgae proteins in producing peptide-based functional foods for promoting cardiovascular health. Trends Food Sci Technol 2017;59:30–6.
DOI: https://doi.org/10.1016/j.tifs.2016.10.026
Okagu IU, Ezeorba TPC, Aham EC, et al. Recent findings on the cellular and molecular mechanisms of action of novel food- derived antihypertensive peptides. Food Chem Oxf 2022;4:100078.
DOI: https://doi.org/10.1016/j.fochms.2022.100078
Gao X, Chen Y, Chen Z, et al. Identification and antimicrobial activity evaluation of three peptides from laba garlic and the related mechanism. Food Funct 2019;4486–96.
DOI: https://doi.org/10.1039/C9FO00236G
Rasaratnam K, Nantasenamat C, Phaonakrop et al. A novel peptide isolated from garlic shows anti-cancer effect against leukemic cell lines via interaction with Bcl-2 family proteins. Chem Biol Drug Des 2021;97:1017–28.
DOI: https://doi.org/10.1111/cbdd.13831
Kangueane P, Nilofer C. Protein-Protein Binding. In: Kangueane P, Nilofer C, editors. Protein-Protein and Domain-Domain Interactions. Singapore: Springer Singapore; 2018. p. 15–33. Available from: https://doi.org/10.1007/978-981-10-7347-2_2
DOI: https://doi.org/10.1007/978-981-10-7347-2_2
Bakail M, Ochsenbein F. Targeting protein–protein interactions, a wide open field for drug design. C R Chim 2016;19:19–27.
DOI: https://doi.org/10.1016/j.crci.2015.12.004
Dong Xu, Yang Zhang. Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J 2011;101:2525–34.
DOI: https://doi.org/10.1016/j.bpj.2011.10.024
Nakamura T, Furunaka H, Miyata T, et al. Tachyplesin, a class of antimicrobial peptide from the hemocytes of the horseshoe crab (Tachypleus tridentatus). Isolation and chemical structure. J Biol Chem 1988;263:16709–13.
DOI: https://doi.org/10.1016/S0021-9258(18)37448-9
Wiederstein Sippl. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 2007;35:W407–10.
DOI: https://doi.org/10.1093/nar/gkm290
Doytchinova IA, Flower DR. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinform 2007;8:4.
DOI: https://doi.org/10.1186/1471-2105-8-4
Mooney C, Haslam NJ, Pollastri G, Shields DC. Towards the improved discovery and design of functional peptides: common features of diverse classes permit generalized prediction of bioactivity. PLoS One 2012;7:e45012.
DOI: https://doi.org/10.1371/journal.pone.0045012
Gupta S, Kapoor P, Chaudhary K, et al. Open source drug discovery consortium; Raghava, G. P. S. In silico approach for predicting toxicity of peptides and proteins. PLoS One 2013;13:e73957.
DOI: https://doi.org/10.1371/journal.pone.0073957
Yan Y, Zhan, D, Zho P, et al. HDOCK: web server for protein-protein and protein- DNA/RNA docking based on hybrid strategy. Nucleic Acids Res 2017;45:W365.
DOI: https://doi.org/10.1093/nar/gkx407
Yan Y, Tao H, He J, Huang SY. The HDOCK server for integrated protein–protein docking. Nat Protoc 2020;15:1829–52.
DOI: https://doi.org/10.1038/s41596-020-0312-x
Newell DG, Koopmans M, Verhoef L, et al. Food-borne diseases—The challenges of 20 years ago persist while new ones continue to emerge. Int J Food Microbiol 2010;139:S3–15.
DOI: https://doi.org/10.1016/j.ijfoodmicro.2010.01.021
Wimley WC, Hristova K. Antimicrobial peptides: successes, challenges and unanswered questions. J Membr Biol 2011;239:27–34.
DOI: https://doi.org/10.1007/s00232-011-9343-0
Gao X, Wang C, Chen Z, Chen Y, et al. Effects of N-trans-feruloyltyramine isolated from laba garlic on antioxidant, cytotoxic activities and H2O2-induced oxidative damage in HepG2 and L02 cells. Food Chem Toxicol 2019;130:130–41.
DOI: https://doi.org/10.1016/j.fct.2019.05.021
Eijlande RT, Abee T, Kuipers OP. Bacterial spores in food: How phenotypic variability complicates prediction of spore properties and bacterial behavior. Curr Opin Biotechnol 2011;22:180–86.
DOI: https://doi.org/10.1016/j.copbio.2010.11.009
Gharsallaoui A, Oulahal N, Joly C, Degraeve P. Nisin as a food preservative: Part 1: Physicochemical properties, antimicrobial activity, and main uses. Crit Rev Food Sci Nutr 2016;56:1262–74.
DOI: https://doi.org/10.1080/10408398.2013.763765
Liu F, Baggerman G, Schoofs L, Wets G. The construction of a bioactive peptide database in Metazoa. J Proteome Res 2008;7:4119–31.
DOI: https://doi.org/10.1021/pr800037n
Bai B, Chen LL, Li QL, et al. Preparation and functional exploration of cysteine peptides from fresh garlic scales for improving bioavailability of food legume iron and zinc. Chin J Anal Chem 2014;42:1507–12.
DOI: https://doi.org/10.1016/S1872-2040(14)60776-3
Craik DJ, Fairlie DP, Liras S, Price, D. The future of peptide-based drugs. Chem Biol Drug Des 2013;81:136–47.
DOI: https://doi.org/10.1111/cbdd.12055
Ciemny M, Kurcinski M, Kamel K, et al. Protein–peptide docking: opportunities and challenges. Drug Discov Today 2018;23:1530–37.
DOI: https://doi.org/10.1016/j.drudis.2018.05.006
How to Cite
Dahab, M., & Aladhadh, M. (2025). Bioinformatics exploration of identified garlic-derived antimicrobial peptides: a food-based approach to quorum sensing inhibition in foodborne pathogens. Journal of Biological Research - Bollettino Della Società Italiana Di Biologia Sperimentale. https://doi.org/10.4081/jbr.2025.13130
Copyright (c) 2025 the Author(s)
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
PAGEPress has chosen to apply the Creative Commons Attribution NonCommercial 4.0 International License (CC BY-NC 4.0) to all manuscripts to be published.