{ "abstract": "Background\n\nCommunity-acquired pneumonia (CAP) remains a major global health concern. Mycoplasma pneumoniae (M. pneumoniae) and Chlamydia pneumoniae (C. pneumoniae) are important atypical CAP pathogens, and reported coinfection may complicate diagnosis and management. However, no licensed vaccine simultaneously targeting both pathogens is currently available. In this context, mRNA-based multi-epitope vaccines represent a promising platform for bivalent vaccine design because they allow the integration of multiple epitopes into a single construct and may support both humoral and cellular immune responses. This study aimed to design bivalent multi-epitope mRNA vaccine candidates against M. pneumoniae and C. pneumoniae using an immunoinformatics-based strategy.Methods\n\nConserved cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and linear B lymphocyte (LBL) epitopes were screened from selected antigenic proteins. Two constructs, MCV1 and MCV2, were assembled with distinct N-terminal immunostimulatory or helper-epitope modules and evaluated for antigenicity, safety, physicochemical and structural properties, receptor docking, three independent 100-ns molecular dynamics simulations, replicate-level MM-PBSA, immune simulation, population coverage, human codon optimization, and RNA secondary structure.Results\n\nA total of 11 CTL, 5 HTL, and 14 LBL epitopes with ≥ 90% conservancy among the analyzed strain sequences were selected. Both core constructs were predicted to be antigenic, non-toxic, non-allergenic, and structurally acceptable. HADDOCK refinement yielded cluster-level scores of - 394.3 ± 7.3 for MCV1-TLR2 and - 399.0 ± 5.5 for the exploratory MCV2-TLR4 complex. Across three independent trajectories, MM-PBSA total binding free energies were - 125.19 ± 20.13 and - 126.87 ± 12.73 kcal/mol, respectively. C-ImmSim generated modeled profiles involving humoral and cellular immune components, and the estimated global population coverage was 97.90%. Human codon optimization yielded codon adaptation index values of 0.92 and 0.91 and GC contents of 61.06% and 60.94% for MCV1 and MCV2, respectively.Conclusion\n\nIn this in silico study, two bivalent multi-epitope mRNA vaccine candidates against M. pneumoniae and C. pneumoniae were computationally prioritized. These findings provide a theoretical basis for subsequent experimental validation, while in vitro and in vivo studies are still required to verify their actual immunogenicity, protective efficacy, and safety.", "abstract_shown": true, "affiliations": [ "Department of Respiratory Medicine, Center of Respiratory Medicine, Clinical Research Center for Respiratory Disease, Xiangya Hospital, National Key Clinical Specialty, Branch of National, Central South University, Changsha, 410008, Hunan, China.", "Clinical Research Center for Respiratory Diseases in Hunan Province, Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.", "National Clinical Research Center for Geriatric Disease, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.", "Department of Respiratory and Critical Care Medicine, General Hospital of Beitun City, Xinjiang Production and Construction Corps, 10th Division, No. 979 Bowang East Street, Beitun, 836099, Xinjiang, China.", "Department of Respiratory Medicine, Center of Respiratory Medicine, Clinical Research Center for Respiratory Disease, Xiangya Hospital, National Key Clinical Specialty, Branch of National, Central South University, Changsha, 410008, Hunan, China. 2204150422@csu.edu.cn.", "Clinical Research Center for Respiratory Diseases in Hunan Province, Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. 2204150422@csu.edu.cn.", "National Clinical Research Center for Geriatric Disease, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. 2204150422@csu.edu.cn.", "Department of Respiratory Medicine, Center of Respiratory Medicine, Clinical Research Center for Respiratory Disease, Xiangya Hospital, National Key Clinical Specialty, Branch of National, Central South University, Changsha, 410008, Hunan, China. pinhuapan668@csu.edu.cn.", "Clinical Research Center for Respiratory Diseases in Hunan Province, Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. pinhuapan668@csu.edu.cn.", "National Clinical Research Center for Geriatric Disease, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. pinhuapan668@csu.edu.cn.", "Furong Laboratory, Changsha, 410078, Hunan, China. pinhuapan668@csu.edu.cn." ], "article_type": "research article", "arxiv": null, "author_total": 10, "authors": [ { "affs": [ 0, 1, 2 ], "name": "Xu Wu", "orcid": "0009-0002-4692-5781" }, { "affs": [ 0, 1, 2 ], "name": "Yizhong Xu" }, { "affs": [ 0, 3 ], "name": "Weiwei Zhao" }, { "affs": [ 0, 1, 2 ], "name": "Rongliu Qin" }, { "affs": [ 0, 1, 2 ], "name": "Yuying Luo" }, { "affs": [ 0, 1, 2 ], "name": "Yanqun Hou" }, { "affs": [ 0, 1, 2 ], "name": "Ziyou Zhou" }, { "affs": [ 0, 1, 2 ], "name": "Shiyang Ma" }, { "affs": [ 4, 5, 6 ], "name": "Fei Zhu", "orcid": "0000-0002-9201-8069" }, { "affs": [ 7, 8, 9, 10 ], "name": "Pinhua Pan", "orcid": "0000-0001-5883-0531" } ], "bibtex": "https://research.draconitic.com/paper/bmfxqym80cgn6.bib", "cited_by": 0, "doi": "10.1186/s12866-026-05473-y", "fulltext_url": "https://europepmc.org/articles/PMC13729508", "id": "bmfxqym80cgn6", "issns": [ "1471-2180" ], "landing_url": "https://europepmc.org/article/MED/42972530", "language": "eng", "licence": "CC-BY", "licence_label": "CC BY", "licence_source": "article", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1312|vaccines and immunoinformatics approaches" ] ], "openalex": "W7197004574", "pdf_url": "https://europepmc.org/articles/PMC13729508?pdf=render", "pmcid": "PMC13729508", "pmid": "42972530", "published": "2026-08-06", "publisher": null, "ris": "https://research.draconitic.com/paper/bmfxqym80cgn6.ris", "sources": [ { "first_seen": "2026-11-04T15:20:44Z", "native_id": "MED:42972530", "source": "europepmc", "url": "https://europepmc.org/article/MED/42972530" } ], "subjects": [ { "field": "biochemistry", "origin": "openalex:1312|vaccines and immunoinformatics approaches", "subfield": "molecular-biology" } ], "title": "In silico design of bivalent multi-epitope mRNA vaccine candidates against Mycoplasma pneumoniae and Chlamydia pneumoniae.", "title_text": "In silico design of bivalent multi-epitope mRNA vaccine candidates against Mycoplasma pneumoniae and Chlamydia pneumoniae.", "type": "peer-reviewed", "updated_at": "2026-11-05T03:20:56Z", "url": "https://research.draconitic.com/paper/bmfxqym80cgn6", "venue": "BMC microbiology", "versions": [] }