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Peer-reviewedCC BYBMC microbiology

In silico design of bivalent multi-epitope mRNA vaccine candidates against Mycoplasma pneumoniae and Chlamydia pneumoniae.

  • Xu Wu1,2,3
  • Yizhong Xu1,2,3
  • Weiwei Zhao1,4
  • Rongliu Qin1,2,3
  • Yuying Luo1,2,3
  • Yanqun Hou1,2,3
  • Ziyou Zhou1,2,3
  • Shiyang Ma1,2,3
  • Fei Zhu5,6,7
  • Pinhua Pan8,9,10,11
11 affiliations
  1. 1Department 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.
  2. 2Clinical 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.
  3. 3National Clinical Research Center for Geriatric Disease, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
  4. 4Department 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.
  5. 5Department 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. [email protected].
  6. 6Clinical 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. [email protected].
  7. 7National Clinical Research Center for Geriatric Disease, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. [email protected].
  8. 8Department 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. [email protected].
  9. 9Clinical 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. [email protected].
  10. 10National Clinical Research Center for Geriatric Disease, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. [email protected].
  11. 11Furong Laboratory, Changsha, 410078, Hunan, China. [email protected].
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Abstract

Background

Community-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

Conserved 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

A 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

In 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.

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Cite

BibTeXRIS
BibTeX
@article{wu2026silico,
  title = {{In silico design of bivalent multi-epitope mRNA vaccine candidates against Mycoplasma pneumoniae and Chlamydia pneumoniae.}},
  author = {Xu Wu and Yizhong Xu and Weiwei Zhao and Rongliu Qin and Yuying Luo and Yanqun Hou and Ziyou Zhou and Shiyang Ma and Fei Zhu and Pinhua Pan},
  journal = {BMC microbiology},
  year = {2026},
  month = aug,
  doi = {10.1186/s12866-026-05473-y},
  url = {https://europepmc.org/article/MED/42972530},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - In silico design of bivalent multi-epitope mRNA vaccine candidates against Mycoplasma pneumoniae and Chlamydia pneumoniae.
AU  - Xu Wu
AU  - Yizhong Xu
AU  - Weiwei Zhao
AU  - Rongliu Qin
AU  - Yuying Luo
AU  - Yanqun Hou
AU  - Ziyou Zhou
AU  - Shiyang Ma
AU  - Fei Zhu
AU  - Pinhua Pan
PY  - 2026
DA  - 2026/08/06
JO  - BMC microbiology
DO  - 10.1186/s12866-026-05473-y
UR  - https://europepmc.org/article/MED/42972530
AB  - Background  Community-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  Conserved 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  A 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  In 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.
SN  - 1471-2180
ER  -