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Purpose <p><i>Enterococcus casseliflavus</i> is a Gram-positive bacterium with intrinsic resistance to antibiotics and increasingly associated with immunocompromised patients. Currently, no vaccine is available. The study aimed to computationally design a multi-epitope vaccine candidate against <i>E. casseliflavus</i> using immunoinformatic and molecular modeling approaches.</p> Methods <p>Integrated immunoinformatic and molecular modeling approach applied to design a multi-epitope vaccine construct.</p> Results <p>T-cell epitopes were retrieved and analyzed for vaccine design (EAAAQEAAA, QEAAAAEAA, AAEAATQEA, AQEAAAQEA, AQEAAAAEA). Docking with TLR-4 showed stable binding, with Model 0 displaying a large cluster size (47 members) and a favorable weighted score of − 716.7. A 100 ns. Molecular dynamics simulation indicated stability after 30 ns, with RMSD maintained between 9 and 11 Å, Rg between 19.9 and 20.3 Å, and SASA between 10,000 and 12,000 Ų. RMSF analysis showed limited residue flexibility except for the C-terminus. MM/PBSA revealed a net binding free energy of − 65.63&#xa0;kcal/mol, mainly driven by van der Waals interactions. Immune simulation shows strong IgM and IgG responses, early cytokine induction, and sustained memory cell development. Codon optimization in <i>E. coli</i> K12 produced a 2082&#xa0;bp gene with 50.73% GC content and CAI of 0.997, successfully cloned in silico into pET28a (+) between Eco53KI and EcoRV sites.</p> Conclusion <p>The designed vaccine is structurally stable, non-allergenic, and immunogenic, showing strong receptor interaction and potential against <i>E. casseliflavus</i>, pending experimental validation.</p>

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Subtractive Proteomics Filtration, Immunoinformatic Design and Biophysics-Based Investigation of a Multi-epitopes Vaccine Construct Against Enterococcus casseliflavus

  • 期刊论文

  • 发表日期：

    2026年6月16日

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  • Inayat Ullah,
  • Asad Ullah,
  • Basmah F. Alharbi,
  • Mawahib Ahmed,
  • Kiran Akbar,
  • Ajmal Khan,
  • Sajjad Ahmad

摘要

Purpose

Enterococcus casseliflavus is a Gram-positive bacterium with intrinsic resistance to antibiotics and increasingly associated with immunocompromised patients. Currently, no vaccine is available. The study aimed to computationally design a multi-epitope vaccine candidate against E. casseliflavus using immunoinformatic and molecular modeling approaches.

Methods

Integrated immunoinformatic and molecular modeling approach applied to design a multi-epitope vaccine construct.

Results

T-cell epitopes were retrieved and analyzed for vaccine design (EAAAQEAAA, QEAAAAEAA, AAEAATQEA, AQEAAAQEA, AQEAAAAEA). Docking with TLR-4 showed stable binding, with Model 0 displaying a large cluster size (47 members) and a favorable weighted score of − 716.7. A 100 ns. Molecular dynamics simulation indicated stability after 30 ns, with RMSD maintained between 9 and 11 Å, Rg between 19.9 and 20.3 Å, and SASA between 10,000 and 12,000 Ų. RMSF analysis showed limited residue flexibility except for the C-terminus. MM/PBSA revealed a net binding free energy of − 65.63 kcal/mol, mainly driven by van der Waals interactions. Immune simulation shows strong IgM and IgG responses, early cytokine induction, and sustained memory cell development. Codon optimization in E. coli K12 produced a 2082 bp gene with 50.73% GC content and CAI of 0.997, successfully cloned in silico into pET28a (+) between Eco53KI and EcoRV sites.

Conclusion

The designed vaccine is structurally stable, non-allergenic, and immunogenic, showing strong receptor interaction and potential against E. casseliflavus, pending experimental validation.