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VOL. 11, ISSUE 3 (2026)
An Immunoinformatics approach to design a neoantigen-driven Multi-Epitope Vaccine against Leukemia
Authors
Hemang Bhindi, Dharmendrasinh F Rao, Arav Sharma, Saumya K Patel
Abstract
Leukemia remains a major hematological malignancy with high relapse
rates and limited therapeutic options, highlighting the need for effective
immunotherapeutic strategies. This study employed an integrated
immunoinformatics and structural vaccinology approach to design a multi-epitope
therapeutic vaccine targeting leukemia-associated neoantigens from acute
myeloid leukemia (AML), chronic myeloid leukemia (CML), acute lymphoblastic
leukemia (ALL), and chronic lymphocytic leukemia (CLL). A total of 81 neoantigens
retrieved from the Cancer Epitope Database and Analysis Resource (CEDAR) were
screened for antigenicity, allergenicity, toxicity, and immunogenicity, resulting
in the selection of 7 CTL and 9 HTL epitopes for vaccine construction. The
vaccine incorporated β-defensin-3, the PADRE peptide, suitable linkers, and a
His-tag. Physicochemical analysis indicated favorable stability and solubility,
while structural validation showed 95.1% of residues in the most favored
regions of the Ramachandran plot. Population coverage analysis predicted 99.95%
global HLA coverage. Molecular docking and a 200 ns molecular dynamics
simulation confirmed stable binding to TLR2, and MM-GBSA analysis demonstrated
an increase in binding free energy from −55.54 kcal/mol to −248.13 ± 37.95
kcal/mol following the simulation. Codon optimization yielded a CAI of 1.0 and
a GC content of 53.57%, indicating efficient expression in Escherichia coli.
Furthermore, in silico immune simulation predicted rapid antigen
clearance, strong antibody production, and robust IFN-γ-mediated cellular
immunity. These findings suggest that the designed multi-epitope vaccine is a
promising therapeutic candidate against leukemia and warrants further in
vitro and in vivo validation.
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Pages:140-149
How to cite this article:
Hemang Bhindi, Dharmendrasinh F Rao, Arav Sharma, Saumya K Patel "An Immunoinformatics approach to design a neoantigen-driven Multi-Epitope Vaccine against Leukemia". International Journal of Botany Studies, Vol 11, Issue 3, 2026, Pages 140-149
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