Author

Volta Kellik Setiawan

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Aug 2026

Expression-Guided Immunoinformatics Design of a Recombinant Multi-Epitope Vaccine Candidate for Triple-Negative Breast Cancer Incorporating a MyD88-Derived Immunomodulatory Domain

Triple-negative breast cancer (TNBC) remains a major therapeutic challenge because of its aggressive behavior, molecular heterogeneity, and limited subtype-specific targets. This study used an integrated immunoinformatics workflow to design a recombinant tumor-associated antigen-derived multi-epitope vaccine based on MMP1, CXorf61/CT83, and COL11A1, prioritized according to their tumor-to-normal transcript-expression ratios. Candidate cytotoxic T-lymphocyte, helper T-lymphocyte, and linear B-cell epitopes were screened for predicted HLA binding, antigenicity, allergenicity, toxicity, and IFN-γ-induction potential. The selected epitopes were assembled with PADRE, a MyD88-derived exploratory immunomodulatory domain, class-specific linkers, and a C-terminal histidine tag to generate a 621-amino-acid construct. Combined HLA class I and II analysis predicted 99.36% worldwide population coverage, with 3.14 epitope–HLA hits per individual. The construct was predicted to be antigenic, non-allergenic, soluble, and physicochemically compatible with recombinant production. Structural modeling yielded a ProSA Z-score of −7.43 and 97.45% of residues in favored Ramachandran regions, while disulfide engineering identified ten candidate intramolecular bridges. Docking produced an HDOCK score of −298.65 for the modeled vaccine–TLR4 complex, and flexibility analysis showed an average RMSF of 1.93 Å. Immune simulation predicted Th1-associated cytokine production, T-cell expansion, antibody responses, and memory-cell formation. Codon optimization generated a CAI of 0.95 and a GC content of 53.2%, followed by virtual cloning into pET-28a(+). These findings support the computational feasibility of the proposed vaccine candidate, which requires experimental validation of expression, antigen processing, HLA presentation, immunogenicity, safety, and antitumor activity.

M. R. Afnani, Volta Kellik Setiawan, Anwar Rovik · Natural and Life Sciences Co... · 0 citations

Open access Jul 2026

In silico identification of organosulfur compounds from Allium ascalonicum L. as potential inhibitors of influenza A (H5N1): integrated DFT, docking, and molecular dynamics analysis

Influenza A (H5N1) remains a major public health concern due to its high pathogenicity and ongoing viral evolution, underscoring the need for novel antiviral candidates. In this study, we performed an integrated in silico evaluation of organosulfur compounds derived from Allium ascalonicum L. (shallot) cultivated in the Tolaki-Mekongga region, Sulawesi, Indonesia, targeting key viral proteins including polymerase (PB2), nucleoprotein (NP), and neuraminidase (NA). Density functional theory (DFT) analyses were conducted to characterize the electronic properties of the compounds, while PASS prediction indicated moderate potential antiviral activity for Propanethiol and Dipropyl disulfide. Pharmacokinetic profiling suggested acceptable ADMET properties for several candidates. Molecular docking revealed favorable binding conformations across all targets, with γ-glutamyl-S-propenylcysteine exhibiting the most favorable binding energies among the evaluated organosulfur compounds (PB2: -4.9 kcal/mol; NP: -5.8 kcal/mol; NA: -5.2 kcal/mol). These values were comparable to those of oseltamivir and favipiravir for NP and NA, although weaker binding was observed against PB2. Subsequent simulations of molecular dynamics demonstrated stable protein–ligand complexes over 100 ns, further supporting the predicted binding interactions. Consistently, MM-GBSA calculations indicated favorable binding free energies, particularly for γ-glutamyl-S-propenylcysteine (PB2: -30.52 ± 0.29 kcal/mol; NP: -22.76 ± 0.12 kcal/mol; NA: -26.13 ± 0.35 kcal/mol). Overall, these findings suggest that shallot-derived organosulfur compounds, especially γ-glutamyl-S-propenylcysteine, exhibit potential for interaction with H5N1 viral targets and may warrant further investigation as antiviral candidates. Experimental validation through in vitro and in vivo studies is required to confirm their biological activity and therapeutic potential.

Rangga Adhi Prastika, Alifaghi Pahlevi Ervianto Putra, Muhammad Alesha Fadhana et al. · Frontiers in Virology · 0 citations