Supplementary computational data for CRUISER: a dual-arm peptide vaccine against KRAS, EGFR, PD-L1 and VEGFR2 for non-small cell lung cancer in Vietnamese patients

This repository contains the complete computational pipeline and supplementary data supporting the manuscript "CRUISER: a dual-arm peptide vaccine against KRAS, EGFR, PD-L1 and VEGFR2 for non-small cell lung cancer in Vietnamese patients." CRUISER is a dual-arm therapeutic vaccine restricted to a Vietnamese-specific panel of 12 HLA class I alleles and 13 class II specificities. The T-cell arm (Pool A / CRUISER-A) is a 273-residue recombinant protein carrying eight KRAS and EGFR neoepitopes fused to the chemokine XCL1, targeting the construct to XCR1-positive conventional type 1 dendritic cells. The antibody arm (Pool B) comprises four disulfide-cyclised peptides from the ligand-binding faces of PD-L1 and VEGFR2. Contents are organised into a numbered pipeline structure (01-10) for both pools: epitope screening, antigenicity/toxicity, structure prediction, docking, MD/MM-PBSA, population coverage, immunosimulation, physicochemical/developability, cloning, and reports/structures. Key results: combined population coverage 73.35% in Vietnam vs 46.78% worldwide and 41.23% in Europe; triplicate 100 ns MD simulations benchmarked against a free XCL1:XCR1 positive control confirmed that fusion preserves receptor engagement; epitope-MHC docking confirmed EP024 (ipTM 0.929) and EP044 (ipTM 0.907) binding to HLA-A*11:01. All findings are computational predictions requiring experimental validation. Methods: ff14SB/lipid21/TIP3P force field; GROMACS (CUDA); gmx_MMPBSA 1.6.5; ColabFold 1.6.2 (AlphaFold2-Multimer); IEDB Population Coverage 3.0.2; C-ImmSim.