In silico Investigation of Marine Natural Products Targeting Dual PD-L1 and VISTA as Potential Cancer Immunotherapy Agents

Abstract

Inhibiting overexpressed key immunoregulatory proteins, programmed death-ligand 1 (PD-L1) and V-domain immunoglobulin suppressor of T cell activation (VISTA), represents a critical strategy for restoring antitumor immunity. These proteins are upregulated under hypoxic conditions, leading to immune evasion and drug resistance to monotherapy. In this study, a comprehensive computational workflow, including structure-based pharmacophore screening and validation, molecular docking, predictive toxicity profiling, and molecular dynamics (MD) simulations, was used to explore a marine database for compounds that bind PD-L1 and VISTA simultaneously. The retrospective pharmacophore validation of known actives and decoys confirmed the discriminatory reliability of both PD-L1 and VISTA models. From the common pharmacophore alignment of PD-L1 and VISTA models, 235 marine compounds exhibited RMSD values <2.0 Å. Based on the molecular docking screening of these common hits, CMNPD14606, CMNPD20027, and CMNPD20697 were found to have higher affinities than the reference P17 and S8. Additionally, these hits demonstrated favorable physicochemical profiles; however, the in-silico toxicity profiling revealed modest-to-high genotoxicity and mutagenicity liabilities for all three compounds, which represent key safety limitations. The MD simulations, performed in triplicate for up to 100 ns, confirmed MD stability across independent replicates. The identification of marine-derived compounds addresses the need to overcome resistance to single-checkpoint immunotherapy. Accordingly, these compounds are regarded as earlystage lead scaffolds requiring structural optimization rather than hits with acceptable overall safety profiles. These results suggest the development of dual-targeting PD-L1/VISTA compounds that warrant lead optimization to mitigate toxicity risks before further experimental investigation.