In Silico Prioritization of Potential Protein Interactions for Glutathione-Responsive Abasic Site-Trapping Prodrugs in Non-Small Cell Lung Cancer

Abstract

Non-small cell lung cancer (NSCLC) remains a major cause of cancer-related mortality, and treatment efficacy is frequently limited by acquired resistance and systemic toxicity. Glutathione-responsive abasic site-trapping prodrugs have shown selective anticancer activity in prior experimental studies, but whether their released metabolites also show meaningful interactions with cancer-relevant proteins remains to be established. Here, an integrated in silico workflow combining network pharmacology, molecular docking, molecular dynamics (MD), and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis was used to prioritize testable protein-interaction hypotheses for two glutathione-responsive prodrugs (Compound 1 and Compound 2), their aminooxy-containing products (Compound 4 and Compound 5), and a matched non-trapping control pair (Compound 3 and Compound 6). Twenty-one intersecting compound- and disease-associated targets were identified, and AKT serine/threonine kinase 1 (AKT1), epidermal growth factor receptor (EGFR), tumor necrosis factor (TNF), matrix metalloproteinase 9 (MMP9), and SRC proto-oncogene non-receptor tyrosine kinase (SRC) were prioritized by protein-protein interaction topology. Compound 5 produced the most favorable single AutoDock Vina score with MMP9 (-8.418 kcal·mol⁻¹) and showed comparatively persistent docking-derived poses across the MMP9 and SRC MD trajectories. However, the top-ranked MMP9 pose did not show direct coordination of the catalytic Zn²⁺ ion or direct engagement of His401, Glu402, His405, or His411, so it cannot be assigned a canonical MMP9 inhibitory binding mode. MD and MM-PBSA analyses characterize only trajectory behavior and the relative energetic ranking of these complexes; they do not demonstrate intracellular target engagement, enzyme inhibition, or pathway regulation. The established abasic-site-trapping activity and the newly predicted protein interactions are therefore treated as separate, potentially parallel hypotheses rather than a demonstrated mechanistic chain. Overall, the results prioritize specific compound-target pairs for future testing but do not establish a multi-target anti-NSCLC mechanism.

The authors' abstract, as published at the source. Journal of Visualized Experiments, 2026 · DOI ↗