Integrated computational investigation of Glycosmis pentaphylla-derived compounds against major venom proteins of Daboia russelii

Abstract

Snakebite envenomation remains a significant neglected tropical disease, particularly in South Asia, where Daboia russelii (Russell’s viper) causes substantial morbidity and mortality. Current antivenom therapy is limited by poor efficacy against local tissue damage, high production costs, restricted toxin specificity, and adverse immune reactions, highlighting the need for alternative or adjunct therapeutic strategies. Using an integrated computational and experimental approach, phytocompounds identified from Glycosmis pentaphylla leaf extracts were evaluated as potential inhibitors of major venom proteins. A total of 32 compounds identified by GC-MS were screened against phospholipase A2 (PLA2), snake venom metalloproteinases (SVMPs), snake venom serine proteases (SVSPs), L-amino acid oxidase (LAAO), and snake C-type lectin-like proteins (SNACLECs) using molecular docking. Representative high-affinity protein-ligand complexes were further evaluated by 100 ns molecular dynamics simulations. Pharmacokinetic, toxicity, protein-protein interaction, and pathway enrichment analyses were also performed to assess the therapeutic potential of the identified compounds. Preliminary experimental validation was conducted using trypsin-casein protease inhibition, skim milk agar protease inhibition, and erythrocyte membrane stabilization assays. Compared with N-acetyl cysteine (NAC), β-sitosterol, 3-chloro-5-cholestene, and vitamin E exhibited stronger binding affinities and more stable interactions with multiple venom proteins. Molecular dynamics analyses (RMSD, RMSF, radius of gyration, solvent-accessible surface area, and hydrogen bonding) further supported the stability of the selected protein-ligand complexes. Pharmacokinetic and toxicity predictions indicated acceptable drug-likeness and comparatively safe toxicity profiles for most selected compounds. STRING-based protein-protein interaction and pathway enrichment analyses revealed associations with inflammatory, coagulation, oxidative stress, and extracellular matrix-related pathways involved in venom pathology. The G. pentaphylla extract demonstrated concentration-dependent protease inhibition (56.86% at 5 mg/mL), reduced caseinolytic activity (28.19% inhibition), and significant erythrocyte membrane stabilization (39.23%), providing preliminary experimental support for the computational predictions. Overall, these findings identify G. pentaphylla-derived phytocompounds as potential lead compounds for future antivenom development and provide a computational foundation for subsequent venom-specific biochemical and in vivo validation toward safer and more affordable adjunct therapies for snakebite management.