Exploring the microbial metabolomes for Wnt pathway modulators: a multi-scale computational pipeline targeting...

Colorectal cancer (CRC) is a multifactorial malignancy frequently driven by aberrant activation of the Wnt/β-catenin cascade, which promotes uncontrolled cell proliferation and tumor progression. Tankyrases (TNKS1/TNKS2), members of the PARP family, regulate this pathway by mediating AXIN degradation, thereby stabilizing β-catenin. Inhibition of TNKS can restore AXIN levels and attenuate Wnt signalling, positioning TNKS as a promising therapeutic target. Leveraging the structural diversity, biochemical specificity, and evolutionary refinement of natural microbial compounds, this study screened 36,588 microbial and fungal natural products obtained from the NPATLAS database. High-throughput screening was carried out using Python and the RDKit package, applying stringent physicochemical, structural, and drug-likeliness filters. Exhaustive virtual screening, molecular docking, and 300 ns molecular dynamics (MD) simulations identified two promising candidates, namely Malassezione (NPA018503) and Xenocockiamide B (NPA033189), which exhibited the most favourable and stable binding interactions with TNKS-1, with binding affinities of - 11.45 kcal/mol and - 12.48 kcal/mol, respectively. Further validation through MM-PBSA calculations, Principal component analysis (PCA), DCCM, and free energy landscape (FEL) analyses revealed robust conformational stability and distinct clustering mechanisms of these top hits within the TNKS-1 active site. Density functional theory (DFT) calculations additionally confirmed favourable electronic characteristics for both compounds, including optimal HOMO-LUMO energy gaps and chemical reactivity parameters. Pharmacokinetic profiling indicated high GI absorption, metabolic resilience, and minimal toxicity risk. Although XAV939 is a known TNKS-1 inhibitor, it demonstrated comparatively reduced efficacy across binding and stability metrics. In conclusion, this integrative computational evidence supports microbial-derived compounds as promising natural candidates for TNKS-1 inhibition, offering a new avenue for in vivo validation and structure-guided discovery of next-generation microbe-based therapeutics for colorectal cancer.

The online version contains supplementary material available at 10.1007/s40203-026-00585-9.