Morus Prenylflavonoids as Candidate NLRP3 Inflammasome Inhibitors from an AI-Guided Natural-Product Screen with a Quantified Applicability Domain

Background/Objectives: The NLRP3 (NACHT, LRR and PYD domains-containing protein 3) inflammasome drives interleukin-1β maturation and pyroptosis in chronic inflammatory disease, and no direct inhibitor has been approved. Natural products are a plausible source of new chemical matter for this target, but such collections are too large to dock exhaustively, and the machine-learning rankings used to triage them are routinely acted on without stating the chemistry over which they hold. This study prioritises natural-product candidates for NLRP3 while quantifying that limit explicitly. Methods: In total, 610 compounds with reported NLRP3 IC50 values were curated from ChEMBL and used to benchmark five Morgan fingerprint classifiers across three repeated scaffold-based splits. A three-seed consensus of the calibrated best model ranked 2983 natural products, with a similarity-based applicability domain computed alongside every prediction. The highest-ranked compounds were docked into the NACHT domain inhibitor pocket of NLRP3 (PDB 7ALV), and five finalists entered 500 ns molecular dynamics simulations with molecular mechanics generalised Born surface area (MM-GBSA) interaction energy analysis. Results: XGBoost gave the highest mean held-out area under the receiver operating characteristic curve (AUROC), 0.868 ± 0.052, and its performance tracked chemical similarity: 0.857 ± 0.046 inside the applicability domain against 0.368 ± 0.116 outside it. Only 322 library compounds (11%) fell inside the domain. Feature attribution and R-group decomposition traced the ranking to a flavone series in which hydroxylation was tolerated or mildly favourable, and methoxylation was consistently detrimental. Five of the 48 docked compounds were simulated—the Morus prenylflavonoids kuwanon H, morusin and morusinol, together with the approved drugs vardenafil and carprofen—and none left the pocket. Kuwanon H gave the most favourable MM-GBSA interaction energy, −42.5 ± 4.8 against −28.4 ± 3.0 kcal mol−1 for the crystallographic reference, with morusinol having the lowest ligand root-mean-square deviation (RMSD). Conclusions: Morus prenylflavonoids are prioritised candidates for NLRP3 ATPase, inflammasome activation and cytotoxicity assays. All five compounds lie outside the applicability domain (maximum Tanimoto 0.19–0.23), so the ranking served as triage rather than as a predicted activity, and the structure-based stages carry the prioritisation. The five therefore stand as prioritised candidates for experimental validation, through NLRP3 ATPase and target engagement assays, cellular inflammasome readouts and selectivity counter-screens.