Molecular Dynamics and Virtual Screening of Withania somnifera Phytochemicals as Potential Inhibitors of the Human NLRP9 Pyrin Domain

Inflammation mediated by the NLRP9 inflammasome, a comparatively undercharacterized NOD-like receptor (NLR) family member, represents an emerging therapeutic target in innate immunity and inflammatory disease. The pyrin domain (PYD) of NLRP9 plays a pivotal role in inflammasome assembly through homotypic protein–protein interactions with the adaptor protein ASC, making it a structurally rational target for pharmacological intervention. This study employed an integrated in silico framework to evaluate seven bioactive phytochemicals from Withania somnifera (Ashwagandha)—namely Withanolide A, Withanolide B, Withanolide D, Withanolide E, Withaferin A, Withanone, and Somniferine—as potential inhibitors of the human NLRP9 PYD domain. The NLRP9-PYD structure was generated via homology modeling using SWISS-MODEL and validated by Ramachandran analysis, yielding 93.8% of residues in the most favoured conformational regions. Molecular docking was performed using AutoDock Vina via PyRx, followed by interaction analysis in BIOVIA Discovery Studio. ADMET profiling was conducted using SwissADME, and computational toxicity assessment was performed using ProTox-II. Withanolide B demonstrated the highest binding affinity (−7.8 kcal/mol), followed by Withanolide A (−7.5 kcal/mol) and Withanolide D (−7.3 kcal/mol), with key interactions involving residues Glu14, Arg15, Ser18, and Gln21. All compounds exhibited favorable oral bioavailability, high gastrointestinal absorption, and absence of blood–brain barrier permeability. These findings establish Withanolide B, A, and D as promising lead candidates for NLRP9 inflammasome inhibition, warranting experimental validation.