Computational study on the mechanism of small molecules inhibiting NLRP3 with ensemble docking and molecular dynamic simulations

NLRP3 (Nucleotide-binding oligomerization domain, LRR and pyrin domain-containing protein 3) is a pivotal regulator of inflammation, with strong implications in gout, neurodegenerative diseases, and various inflammatory conditions. Consequently, the exploration of NLRP3 inhibitors is of great significance for the treatment of diseases. MCC950, NP3-146, compound (3), and YQ128 are four highly bioactive NLRP3 inhibitors that show great potential; however, their mechanism of action is currently limited to targeting the ATP binding region (NACHT site) of the NLRP3 protein. To gain deeper insights into the defining features of NLRP3 inhibitors and to develop more potent inhibitors, it is imperative to elucidate the interaction mechanism between NLRP3 and these inhibitors. In this study, we employ a comprehensive computational approach to investigate the binding mechanism between NLRP3 and representative inhibitors. Utilizing the molecular mechanics/generalized Born surface area (MM/GBSA) method, we calculate the binding free energy and pinpoint the key residues involved in the binding of the four inhibitors to NLRP3. The decomposition of binding free energy by the MM/GBSA method reveals that the residues Val71, Arg195, Ile255, Phe419, Arg422, and Met505, situated around the binding pocket, play a crucial role in conferring the high bioactivity of NLRP3 inhibitors. Furthermore, pharmacophore analysis of the four NLRP3 complexes indicates that the primary interaction between the inhibitors and NLRP3 was mainly hydrophobic interaction. Our study provides a profound understanding of the interaction mechanism between NLRP3 and its inhibitors, identifies the key residues involved, and provides theoretical guidance for the design of more efficient NLRP3 inhibitors.