Discovery of Natural Alkaloid Inhibitors of NLRP3 Inflammasome: A Computational Approach Leveraging Brazilian Biodiversity

Abstract

The NLRP3 inflammasome (NLR family pyrin domain-containing 3) plays a central role in the pathogenesis of several chronic inflammatory diseases, including rheumatoid arthritis, type 2 diabetes mellitus, and Alzheimer disease. However, currently available inhibitors, such as MCC950, present important limitations related to hepatotoxicity, highlighting the need for safer therapeutic alternatives. In this study, Brazilian biodiversity was explored as a source of natural alkaloids with potential inhibitory activity against NLRP3 using an integrated computational approach. Initially, 221 alkaloids were subjected to virtual screening by molecular docking, followed by binding free energy refinement using the molecular mechanics/generalized born surface area (MM/GBSA) method. Based on the most favorable energy values, ten compounds were selected for subsequent analysis. Predictive toxicity assessment then enabled the prioritization of three alkaloids, NuBBE_306 (spectaline), NuBBE_452 (canavaline), and NuBBE_453 (leptophylline A), for molecular dynamics simulations, principal component analysis (PCA), free energy landscape (FEL) analysis, and an additional free energy evaluation, with the results compared against the reference inhibitors MCC950 and RM5. Among the evaluated compounds, NuBBE_452 and NuBBE_453 emerged as the most promising candidates, exhibiting high binding affinity, strong conformational stability supported by PCA and FEL analyses, and a more favorable predicted toxicity profile than the reference inhibitors. These findings highlight the potential of Brazilian biodiversity as a source of bioactive molecules and reinforce the applicability of robust computational strategies for identifying novel NLRP3 inhibitors with improved safety profiles. Further experimental studies are required to validate these results.