Treatment of inflammation: Novel inhibitors of the inflammasome

Abstract

NLRP3 (NOD-, LRR- and pyrin domain containing 3) inflammasome is a cytoplasmic protein complex that regulates the activation of inflammatory cytokines. Given its implication in a range of diseases, NLRP3 is an important therapeutic target. The cofactor ATP and the centrosomal kinase NEK7 are important for NLRP3 activation. We have constructed and simulated computational models of full-length monomeric NLRP3 to shed light on the importance of NEK7 and cofactor interactions for its conformation and dynamics in aqueous solution. These computed dynamical trajectories of NLRP3 provide insight into coordinates of deformation that may be key for cofactor binding and inflammasome activation. Moreover, the NLRP3 inflammasome is currently an exciting target for drug discovery due to its role in various inflammatory diseases; however, to date, no NLRP3 inhibitors have reached the clinic. Virtual screening of the ZINC20 drug-like database was performed to design novel small molecule NLRP3 inhibitors using the structure of the NACHT domain (PDB code 7ALV). From this VS, 58 compounds were selected for biological testing in collaboration with Prof. Brough’s and Dr. Kasher’s labs to evaluate the percentage of IL-1 release in response to the treatment of the cells with 10 M of the selected compounds. Then, the most active compounds resulted from the biological screening were used to design 2nd generation inhibitors which will form the basis for future work to design a more potent NLRP3 inhibitors. In a collaboration with Dr. Freeman’s and Prof. Stratford’s labs, a set of meta-substituted 3-arylisoquinolinones have been identified that show substantial cytotoxicity in breast, liver, lung and colon cancer cell lines; these are up to 700-fold more active than the corresponding para-analogues. Docking, molecular dynamics simulations, and free energy analysis suggested that the meta-substituted compounds such as 6-fluoro-3-(meta-fluorophenyl)isoquinolin-1(2H)-one (4) bound well into the colchicine-binding pocket of tubulin. Also, the computed free energy of binding of the para-analogues to tubulin was lower in magnitude than that for meta. Furthermore, a SAR study using 4 as a lead compound was conducted by simulating 4-tubulin interactions with putative compounds D1 – D25. Overall, these findings should stimulate further investigation of the in vivo efficacy of this novel structural class.

Date of Award	1 Aug 2023
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Sally Freeman (Supervisor) & Richard Bryce (Supervisor)