Fragment library screening by X-ray crystallography and hit optimization against thioredoxin glutathione reductase of Schistosoma mansoni

Abstract

Abstract Schistosomiasis is caused by parasites of the genus Schistosoma, which infect more than 200 million people. While praziquantel (PZQ) has been the main drug for controlling schistosomiasis for over four decades, PZQ drug resistant strains have already been reported, highlighting the need to search for new schistosomicidal drugs. S. mansoni survival relies on the redox enzyme thioredoxin glutathione reductase (SmTGR), a validated target for the development of new anti-schistosomal drugs. Here we report a fragment screening campaign of 768 compounds against SmTGR using X-ray crystallography and our efforts to optimize the hits found into potent inhibitors. We observed 49 binding events involving 35 distinct molecular fragments which were found to be distributed across 16 binding sites. Most sites are described for the first time within SmTGR, a noteworthy exception being the “door stop pocket” near the NADPH binding site. Fragments binding to the latter were prioritized to undergo a “SAR by catalog” strategy for optimization into potential inhibitors. A search for compounds containing any of the prioritized fragments as a substructure was made in commercial databases. The ability of these compounds to inhibit SmTGR was predicted based on a binary ML classification model, followed by an analysis of the putative binding mode by molecular docking. The 38 best ranked compounds were purchased and experimentally evaluated for SmTGR inhibition. Compound 14 inhibited 63.6% of enzyme activity at 100 µM and presented an estimated IC50 of 33 µM against SmTGR.