Discovery of Potent, Reversible, and Competitive Cruzain Inhibitors with Trypanocidal Activity: A Structure-Based Drug Design Approach

Abstract

A virtual screening conducted with nearly 4 000 000 compounds from lead-like and fragment-like subsets enabled the identification of a small-molecule inhibitor (1) of the Trypanosoma cruzi cruzain enzyme, a validated drug target for Chagas disease. Subsequent comprehensive structure-based drug design and structure−activity relationship studies led to the discovery of carbamoyl imidazoles as potent, reversible, and competitive cruzain inhibitors. The most potent carbamoyl imidazole inhibitor (45) exhibited high affinity with a K i value of 20 nM, presenting both in vitro and in vivo activity against T. cruzi. Furthermore, the most promising compounds reduced parasite burden in vivo and showed no toxicity at a dose of 100 mg/kg. These carbamoyl imidazoles are structurally attractive, nonpeptidic, and easy to prepare and synthetically modify. Finally, these results further advance our understanding of the noncovalent mode of inhibition of this pharmaceutically relevant enzyme, building strong foundations for drug discovery efforts.

Fragment-to-Lead Medicinal Chemistry Publications in 2020

“… 22 While a string of other 2020 publications describe antimicrobial FBLD hit-finding and exploration studies, they do not meet all the criteria for F2L table inclusion. Examples include studies focused on bacterial targets such as metallo-β-lactamase(MBL)NDM-1, 54 dihydrofolate reductase from M. tuberculosis (MtDHFR), 55 M. tuberculosis MabA (FabG1) 56 and tRNA-modifying enzyme TGT, where a hit fragment opens a transient subpocket that can be exploited by a new series of ligands; 57 tRNA modification enzyme TrmD, 58 fungal targets such as glucosamine 6-phosphate N -acetyltransferase (Gna1), which is a key enzyme in the biosynthesis of an essential fungal cell-wall component; 59 parasite targets such as the cysteine protease enzyme cruzain; 60 allosteric binders for farnesyl pyrophosphate synthase of Trypanosoma brucei ; 61 bromodomain-containing factor 3 of Trypanosoma cruzi ; 62 membrane-bound pyrophosphatases (mPPases); virus targets (e.g., viral DNA-binding proteins Epstein–Barr nuclear antigen 1 (EBNA1) and latency-associated nuclear antigen (LANA); 63 and, as indicated above, several efforts to probe and target SARS-CoV-2 proteins. Another interesting study developed PqsR-targeting quorum-sensing inhibitors (a study that uses biophysical screening and enthalpic efficiency evaluations, and introduces relatively flexible linkers).…”

Multiparameter Optimization of Trypanocidal Cruzain Inhibitors With In Vivo Activity and Favorable Pharmacokinetics

“…This is a major hurdle in the field that can be related to the complex life-cycle biology of T. cruzi, and the many poorly understood aspects of the interplay between the parasite and the host ( Libisch et al, 2021 ). Among the compounds that reached this milestone, we can highlight vinyl sulfone K777, CYP51-inhibitor azoles (including posaconazole), and cruzain-inhibitor triazoles and carbamoyl imidazoles ( Ferraz et al, 2007 ; McKerrow et al, 2009 ; Brak et al, 2010 ; de Souza et al, 2020 ). K777 was a landmark in the field as it was the first compound to show the possibility to enter clinical trials for Chagas disease.…”

Impact of different protonation states on virtual screening performance against cruzain

“…There is no consensus on the protonation states considered for these residues in the docking literature. In different studies, they may be considered neutral (Wiggers et al, 2011, 2013), charged (de Souza et al, 2020; Ferreira et al, 2019; Martins et al, 2018; Pereira et al, 2019; Rogers et al, 2012), or the protonation states may not be described (Assis et al, 2013; Moreira et al, 2014; Palos et al, 2017; Romeiro et al, 2009).…”