Toward the discovery of inhibitors of babesipain-1, a Babesia bigemina cysteine protease: in vitro evaluation, homology modeling and molecular docking studies

Abstract

Babesia bigemina is a protozoan parasite that causes babesiosis, a disease with a world-wide distribution in mammals, principally affecting cattle and man. The unveiling of the genome of B. bigemina is a project in active progress that has already revealed a number of new targets with potential interest for the design of anti-babesiosis drugs. In this context, babesipain-1 has been identified as a proteolytically active enzyme whose three-dimensional structure has not been resolved yet, but which is known to be inhibited by cysteine proteases inhibitors such as E64, ALLN, leupeptin, and vinyl sulfones. In this work, we introduce (1) a homology model of babesipain-1; (2) a comparison between babesipain-1 and falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum; (3) in vitro data for babesipain-1 inhibition by HEDICINs and HECINs, previously reported as modest inhibitors of falcipain-2; and (4) the docked binding conformations of HEDICINs and HECINs in the model of babesipain-1. HEDICINs presented similar preferred binding conformations for both babesipain-1 and falcipain-2. However, in vitro bioassay shows that HEDICINs and HECINs are better inhibitors of babesipain-1 than of falcipain-2, which could be explained by observed differences between the active pockets of these proteins in silico. Results presented herein provide a valuable contribution to future computer-aided molecular design of new babesipain-1 inhibitors.

Novel Non-Peptide Inhibitors against SmCL1 of Schistosoma mansoni: In Silico Elucidation, Implications and Evaluation via Knowledge Based Drug Discovery

“…Therefore, models in this experiment were built based on different alignments resulting from multiple templates using the PSI-Coffee mode of T-Coffee. Following Perez et al [ 51 ], the combination of selected target sequence (SmCL1) and all possible combinations of two to three selected homolog proteins resulted in 41 different alignments. For each alignment, 100 models were constructed, totalling to 4100 models for SmCL1.…”

Comparative Degradome Analysis of the Bovine Piroplasmid Pathogens Babesia bovis and Theileria annulata

“…Due to their predicted functional relevance, different approaches have been applied to identify kinetics parameters, substrate specificity, and/or inhibitors of Babesia spp. C1A proteases, including producing enzymatically active recombinant proteins and in silico modeling and prediction analyses [ 75 , 77 , 78 , 79 ].…”

In Silico Survey and Characterization of Babesia microti Functional and Non-Functional Proteases

“…Recent advances in B. microti gene editing will permit exploring the functional relevance of selected proteases [89,90]. In addition, the application of computer-based inhibitor screening and the use of optimized pipelines to test drug efficacies using in vitro cultures and animal models allows obtaining new therapeutics against human babesiosis in a relatively short period of time [34,91,92].…”