The 26S proteasome in Entamoeba histolytica: Functional annotation and modelling of beta4-beta5 subunits

Abstract

Abstract Background: Proteasomes are conserved proteases that are crucial for proteostasis in eukaryotes. They are promising drug targets for protozoan parasites. Despite this, the 26S proteasomes of the protozoan parasite Entamoeba histolytica has not received much attention. This study reports a comprehensive bioinformatics analysis of the 26S proteasome subunits of Entamoeba histolytica and related Entamoeba species. Results: While showing overall conservation, critical substitutions in structurally and functionally important residues were observed in both regulatory (RP) and core particle (CP) subunits. Comparative sequence analysis suggests that the substrate translocation channel of E. histolytica has a changed polarity, and is possibly wider, compared to host proteasomes. The proteolytic subunits show differences in the substrate binding sites, especially the S1 and S3 binding pockets of the b1 subunit, that show T22M, A27V, T31K R45T substitutions suggesting differences in size and charge of the pockets. Similarly, b2 has T52L and E22V and b5 has A22R, A27S, S115D and E116G substitutions. These changes in the substrate binding pockets suggest differences in substrate preference and susceptibility to inhibitors compared to host proteasomes. Computational models of β4 and β5 subunits, and a docked β4-β5 model were developed. A binding pocket between β4-β5, similar to that of Leishmania tarentolae was observed. Selective inhibitors for visceral leishmaniasis, LXE408 and compound 8, docked well to this pocket. Conclusions: This sequence based analysis predicts potential points of differences from the host proteasomes that can be experimentally tested, and can be utilized to develop selective inhibitors against E. histolytica.