Systematic in silico Evaluation of Leishmania spp. Proteomes for Drug Discovery

Abstract

Leishmaniasis is a group of neglected infectious diseases, with approximately 1. 3 million new cases each year, for which the available therapies have serious limitations. Therefore, it is extremely important to apply efficient and low-cost methods capable of selecting the best therapeutic targets to speed up the development of new therapies against those diseases. Thus, we propose the use of integrated computational methods capable of evaluating the druggability of the predicted proteomes of Leishmania braziliensis and Leishmania infantum, species responsible for the different clinical manifestations of leishmaniasis in Brazil. The protein members of those proteomes were assessed based on their structural, chemical, and functional contexts applying methods that integrate data on molecular function, biological processes, subcellular localization, drug binding sites, druggability, and gene expression. These data were compared to those extracted from already known drug targets (BindingDB targets), which made it possible to evaluate Leishmania proteomes for their biological relevance and treatability. Through this methodology, we identified more than 100 proteins of each Leishmania species with druggability characteristics, and potential interaction with available drugs. Among those, 31 and 37 proteins of L. braziliensis and L. infantum, respectively, have never been tested as drug targets, and they have shown evidence of gene expression in the evolutionary stage of pharmacological interest. Also, some of those Leishmania targets showed an alignment similarity of <50% when compared to the human proteome, making these proteins pharmacologically attractive, as they present a reduced risk of side effects. The methodology used in this study also allowed the evaluation of opportunities for the repurposing of compounds as anti-leishmaniasis drugs, inferring potential interaction between Leishmania proteins and ~1,000 compounds, of which only 15 have already been tested as a treatment for leishmaniasis. Besides, a list of potential Leishmania targets to be tested using drugs described at BindingDB, such as the potential interaction of the DEAD box RNA helicase, TRYR, and PEPCK proteins with the Staurosporine compound, was made available to the public.

Drug Discovery for Cutaneous Leishmaniasis: A Review of Developments in the Past 15 Years

“…Researchers have established several tools useful for broad-spectrum anti-leishmanial drug discovery, including parasites constitutively expressing fluorescent proteins [103,104], differential protein expression of different parasite life stages [49], automated image analysis protocols [105], proteome mining [106], and kinome mining [107]. These tools were useful in identifying several potential drug targets, including inositol phosphorylceramide synthase using purified Leishmania enzyme in a plate-based assay [108], serine proteases through activity-based protein profiling of promastigotes [109], the Lmj_04_BRCT protein domain first characterized via homology modeling and then validated in vitro using intracellular amastigotes [110], cysteine protease CPB2.8(∆)CTE via enzymatic screening followed by intramacrophage screening [111], and the Hsp90 chaperone of promastigote parasites [112].…”