Computational approach for calpain inhibitors discovery with potential antiparasitic activity against Leishmania Infantum. From MS label-free proteomic analysis to hits identification through virtual screening.

Host institution:

Name: University of Chemistry and Technology in Prague (UCT Prague)

Affiliation: Prof. Andrea Brancale, Department of Organic Chemistry, University of Chemistry and Technology Prague, Prague 6 16628, Czech Republic. 

Country: Czech Republic

Scope of the STSM.

 The aim of this STSM is the validation of the selected target (calpain) and the identification of novel compounds that will be tested for their antiparasitic potential (Leishmania spp.). Along with computational bioinformatic approaches, MS proteomic analysis is a powerful way to find biological pathways and, by extension, proteins that are involved in certain conditions to find new druggable targets. These approaches can also help in finding molecules that can overcome drug resistance in parasitic diseases. Based on these assumptions, our group has investigated how this new target could be used to do structure-based virtual screening (SBVS) to find new hit compounds that might be able to treat leishmaniasis. Currently, the lack of an x-ray crystal structure of calpain requires the construction of a homology model of the protein. Validation of the model will then be performed, and the active site will be analyzed and employed for a structure-based virtual screening. Finally, the newly identified compounds will be obtained (purchased or synthesized) and tested in vitro against Leishmania spp. The goal is to identify potential drug candidates that can inhibit calpain and potentially serve as new treatments for leishmaniasis. Once the compounds are tested in vitro, further studies will be conducted to evaluate their efficacy, selectivity, and safety. 

Description of the STSM main achievements and planned follow-up activities 

Description and assessment of whether the STSM achieved its planned goals and expected outcomes, including specific contribution to Action objective and deliverables, or publications resulting from the STSM. Agreed plans for future follow-up collaborations shall also be described in this section. 

After the initial evaluation of the discovered sequence of the up-regulated Calpain protein, we have built a homology model of Leishamnia infantum Calpain based on the sequence similarity between parasites, like other strains of Leishamnia and Trypanosomas, and the isolated sequence. Furthermore, because of the minimal similarity between this sequence and the sequences of other species, we could aim for a specific targeting of this protein. The built model has been optimized and validated using various computational tools to ensure its accuracy and reliability for further drug design studies. Additionally, experimental validation of the model through in vitro and in vivo studies will be crucial to confirming its potential as a drug target for Leishmania infections. Chemdiv and Enamine are commercial databases that provide compound libraries meticulously assessed according to specified criteria. The downloaded libraries have been appropriately organized, resulting in the creation of a comprehensive database containing over 400,000 compounds. The generated library was used for a structure-based virtual screening to discover new potential hits. The screening was conducted in three distinct stages: HTVS, SPVS, and XPVS. The binding energy of the most effective molecules was then determined using the MM-GBSA approach. The highest-rated compounds were subjected to docking with the human calpain protease, and their binding energies were determined. ADME studies were performed on all the 400 selected compounds. We will use the acquired data to select the best one-hundred compounds that will be purchased and biologically evaluated.