Análise comparativa das Ecto-NTPDase 1 de Homo sapiens e Schistosoma mansoni por meio de modelagem tridimensional, dinâmica molecular e docking receptor-ligante

Abstract

Schistosomiasis is a neglected disease caused by parasites of the genus Schistosoma. According to the World Health Organization, over 200 million people worldwide were infected, and 4 to 6 million people only in Brazil. The main treatment is the use of the drug praziquantel, but there are reports in the literature suggesting the parasite’s resistance to praziquantel. This situation raised the need for search new molecular targets and new drugs for treating this disease. A group of proteins as potential targets is NTPDase. These enzymes hydrolyse nucleotides (e.g., ADP and ATP) in the presence of bivalent cations, and they are described in different organisms. In the parasite Schistosoma mansoni, an isoform of NTPDase„ named SmATPDase1 or Sm1, was described as a protein anchored in the plasma membrane of cells in the seed coat of the adult worm. According to the literature, this isoform is the most expressed enzyme in the tegument of adult worms. Due to the location and importance of nucleotide triphosphates in the hemostatic and activation of immune cells, Sm1 has been suggested to be involved in the regulation of nucleotide concentrations around the parasite, which could be a mechanism of immune evasion in schistosomiasis. Based on the above assumptions, it has been proposed the use of Sm1 as a possible target for new schistosomicide drugs. In mammals have been described eight isoforms. Isoform 1 of human NTPDase (HsNTPDase1), also known as CD39, is present in the endothelial cells of blood vessels, and it is responsible for the regulation of extracellular concentrations of ATP and ADP. In this paper, we present 3D models of Sm1 and CD39, constructed by homology modeling technique. Due to the similarity of 3D structures of both models, it was necessary to perform a comparative structural analysis of both enzymes by molecular dynamics simulations and and receptorligand docking. Cavities prediction were made in Sm1’s model and two cavities were selected, the active site and an alternative binding site proposed in this work. After, it was performed molecular dynamics simulations involving models of Sm1 and CD39, and PDB3ZX3 and PDB3CJA templates. Two simulations were performed for each model, one in the presence of ANP (ATP analog) in the active-site and other in the absence. In models’ simulations, structures were coupled to a POPC membrane, and the simulation time was 32ns. Simulation time for templates was 40ns. Simulations showed that the alternative site in Sm1 without ANP presented conformational changes which were not observed in simulations of CD39 and Sm1 with ANP. This suggests that the presence of ligand in the active site contributes in stabilizing the structure of Sm1 and CD39. Druggability and clustering analysis were performed with conformations generated through simulations. In this work, we proposed the use of GLCM methodology with Kmeans algorithm for clustering analysis, aiming to select conformations from trajectories that could be used in receptor-ligand docking. We analyzed the affinity of three ligands (ANP, ARL67153 and praziquantel) in the active site and in the alternative site of Sm1 and CD39 enzymes. The best results for active site were obtained with ANP and ARL67153 ligands, in all simulations. For alternative site, the best results were obtained with conformations from the simulation of Sm1 without ANP in the active site. For CD39’s simulations, none of the ligands were docked within the cavity of alternative site. With regard to praziquantel, the best results were observed in the active site of Sm1 and CD39. It is possible to conclude that the alternative site of Sm1 is a region which can be used for docking of possible inhibitors of this enzyme.