Estudos in silico da proteína TcP21 no contexto da doença de Chagas

Abstract

Chagas disease, caused by Trypanosoma cruzi, remains a significant public health concern, with still limited therapeutic options. In this context, the TcP21 protein, secreted by extracellular amastigote forms, has emerged as a molecular target of interest, involved in alternative and still poorly explored infection pathways. This thesis aimed to characterize TcP21 in silico from two complementary perspectives: the identification and characterization of binding sites on its surface, and the elucidation of potential interaction interfaces in the TcP21–CXCR4 complex. The integration of mixed-solvent molecular dynamics simulations, fragment-based molecular docking, and pharmacophore-based molecular docking followed by molecular dynamics, driven by occupancy-based volumetric maps, enabled the convergent identification of a binding site on TcP21. This site involved the key residues GLU55, ASP52, VAL70, ILE62, and TRP77. The observed interactions, including salt bridges, hydrogen bonds, charge–charge interactions, and π–alkyl contacts, formed an intermolecular network consistent with the recognition of protonated amino, acetamido, and phenyl functional groups. Binding modes of the TcP21–CXCR4 complex were generated by molecular docking and subsequently refined through multireplica molecular dynamics simulations in a biomimetic environment. Consensus analysis of the trajectories, based on a ΔSASA-driven multimetric scoring function and on the evaluation of intermolecular contacts (number, frequency, and temporal stability), revealed a continuous segment in TcP21 (LYS23–PHE39) with typical protein–protein interface properties. In CXCR4, the transmembrane domains TM5, TM6, and TM7 formed a stabilized structural core within the extracellular vestibule, whereas regions such as ECL2 and the N-terminal domain exhibited greater conformational flexibility. The resulting interface displayed a modular organization, predominantly stabilized by van der Waals interactions, with additional electrostatic and polar contributions conferring directional specificity to the molecular recognition process. The integrated analysis of the studies indicated the presence of two functionally specialized regions in TcP21, potentially associated with pharmacophore ligand binding and host receptor recognition, respectively