Exploring Binding\nSites in Chagas Disease Protein\nTcP21 Using Integrated Mixed Solvent Molecular Dynamics Approaches

Chagas disease, caused by the protozoan Trypanosoma cruzi,\nremains\na significant global health burden, particularly in Latin America,\nwhere millions are at risk. This disease predominantly affects socioeconomically\nvulnerable populations, aggravating economic inequality, marginalization,\nand low political visibility. Despite extensive research, effective\ntreatments are still lacking, partly due to the complex biology of\nthe parasite and its infection mechanisms. This study focuses on TcP21,\na novel 21 kDa protein secreted by extracellular amastigotes, which\nhas been implicated in T. cruzi infection\nvia an alternative infective pathway. Although the potential of TcP21\nfor understanding Chagas disease is promising, further exploration\nis necessary, particularly in identifying potential binding sites\non its surface. Computational tools offer a versatile and effective\nstrategy for preliminary binding site assessment, facilitating a more\ncost-efficient allocation of experimental resources. In this study,\nwe employed three independent computational approachesmixed\nsolvent molecular dynamics simulations (MSMD), fragment-based molecular\ndocking, and pharmacophore model docking coupled with molecular dynamics\nsimulationsto identify potential binding sites and provide\ncomprehensive insights into TcP21. The three methodologies converged\non a common site located on the external surface of the protein, characterized\nby key residues such as GLU55, ASP52, VAL70, ILE62, and TRP77. The\nprotonated amino, acetamido, and phenyl groups of the pharmacophore\nprobe were consistently observed to interact with the site via a network\nof salt bridges, hydrogen bonds, charge–charge interactions,\nand alkyl-π interactions, suggesting these groups play a significant\nrole in ligand binding. This study does not aim to propose specific\ntherapeutic hits but to highlight a still unknown and unexplored protein\ninvolved in T. cruzi cell invasion.\nIn this regard, given the strong correlation between the three distinct\napproaches used for mapping, we consider this study offers valuable\ninsights for further research into P21 and its role in Chagas disease.