Exploring Binding Sites in Chagas Disease Protein TcP21 Using Integrated Mixed Solvent Molecular Dynamics Approaches.

Chagas disease, caused by the protozoan Trypanosoma cruzi, remains a significant global health burden, particularly in Latin America, where millions are at risk. This disease predominantly affects socioeconomically vulnerable populations, aggravating economic inequality, marginalization, and low political visibility. Despite extensive research, effective treatments are still lacking, partly due to the complex biology of the parasite and its infection mechanisms. This study focuses on TcP21, a novel 21 kDa protein secreted by extracellular amastigotes, which has been implicated in infection via an alternative infective pathway. Although the potential of TcP21 for understanding Chagas disease is promising, further exploration is necessary, particularly in identifying potential binding sites on its surface. Computational tools offer a versatile and effective strategy for preliminary binding site assessment, facilitating a more cost-efficient allocation of experimental resources. In this study, we employed three independent computational approaches─mixed solvent molecular dynamics simulations (MSMD), fragment-based molecular docking, and pharmacophore model docking coupled with molecular dynamics simulations─to identify potential binding sites and provide comprehensive insights into TcP21. The three methodologies converged on a common site located on the external surface of the protein, characterized by key residues such as GLU55, ASP52, VAL70, ILE62, and TRP77. The protonated amino, acetamido, and phenyl groups of the pharmacophore probe were consistently observed to interact with the site via a network of salt bridges, hydrogen bonds, charge-charge interactions, and alkyl-π interactions, suggesting these groups play a significant role in ligand binding. This study does not aim to propose specific therapeutic hits but to highlight a still unknown and unexplored protein involved in cell invasion. In this regard, given the strong correlation between the three distinct approaches used for mapping, we consider this study offers valuable insights for further research into P21 and its role in Chagas disease.