Computational Structural and Dynamic Insights into the Proposed TcP21–CXCR4 Interaction: A Consensus-Based Multireplica Simulation Approach

Chagas disease, caused by Trypanosoma cruzi, is a neglected tropical disease with limited therapeutic options, underscoring the need for novel targeted strategies. The parasite’s secreted 21 kDa virulence factor, TcP21, promotes extracellular amastigote host-cell invasion and persistence by interacting with the human chemokine receptor CXCR4, a class A G protein-coupled receptor. Despite its biological importance, the structural determinants governing TcP21–CXCR4 complex formation remain unknown. To elucidate the molecular basis of this host–parasite recognition, multiple initial candidate binding modes were generated via molecular docking using the experimentally resolved active-state CXCR4 structure (PDB ID: 8K3Z) and then subjected to extensive multireplica molecular dynamics (MD) simulations within a biomimetic lipid bilayer. Consensus analyses integrating solvent-accessible surface area (SASA), dynamic contact profiling, and hydrogen bond occupancy across independent conformational ensembles were used to characterize recurrent features of the proposed interface. The results support a structural model in which TcP21 engages CXCR4 through a continuous interaction region localized within the LYS23–PHE39 segment, whereas CXCR4 presents a hierarchically organized and distributed interface. Within this model, a relatively stable interaction core involving the TM5, TM6, and TM7 domains is predominantly characterized by van der Waals contacts, while a more conformationally adaptable peripheral anchoring region involving the ECL2, TM1, and N-terminal domains contributes additional intermolecular interactions. The recurrence of these features across independent simulations supports their consideration as candidate determinants of TcP21–CXCR4 recognition, although their structural and biological relevance remains to be experimentally established. Overall, the resulting computational model provides atomistic structural hypotheses for TcP21–CXCR4 recognition and a basis for future experimental studies to examine the predicted interface and assess its potential relevance to TcP21–CXCR4-mediated interactions.