Identification of phyto-immunomodulators of CD8A and PTPRC from Schinus molle as potential therapeutics of chronic chagasic cardiomyopathy via integrative transcriptomics and molecular dynamic simulation approaches
The most terrifying cardiac complication of Trypanosoma cruzi infection is Chronic Chagasic Cardiomyopathy (CCC), which is the complication that occurs in about one-third of the infected individuals and is one of the major causes of non-ischemic heart failure in Latin America. Although fairly disease-burdening, the molecular pathways of CCC immunopathology are not fully studied, and disease-modifying therapy is currently lacking. This study used an integrative computational strategy involving RNA-seq transcriptomics, protein-protein interaction (PPI) network analysis, gene ontology and KEGG pathway enrichment, molecular docking, ADMET profiling, and molecular dynamics simulations to define the host immune transcriptional environment of CCC and determine which phytochemicals may regulate its major regulation targets. RNA-seq analysis of severe CCC cardiac tissue compared to healthy controls (GEO: GSE191081) found 2,973 significantly differentially expressed genes (DEGs), 2,239 of which were upregulated, and 734 of which were downregulated. The analysis of functional enrichment showed that the upregulated genes were most linked to T cell activation, antigen receptor-mediated signaling, cytokine production, and MHC complex assembly, whereas downregulated genes were enriched in potassium ion transport, sarcoplasmic reticulum functioning and cardiomyocyte survival pathways. Multi-algorithm hub gene analysis with cytoHubba on PPI networks revealed 5 core regulatory genes, including CD4, PTPRC, CD8A, IFNG and FCGR3A, that were invariably within the top five network topologies of all five topological models (Degree, MCC, MNC, Closeness, and EPC). Among them, CD8A (PDB: 1CD8) and PTPRC (PDB: 1YGR) were chosen to be screened virtually against 110 drug-like phytochemical compounds of Schinus molle downloaded in the IMPPAT database with and without structure. The highest-ranking compound found in molecular docking relative targeting PTPRC (−7.70 kcal/mol) and CD8A (−6.94 kcal/mol), IMPHY006486, was also found to have strong binding affinities with diverse interactions with the essential active site residues, such as Ser928, Gln882, Phe890 (PTPRC) and Thr30, Phe48, Tyr51 (CD8A). Favorable pharmacokinetic properties of the lead compounds including high intestinal absorption, lack of risk of CYP-mediateddrug interaction and negative AMES mutagenicity were confirmed by ADMET profiling. All four protein-ligand complexes were found to be structurally stable at 100 nanoseconds in molecular dynamics simulations, with moderate backbone RMSD (1.52–2.82 A), maintained components of secondary structure, and maintained protein-ligand interaction fractions over the trajectories. Such results indicate that IMPHY006486, IMPHY004111, and IMPHY003082 emerged as computationally prioritized candidates for further experimental evaluation as potential modulators of CD8A and PTPRC. They should be validated experimentally to demonstrate their therapeutic potential. This is a systems-level and structure-based study that points out important immune hubs in the development of CCC pathogenesis and shows how combined transcriptomics and molecular modeling can identify immunomodulatory candidates faster in the context of Chagas heart disease.