Integrative analysis of miRNA in COVID-19 using machine learning and in-silico approaches

The complex pathophysiology of coronavirus disease 2019 (COVID-19) and the quest for effective therapeutic targets remain critical challenges. While miRNA dysregulation is documented in severe cases, expression profiles during the acute phase of mild infections, particularly in home-recovery settings, remain poorly understood. In this study, key SARS-CoV-2 target genes were identified via gene network analysis. Protein–miRNA interactions were simulated using molecular docking and molecular dynamics (MD) simulations to evaluate binding stability. Subsequently, RT-PCR was employed to quantify miR-451a and miR-21-3p expression in blood samples from severe (n = 23) and mild (n = 22) COVID-19 patients, compared to a healthy control group (n = 24). Molecular docking analysis revealed that miR-451a exhibits a markedly stronger binding affinity for the SARS-CoV-2 main protease (Mpro; 6LU7) compared to miR-21-3p, yielding significantly more negative docking scores of − 298.01 kcal/mol and − 203.11 kcal/mol, respectively. Further in-silico analysis indicated that miR-451a interacts with key cytokines and the MAPK pathway. Clinical quantification confirmed that miR-451a expression was significantly down-regulated in severe patients compared to the control group (p = 0.01). Notably, miR-451a also showed significant differential expression in mild patients recovering at home, whereas miR-21-3p expression did not reach statistical significance. Integrated molecular docking, MD simulations, and principal component analyses (PCA) consistently suggested that miR-451a acts as a potent inhibitor of SARS-CoV-2 Mpro and a negative regulator of inflammation. Unlike previous studies predominantly focused on hospitalized or critical cases, this investigation provides the first evidence of significant miR-451a down-regulation in mild COVID-19 patients during the acute phase of home recovery. Our multi-faceted approach underscores the potential of miR-451a as a crucial regulatory biomarker and a promising candidate for future viral inhibition strategies, effectively highlighting the study’s novelty and clinical relevance.