Molecular mechanism and multi-target inhibitory property of ruxolitinib as potential anti-SARS-CoV-2 agent: Network pharmacology study combined with molecular docking, molecular dynamics simulation and MM-PB(GB)SA analysis

• Ruxolitinib effect on SARS-CoV-2 was due to IFIH1, IRF7 and MX1 gene inhibition. • DDX58/IFIH-mediated interferon-I and -II signaling were significantly downregulated. • Expression of regulatory genes in severe COVID-19 were reversed with ruxolitinib. • Ruxolitinib showed effective binding energies against SARS-CoV-2 enzymes. • The anti-cancer drug ruxolitinib might be repurposed in severe COVID-19. Non-availability of specific therapeutics against COVID-19 led repurposing of approved drugs. The imbalance of cytokines in COVID-19 resembles cancer, and therefore, anti-inflammatory agents might reduce COVID-19 severity. The current study investigates the effect of RUXO (ruxolitinib) treatment in SARS-CoV-2 infected alveolar cells compared to the uninfected one from the GSE147507 dataset, along with its (RUXO) molecular docking to the SARS-CoV-2 druggable targets (3CLpro, helicase, PLpro and spike protein S2 subunit). The PPI (protein-protein interaction) network, functional enrichment and biological process of DEGs (differentially expressed genes) were studied using Cytoscape software and R programming tools. RUXO treatment elicited a similar response equivalent to that of SARS-CoV-2 uninfected cases by inducing defense response in host with the viral infection by RLR and NOD like receptor pathways. The RUXO effectiveness against SARS-CoV-2 was majorly caused by the substantial suppression of IFIH1, IRF7 and MX1 genes and inhibition of DDX58/IFIH1-mediated induction of interferon-I and -II signalling. Molecular docking revealed stable complex formation between RUXO and SARS-CoV-2 target with binding energy ranging from -7.9 kcal to -6.6 kcal. Moreover, molecular dynamics simulation and MM-PB(GB)SA binding free energy calculations justified that RUXO is more effective than the reference antiviral, nirmatrelvir, against the 3CLpro of SARS-CoV-2. Overall, the multitarget inhibitory efficacy of RUXO, thus, explains the usefulness of the drug against SARS-CoV-2 infection causing COVID-19.