Integrated Computational and Experimental Evaluation of selected Flavonoids as a Multi-Target Modulator of Viral Entry and Protease Activity.

Abstract

Flavonoids have been widely investigated for their antiviral and anti-inflammatory properties, but their mechanisms of action often remain insufficiently defined. In the present study, high-purity flavonoids were evaluated using an integrated workflow combining molecular docking, LigPlot+ interaction mapping, surface plasmon resonance (SPR), fluorescence-based TMPRSS2 inhibition assays, and cell-based viability studies. Docking with AutoDock Vina identified Hesperidin as the strongest overall candidate among the compounds evaluated. Hesperidin showed strong active-site engagement with TMPRSS2, including interactions with catalytic residues His296, Asp345, and Ser441, and stable binding within the SARS-CoV-2 main protease (Mpro) pocket. Comparative docking showed weaker or more peripheral interaction patterns for Rutin and moderate Spike binding for Hesperidin and Rutin. Experimental validation demonstrated dose-dependent inhibition of TMPRSS2 activity with an IC50 of 79.1 {micro}M for Hesperidin and 43.5 {micro}M for Hesperetin, while Rutin showed partial inhibition without a defined IC50 in the tested range. In Calu-3 cells, pre-treatment with Hesperidin or Rutin reduced SARS-CoV-2 Spike-induced cytotoxicity by approximately 30% without detectable intrinsic toxicity at the concentrations tested Docking analysis of Hesperidin and Rutin with the SARS-CoV-2 Spike protein revealed moderate interaction patterns involving residues such as Asn343, Ser371, and Val367. Hydrogen bond distances were generally in the range of approximately 2.9-3.3 [A], indicating moderate stabilization compared with the stronger active-site interactions observed for Hesperidin in TMPRSS2. The resulting binding poses suggest that these flavonoids can associate with structurally relevant regions of the Spike receptor-binding domain; however, they do not strongly overlap with the key residues required for ACE2 interaction. Rutin, in particular, exhibited a more peripheral and distributed binding mode within the Spike-ACE2 complex, indicating limited potential for direct disruption of the binding interface. In addition to SARS-CoV-2 targets, docking analysis extended to influenza viral proteins revealed moderate interaction of Hesperidin with hemagglutinin (HA) and strong catalytic-pocket binding of Rutin to neuraminidase (NA), involving key residues associated with enzymatic activity. These findings broaden the scope of the study to include influenza viral entry and release mechanisms, supporting a multi-virus, multi-target framework.