COVID-19 and Flavonoids: In Silico Molecular Dynamics Docking to the Active Catalytic Site of SARS-CoV and SARS-CoV-2 Main Protease

27 Pages Posted: 19 May 2020

Date Written: May 12, 2020


Background: Inhibition of the main protease 3CLpro of SARS-CoV and SARS-CoV-2 is being targeted in the search for antivirals to shorten patient recovery times from COVID-19 disease. We investigated 72 flavonoids for their potential to bind with the active catalytic site of 3CLpro for SARS-CoV and SARS-CoV-2.

Methods: In silico molecular dynamics docking was performed using energy-minimized states of the flavonoids. Three variants of the active catalytic site of the protease 3CLpro were used: one based on x-ray crystallography for SARS-CoV, the second based on x-ray crystallography for SARS-CoV-2, and the third based on a 3D-modelled form of an amino acid sequence alignment of SARS-CoV-2 3CLpro from 8 humans. Docking involved characterization of the best putative pose in the “pocket” of the active site based on altering rotatable bonds in each molecule. The binding energy (kcal/mol) and number of hydrogen bonds were assessed during each pose. Mean binding energy across the 3 variants of 3CLpro was sorted in ascending order to rank each flavonoid, since more negative values indicate stronger binding.

Results: The top 10 flavonoids identified were amentoflavone, gallocatechin gallate, diosmin, epigallocatechin gallate, hidrosmin, catechin gallate, elsamitrucin, pectolinaren, quercetin, and isoquercetin. Other flavonoids investigated with significant binding energies were hesperidin, rutin, rhoifolin, and peurarin.

Conclusions: Many of the flavonoids identified have been reported in studies of in vitro laboratory-based inhibition of 3CLpro as well as in silico docking studies. Altogether, 14 flavonoids have now been identified in multiple studies: amentoflavone, daidzein, diosmin, epigallocatechin gallate, gallocatechin gallate, herbacetin, hesperidin, luteolin, naringin, peurarin, pectolinarin, quercetin, rhoifolin, and rutin. Existing antiviral clinical trials should consider adding an arm for combined therapy involving antiviral+flavonoid(s), assuming synergistic effects of combined therapy. Group sequential and adaptive human clinical trials should also be rapidly initiated though compassionate use to establish synergistic efficacy for one of more these flavonoids with antivirals. If efficacious synergism is observed, combinations of flavonoids could be consumed by the healthy public for prophylactic protection from SARS-CoV-2 infection providing formularies for dosing and frequency are established. Many of these flavonoids are already available as prescription-free supplements, so they are widely available.

Note: Funding: Research was funded by research and development support available from NXG Logic, LLC.

Conflict of Interest: No competing interests declared.

Ethical Approval: Not applicable.

Keywords: Docking, Coronavirus, SARS-CoV-2, SARS-CoV, COVID-19, Drug discovery, Pharmaceutics, Pharmacology, Repurposing, Chemoinformatics, Toxicology, Absorption, Distribution, Metabolism, Excretion, ADME

Suggested Citation

Peterson, Leif, COVID-19 and Flavonoids: In Silico Molecular Dynamics Docking to the Active Catalytic Site of SARS-CoV and SARS-CoV-2 Main Protease (May 12, 2020). Available at SSRN: or

Leif Peterson (Contact Author)

NXG Logic, LLC ( email )

Houston, TX 77030
United States


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