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Coronavirus disease 2019 (COVID-19) is an ongoing global pandemic with very limited specific treatments To fight COVID-19, various traditional antiviral medicines havebeen prescribed in China to infected patients with mild to moderate symptoms and received unexpected success in controlling the disease However, the molecular mechanisms of how these herbal medicines interact with the virus have remained elusive It is well known that the main protease (Mpro) of SARS-CoV-2 plays an important role in maturation of many viral proteins such as the RNA-dependent RNA polymerase Here,we explore the underlying molecular mechanisms of the computationally determined tocandidate–rutin, a key component in many traditional antiviral medicines such as Lianhuaqinwen and Shuanghuanlian, for inhibiting the viral target–Mpro Using in silico methods (docking and molecular dynamics simulations), we revealed the dynamics and energetics of rutin when interacting with the Mpro of SARS-CoV-2, suggesting that the highly hydrophilic rutin molecule can be bound inside the Mpro’ pocket (active site) and possibly inhibit its biological functions In addition, we optimized the structure of rutin and designed a more hydrophobic analog which satisfies the rule of five for western medicines and demonstrated that it possesses a much stronger binding affinity to the SARS-COV-2’s Mpro br /div
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