3.6.1. Flavonoids against SARS-CoV-2 MPro

Using molecular docking, Cherrak et al. identified quercetin-3-O-rhamnoside, myricetin 3-rutinoside, and rutin as the potential inhibitors of SARS-CoV-2 Mpro in decreasing order with binding energies of <sup>−</sup>9.7, <sup>−</sup>9.3, and <sup>−</sup>9.2 kcal.mol−<sup>1</sup> respectively [142]. Another report also confirmed that rutin is a potential flavonoid against the SARS-CoV-2 MPro with a binding energy of −11.187 kcal/mol [143]. A recent study supported the inhibitory effect of rutin on SARS-CoV-2 Mpro via molecular docking with a binding energy −15.63 kcal/mol. Furthermore, ADMET analysis, combinatorial molecular simulations, and hybrid QM/MM approaches concluded that rutin binds very strongly at the active sites of SARS-CoV-2 MPro by forming three hydrogen bonds at His 163, Glu 166, Gln189 residues [144]. Rakshit et al. screened various flavonoids against MPro and identified the top five potential flavonoids in order of rhoifolin, 5,7-dimethoxyflavanone-40-O-b-d-glucopyranoside, baicalin, luteolin, and kaempferol based on their binding energies of −9.28, −8.81, −8.29, −8.14, −8.11 kcal/mol [145]. The inhibitory effect of luteolin against the Mpro is recently confirmed [146]. Fayyaz et al. screened several flavonoids and identified three potentially active flavonoids, whose activities against SARS-CoV-2 Mpro were in the order of rhodiolin > baicalin > silymarin based on their binding energy (−9.05, −8.85, −8.71 kcal/mol respectively) and dissociation constant (0.23, 0.33, 0.41 µm, respectively) using molecular docking and simulation studies [147]. Thioflavonol also inhibits Mpro [148] along with other flavonoids such as apigenin, daidzein, quercetin, kaempferol, luteolin, epigallocatechin, and kaempferol using molecular docking and simulation analysis [104].

The MPro is considered the most promising drug target for SARS-CoV-2 due to its proteolytic activity, cleaving viral polyprotein into independent functional proteins required for SARS-CoV-2 replication [149–151]. The other reason for its therapeutic importance is its dissimilarity to any human cell protease [152–154] and its similarity with the MPro of SARS-CoV [155]. The most common active site residues of MPro were Glu166, His163, and Met165, which were involved in the interaction with most of the flavonoids.

#### 3.6.2. Flavonoids against SARS-CoV-2 Spike Glycoprotein

Rutin inhibits the SARS-CoV-2 spike glycoprotein but with less binding energy (−7.9 kcal/mol) [143]. On the other hand, naringin inhibits the spike glycoprotein more effectively with binding energy −9.8 kcal/mol compared to standard drug dexamethasone with the binding energy of −7.9 kcal/mol [156]. Fayyaz et al. described potentially active flavonoids, whose activities against SARS-CoV-2 spike protein were in the order of rhodiolin > hesperidin (with active site 1) > hesperidin (with active site 2) > silyhermin based on their binding energy (−8.68, −8.53, −8.18, −8.05 kcal/mol, respectively) and dissociation constant (0.43, 0.56, 1.01, 1.25 µm respectively) [147]. The authors showed that hesperidin could bind to two different active sites on the spike glycoprotein with different binding energies. Teli et al. highlighted that rutin could serve as a dual receptor inhibitor against the Mpro and spike glycoprotein of SARS-CoV-2 with improved ADMET parameters.
