key: cord-0732466-mo01t2ix
authors: Raj, Vinit; Lee, Jin-Hyung; Shim, Jae-Jin; Lee, Jintae
title: Antiviral activities of 4H-chromen-4-one scaffold-containing flavonoids against SARS–CoV–2 using computational and in vitro approaches
date: 2022-02-17
journal: J Mol Liq
DOI: 10.1016/j.molliq.2022.118775
sha: 40a9df55e6ae40e2bdebe3a4bc05729a82e16eee
doc_id: 732466
cord_uid: mo01t2ix

The widespread outbreak of the novel coronavirus called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused the main health challenge worldwide. This pandemic has attracted the attention of the research communities in various fields, prompting efforts to discover rapid drug molecules for the treatment of the life-threatening COVID-19 disease. This study is aimed at investigating 4H-chromen-4-one scaffold-containing flavonoids that combat the SARS-CoV-2 virus using computational and in vitro approaches. Virtual screening studies of the molecule’s library for 4H-chromen-4-one scaffold were performed with the recently reported coronavirus main protease (M(pro), also called 3CL(pro)) because it plays an essential role in the maturation and processing of the viral polyprotein. Based on the virtual screening, the top hit molecules such as isoginkgetin and afzelin molecules were selected for further estimating in vitro antiviral efficacies against SARS–CoV–2 in Vero cells. Additionally, these molecules were also docked with RNA-dependent RNA Polymerase (RdRp) to reveal the ligands-protein molecular interaction. In the in vitro study, isoginkgetin showed remarkable inhibition potency against the SARS-CoV-2 virus, with an IC(50) value of 22.81 μM, compared to remdesivir, chloroquine, and lopinavir with IC(50) values of 7.18, 11.63, and 11.49 μM, respectively. Furthermore, the complex stability of isoginkgetin with an active binding pocket of the SARS-CoV-2 M(pro) and RdRp supports its inhibitory potency against the SARS-CoV-2. Thus, isoginkgetin is a potent leading drug candidate and needs to be used in in vivo trials for the treatment of SARS-CoV-2 infected patients.

In the COVID-19 pandemic caused by the virulent nature of human coronavirus called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) [1, 2] , the number of people infected globally is increasing rapidly [3] [4] [5] . In the current scenario, SARS-CoV-2 has caused more than 38 million COVID-19 cases and more than one million deaths globally (https://www.worldometers.info/coronavirus/) compared to the more virulent and less transmitted SARS-CoV outbreak in 2002-2003 (which caused only 800 cases and 774 deaths) [6] . Now, there is an urgent need for antiviral drug molecules to treat COVID-19 patients. positions, primarily at conserved Leu Gln↓ Ser Ala Gly↓ sequences, and leads to the assemblage of the viral replicase complex [7] [8] [9] .

As a reported vital role of the SARS-CoV-2 M pro in virus replication [10] , the SARS-CoV-2 M pro is an essential molecular drug target for the development and discovery of antiviral drug molecules against the novel coronavirus causing COVID-19. Equivalent cleavage specificity has not yet been described for human proteases, and thus, inhibition of the SARS-CoV-2 M pro is unlikely to cause any toxicity in humans [11] . Recently, the X-ray structure of the SARS-CoV-2 M pro has been elucidated (PDB ID: 6Y2F) [10] , and this offers a means of discovering its inhibitors. In general, for the development or repurposing of the antiviral drug against the SAS-CoV-2, S protein, ACE2, TMPRSS2 (transmembrane protease serine 2) RNA-dependent RNA polymerase (RdRp), and PL pro (papain-like protease) are also broadly considered as foremost targets for the antiviral drugs towards SARS likely SARS-CoV-2 and other coronaviruses [12] . Some old drug molecules have been repurposed against the SARS-CoV-2 such as dexamethasone, remdesivir, and avifavir [13] . One of them, remdesivir is an adenosine analogue that inhibits viral RNA polymerase with RdRp. Hence, RdRp is another alternative target for the discovery and development of possible targeted molecules for the treatment of COVID-19 patients.

Moreover, in COVID-19 patients, it has been observed that inflammatory molecule levels (e.g. pro-inflammatory cytokines, IL-1β, IL-6, IL-7, IL-8, IL-9, IL-10, reactive protein fibroblast growth factor, granulocyte-colony-stimulating factor, IFN, tumor necrosis factor, granulocyte-macrophage colony-stimulating factor, macrophage inflammatory protein 1 α, and vascular endothelial growth factor) are higher in the cells of the lung, and lead to acute respiratory distress, severe injury, and death [14, 15] .

Because there are fewer options of marketed repurposed antiviral drugs against the SARS-CoV-2. Owing to the lack of toxicity of natural flavonoids, and the fact that their ability to synergize with conventional drug candidates was established, their functional groups easily interact with cellular targets, and they interrupt various pathways [16] . Thus, these features make flavonoids possible candidates for interacting with the coronavirus life cycle. From the chemical site, flavonoids have the hydroxylated phenolic group that is responsible for their antioxidant activity and are designed with two benzene rings (A-and B-rings) and linked with the heterocycle group pyrene scaffold (C-ring). As previously reported, various pharmacological activities of 4H-chromen-4-one synthetic scaffolds [17] , and the significant advancement of natural flavonoids containing 4H-chromen-4-one scaffold have exhibited good antiviral, antibacterial, anti-inflammatory, anticancer, and antioxidant effects, and they also interrupt the RNA picornavirus and interfere with the replication cycle of DNA viruses [16, 18, 19] . Additionally, ginkgetin, isoginkgetin, and bilobetin are natural flavonoids that these molecules have the 4H-chromen-4-one scaffold and possess significant pharmacological activities [20] [21] [22] . Thus, the importance of all these pharmacological factors has attracted the attention of various research groups to discover and explore the role of 4H-chromen-4-one scaffolds against the current COVID-19 pandemic. Previous in silico studies of various flavonoids with the SARS-CoV-2 M pro have recently been reported [23] [24] [25] [26] [27] [28] , which suggest that natural flavonoids might be effective drug molecules against SARS-CoV-2. In these previous studies, ginkgetin, isoginkgetin, and bilobetin are among a hundred hits, but no one has been yet reported any computational stabilities of isoginkgetin and afzelin with the SARS-CoV-2 M pro or an antiviral in vitro assay against SARS-CoV-2.

4H-chromen-4-one containing flavonoids possess a broad range of biological activities including anti-inflammatory effectiveness [29] . Based on the previous anti-inflammatory role of H-chromen-4-one, we hypothesized that these molecules may be effective drug candidates for the treatment of COVID-19 because the level of the proinflammatory cytokines is high in the lung cells of COVID-19 patients [30] . Likewise, the recent advantage of the RdRp and SARS-CoV-2 M pro targets in the translation of the viral RNA makes them important molecular targets for the development SARS-CoV-2 inhibitors. Additionally, the possible binding of 4Hchromen-4-one scaffold with RdRp and SARS-CoV-2 and its previous biological activities can make them an effective scaffold for the discovery of potential lead molecules against the COVID-19 pandemic. Consequently, 4H-chromen-4-one containing flavonoids maybe act not only suppressing the level of the proinflammatory cytokine in the lung cells of COVID-19 patients but also blocking the RdRp or SARS-CoV-2 M pro active binding site, leading to inhibition of the translation of viral RNA. To corroborate this hypothesis, we performed virtual screening of a series of 4H-chromen-4-one containing flavonoids with the SARS-CoV-2 M pro target. Further, the higher binding energy molecules were selected and redocked with RdRp or SARS-CoV-2 M pro to confirm the conformation binding. The molecular dynamic simulation was further performed to analyze the ligand-receptor complex conformation behavior in aqueous media. Additionally, density functional theory was used to reveal the reactivity of molecules. Finally, in vitro antiviral activities of two flavonoids (namely isoginkgetin and afzelin) were carried out against the SARS-CoV-2 in infected Vero cells. This is the first report on molecular simulation and in vitro antiviral activities of isoginkgetin, and afzelin.

Ligands structures were collected from the PubChem library. The crystal structure of the SARS-CoV-2 M pro protein (PDB: 6LU7) [31] and RNA-dependent RNA polymerase (RdRp), PDB: 6M71 were retrieved from the RCSB protein database (https://www.rcsb.org/) at a resolution of 2.16, 2.90Å, respectively [32] . To refine the proteins' structure, the proteins preparation wizards' tool of the Schrodinger suite was used. Extra co-crystallizing molecules of water were deleted, with the essential number of required hydrogens was included in the complex structure of the SARS-CoV-2, and RdRp proteins.

Two-dimensional structures of 4H-chromen-4-one containing flavonoids (total 96) were downloaded in a simulation description format (SDF) from the PubChem data bank (https://pubchem.ncbi.nlm.nih.gov/). Flavonoids structures were prepared using LigPrep tools of the Schrodinger suite, and all molecular structures were optimized over minimum energy to ensure the essential proper arrangement of molecules in space using a density functional theory (DFT) approach, Gaussian 09 suite [33, 34] . Conformations and bond orders were minimized and refined using the OPLS 2005 force field [35] . After the energy minimization, all molecular structure was saved in pdb files. These prepared ligand libraries were subjected to analysis for structure-based virtual screening with an active binding pocket of the SARS-CoV-2 M pro [36] .

First, the active binding pocket of the SARS-CoV-2 M pro was predicted by the CASTp server ( Fig. 1) . Also, the CASTp server predicted the active binding site of the SARS-CoV-2 M pro was again confirmed by VINA random 25 runs between ligands and the SARS-CoV-2 M pro ( Fig. S1 ). Afterward, the predicted active site was assigned for the grid to the virtual screening,

where drug molecules were treated as rigid entities although the assigned active pocket of the receptor was treated as a flexible entity [37, 38] . To ensure the precision of docking results (such as reliability, validation, and reproducibility), a comparative study of molecular docking was achieved by two molecular docking methods, namely AUTODOCK [39] and VINA [40] .

Also, binding energies, as well as ligand-receptor interactions, were revealed between natural flavonoids and the SARS-CoV-2 M pro by the two computational approaches [39] . For the docking with RdRp protein, ARG553, THR556, THR687 and ALA685 was assigned active pocket. To capture the visualization of complex structure interactions of afzelin and isoginkgetin with the protein, BIOVIA Discovery Studio Visualizer was used. 

For the estimation of pharmacokinetic characteristics of top hit targeted molecules, we carried out ADME study using the QikProp software and swissADME, selecting as following properties; topological polar surface, gastrointestinal absorption, blood-brain barrier permeability, Lipinski violations, bioavailability score, Log Kp (skin permeation), and CYP1A2 inhibitor. An orally active pharmaceutical agent must not have molecular weight >500 g/mol, LogP >5, hydrogen-bond-donating atoms >5, hydrogen-bond-accepting atoms >10, and topological polar surface >140.

To analyze the conformation stabilities of isoginkgetin and afzelin with the SARS-CoV-2 M pro , molecular dynamic simulations were carried out in an explicit water solution using YASARA dynamic software [42] were only predicted for the sidechains of His, Asp, Lys, and Glu residues [43] . Initially, 298 K temperature was assigned and gradually increased to achieve equilibrium. Afterward, an AMBER14 molecular dynamic force field was selected under physiological conditions at 0.9% NaCl, and pH 7.4 for MD simulation [44] . The total energy of the system was minimized initially via steepest descent minimization, as in a previously described method [45] . Finally, the complex system structure was submitted to an MD run of more than 100 ns at a 310 K, constant temperature, and 1ps pressure. MD trajectories were saved for every 250 ps for further analysis. These MD trajectories were subjected to evaluate the RMSD of backbone, heavy atoms by the YASARA template file (md_analysis.mcr). Also, the binding energy of each conformation of complexes was analyzed by the YASARA template file (md_analyzebindenergy.mcr) [46] . The usual conformation stabilities of models were assessed from simulations and root means square deviations (RMSDs). According to the YASARA manual, free binding energies were analyzed without the participation of the entropy term.

YASARA delivers positive binding energies, and thus, higher positive energies show favorable binding with a receptor in the assigned force field, although negative binding energies specify a weak binding. Finally, trajectory analysis data were found via MD simulation and denoted graphically using SigmaPlot 10.0. The flavonoids-SARS-CoV-2 M pro binding conformation complexes were visualized using the Discovery Studio visualization software.

To optimize and evaluate the stability of the chemical structures of flavonoids, frontier molecular orbitals (FMOs) including lowest unoccupied molecular orbitals (LUMO), and highest occupied molecular orbitals (HOMOs) were analyzed using DFT [47] . Also, to determine the stability and reactivity of the orbitals of natural flavonoids, HOMO-LUMO energy gaps for flavonoid molecules were analyzed with the following equation [48] :

Chemical hardness (η) and chemical potentials (μ) were calculated using the energy associated with HOMOs and LUMOs:

Electronegativity (χ) and electrophilicity (ω) were estimated by using ionization potentials (I), which are mostly defined as negative E HOMO values , while electron affinity (A) was defined as being equal to negative E LUMO values :

For optimization of flavonoid chemical structures, B3LYP level theory with acetone as a solvent media was used with a program of the Gaussian 09 suite, where a large gap between HOMO and LUMO orbitals showed better stability in the chemical structure of molecules, and the η value indicates the reactivity of a molecule, i.e. a higher value for η shows less reactivity of the chemical scaffold [47] .

In vitro assessment of antiviral potency of natural flavonoids against SARS-CoV-2

The antiviral activities of flavonoids were estimated per a previously described method [49] , and for this process, viral infected cells were used for antibodies specific to the viral nucleocapsid (N) protein. A dose-response curve (DRC) was made for individual compounds.

The images were analyzed with immunofluorescence using Columbus software (Perkin Elmer). Welgene). For in vitro studies, all reagents were well mixed in DMSO.

DRC analysis was performed using the immunofluorescence method in the previously described protocol [49] . Briefly, 384-tissue culture μClear plates (Greiner Bio-One) were 

To reveal the interactions between natural flavonoids and the SARS-CoV-2 M pro , we performed virtual screening of a series of 4H-chromen-4-one scaffold-containing natural flavonoids in total 96 (Table S1 ). The binding domain of the active pocket of the SARS-CoV-2 M pro was confirmed by the CASTp server and random 25 dockings with the SARS-CoV-2 M pro , where we found that domain 1 of SARS-CoV-2 is the main binding pocket for the drug molecules, which is similar to the previously reported positive control α-ketoamide 13b binding [41] . All 4H-chromen-4-one scaffold-containing molecules were screened with the same predicted active binding site of the SARS-CoV-2 M pro , and as a result, all compound's binding affinities were found in the range -6.0 kcal/mol to -9.7 kcal/mol (VINA) (Table S1) . Furthermore, redocking studies using AUTODOCK were carried out for three good binding flavonoids (below -9 kcal/mol) with the SARS-CoV-2 M pro , showing that binding energies range between -11.3 and 13.5 kcal/mol (Table 1) Also, it was found that isoginkgetin formed eight π-π bonds, and one hydrogen bond with amino acid residues Thr26, Gly113, Asn142, Cys145, His163, Met165, and Glu166 of the SARS-CoV-2 M pro , which have common binding amino acid residues similar to those of positive controls Cys145, Met165, and Glu166 (Fig. 2) . Additionally, isoginkogetin exhibited a better binding conformation compared with chloroquine, remdesivir, and lopinavir as shown in Table 1 . Bilobetin and afzelin showed binding energies of -12.13 and -11.36 kcal/mol, respectively, along with bonds of six π-π, four hydrogens, and ten π-π, one hydrogen, compared to the positive control (at -9.50 kcal/mol). Isoginkgetin has a structural similarity with bilobetin, therefore among them, we have selected isoginkgetin and afzelin for further study. Importantly, molecular docking results collectively suggested that His42, Cys145, Met165, Glu166, and

Gln189 are the common binding amino acids, which are required for binding with the active pocket domain of the SARS-CoV-2 M pro ( Table 1) . Likewise, each selected pose of 4H-chromen-4-one scaffold with RdRp was analyzed for binding affinity and molecular contraction between ligand and active pocket of the receptor, including hydrogen and π-π bonding with amino acid residues (Fig. 3.) . Among all dock complexes, isoginkgetin-RdRp complex revealed the highest -8.30 kcal/mol docking score through the formation of hydrogen bonds and π-π interactions with RdRp amino acid residues (Table S2) . While afzelin-RdRp showed -7.17 kcal/mol lowest docking score by a substantial contribution of 4 π-π and 4 hydrogen bonds interaction. Consequently, isoginkgetin has better conformational binding stability with the active domain of RdRp compared to afzelin. The molecular conformation binding of isoginkgetin with M pro and RdRp suggests that isoginkgetin can bind with both targeted proteins.

Regarding the estimation of molecules sorted from M pro targeted library with their pharmacokinetic characteristic are shown in Table 2 . Based on the calculated pharmacokinetic profile of targeted molecules isoginkgetin, bilobetin, and afzelin, a low level of gastrointestinal absorption was found. Additionally, the one violation of the Lipinski rule was shown by isoginkgetin, and bilobetin due to their >500 g/mol molecular weight while afzelin exhibited the one violation of Lipinski rule owing to NH or OH >5 H-bond donors. As reported that 80 % of the compounds that fail to rule of five are not permeable while 48 % of those that pass are not permeable. All these tested compounds exhibited a considerable range of bioavailability scores.

Hence, these parameters collectively indicate that these molecular are further needed to be investigated in vivo pharmacokinetic parameters. 

Density functional theory was used to determine the frontier molecular orbitals, the highest occupied molecular orbitals, and the lowest unoccupied molecule orbitals, of natural flavonoids.

According to the FMO, the HOMO acts as an electron donor whereas the LUMO acts as an electron acceptor. To reveal the factor affecting such biological properties, molecular reactivities, ionization, and electron affinities of molecules, FMO theory for HOMOs and LUMOs is essential. Thus, it can be suggested that FMO studies can explore significant insights into the molecular mechanism of the active drug molecule. As a result of DFT calculations, isoginkgetin and afzelin showed a similar pattern of energy gaps between HOMOs and LUMOs of 4.15 and 4.18 eV, respectively ( Table 3 ). The slightly similar energy gaps between both the isoginkgetin and afzelin the orbitals suggest that both molecules have similar stabilities. As shown in Fig. 4 , the HOMO is located at the 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one scaffold and the oxygen of the 2H-pyron ring, while the LUMO is at the 5,7-dihydroxy-2- Table 3 , the reactivity order of molecules is as following; isoginkgetin > afzelin. The 

In the solution medium, the motion and conformation stabilities of flavonoid-SARS-CoV-2 M pro complexes were analyzed using MD simulation. The root-mean-square deviation (RMSD) and ligand binding energies were analyzed by using generated trajectories of ligandreceptor complexes overtime over more than 100 ns (Fig. 5) . The average binding energies of isoginkgetin and afzelin were found to be 46.12 and 51.23 kcal/mol, respectively. These 

According to the virtual screening results of flavonoids with the SARS-CoV-2 M pro , two natural flavonoids, isoginkgetin and afzelin, were assigned to be evaluated for their in vitro antiviral activities using SARS-CoV-2-infected Vero cells, as previously reported [49] .

Confocal microscope images of the viral N protein and the cell nuclei were evaluated using the Operetta system (Parkin Elmer), and a DRC was estimated for each distinct tested molecule (Fig. 6 ). Three standard drugs (chloroquine, remdesivir, and lopinavir) were used as positive controls; they have an IC 50 of 11.63, 7.18, and 11.49 μM, respectively, which is similar to earlier reported studies [49] . Isoginkgetin exhibited remarkable antiviral activity against SARS-CoV-2 (an IC 50 value of 22.81 μM) compared to the three positive controls (IC 50 values from 7.18-11.63 μM). However, afzelin showed an IC 50 of more than 100 μM against SARS-CoV-2 (i.e., it showed ineffectiveness against SARS-CoV-2). Isoginkgetin also exhibited higher inhibition of the SARS-CoV-2 virus at a concentration of 50 μM (~84 %), and the Vero cell survival ratio was ~61% (Fig. 6) . Also, it was noticed that inhibition of the SARS-CoV-2 virus increased with increased concentrations (at a 100 μM concentration, ~90% inhibition), but the host cell survival ratio slightly decreased at a concentration of 100 μM (~50%).

Therefore, ~50 μM of isoginkgetin is relatively safe for inhibiting the SARS-CoV-2 in vitro. and SI mean 50% inhibition, 50% cytotoxicity, and selectivity index, respectively.

With the rapid global spread of the COVID-19 pandemic, there are still limited options for the treatment of infected patients [50] , leading to attention from the scientific community and efforts to discover a rapid alternative drug molecule for the treatment of COVID-19. In the present work, we attempted to discover potent flavonoid drug molecules against SARS-CoV-2, because natural flavonoid molecules have a broad range of biological activities with minimal, or no cytotoxicity [51] . We repurposed natural flavonoids for antiviral potency against SARS-CoV-2 using computational and in vitro approaches. From the computational studies, we found that isoginkgetin, bilobetin, and afzelin showed better binding with the well-known SARS-CoV-2 M Pro active binding pocket, and these results were compared to the previously reported M Pro inhibitor namely α-ketoamide 13b [41] . On the other hand, isoginkgetin shows substantial complex stability after 60 ns in MD simulation with the active binding pocket of the SARS-CoV-2 M pro (Fig. 5) and also exhibits chemical structural stability during the DFT calculation.

Based on in silico results and structure similarity between bilobetin, and isoginkgetin, two molecules such as isoginkgetin and afzelin have been selected for further in vitro antiviral assays (Table 1 and Fig. 6 ). Among two flavonoids, in vitro antiviral assay, isoginkgetin showed remarkable antiviral activity against SARS-CoV-2, and the result was compared with three marketed drugs as positive controls such as chloroquine, remdesivir, and lopinavir (Fig.   6 ). A recent study reported that isoginkgetin affects pre-mRNA splicing may be modulating RNA polymerase elongation rates [52, 53] . Based on this previous report [54] of isoginkgetin effect towards pre-mRNA splicing and our current study about the effectiveness of isoginkgetin towards the SARS-CoV-2 suggest that isoginkgetin can be an effective drug candidate for the development of COVID-19 inhibitor. Additionally, the earlier reported anti-inflammatory activity of isoginkgetin, by activating a macrophage suggests that might be a better alternative to reduce the inflammatory markers in the lung [55] . Because inflammatory cytokines are high in the lung cell of COVID-19 patients. To confirm the further anti-inflammatory activity of isoginkgetin towards the lung cells, in vitro and in vivo anti-inflammatory studies are needed.

Although, 12-18 mg/kg doses of isoginkgetin were reported safer in vivo in an animal model for the treatment of cancer [56] . Hence, collectively previous reports and our current study outcomes suggested that isoginkgetin might work against the SARS-CoV-2 [55, 56] . Thus, further in vivo estimation of isoginkgetin against the COVID-19 is part of future interest.

Based on previous biological activities and current COVID-19 research, the plausible mechanism of isoginkgetin can be suggested to inhibit the SARS-CoV-2 because it is well known that the structural features of SARS-CoV-2 contain several proteins like spike glycoprotein (S), the SARS-CoV-2 M pro , chymotrypsin-like main protease, RNA polymerase, and papain-like protease (Fig. 7 ) [57] . The S-protein of SARS-CoV-2 initiates host viral entry through binding with an ACE2 (cellular receptor) using an endosomal pathway [58] [59] [60] , which leads to the release of viral RNA. Importantly, remdesivir was reproposed for targeting RNAdependent RNA polymerase (RdRp) and inhibits the viral RNA synthesis [61] . The critical role of this enzyme in the viral lifecycle, RdRp is an attractive target for the treatment of COVID- 19 . The molecular docking result of the current study reveals the binding interaction of the targeted molecule with RdRp. For the support of this interaction study, in vivo study is part of interest.

The released viral RNA starts the viral translation by converting the viral genome RNA into replicase polyproteins 1ab and pp1a, which are cleaved by the SARS-CoV-2 M pro and a papain-like protease into essential small viral proteins (Fig. 7) . 

In summary, this study was conducted to repurpose natural flavonoids for antiviral activity 

The authors declare they have no conflicts of interest. 

Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication

Towards a novel peptide vaccine for Middle East respiratory syndrome coronavirus and its possible use against pandemic COVID-19

Potential clinical drugs as covalent inhibitors of the priming proteases of the spike protein of SARS-CoV-2

Importation and human-to-human transmission of a novel coronavirus in Vietnam

A computational study to disclose potential drugs and vaccine ensemble for COVID-19 conundrum

Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease

An overview of severe acute respiratory syndrome-coronavirus (SARS-CoV) 3CL protease inhibitors: peptidomimetics and small molecule chemotherapy

Structural Insights into the mechanism of RNA recognition by the N-terminal RNA-binding domain of the SARS-CoV-2 nucleocapsid phosphoprotein

Investigating the potential antiviral activity drugs against SARS-CoV-2 by molecular docking simulation

Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease

Potential therapeutic use of ebselen for COVID-19 and other respiratory viral infections. Free Radic

Coronaviruses-drug discovery and therapeutic options

Dexamethasone in hospitalized patients with Covid-19-preliminary report

AntagomiRs: A novel therapeutic strategy for challenging COVID-19 cytokine storm

Martinez-de-la-Casa, Hypercytokinemia in COVID-19: Tear cytokine profile in hospitalized COVID-19 patients

Roles of flavonoids against coronavirus infection

2H/4H-Chromenes-A versatile biologically attractive scaffold

Flavonoids as antiviral agents for Enterovirus A71 (EV-A71)

Plant Platforms for Efficient Heterologous Protein Production

Biological and chemical aspects of natural biflavonoids from plants: a brief review

Anti-influenza virus activity of biflavonoids

Evaluation of amentoflavone isolated from Cnestis ferruginea Vahl ex DC (Connaraceae) on production of inflammatory mediators in LPS stimulated rat astrocytoma cell line (C6) and THP-1 cells

Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CLPro targeting repurposed drug candidates

Virtual screening of naturally occurring antiviral molecules for SARS-CoV-2 mitigation using docking tool on multiple molecular targets. ChemRxiv. Cambridge: Cambridge Open Engage

In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2

Natural Products as Potential Leads Against Coronaviruses: Could They be Encouraging Structural Models Against SARS-CoV-2? Nat. Products Bioprospect. (2020)

Exploring structurally diverse plant secondary metabolites as a potential source of drug targeting different molecular mechanisms of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pathogenesis: An in silico approach

Medicinal plants as sources of active molecules against COVID-19

Anti-inflammatory effects of flavonoids: genistein, kaempferol, quercetin, and daidzein inhibit STAT-1 and NF-κB activations, whereas flavone, isorhamnetin, naringenin, and pelargonidin inhibit only NF-κB activation along with their inhibitory effect on iNOS expression and NO production in activated macrophages

Neutrophil extracellular traps contribute to immunothrombosis in COVID-19 acute respiratory distress syndrome

Assessment of antiviral potencies of cannabinoids against SARS-CoV-2 using computational and in vitro approaches

Structure of M(pro) from COVID-19 virus and discovery of its inhibitors

Schrödinger Suite. Schrödinger, LLC

Density functional approach to the frontier-electron theory of chemical reactivity

Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field

CASTp 3.0: computed atlas of surface topography of proteins

Structural mechanism underlying capsaicin binding and activation of the TRPV1 ion channel

Advances and challenges in protein-ligand docking

Ligand docking and binding site analysis with PyMOL and Autodock/Vina

AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

New ways to boost molecular dynamics simulations

Computational Drug Discovery and Design

Lipid14: the amber lipid force field

Computational study on human sphingomyelin synthase 1 (hSMS1)

New ways to boost molecular dynamics simulations

Molecular interactions of ceftazidime with bovine serum albumin: Spectroscopic, molecular docking, and DFT analyses

Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs

Supporting the health care workforce during the COVID-19 global epidemic

Flavonoids: A complementary approach to conventional therapy of COVID-19?

Human telomerase RNA processing and quality control

The biflavonoid isoginkgetin is a general inhibitor of Pre-mRNA splicing

Characterisation of the biflavonoid hinokiflavone as a pre-mRNA splicing modulator that inhibits

Inhibition of arachidonate release from rat peritoneal macrophage by biflavonoids

Splicing inhibition enhances the antitumor immune response through increased tumor antigen presentation and altered MHC-I immunopeptidome

How to discover antiviral drugs quickly

Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target

Computational Design of ACE2-Based Peptide Inhibitors of SARS-CoV

Rational vaccine design in the time of COVID-19

Xu, b.r. communications, RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19

COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses

A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping

Graphical Abstract

The authors have declared no conflict of interest