Table 1.

In silico molecular mechanics modeling of drug interaction with SARS-CoV-2

Refs.	Therapeutic agent	Target (Viral subunit)	Suggested drug based on the predicted binding energy
101	Commercially available antiviral drugs.	Mpro, RdRp, helicase, 3'-to-5' exonuclease, endoRNAse 2'-O-ribose methyltransferase.	Atazanavir against all the virus endonucleases.
20	Sofosbuvin and ribavirin, remdesvir, IDX-184 guanosine triphosphate, uracil triphoshate, cinnamaldehyde, thymoquinone.	RdRp.	Sofosbuvir and ribavirin, remdesivir and IDX-184 were shown to tightly bind to the target.
21	7173 purchasable drugs.	Mpro.	Ledipasvir or velpatasvir (minimal side effects) + Epclusa® (velpatasvir/sofosbuvir) and Harvoni® (ledipasvir/sofosbuvir) with inhibitory actions on two viral proteases.
13	Drug repurposing (ZINC database + database of traditional Chinese medicine and natural products).	All the main proteins encoded by SARS-CoV-2: 3-chymotrypsin-like protease (3CLpro), Spike, RdRp and PLpro.	Remdesivir (GS-5734) inhibitor of RdRp. Its efficacy was verified in vitro. It is also hypothesized to inhibit Nsp3b (score=-36.5), RdRp (mfScores=-112.8), E-channel (mfScore=-125.1), and TMPRSS2 (score=-36.23, mfScores=-109.4).
102	FDA-approved drugs against viral protease + in-house database of natural and drug-like compounds of synthetic origin.	Mpro	FDA-approved drugs: remdesivir, saquinavir, darunavir + two natural compounds: flavone and coumarin derivatives.
103	Designed inhibitor.	ACE2-Spike interface.	Designed inhibitors consisting of α1+α2 helixes.
104	Designed inhibitor.	Mpro.	Designed drug that needs to be optimized and tested in vitro and vivo.
22	Zinc15 - Approved drugs in major jurisdictions, including the FDA, i.e. DrugBank approved.	Spike protein + Mpro.	Modeled the action of many approved drugs: zanamivir, indinavir, saquinavir, remdesivir (against Mpro)+flavin adenine dinucleotide (FAD), adeflavin (against both spike and Mpro), and coenzyme A (against spike protein).
23	Specific drug.	Spike via homology modeling (template PDB: 2GHV)+spike-ACE2 interaction (template: PDB:2AjF).	Cobicistat, carfilzomib and ombitasvir.
24	From a specific drug to its possible target.	20 virus protein + 22 human proteins.	Development of molecular docking based webserver, namely D3Targets-2019-nCoV for target prediction (in vitro/in vivo studies), to identify: (1) the potential target proteins and their different conformations were included; (2) all the potential ligand-binding sites with volume larger than 200 A°^3; (3) correlations among some conformations or binding sites was annotated; (4) easily to be updated, and freely accessible.
25	Medicinal plant library (32, 297 potential anti-viral phytochemicals/traditional Chinese medicinal compounds).	Mpro.	5,7,3',4'-tetrahydroxy-2'-(3,3-dimethylallyl) isoflavone.