Screening and evaluation of approved drugs as inhibitors of main protease of SARS-CoV-2

Abstract

The COVID-19 pandemic caused by SARS-CoV-2 has emerged as a global catastrophe. The virus requires main protease for processing the viral polyproteins PP1A and PP1AB translated from the viral RNA. In search of a quick, safe and successful therapeutic agent; we screened various clinically approved drugs for the in-vitro inhibitory effect on 3CL Pro which may be able to halt virus replication. The methods used includes protease activity assay, fluorescence quenching, surface plasmon resonance (SPR), Thermofluor® Assay, Size exclusion chromatography and in-silico docking studies. We found that Teicoplanin as most effective drug with IC 50 ~ 1.5 μM. Additionally, through fluorescence quenching Stern–Volmer quenching constant (K SV ) for Teicoplanin was estimated as 2.5 × 10 5 L·mol −1 , which suggests a relatively high affinity between Teicoplanin and 3CL Pro protease. The SPR shows good interaction between Teicoplanin and 3CL Pro with K D ~ 1.6 μM. Our results provide critical insights into the mechanism of action of Teicoplanin as a potential therapeutic against COVID-19. We found that Teicoplanin is about 10–20 fold more potent in inhibiting protease activity than other drugs in use, such as lopinavir, hydroxychloroquine, chloroquine, azithromycin, atazanavir etc. Therefore, Teicoplanin emerged as the best inhibitor among all drug molecules we screened against 3CL Pro of SARS-CoV-2.

Peptide and peptide-based inhibitors of SARS-CoV-2 entry

“…A study currently available as preprint shows that the SARS-CoV-1 and SARS-CoV-2 cathepsin L cleavage sites are conserved and that teicoplanin also prevents infection of SARS-CoV-2 pseudoparticles with an IC 50 of 1.66 μM [ 91 ]. Additionally, teicoplanin seems to inhibit the viral 3-chymotrypsin-like protease (3CL pro ) of SARS-CoV-2 that is important for viral spread [ 120 ]. In the clinics, teicoplanin has been applied to treat Staphylococcus aureus superinfections that may occur as major complication in COVID-19 patients [ 121 ] that simultaneously might act antiviral.…”

Ligand-based approach for predicting drug targets and for virtual screening against COVID-19

“…The targets for top-ranking ligands are predicted potential targets for the submitted molecule. For example, human histamine N-methyltransferase, 3C-like protease and papain-like protease were predicted to be the top three potential targets of chloroquine, among which 3C-like protease was reported recently based on in vitro results [ 41 , 42 ].…”

AI drug discovery screening for COVID-19 reveals zafirlukast as a repurposing candidate

“…Although the utilized dataset comprises activity toward SARS-CoV 3CLpro, exhibiting above 96% sequence identity to the SARS-CoV-2 3CLpro, in addition to the original dataset [ 25 ], we consider also a manually curated version of the same dataset, based on the following enrichment. We added to the dataset the following known SARS-CoV-2 3CLpro inhibitors 1 as active molecules, based on the already published results: ebselen, disulfiram, tideglusib, carmofur, shikonin, PX-12 [ 26 ], ritonavir [ 27 ], lopinavir, teicoplanin, oseltamivir, nitazoxanide, hydroxychloroquine, famciclovir, chloroquine, azithromycin, atazanavir, amoxicillin, aciclovir [ 28 ], and quercetin [ 29 ]. 2…”

“… 2 Since the following 5 drugs: ebselen, disulfiram, nitazoxanide, famciclovir, and aciclovir are included in the original dataset as inactive molecules and they are according to current research considered as already known SARS-CoV-2 3CLpro inhibitors [ 26 , 28 ], in the manually curated version of the dataset we inlcude them as active molecules. …”