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

Authors: Dai W et al.

Link to paper: https://science.sciencemag.org/content/early/2020/04/21/science.abb4489

Journal/ Pre-Print: Science

Tags:

· Cell Biology

· Drug discovery/Drug repurpose

· Structural biology

· Therapeutics

Research Highlights 

1. Two high potent inhibitors for SARS-CoV-2 Mpro with identified mechanism of action.

2. Compounds reveal antiviral effect in vitro.

3. No acute toxicity in rats at 40 mg/kg, no toxicity at daily doses in rats at 10mg/kg and Beagle dogs at 40 mg/kg.

Summary

The main protease of SARS-CoV-2 Mpro is involved in maturation cleavages within the precursor protein. It features a non-canonical Cys145 and His41 (Cys-His) dyad located in the cleft between domain I and II, which displays the substrate-binding site in which novel compounds were designed and synthesised. The two lead compounds, 11a and 11b, show high inhibitory activity of cleavage of a fluorescently labelled substrate (IC50 values of 0.053 ± 0.005 μM and 0.040 ± 0.002 μM, for 11a and 11b respectively). Both compounds showed antiviral effects in cell culture on Vero E6 cells against nCoV2019BetaCoV/Wuhan/WIV04/2019 24 hpi at MOI = 0.05 (EC50 values of 0.53 ± 0.01 μM and 0.72 ± 0.09 μM using plaque-reduction assay). Both compounds showed no toxic effects in animals.

Impact for SARS-CoV2/COVID19 research efforts

Treat of SARS-CoV2/COVID19 positive individuals

Study Type

· In vitro study

· In vivo study 

Strengths and limitations of the paper

Novelty: Two new compounds binding covalently to Mpro, demonstrating the mechanism of action of these compounds, in vitro functional assays and minimal antiviral assays as well as initial in vivo pharmacokinetic studies.

Standing in the field: There is a Nature Paper Jin et al. 2020 https://www.nature.com/articles/s41586-020-2223-y that also contains the structure and shows similar FRET assays and examines FDA approved drugs – who are much weak inhibitors but already approved that show antiviral efficacy.

Appropriate statistics: Yes for structural work, no for antiviral assays.

Viral model used: Protein MPro expressed in E.coli. For antiviral experiments nCoV 2019BetaCoV/Wuhan/WIV04/2019, a clinical isolate, propagated in Vero E6 cells was used.

Translatability: Treatment of SARS-CoV-2 infected patients.

Main limitations: Antiviral experiments are limited. A low MOI (MOI = 0.05) was used and only one time point to identify total secreted virions via qRT-PCR and infectious virions via plaque assay. No statistical analysis was performed. Green monkey kidney cells (Vero E6) were used rather than lung epithelial.