Abstract
In December 2019, the first cases of infection with a novel coronavirus, SARS-CoV-2, were diagnosed in Wuhan, China. Due to international travel and human-to-human transmission, the virus spread rapidly inside and outside of China. Currently, there is no effective antiviral treatment for coronavirus disease 2019 (COVID-19); therefore, research efforts are focused on the rapid development of vaccines and antiviral drugs. The SARS-CoV-2 main protease constitutes one of the most attractive antiviral drug targets. To address this emerging problem, we have synthesized a combinatorial library of fluorogenic substrates with glutamine in the P1 position. We used it to determine the substrate preferences of the SARS-CoV and SARS-CoV-2 main proteases, using natural and a large panel of unnatural amino acids. On the basis of these findings, we designed and synthesized an inhibitor and two activity-based probes, for one of which we determined the crystal structure of its complex with the SARS-CoV-2 Mpro. Using this approach we visualized SARS-CoV-2 active Mpro within nasopharyngeal epithelial cells of a patient with active COVID-19 infection. The results of our work provide a structural framework for the design of inhibitors as antiviral agents or diagnostic tests.
Competing Interest Statement
Wroclaw University of Science and Technology has filed a patent application covering compounds: Ac-Abu-Tle-Leu-Gln-VS, Biotin-PEG(4)-Abu-Tle-Leu-Gln-VS and Cy5-PEG(4)-Abu-Tle-Leu-Gln-VS as well as related compounds with W.R. and M.D. as inventors.
Abbreviations used
- Abu
- 2-aminobutanoic acid;
- 2-Abz
- 2-(amino)benzoic acid;
- 3-Abz
- 3-(amino)benzoic acid;
- ACC
- 7-amino-4-carbamoylmethylcoumarin;
- Dab
- 2,4-diaminobutyric acid;
- Dht
- dihydrotryptophan;
- HyCoSuL
- Hybrid Combinatorial Substrate Library;
- Orn
- ornithine;
- RFU
- relative fluorescence unit;
- D-Phg
- D-phenylglycine;
- Thz
- thiazolidine-4-carboxylic acid;
- Tle
- tert-leucine;