Molecule of the Month: Coronavirus Proteases
Coronavirus proteases are attractive targets for the design of antiviral drugs.
Exploring the Structure
Bat Coronavirus Main Protease with Inhibitor
Researchers are actively using these structures to search for compounds that block the action of the proteases, for use as antiviral drugs. The diversity of coronaviruses poses a great challenge with this effort: coronaviruses have been classified into four separate genera, and sequence and structural studies have shown that the proteases of these viruses can be very different, so drugs designed to fight one may not be effective against others. One possible way to address this challenge is to try to design a broad-spectrum inhibitor targeted against the progenitor bat coronavirus, such as the one shown here from PDB entry 4yoi, which may then provide a head-start for discovering inhibitors against newly emerging viruses. The active site cysteine and histidine are shown in the illustration, with an inhibitor in turquoise. To explore this structure in more detail, click on the image for an interactive JSmol.
Topics for Further Discussion
- An unusual octameric form of the main protease may be involved in its maturation. You can see it in PDB entry 3iwm.
- You can compare the folds of coronavirus main proteases and serine proteases using the “Structure Align” tool. Try using trypsinogen (PDB entry 1tgs), so that the whole enzyme is one chain for the alignment.
Related PDB-101 Resources
- Browse Viruses
- Browse Coronavirus
- Cui, J., Li, F., Shi, Z.L. (2019) Origin and evolution of pathogenic coronaviruses. Nat. Rev. Microbiol. 17, 181-192.
- 4yoi: St John, S.E., Tomar, S., Stauffer, S.R., Mesecar, A.D. (2015) Targeting zoonotic viruses: Structure-based inhibition of the 3C-like protease from bat coronavirus HKU4-The likely reservoir host to the human coronavirus that causes Middle East Respiratory Syndrome (MERS). Bioorg.Med.Chem. 23: 6036-6048
- 4ow0: Baez-Santos, Y.M., Barraza, S.J., Wilson, M.W., Agius, M.P., Mielech, A.M., Davis, N.M., Baker, S.C., Larsen, S.D., Mesecar, A.D. (2014) X-ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-like Proteases. J.Med.Chem. 57: 2393-2412
- Hilgenfeld, R. (2014) From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design. FEBS J. 281,4085-4096
- 1q2w: Pollack, A. (2003) Company says it mapped part of SARS virus. New York Times, July 30, section C, page 2.
February 2020, David Goodselldoi:10.2210/rcsb_pdb/mom_2020_2