Published:  10:49 AM, 09 February 2020

U.S.-based Protein Data Bank releases novel coronavirus protease structure

U.S.-based Protein Data Bank releases novel coronavirus protease structure


The Protein Data Bank archive (PDB) has released a novel coronavirus protease structure following the
recent novel coronavirus outbreak affecting China and other parts of the world.

According to a report released Friday by University of California, San Diego (UCSD), this move would enable research on this newly-recognized human pathogen and provide a starting point for structure-guided drug discovery.

The structure, showed in the topic of the PDB’s current “Molecule of the Month” feature, is a high-resolution crystal structure of the novel coronavirus 3CL hydrolase (Mpro) as determined by Zihe Rao and Haitao Yang’s research team at ShanghaiTech University.

It is currently the only public-domain 3D structure from this specific coronavirus.

The PDB also released a painting depicting a coronavirus just entering the lungs, surrounded by mucus secreted by respiratory cells, secreted antibodies, and several small immune systems proteins.

The coronavirus 3CL hydrolase (Mpro) enzyme, also known as the main protease, is essential for proteolytic maturation of the virus. It is thought to be a promising target for discovery of small-molecule drugs that would inhibit cleavage of the viral polyprotein and prevent spread of the infection.

“Coronavirus main proteases represent attractive targets for drug discovery and development,” explained Stephen K. Burley, physician-scientist and PDB director and faculty member at Rutgers University and UCSD.

“Three-dimensional structure information freely available from the PDB includes small chemicals bound tightly to the enzyme active site, confirming that they are druggable targets. Some of these structures provide starting points for structure-guided drug discovery of protease inhibitors with drug- like properties suitable for preclinical testing,” said Burley.

Burley said that the PDB hoped that this new structure, and those from SARS and MERS, will help researchers and clinicians address the novel coronavirus health emergency.

The PDB archive is jointly managed by the Worldwide Protein Data Bank partnership, involving data centers in the United States, Europe and Asia. It contains more than 160,000 3D structures for proteins, DNA, and RNA.


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