On June 19, the internationally renowned journal Science reported on its cover an important COVID-19 study from a Chinese research team, who discovered new candidate drug compounds 11a and 11b that target the main protease ( Mpro ) of the coronavirus. The research team believes that these two compounds are highly effective and safe, and have the potential to be developed into new drugs against the coronavirus (SARS-CoV-2).

The study, titled "Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease," was originally published on the biological preprint website bioRxiv on March 28 , published online in Science on April 22, and featured on the cover of Science on June 19.

The research was conducted by the team of Liu Hong, Xu Yechun, and Jiang Hualiang from the Shanghai Institute of Materia Medica, Chinese Academy of Sciences; the team of Yang Haitao and Rao Zihe from ShanghaiTech University; and the team of Zhang Lei and Xiao Gengfu from the Wuhan Institute of Virology, Chinese Academy of Sciences. The corresponding authors are Researcher Liu Hong from the Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Professor Yang Haitao from ShanghaiTech University, Associate Researcher Zhang Lei from the Wuhan Institute of Virology, Chinese Academy of Sciences, and Researcher Xu Yechun from the Shanghai Institute of Materia Medica, Chinese Academy of Sciences.

The new coronavirus is a single-stranded RNA positive-strand enveloped betacoronavirus, and one of its most characterized drug targets is the 3-chymotrypsin-like protease, the main protease ( Mpro , also known as 3CLpro). This enzyme operates on no less than 11 cleavage sites on the large polyprotein 1ab and is essential for processing the polyprotein translated from the viral RNA. Therefore, inhibiting the activity of this enzyme will effectively block viral replication.

In fact, on April 9, the "Anti-COVID-19 Alliance", including the team of Academician Rao Zihe, a professor at Tsinghua University and a distinguished professor at the Institute of Immunochemistry of ShanghaiTech University, and their collaborators, published the high-resolution complex structure of the 2.1Å "main protease-N3" of the new coronavirus, which is also the world's first resolved three-dimensional spatial structure of the new coronavirus protein.

Scientists are already developing a variety of potential drugs for the main protease of the new coronavirus. Previously, the research team identified N3, a potent inhibitor of the main protease of the new coronavirus, through computer-aided drug design; Rolf Hilgenfeld and others from the Institute of Biochemistry at the University of Lübeck in Germany optimized the previous inhibitors by analyzing the structure of Mpro , and also found an α-ketoamide inhibitor called 13b that is suitable for administration by inhalation.

This time, a team from the Shanghai Institute of Materia Medica, Chinese Academy of Sciences , designed and synthesized two peptidomimetic compounds 11a and 11b based on the three-dimensional structure of Mpro .

The researchers showed that the active site of Mpro is highly conserved in all coronaviruses. In the main protease structure of the new coronavirus, domains I and II form a six-stranded antiparallel β-barrel with a substrate-binding pocket in the cleft between them. Due to its high conservation, it can be used as a target for designing broad-spectrum inhibitors, that is, the drug target "pocket".

the substrate binding pocket of SARS (severe acute respiratory syndrome) virus Mpro , the researchers were able to design and synthesize inhibitors against SARS-CoV-2 Mpro .

The binding mode of compounds 11a and 11b with the SARS-CoV-2 main protease complex is similar to the previously reported "main protease-N3" complex structure. The three-dimensional structure analyzed by the researchers shows that both compounds occupy the substrate binding pocket, in which the aldehyde group of the compound and the cysteine residue at position 145 of the protease catalytic site form a covalent bond, locking it firmly.

By displaying the complex structure at 1.5 angstrom resolution, the researchers not only analyzed the precise interaction patterns of compounds 11a and 11b with the main protease, but also revealed the molecular mechanism by which the compounds inhibit viral proteases.

More importantly, the researchers believe that both compounds exhibit good in vivo pharmacokinetic properties and safety, and have the potential to be developed into new drugs against SARS-CoV-2.

The researchers administered 11a to mice by peritoneal and intravenous administration and observed that the drug half-life (the time required for the plasma drug concentration to drop by half) was 4.27 hours and 4.41 hours, respectively. The drug had a high maximum concentration, good metabolic stability, and good bioavailability, reaching 87.8%.

11b showed good pharmacokinetic properties whether it was injected intraperitoneally, subcutaneously or intravenously into mice. The bioavailability of 11b exceeded 80% when administered intraperitoneally and subcutaneously, and its half-life was extended to 5.21 hours when administered intraperitoneally.

The researchers also conducted in vivo toxicity studies on compound 11a in rats and beagle dogs, and the results showed that no obvious toxic reactions were observed in either group of animals. The authors believe that these data indicate that 11a is a good candidate drug compound for further clinical research.

In summary, the two drug candidate compounds targeting the main protease of the new coronavirus discovered by the research team have good inhibitory activity and antiviral effects, and both in vivo and in vitro studies have demonstrated their good pharmacokinetic properties and safety. They are a class of novel, highly effective and safe anti-SARS-CoV-2 virus candidate drugs, which will play a significant role in the next step of anti-new coronavirus drug research and development.