7RVT

A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.

(2022) Eur J Med Chem 240: 114570-114570

• PubMed: 35779291 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.1016/j.ejmech.2022.114570
• Primary Citation of Related Structures:  
  7RVM, 7RVN, 7RVO, 7RVP, 7RVQ, 7RVR, 7RVS, 7RVT, 7RVU, 7RVV, 7RVW, 7RVX, 7RVY, 7RVZ, 7RW0, 7RW1


• PubMed Abstract: 
  

  As an essential enzyme of SARS-CoV-2, the COVID-19 pathogen, main protease (M ^Pro ) is a viable target to develop antivirals for the treatment of COVID-19. By varying chemical compositions at both P2 and P3 positions and the N-terminal protection group, we synthesized 18 tripeptidyl M ^Pro inhibitors that contained also an aldehyde warhead and β-(S-2-oxopyrrolidin-3-yl)-alaninal at the P1 position. Systematic characterizations of these inhibitors were conducted, including their in vitro enzymatic inhibition potency, X-ray crystal structures of their complexes with M ^Pro , their inhibition of M ^Pro transiently expressed in 293T cells, and cellular toxicity and SARS-CoV-2 antiviral potency of selected inhibitors. These inhibitors have a large variation of determined in vitro enzymatic inhibition IC ₅₀ values that range from 4.8 to 650?nM. The determined in vitro enzymatic inhibition IC ₅₀ values reveal that relatively small side chains at both P2 and P3 positions are favorable for achieving high in vitro M ^Pro inhibition potency, the P3 position is tolerable toward unnatural amino acids with two alkyl substituents on the α-carbon, and the inhibition potency is sensitive toward the N-terminal protection group. X-ray crystal structures of M ^Pro bound with 16 inhibitors were determined. In all structures, the M ^Pro active site cysteine interacts covalently with the aldehyde warhead of the bound inhibitor to form a hemithioacetal that takes an S configuration. For all inhibitors, election density around the N-terminal protection group is weak indicating possible flexible binding of this group to M ^Pro . In M ^Pro , large structural variations were observed on residues N142 and Q189. Unlike their high in vitro enzymatic inhibition potency, most inhibitors showed low potency to inhibit M ^Pro that was transiently expressed in 293T cells. Inhibitors that showed high potency to inhibit M ^Pro transiently expressed in 293T cells all contain O-tert-butyl-threonine at the P3 position. These inhibitors also exhibited relatively low cytotoxicity and high antiviral potency. Overall, our current and previous studies indicate that O-tert-butyl-threonine at the P3 site is a key component to achieve high cellular and antiviral potency for tripeptidyl aldehyde inhibitors of M ^Pro .

   View More

---

Organizational Affiliation: 

Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.