8Q71

Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the inhibitor GC-67

Summary for 8Q71

• Entry DOI: 10.2210/pdb8q71/pdb
• Descriptor: 3C-like proteinase nsp5, (2~{S})-1-(3,4-dichlorophenyl)-4-(4-methoxypyridin-3-yl)carbonyl-~{N}-(thiophen-2-ylmethyl)piperazine-2-carboxamide (3 entities in total)
• Functional Keywords: inhibitor, complex, non-covalent, twinning, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus
• Total number of polymer chains: 4
• Total formula weight: 137323.86

Authors

Strater, N.,Muller, C.E.,Sylvester, K.,Weisse, R.H.,Useini, A.,Gao, S.,Song, L.,Liu, Z.,Zhan, P. (deposition date: 2023-08-15, release date: 2023-12-06, Last modification date: 2024-01-31)

Primary citation

Gao, S.,Song, L.,Sylvester, K.,Mercorelli, B.,Loregian, A.,Toth, K.,Weisse, R.H.,Useini, A.,Strater, N.,Yang, M.,Ye, B.,Tollefson, A.E.,Muller, C.E.,Liu, X.,Zhan, P.
Design, Synthesis, and Biological Evaluation of Trisubstituted Piperazine Derivatives as Noncovalent Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors with Improved Antiviral Activity and Favorable Druggability.
J.Med.Chem., 66:16426-16440, 2023

PubMed Abstract: The ongoing transmission of SARS-CoV-2 necessitates the development of additional potent antiviral agents capable of combating the current highly infectious variants and future coronaviruses. Here, we present the discovery of potent nonpeptide main protease (M) inhibitors with prominent antiviral activity and improved pharmacokinetic properties. Three series of 1,2,4-trisubstituted piperazine derivatives were designed and synthesized, and the optimal demonstrated high enzyme-inhibitory potency (IC = 0.19 μM) and exhibited excellent antiviral activity (EC = 0.40 μM), reaching the same level as Nirmatrelvir (EC = 0.38 μM). Additionally, displayed potent antiviral activities against various SARS-CoV-2 variants as well as HCoV-OC43 and HCoV-229E, indicating its potential broad-spectrum anticoronaviral activity. Notably, the pharmacokinetic properties of were somewhat enhanced compared to those of the lead compound. Furthermore, the cocrystal and molecular docking elucidated the mechanism of action. In conclusion, we discovered a novel nonpeptidic M inhibitor with promising antiviral activity and a favorable pharmacokinetic profile.

PubMed: 37992202
DOI: 10.1021/acs.jmedchem.3c01876

Experimental method

X-RAY DIFFRACTION (2.322 Å)