8IGN
Crystal structure of SARS-CoV-2 main protease in complex with RAY1216
Summary for 8IGN
| Entry DOI | 10.2210/pdb8ign/pdb |
| Descriptor | 3C-like proteinase nsp5, (3~{S},3~{a}~{S},6~{a}~{R})-2-[(2~{S})-2-cyclohexyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]ethanoyl]-~{N}-[(2~{S})-4-(cyclopentylamino)-3,4-bis(oxidanylidene)-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide (3 entities in total) |
| Functional Keywords | sars-cov-2, nsp5, main protease, coronavirus, protease inhibitor, alpha-ketoamide inhibitor, peptidomimetic inhibitor, viral protein |
| Biological source | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2) |
| Total number of polymer chains | 2 |
| Total formula weight | 68930.51 |
| Authors | |
| Primary citation | Chen, X.,Huang, X.,Ma, Q.,Kuzmic, P.,Zhou, B.,Zhang, S.,Chen, J.,Xu, J.,Liu, B.,Jiang, H.,Zhang, W.,Yang, C.,Wu, S.,Huang, J.,Li, H.,Long, C.,Zhao, X.,Xu, H.,Sheng, Y.,Guo, Y.,Niu, C.,Xue, L.,Xu, Y.,Liu, J.,Zhang, T.,Spencer, J.,Zhu, Z.,Deng, W.,Chen, X.,Chen, S.H.,Zhong, N.,Xiong, X.,Yang, Z. Preclinical evaluation of the SARS-CoV-2 M pro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir. Nat Microbiol, 9:1075-1088, 2024 Cited by PubMed Abstract: Although vaccines are available for SARS-CoV-2, antiviral drugs such as nirmatrelvir are still needed, particularly for individuals in whom vaccines are less effective, such as the immunocompromised, to prevent severe COVID-19. Here we report an α-ketoamide-based peptidomimetic inhibitor of the SARS-CoV-2 main protease (M), designated RAY1216. Enzyme inhibition kinetic analysis shows that RAY1216 has an inhibition constant of 8.4 nM and suggests that it dissociates about 12 times slower from M compared with nirmatrelvir. The crystal structure of the SARS-CoV-2 M:RAY1216 complex shows that RAY1216 covalently binds to the catalytic Cys145 through the α-ketoamide group. In vitro and using human ACE2 transgenic mouse models, RAY1216 shows antiviral activities against SARS-CoV-2 variants comparable to those of nirmatrelvir. It also shows improved pharmacokinetics in mice and rats, suggesting that RAY1216 could be used without ritonavir, which is co-administered with nirmatrelvir. RAY1216 has been approved as a single-component drug named 'leritrelvir' for COVID-19 treatment in China. PubMed: 38553607DOI: 10.1038/s41564-024-01618-9 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.02 Å) |
Structure validation
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