8E5C

Crystal Structure of SARS CoV-2 Mpro mutant L50F with Nirmatrelvir captured in two conformational states

Summary for 8E5C

• Entry DOI: 10.2210/pdb8e5c/pdb
• Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, ... (6 entities in total)
• Functional Keywords: coronavirus, covid-19, covid, protease, drug resistance, complex, hydrolase, durg discovery, main protease, mpro, substrate complex, pfizer iv compound, l50f, nirmatrelvir, viral protein, viral protein-hydrolase-inhibitor complex, hydrolase-inhibitor complex, hydrolase/inhibitor
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 1
• Total formula weight: 34718.99

Authors

Shaqra, A.M.,Schiffer, C.A. (deposition date: 2022-08-20, release date: 2024-02-07, Last modification date: 2024-04-24)

Primary citation

Flynn, J.M.,Zvornicanin, S.N.,Tsepal, T.,Shaqra, A.M.,Kurt Yilmaz, N.,Jia, W.,Moquin, S.,Dovala, D.,Schiffer, C.A.,Bolon, D.N.A.
Contributions of Hyperactive Mutations in M pro from SARS-CoV-2 to Drug Resistance.
Acs Infect Dis., 10:1174-1184, 2024

PubMed Abstract: The appearance and spread of mutations that cause drug resistance in rapidly evolving diseases, including infections by the SARS-CoV-2 virus, are major concerns for human health. Many drugs target enzymes, and resistance-conferring mutations impact inhibitor binding or enzyme activity. Nirmatrelvir, the most widely used inhibitor currently used to treat SARS-CoV-2 infections, targets the main protease (M) preventing it from processing the viral polyprotein into active subunits. Our previous work systematically analyzed resistance mutations in M that reduce binding to inhibitors; here, we investigate mutations that affect enzyme function. Hyperactive mutations that increase M activity can contribute to drug resistance but have not been thoroughly studied. To explore how hyperactive mutations contribute to resistance, we comprehensively assessed how all possible individual mutations in M affect enzyme function using a mutational scanning approach with a fluorescence resonance energy transfer (FRET)-based yeast readout. We identified hundreds of mutations that significantly increased the M activity. Hyperactive mutations occurred both proximal and distal to the active site, consistent with protein stability and/or dynamics impacting activity. Hyperactive mutations were observed 3 times more than mutations which reduced apparent binding to nirmatrelvir in recent studies of laboratory-grown viruses selected for drug resistance. Hyperactive mutations were also about three times more prevalent than nirmatrelvir binding mutations in sequenced isolates from circulating SARS-CoV-2. Our findings indicate that hyperactive mutations are likely to contribute to the natural evolution of drug resistance in M and provide a comprehensive list for future surveillance efforts.

PubMed: 38472113
DOI: 10.1021/acsinfecdis.3c00560

Experimental method

X-RAY DIFFRACTION (2.2 Å)