Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir

ACS Central Science, Год журнала: 2023, Номер 9(8), С. 1658 - 1669

Опубликована: Июль 24, 2023

The SARS-CoV-2 main protease (Mpro) is the drug target of Pfizer's oral nirmatrelvir. emergence variants with mutations in Mpro raised alarm potential resistance. To identify clinically relevant drug-resistant mutants, we systematically characterized 102 naturally occurring mutants located at 12 residues nirmatrelvir-binding site, among which 22 5 residues, including S144M/F/A/G/Y, M165T, E166 V/G/A, H172Q/F, and Q192T/S/L/A/I/P/H/V/W/C/F, showed comparable enzymatic activity to wild-type (kcat/Km < 10-fold change) while being resistant nirmatrelvir (Ki > increase). X-ray crystal structures were determined for six representative and/or without GC-376/nirmatrelvir. Using recombinant viruses generated from reverse genetics, confirmed resistance antiviral assay that reduced had attenuated viral replication. Overall, our study identified several hotspots warrant close monitoring possible clinical evidence resistance, some have already emerged independent passage assays conducted by others.

Язык: Английский

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Global prevalence of SARS-CoV-2 3CL protease mutations associated with nirmatrelvir or ensitrelvir resistance

EBioMedicine, Год журнала: 2023, Номер 91, С. 104559 - 104559

Опубликована: Апрель 14, 2023

Nirmatrelvir-ritonavir (Paxlovid) and ensitrelvir are 3-chymotrypsin-like cysteine protease (3CLpro) inhibitors which have been approved for the treatment of COVID-19 in 2021 2022, respectively. Previous studies identified 3CLpro mutations that associated with reduced susceptibility to these antivirals. The aim current study was estimate global prevalence inhibitor-resistant SARS-CoV-2 strains.We compiled a list nirmatrelvir or resistance based on either viral replication activity assays, determined their among 13.4 million sequences deposited GISAID as December 14, about 1 year after approval nirmatrelvir-ritonavir. We analyzed different time periods, lineages geographical locations.Overall, 0.5% (67,095/13,446,588) contained at least one mutation shown affect inhibitory activity. did not observe any increasing trend widespread clinical use G15S (2070 per million) T21I (1386 were most prevalent mutations, dominant some lineages. E166V S144E, previously by > 100-folds, found <1 sequences.Our data suggest inhibitor is currently rare. However, continuous genotypic phenotypic surveillance would be crucial early detection resistant mutants.Richard Carol Yu, May Tam Mak Mei Yin, Shaw Foundation Hong Kong, Michael Tong, Marina Lee, Government Consultancy Service, Emergency Key Program Guangzhou Laboratory (See acknowledgements full list).

Язык: Английский

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A new generation Mpro inhibitor with potent activity against SARS-CoV-2 Omicron variants

Signal Transduction and Targeted Therapy, Год журнала: 2023, Номер 8(1)

Опубликована: Март 16, 2023

Abstract Emerging SARS-CoV-2 variants, particularly the Omicron variant and its sublineages, continually threaten global public health. Small molecule antivirals are an effective treatment strategy to fight against virus. However, first-generation either show limited clinical efficacy and/or have some defects in pharmacokinetic (PK) properties. Moreover, with increased use of these drugs across globe, they face great pressure drug resistance. We herein present discovery characterization a new generation antiviral candidate (SY110), which is potent selective inhibitor main protease (M pro ). This compound displayed vitro activity not only predominant sublineage BA.5, but also other highly pathogenic human coronaviruses including SARS-CoV-1 MERS-CoV. In Omicron-infected K18-hACE2 mouse model, oral SY110 significantly lowered viral burdens lung alleviated virus-induced pathology. Importantly, possesses favorable PK properties high exposure bioavailability, outstanding safety profile. Furthermore, exhibited sensitivity several drug-resistance M mutations. Collectively, this investigation provides promising variants SARS-CoV-2.

Язык: Английский

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In vitro and in vivo characterization of SARS-CoV-2 resistance to ensitrelvir

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Июль 15, 2023

Ensitrelvir, an oral antiviral agent that targets a SARS-CoV-2 main protease (3CLpro or Nsp5), is clinically useful against including its omicron variants. Since most subvariants have reduced sensitivity to monoclonal antibody therapies, resistance other antivirals inhibitors such as ensitrelvir major public health concern. Here, repeating passages of in the presence revealed M49L and E166A substitutions Nsp5 are responsible for ensitrelvir. Both vitro virus growth absence The combination allowed largely evade suppressive effect vitro. possessing Nsp5-M49L showed similar pathogenicity wild-type virus, whereas Nsp5-E166A Nsp5-M49L/E166A slightly attenuated. Ensitrelvir treatment hamsters infected with was ineffective; however, nirmatrelvir molnupiravir effective. Therefore, it important closely monitor emergence ensitrelvir-resistant variants guide selection.

Язык: Английский

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Molecular mechanism of ensitrelvir inhibiting SARS-CoV-2 main protease and its variants

Communications Biology, Год журнала: 2023, Номер 6(1)

Опубликована: Июль 5, 2023

Abstract SARS-CoV-2 poses an unprecedented threat to the world as causative agent of COVID-19 pandemic. Among a handful therapeutics developed for prevention and treatment infection, ensitrelvir is first noncovalent nonpeptide oral inhibitor targeting main protease (M pro ) SARS-CoV-2, which recently received emergency regulatory approval in Japan. Here we determined 1.8-Å structure M complex with ensitrelvir, revealed that targets substrate-binding pocket , specifically recognizing its S1, S2, S1' subsites. Further, our comprehensive biochemical structural data have demonstrated even though nirmatrelvir (an FDA-approved drug) belong different types inhibitors, both them remain be effective against s from all five variants concern, suggesting bona fide broad-spectrum target. The molecular mechanisms uncovered this study provide basis future design.

Язык: Английский

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Rapid resistance profiling of SARS-CoV-2 protease inhibitors

npj Antimicrobials and Resistance, Год журнала: 2023, Номер 1(1)

Опубликована: Авг. 20, 2023

Abstract Resistance to nirmatrelvir (Paxlovid) has been shown by multiple groups and may already exist in clinical SARS-CoV-2 isolates. Here a robust cell-based assay is used determine the relative potencies of nirmatrelvir, ensitrelvir, FB2001 against panel main protease (M pro ) variants. The results reveal that these three drugs have at least partly distinct resistance mutation profiles raise possibility latter compounds be effective some instances Paxlovid vice versa .

Язык: Английский

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Structural biology of SARS-CoV-2 Mpro and drug discovery

Current Opinion in Structural Biology, Год журнала: 2023, Номер 82, С. 102667 - 102667

Опубликована: Авг. 4, 2023

Язык: Английский

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Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04

Cell Discovery, Год журнала: 2024, Номер 10(1)

Опубликована: Апрель 9, 2024

Drug resistance poses a significant challenge in the development of effective therapies against SARS-CoV-2. Here, we identified two double mutations, M49K/M165V and M49K/S301P, 3C-like protease (3CLpro) that confer to novel non-covalent inhibitor, WU-04, which is currently phase III clinical trials (NCT06197217). Crystallographic analysis indicates M49K mutation destabilizes WU-04-binding pocket, impacting binding WU-04 more significantly than 3CLpro substrates. The M165V directly interferes with binding. S301P mutation, far from indirectly affects by restricting rotation 3CLpro's C-terminal tail impeding dimerization. We further explored mutations clinically used inhibitors: ensitrelvir nirmatrelvir, revealed trade-off between catalytic activity, thermostability, drug 3CLpro. found at same residue (M49) can have distinct effects on inhibitors, highlighting importance developing multiple antiviral agents different skeletons for fighting These findings enhance our understanding SARS-CoV-2 mechanisms inform therapeutics.

Язык: Английский

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An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations

Science Translational Medicine, Год журнала: 2024, Номер 16(738)

Опубликована: Март 13, 2024

Inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (M pro ) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing severity COVID-19, but presence resistance-conferring mutations sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function against these mutants are thus urgently needed. We hypothesized covalent hepatitis C virus inhibitor boceprevir (BPV) could serve basis for orally bioavailable inhibit SARS-CoV-2 M more efficiently than existing drugs. Performing structure-guided modifications BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, pharmacokinetics, therapeutic efficacy similar or superior to those NTV. A crucial feature ML2006a4 is derivatization ketoamide reactive group improves cell permeability bioavailability. Last, was found be less sensitive several cause resistance NTV ETV occur natural population. Thus, anticipatory design can preemptively address potential mechanisms expand treatment options variants.

Язык: Английский

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COVID-19 therapeutics

Clinical Microbiology Reviews, Год журнала: 2024, Номер 37(2)

Опубликована: Май 21, 2024

SUMMARYSince the emergence of COVID-19 in 2020, an unprecedented range therapeutic options has been studied and deployed. Healthcare providers have multiple treatment approaches to choose from, but efficacy those often remains controversial or compromised by viral evolution. Uncertainties still persist regarding best therapies for high-risk patients, drug pipeline is suffering fatigue shortage funding. In this article, we review antiviral activity, mechanism action, pharmacokinetics, safety therapies. Additionally, summarize evidence from randomized controlled trials on various antivirals discuss unmet needs which should be addressed.

Язык: Английский

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