Fitness effects of mutations to SARS-CoV-2 proteins

Virus Evolution, Год журнала: 2023, Номер 9(2)

Опубликована: Июль 1, 2023

Knowledge of the fitness effects mutations to SARS-CoV-2 can inform assessment new variants, design therapeutics resistant escape, and understanding functions viral proteins. However, experimentally measuring is challenging: we lack tractable lab assays for many proteins, comprehensive deep mutational scanning has been applied only two Here, develop an approach that leverages millions publicly available sequences estimate mutations. We first calculate how independent occurrences each mutation are expected be observed along phylogeny in absence selection. then compare these observations actual effect mutation. These estimates correlate well with measurements. For most genes, synonymous nearly neutral, stop-codon deleterious, amino acid have a range effects. some accessory proteins under little no provide interactive visualizations all (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework describe applicable any virus which number sufficiently large neutral observed.

Язык: Английский

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Fitness effects of mutations to SARS-CoV-2 proteins

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Янв. 31, 2023

Knowledge of the fitness effects mutations to SARS-CoV-2 can inform assessment new variants, design therapeutics resistant escape, and understanding functions viral proteins. However, experimentally measuring is challenging: we lack tractable lab assays for many proteins, comprehensive deep mutational scanning has been applied only two Here develop an approach that leverages millions publicly available sequences estimate mutations. We first calculate how independent occurrences each mutation are expected be observed along phylogeny in absence selection. then compare these observations actual effect mutation. These estimates correlate well with measurements. For most genes, synonymous nearly neutral, stop-codon deleterious, amino-acid have a range effects. some accessory proteins under little no provide interactive visualizations all (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework describe applicable any virus which number sufficiently large neutral observed.

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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Contributions of Hyperactive Mutations in M^pro from SARS-CoV-2 to Drug Resistance

ACS Infectious Diseases, Год журнала: 2024, Номер 10(4), С. 1174 - 1184

Опубликована: Март 12, 2024

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

Язык: Английский

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Study of key residues in MERS-CoV and SARS-CoV-2 main proteases for resistance against clinically applied inhibitors nirmatrelvir and ensitrelvir

npj Viruses, Год журнала: 2024, Номер 2(1)

Опубликована: Июнь 24, 2024

Abstract The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an epidemic, zoonotically emerging pathogen initially reported in Saudi Arabia 2012. MERS-CoV has the potential to mutate or recombine with other coronaviruses, thus acquiring ability efficiently spread among humans and become pandemic. Its high mortality rate of up 35% absence effective targeted therapies call for development antiviral drugs this pathogen. Since beginning SARS-CoV-2 pandemic, extensive research focused on identifying protease inhibitors treatment SARS-CoV-2. Our intention was therefore assess whether these are viable options combating MERS-CoV. To that end, we used previously established assays quantify inhibition SARS-CoV-2, main proteases. Nirmatrelvir inhibited several proteases, whereas ensitrelvir less broadly active. simulate nirmatrelvir’s clinical use against subsequent resistance development, applied a safe, surrogate virus-based system. Using virus, selected hallmark mutations SARS-CoV-2-M pro , such as T21I, M49L, S144A, E166A/K/V L167F. In current study, pool MERS-CoV-M mutants, characterized modelled steric effect catalytic site mutants S142G, S142R, S147Y A171S.

Язык: Английский

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M49L and other drug resistance mutations emerging in individuals after administration of ensitrelvir in Japanese clinical settings

Antiviral Research, Год журнала: 2025, Номер 236, С. 106118 - 106118

Опубликована: Фев. 17, 2025

Язык: Английский

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Targeting Matrix Metalloproteinase-1, Matrix Metalloproteinase-7, and Serine Protease Inhibitor E1: Implications in preserving lung vascular endothelial integrity and immune modulation in COVID-19

International Journal of Biological Macromolecules, Год журнала: 2025, Номер 306, С. 141602 - 141602

Опубликована: Фев. 28, 2025

Язык: Английский

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Molecular mechanisms of drug resistance and compensation in SARS-CoV-2 main protease: the interplay between E166 and L50

mBio, Год журнала: 2025, Номер unknown

Опубликована: Апрель 4, 2025

The SARS-CoV-2 main protease (Mpro) is essential for viral replication and a primary target COVID-19 antivirals. Direct-acting antivirals such as nirmatrelvir, the active component of Paxlovid, Mpro site to block polyprotein cleavage thus replication. However, drug resistance mutations at residue Glu166 (E166) have emerged during in vitro selection studies, raising concerns about durability current antiviral strategies. Here, we investigate molecular basis conferred by E166A E166V against nirmatrelvir related PF-00835231, individually combination with distal mutation L50F. We found that E166 reduce potency up 3,000-fold while preserving substrate cleavage, catalytic efficiency reduced only twofold. This loss was compensated addition L50F double-mutant variants. determined three cocrystal structures variants (E166A, E166V, E166V/L50F) bound PF-00835231. Comparison these wild-type enzyme demonstrated crucial dimerization shaping substrate-binding S1 pocket. Our findings highlight mutability E166, prime inhibitors leverage direct interactions this position, potential emergence highly resistant compensatory These insights support design conserved features avoid side-chain minimize susceptibility resistance. Drug remains great challenge modern medicine. study investigates which confer can retain considerable enzymatic activity through For single- variant enzymes, assessed efficiency, measured its analog cocrystallized caused mutations. results contribute toward understanding mechanisms combinations mutations, pushes resistance-thwarting inhibitor design. principles also apply broadly many quickly evolving targets infectious diseases.

Язык: Английский

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Enhancing the understandings on SARS-CoV-2 main protease (Mpro) mutants from molecular dynamics and machine learning

International Journal of Biological Macromolecules, Год журнала: 2025, Номер unknown, С. 143076 - 143076

Опубликована: Апрель 1, 2025

Язык: Английский

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