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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Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system

Science Advances, Год журнала: 2022, Номер 8(51)

Опубликована: Дек. 21, 2022

The oral protease inhibitor nirmatrelvir is of key importance for prevention severe coronavirus disease 2019 (COVID-19). To facilitate resistance monitoring, we studied acute respiratory syndrome 2 (SARS-CoV-2) escape from in cell culture. Resistant variants harbored combinations substitutions the SARS-CoV-2 main (Mpro). Reverse genetics revealed that E166V and L50F + conferred high infectious culture, replicon, Mpro systems. While L50F, E166V, decreased replication activity, had fitness system. Naturally occurring compensated cost promoted viral escape. Molecular dynamics simulations weakened nirmatrelvir-Mpro binding. Polymerase remdesivir monoclonal antibody bebtelovimab retained activity against nirmatrelvir-resistant variants, combination with enhanced treatment efficacy compared to individual compounds. These findings have implications monitoring ensuring treatments emerging sarbecoviruses.

Язык: Английский

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The Substitutions L50F, E166A, and L167F in SARS-CoV-2 3CLpro Are Selected by a Protease Inhibitor In Vitro and Confer Resistance To Nirmatrelvir

mBio, Год журнала: 2023, Номер 14(1)

Опубликована: Янв. 10, 2023

The SARS-CoV-2 main protease (3CLpro) has an indispensable role in the viral life cycle and is a therapeutic target for treatment of COVID-19. potential 3CLpro-inhibitors to select drug-resistant variants needs be established. Therefore, was passaged vitro presence increasing concentrations ALG-097161, probe compound designed context 3CLpro drug discovery program. We identified combination amino acid substitutions (L50F E166A L167F) that associated with >20× increase 50% effective concentration (EC50) values nirmatrelvir (PF-07321332), PF-00835231, ensitrelvir. While two single (E166A provide low-level resistance inhibitors biochemical assay, triple mutant results highest levels (6× 72×). All are significant loss enzymatic activity, suggesting reduction fitness. Structural biology analysis indicates different reduce number inhibitor/enzyme interactions while binding substrate maintained. These observations will important interpretation development clinical setting. IMPORTANCE Paxlovid first oral antiviral approved infection. Antiviral treatments often viruses. In order guide use novel antivirals, it essential understand risk characterize changes genes proteins. this work, we describe time pathway allows develop against vitro. characteristics may predictive situation. our work management COVID-19 next-generation inhibitors.

Язык: Английский

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Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms

eLife, Год журнала: 2022, Номер 11

Опубликована: Июнь 20, 2022

With the continual evolution of new strains severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that are more virulent, transmissible, and able to evade current vaccines, there is an urgent need for effective anti-viral drugs. The SARS-CoV-2 main protease (M

Язык: Английский

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Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Июнь 21, 2022

Abstract Coronaviruses can evolve and spread rapidly to cause severe disease morbidity mortality, as exemplified by SARS-CoV-2 variants of the COVID-19 pandemic. Although currently available vaccines remain mostly effective against variants, additional treatment strategies are needed. Inhibitors that target essential viral enzymes, such proteases polymerases, represent key classes antivirals. However, clinical use antiviral therapies inevitably leads emergence drug resistance. In this study we implemented a strategy pre-emptively address resistance protease inhibitors targeting main (M pro ) SARS-CoV-2, an enzyme promotes maturation. We solved nine high-resolution cocrystal structures M bound substrate peptides six with cleavage products. These enabled us define envelope , map critical recognition elements, identify evolutionarily vulnerable sites may be susceptible mutations would compromise binding newly developed inhibitors. Our results suggest for developing robust will retain longer-lasting efficacy evolving pathogen.

Язык: Английский

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Accelerating antiviral drug discovery: lessons from COVID-19

Nature Reviews Drug Discovery, Год журнала: 2023, Номер 22(7), С. 585 - 603

Опубликована: Май 12, 2023

Язык: Английский

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ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction

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

Опубликована: Дек. 8, 2023

Predicting the effects of mutations in proteins is critical to many applications, from understanding genetic disease designing novel that can address our most pressing challenges climate, agriculture and healthcare. Despite a surge machine learning-based protein models tackle these questions, an assessment their respective benefits challenging due use distinct, often contrived, experimental datasets, variable performance across different families. Addressing requires scale. To end we introduce ProteinGym, large-scale holistic set benchmarks specifically designed for fitness prediction design. It encompasses both broad collection over 250 standardized deep mutational scanning assays, spanning millions mutated sequences, as well curated clinical datasets providing high-quality expert annotations about mutation effects. We devise robust evaluation framework combines metrics design, factors known limitations underlying methods, covers zero-shot supervised settings. report diverse 70 high-performing various subfields (eg., alignment-based, inverse folding) into unified benchmark suite. open source corresponding codebase, MSAs, structures, model predictions develop user-friendly website facilitates data access analysis.

Язык: Английский

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Learning from prepandemic data to forecast viral escape

Nature, Год журнала: 2023, Номер 622(7984), С. 818 - 825

Опубликована: Окт. 11, 2023

Abstract Effective pandemic preparedness relies on anticipating viral mutations that are able to evade host immune responses facilitate vaccine and therapeutic design. However, current strategies for evolution prediction not available early in a pandemic—experimental approaches require polyclonal antibodies test against 1–16 , existing computational methods draw heavily from strain prevalence make reliable predictions of variants concern 17–19 . To address this, we developed EVEscape, generalizable modular framework combines fitness deep learning model historical sequences with biophysical structural information. EVEscape quantifies the escape potential at scale has advantage being applicable before surveillance sequencing, experimental scans or three-dimensional structures antibody complexes available. We demonstrate trained 2020, is as accurate high-throughput variation SARS-CoV-2 other viruses including influenza, HIV understudied such Lassa Nipah. provide continually revised scores all strains predict probable further forecast emerging tool continuing development ( evescape.org ).

Язык: Английский

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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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Functional map of SARS-CoV-2 3CL protease reveals tolerant and immutable sites

Cell Host & Microbe, Год журнала: 2022, Номер 30(10), С. 1354 - 1362.e6

Опубликована: Авг. 11, 2022

Язык: Английский

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