Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir

Nature, Journal Year: 2022, Volume and Issue: 613(7944), P. 558 - 564

Published: Nov. 9, 2022

Nirmatrelvir, an oral antiviral targeting the 3CL protease of SARS-CoV-2, has been demonstrated to be clinically useful against COVID-19 (refs. 1,2). However, because SARS-CoV-2 evolved become resistant other therapeutic modalities3-9, there is a concern that same could occur for nirmatrelvir. Here we examined this possibility by in vitro passaging nirmatrelvir using two independent approaches, including one on large scale. Indeed, highly viruses emerged from both and their sequences showed multitude mutations. In experiment peformed with many replicates, 53 viral lineages were selected mutations observed at 23 different residues enzyme. Nevertheless, several common mutational pathways resistance preferred, majority descending T21I, P252L or T304I as precursor Construction analysis 13 recombinant clones these mediated only low-level resistance, whereas greater required accumulation additional E166V mutation conferred strongest (around 100-fold), but resulted loss replicative fitness was restored compensatory changes such L50F T21I. Our findings indicate does readily arise via multiple vitro, specific herein form strong foundation which study mechanism detail inform design next-generation inhibitors.

Language: Английский

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

ACS Central Science, Journal Year: 2023, Volume and Issue: 9(8), P. 1658 - 1669

Published: July 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.

Language: Английский

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Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: June 28, 2022

ABSTRACT The SARS-CoV-2 main protease (M pro ) is the drug target of Pfizer’s oral Paxlovid. emergence variants with mutations in M raised alarm potential resistance. In this study, we identified 100 naturally occurring located at nirmatrelvir binding site, among which 20 mutants, including S144M/F/A/G/Y, M165T, E166G, H172Q/F, and Q192T/S/L/A/I/P/H/V/W/C/F, showed comparable enzymatic activity to wild-type (k cat /K m <10-fold change) resistance (K i >10-fold increase). X-ray crystal structures were determined for seven representative mutants and/or without GC-376/nirmatrelvir. Viral growth assay that reduced led attenuated viral replication. Overall, our study several resistant hot spots warrant close monitoring possible clinical evidence Paxlovid One Sentence Summary viruses have been from isolates.

Language: Английский

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Alkyne Derivatives of SARS-CoV-2 Main Protease Inhibitors Including Nirmatrelvir Inhibit by Reacting Covalently with the Nucleophilic Cysteine

Journal of Medicinal Chemistry, Journal Year: 2023, Volume and Issue: 66(4), P. 2663 - 2680

Published: Feb. 9, 2023

Nirmatrelvir (PF-07321332) is a nitrile-bearing small-molecule inhibitor that, in combination with ritonavir, used to treat infections by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). interrupts the viral life cycle inhibiting SARS-CoV-2 main protease (Mpro), which essential for processing polyproteins into functional nonstructural proteins. We report studies reveal that derivatives of nirmatrelvir and other Mpro inhibitors nonactivated terminal alkyne group positioned similarly electrophilic nitrile can efficiently inhibit isolated replication cells. Mass spectrometric crystallographic evidence shows apparent irreversible covalent reactions active site cysteine (Cys145), while analogous nitriles react reversibly. The results highlight potential inhibition nucleophilic proteases alkynes, which, contrast nitriles, be functionalized at their position optimize selectivity, as well pharmacodynamic pharmacokinetic properties.

Language: Английский

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Discovery of First-in-Class PROTAC Degraders of SARS-CoV-2 Main Protease

Journal of Medicinal Chemistry, Journal Year: 2024, Volume and Issue: 67(8), P. 6495 - 6507

Published: April 12, 2024

We have witnessed three coronavirus (CoV) outbreaks in the past two decades, including COVID-19 pandemic caused by SARS-CoV-2. Main protease (MPro), a highly conserved among various CoVs, is essential for viral replication and pathogenesis, making it prime target antiviral drug development. Here, we leverage proteolysis targeting chimera (PROTAC) technology to develop new class of small-molecule antivirals that induce degradation SARS-CoV-2 MPro. Among them, MPD2 was demonstrated effectively reduce MPro protein levels 293T cells, relying on time-dependent, CRBN-mediated, proteasome-driven mechanism. Furthermore, exhibited remarkable efficacy diminishing SARS-CoV-2-infected A549-ACE2 cells. also displayed potent activity against strains enhanced potency nirmatrelvir-resistant viruses. Overall, this proof-of-concept study highlights potential targeted as an innovative approach developing could fight drug-resistant variants.

Language: Английский

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Oral Antiviral Treatment for COVID-19: A Comprehensive Review on Nirmatrelvir/Ritonavir

Viruses, Journal Year: 2022, Volume and Issue: 14(11), P. 2540 - 2540

Published: Nov. 17, 2022

Despite the rapid development of efficient and safe vaccines against COVID-19, need to confine pandemic treat infected individuals on an outpatient basis has led approval oral antiviral agents. Taking into account viral kinetic pattern SARS-CoV-2, it is high importance intervene at early stages disease. A protease inhibitor called nirmatrelvir coupled with ritonavir (NMV/r), which acts as a CYP3A inhibitor, delivered formulation, shown much promise in preventing disease progression high-risk patients no for supplemental oxygen administration. Real-world data seem confirm drug combination’s efficacy safety all variants concern adult populations. Although, not fully clarified, rebound recurrence COVID-19 symptoms have been described following treatment; however, more potential resistance issues concerning Mpro gene, drug’s therapeutic target, are needed. NMV/r gamechanger fight by hospitalizations halting severity; therefore, research future greater awareness its use warranted.

Language: Английский

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Adjusted green HPLC determination of nirmatrelvir and ritonavir in the new FDA approved co-packaged pharmaceutical dosage using supported computational calculations

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Jan. 4, 2023

The greening of analytical methods has gained interest in the quantitative analysis field to reduce environmental impact and improve safety health conditions for analysts. Nirmatrelvir plus ritonavir is a new FDA approved co-packaged medication developed treatment COVID-19. aim this research was develop green fitted HPLC method using pre experimental computational testing different stationary phases as well selecting mobile phase regarding chemistry principles. Computational study designed test physical interaction between nirmatrelvir columns (C8, C18, Cyano column). showed that C18 column better simultaneous cited drugs. Regarding point view, consisted ethanol: water (80:20, v/v) provided an efficient chromatographic separation within short run time, reasonable resolution excellent sensitivity. Isocratic elution performed on selected adjusted at flow rate 1 mL/min UV detection 215 nm. system allowed complete baseline with retention times 4.9 min 6.8 ritonavir. succeeded determine over concentration range 1.0-20.0 μg/mL pure form pharmaceutical dosage form. Greenness profiles applied assessed eco-scale, procedure index AGREE evaluation method. results revealed adherence described authors hope provide promising challenge achieving goals through integrating tools applying them assessment metrics.

Language: Английский

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Molecular medicinal insights into scaffold hopping-based drug discovery success

Drug Discovery Today, Journal Year: 2023, Volume and Issue: 29(1), P. 103845 - 103845

Published: Nov. 26, 2023

Language: Английский

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A MERS-CoV antibody neutralizes a pre-emerging group 2c bat coronavirus

Science Translational Medicine, Journal Year: 2023, Volume and Issue: 15(715)

Published: Sept. 27, 2023

The repeated emergence of zoonotic human betacoronaviruses (β-CoVs) dictates the need for broad therapeutics and conserved epitope targets countermeasure design. Middle East respiratory syndrome (MERS)–related coronaviruses (CoVs) remain a pressing concern global health preparedness. Using metagenomic sequence data CoV reverse genetics, we recovered full-length wild-type MERS-like BtCoV/ li /GD/2014-422 (BtCoV-422) recombinant virus, as well two reporter viruses, evaluated their potential susceptibility to currently available countermeasures. Similar MERS-CoV, BtCoV-422 efficiently used other mammalian dipeptidyl peptidase protein 4 (DPP4) proteins entry receptors an alternative DPP4-independent infection route in presence exogenous proteases. also replicated primary airway, lung endothelial, fibroblast cells, although less than MERS-CoV. However, shows minor signs 288/330 DPP4 transgenic mice. Several antivirals, including nucleoside analogs 3C-like/M pro protease inhibitors, demonstrated potent inhibition against vitro. Serum from mice that received MERS-CoV mRNA vaccine showed reduced neutralizing activity BtCoV-422. Although most MERS-CoV–neutralizing monoclonal antibodies (mAbs) had limited activity, one anti-MERS receptor binding domain mAb, JC57-11, neutralized potently. A cryo–electron microscopy structure JC57-11 complex with spike revealed mechanism cross-neutralization involving occlusion site, highlighting its broadly mAb group 2c CoVs use receptor. These studies provide critical insights into candidates development.

Language: Английский

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The impact of SARS-CoV-2 3CL protease mutations on nirmatrelvir inhibitory efficiency. Computational insights into potential resistance mechanisms

Chemical Science, Journal Year: 2023, Volume and Issue: 14(10), P. 2686 - 2697

Published: Jan. 1, 2023

The use of antiviral drugs can promote the appearance mutations in target protein that increase resistance virus to treatment. This is also case nirmatrelvir, a covalent inhibitor 3CL protease, or main SARS-CoV-2. In this work we show how by-residue decomposition noncovalent interactions established between drug and enzyme, combination with an analysis naturally occurring mutations, be used detect potential protease conferring nirmatrelvir. We investigate consequences these on reaction mechanism form enzyme-inhibitor complex using QM/MM methods. particular, E166V variant displays smaller binding affinity nirmatrelvir larger activation free energy for formation complex, both factors contributing observed treatment drug. conclusions derived from our anticipate introduction fitness landscape design new inhibitors adapted some possible mechanisms.

Language: Английский

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