SARS-CoV-2 3CL ^pro mutations selected in a VSV-based system confer resistance to nirmatrelvir, ensitrelvir, and GC376

Science Translational Medicine, Год журнала: 2022, Номер 15(678)

Опубликована: Окт. 4, 2022

Protease inhibitors are among the most powerful antiviral drugs. Nirmatrelvir is first protease inhibitor specifically developed against SARS-CoV-2 3CLpro that has been licensed for clinical use. To identify mutations confer resistance to this inhibitor, we engineered a chimeric vesicular stomatitis virus (VSV) expressed polyprotein composed of VSV glycoprotein (G), 3CLpro, and polymerase (L). Viral replication was thus dependent on autocatalytic processing precursor protein by release functional viral proteins G L, effectively inhibited nirmatrelvir. Using system, applied nirmatrelvir select mutations. Resistance confirmed retesting selected in additional VSV-based systems, an independently cellular biochemical assay, recombinant system. We demonstrate some mutants cross-resistant ensitrelvir GC376, whereas others less resistant these compounds. Furthermore, found already existed sequences have deposited NCBI GISAID databases, indicating were present circulating strains.

Язык: Английский

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Small molecules in the treatment of COVID-19

Signal Transduction and Targeted Therapy, Год журнала: 2022, Номер 7(1)

Опубликована: Дек. 5, 2022

Abstract The outbreak of COVID-19 has become a global crisis, and brought severe disruptions to societies economies. Until now, effective therapeutics against are in high demand. Along with our improved understanding the structure, function, pathogenic process SARS-CoV-2, many small molecules potential anti-COVID-19 effects have been developed. So far, several antiviral strategies were explored. Besides directly inhibition viral proteins such as RdRp M pro , interference host enzymes including ACE2 proteases, blocking relevant immunoregulatory pathways represented by JAK/STAT, BTK, NF-κB, NLRP3 pathways, regarded feasible drug development. development treat achieved strategies, computer-aided lead compound design screening, natural product discovery, repurposing, combination therapy. Several representative remdesivir paxlovid proved or authorized emergency use countries. And candidates entered clinical-trial stage. Nevertheless, due epidemiological features variability issues it is necessary continue exploring novel COVID-19. This review discusses current findings for treatment. Moreover, their detailed mechanism action, chemical structures, preclinical clinical efficacies discussed.

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

Journal of Medicinal Chemistry, Год журнала: 2023, Номер 66(4), С. 2663 - 2680

Опубликована: Фев. 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.

Язык: Английский

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Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6

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

Опубликована: Апрель 21, 2023

Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across world and effectively evaded immune responses, its viral fitness in cell animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent genomes is challenging because length genome (~30 kb). Here, we present a plasmid-based assembly rescue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons single ligation reaction with >80% efficiency. Fully sequenced stocks can be generated 1 3 weeks, respectively. By testing series naturally occurring well Delta-Omicron chimeric replicons, show nonstructural protein 6 harbors critical attenuating mutations, which dampen RNA replication reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study reveals deficits function underlying attenuation.

Язык: Английский

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In vitro and in vivo characterization of SARS-CoV-2 strains resistant to nirmatrelvir

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

Опубликована: Июль 4, 2023

Nirmatrelvir, an oral antiviral agent that targets a SARS-CoV-2 main protease (3CLpro), is clinically useful against infection with including its omicron variants. Since most subvariants have reduced sensitivity to many monoclonal antibody therapies, potential resistance nirmatrelvir major public health concern. Several amino acid substitutions been identified as being responsible for susceptibility nirmatrelvir. Among them, we selected L50F/E166V and L50F/E166A/L167F in the 3CLpro because these combinations of are unlikely affect virus fitness. We prepared characterized delta variants possessing Nsp5-L50F/E166V Nsp5-L50F/E166A/L167F. Both mutant viruses showed decreased their growth VeroE6/TMPRSS2 cells was delayed. attenuated phenotypes male hamster model, maintained airborne transmissibility, were outcompeted by wild-type co-infection experiments absence nirmatrelvir, but less so presence drug. These results suggest Nsp5-L50F/E166A/L167F do not become dominant nature. However, it important closely monitor emergence nirmatrelvir-resistant resistant additional compensatory mutations could emerge, outcompete virus, dominant.

Язык: 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, Год журнала: 2023, Номер 14(10), С. 2686 - 2697

Опубликована: Янв. 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.

Язык: Английский

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Combinations of Host- and Virus-Targeting Antiviral Drugs Confer Synergistic Suppression of SARS-CoV-2

Microbiology Spectrum, Год журнала: 2022, Номер 10(5)

Опубликована: Окт. 3, 2022

Imagine a future viral pandemic where if you test positive for the new virus, can quickly take some medicines at home few days so that do not get too sick. To date, only single drugs have been approved outpatient use against SARS-CoV-2, and we are learning these limitations may succumb to drug resistance.

Язык: Английский

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Predicting Antiviral Resistance Mutations in SARS-CoV-2 Main Protease with Computational and Experimental Screening

Biochemistry, Год журнала: 2022, Номер 61(22), С. 2495 - 2505

Опубликована: Ноя. 3, 2022

The main protease (Mpro) of SARS-CoV-2 is essential for viral replication and has been the focus many drug discovery efforts since start COVID-19 pandemic. Nirmatrelvir (NTV) an inhibitor Mpro that used in combination Paxlovid treatment mild to moderate COVID-19. However, with increased use NTV across globe, there a possibility future lineages will evolve resistance NTV. Early prediction monitoring mutations could allow measures slow spread development new compounds activity against resistant strains. In this work, we have silico mutational scanning docking identify potential mutations. Subsequent vitro experiments revealed five (N142L, E166M, Q189E, Q189I, Q192T) reduce potency previously identified non-covalent cyclic peptide Mpro. E166M mutation reduced half-maximal inhibitory concentration (IC50) 24-fold 118-fold inhibitor. Our findings inform ongoing genomic surveillance emerging lineages.

Язык: Английский

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A strategy for evaluating potential antiviral resistance to small molecule drugs and application to SARS-CoV-2

Scientific Reports, Год журнала: 2023, Номер 13(1)

Опубликована: Янв. 10, 2023

Alterations in viral fitness cannot be inferred from only mutagenesis studies of an isolated protein. To-date, no systematic analysis has been performed to identify mutations that improve virus and reduce drug efficacy. We present a generic strategy evaluate which might diminish efficacy applied it assess how SARS-CoV-2 evolution may affect the current approved/candidate small-molecule antivirals for Mpro, PLpro, RdRp. For each target, we determined drug-interacting residues available structures selection pressure genomes. This enabled identification promising target regions can develop resistance. Our utilizing sequence structural information genomic protein structure databanks rapidly any emerging variants aid antiviral design future pathogens.

Язык: Английский

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