Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors

Science Advances, Journal Year: 2023, Volume and Issue: 9(13)

Published: March 31, 2023

Vaccines and drugs have helped reduce disease severity blunt the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, ongoing virus transmission, continuous evolution, increasing selective pressures potential to yield viral variants capable resisting these interventions. Here, we investigate susceptibility natural main protease [Mpro; 3C-like (3CLpro)] SARS-CoV-2 inhibitors. Multiple single amino acid changes in Mpro confer resistance nirmatrelvir (the active component Paxlovid). An additional clinical-stage inhibitor, ensitrelvir (Xocova), shows a different mutation profile. Importantly, phylogenetic analyses indicate that several resistant pre-existed introduction into human population are spreading. These results encourage monitoring development inhibitors other antiviral with mechanisms action profiles for combinatorial therapy.

Language: Английский

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

Science Translational Medicine, Journal Year: 2022, Volume and Issue: 15(678)

Published: Oct. 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.

Language: Английский

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Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease

Journal of Biological Chemistry, Journal Year: 2023, Volume and Issue: 299(3), P. 103004 - 103004

Published: Feb. 10, 2023

SARS-CoV-2 is the causative agent of COVID-19. The main viral protease (Mpro) an attractive target for antivirals. clinically approved drug nirmatrelvir and clinical candidate ensitrelvir have so far showed great potential treatment infection. However, broad use antivirals often associated with resistance generation. Herein, we enzymatically characterized 14 naturally occurring Mpro polymorphisms that are close to binding site these Nirmatrelvir retained its potency against most tested, while mutants G143S Q189K were diminished inhibition constants. For ensitrelvir, constants observed M49I, G143S, R188S, but not Q189K, suggesting a distinct profile between inhibitors. In addition, crystal structures selected revealed interactions critical loss potency. conclusion, our data will assist monitoring resistant strains, support design combined therapy, as well development next generation

Language: Английский

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

EBioMedicine, Journal Year: 2023, Volume and Issue: 91, P. 104559 - 104559

Published: April 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).

Language: Английский

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Bench-to-bedside: Innovation of small molecule anti-SARS-CoV-2 drugs in China

European Journal of Medicinal Chemistry, Journal Year: 2023, Volume and Issue: 257, P. 115503 - 115503

Published: May 18, 2023

Language: Английский

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

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: March 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.

Language: Английский

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Multidrug-resistant mutations to antiviral and antibody therapy in an immunocompromised patient infected with SARS-CoV-2

Med, Journal Year: 2023, Volume and Issue: 4(11), P. 813 - 824.e4

Published: Sept. 7, 2023

Antiviral and antibody therapies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are being recommended high-risk patients, but the potential development of multidrug-resistant mutations in immunocompromised patients is unclear.To investigate treatment course cases prolonged viral shedding an patient with SARS-CoV-2 infection, we conducted longitudinal measurements laboratory tests, chest computed tomography (CT) image evaluations, titers, antigen levels nasopharyngeal swabs. Furthermore, performed whole-genome sequencing digital PCR analysis to examine mechanisms drug resistance.We present a case 65-year-old man history malignant lymphoma who was treated multiple antiviral therapies, including sotrovimab, remdesivir, paxlovid (nirmatrelvir/ritonavir), molnupiravir. Initially, decreased after treatments. However, virus rebounded, showed no virologic response. The genome revealed single Omicron subvariant (BA.1.1), which evolved within host during disease progression. viruses had acquired resistance nirmatrelvir (3 chymotrypsin-like protease [3CLpro] E166 A/V), sotrovimab (spike P337L E340K), remdesivir (RNA-dependent RNA polymerase [RdRp] V166L).Our results indicate that survival fitness persist infected subpopulation selection pressure.This study supported by JSPS KAKENHI Early-Career Scientists 18K16292 (Y.H.), Grant-in-Aid Scientific Research (B) 20H03668 23H02955 YASUDA Medical Foundation Uehara Memorial Takeda Science Kato Bioscience (Y.H.).

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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Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model

Science, Journal Year: 2024, Volume and Issue: 383(6690), P. 1434 - 1440

Published: March 28, 2024

The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. papain-like protease (PL pro ) is a promising but challenging drug target. We designed synthesized 85 noncovalent PL inhibitors that bind to recently discovered ubiquitin binding site the known BL2 groove pocket near S4 subsite. Leads inhibited with inhibitory constant K i values from 13.2 88.2 nanomolar. co-crystal structures eight leads revealed their interaction modes. in vivo lead Jun12682 its variants, including nirmatrelvir-resistant strains EC 50 0.44 2.02 micromolar. Oral treatment improved survival reduced lung viral loads lesions infection mouse model, suggesting are antiviral candidates.

Language: Английский

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

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: April 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.

Language: Английский

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