Mechanism and spectrum of inhibition of a 4′-cyano modified nucleotide analog against diverse RNA polymerases of prototypic respiratory RNA viruses DOI Creative Commons
Calvin J. Gordon, Simon Walker, Egor P. Tchesnokov

et al.

Journal of Biological Chemistry, Journal Year: 2024, Volume and Issue: 300(8), P. 107514 - 107514

Published: June 28, 2024

The development of safe and effective broad-spectrum antivirals that target the replication machinery respiratory viruses is high priority in pandemic preparedness programs. Here, we studied mechanism action a newly discovered nucleotide analog against diverse RNA-dependent RNA polymerases (RdRps) prototypic viruses. GS-646939 active 5'-triphosphate metabolite 4'-cyano modified C-adenosine phosphoramidate prodrug GS-7682. Enzyme kinetics show RdRps human rhinovirus type 16 (HRV-16) enterovirus 71 incorporate with unprecedented selectivity; incorporated 20-50-fold more efficiently than its natural ATP counterpart. RdRp complex syncytial virus metapneumovirus similar efficiency. In contrast, influenza B shows clear preference for mitochondrial polymerase does not significant incorporation GS-646939. Once into nascent strand, acts as chain terminator although higher NTP concentrations can partially overcome inhibition some polymerases. Modeling biochemical data suggest 4'-modification inhibits translocation. Comparative studies GS-443902, triphosphate form 1'-cyano prodrugs remdesivir obeldesivir, reveal only different mechanisms inhibition, but also differences spectrum viral conclusion, modifications analogs provide complementary strategies to several families

Language: Английский

A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors DOI Creative Commons
Liming Yan,

Yucen Huang,

Ji Ge

et al.

Cell, Journal Year: 2022, Volume and Issue: 185(23), P. 4347 - 4360.e17

Published: Oct. 4, 2022

Language: Английский

Citations

37
Developing nucleoside tailoring strategies against SARS-CoV-2 via ribonuclease targeting chimera DOI Creative Commons
Yuan‐Qin Min, Wei Xiong,

Wei Shen

et al.

Science Advances, Journal Year: 2024, Volume and Issue: 10(15)

Published: April 10, 2024

In response to the urgent need for potent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) therapeutics, this study introduces an innovative nucleoside tailoring strategy leveraging ribonuclease targeting chimeras. By seamlessly integrating L recruiters into nucleosides, we address RNA recognition challenges and effectively inhibit replication in human cells. Notably, nucleosides tailored at ribose 2'-position outperform those modified nucleobase. Our vivo validation using hamster models further bolsters promise of approach, positioning it as a valuable asset development antiviral drugs.

Language: Английский

Citations

8
Favipiravir Analogues as Inhibitors of SARS-CoV-2 RNA-Dependent RNA Polymerase, Combined Quantum Chemical Modeling, Quantitative Structure–Property Relationship, and Molecular Docking Study DOI Creative Commons
Magdalena Latosińska, Jolanta Natalia Latosińska

Molecules, Journal Year: 2024, Volume and Issue: 29(2), P. 441 - 441

Published: Jan. 16, 2024

Our study was motivated by the urgent need to develop or improve antivirals for effective therapy targeting RNA viruses. We hypothesized that analogues of favipiravir (FVP), an inhibitor RNA-dependent polymerase (RdRp), could provide more nucleic acid recognition and binding processes while reducing side effects such as cardiotoxicity, hepatotoxicity, teratogenicity, embryotoxicity. proposed a set FVP together with their forms triphosphate new SARS-CoV-2 RdRp inhibitors. The main aim our investigate changes in mechanism capacity resulting from these modifications. Using three different approaches, QTAIM, QSPR, MD, differences reactivity, toxicity, efficiency, ability be incorporated were assessed. Two quantum chemical reactivity descriptors, relative electro-donating electro-accepting power, defined successfully applied. Moreover, quantitative method comparing modes developed based on mathematical metrics atypical radar plot. These methods deep insight into desirable properties responsible inhibiting RdRp, allowing ligands conveniently screened. modification structure seems its enhance productive mode binding. In particular, two (the trifluoro- cyano-) bind very strongly template, primer, cofactors, thus may constitute good alternative FVP.

Language: Английский

Citations

7
The oral nucleoside prodrug GS-5245 is efficacious against SARS-CoV-2 and other endemic, epidemic, and enzootic coronaviruses DOI
David R. Martinez, Fernando R. Moreira, Nicholas Catanzaro

et al.

Science Translational Medicine, Journal Year: 2024, Volume and Issue: 16(748)

Published: May 22, 2024

Despite the wide availability of several safe and effective vaccines that prevent severe COVID-19, persistent emergence acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants concern (VOCs) can evade vaccine-elicited immunity remains a global health concern. In addition, SARS-CoV-2 VOCs therapeutic monoclonal antibodies underscores need for additional, variant-resistant treatment strategies. Here, we characterize antiviral activity GS-5245, obeldesivir (ODV), an oral prodrug parent nucleoside GS-441524, which targets highly conserved viral RNA-dependent RNA polymerase (RdRp). We show GS-5245 is broadly potent in vitro against alphacoronavirus HCoV-NL63, SARS-CoV, SARS-CoV-related bat-CoV RsSHC014, Middle East (MERS-CoV), WA/1, transmissible BA.1 Omicron variant. Moreover, mouse models (WA/1 B1.1.529), MERS-CoV, RsSHC014 pathogenesis, observed dose-dependent reduction replication, body weight loss, lung injury, pulmonary function with therapy. Last, demonstrate combination main protease (M

Language: Английский

Citations

7
Kill or corrupt: Mechanisms of action and drug-resistance of nucleotide analogues against SARS-CoV-2 DOI Creative Commons
Ashleigh Shannon, Bruno Canard

Antiviral Research, Journal Year: 2022, Volume and Issue: 210, P. 105501 - 105501

Published: Dec. 22, 2022

Language: Английский

Citations

25
A mutation in the coronavirus nsp13-helicase impairs enzymatic activity and confers partial remdesivir resistance DOI Creative Commons
Samantha L. Grimes, Young Joo Choi,

Anoosha Banerjee

et al.

mBio, Journal Year: 2023, Volume and Issue: unknown

Published: June 20, 2023

ABSTRACT Coronaviruses (CoVs) encode nonstructural proteins 1–16 (nsps 1–16) which form replicase complexes that mediate viral RNA synthesis. Remdesivir (RDV) is an adenosine nucleoside analog antiviral inhibits CoV RDV resistance mutations have been reported only in the protein 12 RNA-dependent polymerase (nsp12-RdRp). We here show a substitution mutation nsp13-helicase (nsp13-HEL A335V) of betacoronavirus murine hepatitis virus (MHV) was selected during passage with parent compound confers partial independently and additively when expressed co-selected nsp12-RdRp. The MHV A335V did not enhance replication or competitive fitness compared to WT remained sensitive active cytidine molnupiravir (MOV). Biochemical analysis SARS-CoV-2 helicase encoding homologous (A336V) demonstrates mutant retained ability associate core nsps 7, 8, but had impaired unwinding ATPase activity. Together, these data identify novel determinant nsp13-HEL enzymatic activity, define new genetic pathway for resistance, demonstrate importance surveillance testing arise genomes. IMPORTANCE Despite development effective vaccines against COVID-19, continued circulation emergence variants support need antivirals such as RDV. Understanding pathways essential emerging variants, combination therapies, identifying potential targets inhibition. also impairs functions, supporting studying individual cooperative functions 7–16 has GISAID database genomes, highlighting helicase.

Language: Английский

Citations

14
Discovery of C-Linked Nucleoside Analogues with Antiviral Activity against SARS-CoV-2 DOI
Eugen F. Mesaros, Benjamin J. Dugan, Min Gao

et al.

ACS Infectious Diseases, Journal Year: 2024, Volume and Issue: 10(5), P. 1780 - 1792

Published: April 23, 2024

The recent COVID-19 pandemic underscored the limitations of currently available direct-acting antiviral treatments against acute respiratory RNA-viral infections and stimulated major research initiatives targeting anticoronavirus agents. Two novel nsp5 protease (MPro) inhibitors have been approved, nirmatrelvir ensitrelvir, along with two existing nucleos(t)ide analogues repurposed as nsp12 polymerase inhibitors, remdesivir molnupiravir, but a need still exists for therapies improved potency systemic exposure oral dosing, better metabolic stability, reduced resistance toxicity risks. Herein, we summarize our toward identifying that led to nucleoside 10e 10n, which showed favorable pan-coronavirus activity in cell-infection screens, were metabolized active triphosphate nucleotides cell-incubation studies, demonstrated target (nsp12) engagement biochemical assays.

Language: Английский

Citations

5
Effects of natural RNA modifications on the activity of SARS‐CoV‐2 RNA‐dependent RNA polymerase DOI

Ivan Petushkov,

Daria Esyunina, Andrey Kulbachinskiy

et al.

FEBS Journal, Journal Year: 2022, Volume and Issue: 290(1), P. 80 - 92

Published: Aug. 2, 2022

RNA-dependent RNA polymerase (RdRp) plays a key role in the replication of viruses, including SARS-CoV-2. Processive synthesis by RdRp is crucial for successful genome and expression, especially case very long coronaviral genomes. Here, we analysed activity SARS-CoV-2 (the nsp12-nsp7-nsp8 complex) on synthetic primer-templates various structures, substrates with mismatched primers or template modifications. It has been shown that cannot efficiently extend containing mismatches no intrinsic cleavage to remove primer 3'-end, thus necessitating action exoribonuclease proofreading. Similar DNA-dependent polymerases, can perform processive pyrophosphorolysis nascent product but this reaction also blocked presence mismatches. Furthermore, have demonstrated several natural post-transcriptional modifications template, which do not prevent complementary interactions (N6-methyladenosine, 5-methylcytosine, inosine pseudouridine), change processivity. At same time, certain bases ribose residues strongly block synthesis, either prior nucleotide incorporation (3-methyluridine 1-methylguanosine) immediately after it (2'-O-methylation). The results demonstrate be inhibited common suggesting way design novel antiviral compounds.

Language: Английский

Citations

17
Transcription Kinetics in the Coronavirus Life Cycle DOI Creative Commons
Katarzyna Grelewska‐Nowotko, Ahmed Eısa Elhag, Tomasz W. Turowski

et al.

Wiley Interdisciplinary Reviews - RNA, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 1, 2025

Coronaviruses utilize a positive-sense single-strand RNA, functioning simultaneously as mRNA and the genome. An RNA-dependent RNA polymerase (RdRP) plays dual role in transcribing genes replicating genome, making RdRP critical target therapies against coronaviruses. This review explores recent advancements understanding coronavirus transcription machinery, discusses it within virus infection context, incorporates kinetic considerations on activity. We also address steric limitations replication, particularly during early phases, outline hypothesis regarding translation-transcription conflicts, postulating existence of mechanisms that resolve these issues. In cells infected by coronaviruses, abundant structural proteins are synthesized from subgenomic fragments (sgRNAs) produced via discontinuous transcription. During elongation, can skip large sections viral resulting creation shorter sgRNAs reflects stoichiometry proteins. Although precise mechanism remains unknown, we discuss hypotheses involving long-distance RNA-RNA interactions, helicase-mediated backtracking, dissociation reassociation RdRP, dimerization.

Language: Английский

Citations

0
A post-assembly conformational change makes the SARS-CoV-2 polymerase elongation-competent DOI Creative Commons
Misha Klein, Arnab Das, Subhas Chandra Bera

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 11, 2025

Abstract Coronaviruses (CoV) encode sixteen non-structural proteins (nsps), most of which form the replication-transcription complex (RTC). The RTC contains a core composed one nsp12 RNA-dependent RNA polymerase (RdRp), two nsp8s and nsp7. recruits other nsps to synthesize all viral RNAs within infected cell. While essential for replication, mechanism by assembles into processive remains poorly understood. We show that preferentially first having nsp12-polymerase bind template, followed subsequent association nsp7 nsp8. Once assembled on requires hundreds seconds undergo conformational change enables elongation. In absence RNA, (apo-)RTC several hours adopt its elongation-competent conformation. propose this obligatory activation step facilitates recruitment additional nsp’s efficient synthesis may represent promising target therapeutic interventions.

Language: Английский

Citations

0