Conserved Characteristics of NMPylation Activities of Alpha- and Betacoronavirus NiRAN Domains DOI
Heiko Slanina, Ramakanth Madhugiri,

Kai Wenk

и другие.

Journal of Virology, Год журнала: 2023, Номер 97(6)

Опубликована: Май 18, 2023

Coronavirus genome replication and expression are mediated by the viral replication-transcription complex (RTC) which is assembled from multiple nonstructural proteins (nsp). Among these, nsp12 represents central functional subunit. It harbors RNA-directed RNA polymerase (RdRp) domain contains, at its N terminus, an additional called NiRAN widely conserved in coronaviruses other nidoviruses. In this study, we produced bacterially expressed coronavirus nsp12s to investigate compare NiRAN-mediated NMPylation activities representative alpha- betacoronaviruses. We found that four domains characterized date have a number of properties, including (i) robust nsp9-specific appear operate largely independently C-terminal RdRp domain, (ii) nucleotide substrate preference for UTP followed ATP nucleotides, (iii) dependence on divalent metal ions, with Mn2+ being preferred over Mg2+, (iv) key role N-terminal residues (particularly Asn2) nsp9 efficient formation covalent phosphoramidate bond between NMP amino group nsp9. context, mutational analysis confirmed conservation critical Asn2 across different subfamilies family Coronaviridae, as shown studies using chimeric variants six were replaced those corona-, pito- letovirus homologs. The combined data previous reveal remarkable degree among activities, supporting enzymatic activity synthesis processing. IMPORTANCE There strong evidence large nidoviruses evolved unique RdRp-associated but not most viruses. Previous mainly focused severe acute respiratory syndrome 2 (SARS-CoV-2) suggested functions such NMPylation/RNAylation nsp9, guanylyltransferase involved canonical and/or unconventional capping pathways, functions. To help resolve partly conflicting information specificities ion requirements reported previously SARS-CoV-2 activity, extended these earlier characterizing betacoronavirus domains. study revealed features protein specificity requirements, very well genetically divergent coronaviruses, suggesting potential avenues future antiviral drug development targeting essential enzyme.

Язык: Английский

Identification of potent multi-target antiviral natural compounds from the fungal metabolites against aspartyl viral polymerases DOI Creative Commons

Zohreh Sahhaf Razavi,

Ali Ramazani,

Armin Zarei

и другие.

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Март 13, 2025

Since viral polymerases are responsible for replication, they a prime target in antiviral drug development. The present study evaluated the potential of 174 secondary metabolites Sordariales order against aspartyl polymerases, including hepatitis C virus nonstructural protein 5B (HCV NS5B) and Severe acute respiratory syndrome coronavirus 2 RNA-dependent RNA polymerase (SARS CoV-2 RdRp). A two-step virtual screening was performed, identifying 76 ligands binding to active site, while 10 showed energies below -7 kcal/mol. Ligands 1–3 exhibited better affinities than Ribavirin. Lig-3 demonstrated most intense interaction. These interacted through hydrogen bonding hydrophobic interactions with key catalytic motifs that may disrupt replication by inhibiting activities. Next, effects these induced structure dynamics were analyzed 300 ns molecular (MD) simulations, showing ligand altered structural critical NTP template binding. RMSF PCA analyses revealed reduced mobility significant destabilization, particularly Lig-1 SARS-CoV-2 RdRp Lig-2 HCV NS5B. Additionally, Rg SASA indicated compression ligand-bound complexes, corroborating hypothesis enzymatic inhibition. MM/PBSA analysis highlighted as having stronger RdRp, displayed higher With promising ADME/T properties, is multi-target candidate NS5B meriting further vitro vivo investigations.

Язык: Английский

Процитировано

0
An Overview on Anti-COVID-19 Drug Achievements and Challenges Ahead DOI
Mehdi Valipour, Hamid Irannejad, Hossein Keyvani

и другие.

ACS Pharmacology & Translational Science, Год журнала: 2023, Номер 6(9), С. 1248 - 1265

Опубликована: Авг. 16, 2023

The appearance of several coronavirus pandemics/epidemics during the last two decades (SARS-CoV-1 in 2002, MERS-CoV 2012, and SARS-CoV-2 2019) indicates that humanity will face increasing challenges from coronaviruses future. emergence new strains with similar transmission characteristics as mortality rates to SARS-CoV-1 (∼10% mortality) or (∼35% future is a terrifying possibility. Therefore, getting enough preparations such risks an inevitable necessity. present study aims review drug achievements fight against combined perspective derived pharmacology, pharmacotherapy, medicinal chemistry insights. Appreciating all efforts made past few years, there strong evidence desired results have not yet been achieved research this area should still be pursued seriously. By expressing some pessimistic possibilities concluding discovery pharmacotherapy COVID-19 successful so far, short essay tries draw attention responsible authorities more prepared epidemics/pandemics.

Язык: Английский

Процитировано

9
Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain DOI Creative Commons
Gabriel I. Small, Olga Fedorova, Paul Dominic B. Olinares

и другие.

Molecular Cell, Год журнала: 2023, Номер 83(21), С. 3921 - 3930.e7

Опубликована: Окт. 26, 2023

Язык: Английский

Процитировано

9
No Remdesivir Resistance Observed in the Phase 3 Severe and Moderate COVID-19 SIMPLE Trials DOI Creative Commons
Charlotte Hedskog, Christoph D. Spinner, Ulrike Protzer

и другие.

Viruses, Год журнала: 2024, Номер 16(4), С. 546 - 546

Опубликована: Март 31, 2024

Remdesivir (RDV) is a broad-spectrum nucleotide analog prodrug approved for the treatment of COVID-19 in hospitalized and non-hospitalized patients with clinical benefit demonstrated multiple Phase 3 trials. Here we present SARS-CoV-2 resistance analyses from SIMPLE studies evaluating RDV participants severe or moderate disease. The enrolled radiologic evidence pneumonia room-air oxygen saturation ≤94% >94%, respectively. Virology sample collection was optional study protocols. Sequencing related viral load data were obtained retrospectively at subset sites local sequencing capabilities (10 183 sites) timepoints detectable load. Among both baseline post-baseline treated RDV, emergent Nsp12 substitutions observed 4 19 (21%) none 2 study. following 5 emerged: T76I, A526V, A554V, E665K, C697F. C697F had an EC50 fold change ≤1.5 relative to wildtype reference using subgenomic replicon system, indicating no significant susceptibility RDV. phenotyping E665K could not be determined due lack replication. These reveal relevant emergence further confirm established efficacy profile high barrier patients.

Язык: Английский

Процитировано

3
Transcription Kinetics in the Coronavirus Life Cycle DOI Creative Commons
Katarzyna Grelewska‐Nowotko, Ahmed Eısa Elhag, Tomasz W. Turowski

и другие.

Wiley Interdisciplinary Reviews - RNA, Год журнала: 2025, Номер 16(1)

Опубликована: Янв. 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.

Язык: Английский

Процитировано

0
Remdesivir and Obeldesivir Retain Potent Antiviral Activity Against SARS-CoV-2 Omicron Variants DOI Creative Commons

Lauren Rodriguez,

J. Lizbeth Reyes Zamora, Dong Han

и другие.

Viruses, Год журнала: 2025, Номер 17(2), С. 168 - 168

Опубликована: Янв. 25, 2025

As new SARS-CoV-2 variants continue to emerge, it is important evaluate the potency of antiviral drugs support their continued use. Remdesivir (RDV; VEKLURY®) an approved treatment for COVID-19, and obeldesivir (ODV) are inhibitors RNA-dependent RNA polymerase Nsp12. Here we show these two compounds retain activity against Omicron BA.2.86, BF.7, BQ.1, CH.1.1, EG.1.2, EG.5.1, EG.5.1.4, FL.22, HK.3, HV.1, JN.1, JN.1.7, JN.1.18, KP.2, KP.3, LB.1, XBB.1.5, XBB.1.5.72, XBB.1.16, XBB.2.3.2, XBC.1.6, XBF when compared with reference strains. Genomic analysis identified 29 Nsp12 polymorphisms in previous variants. Phenotypic confirmed no impact on RDV or ODV suggests containing remain susceptible both compounds. These data use context circulating development as therapeutic.

Язык: Английский

Процитировано

0
Covalent inhibition of the SARS-CoV-2 NiRAN domain via an active-site cysteine DOI Creative Commons
Genaro Hernandez, Adam Osinski, Abir Majumdar

и другие.

Journal of Biological Chemistry, Год журнала: 2025, Номер unknown, С. 108378 - 108378

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

0
Structural basis of SARS-CoV-2 polymerase inhibition by nonnucleoside inhibitor HeE1-2Tyr DOI Creative Commons
Florian Kabinger,

Valerie Doze,

Jana Schmitzová

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2025, Номер 122(10)

Опубликована: Март 4, 2025

Targeting the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 with small molecules is a promising therapeutic strategy against COVID-19, but potent and safe inhibitors are lacking. HeE1-2Tyr, nonnucleoside inhibitor Dengue virus RdRp, was also shown to inhibit RdRp in vitro have antiviral activity cells, underlying mechanism remains unclear. Here, we elucidate molecular HeE1-2Tyr-mediated inhibition. Biochemical assays confirm that HeE1-2Tyr inhibits an IC 50 5 µM show it competes binding vitro. Structural analysis using cryo-EM reveals stack three binds site RdRp. The identification conserved its intriguing inhibition stacked outcompete may facilitate further development pan-corona inhibitors.

Язык: Английский

Процитировано

0
In silico studies to understand the interactions of flavonoid inhibitor with nsp12-RNA dependent RNA polymerase of SARS-CoV-2 and its homologs DOI

Shamiya Anwar Kizhakkiniyakath,

Tejaswini Choudhury,

Madhan Vishal Rajan

и другие.

Biochemistry and Biophysics Reports, Год журнала: 2025, Номер 42, С. 101975 - 101975

Опубликована: Март 13, 2025

Язык: Английский

Процитировано

0
Structural Biology of the SARS-CoV-2 replication–transcription complex DOI Creative Commons
Cameron D. Fyfe, Cromarte Rogers, Alexander Matthew Payne

и другие.

Crystallography Reviews, Год журнала: 2025, Номер unknown, С. 1 - 20

Опубликована: Март 18, 2025

Язык: Английский

Процитировано

0