Insights into RNA-dependent RNA Polymerase Inhibitors as Anti-influenza Virus Agents.

2020 ◽  
Vol 27 ◽  
Author(s):  
Ilaria Giacchello ◽  
Francesca Musumeci ◽  
Ilaria D’Agostino ◽  
Chiara Greco ◽  
Giancarlo Grossi ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Viral Infections ◽  
Rna Dependent Rna Polymerase ◽  
Potential Strength ◽  
Fda Approval ◽  
Promising Target ◽  
New Strategy ◽  
High Conservation ◽  
New Compounds ◽  
Selection Of

Background: Influenza is a seasonal disease which affects millions of people every year and has a significant economic impact. Vaccines are the best strategy to fight this viral pathology, but they are not always available or administrable, prompting the search for antiviral drugs. RNA-dependent RNA polymerase (RdRp) recently emerged as a promising target, because of its key role in viral replication and its high conservation among viral strains. Discussion: This review presents an overview of the most interesting RdRp inhibitors that have appeared in the literature since 2000. Compounds already approved or in clinical trials and a selection of inhibitors endowed with different scaffolds are described, along with the main features responsible for their activity. Results: RdRp inhibitors are emerging as a new strategy to fight viral infections, and the importance of this class of drugs has been confirmed by the FDA approval of baloxavir marboxil in 2018. Despite the complexity of the RdRp machine makes the identification of new compounds a challenging research topic, it is likely that in the coming years this field will attract the interest of a number of academic and industrial scientists because of the potential strength of this therapeutic approach.

scholarly journals A Parallel Phenotypic Versus Target-Based Screening Strategy for RNA-Dependent RNA Polymerase Inhibitors of the Influenza A Virus

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 826 ◽  
Author(s):  
Xiujuan Zhao ◽  
Yanyan Wang ◽  
Qinghua Cui ◽  
Ping Li ◽  
Lin Wang ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Influenza A Virus ◽  
Influenza A ◽  
Screening Strategy ◽  
Control Analysis ◽  
Virus Infections ◽  
Rdrp Activity ◽  
Rna Dependent Rna Polymerase ◽  
Virus Rna ◽  
Promising Target

Influenza A virus infections cause significant morbidity and mortality, and novel antivirals are urgently needed. Influenza RNA-dependent RNA polymerase (RdRp) activity has been acknowledged as a promising target for novel antivirals. In this study, a phenotypic versus target-based screening strategy was established to identify the influenza A virus inhibitors targeting the virus RNA transcription/replication steps by sequentially using an RdRp-targeted screen and a replication-competent reporter virus-based approach using the same compounds. To demonstrate the utility of this approach, a pilot screen of a library of 891 compounds derived from natural products was carried out. Quality control analysis indicates that the primary screen was robust for identification of influenza A virus inhibitors targeting RdRp activity. Finally, two hit candidates were identified, and one was validated as a putative RdRp inhibitor. This strategy can greatly reduce the number of false positives and improve the accuracy and efficacy of primary screening, thereby providing a powerful tool for antiviral discovery.

scholarly journals A Library of Nucleotide Analogues Terminate RNA Synthesis Catalyzed by Polymerases of Coronaviruses Causing SARS and COVID-19

2020 ◽  
Author(s):  
Steffen Jockusch ◽  
Chuanjuan Tao ◽  
Xiaoxu Li ◽  
Thomas K. Anderson ◽  
Minchen Chien ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Safety Profile ◽  
Rna Synthesis ◽  
Viral Infections ◽  
Nucleoside Triphosphate ◽  
Exonuclease Activity ◽  
Base Pairs ◽  
Rna Dependent Rna Polymerase ◽  
Nucleotide Analogues ◽  
Tenofovir Alafenamide

AbstractSARS-CoV-2, a member of the coronavirus family, is responsible for the current COVID-19 worldwide pandemic. We previously demonstrated that five nucleotide analogues inhibit the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), including the active triphosphate forms of Sofosbuvir, Alovudine, Zidovudine, Tenofovir alafenamide and Emtricitabine. We report here the evaluation of a library of additional nucleoside triphosphate analogues with a variety of structural and chemical features as inhibitors of the RdRps of SARS-CoV and SARS-CoV-2. These features include modifications on the sugar (2’ or 3’ modifications, carbocyclic, acyclic, or dideoxynucleotides) or on the base. The goal is to identify nucleotide analogues that not only terminate RNA synthesis catalyzed by these coronavirus RdRps, but also have the potential to resist the viruses’ exonuclease activity. We examined these nucleotide analogues with regard to their ability to be incorporated by the RdRps in the polymerase reaction and then prevent further incorporation. While all 11 molecules tested displayed incorporation, 6 exhibited immediate termination of the polymerase reaction (Carbovir triphosphate, Ganciclovir triphosphate, Stavudine triphosphate, Entecavir triphosphate, 3’-O-methyl UTP and Biotin-16-dUTP), 2 showed delayed termination (Cidofovir diphosphate and 2’-O-methyl UTP), and 3 did not terminate the polymerase reaction (2’-fluoro-dUTP, 2’-amino-dUTP and Desthiobiotin-16-UTP). The coronavirus genomes encode an exonuclease that apparently requires a 2’ -OH group to excise mismatched bases at the 3’-terminus. In this study, all of the nucleoside triphosphate analogues we evaluated form Watson-Cricklike base pairs. All the nucleotide analogues which demonstrated termination either lack a 2’-OH, have a blocked 2’-OH, or show delayed termination. These nucleotides may thus have the potential to resist exonuclease activity, a property that we will investigate in the future. Furthermore, prodrugs of five of these nucleotide analogues (Brincidofovir/Cidofovir, Abacavir, Valganciclovir/Ganciclovir, Stavudine and Entecavir) are FDA approved for other viral infections, and their safety profile is well known. Thus, they can be evaluated rapidly as potential therapies for COVID-19.

scholarly journals In vitro selection of RNA aptamers that bind the RNA-dependent RNA polymerase of hepatitis C virus: A possible role of GC-rich RNA motifs in NS5B binding

Virology ◽  
2009 ◽  
Vol 388 (1) ◽  
pp. 91-102 ◽  
Author(s):  
Hiroshi Kanamori ◽  
Kazuhito Yuhashi ◽  
Yasutoshi Uchiyama ◽  
Tatsuhiko Kodama ◽  
Shin Ohnishi
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Rna Polymerase ◽  
In Vitro Selection ◽  
Rna Aptamers ◽  
Rna Dependent Rna Polymerase ◽  
Rna Motifs ◽  
Selection Of

scholarly journals Computational selection of flavonoid compounds as inhibitors against SARS-CoV-2 main protease, RNA-dependent RNA polymerase and spike proteins: A molecular docking study

2021 ◽  
Vol 28 (1) ◽  
pp. 448-458
Author(s):  
Marimuthu Ragavan Rameshkumar ◽  
Purushothaman Indu ◽  
Narasingam Arunagirinathan ◽  
Babu Venkatadri ◽  
Hamed A. El-Serehy ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Rna Dependent Rna Polymerase ◽  
Flavonoid Compounds ◽  
Main Protease ◽  
Selection Of ◽  
Spike Proteins

Selection of a Thiazole Urea-Resistant Variant of Bovine Viral Diarrhoea Virus That Maps to the RNA-Dependent RNA Polymerase

2002 ◽  
Vol 13 (5) ◽  
pp. 315-323 ◽  
Author(s):  
Robert W King ◽  
Helen T Scarnati ◽  
E Scott Priestley ◽  
Indawati De Lucca ◽  
Anu Bansal ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Bovine Viral Diarrhoea Virus ◽  
Fold Increase ◽  
Bovine Viral Diarrhoea ◽  
Wild Type ◽  
Rna Dependent Rna Polymerase ◽  
Resistant Variant ◽  
Diarrhoea Virus ◽  
Template Selection ◽  
Selection Of

By passing wild type bovine viral diarrhoea virus (BVDV) in increasing concentrations of DPC-A69280–29, a thiazole urea class compound that inhibits BVDV replication, we were able to select several variants of BVDV that exhibited decreased susceptibility to this compound. When the non-structural genes of these variants were sequenced and compared with wild type, only one change was common to all the variants that also exhibited resistance to DPC-A69280–29 (>10-fold increase in IC50). This change was a T-to-A transversion at position 11198 of the BVDV genome, which would cause a predicted substitution of isoleucine for phenylalanine at amino acid 78 of the RNA-dependent RNA polymerase (RdRp). This substitution would occur in a region of the BVDV RdRp which has been proposed to be important for the formation of the RdRp homodimer that is essential for the activity of the enzyme. However, since DPC-69280-29 inhibits BVDV replication by interfering with the initiation of viral RNA synthesis, we discuss the possibility that this region of the BVDV RdRp also may play a role in the initiation process. Furthermore, since this region is located fairly close to the template RNA, we also propose that the role it plays may involve either template selection, stabilization or processivity.

Selection of DNA Aptamers That Bind the RNA-Dependent RNA Polymerase of Hepatitis C Virus and Inhibit Viral RNA SynthesisIn Vitro

2003 ◽  
Vol 13 (6) ◽  
pp. 455-463 ◽  
Author(s):  
Pantxika Bellecave ◽  
Marie-Line Andreola ◽  
Michel Ventura ◽  
Laura Tarrago-Litvak ◽  
Simon Litvak ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Rna Polymerase ◽  
Viral Rna ◽  
Dna Aptamers ◽  
Rna Dependent Rna Polymerase ◽  
Selection Of

scholarly journals Selection of 3′-Template Bases and Initiating Nucleotides by Hepatitis C Virus NS5B RNA-Dependent RNA Polymerase

2002 ◽  
Vol 76 (14) ◽  
pp. 7030-7039 ◽  
Author(s):  
Jae Hoon Shim ◽  
Gary Larson ◽  
Jim Zhen Wu ◽  
Zhi Hong
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Rna Polymerase ◽  
Rna Synthesis ◽  
De Novo ◽  
Nonstructural Protein ◽  
Initiation Site ◽  
De Novo Synthesis ◽  
Rna Dependent Rna Polymerase ◽  
Selection Of

ABSTRACT De novo RNA synthesis by hepatitis C virus (HCV) nonstructural protein 5B (NS5B) RNA-dependent RNA polymerase has been investigated using short RNA templates. Various templates including those derived from the HCV genome were evaluated by examining the early steps of de novo RNA synthesis. NS5B was shown to be able to produce an initiation dinucleotide product from templates as short as 4-mer and from the 3′-terminal sequences of both plus and minus strands of the HCV RNA genome. GMP, GDP, and guanosine were able to act as an initiating nucleotide in de novo RNA synthesis, indicating that the triphosphate moiety is not absolutely required by an initiating nucleotide. Significant amounts of the initiation product accumulated in de novo synthesis, and elongation from the dinucleotide was observed when large amounts of dinucleotide were available. This result suggests that NS5B, a template, and incoming nucleotides are able to form an initiation complex that aborts frequently by releasing the dinucleotide product before transition to an elongation complex. The transition is rate limiting. Furthermore, we discovered that the secondary structure of a template was not essential for de novo initiation and that 3′-terminal bases of a template conferred specificity in selection of an initiation site. Initiation can occur at the +1, +2, or +3 position numbered from the 3′ end of a template depending on base composition. Pyrimidine bases at any of the three positions are able to serve as an initiation site, while purine bases at the +2 and +3 positions do not support initiation. This result implies that HCV possesses an intrinsic ability to ensure that de novo synthesis is initiated from the +1 position and to maintain the integrity of the 3′ end of its genome. This assay system should be an important tool for investigating the detailed mechanism of de novo initiation by HCV NS5B as well as other viral RNA polymerases.

scholarly journals Viperin Reveals Its True Function

2020 ◽  
Vol 7 (1) ◽  
pp. 421-446 ◽  
Author(s):  
Efraín E. Rivera-Serrano ◽  
Anthony S. Gizzi ◽  
Jamie J. Arnold ◽  
Tyler L. Grove ◽  
Steven C. Almo ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Enzymatic Activity ◽  
Rna Synthesis ◽  
Viral Infections ◽  
Innate Immune ◽  
Biological Functions ◽  
Restriction Factors ◽  
Rna Dependent Rna Polymerase ◽  
Immune Pathways ◽  
Antiviral Mechanism

Most cells respond to viral infections by activating innate immune pathways that lead to the induction of antiviral restriction factors. One such factor, viperin, was discovered almost two decades ago based on its induction during viral infection. Since then, viperin has been shown to possess activity against numerous viruses via multiple proposed mechanisms. Most recently, however, viperin was demonstrated to catalyze the conversion of cytidine triphosphate (CTP) to 3′-deoxy-3′,4′-didehydro-CTP (ddhCTP), a previously unknown ribonucleotide. Incorporation of ddhCTP causes premature termination of RNA synthesis by the RNA-dependent RNA polymerase of some viruses. To date, production of ddhCTP by viperin represents the only activity of viperin that links its enzymatic activity directly to an antiviral mechanism in human cells. This review examines the multiple antiviral mechanisms and biological functions attributed to viperin.

Sign in / Sign up

Export Citation Format

Share Document