Faculty Opinions recommendation of Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency.

Effective treatments for coronavirus disease 2019 (COVID-19) are urgently needed to control this current pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Replication of SARS-CoV-2 depends on the viral RNA-dependent RNA polymerase (RdRp), which is the likely target of the investigational nucleotide analogue remdesivir (RDV). RDV shows broad-spectrum antiviral activity against RNA viruses, and previous studies with RdRps from Ebola virus and Middle East respiratory syndrome coronavirus (MERS-CoV) have revealed that delayed chain termination is RDV's plausible mechanism of action. Here, we expressed and purified active SARS-CoV-2 RdRp composed of the nonstructural proteins nsp8 and nsp12. Enzyme kinetics indicated that this RdRp efficiently incorporates the active triphosphate form of RDV (RDV-TP) into RNA. Incorporation of RDV-TP at position i caused termination of RNA synthesis at position i+3. We obtained almost identical results with SARS-CoV, MERS-CoV, and SARS-CoV-2 RdRps. A unique property of RDV-TP is its high selectivity over incorporation of its natural nucleotide counterpart ATP. In this regard, the triphosphate forms of 2′-C-methylated compounds, including sofosbuvir, approved for the management of hepatitis C virus infection, and the broad-acting antivirals favipiravir and ribavirin, exhibited significant deficits. Furthermore, we provide evidence for the target specificity of RDV, as RDV-TP was less efficiently incorporated by the distantly related Lassa virus RdRp, and termination of RNA synthesis was not observed. These results collectively provide a unifying, refined mechanism of RDV-mediated RNA synthesis inhibition in coronaviruses and define this nucleotide analogue as a direct-acting antiviral.

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Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action

Journal of Biological Chemistry ◽

10.1074/jbc.ac120.015720 ◽

2020 ◽

Vol 295 (47) ◽

pp. 16156-16165 ◽

Cited By ~ 3

Author(s):

Egor P. Tchesnokov ◽

Calvin J. Gordon ◽

Emma Woolner ◽

Dana Kocinkova ◽

Jason K. Perry ◽

...

Keyword(s):

Rna Polymerase ◽

Structural Model ◽

Antiviral Agent ◽

Product Formation ◽

Chain Termination ◽

Rna Dependent Rna Polymerase ◽

Biologically Relevant ◽

Direct Acting Antiviral ◽

Dependent Inhibition ◽

Direct Acting

Remdesivir (RDV) is a direct-acting antiviral agent that is used to treat patients with severe coronavirus disease 2019 (COVID-19). RDV targets the viral RNA-dependent RNA polymerase (RdRp) of severe acute respiratory syndrome coronavirus 2 (SARS–CoV-2). We have previously shown that incorporation of the active triphosphate form of RDV (RDV-TP) at position i causes delayed chain termination at position i + 3. Here we demonstrate that the S861G mutation in RdRp eliminates chain termination, which confirms the existence of a steric clash between Ser-861 and the incorporated RDV-TP. With WT RdRp, increasing concentrations of NTP pools cause a gradual decrease in termination and the resulting read-through increases full-length product formation. Hence, RDV residues could be embedded in copies of the first RNA strand that is later used as a template. We show that the efficiency of incorporation of the complementary UTP opposite template RDV is compromised, providing a second opportunity to inhibit replication. A structural model suggests that RDV, when serving as the template for the incoming UTP, is not properly positioned because of a significant clash with Ala-558. The adjacent Val-557 is in direct contact with the template base, and the V557L mutation is implicated in low-level resistance to RDV. We further show that the V557L mutation in RdRp lowers the nucleotide concentration required to bypass this template-dependent inhibition. The collective data provide strong evidence to show that template-dependent inhibition of SARS–CoV-2 RdRp by RDV is biologically relevant.

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Remdesivir and Ledipasvir among the FDA-Approved Antiviral Drugs Have Potential to Inhibit SARS-CoV-2 Replication

Cells ◽

10.3390/cells10051052 ◽

2021 ◽

Vol 10 (5) ◽

pp. 1052

Author(s):

Rameez Hassan Pirzada ◽

Muhammad Haseeb ◽

Maria Batool ◽

MoonSuk Kim ◽

Sangdun Choi

Keyword(s):

Antiviral Drugs ◽

Effective Concentration ◽

Nonstructural Proteins ◽

Rna Dependent Rna Polymerase ◽

Direct Acting Antiviral ◽

Rapid Spread ◽

Half Maximal Effective Concentration ◽

Dynamics Simulations ◽

Direct Acting ◽

Transcription And Replication

The rapid spread of the virus, the surge in the number of deaths, and the unavailability of specific SARS-CoV-2 drugs thus far necessitate the identification of drugs with anti-COVID-19 activity. SARS-CoV-2 enters the host cell and assembles a multisubunit RNA-dependent RNA polymerase (RdRp) complex of viral nonstructural proteins that plays a substantial role in the transcription and replication of the viral genome. Therefore, RdRp is among the most suitable targets in RNA viruses. Our aim was to investigate the FDA approved antiviral drugs having potential to inhibit the viral replication. The methodology adopted was virtual screening and docking of FDA-approved antiviral drugs into the RdRp protein. Top hits were selected and subjected to molecular dynamics simulations to understand the dynamics of RdRp in complex with these drugs. The antiviral activity of the drugs against SARS-CoV-2 was assessed in Vero E6 cells. Notably, both remdesivir (half-maximal effective concentration (EC50) 6.6 μM, 50% cytotoxicity concentration (CC50) > 100 µM, selectivity index (SI) = 15) and ledipasvir (EC50 34.6 μM, CC50 > 100 µM, SI > 2.9) exerted antiviral action. This study highlights the use of direct-acting antiviral drugs, alone or in combination, for better treatments of COVID-19.

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Computer-aided identification of a series of novel ligands showing high potency as hepatitis C virus NS3/4A protease inhibitors

Bulletin of the National Research Centre ◽

10.1186/s42269-020-00467-w ◽

2021 ◽

Vol 45 (1) ◽

Author(s):

Stephen Ejeh ◽

Adamu Uzairu ◽

Gideon Adamu Shallangwa ◽

Stephen E. Abechi

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Binding Energy ◽

Protease Inhibitor ◽

Protease Inhibitors ◽

Antiviral Agents ◽

High Potency ◽

Direct Acting Antiviral ◽

Direct Acting ◽

Direct Acting Antiviral Agents

Abstract Background Hepatitis C virus (HCV) is a global medical condition that causes several life-threatening chronic diseases in the liver. The conventional interferon-free treatment regimens are currently in use by a blend of direct-acting antiviral agents (DAAs) aiming at the viral NS3 protease. However, major concerns may be the issue of DAA-resistant HCV strains and the limited availability to the DAAs due to their high price. Due to this crisis, the developments of a new molecule with high potency as an NS3/4A protease inhibitor of the hepatitis-C virus remain a high priority for medical research. This study aimed to use in-silico methods to identify high potent molecule as an NS3/4A protease inhibitor and investigating the binding energy of the identified molecule in comparison with approved direct-acting antiviral agents (Telaprevir, Simeprevir, and Voxilaprevir) through molecular docking. Results The model obtained by in-silico method have the following statistical records, coefficient of determination (r2) of 0.7704, cross-validation (q2LOO = 0.6914); external test set (r2(pred) = 0.7049) and Y-randomization assessment (cR2p = 0.7025). The results from the model were used to identify 12 new potential human HCV NS3/4A protease inhibitors, and it was observed that the identified molecule is well-fixed when docked with the receptor and was found to have the lowest binding energy of − 10.7, compared to approved direct-acting antiviral agents (Telaprevir, Simeprevir, and Voxilaprevir) with − 9.5, − 10.0, − 10.5 binding energy, respectively. Conclusion The binding affinity (− 10.7) of the newly identified molecule docked with 3D structures of HCV NS3/4a protease/helicase (PDB ID: 4A92) was found to be better than that of Telaprevir, Simeprevir, and Voxilaprevir (approved direct-acting antiviral agents) which are − 9.5, − 10.0, and − 10.5, respectively. Hence, a novel molecule was identified showing high potency as HCV NS3/4a protease inhibitors.

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Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase

ACS Omega ◽

10.1021/acsomega.0c02096 ◽

2020 ◽

Vol 5 (29) ◽

pp. 18356-18366 ◽

Cited By ~ 1

Author(s):

Mohammed Ahmad ◽

Abhisek Dwivedy ◽

Richard Mariadasse ◽

Satish Tiwari ◽

Deepsikha Kar ◽

...

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Rna Polymerase ◽

Small Molecule ◽

Small Molecule Inhibitors ◽

Rna Dependent Rna Polymerase

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Early combination treatment with existing HIV antivirals: an effective treatment for COVID-19?

10.21203/rs.3.rs-35791/v1 ◽

2020 ◽

Author(s):

Roberto Nico Dallocchio ◽

Alessandro Dessì ◽

Andrea De Vito ◽

Giovanna Delogu ◽

Pier Andrea ◽

...

Keyword(s):

Clinical Trials ◽

Molecular Docking ◽

Severe Acute Respiratory Syndrome ◽

Rna Polymerase ◽

Protease Inhibitor ◽

Combination Treatment ◽

Binding Sites ◽

Nucleoside Analogues ◽

Rna Dependent Rna Polymerase ◽

Protein Pocket

Abstract Since no effective therapy exists, we aimed to test existing HIV antivirals for combination treatment of Coronavirus disease 19 (COVID-19). Our molecular docking findings suggest that lopinavir, ritonavir, darunavir, and atazanavir activated interactions with the key binding sites of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) protease with a better Ki for lopinavir, ritonavir, and darunavir. Furthermore, we evidenced the ability of remdesivir, tenofovir, emtricitabine, and lamivudine to be incorporated in SARS-CoV-2 RNA-dependent RNA polymerase in the same protein pocket where poses the corresponding natural nucleoside substrates with comparable Ki and activating similar interactions. In principle, the four antiviral nucleotides might be used effectively against SARS-CoV-2. The combination of a protease inhibitor and two nucleoside analogues should be evaluated in clinical trials for the treatment of COVID-19.

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TMPRSS2 and RNA-Dependent RNA Polymerase Are Effective Targets of Therapeutic Intervention for Treatment of COVID-19 Caused by SARS-CoV-2 Variants (B.1.1.7 and B.1.351)

Microbiology Spectrum ◽

10.1128/spectrum.00472-21 ◽

2021 ◽

Author(s):

Jihye Lee ◽

JinAh Lee ◽

Hyeon Ju Kim ◽

Meehyun Ko ◽

Youngmee Jee ◽

...

Keyword(s):

Public Health ◽

Monoclonal Antibodies ◽

Severe Acute Respiratory Syndrome ◽

Rna Polymerase ◽

Causative Agent ◽

Therapeutic Intervention ◽

Human Society ◽

Rna Dependent Rna Polymerase ◽

Global Problems

The coronavirus disease 2019 (COVID-19) pandemic is causing unprecedented global problems in both public health and human society. While some vaccines and monoclonal antibodies were successfully developed very quickly and are currently being used, numerous variants of the causative agent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging and threatening the efficacy of vaccines and monoclonal antibodies.

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