Journal: Journal of Biomolecular Structure & Dynamics

Article Title: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2

doi: 10.1080/07391102.2020.1796804

Figure Lengend Snippet: Binding affinity of the five drugs with different crystal structures of RdRp and Mpro (AutoDock Vina scores are in kcal/mol).

Article Snippet: The molecular docking approach using AutoDock Vina protocol predicted the binding affinity and the interaction of the selected antiviral drugs with RdRp and Mpro.

Techniques: Binding Assay

Journal: Journal of Biomolecular Structure & Dynamics

Article Title: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2

doi: 10.1080/07391102.2020.1796804

Figure Lengend Snippet: Domain organization and interaction of both proteins with drugs. The inter-domain borders are labeled with amino acid residue numbers. (A) 3 D structure of RdRp (Fingers-Blue; Palm-Red; Thumb-Green) interacting with drugs (B) 3 D structure of Mpro (Domain I-Green; Domain II-Red; Domain III-Blue) interacting with drugs. Cobicistat is shown in Orange; Daclatasvir in Green; Raltegravir in Pink; Simeprevir in Violet; Remdesivir in Yellow.

Article Snippet: The molecular docking approach using AutoDock Vina protocol predicted the binding affinity and the interaction of the selected antiviral drugs with RdRp and Mpro.

Techniques: Labeling, Residue

Journal: Journal of Biomolecular Structure & Dynamics

Article Title: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2

doi: 10.1080/07391102.2020.1796804

Figure Lengend Snippet: Binding pose of Raltegravir and Simeprevir over the course of 100 ns simulation. The crystal structures of RdRp and Mpro are shown as white surface with Raltegravir (red) and Simeprevir (yellow) as spheres in (A) and (B) respectively.

Article Snippet: The molecular docking approach using AutoDock Vina protocol predicted the binding affinity and the interaction of the selected antiviral drugs with RdRp and Mpro.

Techniques: Binding Assay

Journal: Journal of Biomolecular Structure & Dynamics

Article Title: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2

doi: 10.1080/07391102.2020.1796804

Figure Lengend Snippet: PCA analysis of RdRp and Mpro. (A) RdRp PCA model: The scores plot presented four data clusters in different colors, where each dot represented one time point. The clustering is attributable to: apo-RdRp (yellow), Raltegravir-RdRp complex (cyan), Remdesivir-RdRp complex (orange), Simeprevir-RdRp complex (green). (B) Mpro PCA model: The scores plot presented four data clusters in different colors, where each dot represented one time point. The clustering is attributable to: apo-Mpro (cyan), Raltegravir-Mpro complex (yellow), Remdesivir-Mpro complex (orange), Simeprevir-Mpro complex (green).

Article Snippet: The molecular docking approach using AutoDock Vina protocol predicted the binding affinity and the interaction of the selected antiviral drugs with RdRp and Mpro.

Techniques:

Journal: Journal of Biomolecular Structure & Dynamics

Article Title: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2

doi: 10.1080/07391102.2020.1796804

Figure Lengend Snippet: Histogram of the binding free energy for (A) Remdesivir-RdRp, (B) Raltegravir-RdRp (C) Simeprevir-RdRp and (D) Remdesivir-Mpro (E) Raltegravir-Mpro (F) Simeprevir-Mpro. Here, the red color curve represents Gaussian fit.

Article Snippet: The molecular docking approach using AutoDock Vina protocol predicted the binding affinity and the interaction of the selected antiviral drugs with RdRp and Mpro.

Techniques: Binding Assay

Journal: Viruses

Article Title: Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

doi: 10.3390/v14030456

Figure Lengend Snippet: Diagrammatic sketch of the genome organization of SsEV11. ( A ) The information of Contig 2 obtained by virome sequencing and specific primers used for viral detection and rapid amplification of cDNA ends (RACE)-. The gray areas on both sides represent the RACE-OLOGO ligated using RACE method.Arrows represent direction and positions of the primers; F, F1 and F2 are primers ERV-F, ERV-F1 and ERV-F2; R, R1 and R2 are primers ERV-R, ERV-R1 and ERV-R2; Ra2 and Ra3 are primers Race2 and Race3. ( B ) The genome organization of SsEV11, showing 5′ and 3′ untranslated regions (UTR) and open reading flame (ORF) region. ( C ) The polyprotein encoded by the ORF of SsEV11 and its conserved function domains MTR, CRR, DEADc, Hel and RdRp. the Arabic numerals show the amino acid position of each conserved domain.

Article Snippet: Identity matrix diagram of aa sequence of RdRp domain was carried out online using Clustal Omega program ( https://www.ebi.ac.uk/Tools/msa/clustalo/ , accessed on 20 May 2021) and RStudio.

Techniques: Sequencing, Rapid Amplification of cDNA Ends

Journal: Viruses

Article Title: Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

doi: 10.3390/v14030456

Figure Lengend Snippet: Alignment of RdRp domain of selected endornaviruses and endorna-like viruses. Conserved motifs are marked by Roman numerals from I to VIII. “Alpha” and “beta” represent alphaendornavirus and betaendornavirus, respectively; “Gamma” represents proposed gammaendornaviruses or endorna-like viruses. Novel endornavirus is highlighted with red characters.

Article Snippet: Identity matrix diagram of aa sequence of RdRp domain was carried out online using Clustal Omega program ( https://www.ebi.ac.uk/Tools/msa/clustalo/ , accessed on 20 May 2021) and RStudio.

Techniques:

Journal: Viruses

Article Title: Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

doi: 10.3390/v14030456

Figure Lengend Snippet: BLASTp analysis of polyprotein, RdRp, Hel, and Mtr domains between Sclerotinia sclerotiorum endornavirus 11 and selected endornaviruses.

Article Snippet: Identity matrix diagram of aa sequence of RdRp domain was carried out online using Clustal Omega program ( https://www.ebi.ac.uk/Tools/msa/clustalo/ , accessed on 20 May 2021) and RStudio.

Techniques: Sequencing, Virus

Journal: Viruses

Article Title: Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

doi: 10.3390/v14030456

Figure Lengend Snippet: Phylogenetic analysis of SsEV11 and other selected endornaviruses and endorna-like viruses based on the RdRP domain using Maximum Likelihood program with 1000 bootstrap replicates. GenBank accession numbers and virus names are listed in . Viruses written in blue are those infecting or associated with insects, written in red is newly identified virus.

Article Snippet: Identity matrix diagram of aa sequence of RdRp domain was carried out online using Clustal Omega program ( https://www.ebi.ac.uk/Tools/msa/clustalo/ , accessed on 20 May 2021) and RStudio.

Techniques: Virus

Journal: Viruses

Article Title: Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

doi: 10.3390/v14030456

Figure Lengend Snippet: Matrix diagram of amino acid identities of RdRp domain among selected endornaviruses and endornalike viruses by using Clustal Omega 2.1. Alpha, Beta, and Gamma represent alphaendornaviruses, betaendornaviruses, and proposed gammaendornavirus, respectively; the cutoff values were 25%. The information of selected viruses and their RdRp domains are listed in . Viruses written in blue are viruses that infect insects. Newly identified endornavirus is written in red. Alignment analysis was carried out on website https://www.ebi.ac.uk/Tools/msa/clustalo/ , accessed on 20 May 2021.

Article Snippet: Identity matrix diagram of aa sequence of RdRp domain was carried out online using Clustal Omega program ( https://www.ebi.ac.uk/Tools/msa/clustalo/ , accessed on 20 May 2021) and RStudio.

Techniques:

Journal: Viruses

Article Title: Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

doi: 10.3390/v14030456

Figure Lengend Snippet: BLAST analysis of the RdRp domain of SsEV11 and selected endorna-like viruses.

Article Snippet: Identity matrix diagram of aa sequence of RdRp domain was carried out online using Clustal Omega program ( https://www.ebi.ac.uk/Tools/msa/clustalo/ , accessed on 20 May 2021) and RStudio.

Techniques: Virus

Journal: EMBO Molecular Medicine

Article Title: A siRNA targets and inhibits a broad range of SARS‐CoV‐2 infections including Delta variant

doi: 10.15252/emmm.202115298

Figure Lengend Snippet: Flowchart for the selection strategy. The selection criteria and sequence numbers remaining at the end of each stage were individually indicated. Vero E6 cells were transfected with 10 nM of siRNA before infection by SARS‐CoV‐2 at a multiplicity of infection (MOI) of 0.1 after 24 h. The numbers of viral RNA copies were quantitated with RT‐qPCR. The negative control siRNA served as the control and is abbreviated as “Ctrl.” C1–C11 represent the final candidate sequences after selection. The siRNAs capable of inhibiting up to 99% of viral envelope gene expression with P ‐values < 0.005 compared with Ctrl siRNA are marked with *. P ‐value by Student’s t ‐test. Vero E6 cells were transfected with 10 nM of siRNA before infection by SARS‐CoV‐2 at a MOI of 0.1 after 24 h. The number of infectious virions were quantitated with plaque‐forming assay. The siRNAs capable of inhibiting up to 99% of plaque‐forming virions production with P ‐values < 0.0001 compared with Ctrl siRNA are marked with *. P ‐value by Student’s t ‐test. IC 50 and sequences of modified siRNA C6G25S, C8G25S, and C10G31A. Vero E6 cells were transfected with 10, 2, 0.4, 0.08, or 0.016 nM of each modified siRNA and challenged with virus at MOI of 0.1. Plaque‐forming virions were detected 24 h after infection. The sequences and chemical modifications of sense (S) and antisense (AS) strand of each siRNA are presented with 2′‐F and 2′‐OMe modifications as green and black squares, respectively. No modified RNA residues and phosphorothioate interlinkages are depicted as white squares and red dots, respectively. IC 50 of C6 and the fully modified C6G25S. Vero E6 cells were transfected with 10, 2, 0.4, 0.08, or 0.016 nM of C6 or C6G25S before virus infection at an MOI of 0.1. The viral RNA was quantitated by RT‐qPCR at 24 h after infection. IC 50 data for viral RdRp inhibition by C6G25S. Vero E6 cells were transfected with 10, 2, 0.4, 0.08, or 0.016 nM of C6G25S before virus infection at an MOI of 0.1. The viral RNA was quantitated by RT‐qPCR at 24 h after infection. Data information: Data were analyzed with GraphPad Prism 5 software and presented as mean ± SD of three biological replicates in (B–F).

Article Snippet: The lower part of Fig shows the sequence alignment of C6 and RdRp , which is located in the 5‐prime region of ORF1b .

Techniques: Selection, Sequencing, Transfection, Infection, Quantitative RT-PCR, Negative Control, Control, Gene Expression, Modification, Virus, Inhibition, Software

Journal: EMBO Molecular Medicine

Article Title: A siRNA targets and inhibits a broad range of SARS‐CoV‐2 infections including Delta variant

doi: 10.15252/emmm.202115298

Figure Lengend Snippet: siRNA candidates against SARS‐CoV‐2.

Article Snippet: The lower part of Fig shows the sequence alignment of C6 and RdRp , which is located in the 5‐prime region of ORF1b .

Techniques: Sequencing

Journal: EMBO Molecular Medicine

Article Title: A siRNA targets and inhibits a broad range of SARS‐CoV‐2 infections including Delta variant

doi: 10.15252/emmm.202115298

Figure Lengend Snippet: C6 targets a highly conserved region of the virus RdRp (accession number: NC_045512.2). The figure shows a genome map for five variants of concern (VOC), two variants of interests (VOI), and five other variants. Dots above the genome indicate the locations of typical mutations for each variant. Important amino acid mutations listed in the Spike mutations of interest on the European Centre for Disease Prevention and Control (ECDC) website are labeled in red. Other mutations are labeled in black. The target site and sequence for C6G25 recognition on RdRp is shown below the map. C6G25 sequence is shown in red and the viral sequence in black. IC 50 for C6G25S against different variants. Vero E6 cells were transfected with 10, 2, 0.4, 0.08, or 0.016 nM of C6G25S before infection with different strains of SARS‐CoV‐2. The viral RNA was quantitated by RT‐qPCR at 24 h after infection. Data are presented as mean ± SD of three biological replicates. Source data are available online for this figure.

Article Snippet: The lower part of Fig shows the sequence alignment of C6 and RdRp , which is located in the 5‐prime region of ORF1b .

Techniques: Virus, Variant Assay, Control, Labeling, Sequencing, Transfection, Infection, Quantitative RT-PCR

Journal: Journal of Clinical Virology

Article Title: Comparison of commercial realtime reverse transcription PCR assays for the detection of SARS-CoV-2

doi: 10.1016/j.jcv.2020.104510

Figure Lengend Snippet: Details of the compared PCR kits.

Article Snippet: Hecin Scientific , RdRp , 25 , ND.

Techniques: Multiplex Assay, Diagnostic Assay, Reverse Transcription Polymerase Chain Reaction

Journal: Journal of Clinical Virology

Article Title: Comparison of commercial realtime reverse transcription PCR assays for the detection of SARS-CoV-2

doi: 10.1016/j.jcv.2020.104510

Figure Lengend Snippet: Sensitivity and specificity of the PCR kits.

Article Snippet: Hecin Scientific , RdRp , 25 , ND.

Techniques:

Journal: Expert Review of Molecular Diagnostics

Article Title: Spectroscopy as a tool for detection and monitoring of Coronavirus (COVID-19)

doi: 10.1080/14737159.2020.1766968

Figure Lengend Snippet: Detection methods used for COVID-19 (Sheridan et al. [ 4 ]).

Article Snippet: 14 , SARS-CoV-2 E, RdRP or N gene CE-IVD 7 virus Respiratory Panel multiplex RT-PCR , TIB Molbiol (Berlin, Germany) also via Roche Diagnostics.

Techniques: Acid Assay, Control, Reverse Transcription, Diagnostic Assay, Real-time Polymerase Chain Reaction, Virus, Multiplex Assay

Journal: International Journal of Molecular Sciences

Article Title: An Update on SARS-CoV-2 Clinical Trial Results—What We Can Learn for the Next Pandemic

doi: 10.3390/ijms25010354

Figure Lengend Snippet: The coronavirus life cycle and the mechanistic actions of antiviral drugs within the viral replication process, using SARS-CoV-2 as an example. The virus-cell membrane fusion was induced by the binding of spike protein to the host cellular receptor angiotensin-converting enzyme 2 (ACE2), together with the cell surface transmembrane serine protease 2 (TMPRSS2). Following viral entry, the release of the viral genome is followed by the immediate translation of viral proteins and the formation of the viral replication and transcription complex. The 3-chymotrypsin-like protease (CL pro )/main protease (M pro ) and papain-like protease (PL pro ) cleave the virus polypeptide into 16 non-structural proteins. Structural glycoproteins are synthesised in the endoplasmic reticulum (ER) membrane for transit through the endoplasmic reticulum-to-Golgi intermediate compartment (ERGIC). Newly synthesised genomic RNA is encapsulated and buds into the ERGIC to form a virion. New virions leave the cell via lysosomes and are then able to infect new susceptible cells. SARS-CoV-2 infection activates the acid sphingomyelinase/ceramide system, resulting in the formation of ceramide-enriched membrane domains that serve viral entry and infection by clustering ACE2. The directly acting antivirals (DAA) mechanisms include the monoclonal antibodies that target the spike protein of the virus, M pro inhibitor, nucleoside analogues, and RNA-dependent RNA polymerase (RdRp) inhibitor. The host-targeting antivirals (HTA) include the inhibitors of viral entry, functional inhibitors of acid sphingomyelinase activity (FIASMA), and inhibitors of viral glycoprotein processing. The immunomodulatory drugs modify the negative effects of an overreacting immune system, such as the interleukins and JAK ½ inhibitors. Adapted from “Coronavirus Replication Cycle”, by BioRender.com (2023). Retrieved from https://app.biorender.com/biorender-templates , accessed on 20 April 2023.

Article Snippet: Favipiravir is a guanine analogue that selectively inhibits the RdRp and has been developed as a novel antiviral compound against influenza by Toyama Chemical Co. Favipiravir has been evaluated against SARS-CoV-2 infection in multiple clinical trials , with no significant effects on hospitalisation and mortality even when administered within 5 days of symptoms developing [ ].

Techniques: Virus, Membrane, Binding Assay, Infection, Analogues, Functional Assay, Activity Assay

Journal: International Journal of Molecular Sciences

Article Title: An Update on SARS-CoV-2 Clinical Trial Results—What We Can Learn for the Next Pandemic

doi: 10.3390/ijms25010354

Figure Lengend Snippet: Biologicals and small molecule antiviral drugs granted full approval or emergency use authorisation (EUA) for the treatment of COVID-19 from the Food and Drug Administration (FDA) *.

Article Snippet: Favipiravir is a guanine analogue that selectively inhibits the RdRp and has been developed as a novel antiviral compound against influenza by Toyama Chemical Co. Favipiravir has been evaluated against SARS-CoV-2 infection in multiple clinical trials , with no significant effects on hospitalisation and mortality even when administered within 5 days of symptoms developing [ ].

Techniques: Recombinant

Journal: International Journal of Molecular Sciences

Article Title: An Update on SARS-CoV-2 Clinical Trial Results—What We Can Learn for the Next Pandemic

doi: 10.3390/ijms25010354

Figure Lengend Snippet: Small molecule directly acting antivirals (DAA) tested in clinical trials for COVID-19.

Article Snippet: Favipiravir is a guanine analogue that selectively inhibits the RdRp and has been developed as a novel antiviral compound against influenza by Toyama Chemical Co. Favipiravir has been evaluated against SARS-CoV-2 infection in multiple clinical trials , with no significant effects on hospitalisation and mortality even when administered within 5 days of symptoms developing [ ].

Techniques: Protease Inhibitor, Infection, Virus, Variant Assay, Activity Assay