The Antiviral Effect of the Chemical Compounds Targeting DED/EDh Motifs of the Viral Proteins on Lymphocytic Choriomeningitis Virus and SARS-CoV-2

Abstract

Arenaviruses and coronaviruses include several human pathogenic viruses, such as Lassa virus, Lymphocytic choriomeningitis virus (LCMV), SARS-CoV, MERS-CoV, and SARS-CoV-2. Although these viruses belong to different virus families, they possess a common motif, the DED/EDh motif, known as an exonuclease (ExoN) motif. In this study, proof-of-concept studies, in which the DED/EDh motif in these viral proteins, NP for arenaviruses, and nsp14 for coronaviruses, could be a drug target, were performed. Docking simulation studies between two structurally different chemical compounds, ATA and PV6R, and the DED/EDh motifs in these viral proteins indicated that these compounds target DED/EDh motifs. The concentration which exhibited modest cell toxicity was used with these compounds to treat LCMV and SARS-CoV-2 infections in two different cell lines, A549 and Vero 76 cells. Both ATA and PV6R inhibited the post-entry step of LCMV and SARS-CoV-2 infection. These studies strongly suggest that DED/EDh motifs in these viral proteins could be a drug target to combat two distinct viral families, arenaviruses and coronaviruses.

A dsRNA-binding mutant reveals only a minor role of exonuclease activity in interferon antagonism by the arenavirus nucleoprotein

“…TCRV NP(E388A)) samples, and generated an initial Z’-factor of 0.24 ( S4 Fig , panel A). Further, using this approach we could show that nucleotide release by TCRV NP in this assay was strongly blocked by the known nuclease inhibitor Aurintricarboxylic acid (ATA) at concentrations of 10uM and above ( S4 Fig , panel B), which is broadly consistent with previous reports for the inhibition of other arenavirus NPs [ 35 , 36 ]. Importantly, in addition to supporting the potential utility of this assay for drug-screening applications, it also confirms that nucleotide release in this assay is a specific result of ExoN activity by TCRV NP.…”

“…This suggests that while the assay could benefit from further optimization, it indeed has potential utility in high-throughput-based approaches, including drug screening. This is supported by our ability to detect dose-dependent inhibition of TCRV ExoN activity by a known inhibitor (ATA, S4 Fig ) in a range of concentrations similar to those used in other studies [ 35 , 36 ].…”

“…These approaches proved to be easily adaptable to studying the arenavirus NP ExoN activity and required only minor modifications of the buffer (to eliminate EDTA and accommodate an apparent preference for Mn 2+ within the arenavirus NP ExoN active site [ 21 ]), and switching to the preferred dsRNA substrate [ 22 , 23 ]. Using this approach, we could clearly see ExoN activity in lysates expressing NPs from both OW and NW arenaviruses ( S3 Fig ) and show that these signals were reduced by treatment with a known nuclease inhibitor (ATA; S4 Fig ) [ 35 , 36 ]. Interestingly, while studies performed in a viral context have clearly suggested that there are differences in the effectiveness with which the ExoN domains of OW and NW arenaviruses are able to degrade dsRNA [ 10 ], we did not see prominent differences when examining cell lysates transfected with different arenavirus NPs (i.e.…”

Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

“…Because the 3D experimental structures of SARS-CoV-2 proteins were largely unknown at the early stage of the epidemic, homology modeling was widely applied to predict 3D structures of SARS-CoV-2 proteins, such as Mpro, ,,− S protein or variants, ,− RdRp, − ,,,,,,− PLpro, E protein, ,,− N protein, and others. ,,,,,− Some host proteins that interact with SARS-CoV-2 were also predicted, such as ACE2, ,, TMPRSS2, − B cell epitopes, and CD147 . Some 3D structures of vaccine proteins − were also built by homology modeling.…”

Analogs of the Catechol Derivative Dynasore Inhibit HIV-1 Ribonuclease H, SARS-CoV-2 nsp14 Exoribonuclease, and Virus Replication

“…Both HIV-1 RNase H and SARS-CoV-2 ExoN domains are dependent on Mg 2+ ions, which coordinate to DEDD motifs of acidic amino acids in the active sites [ 23 , 24 , 25 ]. The DEDD motif of viral proteins is a potential drug target [ 26 ]. Various catechol-based HIV-1 RNase H inhibitors, such as garcinol and a thienopyrimidine compound, were previously identified, which can coordinate Mg 2+ of the active site, thus blocking binding and cleavage of the RNA substrate [ 27 , 28 ].…”