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Structures of nsp1 (A) Initial structure before starting the simulation. (B) Structure of the complex at 50 ns in the 0th replica (i.e., the simulation with the unscaled potential). (C) Structures from superimposition of 20 representative snapshots of the nsp1-SL1 complex. Snapshots were obtained from a weighted random sampling. Different snapshots from SL1 are colored differently. (D) Nsp1 segmentation used in the analysis: (i) residues 1 to 18, green; (ii) residues 31 to 50, cyan; (iii) residues 74 to 90, magenta; (iv) residues 121 to 146, orange; (v) residues 147 to 180, blue.
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Nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a 180-residue protein that blocks translation of host mRNAs in SARS-CoV-2-infected cells. Although it is known that SARS-CoV-2’s own RNA evades nsp1’s host translation shutoff, the molecular mechanism underlying the evasion was poorly understood. We pe...
Citations
... Several models have been proposed to explain the escape of viral mRNA from degradation. The most reliable one suggests that viral mRNAs containing the SL1 interact with Nsp1 and, in association with cellular factor(s), induce a conformational change in Nsp1 that unplugs its C-terminal domain from the 40S entry channel, thereby allowing mRNA translation [36,[47][48][49]. Specific mutations within NTD of Nsp1 (R 99 A and R 124 A/K 125 A) have negative effects on the translation of SARS-CoV-2 leader mRNA, instead. ...
Non-structural protein 1 (Nsp1) represents one of the most crucial SARS-CoV-2 virulence factors by inhibiting the translation of host mRNAs and promoting their degradation. We selected naturally occurring virus lineages with specific Nsp1 deletions located at both the N- and C-terminus of the protein. Our data provide new insights into how Nsp1 coordinates these functions on host and viral mRNA recognition. Residues 82–85 in the N-terminal part of Nsp1 likely play a role in docking the 40S mRNA entry channel, preserving the inhibition of host gene expression without affecting cellular mRNA decay. Furthermore, this domain prevents viral mRNAs containing the 5′-leader sequence to escape translational repression. These findings support the presence of distinct domains within the Nsp1 protein that differentially modulate mRNA recognition, translation and turnover. These insights have implications for the development of drugs targeting viral proteins and provides new evidences of how specific mutations in SARS-CoV-2 Nsp1 could attenuate the virus.
... In all cases, the binding pocket of amentoflavone includes residues of the flexible C-terminal region of the protein. For the cluster 1 (Fig. 6A), important interactions include the H-bonds with Arg124 and Gln158, π interactions with Asp75 and Gly168 (Fig. 4A1); it has been demonstrated that Arg124 strongly interacts with the phosphate backbone of SARS-CoV-2 RNA 5′-untranslated region and also Asp75 sometimes formed hydrogen bonds with the bases of it [40], furthermore protein uS5 of the 40S ribosome subunit interacts within a hydrophobic surface which involves this residue and other adjacent ones, including Gln158 and Gly168 [41]. In the case of cluster 2 (Fig. 6B), we can appreciate in Fig. 4A2 that more H-bonds were formed compared to the previous cluster, standing out the interactions with Phe157 and Gly168 which are included in the hydrophobic surface above mentioned [41]. ...
Despite the development of vaccines against COVID-19 disease and the multiple efforts to find efficient drugs as treatment for this virus, there are too many social, political, economic, and health inconveniences to incorporate a fully accessible plan of prevention and therapy against SARS-CoV-2. In this sense, it is necessary to find nutraceutical/pharmaceutical drugs as possible COVID-19 preventives/treatments. Based on their beneficial effects, flavonoids are one of the most promising compounds. Therefore, using virtual screening, 478 flavonoids obtained from the KEGG database were evaluated against non-structural proteins Nsp1, Nsp3, Nsp5, Nsp12, and Nsp15, which are essential for the virus-host cell infection, searching for possible multitarget flavonoids. Amentoflavone, a biflavonoid found mainly in Ginkgo biloba, Lobelia chinensis, and Byrsonima intermedia, can interact and bind with the five proteins, suggesting its potential as a multitarget inhibitor. Molecular docking calculations and structural analysis (RMSD, number of H bonds, and clustering) performed from molecular dynamics simulations of the amentoflavone-protein complex support this potential. The results shown here are theoretical evidence of the probable multitarget inhibition of non-structural proteins of SARS-CoV-2 by amentoflavone, which has wide availability, low cost, no side effects, and long history of use. These results are solid evidence for future in vitro and in vivo experiments aiming to validate amentoflavone as an inhibitor of the Nsp1, 3, 5, 12, and 15 of SARS-CoV-2.Graphical Abstract
... For instance, SARS-CoV-2 5 -UTR structures obtained from modeling were used for virtual docking simulations of amiloride-based small molecules [59]. The RNAComposer model of the 5 -UTR stem loop SL1 was used to investigate its binding to the nonstructural protein 1 of SARS-CoV-2 (nsp1) using MD simulation [60]. Furthermore, the homology model for the SARS-CoV-2 stem loop II motif (S2M) was explored as a potential drug target by docking a library of FDA-approved drugs [61]. ...
RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5′- and 3′-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.
Citation: Gumna, J.; Antczak, M.; Adamiak, R.W.; Bujnicki, J.M.; Chen, S.-J.; Ding, F.; Ghosh, P.; Li, J.; Mukherjee, S.; Nithin, C.; et al. Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models. Int. J. Mol. Sci. 2022, 23, 9630. https://doi.org/10.3390/ijms23179630
... The C-terminal residues 131-180 of the nonstructural protein 1 (nsp1) are intrinsically disordered in an aqueous environment and are prone to self-aggregation [218]. The potential binding of nsp1 to mRNA may be responsible for mediating mechanisms behind the successful evasion of host translation shutoff by nsp1 [236,237]. Conformational changes of nsp1 due to electrostatic interactions in the IDRs of nsp1 allow highly flexible and indiscriminate access to binding partners such as host mRNA export receptor heterodimer NXF1-NXT1 and the ribosomal 40S subunit [164,218,227]. Widely known as a pathogenic virulence factor, nsp1 effectively shuts down host mRNA translation to prevent expression of IFNs and ISGs by binding with the 40S and 80S ribosomes to form ribosomal complexes in vitro and in vivo [138,164,238]. ...
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of “viral factories” by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
Nonstructural protein 1 (nsp1) of the severe acute respiratory syndrome coronavirus (SCOV1 and SCOV2) acts as a host shutoff protein by blocking the translation of host mRNAs and triggering their decay. Surprisingly, viral RNA, which resembles host mRNAs containing a 5′-cap and a 3′-poly(A) tail, escapes significant translation inhibition and RNA decay, aiding viral propagation. Current literature proposes that, in SCOV2, nsp1 binds the viral RNA leader sequence, and the interaction may serve to distinguish viral RNA from host mRNA. However, a direct binding between SCOV1 nsp1 and the corresponding RNA leader sequence has not been established yet. Here, we show that SCOV1 nsp1 binds to the SCOV1 RNA leader sequence but forms multiple complexes at a high concentration of nsp1. These complexes are marginally different from complexes formed with SCOV2 nsp1. Finally, mutations of the RNA stem-loop did not completely abolish RNA binding by nsp1, suggesting that an RNA secondary structure is more important for binding than the sequence itself. Understanding the nature of binding of nsp1 to viral RNA will allow us to understand how this viral protein selectively suppresses host gene expression.
Nonstructural protein 1 (nsp1) is a coronavirus (CoV) virulence factor that restricts cellular gene expression by inhibiting translation through blocking the mRNA entry channel of the 40S ribosomal subunit and by promoting mRNA degradation. We perform a detailed structure-guided mutational analysis of SARS-CoV-2 nsp1, revealing insight into how it coordinates these activities against host but not viral mRNA. We find that residues in the N-terminal and central regions of nsp1 not involved in docking into the 40S mRNA entry channel nonetheless stabilize its association with the ribosome and mRNA, both enhancing its restriction of host gene expression and enabling mRNA containing the SARS-CoV-2 leader sequence to escape translational repression. These data support a model in which viral mRNA binding functionally alters the association of nsp1 with the ribosome, which has implications for drug targeting and understanding how engineered or emerging mutations in SARS-CoV-2 nsp1 could attenuate the virus.
The on-going pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to unprecedented medical and socioeconomic crises. Although the viral pathogenesis remains elusive, deficiency of effective antiviral interferon (IFN) responses upon SARS-CoV-2 infection has been recognized as a hallmark of COVID-19 contributing to the disease pathology and progress. Recently, multiple proteins encoded by SARS-CoV-2 have been shown to act as potential IFN antagonists with diverse possible mechanisms. Here, we summarize and discuss the strategies of SARS-CoV-2 for evasion of innate immunity (particularly the antiviral IFN responses), understanding of which will facilitate not only the elucidation of SARS-CoV-2 infection and pathogenesis but also the development of antiviral intervention therapies.
