Abstract
Non-structural protein 1 (Nsp1) is a virulence factor found in all beta coronaviruses (b-CoVs). Recent studies have shown that Nsp1 of SARS-CoV-2 virus interacts with the nuclear export receptor complex, which includes nuclear RNA export factor 1 (NXF1) and nuclear transport factor 2-like export factor 1 (NXT1). The NXF1–NXT1 complex plays a crucial role in the transport of host messenger RNA (mRNA). Nsp1 interferes with the proper binding of NXF1 to mRNA export adaptors and its docking to the nuclear pore complex. We propose that drugs targeting the binding surface between Nsp1 and NXF1–NXT1 may be a useful strategy to restore host antiviral gene expression. Exploring this strategy forms the main goals of this paper. Crystal structures of Nsp1 and the heterodimer of NXF1–NXT1 have been determined. We modeled the docking of Nsp1 to the NXF1–NXT1 complex, and discovered repurposed drugs that may interfere with this binding. To our knowledge, this is the first attempt at drug-repurposing of this complex. We used structural analysis to screen 1993 FDA-approved drugs for docking to the NXF1–NXT1 complex. The top hit was ganirelix, with a docking score of −14.49. Ganirelix competitively antagonizes the gonadotropin releasing hormone receptor (GNRHR) on pituitary gonadotrophs, and induces rapid, reversible suppression of gonadotropin secretion. The conformations of Nsp1 and GNRHR make it unlikely that they interact with each other. Additional drug leads were inferred from the structural analysis of this complex, which are discussed in the paper. These drugs offer several options for therapeutically blocking Nsp1 binding to NFX1–NXT1, which may normalize nuclear export in COVID-19 infection.
Highlights
Introduction published maps and institutional affilAlmost 2 years into the pandemic, we have lost more than 750,000 lives in the UnitedStates alone to coronavirus disease 2019 (COVID-19)
We took a fresh approach by assessing SARS-CoV-2 Non-structural protein 1 (Nsp1) domain and translational suppression of the nuclear RNA export factor 1 (NXF1, Gene ID: 10482) and nuclear transport factor 2-like export factor 1 (NXT1, Gene ID: 29107) proteins [5,6,7]
NTF2-like domains of NXF1 complexed with NXT1 (PDB-ID 4WYK), and crystal structures of NSP1 from SARS-CoV-2 (PDB-ID: 7K3N) were used in this study
Summary
Protein Data Bank (rcsb.org (accessed on 1 August 2021)): 3D-protein structures used in this manuscript were retrieved from the Protein Data Bank structure of the LRR and NTF2-like domains of NXF1 complexed with NXT1 (PDB-ID 4WYK), and crystal structures of NSP1 from SARS-CoV-2 (PDB-ID: 7K3N) were used in this study. Protein–Protein Docking: Docking of Nsp (PDB-ID: 7K3N) to the structure of the LRR and NTF2-like domains of NXF1 complexed with NXT1 Software: 1993 FDA-approved drugs were obtained from the e-drug database for docking analysis in SDF format [30]. These drugs were docked to the structure of the LRR and NTF2-like domains of NXF1 complexed with NXT1 (PDB-ID: 4WYK) using the Molecular. We have added the functional classifications to Table 1
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