Structural biology of SARS-CoV-2 leader protein (nsp1)

References

• Vankadari N, Jeyasankar NN, Lopes WJ. Structure of the SARS-CoV-2 Nsp1/5′-untranslated region complex and implications for potential therapeutic targets, a vaccine, and virulence. J Phys Chem Lett. 2020;11:9659–9668. doi:10.1021/acs.jpclett.0c02818
   PubMed Web of Science ®Google Scholar
• Anwar MU, Adnan F, Abro A, et al. Combined deep learning and molecular docking simulations approach identifies potentially effective FDA approved drugs for repurposing against SARS-CoV-2. Comput Biol Med. 2020 [cited 2022 Apr 13];141:105049. doi:10.1016/j.compbiomed.2021.105049. Available from: https://chemrxiv.org/engage/chemrxiv/article-details/60c74a96f96a007f8228747a.
   Web of Science ®Google Scholar
• Schubert K, Karousis ED, Jomaa A, et al. SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Nat Struct Mol Biol. 2020;27:959–966. doi:10.1038/s41594-020-0511-8
   PubMed Web of Science ®Google Scholar
• de Lima Menezes G, da Silva RA. Identification of potential drugs against SARS-CoV-2 non-structural protein 1 (nsp1). J Biomol Struct Dyn. 2021;39:5657–5667. doi:10.1080/07391102.2020.1792992
   PubMed Web of Science ®Google Scholar
• Yoshimoto FK. The proteins of severe acute respiratory syndrome coronavirus-2 (SARS CoV-2 or n-COV19), the cause of COVID-19. Protein J. 2020;39:198–216. doi:10.1007/s10930-020-09901-4
   PubMed Web of Science ®Google Scholar
• Thoms M, Buschauer R, Ameismeier M, et al. Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science. 2020;369:1249–1255. doi:10.1126/science.abc8665
   PubMed Web of Science ®Google Scholar
• Yuan S, Peng L, Park JJ, et al. Nonstructural protein 1 of SARS-CoV-2 is a potent pathogenicity factor redirecting host protein synthesis machinery toward viral RNA. Mol Cell. 2020;80:1055–1066.e6. doi:10.1016/j.molcel.2020.10.034
   PubMed Web of Science ®Google Scholar
• Tirumalai MR, Rivas M, Tran Q, et al. The peptidyl transferase center: a window to the past. Microbiol Mol Biol Rev. 2021; 85:e00104-21.
   PubMed Web of Science ®Google Scholar
• Khatter H, Myasnikov AG, Natchiar SK, et al. Structure of the human 80S ribosome. Nature. 2015;520:640–645. doi:10.1038/nature14427
   PubMed Web of Science ®Google Scholar
• Altschul SF, Madden TL, Schäffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. doi:10.1093/nar/25.17.3389
   PubMed Web of Science ®Google Scholar
• Connor RF, Roper RL. Unique SARS-CoV protein nsp1: bioinformatics, biochemistry and potential effects on virulence. Trends Microbiol. 2007;15:51–53. doi:10.1016/j.tim.2006.12.005
   PubMed Web of Science ®Google Scholar
• Min Y-Q, Mo Q, Wang J, et al. SARS-CoV-2 nsp1: bioinformatics, potential structural and functional features, and implications for drug/vaccine designs. Front Microbiol. 2020;11:587317. doi:10.3389/fmicb.2020.587317
   PubMed Web of Science ®Google Scholar
• Almeida MS, Johnson MA, Herrmann T, et al. Novel β-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus. J Virol. 2007;81:3151–3161. doi:10.1128/JVI.01939-06
   PubMed Web of Science ®Google Scholar
• Jansson AM. Structure of alphacoronavirus transmissible gastroenteritis virus nsp1 has implications for coronavirus nsp1 function and evolution. J Virol. 2013;87:2949–2955. doi:10.1128/JVI.03163-12
   PubMed Web of Science ®Google Scholar
• Shen Z, Ye G, Deng F, et al. Structural basis for the inhibition of host gene expression by porcine epidemic diarrhea virus nsp1. J Virol. 2018;92:e01896-17.
   PubMed Web of Science ®Google Scholar
• Clark LK, Green TJ, Petit CM. Structure of nonstructural protein 1 from SARS-CoV-2. J Virol. 2021;95:e02019-20.
   PubMed Web of Science ®Google Scholar
• Ma S, Damfo S, Lou J, et al. Two ligand-binding sites on SARS-CoV-2 non-structural protein 1 revealed by fragment-based X-ray screening. Int J Mol Sci. 2022;23:12448. doi:10.3390/ijms232012448
   PubMed Web of Science ®Google Scholar
• Wang Y, Kirkpatrick J, zur Lage S, et al. 1H, 13c, and 15N backbone chemical-shift assignments of SARS-CoV-2 non-structural protein 1 (leader protein). Biomol NMR Assign. 2021;15:287–295. doi:10.1007/s12104-021-10019-6
   PubMed Web of Science ®Google Scholar
• Croll T, Diederichs K, Fischer F, et al. Making the invisible enemy visible [Internet]. bioRxiv; 2020 [cited 2022 Jun 2]. Available from: https://www.biorxiv.org/content/10.11012020.10.07.307546v2.
   Google Scholar
• Agback T, Dominguez F, Frolov I, et al. 1 H, 13 C and 15 N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution. PLoS One. 2021;16(12):e0251834. doi:10.1371/journal.pone.0251834
   PubMed Web of Science ®Google Scholar
• Wang Y, Kirkpatrick J, zur Lage S, et al. Structural insights into the activity regulation of full-length non-structural protein 1 from SARS-CoV-2. Structure. 2023;31:128–137.e5. doi:10.1016/j.str.2022.12.006
   PubMed Web of Science ®Google Scholar
• Prabhu D, Rajamanikandan S, Sureshan M, et al. Modelling studies reveal the importance of the C-terminal inter motif loop of NSP1 as a promising target site for drug discovery and screening of potential phytochemicals to combat SARS-CoV-2. J Mol Graphics Modell. 2021;106:107920. doi:10.1016/j.jmgm.2021.107920
   Google Scholar
• Shi M, Wang L, Fontana P, et al. SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism [Internet]. Cell Biol. 2020 [cited 2022 Apr 13]. Available from: http://biorxiv.org/lookup/doi/10.11012020.09.18.302901.
   Google Scholar
• Huang C, Lokugamage KG, Rozovics JM, et al. SARS coronavirus nsp1 protein induces template-dependent endonucleolytic cleavage of mRNAs: viral mRNAs are resistant to nsp1-induced RNA cleavage. PLoS Pathog. 2011;7:e1002433. doi:10.1371/journal.ppat.1002433
   PubMed Web of Science ®Google Scholar
• Zhang K, Miorin L, Makio T, et al. Nsp1 protein of SARS-CoV-2 disrupts the mRNA export machinery to inhibit host gene expression. Sci Adv. 2021;7:eabe7386. doi:10.1126/sciadv.abe7386
   PubMed Web of Science ®Google Scholar
• Narayanan K, Huang C, Lokugamage K, et al. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells. J Virol. 2008;82:4471–4479. doi:10.1128/JVI.02472-07
   PubMed Web of Science ®Google Scholar
• York A, Fodor E. Biogenesis, assembly, and export of viral messenger ribonucleoproteins in the influenza A virus infected cell. RNA Biol. 2013;10:1274–1282. doi:10.4161/rna.25356
   PubMed Web of Science ®Google Scholar
• Xia H, Cao Z, Xie X, et al. Evasion of type I interferon by SARS-CoV-2. Cell Rep. 2020;33:108234. doi:10.1016/j.celrep.2020.108234
   PubMed Web of Science ®Google Scholar
• Lei X, Dong X, Ma R, et al. Activation and evasion of type I interferon responses by SARS-CoV-2. Nat Commun. 2020;11:3810. doi:10.1038/s41467-020-17665-9
   PubMed Web of Science ®Google Scholar
• Liao Y, Li X, Mou T, et al. Distinct infection process of SARS-CoV-2 in human bronchial epithelial cell lines. J Med Virol. 2020;92:2830–2838. doi:10.1002/jmv.26200
   PubMed Web of Science ®Google Scholar
• Alcorn JF. IL-22 plays a critical role in maintaining epithelial integrity during pulmonary infection. Front Immunol. 2020;11:1160. doi:10.3389/fimmu.2020.01160
   PubMed Web of Science ®Google Scholar
• Costela-Ruiz VJ, Illescas-Montes R, Puerta-Puerta JM, et al. SARS-CoV-2 infection: the role of cytokines in COVID-19 disease. Cytokine Growth Factor Rev. 2020;54:62–75. doi:10.1016/j.cytogfr.2020.06.001
   PubMed Web of Science ®Google Scholar
• Fara A, Mitrev Z, Rosalia RA, et al. Cytokine storm and COVID-19: a chronicle of pro-inflammatory cytokines. Open Biol. 2020;10:200160. doi:10.1098/rsob.200160
   PubMed Web of Science ®Google Scholar
• Gordon DE, Hiatt J, Bouhaddou M, et al. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020;370:eabe9403. doi:10.1126/science.abe9403
   PubMed Web of Science ®Google Scholar
• Chen Z, Wang C, Feng X, et al. Interactomes of SARS-CoV-2 and human coronaviruses reveal host factors potentially affecting pathogenesis. EMBO J. 2021;40:e107776. doi:10.15252/embj.2021107776
   PubMed Web of Science ®Google Scholar
• Kilkenny ML, Veale CE, Guppy A, et al. Structural basis for the interaction of SARS-CoV-2 virulence factor nsp1 with DNA polymerase α–primase. Protein Sci. 2022;31:333–344. doi:10.1002/pro.4220
   PubMed Web of Science ®Google Scholar
• Borsatto A, Akkad O, Galdadas I, et al. Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other β-coronaviruses by simulations and crystallography. eLife. 2022;11:e81167. doi:10.7554/eLife.81167
   PubMed Web of Science ®Google Scholar
• Züst R, Cervantes-Barragán L, Kuri T, et al. Coronavirus non-structural protein 1 is a major pathogenicity factor: implications for the rational design of coronavirus vaccines. PLoS Pathog. 2007;3:e109. doi:10.1371/journal.ppat.0030109
   PubMed Web of Science ®Google Scholar
• Hojyo S, Uchida M, Tanaka K, et al. How COVID-19 induces cytokine storm with high mortality. Inflamm Regen. 2020;40:37. doi:10.1186/s41232-020-00146-3
   PubMed Web of Science ®Google Scholar
• Zhao K, Ke Z, Hu H, et al. Structural basis and function of the N terminus of SARS-CoV-2 nonstructural protein 1. Microbiol Spectr. 2021;9:e00169-21.
   Web of Science ®Google Scholar
• Semper C, Watanabe N, Savchenko A. Structural characterization of nonstructural protein 1 from SARS-CoV-2. iScience. 2021;24:101903. doi:10.1016/j.isci.2020.101903
   PubMed Web of Science ®Google Scholar
• Ma S, Mykhaylyk V, Bowler MW, et al. High-confidence placement of fragments into electron density using anomalous diffraction – a case study using hits targeting SARS-CoV-2 non-structural protein 1. Int J Mol Sci. 2023;24(13):11197. doi:10.3390/ijms241311197
   PubMed Web of Science ®Google Scholar