Suramin Disturbs the Association of the N-Terminal Domain of SARS-CoV-2 Nucleocapsid Protein with RNA
Abstract
:1. Introduction
2. Results and Discussion
2.1. Suramin Disturbs the Association of SARS-CoV-2 N-NTD with RNA
2.2. Suramin Has a Higher Affinity for Binding SARS-CoV-2 N-NTD Than RNA
2.3. Suramin Shares Similar Binding Areas with RNA on SARS-CoV-2 N-NTD
2.4. Structural Model of the SARS-CoV-2 N-NTD-Suramin Complex
2.5. Suramin Binding Changes the Dynamics Property of SARS-CoV-2 N-NTD
3. Materials and Methods
3.1. Cloning, Expression and Purification
3.2. Gel Mobility Shift Assay
3.3. BLI Assays
3.4. NMR Titration Assays
3.5. Molecular Docking
3.6. NMR Relaxation Measurements
3.7. Reduced Spectral Density Mapping
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Sample Availability
References
- Wu, F.; Zhao, S.; Yu, B.; Chen, Y.M.; Wang, W.; Song, Z.G.; Hu, Y.; Tao, Z.W.; Tian, J.H.; Pei, Y.Y.; et al. A new coronavirus associated with human respiratory disease in China. Nature 2020, 579, 265–269. [Google Scholar] [CrossRef] [Green Version]
- Perdikari, T.M.; Murthy, A.C.; Ryan, V.H.; Watters, S.; Naik, M.T.; Fawzi, N.L. SARS-CoV-2 nucleocapsid protein phase-separates with RNA and with human hnRNPs. EMBO J. 2020, 39, e106478. [Google Scholar] [CrossRef]
- Chang, C.K.; Hou, M.H.; Chang, C.F.; Hsiao, C.D.; Huang, T.H. The SARS coronavirus nucleocapsid protein—Forms and functions. Antivir. Res. 2014, 103, 39–50. [Google Scholar] [CrossRef]
- McBride, R.; van Zyl, M.; Fielding, B.C. The Coronavirus Nucleocapsid Is a Multifunctional Protein. Viruses 2014, 6, 2991–3018. [Google Scholar] [CrossRef] [Green Version]
- Wei, D.Q.; Zhang, R.; Du, Q.S.; Gao, W.N.; Li, Y.; Gao, H.; Wang, S.Q.; Zhang, X.; Li, A.X.; Sirois, S.; et al. Anti-SARS drug screening by molecular docking. Amino. Acids 2006, 31, 73–80. [Google Scholar] [CrossRef]
- Zhang, R.; Wei, D.-Q.; Du, Q.-S.; Chou, K.-C. Molecular modeling studies of peptide drug candidates against SARS. Med. Chem. 2006, 2, 309–314. [Google Scholar] [CrossRef] [PubMed]
- Cong, Y.; Ulasli, M.; Schepers, H.; Mauthe, M.; V’Kovski, P.; Kriegenburg, F.; Thiel, V.; de Haan, C.A.M.; Reggiori, F. Nucleocapsid Protein Recruitment to Replication-Transcription Complexes Plays a Crucial Role in Coronaviral Life Cycle. J. Virol. 2020, 94, e01925-19. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Stohlman, S.A.; Baric, R.S.; Nelson, G.N.; Soe, L.H.; Welter, L.M.; Deans, R.J. Specific interaction between coronavirus leader RNA and nucleocapsid protein. J. Virol. 1988, 62, 4288–4295. [Google Scholar] [CrossRef] [Green Version]
- Nelson, G.W.; Stohlman, S.A.; Tahara, S.M. High affinity interaction between nucleocapsid protein and leader/intergenic sequence of mouse hepatitis virus RNA. J. Gen. Virol. 2000, 81, 181–188. [Google Scholar] [CrossRef] [PubMed]
- Du, L.Y.; Zhao, G.Y.; Lin, Y.P.; Chan, C.; He, Y.X.; Jiang, S.B.; Wu, C.Y.; Jin, D.Y.; Yuen, K.Y.; Zhou, Y.S.; et al. Priming with rAAV encoding RBD of SARS-CoV S protein and boosting with RBD-specific peptides for T cell epitopes elevated humoral and cellular immune responses against SARS-CoV infection. Vaccine 2008, 26, 1644–1651. [Google Scholar] [CrossRef] [PubMed]
- Surjit, M.; Liu, B.P.; Chow, V.T.K.; Lal, S.K. The nucleocapsid protein of severe acute respiratory syndrome-coronavirus inhibits the activity of cyclin-cyclin-dependent kinase complex and blocks S phase progression in mammalian cells. J. Biol. Chem. 2006, 281, 10669–10681. [Google Scholar] [CrossRef] [Green Version]
- Ma, J.; Zhu, F.; Zhao, M.; Shao, F.; Yu, D.; Ma, J.; Zhang, X.; Li, W.; Qian, Y.; Zhang, Y.; et al. SARS-CoV-2 nucleocapsid suppresses host pyroptosis by blocking Gasdermin D cleavage. EMBO J. 2021, 40, e108249. [Google Scholar] [CrossRef]
- Chen, K.L.; Xiao, F.; Hu, D.W.; Ge, W.W.; Tian, M.F.; Wang, W.B.; Pan, P.; Wu, K.L.; Wu, J.G. SARS-CoV-2 Nucleocapsid Protein Interacts with RIG-I and Represses RIG-Mediated IFN-beta Production. Viruses 2021, 13, 47. [Google Scholar] [CrossRef]
- Khan, M.T.; Irfan, M.; Ahsan, H.; Ahmed, A.; Kaushik, A.C.; Khan, A.S.; Chinnasamy, S.; Ali, A.; Wei, D.Q. Structures of SARS-CoV-2 RNA-Binding Proteins and Therapeutic Targets. Intervirology 2021, 64, 55–68. [Google Scholar] [CrossRef] [PubMed]
- Peng, Y.; Du, N.; Lei, Y.Q.; Dorje, S.; Qi, J.X.; Luo, T.R.; Gao, G.F.; Song, H. Structures of the SARS-CoV-2 nucleocapsid and their perspectives for drug design. EMBO J. 2020, 39, e105938. [Google Scholar] [CrossRef] [PubMed]
- Bai, Z.; Cao, Y.; Liu, W.; Li, J. The SARS-CoV-2 Nucleocapsid Protein and Its Role in Viral Structure, Biological Functions, and a Potential Target for Drug or Vaccine Mitigation. Viruses 2021, 13, 1115. [Google Scholar] [CrossRef]
- Tatar, G.; Ozyurt, E.; Turhan, K. Computational drug repurposing study of the RNA binding domain of SARS-CoV-2 nucleocapsid protein with antiviral agents. Biotechnol. Prog. 2021, 37, e3110. [Google Scholar] [CrossRef] [PubMed]
- Redzic, J.S.; Lee, E.; Born, A.; Issaian, A.; Henen, M.A.; Nichols, P.J.; Blue, A.; Hansen, K.C.; D’Alessandro, A.; Vogeli, B.; et al. The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region. J. Mol. Biol. 2021, 433, 167108. [Google Scholar] [CrossRef]
- Dinesh, D.C.; Chalupska, D.; Silhan, J.; Koutna, E.; Nencka, R.; Veverka, V.; Boura, E. Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein. PLoS Pathog. 2020, 16, e1009100. [Google Scholar] [CrossRef]
- Yang, M.; He, S.; Chen, X.; Huang, Z.; Zhou, Z.; Zhou, Z.; Chen, Q.; Chen, S.; Kang, S. Structural Insight Into the SARS-CoV-2 Nucleocapsid Protein C-Terminal Domain Reveals a Novel Recognition Mechanism for Viral Transcriptional Regulatory Sequences. Front. Chem. 2021, 8, 624765. [Google Scholar] [CrossRef]
- Jia, Z.; Liu, C.; Chen, Y.; Jiang, H.; Wang, Z.; Yao, J.; Yang, J.; Zhu, J.; Zhang, B.; Yuchi, Z. Crystal structures of the SARS-CoV-2 nucleocapsid protein C-terminal domain and development of nucleocapsid-targeting nanobodies. FEBS J. 2022, 289, 3813–3825. [Google Scholar] [CrossRef]
- Matsuo, T. Viewing SARS-CoV-2 Nucleocapsid Protein in Terms of Molecular Flexibility. Biology 2021, 10, 454. [Google Scholar] [CrossRef] [PubMed]
- Wu, C.; Qavi, A.J.; Hachim, A.; Kavian, N.; Cole, A.R.; Moyle, A.B.; Wagner, N.D.; Sweeney-Gibbons, J.; Rohrs, H.W.; Gross, M.L.; et al. Characterization of SARS-CoV-2 N protein reveals multiple functional consequences of the C-terminal domain. iScience 2020, 24, 102681. [Google Scholar] [CrossRef] [PubMed]
- Guy, R.K.; DiPaola, R.S.; Romanelli, F.; Dutch, R.E. Rapid repurposing of drugs for COVID-19. Science 2020, 368, 829–830. [Google Scholar] [CrossRef] [PubMed]
- Salgado-Benvindo, C.; Thaler, M.; Tas, A.; Ogando, N.S.; Bredenbeek, P.J.; Ninaber, D.K.; Wang, Y.; Hiemstra, P.S.; Snijder, E.J.; van Hemert, M.J. Suramin Inhibits SARS-CoV-2 Infection in Cell Culture by Interfering with Early Steps of the Replication Cycle. Antimicrob. Agents Chemother. 2020, 64, e00900-20. [Google Scholar] [CrossRef]
- Eberle, R.J.; Olivier, D.S.; Amaral, M.S.; Gering, I.; Willbold, D.; Arni, R.K.; Coronado, M.A. The Repurposed Drugs Suramin and Quinacrine Cooperatively Inhibit SARS-CoV-2 3CL(pro) In Vitro. Viruses 2021, 13, 873. [Google Scholar] [CrossRef]
- Yin, W.; Luan, X.; Li, Z.; Zhou, Z.; Wang, Q.; Gao, M.; Wang, X.; Zhou, F.; Shi, J.; You, E.; et al. Structural basis for inhibition of the SARS-CoV-2 RNA polymerase by suramin. Nat. Struct. Mol. Biol. 2021, 28, 319–325. [Google Scholar] [CrossRef]
- Hawking, F. Suramin: With special reference to onchocerciasis. Adv. Pharmacol. Chemother. 1978, 15, 289–322. [Google Scholar] [CrossRef] [PubMed]
- Morgan, H.P.; McNae, I.W.; Nowicki, M.W.; Zhong, W.; Michels, P.A.M.; Auld, D.S.; Fothergill-Gilmore, L.A.; Walkinshaw, M.D. The Trypanocidal Drug Suramin and Other Trypan Blue Mimetics Are Inhibitors of Pyruvate Kinases and Bind to the Adenosine Site. J. Biol. Chem. 2011, 286, 31232–31240. [Google Scholar] [CrossRef] [Green Version]
- Huang, Q.L.; Yu, L.P.; Petros, A.M.; Gunasekera, A.; Liu, Z.H.; Xu, N.; Hajduk, P.; Mack, J.; Fesik, S.W.; Olejniczak, E.T. Structure of the N-terminal RNA-binding domain of the SARS CoV nucleocapsid protein. Biochemistry 2004, 43, 6059–6063. [Google Scholar] [CrossRef]
- Farrow, N.A.; Zhang, O.W.; Szabo, A.; Torchia, D.A.; Kay, L.E. Spectral Density-Function Mapping Using 15N Relaxation data Exclusively. J. Biomol. NMR 1995, 6, 153–162. [Google Scholar] [CrossRef] [PubMed]
- Spyracopoulos, L. A suite of Mathematica notebooks for the analysis of protein main chain N-15 NMR relaxation data. J. Biomol. NMR 2006, 36, 215–224. [Google Scholar] [CrossRef] [PubMed]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Guo, C.; Xu, H.; Li, X.; Yu, J.; Lin, D. Suramin Disturbs the Association of the N-Terminal Domain of SARS-CoV-2 Nucleocapsid Protein with RNA. Molecules 2023, 28, 2534. https://doi.org/10.3390/molecules28062534
Guo C, Xu H, Li X, Yu J, Lin D. Suramin Disturbs the Association of the N-Terminal Domain of SARS-CoV-2 Nucleocapsid Protein with RNA. Molecules. 2023; 28(6):2534. https://doi.org/10.3390/molecules28062534
Chicago/Turabian StyleGuo, Chenyun, Hao Xu, Xiao Li, Jiaxin Yu, and Donghai Lin. 2023. "Suramin Disturbs the Association of the N-Terminal Domain of SARS-CoV-2 Nucleocapsid Protein with RNA" Molecules 28, no. 6: 2534. https://doi.org/10.3390/molecules28062534