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. 2023 Mar 10;28(6):2534.
doi: 10.3390/molecules28062534.

Suramin Disturbs the Association of the N-Terminal Domain of SARS-CoV-2 Nucleocapsid Protein with RNA

Chenyun Guo  1 , Hao Xu  1 , Xiao Li  1 , Jiaxin Yu  1 , Donghai Lin  1
Affiliations

Suramin Disturbs the Association of the N-Terminal Domain of SARS-CoV-2 Nucleocapsid Protein with RNA

Chenyun Guo et al. Molecules. .

Abstract

Suramin was originally used as an antiparasitic drug in clinics. Here, we demonstrate that suramin can bind to the N-terminal domain of SARS-CoV-2 nucleocapsid protein (N-NTD) and disturb its interaction with RNA. The BLI experiments showed that N-NTD interacts suramin with a dissociate constant (Kd = 2.74 μM) stronger than that of N-NTD with ssRNA-16 (Kd = 8.37 μM). Furthermore, both NMR titration experiments and molecular docking analysis suggested that suramin mainly binds to the positively charged cavity between the finger and the palm subdomains of N-NTD, and residues R88, R92, R93, I94, R95, K102 and A156 are crucial for N-NTD capturing suramin. Besides, NMR dynamics experiments showed that suramin-bound N-NTD adopts a more rigid structure, and the loop between β2-β3 exhibits fast motion on the ps-ns timescale, potentially facilitating suramin binding. Our findings not only reveal the molecular basis of suramin disturbing the association of SARS-CoV-2 N-NTD with RNA but also provide valuable structural information for the development of drugs against SARS-CoV-2.

Keywords: N-NTD; NMR; SARS-CoV-2; protein interaction; suramin.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The chemical structure of suramin.
Figure 2
Figure 2
EMSA experiment for suramin disturbing the association between SARS-CoV-2 N-NTD and ssRNA-16. Lane 1: free ssRNA-16; lane 2: mixture of N-NTD with ssRNA-16 at the molar ratio of 1:1; lane 3–9: mixture of N-NTD with ssRNA-16 and suramin at molar ratios of 1:1:1, 1:1:2.5, 1:1:5, 1:1:7.5, 1:1:10, 1:1:15, 1:1:20; lane 10: suramin; lane 11: mixture of suramin with ssRNA-16 at the ratio of 1:1.
Figure 3
Figure 3
BLI experiments for detecting the interaction of SARS-CoV-2 N-NTD with suramin (a) or ssRNA-16 (b).
Figure 4
Figure 4
Binding site comparison of ssRNA-16 and suramin on SARS-CoV-2 N-NTD. (a) 2D 1H-15N HSQC spectra of N-NTD titrated with ssRNA-16. (b) Mapping the residues perturbed during the RNA titration on the 3D structure of N-NTD (PDB ID: 6YI3). (c) 2D 1H-15N HSQC spectra of N-NTD titrated with suramin. (d) Mapping the residues perturbed during the suramin titration on the 3D structure of N-NTD (PDB ID: 6YI3). The broad peaks are indicated in the dashed rectangles in the spectra and the corresponding residues are shown in yellow in the structure, while the shifted peaks are indicated as arrows and the corresponding residues are shown in green.
Figure 5
Figure 5
Structural model of the SARS-CoV-2 N-NTD-suramin complex. (a) The docking model was built using HADDOCK. Suramin is shown in grey. (b) Schematic diagram of intermolecular interactions in the structural model of N-NTD-suramin produced using PLIP 2.2.0 online software.
Figure 6
Figure 6
Affinity comparison of SARS-CoV-2 N-NTD WT and mutants for binding suramin. The dashed line denotes the relative binding affinity of 50%.
Figure 7
Figure 7
NMR-measured backbone relaxation parameters R1, R2 and hNOE values of free N-NTD and suramin-bound N-NTD.
Figure 8
Figure 8
Calculated spectral density parameters of free N-NTD and suramin-bound N-NTD.
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References

    1. 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. doi: 10.1038/s41586-020-2008-3. - DOI - PMC - PubMed
    1. 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. doi: 10.15252/embj.2020106478. - DOI - PMC - PubMed
    1. 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. doi: 10.1016/j.antiviral.2013.12.009. - DOI - PMC - PubMed
    1. McBride R., van Zyl M., Fielding B.C. The Coronavirus Nucleocapsid Is a Multifunctional Protein. Viruses. 2014;6:2991–3018. doi: 10.3390/v6082991. - DOI - PMC - PubMed
    1. 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. doi: 10.1007/s00726-006-0361-7. - DOI - PMC - PubMed