Theranostics 2021; 11(8):3853-3867. doi:10.7150/thno.55647

Research Paper

MERS-CoV and SARS-CoV-2 replication can be inhibited by targeting the interaction between the viral spike protein and the nucleocapsid protein

Byoung Kwon Park1*, Jinsoo Kim2*, Sangkyu Park3*, Dongbum Kim1, Minyoung Kim2, Kyeongbin Baek2, Joon-Yong Bae4, Man-Seong Park4, Won-Keun Kim1,2, Younghee Lee3✉, Hyung-Joo Kwon1,2✉

1. Institute of Medical Science, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea.
2. Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea.
3. Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea.
4. Department of Microbiology, College of Medicine, and the Institute for Viral Diseases, Korea University, Seoul 02841, Republic of Korea.
*These authors contributed equally to this work.

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Citation:
Park BK, Kim J, Park S, Kim D, Kim M, Baek K, Bae JY, Park MS, Kim WK, Lee Y, Kwon HJ. MERS-CoV and SARS-CoV-2 replication can be inhibited by targeting the interaction between the viral spike protein and the nucleocapsid protein. Theranostics 2021; 11(8):3853-3867. doi:10.7150/thno.55647. Available from https://www.thno.org/v11p3853.htm

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Abstract

Background: The molecular interactions between viral proteins form the basis of virus production and can be used to develop strategies against virus infection. The interactions of the envelope proteins and the viral RNA-binding nucleocapsid (N) protein are essential for the assembly of coronaviruses including the Middle East respiratory syndrome coronavirus (MERS-CoV).

Methods: Using co-immunoprecipitation, immunostaining, and proteomics analysis, we identified a protein interacting with the spike (S) protein in the cells infected with MERS-CoV or SARS-CoV-2. To confirm the interaction, synthetic peptides corresponding to the C-terminal domain of the S protein (Spike CD) were produced and their effect on the interaction was investigated in vitro. In vivo effect of the Spike CD peptides after cell penetration was further investigated using viral plaque formation assay. Phylogeographic analyses were conducted to deduce homology of Spike CDs and N proteins.

Results: We identified a direct interaction between the S protein and the N protein of MERS-CoV that takes place during virus assembly in infected cells. Spike CD peptides of MERS-CoV inhibited the interaction between the S and N proteins in vitro. Furthermore, cell penetration by the synthetic Spike CD peptides inhibited viral plaque formation in MERS-CoV-infected cells. Phylogeographic analyses of Spike CDs and N proteins showed high homology among betacoronavirus lineage C strains. To determine if Spike CD peptides can inhibit the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we used the same strategy and found that the SARS-CoV-2 Spike CD peptide inhibited virus replication in SARS-CoV-2-infected cells.

Conclusions: We suggest that the interaction between the S protein and the N protein can be targeted to design new therapeutics against emerging coronaviruses, including SARS-CoV-2.

Keywords: MERS-CoV, SARS-CoV-2, nucleocapsid protein, spike protein, targeting