The nucleocapsid protein of zoonotic betacoronaviruses is an attractive target for antiviral drug discovery

Abstract

Betacoronaviruses are in one genera of coronaviruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome-related coronavirus (MERS-CoV), etc. These viruses threaten public health and cause dramatic economic losses. The nucleocapsid (N) protein is a structural protein of betacoronaviruses with multiple functions such as forming viral capsids with viral RNA, interacting with viral membrane protein to form the virus core with RNA, binding to several cellular kinases for signal transductions, etc. In this review, we highlighted the potential of the N protein as a suitable antiviral target from different perspectives, including structure, functions, and antiviral strategies for combatting betacoronaviruses.

Keywords: Antiviral; Betacoronavirus; Coronavirus N; Nucleocapsid protein; Protein-protein interaction.

Graphical abstract

Fig. 1

Structure of the β-CoV N protein. (A) C-I-TASSER structure model. The ribbon representations of the structures of NTD (N-terminal RNA-binding domain, red box) and CTD (C-terminal dimerization domain, yellow box) are generated with PyMOL from coordinates in the protein data bank (PDB IDs: NTD, 6M3M; CTD, 6WJI). The relative orientation of NTD, CTD, and CLK are drawn randomly to reflect the dynamic nature of the N protein. (B) CTD. (C) NTD. (D) CTD dimer. (E) Electrostatic surface of the NTD. Blue denotes positive charge potential. Red denotes negative charge potential. Pocket in the square indicates the RNA binding site of NTD; this pocket is various among β-CoVs. (F) The domain organization of the β-CoV N protein. (G) The crystal packing of the CTD 24-mer. Yellow and orange ribbons represent β-CoV viral RNA strands wrapping around the helical oligomer structure. (H) Schematic of the docking of NTD onto the CTD 24–mer complex. The NTD domains are represented by red ellipsoids. Structures were generated using PyMOL (The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Domain architectures of β-CoVs N protein. NTD: N-terminal RNA-binding domain; CTD: C-terminal dimerization domain. Multiple sequence alignment of SARS-CoV-2 N-NTD (GenBank: NC_045512.2) with SARS-CoV N-NTD (GenBank: NC_004718.3), MERS-CoV N-NTD (GenBank: NC_019843.3), HCoV-OC43 N-NTD (GenBank: NC_006213.1), HCoV-HKU1 (GenBank: NC_006577.2), Tylonycteris bat coronavirus HKU4 (GenBank: MH002339.1). Red arrows indicate conserved residues for ribonucleotide binding sites, dash-bordered boxes indicate variability of residues in the structural comparisons. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 3

Schematic describing the rationale used in designing the allosteric stabilizer of this study. An orthosteric stabilizer is used to bind to the non-native interaction interface of the NTD and stabilize the abnormal interaction between proteins. Then the CTD cannot be packed correctly.