Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein

Abstract

The advent of severe acute respiratory syndrome (SARS) in the 21st century and the recent outbreak of Middle-East respiratory syndrome (MERS) highlight the importance of coronaviruses (CoVs) as human pathogens, emphasizing the need for development of novel antiviral strategies to combat acute respiratory infections caused by CoVs. Recent studies suggest that nucleocapsid (N) proteins from coronaviruses and other viruses can be useful antiviral drug targets against viral infections. This review aims to provide readers with a concise survey of the structural features of coronavirus N proteins and how these features provide insights into structure-based development of therapeutics against coronaviruses. We will also present our latest results on MERS-CoV N protein and its potential as an antiviral drug target.

Figure 1

(a) Domain organization of human coronavirus nucleocapsid protein. MHV: mouse hepatitis virus; IBV: avian infectious bronchitis virus. (b) A schematic mechanism of the oligomeric N protein complexed with RNA showing that the N proteins form a tetramer through the interactions between the C-terminal domains and C-terminal tails of the dimer. (c) Ribbon representation of HCoV-OC43 N-NTD structure (left). Ribbon representation of HCoV-OC43 N-NTD structure with AMP depicted as a stick structure (middle). Electrostatic surface of the HCoV-OC43 N-NTD–AMP complex (right). Blue denotes positive charge potential, red indicates negative charge potential. (d) Detailed stereoview of the interactions at the AMP-binding site. The dotted green lines represent H-bonds. (e) Ribbon representation of the SARS-CoV N-C-terminal-domain (CTD) dimer structure.

Figure 2

(a) Chemical structure of N-(6-oxo-5,6-dihydrophenanthridin-2-yl)(N,N-dimethylamino)acetamide hydrochloride (PJ34). (b) Structural overview of human coronavirus OC43 (HCoV-OC43) N-N-terminal-domain(NTD)–PJ34 complex. A ribbon representation of the HCoV-OC43 N-NTD with PJ34 depicted as a stick model is shown on the left, whereas the electrostatic surface of the HCoV-OC43 N-NTD–PJ34 complex is shown on the right. Blue denotes positive charge potential, red indicates negative charge potential. (c) Detailed view of the interactions between PJ34 and HCoV-OC43 N-NTD, with the H-bonds depicted as green dotted lines. (d) Three general guidelines for the design of compounds that bind to the nucleotide-binding pocket of CoV N-NTD, deduced from the molecular structures of PJ34 and AMP. (e) Chemical structure of 6-chloro-7-(2-morpholin-4-yl-ethylamino) quinoxaline-5, 8-dione (H3) (left) and a detailed view of the interactions between H3 and HCoV-OC43 N-NTD. H-bonds mediated by the side- and main-chain atoms are marked as red and black dotted lines, respectively. Anion-π and stacking interactions are denoted in blue and green dashed lines, respectively. (f) Chemical structure of (−)-catechin gallate and (−)-gallocatechin gallate.

Figure 3

(a) Ribbon representation of Middle-East respiratory syndrome coronavirus (MERS-CoV) N-N-terminal-domain (NTD) structure (left). Electrostatic surface of the MERS-CoV N-NTD structure (right). Blue denotes positive charge potential, red indicates negative charge potential. (b) Structural superimposition of the conserved residues of MERS-CoV N-NTD (green) involved in RNA binding with N-NTDs from severe acute respiratory syndrome coronavirus (SARS-CoV) (magenta) (PDB code: 2ofz) and human coronavirus OC43 (HCoV-OC43) (cyan) (PDB code: 3v3p). (c) Putative drug-binding sites predicted by metaPocket are shown as brown spheres on the MERS-CoV N-NTD structure. (d) Front (left) and back (right) views of the modeled dimer structure of MERS-CoV N-C-terminal-domain (CTD). The two red arrows indicate the position of the two pyramidal hydrophobic cores that stabilize the CTD dimer.