Minireview of progress in the structural study of SARS-CoV-2 proteins

Abstract

A severe form of pneumonia, named coronavirus disease 2019 (COVID-19) by the World Health Organization, broke out in China and rapidly developed into a global pandemic, with millions of cases and hundreds of thousands of deaths reported globally. The novel coronavirus, which was designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of COVID-19. On the basis of experience accumulated following previous SARS-CoV and MERS-CoV outbreaks and research, a series of studies have been conducted rapidly, and major progress has been achieved with regard to the understanding of the phylogeny and genomic organization of SARS-CoV-2 in addition its molecular mechanisms of infection and replication. In the present review, we summarized crucial developments in the elucidation of the structure and function of key SARS-CoV-2 proteins, especially the main protease, RNA-dependent RNA polymerase, spike glycoprotein, and nucleocapsid protein. Results of studies on their associated inhibitors and drugs have also been highlighted.

Keywords: 3CLpro, 3C-like protease; 6-HB, six-helix bundle; ACE2, angiotensin-converting enzyme 2; COVID-19; COVID-19, coronavirus disease 2019; CatB/L, cysteine proteases-cathepsin B and L; Drug-screening; E protein, Envelope protein; Genome-encoded proteins; HR1, heptad repeat 1; HR2, heptad repeat 2; M protein, Membrane protein; MERS-CoV, the Middle Eastern respiratory syndrome coronavirus; Mpro, Main protease; N protein, Nucleocapsid protein; NSP, non-structural protein; ORF, Open reading frame; PD, peptidase domain; RBD, receptor-binding domain; RBM, receptor-binding motif; RMP, The remdesivir monophosphate; RdRp, RNA-dependent RNA polymerase; S protein, Spike glycoprotein; SARS-CoV, severe acute respiratory syndrome coronavirus; SARS-CoV-2; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; Structure-based screening; gRNA, genomic RNA; sgRNA, subgenomic RNA.

Graphical abstract

Fig. 1

Schematic presentation of the SARS-CoV-2 genome organization, and the primary structures of M^pro, NSP12, S protein and N protein. The SARS-CoV-2 genome consists of ∼30 Kb RNA strand. There are 14 ORFs. The first two ORFs at 5′ untranslated regions code for polyprotein (pp1a/ab) that are segmented into 16 NSPs required for virus replication, followed by four structural proteins for spike glycoprotein(S), envelope protein(E), membrane protein(M), and nucleocapsid protein(N). At the 3′ terminus, there are nine accessory proteins (3a, 3b, 6, 7a, 7b, 8, 9b, 9c, and 10). M^pro consists of three domains, Domains I (8–101 aa), II (102–184 aa) and III (201–303 aa). NSP12 has three domains, the RdRp domain (367–920 aa), NiRAN domain (4–28 aa and 69–249 aa) and interface domain (250–365 aa). The RdRp domain consists of three subdomains: the finger subdomain (66–581 and 621–679 aa), the palm subdomain (582–620 and 680–815 aa), and the thumb subdomain (816–920 aa). S glycoprotein is divided into two subunits by protease at the S1/S2 protease cleavage site, Its S1 subunit contains NTD (14–305 aa), RBD (319 –541 aa), and RBM (437–508 aa). Its S2 subunit contains FP (788–806 aa), HR1 (912–984 aa), HR2 (1163–1213 aa), TM (1214–1237 aa) and CP (1238–1273 aa). N protein encompasses two conserved domains, namely the N1b domain (49–175aa), and N2b domain (247–365aa), and three short regions [N1a (1–49aa), N2a (174–247aa), and spacer B/N3 (365–419aa)]. The white box represents loop or non-special structural domain connecting the two domains on either side.

Fig. 2

General structure of a SARS-CoV-2 virion, the pre- and post-fusion states of the SARS-CoV-2 S glycoprotein, and some effective inhibitors targeting different proteins to impair SARS-CoV-2 infection. SARS-CoV-2 enters host cells mainly through the trimeric S glycoprotein (PDB ID: 6VSB, 6VYB/6VXX) containing RBD which binds to the human receptor ACE2 (PDB ID: 6M17). A previously characterized SARS-CoV monoclonal antibody CR3022 could bind to the SARS-CoV-2 RBD (PDB ID: 6W41); the epitope can potentially confer in vivo protection. The recombinant soluble human ACE2 can bind to RBD of the S protein to block the pre-fusion stage of SARS-CoV-2 infection. The TMPRSS2 for S protein priming can be inhibited by camostat mesylate, which in turn would block SARS-CoV-2 infection. After receptor binding of the S1 subunit to support membrane fusion and viral infection, the S2 subunit is exposed and undergoes a conformational change from a pre-fusion to a post-fusion state (PDB ID: 6LXT). The inhibitor EK1C4 targets the S2 to inhibit viral infection. In cells, SARS-CoV-2 RNA translates to different proteins, such as NSP12 (PDB ID: 7BV1), N protein (PDB ID: 6M3M & 6WZO) and M^pro (PDB ID: 6Y2G). Several compounds (N3, α-ketoamide,11a and 11b) have been identified to exhibit high inhibitory activity against SARS-CoV-2 M^pro activity and viral infection.