Structure genomics of SARS-CoV-2 and its Omicron variant: drug design templates for COVID-19

Abstract

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has brought an unprecedented public health crisis and persistently threatens to humanity. With tireless efforts from scientists around the world, understanding of the biology of coronavirus has been greatly enhanced over the past 2 years. Structural biology has demonstrated its powerful impact on uncovering structures and functions for the vast majority of SARS-CoV-2 proteins and guided the development of drugs and vaccines against COVID-19. In this review, we summarize current progress in the structural biology of SARS-CoV-2 and discuss important biological issues that remain to be addressed. We present the examples of structure-based design of Pfizer's novel anti-SARS-CoV-2 drug PF-07321332 (Paxlovid), Merck's nucleotide inhibitor molnupiravir (Lagevrio), and VV116, an oral drug candidate for COVID-19. These examples highlight the importance of structure in drug discovery to combat COVID-19. We also discussed the recent variants of Omicron and its implication in immunity escape from existing vaccines and antibody therapies.

Keywords: COVID-19; SARS-CoV-2; drug design; omicron; structural biology; vaccine development.

Fig. 1. The genome of SARS-CoV-2 and its coded proteins.

a The organization of SARS-CoV-2 genome. b Schematic illustrations of the secondary structure of the frameshift stimulation element −1 programmed ribosomal frameshifting, with different functional regions labeled and colored accordingly. c The rectangle depicts the nsps derived from processing of the pp1a and pp1ab polyproteins. Labels indicate protein names. The position of blue arrow indicates cleavage site of PL^pro, and position of red arrow indicates the site of M^pro. d Domain architectures of SARS-CoV-2 genome coded proteins and summary of structural characterization of individual proteins. Bars above domain architectures indicate regions of the proteins for which high-resolution structures area are available. Ubl ubiquitin-like domain, MD macrodomain, SUD SARS unique domain, PL^pro papain-like protease, NAB nucleic acid-binding domain, TM transmembrane domain, Y Y region, NTD N-terminal domain, CTD C-terminal domain.

Fig. 2. Structures of the SARS-CoV-2 holo-RdRp and RTX.

a The schematic diagram for the domain organization of the holo-RdRp, containing nsp12, nsp7, nsp8-1 and nsp8-2 (PDB: 7C2K). Two views of the cartoon model of the cryo-EM structure of holo-RdRp. The subdomains and components of the holo-RdRp are colored as follows: β-hairpin, chocolate; NiRAN, light orange; Interface, light magenta; Fingers, bright orange; Palm, lime; Thumb, pale cyan; nsp7, marine; nsp8-1, pink; nsp8- 2, fire brick; template RNA, red; product RNA, deepteal. b Zoom in views of holo-RdRp bound to inhibitors, Favipiravir at +1 (PDB: 7AAP, 7CTT), Remedisivir at +1 (PDB: 7BV2), Remedisivir at −1 (PDB: 7C2K), Remedisivir at −3 (PDB: 7B3B), Remedisivir at +1, −1, −2, −3 (PDB: 7L1F), Suramin (PDB: 7D4F), Molnupiravir at template RNA, the four inhibitors are indicated in different colors. Proteins and RNA are shown in cartoon representation, and inhibitors are shown as sticks. Nsp12 is shown in transparent gray. Ligand atom color code: O atoms, red; N atoms, blue; P atoms, salmon; Mg²⁺ ion, green. 2D structures of five drugs are presented. c The schematic diagram for the domain organization of the RTC, containing nsp12, nsp7, nsp8-1, nsp8-2, nsp9, nsp13-1 and nsp13-2 (PDB: 7CYQ). Two views of the cartoon model of the cryo-EM structure of RTC. The subdomains and components of the holo-RdRp are colored as follows: the subdomains and components of the RTC are colored as follows: β-hairpin, chocolate; NiRAN, light orange; Interface, light magenta; Fingers, bright orange; Palm, lime; Thumb, pale cyan; nsp7, marine; nsp8-1, pink; nsp8-2, fire brick; nsp9, purple blue; nsp13-1, wheat; nsp13-2, dark salmon; template RNA, red; product RNA, deep-teal.

Fig. 3. The structures of S protein.

a Schematic of SARS-CoV-2 S protein domain architecture. The S1 and S2 subunits are indicated, with diamond representing the locations of furin cleavage site. SP signal peptide, RBD receptor-binding domain, RBM receptor-binding motif, SD1 subdomain 1, SD2 subdomain 2, FP fusion peptide, HR1 heptad repeat 1, HR2 heptad repeat 2, TM transmembrane region, CT cytoplasmic tail. b Side and top views of the prefusion structure of the SARS-CoV-2 S protein with all RBD in the “down” conformation (PDB: 6VXX). Protein is shown in cartoon representation, and glycosyls are shown as sticks. c Side view of the prefusion structure of the SARS-CoV-2 S protein with one RBD in the “up” conformation (PDB: 6XKL). d Side and top views of the post-fusion structure of the SARS-CoV-2 S protein (PDB: 6M3W). e Structure of the SARS-CoV-2 RBD complexed with ACE2 (PDB: 6LZG). ACE2 is shown in yellow. The RBD is shown in cyan. Key contacting residues are shown as sticks at the SARS-CoV-2 RBD–ACE2 interfaces. f Side and top views of superimposed three cryo-EM structures of SARS-CoV-2 S in complex with nAbs. S2E12 (represented as a cyan surface) binds to the “up” conformation of SARS-CoV-2 S RBD (PDB: 7K4N); S2M11 (represented as a brown surface) binds to the “down” conformation of SARS-CoV-2 S RBD (PDB: 7K43); 4A8 (represented as a magento surface) binds to the NTD of SARS-CoV-2 S (PDB: 7C2L). g Amino acids mutated in the Omicron variant S protein.

Fig. 4. In situ structures of SARS-CoV-2 virions.

a Cryo-EM map of SARS-CoV-2 virion structure. The S proteins with different conformations are distributed over the virion surface and can be tilted to different directions (EMD-30430). b A tilted conformation of S trimer is presented in the upper plots, while a Y-shaped spike pairs having two heads and one combined stem are presented in the lower plots. c Side view of cryo-EM map of SARS-CoV-2 virion structure, displaying RNPs assembled in the virus envelope. d Side and top views of in situ structure of SARS-CoV-2 RNP (EMD-30429). e Tomograms showing SARS-CoV-2 virions in VeroE6 cells (EMD-11865). f Tomograms showing DMVs in SARS-CoV-2 affected VeroE6 cells (EMD-11866). g Different views of the EM structure of the MHV-induced pore complex embedded in the DMVs membranes (EMD-11514).

Fig. 5. High-resolution structures of SARS-CoV-2 proteins.

Crystal structure of SARS-CoV-2 nsp1 (PDB: 7K7P); Cryo-EM structure of the SARS-CoV-2 nsp2 (PDB: 7MSW); crystal structure of the SARS-CoV-2 PL^pro with GRL0617 (PDB: 7CMD); crystal structure of the SARS-CoV-2 M^pro in complex with an inhibitor N3 (PDB: 6LU7); crystal structure of the SARS-CoV-2 Nsp9 in complex with a peptide (PDB: 6WC1); crystal structure of the SARS-CoV-2 nsp10 (PDB: 6ZCT); crystal structure of SARS-CoV-2 nsp10 bound to nsp14-exoribonuclease domain (PDB: 7DIY); crystal structure of SARS-CoV-2 nsp10 in complex with nsp16 (PDB: 6W4H); crystal structure of the SARS-CoV-2 nsp15 endoribonuclease (PDB: 6VWW); crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain (PDB: 6M3M); crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal RNA binding domain (PDB: 6WZO); Cryo-EM structure of SARS-CoV-2 ORF3a (PDB: 7KJR); the crystal structure of the SARS-CoV-2 ORF7a ectodomain (PDB: 7CI3); the crystal structure of SARS-CoV-2 ORF8 accessory protein (PDB: 7JTL); the crystal structure of SARS-CoV-2 ORF9b accessory protein (PDB: 6Z4U).

Fig. 6. The structures of SARS-CoV-2 M^pro in complex with inhibitors.

a Chemical structure of PF-07321332, Boceprevir and GC376. b The comparison of SARS-CoV-2 M^pro-PF-07321332 complex structure with that of SARS-CoV-2 M^pro-boceprevir. c The comparison of SARS-CoV-2 M^pro-PF-07321332 complex structure with that of SARS-CoV-2 M^pro-GC376.