Unlocking COVID therapeutic targets: A structure-based rationale against SARS-CoV-2, SARS-CoV and MERS-CoV Spike

Abstract

There are no approved target therapeutics against SARS-CoV-2 or other beta-CoVs. The beta-CoV Spike protein is a promising target considering the critical role in viral infection and pathogenesis and its surface exposed features. We performed a structure-based strategy targeting highly conserved druggable regions resulting from a comprehensive large-scale sequence analysis and structural characterization of Spike domains across SARSr- and MERSr-CoVs. We have disclosed 28 main consensus druggable pockets within the Spike. The RBD and SD1 (S1 subunit); and the CR, HR1 and CH (S2 subunit) represent the most promising conserved druggable regions. Additionally, we have identified 181 new potential hot spot residues for the hSARSr-CoVs and 72 new hot spot residues for the SARSr- and MERSr-CoVs, which have not been described before in the literature. These sites/residues exhibit advantageous structural features for targeted molecular and pharmacological modulation. This study establishes the Spike as a promising anti-CoV target using an approach with a potential higher resilience to resistance development and directed to a broad spectrum of Beta-CoVs, including the new SARS-CoV-2 responsible for COVID-19. This research also provides a structure-based rationale for the design and discovery of chemical inhibitors, antibodies or other therapeutic modalities successfully targeting the Beta-CoV Spike protein.

Keywords: ACE2, angiotensin-converting enzyme2; Bat-SL-CoVs, bat SARS-like coronavirus; Beta-CoVs, betacoronavirus; Betacoronavirus; CC, conserved cluster; CD, connector domain; CDP, consensus druggable pocket; CDR, consensus druggable residue; CH, central helix; CP, cytoplasmic domain; CR, connecting region; CS, conservation score; CoVs, coronavirus; Coronavirus disease; DGSS, DoGSiteScorer; DPP4, dipeptidyl peptidase-4; Druggability prediction; FP, fusion peptide; HR1, heptad repeat 1; HR2, heptad repeat 2; MERS-CoVs, middle east respiratory syndrome coronavirus; MERSr-CoVs, middle east respiratory syndrome-related coronavirus; MSA, multiple sequence alignment; NTD, N-terminal domain; Novel antiviral targets; PDB, Protein Data Bank; PDS, PockDrug-Server; RBD, Receptor-Binding Domain; S, Spike; SARS-CoV-2; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; SARS-CoVs, severe acute respiratory syndrome coronavirus; SARSr-CoVs, severe acute respiratory syndrome-related coronavirus; SD1, subdomain 1; SD2, subdomain 2; SF, SiteFinder from MOE; SP, small pocket; Sequence conservation; Spike protein; Sv, shorter variant; T-RHS, top-ranked hot spots; TMPRSS2, transmembrane protease serine 2; aa, amino acid; hSARSr-CoVs, human Severe acute respiratory syndrome-related coronavirus; nts, nucleotides.

Graphical abstract

Fig. 1

Three-dimensional sequence conservation of the human SARSr-CoVs (A) and SARSr- and MERSr-CoVs (B) Spike protomers (PDB ID: 6VYB). The cs are mapped onto the S protein structures. The figure is coloured based on cs: the highest conservation positions are highlighted in shades of blue and the red regions indicate low conservation according to the cs scale. The S1 and S2 domains resolved are indicated in black and grey, respectively, in the hSARSr-CoV protomer. NTD: N-terminal domain; RBD: receptor-binding domain; SD: subdomain; FP: fusion peptide; CR: connecting region, HR: heptad repeat; CH: central helix. The figures were produced with PyMOL Molecular Graphics System . (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Overall alignment of Spike-RBD druggability along with the conservation scores for each residue position. The druggability prediction was based on the descriptors algorithm of each pocket bioinformatics tool: SF, DGSS and PDS. The potential conserved druggable sites/residues are marked with an asterisk and the T-RHS are marked with a target. The conserved druggable pockets allocated to each site/residue along with the secondary structure elements are indicated at the top of the picture.

Fig. 3

Mapping results of the highest-ranked consensus druggable pockets onto the Spike-RBD crystallographic structure of SARS-CoV-2 (PDB: 6VW1). The top-ranked pockets: CDP1 to CDP5 are highlighted in shades of pink, pale blue, orange, green, yellow and cyan, respectively. The number and aa composition of each CDP are shown in Supplemental Table S-2. The figures were produced with PyMOL Molecular Graphics System . (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 4

Mapping results of the highest-ranked consensus druggable pockets onto the Spike trimer crystallographic structure of SARS-CoV-2 (PDB: 6VYB). The top-ranked pockets: CDP5T-S1, CDP6T-S1, CDP9T-S1, CDP2T-S2, CDP4T-S2, CDP8T-S2, CDP2T-S1S2, CDP3T-S1S2, CDP5T-S1S2 are highlighted in shades of yellow, turquoise, pale blue, cyan, orange, pink, grey, green and raspberry, respectively. The number and aa composition of each CDP are shown in Supplemental Table S-2. The figures were produced with PyMOL Molecular Graphics System . (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 5

Overall alignment of Spike S1 and S2 druggability along with the conservation scores for each residue position. The druggability prediction was based on the descriptors algorithm of each pocket bioinformatics tool: SF and DGSS; and for all the predicted S state conformation (open, semi-open and open). The potential conserved druggable sites/residues are marked with an asterisk and the T-RHS are marked with a target. The conserved druggable residues shared by the S monomer and trimer conformations for the hSARSr-CoVs are coloured in blue; and the conserved druggable pockets allocated to each site/residue are indicated at the top of the picture. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)