Tracking mutation progression on SARS-CoV-2 druggable cavities, epitopes, and binding interfaces

Date: 12/1/2021
Tracking the evolution of the SARS-CoV-2 viral components is vital for identifying potential efficacy shifts for existing and novel therapeutics (e.g. the Pfizer mRNA vaccine, Casirivimab, Indevimab, Bamlanivimab, Remdesivir) as well as understanding potential causes of increased virulence, e.g. the destabilising Spike glycoprotein D614G mutation, and mutations in the UK and South African variants that facilitate the viral spike activation and viral-host membrane fusion. Furthermore, viral mutations can affect interactions with human proteins, thus altering the virus - host interactome. Such mutations can impact cell signalling and, from the point of view of drug discovery, may introduce new therapeutic opportunities via novel virus - host protein interactions or negate existing ones should mutations diminish established virus - host protein interactions.
canSARS, utilises canSAR-3D (the unique 3D structural component of canSAR, that uses artificial intelligence approaches to identify and predict the 'ligandability' of proteins with known 3D structure) in conjunction with the canSARS druggable core networks (Druggable Interactome report), to triage the comprehensive GISAID SARS-CoV-2 mutation data provided by CoV-GLUE with additional literature curation of epitope sites on viral components (e.g. Shrock et al., 2020).
In this report we compare and contrast two snapshots of the mutational landscape of SARS-CoV-2, the first from mid-June 2020 (217,204 protein coding mutations) and the second from mid-November 2020 (1,197,272 protein coding mutations): with additional literature curation of epitope sites on viral components (e.g. Shrock et al., 2020).
Overall Mutational Profile SARS-CoV-2 image Overall Mutational Profile SARS-CoV-2
Despite the significant increase in the reported number of mutations between the two snapshots, their relative distribution is comparable, with two notable exceptions: an 3.7% increase in mutations occurring in the Spike glycoprotein and a 5.9% decrease in mutations targeting ORF3a, implicated in induction of cell apoptosis, both components playing a pivotal role in the pathogenicity of this deadly coronavirus.
The majority of mutations focus on 6 viral proteins: S (21.8% as of November 2020), N (18.1%), ORF3a (7.0%) and polyprotein components Nsp12 (Pol), Nsp3 (PL-PRO) and Nsp2 (16.4%, 7.9%, 6.8% respectively). A closer inspection of the individual viral component profiles often highlights mutation hotspots, which could influence drug discovery decisions as presented above. Here we focus on the Spike glycoprotein and the Nsp12 polyprotein component (Pol), which are currently targeted by approved therapeutics and vaccines. Mutational profile of the Spike glycoprotein are available here.

Mutational profile of the Spike glycoprotein

As of November 2020, 261,401 mutations were targeting the Spike glycoprotein. The vast majority map on 3D structure, most targeting protein binding interfaces:
Spike glycoprotein mutation counts Spike glycoprotein mutation counts
Significantly, mutations have started emerging in ligandable cavities and interfaces, though their rates are currently quite low. A closer inspection reveals that the dominant mutation is indeed the D614G amino acid change which results in increased ACE2 binding and fusion (Yurkovetskiy et al., 2020, Teruel et al - preprint DOI, Published). This mutation was already prevalent, yet not as a dominant proponent in the June 2020 mutational landscape:
Spike glycoprotein mutation lollipop plot Spike glycoprotein mutation lollipop plot
Residues 331 – 524 in the Receptor Binding Domain (RBD) are not targeted as extensively by mutations. These residues form the basis of the Pfizer mRNA vaccine. A number of other highly immunogenic epitope sites, proposed by Shrock et al., 2020, also exhibit far lower mutation rates and are highlighted in magenta in the above lollipop plots.

Mutational profile of Nsp12 (Pol)

The Polymerase component of SARS2 harbours 196,086 mutations as of mid-November 2020 (16.4% of all mutations). The most dominant mutation, P323L, accounts for 80% of all Nsp12 mutations:
Nsp12 (Pol) mutation lollipop plot Nsp12 (Pol) mutation lollipop plot
Proline 323 forms part of the Nsp8 binding interface and participates in Hydrogen bonding with the Nsp8 Asparagine residue 118. Note that a number of epitopes have been identified by Shrock et al., 2020 using triple Ala mutagenesis (shown in blue in the above lollipop plot), presenting opportunities in the Nsp12 binding interfaces with Nsp7 and Nsp8.
The Remdesivir ligandable cavity identified by canSAR-3D comprises 38 amino acids exhibiting comparatively low mutation rates (see table below). However there are mutations emerging in residues N691, K545 and S682 which are important for Remdesivir binding:
Remdesivir-cavity-binding image Remdesivir cavity binding
Remdesivir-ligandable-cavity-using-canSAR-3D Mutation incidence within canSAR-3D identified Remdesivir binding ligandable pocket
The canSAR-3D ligandable cavity residues are shown as a molecular surface, using a rainbow spectrum for indicating mutation rates (blue = low, red = high). The Remdesivir molecule is shown in red, and the three most significantly mutated residues are highlighted.
Following the recent FDA approval of Remdesivir for covid19 treatment it will be important to monitor whether the mutation rate in this cavity increases.
The next full mutational profile update for SARS-CoV-2 is scheduled for February 2021, to mark the first year of the covid19 pandemic.