Comparative Analyses of ACE2 Receptor Binding Corona Viruses that Cause Mild versus Severe Acute Respiratory Syndrome in Humans

Aim: To analyze the spike proteins and Replication-Transcription Complexes (RTCs) of the Mild and Severe Acute Respiratory Syndrome (SARS) and SARS-related coronaviruses (CoVs) to find out the similarities and differences between them, as both of groups bind to angiotensin-converting enzyme 2 (ACE2) receptor for human cell entry.

Study Design: Bioinformatics, Biochemical, Site-Directed Mutagenesis (SDM), X-ray crystallographic, cryo-Electron microscopic (cryo-EM) and Mass Spectrometric (MS) data were analyzed.

Methodology: The protein sequence data for spike proteins and the proteins of the RTCs, viz. the RNA- dependent RNA polymerases (RdRps), primases and the nonstructural protein 7 (NSP7) were obtained from PUBMED and SWISS-PROT databases. The advanced version of Clustal Omega was used for protein sequence analysis. Along with the conserved motifs identified by the bioinformatics analysis, the data already available by biochemical and SDM experiments and X-ray crystallographic and cryo-EM studies on these proteins were used to confirm the possible amino acids involved in ACE2 receptor binding and active sites of the RTCs. For identification of probable N-linked and O-linked glycosylation sites, NetNGlyc 1.0 and NetOGlyc 4.0 tools of Technical University of Denmark were used. ExPASy tool was used for pI analysis.

Results: The spike protein of human CoV (HCoV)-NL63 is ~90 amino acids longer than the spike proteins of SARS and SARS-related CoVs. The additions are mostly found in the N-terminal regions and few insertions are also found in the crucial receptor binding domain (RBD). The SARS and SARS-related CoVs and HCoV-NL63 showed several conserved residues, motifs and large peptide regions. The most important aspect between the recent pandemic causing SARS-CoV-2 and HCoV-NL63 is a unique but different tetrapeptide insertions very close to the S1/S2 cleavage region, i.e., -PRRA- and -IPVR-, respectively. The next cleavage point S2’ and the transmembrane domains are conserved between the two groups. The RdRps are highly conserved between the two groups. The catalytic regions, catalytic amino acids and the NTP selection tripeptide regions are completely conserved between SARS-CoVs and HCoV-NL63. However, one of the metal binding sites, viz. the universal –GDD- reported in all RdRps is aligning with– KDG- in the RdRp of HCoV-NL63. The other metal binding site, viz. –SDD- is completely conserved in both the groups. The NiRAN domains of the RdRps differed from the possible catalytic amino acid and NTP selection tripeptide regions. The primases (NSP8) and the NSP7 subunits of the RTC are highly conserved in both the groups. The NSP8 and NSP7 subunits exhibit closer similarities between the MERS-CoV and HCoV-NL63. Unlike other SARS and SARS-related CoVs, the HCoV-NL63 possesses only a single accessory protein. Interestingly, a large number of amino acids are replaced with Ns in the spike proteins (which is also reflected in the number of N-linked glycosylation sites in it) as well as in the RTC.

Conclusions: Detailed analysis revealed several unique features in the HCoV-NL63 pathogen. As all the pandemic strains like SARS-CoV-1, SARS-CoV-2 and the milder HCoV-NL63 strain, use the same ACE2 receptor for entry into human cells, the frequent infection of humans by HCoV-NL63, especially in children, suggests that there is an ample opportunity for highly pathogenic variants to evolve in the future.