SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus-Host Interaction

Abstract

The recently emerged SARS-CoV-2 is the cause of the global health crisis of the coronavirus disease 2019 (COVID-19) pandemic. No evidence is yet available for CoV infection into hosts upon zoonotic disease outbreak, although the CoV epidemy resembles influenza viruses, which use sialic acid (SA). Currently, information on SARS-CoV-2 and its receptors is limited. O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells. SARS-CoV-2 hemagglutinin-esterase (HE) acts as the classical glycan-binding lectin and receptor-degrading enzyme. Most β-CoVs recognize 9-O-acetyl-SAs but switched to recognizing the 4-O-acetyl-SA form during evolution of CoVs. Type I HE is specific for the 9-O-Ac-SAs and type II HE is specific for 4-O-Ac-SAs. The SA-binding shift proceeds through quasi-synchronous adaptations of the SA-recognition sites of the lectin and esterase domains. The molecular switching of HE acquisition of 4-O-acetyl binding from 9-O-acetyl SA binding is caused by protein-carbohydrate interaction (PCI) or lectin-carbohydrate interaction (LCI). The HE gene was transmitted to a β-CoV lineage A progenitor by horizontal gene transfer from a 9-O-Ac-SA-specific HEF, as in influenza virus C/D. HE acquisition, and expansion takes place by cross-species transmission over HE evolution. This reflects viral evolutionary adaptation to host SA-containing glycans. Therefore, CoV HE receptor switching precedes virus evolution driven by the SA-glycan diversity of the hosts. The PCI or LCI stereochemistry potentiates the SA-ligand switch by a simple conformational shift of the lectin and esterase domains. Therefore, examination of new emerging viruses can lead to better understanding of virus evolution toward transitional host tropism. A clear example of HE gene transfer is found in the BCoV HE, which prefers 7,9-di-O-Ac-SAs, which is also known to be a target of the bovine torovirus HE. A more exciting case of such a switching event occurs in the murine CoVs, with the example of the β-CoV lineage A type binding with two different subtypes of the typical 9-O-Ac-SA (type I) and the exclusive 4-O-Ac-SA (type II) attachment factors. The protein structure data for type II HE also imply the virus switching to binding 4-O acetyl SA from 9-O acetyl SA. Principles of the protein-glycan interaction and PCI stereochemistry potentiate the SA-ligand switch via simple conformational shifts of the lectin and esterase domains. Thus, our understanding of natural adaptation can be specified to how carbohydrate/glycan-recognizing proteins/molecules contribute to virus evolution toward host tropism. Under the current circumstances where reliable antiviral therapeutics or vaccination tools are lacking, several trials are underway to examine viral agents. As expected, structural and non-structural proteins of SARS-CoV-2 are currently being targeted for viral therapeutic designation and development. However, the modern global society needs SARS-CoV-2 preventive and therapeutic drugs for infected patients. In this review, the structure and sialobiology of SARS-CoV-2 are discussed in order to encourage and activate public research on glycan-specific interaction-based drug creation in the near future.

Keywords: SARS-CoV-2; entry receptor; evolutionary adaptation; glycosylation; hemagglutinin-esterase; sialic acid O-acetylation; virus–host interaction.

Figure 1

Cellular glycans are recognized by infectious agents including viruses and bacteria through protein–carbohydrate interaction (PCI) or lectin–carbohydrate interaction (LCI). The carbohydrates are uses as cellular adhesion sites in eukaryotic cells. Host cell surfaced and cytosolic glycans include glycoproteins, glycolipids and proteoglycans with minor glycan species of O-GlcNAc present in nucleus and cytosols.

Figure 2

Diverse structures of sialic acids (SA). (A) Neuraminic acid; (NeuC); (B) N-acetyl neuraminic acid (NeuAc); (C) N-glycolyl neuraminic acid (NeuGc); (D) N, O-diacetyl neuraminic acid (occurs in horse); (E) N, O-diacetyl neuraminic acid (occurs in bovine); (F) N-acetyl O-diacetyl neuraminic acid (occurs in bovine).

Figure 3

SA linkages of α2-3, α2-6, α2-8 or α2-9 to the SA or Gal residues.

Figure 4

Formation of α2,3 ST or α2,6 SA structures by α 2,3- and 2,6-sialyltransferase (ST) using substrates such as Galβ-1,4-GlcNAc.

Figure 5

Action sites of viral SA-O-acetylesterases (C4, C7, C8 and C9) specific for 4-O-SA-, 7-O-SA-, 8-O-SA and 9-O-SA and neuraminidases [6].

Figure 6

CasD1, SA O-acetyltransferase, transfers acetyl groups to C7 position of SA (Neu5Ac), from which it migrates to the C9 position (Neu5,9Ac2). The additional acetyl group is added to C7 of SA (Neu5,7,9Ac3) by the same CasD1. The SA O-acetylesterase cleaves of the acetyl groups.

Figure 7

SARS-CoV-2 uses angiotensin-converting enzyme 2 (ACE2) for cell entry through TMPRSS2 priming of S glycoprotein.

Figure 8

Endoplasmic-reticulum (ER) stress responses and COVID-19 receptor (S glycoprotein binding site). Balance of ER stress and unfolded protein response (UPR) are regulated. ER-stress sensor proteins are IRE1 (inositol requiring 1), ATF6 (activating TF 6) and PERK (PKR-like ER kinase).

Figure 9

Structure of glycosaminoglycan (GAG)-linkage tetrasaccharide, GluAβ1,3Galβ1,3Galβ1,4Xylβ-O-serine and HS; (A) HS structure; (B) Sulfation of sugar residues; (C) Synthesis and localization of HS in host cells. Glycosyltransferases involved in GAG synthesis include (i) GlcAT-II (glucuronosyltransferase) and (ii) GlcNAcT-II (N-acetylglucosaminyltransferase II) for heparan sulfate synthesis. β-D-glucuronic acid (GlcA), α-L-iduronic acid (IdoA) and 2-O-sulfo-α-L-iduronic acid (IdoA(2S) are composed [124].

Figure 10

Structures of (A) CLQ and (B) CLQ-related CLQ-OH as predicted UDP-GlcNAc 2-epimerase inhibitors.