The Sialoside-Binding Pocket of SARS-CoV-2 Spike Glycoprotein Structurally Resembles MERS-CoV

Abstract

COVID-19 novel coronavirus (CoV) disease caused by severe acquired respiratory syndrome (SARS)-CoV-2 manifests severe lethal respiratory illness in humans and has recently developed into a worldwide pandemic. The lack of effective treatment strategy and vaccines against the SARS-CoV-2 poses a threat to human health. An extremely high infection rate and multi-organ secondary infection within a short period of time makes this virus more deadly and challenging for therapeutic interventions. Despite high sequence similarity and utilization of common host-cell receptor, human angiotensin-converting enzyme-2 (ACE2) for virus entry, SARS-CoV-2 is much more infectious than SARS-CoV. Structure-based sequence comparison of the N-terminal domain (NTD) of the spike protein of Middle East respiratory syndrome (MERS)-CoV, SARS-CoV, and SARS-CoV-2 illustrate three divergent loop regions in SARS-CoV-2, which is reminiscent of MERS-CoV sialoside binding pockets. Comparative binding analysis with host sialosides revealed conformational flexibility of SARS-CoV-2 divergent loop regions to accommodate diverse glycan-rich sialosides. These key differences with SARS-CoV and similarity with MERS-CoV suggest an evolutionary adaptation of SARS-CoV-2 spike glycoprotein reciprocal interaction with host surface sialosides to infect host cells with wide tissue tropism.

Keywords: MERS-CoV; N-terminal domain; SARS-CoV-2; spike glycoprotein.

Figure 1

Phylogenetic, sequence and structural analysis of SARS-CoV-2 with close members of betacoronavirus family. (a) Evolutionary analysis of the spike protein of human-infecting coronaviruses. The phylogenetic tree was drawn by using the maximum likelihood method and scaled with branch lengths measured in the number of substitutions per site. (b) Sequence alignment of the N-terminal domain (NTD) of SARS-CoV, SARS-CoV-2, and MERS-CoV shows the divergent loop regions of an otherwise highly similar protein sequence. The β4-β5, β9-β10, and β14-β15 loop regions are highlighted by red, green, and blue box, respectively. The α-helices and β-strands are represented as pink bars and cyan arrows, respectively. (c) The tertiary structure of NTD of the spike protein of SARS-CoV-2. The β4-β5 (red) and β14-β15 (blue) loops are important components of the predicted sialoside-binding pocket of SARS-CoV-2 spike glycoprotein.

Figure 2

Binding between the docked sialoside derivatives and the NTD of SARS-CoV-2 glycoprotein. The key amino acid side chains surrounding (a) 5-N-acetyl neuraminic acid (Neu5Ac, orange), (b) α2,3-sialyl-N-acetyl-lactosamine (2,3-SLN, teal), (c) α2,6-sialyl-N-acetyl-lactosamine (2,6-SLN, pink) (d) 5-N-glycolyl neuraminic acid (Neu5Gc, dark grey), and (e) sialyl Lewis^X (sLeX, light grey) are shown. (f) The flexibility of β14-β15 loop (Leu244-Gly261) enables binding of a wide variety of sialosides. The NTD of SARS-CoV-2 glycoprotein is shown as purple ribbons and sialoside derivatives are shown as ball and stick models. The amino acids side chains interacting with sialosides are shown as purple sticks.

Figure 3

Protein-ligand interactions between the NTD of SARS-CoV-2 glycoprotein and (a) 5-N-acetyl neuraminic acid (Neu5Ac, orange), (b) α2,3-sialyl-N-acetyl-lactosamine (2,3-SLN, teal), (c) α2,6-sialyl-N-acetyl-lactosamine (2,6-SLN, pink), (d) 5-N-glycolyl neuraminic acid (Neu5Gc, dark grey) and (e) sialyl Lewis^X (sLeX, light grey) are shown. Dashed green lines show electrostatic interactions formed between the SARS-CoV-2 glycoprotein amino acid residues and the ligand. Hydrophobic contacts are shown as filled circles, where the orientation and size of the opaque ellipsoid mark the directionality and strength of hydrophobic interactions. In all panels, nitrogen, carbon, and oxygen atoms are colored blue, black, and red, respectively.