Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain

Zachariah P Schuurs; Edward Hammond; Stefano Elli; Timothy R Rudd; Courtney J Mycroft-West; Marcelo A Lima; Mark A Skidmore; Richard Karlsson; Yen-Hsi Chen; Ieva Bagdonaite; Zhang Yang; Yassir A Ahmed; Derek J Richard; Jeremy Turnbull; Vito Ferro; Deirdre R Coombe; Neha S Gandhi

doi:10.1016/j.csbj.2021.05.002

Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain

Comput Struct Biotechnol J. 2021:19:2806-2818. doi: 10.1016/j.csbj.2021.05.002. Epub 2021 May 4.

Authors

Zachariah P Schuurs¹, Edward Hammond², Stefano Elli³, Timothy R Rudd⁴, Courtney J Mycroft-West⁵, Marcelo A Lima⁵, Mark A Skidmore⁵, Richard Karlsson⁶, Yen-Hsi Chen⁶, Ieva Bagdonaite⁶, Zhang Yang⁶, Yassir A Ahmed⁷, Derek J Richard⁸, Jeremy Turnbull^{6

7}, Vito Ferro^{9

10}, Deirdre R Coombe¹⁰, Neha S Gandhi¹

Affiliations

¹ QUT, Centre for Genomics and Personalised Health, Cancer and Ageing Research Program, School of Chemistry and Physics, Faculty of Science and Engineering, Institute of Health and Biomedical Innovation, 2 George Street, Brisbane, QLD 4000, Australia.
² Zucero Therapeutics Ltd, 1 Westlink Court, Brisbane, Queensland, Australia.
³ Istituto di Ricerche Chimiche e Biochimiche "G.Ronzoni", via Giuseppe Colombo 81, 20133 Milano, Italy.
⁴ National Institute for Biological Standards and Control, Analytical and Biological Sciences Division, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK.
⁵ Molecular & Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire ST5 5BG, UK.
⁶ Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark.
⁷ Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
⁸ QUT, Centre for Genomics and Personalised Health, Cancer & Ageing Research Program, Institute of Health and Biomedical Innovation at the Translational Research Institute (TRI), 37 Kent Street, Woolloongabba, Queensland 4102, Australia.
⁹ School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
¹⁰ Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia.

Abstract

SARS-CoV-2 has rapidly spread throughout the world's population since its initial discovery in 2019. The virus infects cells via a glycosylated spike protein located on its surface. The protein primarily binds to the angiotensin-converting enzyme-2 (ACE2) receptor, using glycosaminoglycans (GAGs) as co-receptors. Here, we performed bioinformatics and molecular dynamics simulations of the spike protein to investigate the existence of additional GAG binding sites on the receptor-binding domain (RBD), separate from previously reported heparin-binding sites. A putative GAG binding site in the N-terminal domain (NTD) of the protein was identified, encompassing residues 245-246. We hypothesized that GAGs of a sufficient length might bridge the gap between this site and the PRRARS furin cleavage site, including the mutation S247R. Docking studies using GlycoTorch Vina and subsequent MD simulations of the spike trimer in the presence of dodecasaccharides of the GAGs heparin and heparan sulfate supported this possibility. The heparan sulfate chain bridged the gap, binding the furin cleavage site and S247R. In contrast, the heparin chain bound the furin cleavage site and surrounding glycosylation structures, but not S247R. These findings identify a site in the spike protein that favors heparan sulfate binding that may be particularly pertinent for a better understanding of the recent UK and South African strains. This will also assist in future targeted therapy programs that could include repurposing clinical heparan sulfate mimetics.

Keywords: COVID-19; Coronavirus; Cosolvent MD simulations; Heparan sulfate; Heparin; SARS-CoV-2; Spike protein.