key: cord-0890089-uuws2nen
authors: Vankadari, Naveen
title: Structural interactions between pandemic SARS-CoV-2 spike glycoprotein and human Furin protease
date: 2020-04-11
journal: bioRxiv
DOI: 10.1101/2020.04.10.036533
sha: ffe5049d4a9928890638f93bfc0b2f1113df2416
doc_id: 890089
cord_uid: uuws2nen

The SARS-CoV-2 pandemic is an urgent global public health emergency and warrants investigating molecular and structural studies addressing the dynamics of viral proteins involved in host cell adhesion. The recent comparative genomic studies highlight the insertion of Furin protease site in the SARS-CoV-2 spike glycoprotein alerting possible modification in the viral spike protein and its eventual entry to host cell and presence of Furin site implicated to virulence. Here we structurally show how Furin interacts with the SARS-CoV-2 spike glycoprotein homotrimer at S1/S2 region, which underlined the mechanism and mode of action, which is a key for host cell entry. Unravelling the structural features of biding site opens the arena in rising bonafide antibodies targeting to block the Furin cleavage and have great implications in the development of Furin inhibitors or therapeutics.

The pandemic Corona Virus Disease 2019 (COVID-19) caused by Severe Acute 30

Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is an urgent public health emergency 31 and made a serious impact on global health and economy (1). To date, more than 86,000 32 deaths and 1.5 million confirmed positive cases were reported globally, making the most 33 contagious pandemic in the last decade (www.coronavirus.gov). Since the initial reports on 34 2 this pneumonia-causing novel coronavirus (SARS-CoV-2) in Wuhan, China , mortality and 35 morbidity are increasing exponentially around the globe despite several antiviral and 36 antibody treatments (2). Most available neutralising antibodies in use are targeting the SARS-37

CoV-2 spike glycoprotein, which is essential for host cell adhesion via ACE2 and CD26 38 receptors (3, 4), but infection control is still insignificant. Meanwhile, several antiviral drugs 39 (Ritonavir, Lopinavir, Chloroquine, Remdesivir and others) targeting different host and viral 40 proteins are been clinically evaluating and repurposing to combat SARS-CoV-2 infection (2, 41 5). With the drastic increasing number of the positive cases around the world (www.cdc.gov), 42 moderate response to antivirals under clinical trials and poor response to antibodies targeting 43 spike SARS-CoV-2 spike glycoprotein is a serious concern and warrants detail understanding 44 of the molecular and structural features of SARS-CoV-2 structural proteins in native 45 condition and post-viral infection. This will abet in understanding the dynamics and 46 mechanism of viral action on the human cell. The overall complex structure shows three Furin proteases binding to the mid or 89 equatorial region (mid region of S1 and S2 domain (S1/S2)) of SARS-CoV-2 spike 90 glycoprotein homo-trimer at the off-centric and adjacent side of spike trimer ( Fig. 1 R298, W328 and Q346 (10, 11) ( Fig. 2 and S2) . Interestingly, these residues are also well-100 positioned to interact with the viral spike protein cleavage site in our complex structure and 101 the entire substrate-binding pocket of Furin protease appears like a canyon-like crevice, 4 which can accommodate a large portion of target protein/peptide. The results show that the 103 SARS-CoV-2 spike glycoprotein amino acid residues N657 to Q690 are the prime interacting 104 residues with the Furin protease. The position and orientation of these unique residues 105 involved in Furin recognition are well exposed and organise in a flexible loop. The spike 106 protein residues N657, N658, E661, Y660, T678, N679, S680, R682, R683, R685, S689, 107 Q690 makes the strong interaction with the Furin protease ( Fig. 2A) . The interaction between 108 the viral spike glycoprotein and Furin protease is mediated via several van der Waals or by 109 hydrogen bonding. Furthermore, the entire cleavage loop of viral spike protein fits into the 110 canyon-like substrate-binding pocket of Furin protease. It is quite interesting to notice that 111 none of the previously known coronaviruses had this novel Furin protease cleavage site in the 112 spike glycoprotein, which accentuates the novelty and uniqueness of SARS-CoV-2. In 113 addition, previous reports on the glycosylation of spike glycoprotein show that Furin 114 cleavage site in the SARS-CoV-2 spike glycoprotein is not targeted by the glycosylation, 115 hence this cleavage loop is completely solvent-exposed (4). This further corroborates the 116 potential attack of Furin protease over the S1/S2 cleavage site in the SARS-CoV-2 spike 117 glycoprotein. Based on the Furin binding mode and structural interaction, we propose the 118 following supposition. The binding and cleaving (priming) the spike glycoprotein at S1/S2 119 region by Furin protease might cut the spike glycoprotein into N-terminal S1 domain 120 spike glycoproteins also could make the ACE2 and CD26 inhibitors of least effective, as 129 upon cleavage the N-terminal S1 domains are not required for the cell penetration. This also 130 raises a caution that while making neutralizing antibodies targeting SARS-CoV-2 spike 131 glycoprotein, these cleavage activities need to be considered. Hence, we speculate that 132 antibodies against S2 domain and drugs targeting S1 trimerization could be more promising. 

Clinical features of patients infected with 2019 novel coronavirus in 172

Therapeutic and triage strategies for 2019 novel coronavirus disease in 174 fever clinics

Structure, Function, and Antigenicity of the SARS-CoV

Emerging WuHan (COVID-19) coronavirus: glycan shield 178 and structure prediction of spike glycoprotein and its interaction with human CD26

Therapeutic options for the 2019 novel coronavirus (2019-181 nCoV)

A pneumonia outbreak associated with a new coronavirus of probable 183 bat origin

Evolution of the novel coronavirus from the ongoing Wuhan outbreak and 186 modeling of its spike protein for risk of human transmission. SCIENCE CHINA Life 187 Sciences

The proximal 189 origin of SARS-CoV-2

Protective role for the N-terminal domain of alpha-dystroglycan 191

in Influenza A virus proliferation

The crystal structure of the proprotein processing proteinase furin 194 explains its stringent specificity

Structure of the 196 unliganded form of the proprotein convertase furin suggests activation by a substrate-197 induced mechanism

Cryo-EM structure of the 2019-nCoV spike in the prefusion 199 conformation

Proteolytic activation of the spike protein at a novel RRRR/S 201 motif is implicated in furin-dependent entry, syncytium formation, and infectivity of 202 coronavirus infectious bronchitis virus in cultured cells