scholarly journals Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

2020 ◽  
Vol 124 (33) ◽  
pp. 7128-7137 ◽  
Author(s):  
Hyeonuk Woo ◽  
Sang-Jun Park ◽  
Yeol Kyo Choi ◽  
Taeyong Park ◽  
Maham Tanveer ◽  
...  
Keyword(s):  
Full Length ◽  
Spike Protein ◽  
Viral Membrane ◽  
Protein Model

scholarly journals Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane

2020 ◽  
Author(s):  
Hyeonuk Woo ◽  
Sang-Jun Park ◽  
Yeol Kyo Choi ◽  
Taeyong Park ◽  
Maham Tanveer ◽  
...  
Keyword(s):  
Modeling And Simulation ◽  
Structure Prediction ◽  
De Novo ◽  
Protein Structures ◽  
Full Length ◽  
Loop Modeling ◽  
S Protein ◽  
Viral Membrane ◽  
Protein Model ◽  
Dynamics Simulations

ABSTRACTThis technical study describes all-atom modeling and simulation of a fully-glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB:6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXY modeling suite. Then, using the recently-determined most occupied glycoforms, 22 N-glycans and 1 O-glycan of each monomer were modeled using Glycan Reader & Modeler in CHARMM-GUI. These fully-glycosylated full-length S protein model structures were assessed and further refined against the low-resolution data in their respective experimental maps using ISOLDE. We then used CHARMM-GUI Membrane Builder to place the S proteins in a viral membrane and performed all-atom molecular dynamics simulations. All structures are available in CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19), so researchers can use these models to carry out innovative and novel modeling and simulation research for the prevention and treatment of COVID-19.

scholarly journals SARS-CoV-2 full length spike protein for COVID-19 vaccine development and diagnostic testing

2021 ◽  
Vol 147 (2) ◽  
pp. AB152
Author(s):  
Crystal Richardson ◽  
Mayuresh Abhyankar ◽  
Jillian Bracaglia ◽  
Sayeh Agah ◽  
Zachary Schuhmacher ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Diagnostic Testing ◽  
Full Length ◽  
Spike Protein

scholarly journals Modified Vaccinia Ankara Based SARS-CoV-2 Vaccine Expressing Full-Length Spike Induces Strong Neutralizing Antibody Response

2020 ◽  
Author(s):  
Nanda Kishore Routhu ◽  
Sailaja Gangadhara ◽  
Narayanaiah Cheedarla ◽  
Ayalnesh Shiferaw ◽  
Sheikh Abdul Rahman ◽  
...  
Keyword(s):  
Antibody Response ◽  
Room Temperature ◽  
Vaccine Candidate ◽  
Neutralizing Antibody ◽  
Antibody Responses ◽  
Full Length ◽  
Spike Protein ◽  
Strongly Correlated ◽  
Igg Antibodies ◽  
Potential Vaccine

AbstractThere is a great need for the development of vaccines for preventing SARS-CoV-2 infection and mitigating the COVID-19 pandemic. Here, we developed two modified vaccinia Ankara (MVA) based vaccines which express either a membrane anchored full-length spike protein (MVA/S) stabilized in a prefusion state or the S1 region of the spike (MVA/S1) which forms trimers and is secreted. Both immunogens contained the receptor-binding domain (RBD) which is a known target of antibody-mediated neutralization. Following immunizations with MVA/S or MVA/S1, both spike protein recombinants induced strong IgG antibodies to purified full-length SARS-CoV-2 spike protein. The MVA/S induced a robust antibody response to purified RBD, S1 and S2 whereas MVA/S1 induced an antibody response to the S1 region outside of the RBD region. Both vaccines induced an antibody response in the lung and that was associated with induction of bronchus-associated lymphoid tissue. MVA/S but not MVA/S1 vaccinated mice generated robust neutralizing antibody responses against SARS-CoV-2 that strongly correlated with RBD antibody binding titers. Mechanistically, S1 binding to ACE-2 was strong but reduced following prolonged pre-incubation at room temperature suggesting confirmation changes in RBD with time. These results demonstrate MVA/S is a potential vaccine candidate against SARS-CoV-2 infection.

scholarly journals Rapid, high-yield production of full-length SARS-CoV-2 spike ectodomain by transient gene expression in CHO cells

2020 ◽  
Author(s):  
Matthew Stuible ◽  
Christian Gervais ◽  
Simon Lord-Dufour ◽  
Sylvie Perret ◽  
Denis L’Abbe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mammalian Cells ◽  
Affinity Purification ◽  
Transient Gene Expression ◽  
Full Length ◽  
Spike Protein ◽  
Hek293 Cells ◽  
High Yield ◽  
Diagnostic Tools ◽  
Purification Method

ABSTRACTRecombinant forms of the spike protein of SARS-CoV-2 and related viruses have proven difficult to produce with good yields in mammalian cells. Given the panoply of potential COVID-19 diagnostic tools and therapeutic candidates that require purified spike protein and its importance for ongoing SARS-CoV-2 research, we have explored new approaches for spike production and purification. Three transient gene expression methods based on PEI-mediated transfection of CHO or HEK293 cells in suspension culture in chemically-defined media were compared for rapid production of full-length SARS-CoV-2 ectodomain. A high-cell-density protocol using DXB11-derived CHOBRI/rcTA cells gave substantially better yields than the other methods. Different forms of the spike were expressed, including the wild-type SARS-CoV-2 sequence and a mutated/stabilized form (to favor expression of the full-length spike in prefusion conformation), with and without fusion to putative trimerization domains. An efficient two-step affinity purification method was also developed. Ultimately, we have been able to produce highly homogenous preparations of full-length spike, both monomeric and trimeric, with yields of 100-150 mg/L. The speed and productivity of this method support further development of CHO-based approaches for recombinant spike protein manufacturing.

scholarly journals Enoxaparin and Pentosan Polysulfate Bind to the SARS-CoV-2 Spike Protein and Human ACE2 Receptor, Inhibiting Vero Cell Infection

Biomedicines ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 49
Author(s):  
Maria Ennemoser ◽  
Julia Rieger ◽  
Eva Muttenthaler ◽  
Tanja Gerlza ◽  
Kurt Zatloukal ◽  
...  
Keyword(s):  
Heparan Sulfate ◽  
Viral Transmission ◽  
Full Length ◽  
Spike Protein ◽  
Target Cells ◽  
Pentosan Polysulfate ◽  
Cell Infection ◽  
Virus Surface ◽  
Kd Values

As with many other pathogens, SARS-CoV-2 cell infection is strongly dependent on the interaction of the virus-surface Spike protein with the glycosaminoglycans of target cells. The SARS-CoV-2 Spike glycoprotein was previously shown to interact with cell-surface-exposed heparan sulfate and heparin in vitro. With the aim of using Enoxaparin as a treatment for COVID-19 patients and as prophylaxis to prevent interpersonal viral transmission, we investigated GAG binding to the Spike full-length protein, as well as to its receptor binding domain (RBD) in solution by isothermal fluorescence titration. We found that Enoxaparin bound to both protein variants with similar affinities, compared to the natural GAG ligand heparan sulfate (with Kd-values in the range of 600–680 nM). Using size-defined Enoxaparin fragments, we discovered the optimum binding for dp6 or dp8 for the full-length Spike protein, whereas the RBD did not exhibit a significant chain-length-dependent affinity for heparin oligosaccharides. The soluble ACE2 receptor was found to interact with unfractionated GAGs in the low µM Kd range, but with size-defined heparins with clearly sub-µM Kd-values. Interestingly, the structural heparin analogue, pentosan polysulfate (PPS), exhibited high binding affinities to both Spike variants as well as to the ACE2 receptor. In viral infection experiments, Enoxaparin and PPS both showed a strong inhibition of infection in a concentration range of 50–500 µg/mL. Both compounds were found to retain their inhibitory effects at 500 µg/mL in a natural biomatrix-like human sputum. Our data suggest the early topical treatment of SARS-CoV-2 infections with inhaled Enoxaparin; some clinical studies in this direction are already ongoing, and they further imply an oral or nasal prophylactic inactivation of the virus by Enoxaparin or PPS for the prevention of inter-personal viral transmission.

scholarly journals Cost-effective serological test to determine exposure to SARS-CoV-2: ELISA based on the receptor-binding domain of the spike protein (Spike-RBDN318-V510) expressed in Escherichia coli

2020 ◽  
Author(s):  
Alan Roberto Marquez-Ipiña ◽  
Everardo Gonzalez-Gonzalez ◽  
Iram Pablo Rodriguez-Sanchez ◽  
Itzel Montserrat Lara-Mayorga ◽  
Luis Alberto Mejia-Manzano ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Serological Test ◽  
Cost Effective ◽  
Binding Domain ◽  
Full Length ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Cost Effective Alternative ◽  
Virus Exposure ◽  
Straightforward Approach

Massive worldwide serological testing for SARS-CoV-2 is needed to determine the extent of virus exposure in a particular region, the ratio of symptomatic to asymptomatic infected persons, and the duration and extent of immunity after infection. To achieve this aim, the development and production of reliable and cost-effective SARS-CoV-2 antigens is critical. Here, we report the bacterial production of the peptide S-RBDN318-V510, which contains the receptor binding domain of the SARS-CoV-2 spike protein. We purified this peptide using a straightforward approach involving bacterial lysis, his-tag mediated affinity chromatography, and imidazole-assisted refolding. The antigen performances of S RBDN318 V510 and a commercial full-length spike protein were compared in two distinct ELISAs. In direct ELISAs, where the antigen was directly bound to the ELISA surface, both antigens discriminated sera from non-exposed and exposed individuals. However, the discriminating resolution was better in ELISAs that used the full-spike antigen than the S-RBDN318-V510. Attachment of the antigens to the ELISA surface using a layer of anti-histidine antibodies gave equivalent resolution for both S-RBDN318-V510 and the full length spike protein. Our results demonstrate that ELISA-functional SARS-CoV-2 antigens can be produced in bacterial cultures. S-RBDN318-V510 is amenable to massive production and may represent a cost-effective alternative to the use of structurally more complex antigens in serological COVID-19 testing.

Structure, Dynamics, Receptor Binding, and Antibody Binding of Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane

2020 ◽  
Author(s):  
Yeol Kyo Choi ◽  
Yiwei Cao ◽  
Martin Frank ◽  
Hyeonuk Woo ◽  
Sang-Jun Park ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Vaccine Development ◽  
Accessible Surface Area ◽  
Full Length ◽  
S Protein ◽  
Viral Membrane ◽  
Accessible Surface ◽  
Dynamics Simulations ◽  
The Impact ◽  
Insight Into

ABSTRACTThe spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates host cell entry by binding to angiotensin-converting enzyme 2 (ACE2), and is considered the major target for drug and vaccine development. We previously built fully-glycosylated full-length SARS-CoV-2 S protein models in a viral membrane including both open and closed conformations of receptor binding domain (RBD) and different templates for the stalk region. In this work, multiple μs-long all-atom molecular dynamics simulations were performed to provide deeper insight into the structure and dynamics of S protein, and glycan functions. Our simulations reveal that the highly flexible stalk is composed of two independent joints and most probable S protein orientations are competent for ACE2 binding. We identify multiple glycans stabilizing the open and/or closed states of RBD, and demonstrate that the exposure of antibody epitopes can be captured by detailed antibody-glycan clash analysis instead of a commonly-used accessible surface area analysis that tends to overestimate the impact of glycan shielding and neglect possible detailed interactions between glycan and antibody. Overall, our observations offer structural and dynamic insight into SARS-CoV-2 S protein and potentialize for guiding the design of effective antiviral therapeutics.

scholarly journals Phage display of functional, full-length human and viral membrane proteins

2008 ◽  
Vol 18 (22) ◽  
pp. 5937-5940 ◽  
Author(s):  
Sudipta Majumdar ◽  
Agnes Hajduczki ◽  
Aaron S. Mendez ◽  
Gregory A. Weiss
Keyword(s):  
Membrane Proteins ◽  
Phage Display ◽  
Full Length ◽  
Viral Membrane
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