Development of a Vaccine against SARS-CoV-2 Based on the Receptor-Binding Domain Displayed on Virus-Like Particles

The ongoing coronavirus disease (COVID-19) pandemic is caused by a new coronavirus (severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2)) first reported in Wuhan City, China. From there, it has been rapidly spreading to many cities inside and outside China. Nowadays, more than 110 million cases with deaths surpassing 2 million have been recorded worldwide, thus representing a major health and economic issues. Rapid development of a protective vaccine against COVID-19 is therefore of paramount importance. Here, we demonstrated that the recombinantly expressed receptor-binding domain (RBD) of the spike protein can be coupled to immunologically optimized virus-like particles derived from cucumber mosaic virus (CuMVTT). The RBD displayed CuMVTT bound to ACE2, the viral receptor, demonstrating proper folding of RBD. Furthermore, a highly repetitive display of the RBD on CuMVTT resulted in a vaccine candidate that induced high levels of specific antibodies in mice, which were able to block binding of the spike protein to ACE2 and potently neutralize SARS-CoV-2 virus in vitro.

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Development of a COVID-19 vaccine based on the receptor binding domain displayed on virus-like particles

10.1101/2020.05.06.079830 ◽

2020 ◽

Cited By ~ 6

Author(s):

Lisha Zha ◽

Hongxin Zhao ◽

Mona O. Mohsen ◽

Liang Hong ◽

Yuhang Zhou ◽

...

Keyword(s):

Receptor Binding ◽

Vaccine Candidate ◽

Rapid Development ◽

Binding Domain ◽

Spike Protein ◽

Receptor Binding Domain ◽

Viral Receptor ◽

Virus Like Particles ◽

The City

AbstractThe recently ermerging disease COVID-19 is caused by the new SARS-CoV-2 virus first detected in the city of Wuhan, China. From there it has been rapidly spreading inside and outside China. With initial death rates around 4%, COVID-19 patients at longer distances from Wuhan showed reduced mortality as was previously observed for the SARS coronavirus. However, the new coronavirus spreads more strongly, as it sheds long before onset of symptoms or may be transmitted by people without symptoms. Rapid development of a protective vaccine against COVID-19 is therefore of paramount importance. Here we demonstrate that recombinantly expressed receptor binding domain (RBD) of the spike protein homologous to SARS binds to ACE2, the viral receptor. Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus resulted in a vaccine candidate (RBD-CuMVTT) that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized the SARS-CoV-2 virus in vitro.

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Stereotypic neutralizing VH antibodies against SARS-CoV-2 spike protein receptor binding domain in COVID-19 patients and healthy individuals

Science Translational Medicine ◽

10.1126/scitranslmed.abd6990 ◽

2021 ◽

pp. eabd6990

Author(s):

Sang Il Kim ◽

Jinsung Noh ◽

Sujeong Kim ◽

Younggeun Choi ◽

Duck Kyun Yoo ◽

...

Keyword(s):

B Cells ◽

Receptor Binding ◽

Neutralizing Antibodies ◽

De Novo ◽

Binding Domain ◽

Host Cells ◽

Spike Protein ◽

Receptor Binding Domain ◽

Healthy Individuals

Stereotypic antibody clonotypes exist in healthy individuals and may provide protective immunity against viral infections by neutralization. We observed that 13 out of 17 patients with COVID-19 had stereotypic variable heavy chain (VH) antibody clonotypes directed against the receptor-binding domain (RBD) of SARS-CoV-2 spike protein. These antibody clonotypes were comprised of immunoglobulin heavy variable (IGHV)3-53 or IGHV3-66 and immunoglobulin heavy joining (IGHJ)6 genes. These clonotypes included IgM, IgG3, IgG1, IgA1, IgG2, and IgA2 subtypes and had minimal somatic mutations, which suggested swift class switching after SARS-CoV-2 infection. The different immunoglobulin heavy variable chains were paired with diverse light chains resulting in binding to the RBD of SARS-CoV-2 spike protein. Human antibodies specific for the RBD can neutralize SARS-CoV-2 by inhibiting entry into host cells. We observed that one of these stereotypic neutralizing antibodies could inhibit viral replication in vitro using a clinical isolate of SARS-CoV-2. We also found that these VH clonotypes existed in six out of 10 healthy individuals, with IgM isotypes predominating. These findings suggest that stereotypic clonotypes can develop de novo from naïve B cells and not from memory B cells established from prior exposure to similar viruses. The expeditious and stereotypic expansion of these clonotypes may have occurred in patients infected with SARS-CoV-2 because they were already present.

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Heteromerization As a Mechanism Modulating the Affinity of the ACE2 Receptor to the Receptor Binding Domain of SARS-CoV-2 Spike Protein

Current Proteomics ◽

10.2174/1570164618999201216112244 ◽

2020 ◽

Vol 18 ◽

Author(s):

Diego Guidolin ◽

Cinzia Tortorella ◽

Deanna Anderlini ◽

Manuela Marcoli ◽

Guido Maura

Keyword(s):

Receptor Binding ◽

Binding Domain ◽

G Protein Coupled Receptors ◽

Spike Protein ◽

Macromolecular Complex ◽

Receptor Binding Domain ◽

Viral Receptor ◽

Angiotensin Converting Enzyme 2 ◽

Quaternary Structures ◽

G Protein Coupled

Background: Angiotensin Converting Enzyme 2 (ACE2) is primarily involved in the maturation of angiotensin. It also represents the main receptor for the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) that caused the serious epidemics COVID-19. Available evidence indicates that at the cell membrane ACE2 can form heteromeric complexes with other membrane proteins, including the amino acid transporter B0AT1 and G Protein-Coupled Receptors (GPCR). Objective: It is well known that during the formation of quaternary structures, the configuration of each single monomer is re-shaped by its interaction pattern in the macromolecular complex. Therefore, it can be hypothesized that the affinity of ACE2 to the viral receptor binding domain (RBD), when in a heteromeric complex, may depend on the associated partner. Method: By using established docking and molecular dynamics procedures, the reshaping of monomer was explored in silico to predict possible heterodimeric structures between ACE2 and GPCR, such as angiotensin and bradykinin receptors. The associated possible changes in binding affinity between the viral RBD and ACE2 when in the heteromeric complexes were also estimated. Results and Conclusion: The results provided support to the hypothesis that the heteromerization state of ACE2 may modulate its affinity to the viral RBD. If experimentally confirmed, ACE2 heteromerization may contribute to explain the observed differences in susceptibility to virus infection among individuals and to devise new therapeutic opportunities.

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SARS-CoV-2 Prion-Like Domains in Spike Proteins Enables Higher Affinity to ACE2

10.20944/preprints202003.0422.v1 ◽

2020 ◽

Author(s):

George Tetz ◽

Victor Tetz

Keyword(s):

Receptor Binding ◽

Cell Receptor ◽

Binding Domain ◽

Spike Protein ◽

Striking Difference ◽

Receptor Binding Domain ◽

Viral Receptor ◽

Functional Roles ◽

Binding Domains ◽

Spike Proteins

Currently, the world is struggling with the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Prion-like domains are critical for virulence and the development of therapeutic targets; however, the prion-like domains in the SARS-CoV-2 proteome have not been analyzed. In this in silico study, using the PLAAC algorithm, we identified the presence of prion-like domains in SARS-CoV-2 spike protein. Compared with other viruses, a striking difference was observed in the distribution of prion-like domains in the spike, since SARS-CoV-2 was the only coronavirus with a prion-like domain found in the receptor-binding domain of the S1 region of the spike protein. The presence and unique distribution of prion-like domains in the SARS-CoV-2 receptor-binding domains of spike proteins is particularly interesting, since although SARS-CoV-2 and SARS-CoV S share the same host cell receptor, angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 demonstrates a 10- to 20-fold higher affinity for ACE2. Finally, we identified prion-like domains in the α1 helix of the ACE2 receptor that interacts with the viral receptor-binding domain of SARS-CoV-2. Taken together, the present findings indicate that the identified PrDs in the SARS-CoV-2 receptor-binding domain (RBD) and ACE2 region that interacts with RBD have important functional roles in viral adhesion and entry.

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A Drug Repurposing Approach for Antimalarials Interfering with SARS-CoV-2 Spike Protein Receptor Binding Domain (RBD) and Human Angiotensin-Converting Enzyme 2 (ACE2)

Pharmaceuticals ◽

10.3390/ph14100954 ◽

2021 ◽

Vol 14 (10) ◽

pp. 954

Author(s):

Paolo Coghi ◽

Li Jun Yang ◽

Jerome P. L. Ng ◽

Richard K. Haynes ◽

Maurizio Memo ◽

...

Keyword(s):

Angiotensin Converting Enzyme ◽

Receptor Binding ◽

Cell Invasion ◽

Binding Domain ◽

Spike Protein ◽

Interaction Patterns ◽

Receptor Binding Domain ◽

Converting Enzyme ◽

Angiotensin Converting Enzyme 2

Host cell invasion by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is mediated by the interaction of the viral spike protein (S) with human angiotensin-converting enzyme 2 (ACE2) through the receptor-binding domain (RBD). In this work, computational and experimental techniques were combined to screen antimalarial compounds from different chemical classes, with the aim of identifying small molecules interfering with the RBD-ACE2 interaction and, consequently, with cell invasion. Docking studies showed that the compounds interfere with the same region of the RBD, but different interaction patterns were noted for ACE2. Virtual screening indicated pyronaridine as the most promising RBD and ACE2 ligand, and molecular dynamics simulations confirmed the stability of the predicted complex with the RBD. Bio-layer interferometry showed that artemisone and methylene blue have a strong binding affinity for RBD (KD = 0.363 and 0.226 μM). Pyronaridine also binds RBD and ACE2 in vitro (KD = 56.8 and 51.3 μM). Overall, these three compounds inhibit the binding of RBD to ACE2 in the μM range, supporting the in silico data.

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501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to Bamlanivimab in vitro

10.1101/2021.02.16.431305 ◽

2021 ◽

Author(s):

Haolin Liu ◽

Pengcheng Wei ◽

Qianqian Zhang ◽

Zhongzhou Chen ◽

Katja Aviszus ◽

...

Keyword(s):

South Africa ◽

Binding Affinity ◽

Receptor Binding ◽

Binding Domain ◽

Therapeutic Antibody ◽

Spike Protein ◽

Receptor Binding Domain ◽

Human Receptor

AbstractWe generated several versions of the receptor binding domain (RBD) of the Spike protein with mutations existing within newly emerging variants from South Africa and Brazil. We found that the mutant RBD with K417N, E484K, and N501Y exchanges has higher binding affinity to the human receptor compared to the wildtype RBD. This mutated version of RBD also completely abolishes the binding to a therapeutic antibody, Bamlanivimab, in vitro.

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Rapid Development of SARS-CoV-2 Spike Protein Receptor-Binding Domain Self-Assembled Nanoparticle Vaccine Candidates

ACS Nano ◽

10.1021/acsnano.0c08379 ◽

2021 ◽

Vol 15 (2) ◽

pp. 2738-2752 ◽

Cited By ~ 1

Author(s):

Yin-Feng Kang ◽

Cong Sun ◽

Zhen Zhuang ◽

Run-Yu Yuan ◽

Qingbing Zheng ◽

...

Keyword(s):

Receptor Binding ◽

Rapid Development ◽

Binding Domain ◽

Spike Protein ◽

Receptor Binding Domain ◽

Vaccine Candidates ◽

Protein Receptor ◽

Self Assembled

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Comparison of Clinically Approved Molecules on SARS-CoV-2 Drug Target Proteins: A Molecular Docking Study

10.26434/chemrxiv.12090828.v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Hasan Cubuk ◽

Mehmet Ozbil

Keyword(s):

Drug Design ◽

Receptor Binding ◽

Binding Domain ◽

Spike Protein ◽

Receptor Binding Domain ◽

Molecular Docking Study ◽

Design Studies ◽

Target Proteins ◽

Main Protease

There are numerous drug design studies conducted all over the globe. Most of these studies target the receptor-binding domain of spike protein of SASR-CoV-2, which is known to bind human ACE2 receptor and SARS-CoV-2 main protease, vital for the virus’ replication. However, there might be a third target, human furin protease, which cleaves the virus’ S1-S2 domains taking active role in its entry into the host cell. In this study we docked five clinically used drug molecules, favipiravir, hydroxychloroquine, remdesivir, lopinavir, and ritonavir onto three target proteins, receptor binding domain of SARS-CoV-2 spike protein, SARS-CoV-2 main protease, and human furin protease. Computational results clearly showed that all ligands provided higher binding affinities towards furin protease, except hydroxychloroquine and ritonavir yielding the highest binding affinity. This proves that furin protease might be targeted for drug design studies and must be further explored in vitro and in vivo.

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Sybodies targeting the SARS-CoV-2 receptor-binding domain

10.1101/2020.04.16.045419 ◽

2020 ◽

Cited By ~ 19

Author(s):

Justin D Walter ◽

Cedric A.J. Hutter ◽

Iwan Zimmermann ◽

Marianne Wyss ◽

Pascal Egloff ◽

...

Keyword(s):

Receptor Binding ◽

Therapeutic Potential ◽

Rapid Development ◽

Combinatorial Libraries ◽

Binding Domain ◽

Sequence Information ◽

Receptor Binding Domain ◽

Population Immunity ◽

Novel Coronavirus

The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has resulted in a global health and economic crisis of unprecedented scale. The high transmissibility of SARS-CoV-2, combined with a lack of population immunity and prevalence of severe clinical outcomes, urges the rapid development of effective therapeutic countermeasures. Here, we report the generation of synthetic nanobodies, known as sybodies, against the receptor-binding domain (RBD) of SARS-CoV-2. In an expeditious process taking only twelve working days, sybodies were selected entirely in vitro from three large combinatorial libraries, using ribosome and phage display. We obtained six strongly enriched sybody pools against the isolated RBD and identified 63 unique anti-RBD sybodies which also interact in the context of the full-length SARS-CoV-2 spike ectodomain. Among the selected sybodies, six were found to bind to the viral spike with double-digit nanomolar affinity, and five of these also showed substantial inhibition of RBD interaction with human angiotensin-converting enzyme 2 (ACE2). Additionally, we identified a pair of anti-RBD sybodies that can simultaneously bind to the RBD. It is anticipated that compact binders such as these sybodies could feasibly be developed into an inhalable drug that can be used as a convenient prophylaxis against COVID-19. Moreover, generation of polyvalent antivirals, via fusion of anti-RBD sybodies to additional small binders recognizing secondary epitopes, could enhance the therapeutic potential and guard against escape mutants. We present full sequence information and detailed protocols for the identified sybodies, as a freely accessible resource.

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Human Surfactant Protein D Binds S1 and Receptor Binding Domain of Spike protein and acts as an entry inhibitor of SARS-CoV-2 Pseudotyped viral particles in vitro

10.1101/2020.12.18.423418 ◽

2020 ◽

Author(s):

Miao-Hsi Hsieh ◽

Nazar beirag ◽

Valarmathy Murugaiah ◽

Yu-Chi Chou ◽

Wen-Shuo Kuo ◽

...

Keyword(s):

Receptor Binding ◽

Protective Role ◽

Binding Domain ◽

Spike Protein ◽

Entry Inhibitor ◽

Surfactant Protein D ◽

Receptor Binding Domain ◽

Immune Molecule

AbstractHuman SP-D is a potent innate immune molecule whose presence at pulmonary mucosal surfaces allows immune surveillance role against pulmonary pathogens. Higher levels of serum SP-D have been reported in patients with severe acute respiratory syndrome coronavirus-1 (SARS-CoV). Studies have suggested the ability of human SP-D to recognise spike glycoprotein of SARS-CoV; its interaction with HCoV-229E strain leads to viral inhibition in human bronchial epithelial (16HBE) cells. Previous studies have reported that a recombinant fragment of human SP-D (rfhSP-D) composed of 8 Gly-X-Y repeats, neck and CRD region, can act against a range of viral pathogens including influenza A Virus and Respiratory Syncytial Virus in vitro, in vivo and ex vivo models. In this context, this study was aimed at examining the likely protective role of rfhSP-D against SARS-CoV-2 infection. rfhSP-D showed a dose-responsive binding to S1 spike protein of SARS-CoV-2 and its receptor binding domain. Importantly, rfhSP-D inhibited interaction of S1 protein with the HEK293T cells overexpressing Angiotensin Converting Enzyme 2. The protective role of rfhSP-D against SARS-CoV-2 infection as an entry inhibitor was further validated by the use of pseudotyped lentiviral particles expressing SARS-CoV-2 S1 protein; ~0.5 RLU fold reduction in viral entry was seen following rfhSP-D treatment (10 μg/ml). The results highlight the therapeutic potential of rfhSP-D in SARS-CoV-2 infection and merits pre-clinical studies in murine models.

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