scholarly journals A thermostable, closed, SARS-CoV-2 spike protein trimer

2020 ◽  
Author(s):  
Xiaoli Xiong ◽  
Kun Qu ◽  
Katarzyna A. Ciazynska ◽  
Myra Hosmillo ◽  
Andrew P. Carter ◽  
...  
Keyword(s):  
Immune System ◽  
Receptor Binding ◽  
Conformational Flexibility ◽  
Cell Entry ◽  
Spike Protein ◽  
Receptor Binding Site ◽  
S Protein ◽  
Vaccine Candidates ◽  
Diagnostic Assays ◽  
Potential Applications

AbstractThe spike (S) protein of SARS-CoV-2 mediates receptor binding and cell entry and is the dominant target of the immune system. S exhibits substantial conformational flexibility. It transitions from closed to open conformations to expose its receptor binding site, and subsequently from prefusion to postfusion conformations to mediate fusion of viral and cellular membranes. S protein derivatives are components of vaccine candidates and diagnostic assays, as well as tools for research into the biology and immunology of SARS-CoV-2. Here we have designed mutations in S which allow production of thermostable, crosslinked, S protein trimers that are trapped in the closed, pre-fusion, state. We have determined the structures of crosslinked and non-crosslinked proteins, identifying two distinct closed conformations of the S trimer. We demonstrate that the designed, thermostable, closed S trimer can be used in serological assays. This protein has potential applications as a reagent for serology, virology and as an immunogen.

scholarly journals SARS-CoV-2 spike protein arrested in the closed state induces potent neutralizing responses

2021 ◽  
Author(s):  
George W. Carnell ◽  
Katarzyna A. Ciazynska ◽  
David A. Wells ◽  
Xiaoli Xiong ◽  
Ernest T. Aguinam ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Neutralizing Antibody ◽  
Protein S ◽  
Spike Protein ◽  
Receptor Binding Site ◽  
S Protein ◽  
Closed State ◽  
S Proteins ◽  
Protein Constructs

AbstractThe majority of SARS-CoV-2 vaccines in use or in advanced clinical development are based on the viral spike protein (S) as their immunogen. S is present on virions as pre-fusion trimers in which the receptor binding domain (RBD) is stochastically open or closed. Neutralizing antibodies have been described that act against both open and closed conformations. The long-term success of vaccination strategies will depend upon inducing antibodies that provide long-lasting broad immunity against evolving, circulating SARS-CoV-2 strains, while avoiding the risk of antibody dependent enhancement as observed with other Coronavirus vaccines. Here we have assessed the results of immunization in a mouse model using an S protein trimer that is arrested in the closed state to prevent exposure of the receptor binding site and therefore interaction with the receptor. We compared this with a range of other modified S protein constructs, including representatives used in current vaccines. We found that all trimeric S proteins induce a long-lived, strongly neutralizing antibody response as well as T-cell responses. Notably, the protein binding properties of sera induced by the closed spike differed from those induced by standard S protein constructs. Closed S proteins induced more potent neutralising responses than expected based on the degree to which they inhibit interactions between the RBD and ACE2. These observations suggest that closed spikes recruit different, but equally potent, virus-inhibiting immune responses than open spikes, and that this is likely to include neutralizing antibodies against conformational epitopes present in the closed conformation. Together with their improved stability and storage properties we suggest that closed spikes may be a valuable component of refined, next-generation vaccines.

Molecular Mechanics Investigation on Conformational Flexibility of 14β Steroids in Drug-Receptor Interactions

1986 ◽  
Vol 41 (3) ◽  
pp. 297-300 ◽  
Author(s):  
Martin Bohl ◽  
Manfred Wunderwald
Keyword(s):  
Atpase Activity ◽  
Molecular Mechanics ◽  
Receptor Binding ◽  
Conformational Changes ◽  
Conformational Flexibility ◽  
Receptor Binding Site ◽  
Receptor Interactions ◽  
Drug Receptor ◽  
Potential Inhibitors ◽  
Steroid Structure

The interaction between two 14 β steroids being still unsynthesized and a model receptor binding site is theoretically studied by a molecular mechanics scheme. Both com pounds containing seven-membered rings in the 17 β position are found to form stable hydrogen bonds to the receptor and can be attributed to be potential inhibitors of the Na +,K + -ATPase activity. Substantial steroid conformational changes necessary for an efficient receptor binding are calculated to reduce the interaction energy by only 10 kJ mol -1. Therefore, alterations in steroid structure should be generally taken into consideration in the investigation of steroid-receptor interactions.

scholarly journals Mutations in Spike Protein of SARS-CoV-2 Modulate Receptor Binding, Membrane Fusion and Immunogenicity: An Insight into Viral Tropism and Pathogenesis of COVID-19

2020 ◽  
Author(s):  
Dr. Priyanka Saha ◽  
Ranabir Majumder ◽  
sourabrata chakraborty ◽  
Amit Kumar Srivastava ◽  
Mahitosh Mandal ◽  
...  
Keyword(s):  
Host Cell ◽  
Cell Entry ◽  
Spike Protein ◽  
Antigenic Determinants ◽  
Chimeric Antibody ◽  
Radius Of Gyration ◽  
S Protein ◽  
Viral Tropism ◽  
Host Cell Entry ◽  
High Degree

<p>SARS-CoV-2 uses RBD of Spike (S) protein to attach with human cell via ACE2 receptor, followed by protease priming at S1/S2 site resulted in host cell entry and pathogenesis. In this context, we focused our aim in studying natural mutations harboring in Spike protein of SARS-CoV-2. We have analyzed 420 COVID-19 cases. G476S and V483G mutation are observed which lies in the RBD region where as the prevalent D614G mutation is observed in the vicinity of S1/S2 site. Interestingly MD simulation supports strong favorable interaction of ACE2 with RBD region containing V483A mutation as compared to G476S and reference wild Wuhan S protein. Radius of gyration analysis also showed high degree of compactness in V483A. The landscape plot and Gibbs free energy also support our findings. Overall, our study indicates that V483G in the RBD region can enhance its binding with the human ACE2 receptor. Interestingly D614G mutation in vicinity of S1/S2 region introduced a new cleavage site specific for a serine protease elastase that is anticipated to broaden the virus host cell tropism. Hence, both V483A and D614G mutations led to enhanced and broaden the virus host cell entry and transmission of the disease. Further epitope mapping analysis revealed G476S and D614G mutations as antigenic determinants and thus these mutations are important while designing a therapeutics vaccine or chimeric antibody. This finding will help in further understanding the role of such arising mutations in modulating immunogenicity, viral tropism and pathogenesis of the disease, which in lieu will help in designing vaccine more precisely to mitigate pandemic COVID-19. </p> <p> </p>

scholarly journals Mutations in the Spike Protein of Middle East Respiratory Syndrome Coronavirus Transmitted in Korea Increase Resistance to Antibody-Mediated Neutralization

2018 ◽  
Vol 93 (2) ◽  
Author(s):  
Hannah Kleine-Weber ◽  
Mahmoud Tarek Elzayat ◽  
Lingshu Wang ◽  
Barney S. Graham ◽  
Marcel A. Müller ◽  
...  
Keyword(s):  
Middle East ◽  
Protein Binding ◽  
Receptor Binding ◽  
Viral Entry ◽  
Middle East Respiratory Syndrome ◽  
Spike Protein ◽  
Target Cells ◽  
S Protein ◽  
Hospital Outbreak ◽  
The Republic

ABSTRACT Middle East respiratory syndrome coronavirus (MERS-CoV) poses a threat to public health. The virus is endemic in the Middle East but can be transmitted to other countries by travel activity. The introduction of MERS-CoV into the Republic of Korea by an infected traveler resulted in a hospital outbreak of MERS that entailed 186 cases and 38 deaths. The MERS-CoV spike (S) protein binds to the cellular protein DPP4 via its receptor binding domain (RBD) and mediates viral entry into target cells. During the MERS outbreak in Korea, emergence and spread of viral variants that harbored mutations in the RBD, D510G and I529T, was observed. Counterintuitively, these mutations were found to reduce DPP4 binding and viral entry into target cells. In this study, we investigated whether they also exerted proviral effects. We confirm that changes D510G and I529T reduce S protein binding to DPP4 but show that this reduction only translates into diminished viral entry when expression of DPP4 on target cells is low. Neither mutation modulated S protein binding to sialic acids, S protein activation by host cell proteases, or inhibition of S protein-driven entry by interferon-induced transmembrane proteins. In contrast, changes D510G and I529T increased resistance of S protein-driven entry to neutralization by monoclonal antibodies and sera from MERS patients. These findings indicate that MERS-CoV variants with reduced neutralization sensitivity were transmitted during the Korean outbreak and that the responsible mutations were compatible with robust infection of cells expressing high levels of DPP4. IMPORTANCE MERS-CoV has pandemic potential, and it is important to identify mutations in viral proteins that might augment viral spread. In the course of a large hospital outbreak of MERS in the Republic of Korea in 2015, the spread of a viral variant that contained mutations in the viral spike protein was observed. These mutations were found to reduce receptor binding and viral infectivity. However, it remained unclear whether they also exerted proviral effects. We demonstrate that these mutations reduce sensitivity to antibody-mediated neutralization and are compatible with robust infection of target cells expressing large amounts of the viral receptor DPP4.

scholarly journals A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 724
Author(s):  
Paola Cristina Resende ◽  
Tiago Gräf ◽  
Anna Carolina Dias Paixão ◽  
Luciana Appolinario ◽  
Renata Serrano Lopes ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Receptor Binding ◽  
Binding Domain ◽  
The Other ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
S Protein ◽  
Other Hand

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in Brazil was dominated by two lineages designated as B.1.1.28 and B.1.1.33. The two SARS-CoV-2 variants harboring mutations at the receptor-binding domain of the Spike (S) protein, designated as lineages P.1 and P.2, evolved from lineage B.1.1.28 and are rapidly spreading in Brazil. Lineage P.1 is considered a Variant of Concern (VOC) because of the presence of multiple mutations in the S protein (including K417T, E484K, N501Y), while lineage P.2 only harbors mutation S:E484K and is considered a Variant of Interest (VOI). On the other hand, epidemiologically relevant B.1.1.33 deriving lineages have not been described so far. Here we report the identification of a new SARS-CoV-2 VOI within lineage B.1.1.33 that also harbors mutation S:E484K and was detected in Brazil between November 2020 and February 2021. This VOI displayed four non-synonymous lineage-defining mutations (NSP3:A1711V, NSP6:F36L, S:E484K, and NS7b:E33A) and was designated as lineage N.9. The VOI N.9 probably emerged in August 2020 and has spread across different Brazilian states from the Southeast, South, North, and Northeast regions.

scholarly journals A potential SARS-CoV-2 variant of interest (VOI) harboring mutation E484K in the Spike protein was identified within lineage B.1.1.33 circulating in Brazil

2021 ◽  
Author(s):  
Paola Cristina Resende ◽  
Tiago Gräf ◽  
Anna Carolina Dias Paixão ◽  
Luciana Appolinario ◽  
Renata Serrano Lopes ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Binding Domain ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
S Protein

SummaryThe SARS-CoV-2 epidemic in Brazil was dominated by two lineages designated as B.1.1.28 and B.1.1.33. Two SARS-CoV-2 variants harboring mutations at the receptor-binding domain of the Spike (S) protein, designated as lineages P.1 and P.2, evolved within lineage B.1.1.28 and are rapidly spreading in Brazil. Lineage P.1 is considered a Variant of Concern (VOC) because of the presence of multiple mutations in the S protein (including K417T, E484K, N501Y), while lineage P.2 only harbors mutation S:E484K and is considered a Variant of Interest (VOI). Here we report the identification of a new SARS-CoV-2 VOI within lineage B.1.1.33 that also harbors mutation S:E484K and was detected in Brazil between November 2020 and February 2021. This VOI displayed four non-synonymous lineage-defining mutations (NSP3:A1711V, NSP6:F36L, S:E484K, and NS7b:E33A) and was designated as lineage N.9. The VOI N.9 probably emerged in August 2020 and has spread across different Brazilian states from the Southeast, South, North and Northeast regions.

scholarly journals Neutralization of N501Y mutant SARS-CoV-2 by BNT162b2 vaccine-elicited sera

2021 ◽  
Author(s):  
Pei-Yong Shi ◽  
Xuping Xie ◽  
Jing Zou ◽  
Camila Fontes-Garfias ◽  
Hongjie Xia ◽  
...  
Keyword(s):  
South Africa ◽  
United Kingdom ◽  
Binding Site ◽  
Receptor Binding ◽  
Cell Entry ◽  
Receptor Binding Site ◽  
Viral Receptor ◽  
The United Kingdom ◽  
Human Sera

Abstract Rapidly spreading variants of SARS-CoV-2 that have arisen in the United Kingdom and South Africa share the spike N501Y substitution, which is of particular concern because it is located in the viral receptor binding site for cell entry and increases binding to the receptor. We generated isogenic N501 and Y501 SARS-CoV-2. Twenty human sera from the mRNA-based vaccine BNT162b2 trial exhibited equivalent neutralizing titers to the N501 and Y501 viruses.

scholarly journals Cell entry mechanisms of SARS-CoV-2

2020 ◽  
Vol 117 (21) ◽  
pp. 11727-11734 ◽  
Author(s):  
Jian Shang ◽  
Yushun Wan ◽  
Chuming Luo ◽  
Gang Ye ◽  
Qibin Geng ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Receptor Binding ◽  
Immune Surveillance ◽  
Intervention Strategies ◽  
Cell Entry ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Wide Spread ◽  
Virus Surface ◽  
Protease Activation

A novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) is causing the global coronavirus disease 2019 (COVID-19) pandemic. Understanding how SARS-CoV-2 enters human cells is a high priority for deciphering its mystery and curbing its spread. A virus surface spike protein mediates SARS-CoV-2 entry into cells. To fulfill its function, SARS-CoV-2 spike binds to its receptor human ACE2 (hACE2) through its receptor-binding domain (RBD) and is proteolytically activated by human proteases. Here we investigated receptor binding and protease activation of SARS-CoV-2 spike using biochemical and pseudovirus entry assays. Our findings have identified key cell entry mechanisms of SARS-CoV-2. First, SARS-CoV-2 RBD has higher hACE2 binding affinity than SARS-CoV RBD, supporting efficient cell entry. Second, paradoxically, the hACE2 binding affinity of the entire SARS-CoV-2 spike is comparable to or lower than that of SARS-CoV spike, suggesting that SARS-CoV-2 RBD, albeit more potent, is less exposed than SARS-CoV RBD. Third, unlike SARS-CoV, cell entry of SARS-CoV-2 is preactivated by proprotein convertase furin, reducing its dependence on target cell proteases for entry. The high hACE2 binding affinity of the RBD, furin preactivation of the spike, and hidden RBD in the spike potentially allow SARS-CoV-2 to maintain efficient cell entry while evading immune surveillance. These features may contribute to the wide spread of the virus. Successful intervention strategies must target both the potency of SARS-CoV-2 and its evasiveness.

scholarly journals Domains and Functions of Spike Protein in SARS-Cov-2 in the Context of Vaccine Design

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 109
Author(s):  
Xuhua Xia
Keyword(s):  
Membrane Fusion ◽  
Receptor Binding ◽  
Viral Entry ◽  
Vaccine Development ◽  
Cell Entry ◽  
Spike Protein ◽  
Structural Domains ◽  
Theoretical Approaches ◽  
A Cell ◽  
And Function

The spike protein in SARS-CoV-2 (SARS-2-S) interacts with the human ACE2 receptor to gain entry into a cell to initiate infection. Both Pfizer/BioNTech’s BNT162b2 and Moderna’s mRNA-1273 vaccine candidates are based on stabilized mRNA encoding prefusion SARS-2-S that can be produced after the mRNA is delivered into the human cell and translated. SARS-2-S is cleaved into S1 and S2 subunits, with S1 serving the function of receptor-binding and S2 serving the function of membrane fusion. Here, I dissect in detail the various domains of SARS-2-S and their functions discovered through a variety of different experimental and theoretical approaches to build a foundation for a comprehensive mechanistic understanding of how SARS-2-S works to achieve its function of mediating cell entry and subsequent cell-to-cell transmission. The integration of structure and function of SARS-2-S in this review should enhance our understanding of the dynamic processes involving receptor binding, multiple cleavage events, membrane fusion, viral entry, as well as the emergence of new viral variants. I highlighted the relevance of structural domains and dynamics to vaccine development, and discussed reasons for the spike protein to be frequently featured in the conspiracy theory claiming that SARS-CoV-2 is artificially created.

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