Trimeric receptor-binding domain of SARS-CoV-2 acts as a potent inhibitor of ACE2 receptor-mediated viral entry

Basavarajappa, Shrikanth C.; Liu, Angela Rose; Bruchez, Anna; Li, Zhenlu; Suzart, Vinicius G.; Z, Liu; Chen, Yinghua; Xiao, Tsan Sam; Buck, Matthias; Ramakrishnan, Parameswaran

doi:10.1016/j.isci.2022.104716

Cited by 9 publications

(12 citation statements)

References 54 publications

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“…Based on observations made by researchers at one of the public junior high schools in Yogyakarta, it is known that that this application has not been used, even though this application has advantages that can make students better understand the concept of the existing material [46]- [50]. This is in accordance with several studies using mindfulness that have been carried out where maps are able to improve students' conceptual understanding abilities [51]- [55]. Because of these advantages, the researcher intends to conduct research to determine the analysis of the need for using mind map applications to improve students' conceptual understanding abilities.…”

Section: Introduction Human Development By Humanizing Humanssupporting

confidence: 67%

I Mind Map Application Needs Analysis to Improve Students’ Mathematical Concept Understanding Ability

Pertiwi

Khuzaini

Beneditha³

et al. 2022

JOAW

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The ability to understand concepts is the mastery of the material in which students recognize, know, and are able to re-express concepts in a form that is easier to understand. However, students’ conceptual understanding skills still tend to be low. So it takes teaching materials that integrate these abilities. For this reason, this study aims to analyze the need for teaching materials based on mind map applications to improve students’ conceptual understanding skills. A mind map is a mind map in the form of a diagram that visually describes ideas, concepts, information, or other things. This type of research is descriptive qualitative. The research was conducted in one of the public junior high schools in Yogyakarta. The subjects in this study were 32 students of class IXA. Data collection techniques used interviews, concept understanding ability tests, and preliminary study questionnaires. While the data analysis technique uses the Miles and Huberman model which consists of data collection, data reduction, data presentation, and drawing conclusions. The results showed that teachers had not implemented mind map-assisted learning, students’ conceptual understanding abilities tended to be low, students were interested in learning using mind map applications because students could develop ways of thinking and make them more active during learning

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Section: Introduction Human Development By Humanizing Humanssupporting

confidence: 67%

I Mind Map Application Needs Analysis to Improve Students’ Mathematical Concept Understanding Ability

Pertiwi

Khuzaini

Beneditha³

et al. 2022

JOAW

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“…Studies published early in the pandemic demonstrated that a DNA vaccine containing the RBD along with a trimerization tag was able to elicit a protective immune response in a model of rhesus macaques [50]. It has been shown that trimeric RBD interacts with greater affinity with ACE2 receptor molecules on the cell surface than monomeric RBD [51]. Therefore, production of antibodies that recognize the trimeric structure may be more effective in inhibiting this binding.…”

Section: Discussionmentioning

confidence: 99%

“…Neutralizing antibodies are known to target the receptor-binding domain, which is 90% neutralizing in convalescent sera [49], supporting the use of RBD as an antigen for vaccines. Studies published early in the pandemic demonstrated that a DNA vaccine containing the RBD along with a trimerization tag was able to elicit a protective immune response in a model of rhesus macaques [50]. It has been shown that trimeric RBD interacts with greater affinity with ACE2 receptor molecules on the cell surface than monomeric RBD [51].…”

Section: Discussionmentioning

confidence: 99%

“…For instance, immunization of rhesus macaques with various forms of protein S showed protective humoral and cellular responses, in addition to neutralizing antibody titers (J. Yu et al, 2020). Today, there are more than 400 preparations in clinical development and preclinical development (https://www.who.int/publications/m/item/draft-landscapeof-covid-19-candidate-vaccines).…”

Section: Introductionmentioning

confidence: 99%

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Development and characterization of a multimeric recombinant protein based on the spike protein receptor binding domain of SARS-CoV-2 that can neutralize virus infection

Lima

Ferreira

Oliva

et al. 2023

Preprint

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Background: The SARS-CoV-2 virus, responsible for the COVID-19 pandemic, has four structural proteins and sixteen non-structural proteins. The S-protein is one of the structural proteins exposed on the surface of the virus and is the main target for producing neutralizing antibodies and vaccines. The S-protein forms a trimer that can bind the angiotensin-converting enzyme 2 (ACE2) through its receptor binding domain (RBD) for cell entry. Methods: We stably expressed in a constitutive manner in HEK293 cells a new recombinant protein containing a signal sequence of immunoglobulin to produce an extended C-terminal portion of the RBD followed by a region responsible for the trimerization inducer of the bacteriophage T4, and a sequence of 6 histidines. The protein was produced and released in the culture supernatant of cells and was purified by Ni-agarose column and exclusion chromatography. It was then characterized by SDS-polyacrylamide gel and used as antigen to generate protective antibodies to inhibit ACE2 receptor interaction and virus entry into Vero cells. Results: The purified protein displayed a molecular mass of 135 kDa and with a secondary structure like the monomeric RBD. Electrophoresis analysis in SDS-polyacrylamide gel with and without reducing agents, and in the presence of crosslinkers indicated that it forms a multimeric structure composed of trimers and hexamers. The purified protein was able to bind the ACE2 receptor and generated high antibody titers in mice (1:10000), capable of inhibiting the binding of biotin labeled ACE2 to the virus S1 subunit, and to neutralize the entry of the SARS-CoV-2 Wuhan strain into cells. Conclusion: Our results characterize a new multimeric protein based on S1 subunit to combat COVID-19, as a possible immunogen or antigen for diagnosis.

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“…Each S protein protomer is composed of two functional subunits; the S1 subunit is responsible for binding to the host receptor and contains an N-terminal domain (NTD) and a receptor-binding domain (RBD); the S2 subunit is responsible for facilitating viral cell membrane fusion through the membrane fusion machinery . Binding of the trimeric S protein onto ACE2 only occurs when at least one RBD of the S1 subunit from the trimer is elevated and rotated away from the S2 subunit to expose its receptor-binding surface. , Figure a displays a 3D structure of an RBD protein that resembles an outward-facing human body, along with nomenclatures of the protein regions for parts of the body. Inhibitors that target S glycoproteins typically prevent virus–membrane fusion by interfering with the interaction between RBD and ACE2 (see Figure b) as analogous to the body carrying an object on the shoulder …”

Section: Introductionmentioning

confidence: 99%

Allosteric Signal within the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein Mediated by a Class 3 Monoclonal Antibody Revealed through Molecular Dynamics Simulations and Protein Residue Networks

Boonserm,

Somsoros,

Khunrae

et al. 2024

ACS Omega

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This study investigated the allosteric action within the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein caused by class 3 monoclonal antibody (mAb) binding. As the emergence of SARS-CoV-2 variants has raised concerns about the effectiveness of treatments by antibodies, targeting the highly conserved class 3 epitopes has become an alternative strategy of antibody design. Simulations of explicitly solvated RBD of the BA.2.75 omicron subvariants were carried out both in the presence and in the absence of bebtelovimab, as a model example of class 3 monoclonal antibodies against the RBD of the SARS-CoV-2 spike protein. The comparative analysis showed that bebtelovimab's binding on two α helices at the epitope region disrupted the nearby interaction network, which triggered a denser interaction network formation on the opposite side of the receptor-binding motif (RBM) region and resulted in a "close" conformation that could prevent the ACE2 binding. A better understanding of this allosteric action could lead to the development of alternative mAbs for further variants of concern. In terms of computational techniques, the communicability matrix could serve as a tool to visualize the effects of allostery, as the pairs of amino acids or secondary structures with high communicability could pinpoint the possible sites to transfer the allosteric signal. Additionally, the communicability gain/loss matrix could help elucidate the consequences of allosteric actions, which could be employed along with other allostery quantification techniques in some previous studies.

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Trimeric receptor-binding domain of SARS-CoV-2 acts as a potent inhibitor of ACE2 receptor-mediated viral entry

Cited by 9 publications

References 54 publications

I Mind Map Application Needs Analysis to Improve Students’ Mathematical Concept Understanding Ability

I Mind Map Application Needs Analysis to Improve Students’ Mathematical Concept Understanding Ability

Development and characterization of a multimeric recombinant protein based on the spike protein receptor binding domain of SARS-CoV-2 that can neutralize virus infection

Allosteric Signal within the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein Mediated by a Class 3 Monoclonal Antibody Revealed through Molecular Dynamics Simulations and Protein Residue Networks

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