Discovery of Aptamers Targeting Receptor-Binding Domain of the SARS-CoV-2 Spike Glycoprotein

Song, Yanling; Song, Jia; Wei, Xinyu; Huang, Mengjiao; Sun, Miao; Zhu, Lin; Lin, Bingqianp; Shen, Haicong; Zhu, Zhenbo; Yang, Chaoyong

doi:10.26434/chemrxiv.12053535.v1

Cited by 47 publications

(82 citation statements)

References 35 publications

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“…This charge distribution will create a speci c resistivity of the intrinsic silicon channel. While it has been reported [17] and proven by the response of the TFT sensor that the aptamer binds to the spike protein, what is unknown is the exact binding location of the protein and how the local charge distribution of the protein is arranged. The observed effect could be explained if the presence of the protein were to limit or shield the effect of the charges on the aptamer, while not adding any additional charge contribution of its own.…”

Section: Resultsmentioning

confidence: 99%

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Silicon thin film transistor-based aptamer sensor for COVID-19 detection

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Laumier

Sandall

et al. 2020

Preprint

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Since the beginning of the coronavirus disease 2019 (COVID-19) in December 2019 and the current lack to date of specific drugs or vaccinations to cope with the disease, it has become apparent that the surest way of dealing with this is through early diagnosis and management. Current testing has shown to be unable to rapidly and accurately provide the results required to restrict the spread. Here we report the use of an intrinsic silicon thin film transistor functionalised with aptamers designed to attach to the spike protein of COVID-19. It is shown that a linear response can be obtained in a concentration of 10 fM and 10 pM, and that the relative response is independent of the applied potential allowing a sensory system to fine tune the applied potential to facilitate the interpretation of the results.

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Section: Resultsmentioning

confidence: 99%

“…An aptamer that was previously reported to bind to the spike protein of the COVID-19 virus was used [17]. The sequence is 5'-CAGCACCGACCTTGTGCTTTGGGAGTGCTGGTCCAAGGGCGTTAATGGACA-3'.…”

Section: Methodsmentioning

confidence: 99%

Silicon thin film transistor-based aptamer sensor for COVID-19 detection

Farrow

Laumier

Sandall

et al. 2020

Preprint

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“…Animal and human coronaviruses evolve to acquire the same host receptors and attachment factors and overcome the interspecies barrier from animals to human. Specifically, S glycoprotein interaction with its binding receptor determines host tropism, pathogenicity and therapeutic clues [ 80 ]. CoVs recognize multiple host receptors via distinct S domains.…”

Section: Covs Infection Of Human Hostsmentioning

confidence: 99%

“…MHV S1 protein also evolutionarily acquired murine CEACAM1a-recognizing activity [ 102 ]. Therefore, CoVs are under evolution to adapt their host receptor interaction to infect cross-species hosts [ 80 , 103 ]. On the host side, to escape the lethal pressure from CoV infections, hosts have also evolved to acquire SA-binding proteins such as siglecs to inhibit or activate the innate immune cells.…”

Section: Covs Infection Of Human Hostsmentioning

confidence: 99%

SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction

Kim

2020

IJMS

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The recently emerged SARS-CoV-2 is the cause of the global health crisis of the coronavirus disease 2019 (COVID-19) pandemic. No evidence is yet available for CoV infection into hosts upon zoonotic disease outbreak, although the CoV epidemy resembles influenza viruses, which use sialic acid (SA). Currently, information on SARS-CoV-2 and its receptors is limited. O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells. SARS-CoV-2 hemagglutinin-esterase (HE) acts as the classical glycan-binding lectin and receptor-degrading enzyme. Most β-CoVs recognize 9-O-acetyl-SAs but switched to recognizing the 4-O-acetyl-SA form during evolution of CoVs. Type I HE is specific for the 9-O-Ac-SAs and type II HE is specific for 4-O-Ac-SAs. The SA-binding shift proceeds through quasi-synchronous adaptations of the SA-recognition sites of the lectin and esterase domains. The molecular switching of HE acquisition of 4-O-acetyl binding from 9-O-acetyl SA binding is caused by protein–carbohydrate interaction (PCI) or lectin–carbohydrate interaction (LCI). The HE gene was transmitted to a β-CoV lineage A progenitor by horizontal gene transfer from a 9-O-Ac-SA–specific HEF, as in influenza virus C/D. HE acquisition, and expansion takes place by cross-species transmission over HE evolution. This reflects viral evolutionary adaptation to host SA-containing glycans. Therefore, CoV HE receptor switching precedes virus evolution driven by the SA-glycan diversity of the hosts. The PCI or LCI stereochemistry potentiates the SA–ligand switch by a simple conformational shift of the lectin and esterase domains. Therefore, examination of new emerging viruses can lead to better understanding of virus evolution toward transitional host tropism. A clear example of HE gene transfer is found in the BCoV HE, which prefers 7,9-di-O-Ac-SAs, which is also known to be a target of the bovine torovirus HE. A more exciting case of such a switching event occurs in the murine CoVs, with the example of the β-CoV lineage A type binding with two different subtypes of the typical 9-O-Ac-SA (type I) and the exclusive 4-O-Ac-SA (type II) attachment factors. The protein structure data for type II HE also imply the virus switching to binding 4-O acetyl SA from 9-O acetyl SA. Principles of the protein–glycan interaction and PCI stereochemistry potentiate the SA–ligand switch via simple conformational shifts of the lectin and esterase domains. Thus, our understanding of natural adaptation can be specified to how carbohydrate/glycan-recognizing proteins/molecules contribute to virus evolution toward host tropism. Under the current circumstances where reliable antiviral therapeutics or vaccination tools are lacking, several trials are underway to examine viral agents. As expected, structural and non-structural proteins of SARS-CoV-2 are currently being targeted for viral therapeutic designation and development. However, the modern global society needs SARS-CoV-2 preventive and therapeutic drugs for infected patients. In this review, the structure and sialobiology of SARS-CoV-2 are discussed in order to encourage and activate public research on glycan-specific interaction-based drug creation in the near future.

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“…Song et al have developed new aptamers targeting S protein of SARS-CoV-2 and particularly receptor binding domain (RBD). The authors reported K d values of 5.8 and 19.9 nM for CoV2-RBD-1C and CoV2-RBD-4C DNA aptamers respectively ( Song et al, 2020 ). The aptamers needs to be further evaluated for their ability to interfere and disrupt binding between host ACE2 and RBD of spike protein both in vitro and in vivo .…”

Section: Introductionmentioning

confidence: 99%

Repurposing of SARS-CoV nucleocapsid protein specific nuclease resistant RNA aptamer for therapeutics against SARS-CoV-2

Parashar

Poddar

Chakrabarti

et al. 2020

Infection, Genetics and Evolution

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COVID-19 pandemic is rapidly advancing among human population. Development of new interventions including therapeutics and vaccines against SARS-CoV-2 will require time and validation before it could be made available for public use. Keeping in view of the emergent and evolving situation the motive is to repurpose and test the immediate efficacy of available drugs and therapeutics against COVID-19. Through this article we propose and discuss the possibility of repurposing the available nuclease resistant RNA aptamer against the nucleocapsid protein of SARS-CoV as a potential therapeutic agent for COVID-19.

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Discovery of Aptamers Targeting Receptor-Binding Domain of the SARS-CoV-2 Spike Glycoprotein

Cited by 47 publications

References 35 publications

Silicon thin film transistor-based aptamer sensor for COVID-19 detection

Silicon thin film transistor-based aptamer sensor for COVID-19 detection

SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction

Repurposing of SARS-CoV nucleocapsid protein specific nuclease resistant RNA aptamer for therapeutics against SARS-CoV-2

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