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BIT Team Screened and Obtained Neutralizing Nucleic Acid Aptamers against the COVID-19

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Since December 2019, the Covid-2019 has sickened about 180 million people worldwide and killed about 3.8 million people. The rapid spread between people is one of the most notable features of SARS-CoV-2. It is the main transmission mechanism of SARS-CoV-2 that the Spike protein binds to the host cell angiotensin-converting enzyme (ACE2) receptor to initiate the infection process. Among them, the RBD domain of the S1 subunit of the Spike protein promotes the recognition and binding of SARS-CoV-2 and ACE2; at the same time, the S2 subunit triggers membrane fusion and mediates the injection of the viral genome into the host cytoplasm. Therefore, blocking the combination of ACE2 and RBD is considered to be a key strategy to inhibit the infection and spread of SARS-CoV-2. At present, although a variety of virus and host therapies such as remdesivir, chloroquine, interferon, tocilizumab, convalescent plasma, neutralizing antibodies, and traditional Chinese medicine have been used to prevent and treat COVID-19, however, there are no targeted specific therapeutic drugs. Nucleic acid-based therapeutics have great potential in the prevention and treatment of COVID-19 (or other infectious diseases) due to their rapid development, high target specificity and few side effects. The development of a treatment plan based on aptamers (Aptamer) is a potentially effective method to control COVID-19.

Recently, the team of researcher Huang Yuanyu from the Advanced Research Institute of Multidisciplinary Sciences of BIT published a paper titled Identification of SARS-CoV-2-against aptamer with high neutralization activity by blocking the RBD domain of spike protein 1 in Signal Transduction and Targeted Therapy (China Science and Technology Journal Excellence Action Plan Leading Journal, IF="18.187) , in which SARS-CoV-2 neutralizing active nucleic acid aptamers that can block the RBD domain of the S1 subunit were screened and identified.

Based on capillary electrophoresis (CE), this research applies CE-Based SELEX to screen high-affinity and specific nucleic acid aptamers of the S1 subunit. In order to ensure the evolution efficiency of the affinity and specificity of the candidate sequence, the SELEX strategy combining positive, negative and complex background screening process were adopted to continuously reduce the concentration of the target protein to increase the screening pressure. Finally, 6 DNA aptamers nCoV-S1-Apts (KD = "0.118±0.033~85.610±14.219" nM) with high affinity to the S1 subunit were obtained.

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Specificity and toxicity evaluation results show that nCoV-S1-Apts has high specificity, anti-plasma protein interference characteristics and low toxicity, which is beneficial to reduce potential off-target effects and cytotoxicity. Furthermore, it is predicted by molecular docking that nCoV-S1-Apt1 can bind to the RBD domain of the S1 subunit, covering the two main active sites that it binds to ACE2. At the same time, this was confirmed by the binding experiment of RBD protein, so nCoV-S1-Apt1 has the potential to be used as an effective inhibitor of RBD domain.

In order to evaluate the recognition and detection potential of nCoV-S1Apt1, this study established an AuNPs colorimetric method that can quickly and specifically detect the S1 subunit in human serum with a detection limit of 3.125 nM. At the same time, the FAM-labeled nCoV-S1-Apt1 can be used as a fluorescent probe to capture the S1 subunit and SARS-CoV-2 pseudovirus in human serum, with good recognition and detection linearity in the range of 102-105 virus particles.

In order to confirm the multi-scale inhibitory effect of nCoV-S1-Apt1 on SARS-CoV-2, this study carried out inhibition experiments from three levels of RBD, S1 subunit and pseudovirus. The results show that nCoV-S1-Apt1 can reduce SARS-CoV-2 infection by binding to the RBD of S1, hindering the recognition and interaction between S1 and ACE2, which shows that it has good application potential as a new type of nucleic acid neutralizer against SARS-CoV-2 infection.

In summary, this study screened and identified the nucleic acid aptamer of the S1 protein, and verified the application ability of the aptamer in the prevention, treatment and detection of COVID-19, also providing potential tools for the design of fusion nucleic acid inhibitors, virus neutralizing oligonucleotides or targeted delivery systems. In addition, the study also proposed a multi-scale target-based virus-neutralizing nucleic acid aptamer screening and identification strategy.

Yang Ge, a postdoctoral fellow at the Advanced Research Institute of Multidisciplinary Sciences and School of Life Sciences, BIT, is the first author of the paper, and researcher Huang Yuanyu is the corresponding author. This research was strongly supported by Professor Qu Feng from BIT.

Details of  the paper:

Ge Yang, Ziyue Li, Irfan Mohammed, Liping Zhao, Wei Wei, Haihua Xiao, Weisheng Guo, Yongxiang Zhao, Feng Qu & Yuanyu Huang*. Identification of SARS-CoV-2-against aptamer with high neutralization activity by blocking the RBD domain of spike protein 1. Signal Transduction and Targeted Therapy 2021; 6(1):227. DOI: 10.1038/s41392-021-00649-6

Teacher homepage: https://www.x-mol.com/groups/Yuanyu_Huang-BIT

Link to the paper: https://www.nature.com/articles/s41392-021-00649-6