Designing of peptide aptamer targeting the receptor-binding domain of spike protein of SARS-CoV-2: an in silico study

Devi, Arpita; Chaitanya, Nyshadham S.N.

doi:10.1007/s11030-020-10171-6

Cited by 20 publications

(18 citation statements)

References 61 publications

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“…Thus, aptamers can be widely used for the detection of SARS-CoV-2. Similar studies have been reported by others ( Chen et al, 2020b ; Zhang L. et al, 2020 ; Song et al, 2020 ; Acquah et al, 2021 ; Devi and Chaitanya, 2021 ; Sun et al, 2021 ). Although aptamers have not been combined with LFAs for direct diagnosis of virus particles so far, it is believed that the assay, combined with the merits of aptamers and LFA is a promising tool for rapid detection of SARS-CoV-2 in the future.…”

Section: Diagnosis Methodssupporting

confidence: 92%

Recent Progress on Rapid Lateral Flow Assay-Based Early Diagnosis of COVID-19

Zhang

Chai

et al. 2022

Front. Bioeng. Biotechnol.

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The outbreak of the coronavirus disease 2019 (COVID-19) has resulted in enormous losses worldwide. Through effective control measures and vaccination, prevention and curbing have proven significantly effective; however, the disease has still not been eliminated. Therefore, it is necessary to develop a simple, convenient, and rapid detection strategy for controlling disease recurrence and transmission. Taking advantage of their low-cost and simple operation, point-of-care test (POCT) kits for COVID-19 based on the lateral flow assay (LFA) chemistry have become one of the most convenient and widely used screening tools for pathogens in hospitals and at home. In this review, we introduce essential features of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, compare existing detection methods, and focus on the principles, merits and limitations of the LFAs based on viral nucleic acids, antigens, and corresponding antibodies. A systematic comparison was realized through summarization and analyses, providing a comprehensive demonstration of the LFA technology and insights into preventing and curbing the COVID-19 pandemic.

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Section: Diagnosis Methodssupporting

confidence: 92%

Recent Progress on Rapid Lateral Flow Assay-Based Early Diagnosis of COVID-19

Zhang

Chai

et al. 2022

Front. Bioeng. Biotechnol.

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“…Similar efforts are made for the detection of IgG, IgM-based LFAs [ 157 , 158 ] and antigen-based testing [ 159 ]. Furthermore, aptamer-based LFAs are being taken on account due to high sensitivity, long shelf life and cost effectiveness [ 160 , 161 , 162 ]. Based on the available genomic data, the LFAs can be used to design the newly mutant strains of SARS-CoV-2.…”

Section: Biosensorsmentioning

confidence: 99%

Advancements in Testing Strategies for COVID-19

et al. 2022

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The SARS-CoV-2 coronavirus, also known as the disease-causing agent for COVID-19, is a virulent pathogen that may infect people and certain animals. The global spread of COVID-19 and its emerging variation necessitates the development of rapid, reliable, simple, and low-cost diagnostic tools. Many methodologies and devices have been developed for the highly sensitive, selective, cost-effective, and rapid diagnosis of COVID-19. This review organizes the diagnosis platforms into four groups: imaging, molecular-based detection, serological testing, and biosensors. Each platform’s principle, advancement, utilization, and challenges for monitoring SARS-CoV-2 are discussed in detail. In addition, an overview of the impact of variants on detection, commercially available kits, and readout signal analysis has been presented. This review will expand our understanding of developing advanced diagnostic approaches to evolve into susceptible, precise, and reproducible technologies to combat any future outbreak.

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“…Chen et al [ 15 ] showed that aptamers designed based on an aptamer for SARS-CoV N protein can still have high-affinity binding for the SARS-CoV-2 N protein, and these aptamers have the potential to be used in antiviral therapy by interfering with the N protein function. Furthermore, other types of aptamers, such as the peptide [ 16 ] and quadruplex [ 17 ] aptamers, have been designed by in-silico methods for targeting the S protein of SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

“…Compared with empirical methods, computational in-silico methods have several advantages, such as low cost, a simple process, and queries that can be investigated irrespective of practical limitations that hinder experiments. Therefore, numerous studies have reported the use of in-silico approaches to screen or design aptamers, targeting a variety of biomolecules [ 16 , 17 , 22 , 25 , 26 , 27 ].…”

Section: Introductionmentioning

confidence: 99%

In-Silico Selection of Aptamer Targeting SARS-CoV-2 Spike Protein

Lin

Chen

Hwu

et al. 2022

IJMS

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Aptamers are single-stranded, short DNA or RNA oligonucleotides that can specifically bind to various target molecules. To diagnose the infected cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in time, numerous conventional methods are applied for viral detection via the amplification and quantification of DNA or antibodies specific to antigens on the virus. Herein, we generated a large number of mutated aptamer sequences, derived from a known sequence of receptor-binding domain (RBD)-1C aptamer, specific to the RBD of SARS-CoV-2 spike protein (S protein). Structural similarity, molecular docking, and molecular dynamics (MD) were utilized to screen aptamers and characterize the detailed interactions between the selected aptamers and the S protein. We identified two mutated aptamers, namely, RBD-1CM1 and RBD-1CM2, which presented better docking results against the S protein compared with the RBD-1C aptamer. Through the MD simulation, we further confirmed that the RBD-1CM1 aptamer can form the most stable complex with the S protein based on the number of hydrogen bonds formed between the two biomolecules. Based on the experimental data of quartz crystal microbalance (QCM), the RBD-1CM1 aptamer could produce larger signals in mass change and exhibit an improved binding affinity to the S protein. Therefore, the RBD-1CM1 aptamer, which was selected from 1431 mutants, was the best potential candidate for the detection of SARS-CoV-2. The RBD-1CM1 aptamer can be an alternative biological element for the development of SARS-CoV-2 diagnostic testing.

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Designing of peptide aptamer targeting the receptor-binding domain of spike protein of SARS-CoV-2: an in silico study

Cited by 20 publications

References 61 publications

Recent Progress on Rapid Lateral Flow Assay-Based Early Diagnosis of COVID-19

Recent Progress on Rapid Lateral Flow Assay-Based Early Diagnosis of COVID-19

Advancements in Testing Strategies for COVID-19

In-Silico Selection of Aptamer Targeting SARS-CoV-2 Spike Protein

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