In silico design of quadruplex aptamers against the spike protein of SARS-CoV-2

Behbahani, Mandana; Mohabatkar, Hassan; Hosseini, Barumand

doi:10.1016/j.imu.2021.100757

Cited by 13 publications

(11 citation statements)

References 34 publications

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“…So far, many attempts have been given to find an inhibitor agent against SARS-CoV-2, among which application of natural products has been the subject of many studies. In these studies, in silico assays have been very helpful for screening of the potential therapeutics (Teli et al 2021 ) and even designing or optimizing new therapeutics (Behbahani et al 2021 ). In this regard, a study by Kurniawan et al investigated the efficacy of Brazilein sappan wood as a potential inhibitor for spike (S) glycoprotein, papain-like proteinase, and main protease of SARS-CoV-2 by using the platform provided via bioinformatics methods.…”

Section: Discussionmentioning

confidence: 99%

In Silico Analysis of Inhibiting Papain-like Protease from SARS-CoV-2 by Using Plant-Derived Peptides

Moradi

Golmohammadi

Najafi

et al. 2021

Int J Pept Res Ther

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SARS-CoV-2 is a corona virus that has been the cause for one of the deadliest pandemics of history, started since 2019. Suppressing the activity of the critical enzymes in the SARS-CoV-2 could potentially inhibit a vital step in viral life cycle. Papain-like protease (PLpro) could be regarded as a critical enzyme in viral replication of SARS-CoV-2. In this research, it was aimed to suppress the activity of PLpro enzyme by using potential plant-derived protease inhibitor peptides. For this purpose, 11 plant derived peptides that could potentially inhibit protease activity were selected from literature. The structures of the PLpro and the peptide ligands were acquired from PDB (protein data bank) and after structural optimization, were docked by using HADDOCK 2.4 program. Analyzing the results indicated that VcTI from Veronica hederifolia provides effective molecular interactions at both liable Zn site and classic active site of PLpro, making it a potential inhibitory ligand for this enzyme that could be used for halting the replication of SARS-CoV-2. Molecular dynamic assay confirmed that the selected receptor and ligand complex was stable. Future in vitro and in vivo investigations are required to verify the efficiency of this compound as a potential therapeutic against SARS-CoV-2 infection. Supplementary Information The online version contains supplementary material available at 10.1007/s10989-021-10331-8.

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Section: Discussionmentioning

confidence: 99%

In Silico Analysis of Inhibiting Papain-like Protease from SARS-CoV-2 by Using Plant-Derived Peptides

Moradi

Golmohammadi

Najafi

et al. 2021

Int J Pept Res Ther

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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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“… 48 Other high affinity spike protein-binding aptamers ( K D in the low nanomolar range) have also been reported, 49 − 53 and in silico modeling has also been used to predict aptamers for binding the spike protein. 54 − 56 …”

Section: Introductionmentioning

confidence: 99%

“…Aptamer 1C was later used for the development of a surface-enhanced Raman spectrometry (SERS)-based aptasensor for the detection of sub-picomolar concentrations of the spike protein, while aptamer 4C immobilized on gold nanostars was exploited for spike protein detection using distance-dependent nanoparticle surface energy transfer (NSET) spectroscopy, achieving an LOD of 1.7 fM . Other high affinity spike protein-binding aptamers ( K D in the low nanomolar range) have also been reported, − and in silico modeling has also been used to predict aptamers for binding the spike protein. − …”

Section: Introductionmentioning

confidence: 99%

Aptamer Sandwich Assay for the Detection of SARS-CoV-2 Spike Protein Antigen

et al. 2021

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The novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) emerged at the end of 2019, resulting in the ongoing COVID-19 pandemic. The high transmissibility of the virus and the substantial number of asymptomatic individuals have led to an exponential rise in infections worldwide, urgently requiring global containment strategies. Reverse transcription-polymerase chain reaction is the gold standard for the detection of SARS-CoV-2 infections. Antigen tests, targeting the spike (S) or nucleocapsid (N) viral proteins, are considered as complementary tools. Despite their shortcomings in terms of sensitivity and specificity, antigen tests could be deployed for the detection of potentially contagious individuals with high viral loads. In this work, we sought to develop a sandwich aptamer-based assay for the detection of the S protein of SARS-CoV-2. A detailed study on the binding properties of aptamers to the receptor-binding domain of the S protein in search of aptamer pairs forming a sandwich is presented. Screening of aptamer pairs and optimization of assay conditions led to the development of a laboratory-based sandwich assay able to detect 21 ng/mL (270 pM) of the protein with negligible cross-reactivity with the other known human coronaviruses. The detection of 375 pg of the protein in viral transport medium demonstrates the compatibility of the assay with clinical specimens. Finally, successful detection of the S antigen in nasopharyngeal swab samples collected from suspected patients further establishes the suitability of the assay for screening purposes as a complementary tool to assist in the control of the pandemic.

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In silico design of quadruplex aptamers against the spike protein of SARS-CoV-2

Cited by 13 publications

References 34 publications

In Silico Analysis of Inhibiting Papain-like Protease from SARS-CoV-2 by Using Plant-Derived Peptides

In Silico Analysis of Inhibiting Papain-like Protease from SARS-CoV-2 by Using Plant-Derived Peptides

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

Aptamer Sandwich Assay for the Detection of SARS-CoV-2 Spike Protein Antigen

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