Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 May 22;23(10):5810.
doi: 10.3390/ijms23105810.

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

Yu-Chao Lin  1   2 , Wen-Yih Chen  3 , En-Te Hwu  4 , Wen-Pin Hu  5   6
Affiliations

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

Yu-Chao Lin et al. Int J Mol Sci. .

Abstract

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.

Keywords: COVID-19; DNA aptamer; SARS-CoV-2; aptamer–protein interaction; infectious disease; molecular dynamics simulation; spike protein.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Best docking pose of RBD-1C aptamer against the S protein (visualization software: DS 4.1). Amino acids and nucleotides involved in the binding interface of the S protein/RBD-1C complex are marked with yellow. The close-up view presents the amino acids and nucleotides in the binding interface marked by labels.
Figure 2
Figure 2
Sequence information of aptamers. (A) Sequences of the two best selected aptamers (RBD-1CM1 and RBD-1CM2) and RBD-1C aptamer. (B) Image of sequence alignment for three sequences (created by WebLogo) [29]. The mutated nucleotides are marked in this image.
Figure 3
Figure 3
RMSD plots of the S protein/aptamer complexes during the MD simulation for (A) the S protein/RBD-1C complex, (B) S protein/RBD-1CM1 complex, and (C) S protein/RBD-1CM2 complex.
Figure 3
Figure 3
RMSD plots of the S protein/aptamer complexes during the MD simulation for (A) the S protein/RBD-1C complex, (B) S protein/RBD-1CM1 complex, and (C) S protein/RBD-1CM2 complex.
Figure 4
Figure 4
Total energy plots for (A) the S protein/RBD-1C complex, (B) S protein/RBD-1CM1 complex, and (C) S protein/RBD-1CM2 complex during the MD simulation.
Figure 5
Figure 5
Number of hydrogen bonds of (A) the S protein/RBD-1C complex, (B) S protein/RBD-1CM1 complex, and (C) S protein/RBD-1CM2 complex during the 10 ns MD simulation.
Figure 6
Figure 6
Visualization of the hydrogen bonds formed by the DNA aptamer and S protein in the last frame of MD simulation using PyMOL 2.5. The aptamer is colored in light green, the S protein in light blue, and hydrogen bonds shown by red dashed lines. (A) Three H-bonds formed in the binding interface of the S protein/RBD-1C complex, (B) seven H-bonds in the binding interface of the S protein/RBD-1CM1 complex, and (C) five H-bonds in the binding interface of the S protein/RBD-1CM2 complex.
Figure 7
Figure 7
Representative time dependencies of Δ mass changes in the aptamer-immobilized chips respond-ing to the S protein. The S protein started to flow over the chip surface at arrow A (at 42 s) and the flow was changes to 1X PBS buffer at arrow B (at 282 s).
Figure 8
Figure 8
Schematic showing the workflow for the in-silico selection of aptamer target SARS-CoV-2 S protein.
Figure 9
Figure 9
Secondary structure of the RBD-1C aptamer was predicted by the RNAfold web server [45]. In this structure, 2 hairpins (at two ends) and 1 internal loop can be observed.
See this image and copyright information in PMC

References

    1. Petersen E., Koopmans M., Go U., Hamer D.H., Petrosillo N., Castelli F., Storgaard M., Al Khalili S., Simonsen L. Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics. Lancet Infect. Dis. 2020;20:e238–e244. doi: 10.1016/S1473-3099(20)30484-9. - DOI - PMC - PubMed
    1. Yeung M.L., Teng J.L.L., Jia L., Zhang C., Huang C., Cai J.P., Zhou R., Chan K.H., Zhao H., Zhu L., et al. Soluble ACE2-mediated cell entry of SARS-CoV-2 via interaction with proteins related to the renin-angiotensin system. Cell. 2021;184:2212–2228.e12. doi: 10.1016/j.cell.2021.02.053. - DOI - PMC - PubMed
    1. Huang Y., Yang C., Xu X.F., Xu W., Liu S.W. Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacol. Sin. 2020;41:1141–1149. doi: 10.1038/s41401-020-0485-4. - DOI - PMC - PubMed
    1. Xia S., Liu M., Wang C., Xu W., Lan Q., Feng S., Qi F., Bao L., Du L., Liu S., et al. Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion. Cell Res. 2020;30:343–355. doi: 10.1038/s41422-020-0305-x. - DOI - PMC - PubMed
    1. Igloi Z., Velzing J., van Beek J., van de Vijver D., Aron G., Ensing R., Benschop K., Han W., Boelsums T., Koopmans M., et al. Clinical evaluation of Roche SD Biosensor rapid antigen test for SARS-CoV-2 in municipal health service testing site, the Netherlands. Emerg. Infect. Dis. 2021;27:1323–1329. doi: 10.3201/eid2705.204688. - DOI - PMC - PubMed