In silico evaluation of potential murine M49 DNA aptamer on ORF7a of SARS-COV-2: A similar target

Nor Azlina Ahmad; Razauden Zulkifli; Huszalina Hussin; Syazwani İtri Amran; Muhammad Helmi Nadri; Saiful Izwan Abdul Razak; Sabrinah Adam; Farahwahida Mohd Yusof Yusof

In silico evaluation of potential murine M49 DNA aptamer on ORF7a of SARS-COV-2: A similar target

Abstract

DNA aptamers are short nucleotides with a high affinity for their target. However, the process of isolating aptamers via the systematic evolution of ligands by exponential enrichment (SELEX) procedure is laborious. Therefore, an in silico approach is used to screen potential DNA aptamer candidates as a kickstart specifically for ORF7a of SARS-COV-2. By applying the TM-align program, the murine receptor (CD200R) protein was found to have structural similarities with ORF7a. Based on the literature, this CD200R protein is successfully bound by M49 DNA aptamers experimentally. Herein, the 3D structure of the M49 DNA aptamer was generated using Mfold, RNA Composer webserver, Discovery Studio Visualizer, and UCSF Chimera software, and the docking simulation was predicted using the HDOCK webserver. The binding energy scores for the M49-CD200R complex were slightly higher than those for the M49-ORF7a complex with -233.78 and -220.11, respectively. The molecular interaction in the complexes was contributed by the hydrogen bond. In conclusion, the M49 aptamer of CD200R protein can bind to the other similar target, the ORF7a protein of SARS-COV-2. Even though CD200R and ORF7a proteins share structural similarities, the binding sites of the individual complex are distinct. The current study shows that two different proteins with structural similarities may have a possibility to share the same DNA aptamer. This strategy may result in efficient aptamer discovery using an in silico method as a first step.

Keywords

References

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Details

Primary Language

English

Subjects

Pharmacology and Pharmaceutical Sciences (Other)

Journal Section

Research Article

Authors

Nor Azlina Ahmad
0000-0002-7676-2904
Malaysia

Razauden Zulkifli ^*
0000-0003-1925-0969
Malaysia

Huszalina Hussin
0000-0001-8564-1138
Malaysia

Syazwani İtri Amran
0000-0002-5873-5291
Malaysia

Muhammad Helmi Nadri
0000-0002-2506-2043
Malaysia

Saiful Izwan Abdul Razak This is me
0000-0001-7477-0284
Malaysia

Sabrinah Adam This is me
0000-0001-6765-8104
Malaysia

Farahwahida Mohd Yusof Yusof This is me
0000-0003-4834-8527
Malaysia

Publication Date

June 28, 2025

Submission Date

January 23, 2022

Acceptance Date

June 10, 2022

Published in Issue

Year 2023 Volume: 27 Number: 1

IZ

https://izlik.org/JA25YB44PF

Cite

RIS / Bibtex

APA

Ahmad, N. A., Zulkifli, R., Hussin, H., Amran, S. İ., Nadri, M. H., Razak, S. I. A., Adam, S., & Yusof, F. M. Y. (2025). In silico evaluation of potential murine M49 DNA aptamer on ORF7a of SARS-COV-2: A similar target. Journal of Research in Pharmacy, 27(1), 232-240. https://izlik.org/JA25YB44PF

AMA

1.Ahmad NA, Zulkifli R, Hussin H, et al. In silico evaluation of potential murine M49 DNA aptamer on ORF7a of SARS-COV-2: A similar target. J. Res. Pharm. 2025;27(1):232-240. https://izlik.org/JA25YB44PF

Chicago

Ahmad, Nor Azlina, Razauden Zulkifli, Huszalina Hussin, et al. 2025. “In Silico Evaluation of Potential Murine M49 DNA Aptamer on ORF7a of SARS-COV-2: A Similar Target”. Journal of Research in Pharmacy 27 (1): 232-40. https://izlik.org/JA25YB44PF.

EndNote

Ahmad NA, Zulkifli R, Hussin H, Amran Sİ, Nadri MH, Razak SIA, Adam S, Yusof FMY (June 1, 2025) In silico evaluation of potential murine M49 DNA aptamer on ORF7a of SARS-COV-2: A similar target. Journal of Research in Pharmacy 27 1 232–240.

IEEE

[1]N. A. Ahmad et al., “In silico evaluation of potential murine M49 DNA aptamer on ORF7a of SARS-COV-2: A similar target”, J. Res. Pharm., vol. 27, no. 1, pp. 232–240, June 2025, [Online]. Available: https://izlik.org/JA25YB44PF

ISNAD

Ahmad, Nor Azlina - Zulkifli, Razauden - Hussin, Huszalina - Amran, Syazwani İtri - Nadri, Muhammad Helmi - Razak, Saiful Izwan Abdul - Adam, Sabrinah - Yusof, Farahwahida Mohd Yusof. “In Silico Evaluation of Potential Murine M49 DNA Aptamer on ORF7a of SARS-COV-2: A Similar Target”. Journal of Research in Pharmacy 27/1 (June 1, 2025): 232-240. https://izlik.org/JA25YB44PF.

JAMA

1.Ahmad NA, Zulkifli R, Hussin H, Amran Sİ, Nadri MH, Razak SIA, Adam S, Yusof FMY. In silico evaluation of potential murine M49 DNA aptamer on ORF7a of SARS-COV-2: A similar target. J. Res. Pharm. 2025;27:232–240.

MLA

Ahmad, Nor Azlina, et al. “In Silico Evaluation of Potential Murine M49 DNA Aptamer on ORF7a of SARS-COV-2: A Similar Target”. Journal of Research in Pharmacy, vol. 27, no. 1, June 2025, pp. 232-40, https://izlik.org/JA25YB44PF.

Vancouver

1.Nor Azlina Ahmad, Razauden Zulkifli, Huszalina Hussin, Syazwani İtri Amran, Muhammad Helmi Nadri, Saiful Izwan Abdul Razak, Sabrinah Adam, Farahwahida Mohd Yusof Yusof. In silico evaluation of potential murine M49 DNA aptamer on ORF7a of SARS-COV-2: A similar target. J. Res. Pharm. [Internet]. 2025 Jun. 1;27(1):232-40. Available from: https://izlik.org/JA25YB44PF