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

Makale detayları

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

Yazarlar:

Nor Azlina Ahmad | Razauden Zulkifli | Huszalina Hussin | Syazwani İtri Amran | Muhammad Helmi Nadri

Yayıncı:

Marmara University

Ana Başlıklar:

Pharmacology and Pharmaceutical Sciences (Other)

Dergi:

Journal of Research in Pharmacy Vol.27 Issue 1, pp.232-240

Belge Tipi:

Makale

Yayın Tarihi:

6/2025

Belge Dili:

İngilizce

Document ID (Org No.):

2001345954

pISSN:

2630-6344

Anahtar kelimeler:

Özet:

 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.

 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.

 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.

 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.

Makale detayları

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

Yazarlar:

Nor Azlina Ahmad | Razauden Zulkifli | Huszalina Hussin | Syazwani İtri Amran | Muhammad Helmi Nadri

Yayıncı:

Marmara University

Ana Başlıklar:

Pharmacology and Pharmaceutical Sciences (Other)

Dergi:

Journal of Research in Pharmacy Vol.27 Issue 1, pp.232-240

Belge Tipi:

Makale

Yayın Tarihi:

6/2025

Belge Dili:

İngilizce

Document ID (Org No.):

2001345954

pISSN:

2630-6344

SARS-COV-2

ORF7a

DNA aptamer

molecular docking

Sayı

Makale detayları

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

Yazarlar: Nor Azlina Ahmad | Razauden Zulkifli | Huszalina Hussin | Syazwani İtri Amran | Muhammad Helmi Nadri

Yayıncı: Marmara University

Ana Başlıklar: Pharmacology and Pharmaceutical Sciences (Other)

Dergi: Journal of Research in Pharmacy Vol.27 Issue 1, pp.232-240

Belge Tipi: Makale

Yayın Tarihi: 6/2025

Belge Dili: İngilizce

Document ID (Org No.): 2001345954

pISSN: 2630-6344

SARS-COV-2

ORF7a

DNA aptamer

molecular docking

Sayı

Yazarlar:

Nor Azlina Ahmad | Razauden Zulkifli | Huszalina Hussin | Syazwani İtri Amran | Muhammad Helmi Nadri

Yayıncı:

Marmara University

Ana Başlıklar:

Pharmacology and Pharmaceutical Sciences (Other)

Dergi:

Journal of Research in Pharmacy Vol.27 Issue 1, pp.232-240

Belge Tipi:

Makale

Yayın Tarihi:

6/2025

Belge Dili:

İngilizce

Document ID (Org No.):

2001345954

pISSN:

2630-6344