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In silico selection against progesterone receptor DNA-binding domain
Tholasi Nadhan Navien1, Ramesh Thevendran1, Marimuthu Citartan1
1Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
Analytical Biochemistry
|December 24, 2024
Summary
Researchers developed a novel DNA aptamer, PRDBDapt17, for progesterone receptor detection in breast cancer diagnostics. This aptamer offers an alternative to antibodies, showing high binding affinity and potential for broad steroid hormone receptor applications.
Area of Science:
- Biotechnology
- Molecular Biology
- Cancer Diagnostics
Background:
- Progesterone receptor is a key marker in breast cancer diagnostics, typically detected using antibody-based immunohistochemistry.
- Limitations of antibodies necessitate exploring alternative molecular recognition tools like aptamers.
- Conventional SELEX for aptamer selection is rigorous, prompting interest in in silico methods.
Purpose of the Study:
- To perform in silico selection and experimental validation of DNA aptamers targeting the progesterone receptor DNA binding domain (PR DBD).
- To utilize DNA sequences derived from human progesterone response elements (PREs) for aptamer development.
- To assess the potential of aptamers as diagnostic tools for breast cancer and other steroid hormone receptor-related conditions.
Main Methods:
- In silico selection of DNA aptamers against PR DBD using a library of 64 ssDNA sequences.
- Secondary and tertiary structural determination followed by docking simulations using PatchDock.
- Molecular dynamic simulations and experimental validation using direct Enzyme-Linked Aptamer Assay (ELASA).
Main Results:
- PRDBDapt17 emerged as the top candidate aptamer with the highest docking score (11334), confirmed by molecular dynamics.
- Direct ELASA validation showed a limit of detection of 3.91 nM for PRDBDapt17.
- The equilibrium dissociation constant (Kd) was determined to be 366.6 nM, indicating significant binding affinity.
- PRDBDapt17 demonstrated cross-reactivity with estrogen and androgen receptors, suggesting potential as a universal steroid hormone receptor binder.
Conclusions:
- The in silico approach successfully identified PRDBDapt17, a potent DNA aptamer for PR DBD recognition.
- PRDBDapt17 exhibits favorable detection limits and binding affinity, suitable for diagnostic applications.
- Its potential as a universal binder for steroid hormone receptors opens avenues for broader diagnostic utility in hormone-related diseases, including breast cancer.
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