Novel Design of RNA Aptamers as Cancer Inhibitors and Diagnosis Targeting the Tyrosine Kinase Domain of the NT-3 Growth Factor Receptor Using a Computational Sequence-Based Approach.
Ashraf M MuhammadAli ZariNouf H AlsubhiMaryam Hassan Al-ZahraniRana Abdullah AlghamdiMai M LabibPublished in: Molecules (Basel, Switzerland) (2022)
Aptamers, the nucleic acid analogs of antibodies, bind to their target molecules with remarkable specificity and sensitivity, making them promising diagnostic and therapeutic tools. The systematic evolution of ligands by exponential enrichment (SELEX) is time-consuming and expensive. However, regardless of those issues, it is the most used in vitro method for selecting aptamers. Therefore, recent studies have used computational approaches to reduce the time and cost associated with the synthesis and selection of aptamers. In an effort to present the potential of computational techniques in aptamer selection, a simple sequence-based method was used to design a 69-nucleotide long aptamer (mod_09) with a relatively stable structure (with a minimum free energy of -32.2 kcal/mol) and investigate its binding properties to the tyrosine kinase domain of the NT-3 growth factor receptor, for the first time, by employing computational modeling and docking tools.
Keyphrases
- nucleic acid
- growth factor
- tyrosine kinase
- epidermal growth factor receptor
- gold nanoparticles
- sensitive detection
- papillary thyroid
- binding protein
- molecular dynamics
- molecular dynamics simulations
- molecular docking
- protein protein
- squamous cell carcinoma
- cancer therapy
- label free
- risk assessment
- amino acid
- small molecule
- childhood cancer
- case control