Using in silico methods for designing novel aptameric ligands against therapeutic proteins

Using in silico methods for designing novel aptameric ligands against therapeutic proteins
Maryam Tabarzad,^1,* Amirhossein Faraji,²
1. Protein Technology Resaerch Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
2. Protein Technology Resaerch Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
Introduction: Aptamers are single-stranded DNA or RNA structures that interact with specified targets with a high affinity. A wide range of targets, including whole cells of different organisms, inorganic materials, large biomolecules (proteins, peptides, lipids, even other nucleic acids) have been considered for aptamer development. Among them, protein targets are of great importance in medicine due to the value of proteins activities in health and pathogenesis of disease. Selection of aptamers through experimental effort using Systematic Evolution of Ligands by EXponential enrichment (SELEX) or non-SELEX process are time and cost consuming. Therefore, using computational methods for in silico design of aptameric ligands has become an interesting field of research in this regard.
Methods: The publication of Science Direct and PubMed as well as Google Scholar was searched using keywords of “aptamer” AND “protein” AND “in silico design” OR “computational design”.
Results: There an increasing numbers of reports using molecular docking and molecular modelling (MD) simulations methods or using methods based on machine learning and artificial intelligence in the design and prediction of specific aptamers against protein targets, in recent years. Although using these strategies is time- and cost-saving, however, the results of in silico design do not have essentially shown similar potent in vitro or in vivo affinity and activity.
Conclusion: In this review, we discussed different methods have been reported for in silico aptamer design against protein targets, so far; and discussed about their cons and pros.
Keywords: Aptamer, Nucleic acids, Protein, In silico, Design