Development and validation of anti-human Alpha synuclein DNA aptamer using computer modelling techniques-an in silico...

Area of Science:

• Biotechnology
• Computational Biology
• Molecular Diagnostics

Background:

• Nucleic acid aptamers are emerging as sensitive biomarker detection tools.
• Human alpha synuclein (α-syn) is a key biomarker for Parkinson's disease (PD).
• In silico aptamer generation offers potential for higher target affinity than in vitro methods.

Purpose of the Study:

• To computationally design and evaluate a novel DNA aptamer targeting human alpha synuclein (α-syn).
• To compare the binding affinity of the in silico-generated aptamer with a known aptamer (M5-15).

Main Methods:

• Generated a library of DNA sequences using Python scripting.
• Screened sequences for thermodynamic stability using DINAMelt and QuickFold.
• Predicted secondary and 3D structures using MFold and RNA composer.
• Performed virtual screening and molecular docking using CSD-Discovery-GOLD.

Main Results:

• Proposed a novel in silico aptamer, TMG-79, with enhanced affinity for α-syn (-17.77 kcal/mol) compared to M5-15 (-15.9 kcal/mol).
• TMG-79 exhibited superior ChemPLP fitness scoring (53.32) versus M5-15 (32.33).
• Structural analysis suggests TMG-79's flexibility may contribute to its higher affinity.

Conclusions:

• In silico aptamer generation is a powerful tool with the potential to transform aptamer design.
• The novel TMG-79 aptamer demonstrates significant potential for Parkinson's disease diagnostics and research.
• Further in vitro validation is recommended for TMG-79's clinical and research applications.