| Summary: | Background: Biomarker detection strategies have, in recent years, been
moving towards nucleic acid-based detection systems in the form of aptamers,
short oligonucleotide sequences which have shown promise in pre-clinical and
research settings. One such aptamer is M5-15, a DNA aptamer raised against human
alpha synuclein (α-syn) the causative agent in Lewy body and Parkinson’s disease
(PD) associated dementia. While this aptamer has shown promise, in
silico methodologies have demonstrated a capacity to produce aptamers that have
higher affinities for their targets than in vitro generated sequences.
Methods: A Python script random generated library of DNA sequences were
screened based on their thermodynamic stability with the use of DINAMelt
server-QuickFold web server. The selected sequences were examined with MFold in
order to generate secondary structure data that were used to produce 3D data with
the use of RNA composer software. Further on, the structure was corrected and RNA
was replaced with DNA and the virtual screening for α-syn aptamer took
place with a series of molecular docking experiments with the use of
CSD-Discovery-GOLD software. Results: Herein we propose an alternative
in silico generated aptamer we call TMG-79 which demonstrates greater
affinity for the target compared to M5-15 (M5-15 = –15.9 kcal/mol, TMG-79 =
–17.77 kcal/mol) as well as better ChemPLP fitness scoring between the top poses
(M5-15 = 32.33, TMG-79 = 53.32). Structural analysis suggests that while there
are similarities, the greater potential flexibility of TMG-79 could be promoting
greater affinity for the α-syn compared to M5-15. Conclusions:
In silico methods of aptamer generation has the potential to
revolutionise the field of aptamer design. We feel that further development of
TMG-79 and validation in vitro will make it a viable candidate for diagnostic and
research use in the future.
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