Development and validation of anti-human Alpha synuclein DNA aptamer using computer modelling techniques—an in silico study
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 again...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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IMR Press
2022-01-01
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| Series: | Journal of Integrative Neuroscience |
| Subjects: | |
| Online Access: | https://article.imrpress.com/journal/JIN/21/1/10.31083/j.jin2101005/1757-448X-21-1-005.pdf |
| _version_ | 1828264663858544640 |
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| author | Marcus Rock Georgios D. Zouganelis Ana Flavia Belchior de Andrade Samantha J. Drake Athanasios Alexiou Ashraf Albrakati Gaber El-Saber Batiha Thomas Arron Illingworth |
| author_facet | Marcus Rock Georgios D. Zouganelis Ana Flavia Belchior de Andrade Samantha J. Drake Athanasios Alexiou Ashraf Albrakati Gaber El-Saber Batiha Thomas Arron Illingworth |
| author_sort | Marcus Rock |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T04:28:14Z |
| format | Article |
| id | doaj.art-03aa9b3af9574536aefdf674e880f473 |
| institution | Directory Open Access Journal |
| issn | 0219-6352 |
| language | English |
| last_indexed | 2024-04-13T04:28:14Z |
| publishDate | 2022-01-01 |
| publisher | IMR Press |
| record_format | Article |
| series | Journal of Integrative Neuroscience |
| spelling | doaj.art-03aa9b3af9574536aefdf674e880f4732022-12-22T03:02:25ZengIMR PressJournal of Integrative Neuroscience0219-63522022-01-0121100510.31083/j.jin2101005S0219-6352(22)00265-0Development and validation of anti-human Alpha synuclein DNA aptamer using computer modelling techniques—an in silico studyMarcus Rock0Georgios D. Zouganelis1Ana Flavia Belchior de Andrade2Samantha J. Drake3Athanasios Alexiou4Ashraf Albrakati5Gaber El-Saber Batiha6Thomas Arron Illingworth7Human Sciences Research Centre, University of Derby, DE22 1GB Derby, UKHuman Sciences Research Centre, University of Derby, DE22 1GB Derby, UKHuman Sciences Research Centre, University of Derby, DE22 1GB Derby, UKHuman Sciences Research Centre, University of Derby, DE22 1GB Derby, UKDepartment of Science & Engineering, Novel Global Community Educational Foundation, 2770 Hebersham, AustraliaDepartment of Human Anatomy, College of Medicine, Taif University, P.O. BOX 11099, 21944 Taif, Saudi ArabiaDepartment of Pharmacology & Therapeutics, Faculty of Veterinary Medicine, Damanhour University, 22511 Damanhour, AlBeheira, EgyptHuman Sciences Research Centre, University of Derby, DE22 1GB Derby, UKBackground: 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.https://article.imrpress.com/journal/JIN/21/1/10.31083/j.jin2101005/1757-448X-21-1-005.pdfdna aptamersin silico designcomputer aided designalpha synucleinbiomarker detection |
| spellingShingle | Marcus Rock Georgios D. Zouganelis Ana Flavia Belchior de Andrade Samantha J. Drake Athanasios Alexiou Ashraf Albrakati Gaber El-Saber Batiha Thomas Arron Illingworth Development and validation of anti-human Alpha synuclein DNA aptamer using computer modelling techniques—an in silico study Journal of Integrative Neuroscience dna aptamers in silico design computer aided design alpha synuclein biomarker detection |
| title | Development and validation of anti-human Alpha synuclein DNA aptamer using computer modelling techniques—an in silico study |
| title_full | Development and validation of anti-human Alpha synuclein DNA aptamer using computer modelling techniques—an in silico study |
| title_fullStr | Development and validation of anti-human Alpha synuclein DNA aptamer using computer modelling techniques—an in silico study |
| title_full_unstemmed | Development and validation of anti-human Alpha synuclein DNA aptamer using computer modelling techniques—an in silico study |
| title_short | Development and validation of anti-human Alpha synuclein DNA aptamer using computer modelling techniques—an in silico study |
| title_sort | development and validation of anti human alpha synuclein dna aptamer using computer modelling techniques an in silico study |
| topic | dna aptamers in silico design computer aided design alpha synuclein biomarker detection |
| url | https://article.imrpress.com/journal/JIN/21/1/10.31083/j.jin2101005/1757-448X-21-1-005.pdf |
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