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DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design

View ORCID ProfileCameron Andress, Kalli Kappel, View ORCID ProfileMiroslava Cuperlovic-Culf, Hongbin Yan, Yifeng Li
doi: https://doi.org/10.1101/2022.11.30.518473
Cameron Andress
1Department of Computer Science, Brock University, St. Catharines, ON, Canada
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Kalli Kappel
2Broad Institute of MIT and Harvard, Cambridge, MA, United States
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Miroslava Cuperlovic-Culf
3Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada
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Hongbin Yan
4Department of Chemistry, Brock University, St. Catharines, ON, Canada
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Yifeng Li
1Department of Computer Science, Brock University, St. Catharines, ON, Canada
5Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
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  • For correspondence: yli2@brocku.ca
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Abstract

Typical drug discovery and development processes are costly, time consuming and often biased by expert opinion. Aptamers are short, single-stranded oligonucleotides (RNA/DNA) that bind to target proteins and other types of biomolecules. Compared with small-molecule drugs, aptamers can bind to their targets with high affinity (binding strength) and specificity (uniquely interacting with the target only). The conventional development process for aptamers utilizes a manual process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX), which is costly, slow, dependent on library choice and often produces aptamers that are not optimized. To address these challenges, in this research, we create an intelligent approach, named DAPTEV, for generating and evolving aptamer sequences to support aptamer-based drug discovery and development. Using the COVID-19 spike protein as a target, our computational results suggest that DAPTEV is able to produce structurally complex aptamers with strong binding affinities.

Author summary Compared with small-molecule drugs, aptamer drugs are short RNAs/DNAs that can specifically bind to targets with high strength. With the interest of discovering novel aptamer drugs as an alternative to address the long-lasting COVID-19 pandemic, in this research, we developed an artificial intelligence (AI) framework for the in silico design of novel aptamer drugs that can prevent the SARS-CoV-2 virus from entering human cells. Our research is valuable as we explore a novel approach for the treatment of SARS-CoV-2 infection and the AI framework could be applied to address future health crises.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 30, 2022.
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DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design
Cameron Andress, Kalli Kappel, Miroslava Cuperlovic-Culf, Hongbin Yan, Yifeng Li
bioRxiv 2022.11.30.518473; doi: https://doi.org/10.1101/2022.11.30.518473
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DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design
Cameron Andress, Kalli Kappel, Miroslava Cuperlovic-Culf, Hongbin Yan, Yifeng Li
bioRxiv 2022.11.30.518473; doi: https://doi.org/10.1101/2022.11.30.518473

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