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Characterizatio and optimization of an In silico peptide design method to enhance cellular uptake
  • François Charih
François Charih
Carleton University
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Abstract

Owing to their exquisite specificity and, consequently, their advantageous side effect profiles, inhibitory peptides hold great promise as therapeutic agents. However, designing peptides to disrupt a specific protein-protein interactions or to inhibit the activity of targeted enzymes remains a sizeable challenge to this day. While traditional wet lab approaches have yielded successful drug candidates in the past, the labor-intensive and expensive nature of these approaches make computational alternatives particularly attractive. A number of in silico peptide drug design methods have been proposed over the last decade, unlocking an unprecedented opportunity to inexpensively design peptides for a target protein of interest. In this work, we iterate over one such approach developed previously in our laboratory, and show that the existing In silico Peptide Synthesizer can be adjusted to design peptides much shorter than previously possible, facilitating uptake by cells. We characterize this new method, showing the impact of peptide size on its computational and predictive performance. Finally, we present the GUI-based software implementation of this improved peptide design method.