De Novo Generation of Hybrid Ligands with an Ultra-High Affinity to Desired Targets

As affinity reagents can recognize specific biomarkers and subsequently bind to them, they have been essential for developing a variety of diagnostic and therapeutic applications. In particular, early diagnosis and targeted drug delivery require ultra-sensitive affinity reagents which can detect desired targets even at extremely low concentrations; thus, there have been significant efforts to improve the affinity of conventional affinity reagents, such as monoclonal antibodies and nucleic acid aptamers, and in parallel, creation of a new class of ligands have been extensively pursued [1-3]. In this work, by synergistically integrating peptides with nucleic acids, we newly developed hybrid ligands capable of binding to specific targets with an exceptionally high affinity and specificity. Based on a cooperative binding mechanism, when specific epitope-binding peptide motifs are covalently linked with the most optimal structure of nucleic acids that bind to different binding sites, the resulting affinity of the conjugates can be dramatically enhanced. Using our innovative directed evolution technique [4], we directly screened the best hybrid ligands from 10¹⁵ random library, exhibiting subnanomolar binding affinities to streptavidin and coronavirus receptor binding domain.<br/><br/>[1] Kimoto, M., Yamashige, R., Matsunaga, K., Yokoyama, S. & Hirao, I. <i>Nat. Biotechnol.</i> <b>31</b>, 453-457 (2013).<br/>[2] Ahmad, K. M., Xiao, Y. & Soh, H. T. <i>Nucleic Acids Res.</i> <b>40</b>, 11777-11783 (2012).<br/>[3] Chan, K. K.<i> et al. Science</i> <b>369</b>, 1261-1265 (2020).<br/>[4] Oh, S. S., Plakos, K., Lou, X., Xiao, Y. & Soh, H. T. <i>Proc. Natl. Acad. Sci. U.S.A.</i> <b>107</b>, 14053-14058 (2010).