Two-step target recognition for the competitive inhibition activity of an anti-VEGF aptamer

  1. Ichio Shimada1,5,6
  1. 1Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
  2. 2Molecular Profiling Research Center for Drug Discovery and Cellular Molecular Biotechnology Research Institute, National Institute of Advanced Science and Technology, Tokyo 135-0063, Japan
  3. 3Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
  4. 4Research and Development Department, Japan Biological Informatics Consortium, Tokyo 135-0064, Japan
  5. 5Center for Biosystems Dynamics Research, RIKEN, Kanagawa 230-0045, Japan
  6. 6Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City, Hiroshima 739-8528, Japan
  1. Corresponding authors: ichio.shimada{at}riken.jp; koh-takeuchi{at}mol.f.u-tokyo.ac.jp

  1. Handling editor: Adrian Ferre-D'Amare

Abstract

The anti-vascular endothelial growth factor (VEGF) aptamer, t44.27, is a 27-mer RNA that functions as the active component of pegaptanib, an antiangiogenic medicine for neovascular age-related macular degeneration. The t44.27 aptamer is extensively 2′-modified and tightly binds to the heparin-binding domain (HDB) of VEGF165 in a Ca2+-dependent manner. However, the molecular mechanism by which the aptamer selectively recognizes VEGF HDB to antagonize its function is poorly understood. We found that t44.27 binds to VEGF HBD in a two-step manner using a different region in the molecule: a transient interaction using a structured region of t44.27 followed by a tight complex formation with a larger interaction surface. Ca2+ binding stabilizes t44.27 base-pair formation suitable for the initial transient interaction. Meanwhile, the tight complex formation was essential for t44.27 to exert a competitive inhibition of heparin binding to VEGF HBD. These results provide structural insight into how the RNA aptamer specifically interacts with its target molecule to inhibit its activity.

Keywords

  • Received April 11, 2025.
  • Accepted July 22, 2025.

This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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  1. Published in Advance July 31, 2025, doi: 10.1261/rna.080524.125 RNA 31: 1368-1378 © 2025 Takeuchi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society

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