From Screening to Targeted Degradation: Strategies for the Discovery and Optimization of Small Molecule Ligands for PCSK9

  • Cell Chem Biol. 2020 Jan 16;27(1):32-40.e3. doi: 10.1016/j.chembiol.2019.10.002.
Whitney L Petrilli  1 ,  Gregory C Adam  2 ,  Roman S Erdmann  3 ,  Pravien Abeywickrema  4 ,  Vijayalakshmi Agnani  5 ,  Xi Ai  6 ,  Jen Baysarowich  5 ,  Noel Byrne  4 ,  John P Caldwell  7 ,  Wonsuk Chang  7 ,  Edward DiNunzio  5 ,  Zhe Feng  7 ,  Rachael Ford  4 ,  Sookhee Ha  8 ,  Yongcheng Huang  6 ,  Brian Hubbard  6 ,  Jennifer M Johnston  4 ,  Michael Kavana  5 ,  Jean-Marie Lisnock  5 ,  Rui Liang  7 ,  Jun Lu  4 ,  Zhijian Lu  7 ,  Juncai Meng  4 ,  Peter Orth  8 ,  Oksana Palyha  6 ,  Gopal Parthasarathy  4 ,  Scott P Salowe  5 ,  Sujata Sharma  4 ,  Jennifer Shipman  4 ,  Stephen M Soisson  4 ,  Alison M Strack  6 ,  Hyewon Youm  7 ,  Kake Zhao  7 ,  Deborah L Zink  5 ,  Hratch Zokian  5 ,  George H Addona  5 ,  Karen Akinsanya  6 ,  James R Tata  7 ,  Yusheng Xiong  7 ,  Jason E Imbriglio  7
Affiliations
  • 1. Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA. Electronic address: [email protected].
  • 2. Pharmacology, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA. Electronic address: [email protected].
  • 3. Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA; Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA. Electronic address: [email protected].
  • 4. Computational and Structural Chemistry, Merck & Co. Inc., 770 Sumneytown Pike, West Point, PA 19486, USA.
  • 5. In Vitro Pharmacology, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.
  • 6. Cardio Metabolic Diseases, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.
  • 7. Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.
  • 8. Computational and Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.
PMID: 31653597 DOI: 10.1016/j.chembiol.2019.10.002
Abstract

Proprotein convertase substilisin-like/kexin type 9 (PCSK9) is a serine Protease involved in a protein-protein interaction with the low-density lipoprotein (LDL) receptor that has both human genetic and clinical validation. Blocking this protein-protein interaction prevents LDL receptor degradation and thereby decreases LDL Cholesterol levels. Our pursuit of small-molecule direct Binders for this difficult to drug PPI target utilized affinity selection/mass spectrometry, which identified one confirmed hit compound. An X-ray crystal structure revealed that this compound was binding in an unprecedented allosteric pocket located between the catalytic and C-terminal domain. Optimization of this initial hit, using two distinct strategies, led to compounds with high binding affinity to PCSK9. Direct target engagement was demonstrated in the cell lysate with a cellular thermal shift assay. Finally, ligand-induced protein degradation was shown with a Proteasome recruiting tag attached to the high-affinity allosteric ligand for PCSK9.

Keywords
CETSA; PCSK9; affinity selection/mass spectrometry; proximity-driven click chemistry; structure-based drug design; targeted protein degradation.
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