2. Academic Validation
  3. From Screening to Targeted Degradation: Strategies for the Discovery and Optimization of Small Molecule Ligands for PCSK9

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

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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