Antibody targeting of E3 ubiquitin ligases for receptor degradation

Nature. 2022 Oct;610(7930):182-189. doi: 10.1038/s41586-022-05235-6. | PubMed

Hadir Marei¹, Wen-Ting K Tsai², Yee-Seir Kee², Karen Ruiz¹, Jieyan He³, Chris Cox⁴, Tao Sun⁵, Sai Penikalapati⁶, Pankaj Dwivedi⁶, Meena Choi⁶, David Kan⁷, Pablo Saenz-Lopez⁷, Kristel Dorighi⁵, Pamela Zhang², Yvonne T Kschonsak¹, Noelyn Kljavin⁸, Dhara Amin¹, Ingrid Kim², Andrew G Mancini⁸, Thao Nguyen⁸, Chunling Wang¹, Eric Janezic³, Alexander Doan³, Elaine Mai³, Hongkang Xi⁹, Chen Gu¹⁰, Melanie Heinlein⁸, Brian Biehs⁸, Jia Wu⁹, Isabelle Lehoux¹¹, Seth Harris¹², Laetitia Comps-Agrar³, Dhaya Seshasayee⁹, Frederic J de Sauvage⁸, Matthew Grimmer¹, Jing Li³, Nicholas J Agard¹³, Felipe de Sousa E Melo¹⁴

1. Discovery Oncology, Genentech, South San Francisco, CA, USA.
2. Antibody Engineering, Genentech, South San Francisco, CA, USA.
3. Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA.
4. Discovery Immunology, Genentech Inc, South San Francisco, CA, USA.
5. Molecular Biology, Genentech, South San Francisco, CA, USA.
6. Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA.
7. Translational Oncology, Genentech, South San Francisco, CA, USA.
8. Molecular Oncology, Genentech, South San Francisco, CA, USA.
9. Antibody discovery, Genentech, South San Francisco, CA, USA.
10. Protein Chemistry, Genentech, South San Francisco, CA, USA.
11. Biomolecular Resources, Genentech, South San Francisco, CA, USA.
12. Structural Biology, Genentech, South San Francisco, CA, USA.
13. Antibody Engineering, Genentech, South San Francisco, CA, USA. agardn@gene.com.
14. Discovery Oncology, Genentech, South San Francisco, CA, USA. desousaf@gene.com.

Abstract

Most current therapies that target plasma membrane receptors function by antagonizing ligand binding or enzymatic activities. However, typical mammalian proteins comprise multiple domains that execute discrete but coordinated activities. Thus, inhibition of one domain often incompletely suppresses the function of a protein. Indeed, targeted protein degradation technologies, including proteolysis-targeting chimeras1 (PROTACs), have highlighted clinically important advantages of target degradation over inhibition2. However, the generation of heterobifunctional compounds binding to two targets with high affinity is complex, particularly when oral bioavailability is required3. Here we describe the development of proteolysis-targeting antibodies (PROTABs) that tether cell-surface E3 ubiquitin ligases to transmembrane proteins, resulting in target degradation both in vitro and in vivo. Focusing on zinc- and ring finger 3 (ZNRF3), a Wnt-responsive ligase, we show that this approach can enable colorectal cancer-specific degradation. Notably, by examining a matrix of additional cell-surface E3 ubiquitin ligases and transmembrane receptors, we demonstrate that this technology is amendable for 'on-demand' degradation. Furthermore, we offer insights on the ground rules governing target degradation by engineering optimized antibody formats. In summary, this work describes a strategy for the rapid development of potent, bioavailable and tissue-selective degraders of cell-surface proteins.

Presented By Hadir Marei | ORCID iD