Proteolysis-targeting chimeras with reduced off-targets

Tuan M Nguyen; Vedagopuram Sreekanth; Arghya Deb; Praveen Kokkonda; Praveen K Tiwari; Katherine A Donovan; Veronika Shoba; Santosh K Chaudhary; Jaron A M Mercer; Sophia Lai; Ananthan Sadagopan; Max Jan; Eric S Fischer; David R Liu; Benjamin L Ebert; Amit Choudhary

doi:10.1038/s41557-023-01379-8

Proteolysis-targeting chimeras with reduced off-targets

Nat Chem. 2024 Feb;16(2):218-228. doi: 10.1038/s41557-023-01379-8. Epub 2023 Dec 18.

Authors

Tuan M Nguyen^#^{1

2

3}, Vedagopuram Sreekanth^#^{1

2

3}, Arghya Deb^#^{1

2}, Praveen Kokkonda^#^{1

2}, Praveen K Tiwari^{1

2

3}, Katherine A Donovan^{4

5}, Veronika Shoba^{1

2}, Santosh K Chaudhary^{1

2}, Jaron A M Mercer^{6

7

8}, Sophia Lai^{1

7}, Ananthan Sadagopan^{1

9}, Max Jan^{10

11

12}, Eric S Fischer^{4

5}, David R Liu^{6

7

8}, Benjamin L Ebert^{10

11

12}, Amit Choudhary^{13

14

15}

Affiliations

¹ Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
² Department of Medicine, Harvard Medical School, Boston, MA, USA.
³ Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA.
⁴ Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
⁵ Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
⁶ Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁷ Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
⁸ Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
⁹ Massachusetts Institute of Technology, Cambridge, MA, USA.
¹⁰ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
¹¹ Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
¹² Howard Hughes Medical Institute, Boston, MA, USA.
¹³ Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA. achoudhary@bwh.harvard.edu.
¹⁴ Department of Medicine, Harvard Medical School, Boston, MA, USA. achoudhary@bwh.harvard.edu.
¹⁵ Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA. achoudhary@bwh.harvard.edu.

^# Contributed equally.

Abstract

Proteolysis-targeting chimeras (PROTACs) are molecules that induce proximity between target proteins and E3 ligases triggering target protein degradation. Pomalidomide, a widely used E3 ligase recruiter in PROTACs, can independently degrade other proteins, including zinc-finger (ZF) proteins, with vital roles in health and disease. This off-target degradation hampers the therapeutic applicability of pomalidomide-based PROTACs, requiring development of PROTAC design rules that minimize off-target degradation. Here we developed a high-throughput platform that interrogates off-target degradation and found that reported pomalidomide-based PROTACs induce degradation of several ZF proteins. We generated a library of pomalidomide analogues to understand how functionalizing different positions of the phthalimide ring, hydrogen bonding, and steric and hydrophobic effects impact ZF protein degradation. Modifications of appropriate size on the C5 position reduced off-target ZF degradation, which we validated through target engagement and proteomics studies. By applying these design principles, we developed anaplastic lymphoma kinase oncoprotein-targeting PROTACs with enhanced potency and minimal off-target degradation.

MeSH terms

Proteins* / metabolism
Proteolysis
Thalidomide / analogs & derivatives*
Thalidomide / pharmacology
Ubiquitin-Protein Ligases* / metabolism

Substances

pomalidomide
Ubiquitin-Protein Ligases
Proteins
Thalidomide

Abstract

MeSH terms

Substances

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