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Xie H, Li C, Tang H, Tandon I, Liao J, Roberts BL, Zhao Y, Tang W. Development of Substituted Phenyl Dihydrouracil as the Novel Achiral Cereblon Ligands for Targeted Protein Degradation. J Med Chem 2023; 66:2904-2917. [PMID: 36749666 PMCID: PMC10398712 DOI: 10.1021/acs.jmedchem.2c01941] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Glutarimides such as thalidomide, pomalidomide, and lenalidomide are the most frequently used ligands to recruit E3 ubiquitin ligase cereblon (CRBN) for the development of proteolysis-targeting chimeras (PROTACs). Due to the rapid and spontaneous racemization of glutarimides, most CRBN-recruiting PROTACs are synthesized as a mixture of racemates or diastereomers. Since the (S)-enantiomer is primarily responsible for binding to CRBN, the existence of the largely inactive (R)-enantiomer complicates the drug development process. Herein, we report that substituted achiral phenyl dihydrouracil (PDHU) can be used as a novel class of CRBN ligands for the development of PROTACs. Although the parent PDHU has a minimal binding affinity to CRBN, we found that some substituted PDHUs had a comparable binding affinity to lenalidomide. Structural modeling provided a further understanding of the molecular interactions between PDHU ligands and CRBN. PDHUs also have greater stability than lenalidomide. Finally, potent BRD4 degraders were developed by employing trisubstituted PDHUs.
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Affiliation(s)
- Haibo Xie
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Chunrong Li
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Hua Tang
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Ira Tandon
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Junzhuo Liao
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Brett L. Roberts
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Yu Zhao
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Weiping Tang
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706 (USA)
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Yang K, Zhao Y, Nie X, Wu H, Wang B, Almodovar-Rivera CM, Xie H, Tang W. A Cell-Based Target Engagement Assay for the Identification of Cereblon E3 Ubiquitin Ligase Ligands and Their Application in HDAC6 Degraders. Cell Chem Biol 2020; 27:866-876.e8. [PMID: 32413286 DOI: 10.1016/j.chembiol.2020.04.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/04/2020] [Accepted: 04/22/2020] [Indexed: 01/08/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) is a paradigm shift for small-molecule drug discovery. However, limited E3 ubiquitin ligase ligands with cellular activity are available. In vitro binding assays involve the expression and purification of a large amount of proteins and they often yield ligands that are inactive in cell-based assays due to poor cell permeability, stability, and other reasons. Herein, we report the development of a practical and efficient cell-based target engagement assay to evaluate the binding affinity of a small library of cereblon ligands to its E3 ligase in cells. Selected cell-permeable E3 ligase ligands derived from this assay are then used to construct HDAC6 degraders with cellular protein degradation activity. Because the assay does not involve any genetic engineering, it is relatively easy to transfer from one cell type to a different one.
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Affiliation(s)
- Ka Yang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Yu Zhao
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Xueqing Nie
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Hao Wu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Bo Wang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Haibo Xie
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Weiping Tang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA.
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