Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation

Abstract
Data availability
Article and author information
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Abstract

Molecular-glue degraders mediate interactions between target proteins and components of the ubiquitin-proteasome system to cause selective protein degradation. Here, we report a new molecular glue HQ461 discovered by high-throughput screening. Using loss-of-function and gain-of-function genetic screening in human cancer cells followed by biochemical reconstitution, we show that HQ461 acts by promoting an interaction between CDK12 and DDB1-CUL4-RBX1 E3 ubiquitin ligase, leading to polyubiquitination and degradation of CDK12-interacting protein Cyclin K (CCNK). Degradation of CCNK mediated by HQ461 compromised CDK12 function, leading to reduced phosphorylation of a CDK12 substrate, downregulation of DNA damage response genes, and cell death. Structure-activity relationship analysis of HQ461 revealed the importance of a 5-methylthiazol-2-amine pharmacophore and resulted in an HQ461 derivate with improved potency. Our studies reveal a new molecular glue that recruits its target protein directly to DDB1 to bypass the requirement of a substrate-specific receptor, presenting a new strategy for targeted protein degradation.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Sequencing data have been deposited in GEO (GSE153700 and GSE153707).

The following data sets were generated

1. Lv L
2. Chen P
3. Cao L
4. Li Y
5. Zeng Z
6. Cui Y
7. Wu Q
8. Li J
9. Wang JH
10. Dong MQ
11. Qi X
12. Han T
(2020) Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation [CRISPR]
NCBI Gene Expression Omnibus, GSE153700.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE153700
1. Lv L
2. Chen P
3. Cao L
4. Li Y
5. Zeng Z
6. Cui Y
7. Wu Q
8. Li J
9. Wang JH
10. Dong MQ
11. Qi X
12. Han T
(2020) Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger Cyclin K degradation [WES]
NCBI Gene Expression Omnibus, GSE153707.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE153707

Article and author information

Author details

Lu Lv

NIBS, National Institute of Biological Sciences, Beijing, China

Competing interests
Lu Lv, A provisional patent application (PCT/CN2020/095482) has been filed for the application of HQ461 and related small molecules as molecular glues regulating CDK12-DDB1 interaction to degrade CCNK..

"This ORCID iD identifies the author of this article:" 0000-0003-2075-8620
Peihao Chen

NIBS, National Institute of Biological Sciences, Beijing, China

Competing interests
Peihao Chen, A provisional patent application (PCT/CN2020/095482) has been filed for the application of HQ461 and related small molecules as molecular glues regulating CDK12-DDB1 interaction to degrade CCNK..
Longzhi Cao

NIBS, National Institute of Biological Sciences, Beijing, China

Competing interests
Longzhi Cao, A provisional patent application (PCT/CN2020/095482) has been filed for the application of HQ461 and related small molecules as molecular glues regulating CDK12-DDB1 interaction to degrade CCNK..
Yamei Li

NIBS, National Institute of Biological Sciences, Beijing, China

Competing interests
Yamei Li, A provisional patent application (PCT/CN2020/095482) has been filed for the application of HQ461 and related small molecules as molecular glues regulating CDK12-DDB1 interaction to degrade CCNK..
Zhi Zeng

NIBS, National Institute of Biological Sciences, Beijing, China

Competing interests
No competing interests declared.
Yue Cui

NIBS, National Institute of Biological Sciences, Beijing, China

Competing interests
No competing interests declared.
Qingcui Wu

NIBS, National Institute of Biological Sciences, Beijing, China

Competing interests
Qingcui Wu, A provisional patent application (PCT/CN2020/095482) has been filed for the application of HQ461 and related small molecules as molecular glues regulating CDK12-DDB1 interaction to degrade CCNK..
Jiaojiao Li

NIBS, National Institute of Biological Sciences, Beijing, China

Competing interests
Jiaojiao Li, A provisional patent application (PCT/CN2020/095482) has been filed for the application of HQ461 and related small molecules as molecular glues regulating CDK12-DDB1 interaction to degrade CCNK..
Jian-Hua Wang

NIBS, National Institute of Biological Sciences, Beijing, China

Competing interests
No competing interests declared.
Meng-Qiu Dong

NIBS, National Institute of Biological Sciences, Beijing, China

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-6094-1182
Xiangbing Qi

NIBS, National Institute of Biological Sciemces, Beijing, China

For correspondence
qixiangbing@nibs.ac.cn

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-7139-5164
Ting Han

NIBS, National Institute of Biological Sciences, Beijing, China

For correspondence
hanting@nibs.ac.cn

Competing interests
Ting Han, A provisional patent application (PCT/CN2020/095482) has been filed for the application of HQ461 and related small molecules as molecular glues regulating CDK12-DDB1 interaction to degrade CCNK..

"This ORCID iD identifies the author of this article:" 0000-0003-3168-8699

Funding

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.