101
|
Jin YH, Lu MC, Wang Y, Shan WX, Wang XY, You QD, Jiang ZY. Azo-PROTAC: Novel Light-Controlled Small-Molecule Tool for Protein Knockdown. J Med Chem 2020; 63:4644-4654. [DOI: 10.1021/acs.jmedchem.9b02058] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yu-Hui Jin
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Meng-Chen Lu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yan Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wen-Xin Shan
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xuan-Yu Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Zheng-Yu Jiang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
102
|
Sun N, Ren C, Kong Y, Zhong H, Chen J, Li Y, Zhang J, Zhou Y, Qiu X, Lin H, Song X, Yang X, Jiang B. Development of a Brigatinib degrader (SIAIS117) as a potential treatment for ALK positive cancer resistance. Eur J Med Chem 2020; 193:112190. [PMID: 32179332 DOI: 10.1016/j.ejmech.2020.112190] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/24/2020] [Accepted: 02/24/2020] [Indexed: 11/30/2022]
Abstract
EML4-ALK and NPM-ALK fusion proteins possess constitutively activated ALK (anaplastic lymphoma kinase) activity, which in turn leads to the development of non-small cell lung cancer and anaplastic large-cell lymphomas (ALCLs). FDA-approved ALK inhibitor drugs cause significant cancer regression. However, drug resistance eventually occurs and it becomes a big obstacle in clinic. Novel proteolysis targeting chimera (PROTAC) technology platform provides a potential therapeutic strategy for drug resistance. Herein, we designed and synthesized a series of ALK PROTACs based on Brigatinib and VHL-1 conjunction, and screened SIAIS117 as the best degrader which not only blocked the growth of SR and H2228 cancer cell lines, but also degraded ALK protein. In addition, SIAIS117 also showed much better growth inhibition effect than Brigatinib on 293T cell line that exogenously expressed G1202R-resistant ALK proteins. Furthermore, it also degraded G1202R mutant ALK protein in vitro. At last, it has the potentially anti-proliferation ability of small cell lung cancer. Thus, we have successfully generated the degrader SIAIS117 that can potentially overcome resistance in cancer targeted therapy.
Collapse
Affiliation(s)
- Ning Sun
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Chaowei Ren
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Ying Kong
- Jing Medicine Technology (Shanghai), Ltd., Y building, 230 Haike Road, Shanghai, 201210, China
| | - Hui Zhong
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China; Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Jinju Chen
- Jing Medicine Technology (Shanghai), Ltd., Y building, 230 Haike Road, Shanghai, 201210, China
| | - Yan Li
- Jing Medicine Technology (Shanghai), Ltd., Y building, 230 Haike Road, Shanghai, 201210, China
| | - Jianshui Zhang
- Jing Medicine Technology (Shanghai), Ltd., Y building, 230 Haike Road, Shanghai, 201210, China
| | - Yuedong Zhou
- Jing Medicine Technology (Shanghai), Ltd., Y building, 230 Haike Road, Shanghai, 201210, China
| | - Xing Qiu
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Haifan Lin
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China; Yale Stem Cell Center, Yale University, New Haven, CT, 06511, USA.
| | - Xiaoling Song
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China.
| | - Xiaobao Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China.
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China; CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
| |
Collapse
|
103
|
Reynders M, Matsuura BS, Bérouti M, Simoneschi D, Marzio A, Pagano M, Trauner D. PHOTACs enable optical control of protein degradation. SCIENCE ADVANCES 2020; 6:eaay5064. [PMID: 32128406 PMCID: PMC7034999 DOI: 10.1126/sciadv.aay5064] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/22/2019] [Indexed: 05/13/2023]
Abstract
PROTACs (PROteolysis TArgeting Chimeras) are bifunctional molecules that target proteins for ubiquitylation by an E3 ligase complex and subsequent degradation by the proteasome. They have emerged as powerful tools to control the levels of specific cellular proteins. We now introduce photoswitchable PROTACs that can be activated with the spatiotemporal precision that light provides. These trifunctional molecules, which we named PHOTACs (PHOtochemically TArgeting Chimeras), consist of a ligand for an E3 ligase, a photoswitch, and a ligand for a protein of interest. We demonstrate this concept by using PHOTACs that target either BET family proteins (BRD2,3,4) or FKBP12. Our lead compounds display little or no activity in the dark but can be reversibly activated with different wavelengths of light. Our modular approach provides a method for the optical control of protein levels with photopharmacology and could lead to new types of precision therapeutics that avoid undesired systemic toxicity.
Collapse
Affiliation(s)
- Martin Reynders
- Department of Chemistry, New York University, New York, NY 10003, USA
- Department of Chemistry, Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Bryan S. Matsuura
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Marleen Bérouti
- Department of Chemistry, New York University, New York, NY 10003, USA
- Department of Chemistry, Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Daniele Simoneschi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Antonio Marzio
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Dirk Trauner
- Department of Chemistry, New York University, New York, NY 10003, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
- NYU Neuroscience Institute, New York University School of Medicine, New York, NY 10016, USA
| |
Collapse
|
104
|
Verma R, Mohl D, Deshaies RJ. Harnessing the Power of Proteolysis for Targeted Protein Inactivation. Mol Cell 2020; 77:446-460. [PMID: 32004468 DOI: 10.1016/j.molcel.2020.01.010] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/26/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022]
Abstract
Two decades into the twenty-first century, a confluence of breakthrough technologies wielded at the molecular level is presenting biologists with unique opportunities to unravel the complexities of the cellular world. CRISPR/Cas9 allows gene knock-outs, knock-ins, and single-base editing at chromosomal loci. RNA-based tools such as siRNA, antisense oligos, and morpholinos can be used to silence expression of specific genes. Meanwhile, protein knockdown tools that draw inspiration from natural regulatory mechanisms and facilitate elimination of native or degron-tagged proteins from cells are rapidly emerging. The acute and reversible reduction in protein levels enabled by these methods allows for precise determination of loss-of-function phenotypes free from secondary effects or compensatory adaptation that can confound nucleic-acid-based methods that involve slow depletion or permanent loss of a protein. In this Review, we summarize the ingenious ways biologists have exploited natural mechanisms for protein degradation to direct the elimination of specific proteins at will. This has led to advancements not only in basic research but also in the therapeutic space with the introduction of PROTACs into clinical trials for cancer patients.
Collapse
Affiliation(s)
- Rati Verma
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, CA 91320, USA.
| | - Dane Mohl
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | | |
Collapse
|
105
|
Wang Y, Han L, Liu F, Yang F, Jiang X, Sun H, Feng F, Xue J, Liu W. Targeted degradation of anaplastic lymphoma kinase by gold nanoparticle-based multi-headed proteolysis targeting chimeras. Colloids Surf B Biointerfaces 2020; 188:110795. [PMID: 31991291 DOI: 10.1016/j.colsurfb.2020.110795] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/19/2019] [Accepted: 01/12/2020] [Indexed: 02/01/2023]
Abstract
Anaplastic lymphoma kinase (ALK) is a major target in treating non-small-cell lung cancer, and several ALK inhibitors have been developed to antagonize its kinase activity. However, patients treated with inhibitors ultimately develop drug resistance. Therefore, therapies with new mechanisms of action are needed. Proteolysis targeting chimeras (PROTACs) are molecules that comprise a ligand for binding a protein of interest (POI), a connecting linker and a ligand for recruiting E3 ligase, and cause degradation of the target POI. Here, the first multi-headed PROTAC, as a proof of concept, is developed as a gold nanoparticle (GNP)-based drug delivery system for delivering PROTACs to target ALK. Pegylated GNPs loaded with both ceritinib and pomalidomide molecules, termed Cer/Pom-PEG@GNPs, showed good stability in several media. The GNP conjugates potently decreased the levels of ALK fusion proteins in a dose- and time-dependent manner, and specifically inhibited the proliferation of NCI-H2228 cells. In comparison with small molecule PROTACs, the new multi-headed PROTAC promoted the formation of coacervates of POIs/multi-headed PROTAC/E3 ubiquitin ligases, and POI and E3 ubiquitin ligase interacted through multidirectional ligands and a flexible linker, thereby avoiding the need for complicated structure optimization of PROTACs. In conclusion, Cer/Pom-PEG@GNPs can degrade intracellular ALK fusion proteins with minor off-target toxicity and can be applied in patients resistant to ALK inhibitors. As a nano-based drug carrier, Cer/Pom-PEG@GNPs have the potential to enable prolonged circulation and specifically distribute drugs to tumor regions in vivo; thus, further investigation is warranted.
Collapse
Affiliation(s)
- Yingming Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Lingfei Han
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Fulei Liu
- The Joint Laboratory of China Pharmaceutical University and Taian City Central Hospital, Taian City Central Hospital, Taian, Shandong, 271000, China; Pharmaceutical Department, Taian City Central Hospital, Taian, Shandong 271000, China
| | - Fubai Yang
- The Joint Laboratory of China Pharmaceutical University and Taian City Central Hospital, Taian City Central Hospital, Taian, Shandong, 271000, China
| | - Xueyang Jiang
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu 210009, China; The Joint Laboratory of China Pharmaceutical University and Taian City Central Hospital, Taian City Central Hospital, Taian, Shandong, 271000, China
| | - Haopeng Sun
- The Joint Laboratory of China Pharmaceutical University and Taian City Central Hospital, Taian City Central Hospital, Taian, Shandong, 271000, China; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Feng Feng
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu 210009, China; The Joint Laboratory of China Pharmaceutical University and Taian City Central Hospital, Taian City Central Hospital, Taian, Shandong, 271000, China
| | - Jingwei Xue
- The Joint Laboratory of China Pharmaceutical University and Taian City Central Hospital, Taian City Central Hospital, Taian, Shandong, 271000, China.
| | - Wenyuan Liu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, Jiangsu 210009, China.
| |
Collapse
|
106
|
Zeng M, Xiong Y, Safaee N, Nowak RP, Donovan KA, Yuan CJ, Nabet B, Gero TW, Feru F, Li L, Gondi S, Ombelets LJ, Quan C, Jänne PA, Kostic M, Scott DA, Westover KD, Fischer ES, Gray NS. Exploring Targeted Degradation Strategy for Oncogenic KRAS G12C. Cell Chem Biol 2019; 27:19-31.e6. [PMID: 31883964 DOI: 10.1016/j.chembiol.2019.12.006] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/15/2019] [Accepted: 12/06/2019] [Indexed: 12/20/2022]
Abstract
KRAS is the most frequently mutated oncogene found in pancreatic, colorectal, and lung cancers. Although it has been challenging to identify targeted therapies for cancers harboring KRAS mutations, KRASG12C can be targeted by small-molecule inhibitors that form covalent bonds with cysteine 12 (C12). Here, we designed a library of C12-directed covalent degrader molecules (PROTACs) and subjected them to a rigorous evaluation process to rapidly identify a lead compound. Our lead degrader successfully engaged CRBN in cells, bound KRASG12Cin vitro, induced CRBN/KRASG12C dimerization, and degraded GFP-KRASG12C in reporter cells in a CRBN-dependent manner. However, it failed to degrade endogenous KRASG12C in pancreatic and lung cancer cells. Our data suggest that inability of the lead degrader to effectively poly-ubiquitinate endogenous KRASG12C underlies the lack of activity. We discuss challenges for achieving targeted KRASG12C degradation and proposed several possible solutions which may lead to efficient degradation of endogenous KRASG12C.
Collapse
Affiliation(s)
- Mei Zeng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yuan Xiong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Nozhat Safaee
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Christine J Yuan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas W Gero
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Frederic Feru
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Lianbo Li
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Lincoln J Ombelets
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Chunshan Quan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology and the Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Milka Kostic
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - David A Scott
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
107
|
Sun X, Gao H, Yang Y, He M, Wu Y, Song Y, Tong Y, Rao Y. PROTACs: great opportunities for academia and industry. Signal Transduct Target Ther 2019; 4:64. [PMID: 31885879 PMCID: PMC6927964 DOI: 10.1038/s41392-019-0101-6] [Citation(s) in RCA: 346] [Impact Index Per Article: 69.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/17/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023] Open
Abstract
Although many kinds of therapies are applied in the clinic, drug-resistance is a major and unavoidable problem. Another disturbing statistic is the limited number of drug targets, which are presently only 20-25% of all protein targets that are currently being studied. Moreover, the focus of current explorations of targets are their enzymatic functions, which ignores the functions from their scaffold moiety. As a promising and appealing technology, PROteolysis TArgeting Chimeras (PROTACs) have attracted great attention both from academia and industry for finding available approaches to solve the above problems. PROTACs regulate protein function by degrading target proteins instead of inhibiting them, providing more sensitivity to drug-resistant targets and a greater chance to affect the nonenzymatic functions. PROTACs have been proven to show better selectivity compared to classic inhibitors. PROTACs can be described as a chemical knockdown approach with rapidity and reversibility, which presents new and different biology compared to other gene editing tools by avoiding misinterpretations that arise from potential genetic compensation and/or spontaneous mutations. PRTOACs have been widely explored throughout the world and have outperformed not only in cancer diseases, but also in immune disorders, viral infections and neurodegenerative diseases. Although PROTACs present a very promising and powerful approach for crossing the hurdles of present drug discovery and tool development in biology, more efforts are needed to gain to get deeper insight into the efficacy and safety of PROTACs in the clinic. More target binders and more E3 ligases applicable for developing PROTACs are waiting for exploration.
Collapse
Affiliation(s)
- Xiuyun Sun
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Hongying Gao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Yiqing Yang
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084 P. R. China
| | - Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yue Wu
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yugang Song
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yan Tong
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084 P. R. China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001 China
| |
Collapse
|
108
|
Ohoka N, Tsuji G, Shoda T, Fujisato T, Kurihara M, Demizu Y, Naito M. Development of Small Molecule Chimeras That Recruit AhR E3 Ligase to Target Proteins. ACS Chem Biol 2019; 14:2822-2832. [PMID: 31580635 DOI: 10.1021/acschembio.9b00704] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Targeted protein degradation using chimeric small molecules such as proteolysis-targeting chimeras (PROTACs) and specific and nongenetic inhibitors of apoptosis protein [IAP]-dependent protein erasers (SNIPERs) is an emerging modality in drug discovery. Here, we expand the repertoire of E3 ligases capable of ubiquitylating target proteins using this system. By incorporating β-naphthoflavone (β-NF) as a ligand, we developed a novel class of chimeric molecules that recruit the arylhydrocarbon receptor (AhR) E3 ligase complex. β-NF-ATRA, a chimeric degrader directed against cellular retinoic acid binding proteins (CRABPs), induced the AhR-dependent degradation of CRABP-1 and CRABP-2 via the ubiquitin-proteasome pathway. A similar compound ITE-ATRA, in which an alternative AhR ligand was used, also degraded CRABP proteins. Finally, we developed a chimeric compound β-NF-JQ1 that is directed against bromodomain-containing (BRD) proteins using β-NF as an AhR ligand. β-NF-JQ1 induced the interaction of AhR and BRD proteins and displayed effective anticancer activity that correlated with protein knockdown activity. These results demonstrate a novel class of chimeric degrader molecules based on the ability to bring a target protein and an AhR E3 ligase into close proximity.
Collapse
|
109
|
Development of selective mono or dual PROTAC degrader probe of CDK isoforms. Eur J Med Chem 2019; 187:111952. [PMID: 31846828 DOI: 10.1016/j.ejmech.2019.111952] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/27/2019] [Accepted: 12/03/2019] [Indexed: 02/05/2023]
Abstract
Cyclin-dependent kinase (CDK) family members are promising molecular targets in discovering potent inhibitors in disease settings, they function differentially. CDK2, CDK4 and CDK6, directly regulate the cell cycle, while CDK9 primarily modulates the transcription regulation. In discovering inhibitors of these CDKs, toxicity associated with off-target effect on other CDK homologs often posts as a clinical issue and hinders their further therapeutic development. To improve efficacy and reduce toxicity, here, using the Proteolysis Targeted Chimeras (PROTACs) approach, we design and further optimize small molecule degraders targeting multiple CDKs. We showed that heterobifunctional compound A9 selectively degraded CDK2. We also identified a dual-degrader, compound F3, which potently induced degradation of both CDK2 (DC50: 62 nM) and CDK9 (DC50: 33 nM). In human prostate cancer PC-3 cells, compound F3 potently inhibits cell proliferation by effectively blocking the cell cycle in S and G2/M phases. Our preliminary data suggests that PROTAC-oriented CDK2/9 degradation is potentially an effective therapeutic approach.
Collapse
|
110
|
Han X, Zhao L, Xiang W, Qin C, Miao B, Xu T, Wang M, Yang CY, Chinnaswamy K, Stuckey J, Wang S. Discovery of Highly Potent and Efficient PROTAC Degraders of Androgen Receptor (AR) by Employing Weak Binding Affinity VHL E3 Ligase Ligands. J Med Chem 2019; 62:11218-11231. [PMID: 31804827 DOI: 10.1021/acs.jmedchem.9b01393] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Androgen receptor (AR) is a validated therapeutic target for the treatment of metastatic castration-resistant prostate cancer (mCRPC). We report herein our design, synthesis, and biological characterization of highly potent small-molecule proteolysis targeting chimera (PROTAC) AR degraders using a potent AR antagonist and E3 ligase ligands with weak binding affinities to VHL protein. Our study resulted in the discovery of 11 (ARD-266), which effectively induces degradation of AR protein in AR-positive (AR+) LNCaP, VCaP, and 22Rv1 prostate cancer cell lines with DC50 values of 0.2-1 nM. ARD-266 is capable of reducing the AR protein level by >95% in these AR+ prostate cancer cell lines and effectively reduces AR-regulated gene expression suppression. For the first time, we demonstrated that an E3 ligand with micromolar binding affinity to its E3 ligase complex can be successfully employed for the design of highly potent and efficient PROTAC degraders and this finding may have a significant implication for the field of PROTAC research.
Collapse
Affiliation(s)
| | - Lijie Zhao
- School of Pharmaceutical Sciences and Institute of Drug Discovery & Development , Zhengzhou University , Zhengzhou 450001 , China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
111
|
Targeted protein degradation: expanding the toolbox. Nat Rev Drug Discov 2019; 18:949-963. [PMID: 31666732 DOI: 10.1038/s41573-019-0047-y] [Citation(s) in RCA: 485] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 12/19/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) and related molecules that induce targeted protein degradation by the ubiquitin-proteasome system represent a new therapeutic modality and are the focus of great interest, owing to potential advantages over traditional occupancy-based inhibitors with respect to dosing, side effects, drug resistance and modulating 'undruggable' targets. However, the technology is still maturing, and the design elements for successful PROTAC-based drugs are currently being elucidated. Importantly, fewer than 10 of the more than 600 E3 ubiquitin ligases have so far been exploited for targeted protein degradation, and expansion of knowledge in this area is a key opportunity. Here, we briefly discuss lessons learned about targeted protein degradation in chemical biology and drug discovery and systematically review the expression profile, domain architecture and chemical tractability of human E3 ligases that could expand the toolbox for PROTAC discovery.
Collapse
|
112
|
Pfaff P, Samarasinghe KTG, Crews CM, Carreira EM. Reversible Spatiotemporal Control of Induced Protein Degradation by Bistable PhotoPROTACs. ACS CENTRAL SCIENCE 2019; 5:1682-1690. [PMID: 31660436 PMCID: PMC6813558 DOI: 10.1021/acscentsci.9b00713] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 05/09/2023]
Abstract
Off-tissue effects are persistent issues of modern inhibition-based therapies. By merging the strategies of photopharmacology and small-molecule degraders, we introduce a novel concept for persistent spatiotemporal control of induced protein degradation that potentially prevents off-tissue toxicity. Building on the successful principle of bifunctional all-small-molecule Proteolysis Targeting Chimeras (PROTACs), we designed photoswitchable PROTACs (photoPROTACs) by including ortho-F4-azobenzene linkers between both warhead ligands. This highly bistable yet photoswitchable structural component leads to reversible control over the topological distance between both ligands. The azo-cis-isomer is observed to be inactive because the distance defined by the linker is prohibitively short to permit complex formation between the protein binding partners. By contrast, the azo-trans-isomer is active since it can engage both protein partners to form the necessary and productive ternary complex. Importantly, due to the bistable nature of the ortho-F4-azobenzene moiety employed, the photostationary state of the photoPROTAC is persistent, with no need for continuous irradiation. This technique offers reversible on/off switching of protein degradation that is compatible with an intracellular environment and, therefore, could be useful in experimental exploration of biological signaling pathways-such as those crucial for oncogenic signal transduction. Additionally, this strategy may be suitable for therapeutic intervention to address a variety of diseases. By enabling reversible activation and deactivation of protein degradation, photoPROTACs offer advantages over conventional photocaging strategies that irreversibly release active agents.
Collapse
Affiliation(s)
- Patrick Pfaff
- Department
of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Kusal T. G. Samarasinghe
- Department
of Molecular, Cell, and Developmental Biology, Yale University, 260
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Department
of Molecular, Cell, and Developmental Biology, Yale University, 260
Whitney Avenue, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Department
of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Erick M. Carreira
- Department
of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| |
Collapse
|
113
|
Asatsuma-Okumura T, Ito T, Handa H. Molecular mechanisms of cereblon-based drugs. Pharmacol Ther 2019; 202:132-139. [DOI: 10.1016/j.pharmthera.2019.06.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/06/2019] [Indexed: 01/25/2023]
|
114
|
Kong X, Pan P, Sun H, Xia H, Wang X, Li Y, Hou T. Drug Discovery Targeting Anaplastic Lymphoma Kinase (ALK). J Med Chem 2019; 62:10927-10954. [PMID: 31419130 DOI: 10.1021/acs.jmedchem.9b00446] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As a receptor tyrosine kinase of insulin receptor (IR) subfamily, anaplastic lymphoma kinase (ALK) has been validated to play important roles in various cancers, especially anaplastic large cell lymphoma (ALCL), nonsmall cell lung cancer (NSCLC), and neuroblastomas. Currently, five small-molecule inhibitors of ALK, including Crizotinib, Ceritinib, Alectinib, Brigatinib, and Lorlatinib, have been approved by the U.S. Food and Drug Administration (FDA) against ALK-positive NSCLCs. Novel type-I1/2 and type-II ALK inhibitors with improved kinase selectivity and enhanced capability to combat drug resistance have also been reported. Moreover, the "proteolysis targeting chimera" (PROTAC) technique has been successfully applied in developing ALK degraders, which opened a new avenue for targeted ALK therapies. This review provides an overview of the physiological and biological functions of ALK, the discovery and development of drugs targeting ALK by focusing on their chemotypes, activity, selectivity, and resistance as well as potential therapeutic strategies to overcome drug resistance.
Collapse
Affiliation(s)
- Xiaotian Kong
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China.,Institute of Functional Nano and Soft Materials (FUNSOM) , Soochow University , Suzhou , Jiangsu 215123 , China
| | - Peichen Pan
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Hongguang Xia
- Department of Biochemistry & Research Center of Clinical Pharmacy of the First Affiliated Hospital , Zhejiang University , Hangzhou 310058 , China
| | - Xuwen Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM) , Soochow University , Suzhou , Jiangsu 215123 , China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| |
Collapse
|
115
|
Maple HJ, Clayden N, Baron A, Stacey C, Felix R. Developing degraders: principles and perspectives on design and chemical space. MEDCHEMCOMM 2019; 10:1755-1764. [PMID: 31867093 PMCID: PMC6894040 DOI: 10.1039/c9md00272c] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/20/2019] [Indexed: 12/18/2022]
Abstract
Degraders (e.g. PROTACs, SNIPERs, degronimers etc.) are a new modality offering increasing potential both as tools for basic research and therapeutic development.
Degraders (e.g. PROTACs, SNIPERs, degronimers etc.) are a new modality offering increasing potential both as tools for basic research and therapeutic development. They occupy chemical space that lies outside the classical Lipinski ‘Rule of 5’, which poses fresh challenges for achieving cell permeability and oral bioavailability. This study presents a comprehensive database of degrader structures from the peer reviewed literature, including both optimized degraders and first generation compounds, in order to provide a thorough assessment of the chemical space associated with this modality and identify common trends used during the ‘hit to lead’ process. The results provide insights into this new area of chemical space as well as pointers for degrader design, which we anticipate will be useful for researchers entering this field.
Collapse
Affiliation(s)
- Hannah J Maple
- Bio-Techne (Tocris) , The Watkins Building , Atlantic Road, Avonmouth , Bristol , BS11 9QD , UK .
| | - Nat Clayden
- Bio-Techne (Tocris) , The Watkins Building , Atlantic Road, Avonmouth , Bristol , BS11 9QD , UK .
| | - Anne Baron
- Bio-Techne (Tocris) , The Watkins Building , Atlantic Road, Avonmouth , Bristol , BS11 9QD , UK .
| | - Callum Stacey
- Bio-Techne (Tocris) , The Watkins Building , Atlantic Road, Avonmouth , Bristol , BS11 9QD , UK .
| | - Robert Felix
- Bio-Techne (Tocris) , The Watkins Building , Atlantic Road, Avonmouth , Bristol , BS11 9QD , UK .
| |
Collapse
|
116
|
Röth S, Fulcher LJ, Sapkota GP. Advances in targeted degradation of endogenous proteins. Cell Mol Life Sci 2019; 76:2761-2777. [PMID: 31030225 PMCID: PMC6588652 DOI: 10.1007/s00018-019-03112-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/23/2019] [Accepted: 04/16/2019] [Indexed: 01/07/2023]
Abstract
Protein silencing is often employed as a means to aid investigations in protein function and is increasingly desired as a therapeutic approach. Several types of protein silencing methodologies have been developed, including targeting the encoding genes, transcripts, the process of translation or the protein directly. Despite these advances, most silencing systems suffer from limitations. Silencing protein expression through genetic ablation, for example by CRISPR/Cas9 genome editing, is irreversible, time consuming and not always feasible. Similarly, RNA interference approaches warrant prolonged treatments, can lead to incomplete protein depletion and are often associated with off-target effects. Targeted proteolysis has the potential to overcome some of these limitations. The field of targeted proteolysis has witnessed the emergence of many methodologies aimed at targeting specific proteins for degradation in a spatio-temporal manner. In this review, we provide an appraisal of the different targeted proteolytic systems and discuss their applications in understanding protein function, as well as their potential in therapeutics.
Collapse
Affiliation(s)
- Sascha Röth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Luke J Fulcher
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Gopal P Sapkota
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
| |
Collapse
|
117
|
Proteolysis targeting chimeras (PROTACs) in ‘beyond rule-of-five’ chemical space: Recent progress and future challenges. Bioorg Med Chem Lett 2019; 29:1555-1564. [DOI: 10.1016/j.bmcl.2019.04.030] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/11/2019] [Accepted: 04/16/2019] [Indexed: 12/14/2022]
|
118
|
Qiu X, Sun N, Kong Y, Li Y, Yang X, Jiang B. Chemoselective Synthesis of Lenalidomide-Based PROTAC Library Using Alkylation Reaction. Org Lett 2019; 21:3838-3841. [DOI: 10.1021/acs.orglett.9b01326] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xing Qiu
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Ning Sun
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Ying Kong
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yan Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Xiaobao Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Biao Jiang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| |
Collapse
|
119
|
Targeted protein degradation: elements of PROTAC design. Curr Opin Chem Biol 2019; 50:111-119. [PMID: 31004963 DOI: 10.1016/j.cbpa.2019.02.022] [Citation(s) in RCA: 322] [Impact Index Per Article: 64.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 12/26/2022]
Abstract
Targeted protein degradation using Proteolysis Targeting Chimeras (PROTACs) has emerged as a novel therapeutic modality in drug discovery. PROTACs mediate the degradation of select proteins of interest (POIs) by hijacking the activity of E3 ubiquitin ligases for POI ubiquitination and subsequent degradation by the 26S proteasome. This hijacking mechanism has been used to degrade various types of disease-relevant POIs. In this review, we aim to highlight the recent advances in targeted protein degradation and describe the challenges that need to be addressed in order to efficiently develop potent PROTACs.
Collapse
|
120
|
Shibata N, Ohoka N, Hattori T, Naito M. Development of a Potent Protein Degrader against Oncogenic BCR-ABL Protein. Chem Pharm Bull (Tokyo) 2019; 67:165-172. [PMID: 30827996 DOI: 10.1248/cpb.c18-00703] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chromosomal translocation occurs in some cancer cells, resulting in the expression of aberrant oncogenic fusion proteins that include BCR-ABL in chronic myelogenous leukemia (CML). Inhibitors of ABL tyrosine kinase, such as imatinib and dasatinib, exhibit remarkable therapeutic effects, although emergence of drug resistance hampers the therapy during long-term treatment. An alternative approach to treat CML is to downregulate expression of the BCR-ABL protein. Recently, we have devised a protein knockdown system by hybrid molecules named Specific and Nongenetic inhibitor of apoptosis protein [IAP]-dependent Protein Erasers (SNIPER). This system is designed to induce IAP-mediated ubiquitylation and proteasomal degradation of target proteins. In this review, we describe the development of SNIPER against BCR-ABL, and discuss the features and prospect for treatment of CML.
Collapse
Affiliation(s)
- Norihito Shibata
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences
| | - Nobumichi Ohoka
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences
| | - Takayuki Hattori
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences
| | - Mikihiko Naito
- Divisions of Molecular Target and Gene Therapy Products, National Institute of Health Sciences
| |
Collapse
|
121
|
Popow J, Arnhof H, Bader G, Berger H, Ciulli A, Covini D, Dank C, Gmaschitz T, Greb P, Karolyi-Özguer J, Koegl M, McConnell DB, Pearson M, Rieger M, Rinnenthal J, Roessler V, Schrenk A, Spina M, Steurer S, Trainor N, Traxler E, Wieshofer C, Zoephel A, Ettmayer P. Highly Selective PTK2 Proteolysis Targeting Chimeras to Probe Focal Adhesion Kinase Scaffolding Functions. J Med Chem 2019; 62:2508-2520. [DOI: 10.1021/acs.jmedchem.8b01826] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Johannes Popow
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Helmut Berger
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - David Covini
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Christian Dank
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Peter Greb
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Maria Rieger
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | | | | | - Markus Spina
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Nicole Trainor
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | | | | | | | - Peter Ettmayer
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| |
Collapse
|
122
|
Scheepstra M, Hekking KF, van Hijfte L, Folmer RH. Bivalent Ligands for Protein Degradation in Drug Discovery. Comput Struct Biotechnol J 2019; 17:160-176. [PMID: 30788082 PMCID: PMC6369262 DOI: 10.1016/j.csbj.2019.01.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/16/2019] [Accepted: 01/19/2019] [Indexed: 01/19/2023] Open
Abstract
Targeting the "undruggable" proteome remains one of the big challenges in drug discovery. Recent innovations in the field of targeted protein degradation and manipulation of the ubiquitin-proteasome system open up new therapeutic approaches for disorders that cannot be targeted with conventional inhibitor paradigms. Proteolysis targeting chimeras (PROTACs) are bivalent ligands in which a compound that binds to the protein target of interest is connected to a second molecule that binds an E3 ligase via a linker. The E3 protein is usually either Cereblon or Von Hippel-Lindau. Several examples of selective PROTAC molecules with potent effect in cells and in vivo models have been reported. The degradation of specific proteins via these bivalent molecules is already allowing for the study of biochemical pathways and cell biology with more specificity than was possible with inhibitor compounds. In this review, we provide a comprehensive overview of recent developments in the field of small molecule mediated protein degradation, including transcription factors, kinases and nuclear receptors. We discuss the potential benefits of protein degradation over inhibition as well as the challenges that need to be overcome.
Collapse
Key Words
- ABCB1, ATP-binding cassette sub-family B member 1
- AD, Alzheimer's disease
- AHR, aryl hydrogen receptor
- ALK, anaplastic lymphoma kinase
- Aβ, amyloid-β
- BET, bromodomain and extra-terminal
- BTK, Bruton's tyrosine kinase
- Bcl6, B-cell lymphoma 6
- Bivalent ligand
- Brd4, bromodomain 4
- CDK9, cyclin dependent kinase 9
- CK2, Casein kinase 2
- CLIPTAC, click-formed proteolysis targeting chimera
- CRBN, Cereblon
- Chimera
- DC50, the compound concentration that results in 50% target protein degradation
- DHODH, Dihydroorotate dehydrogenase
- Degrader
- ERK1, extracellular signal-regulated kinase 1
- ERRα, estrogen-related receptor alpha
- ERα, estrogen receptor alpha
- EZH2, enhancer of zeste homolog 2
- FLT3, FMS-like tyrosine kinase-3
- FRS2, fibroblast growth factor receptor substrate 2
- GCN5, general control nonderepressible 5
- GPCR, G-protein coupled receptor
- GST, glutathione S-transferase
- HDAC, histone deacetylase
- HTS, high-throughput screening
- MDM2, mouse double-minute 2 homolog
- MetAP-2, methionine aminopeptidase-2
- PCAF, P300/CBP-associated factor
- PEG, polyethylene glycol
- PI3K, phosphatidylinositol-3-kinase
- PLK-1, polo-like kinase 1
- POI, protein of interest
- PROTAC
- PROTAC, proteolysis targeting chimeras
- Proteasome
- Protein degradation
- RAR, retinoic acid receptor
- RIPK2, receptor-interacting serine/threonine-protein kinase 2
- RTK, receptor tyrosine kinase
- SARM, selective androgen receptor modulator
- SNIPER, specific and non-genetic IAP-dependent protein eraser
- TBK1, TANK-Binding kinase 1
- TRIM24, tripartite motif-containing 24 (also known as TIF1α)
- VHL, Von Hippel-Lindau
- cIAP1, cellular inhibitor of apoptosis protein
Collapse
|
123
|
Zhao Q, Lan T, Su S, Rao Y. Induction of apoptosis in MDA-MB-231 breast cancer cells by a PARP1-targeting PROTAC small molecule. Chem Commun (Camb) 2019; 55:369-372. [PMID: 30540295 DOI: 10.1039/c8cc07813k] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) is a major member of the PARP superfamily that is involved in DNA damage signalling and other important cellular processes. Here we report the development of a small molecule targeting PARP1 based on the PROTAC strategy. In the MDA-MB-231 cell line, the representative compound 3 can induce significant PARP1 cleavage and programmed cell death.
Collapse
Affiliation(s)
- Qiuye Zhao
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
| | | | | | | |
Collapse
|
124
|
Han X, Wang C, Qin C, Xiang W, Fernandez-Salas E, Yang CY, Wang M, Zhao L, Xu T, Chinnaswamy K, Delproposto J, Stuckey J, Wang S. Discovery of ARD-69 as a Highly Potent Proteolysis Targeting Chimera (PROTAC) Degrader of Androgen Receptor (AR) for the Treatment of Prostate Cancer. J Med Chem 2019; 62:941-964. [PMID: 30629437 DOI: 10.1021/acs.jmedchem.8b01631] [Citation(s) in RCA: 241] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report herein the discovery of highly potent PROTAC degraders of androgen receptor (AR), as exemplified by compound 34 (ARD-69). ARD-69 induces degradation of AR protein in AR-positive prostate cancer cell lines in a dose- and time-dependent manner. ARD-69 achieves DC50 values of 0.86, 0.76, and 10.4 nM in LNCaP, VCaP, and 22Rv1 AR+ prostate cancer cell lines, respectively. ARD-69 is capable of reducing the AR protein level by >95% in these prostate cancer cell lines and effectively suppressing AR-regulated gene expression. ARD-69 potently inhibits cell growth in these AR-positive prostate cancer cell lines and is >100 times more potent than AR antagonists. A single dose of ARD-69 effectively reduces the level of AR protein in xenograft tumor tissue in mice. Further optimization of ARD-69 may ultimately lead to a new therapy for AR+, castration-resistant prostate cancer.
Collapse
|
125
|
Zou Y, Ma D, Wang Y. The PROTAC technology in drug development. Cell Biochem Funct 2019; 37:21-30. [PMID: 30604499 PMCID: PMC6590639 DOI: 10.1002/cbf.3369] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/28/2022]
Abstract
Currently, a new technology termed PROTAC, proteolysis targeting chimera, has been developed for inducing the protein degradation by a targeting molecule. This technology takes advantage of a moiety of targeted protein and a moiety of recognizing E3 ubiquitin ligase and produces a hybrid molecule to specifically knock down a targeted protein. During the first decade, three pedigreed groups worked on the development of this technology. To date, this technology has been extended by different groups, aiming to develop new drugs against different diseases including cancers. This review summarizes the contributions of the groups for the development of PROTAC. SIGNIFICANCE OF THE STUDY: This review summarized the development of the PROTAC technology for readers and also presented the author's opinions on the application of the technology in tumor therapy.
Collapse
Affiliation(s)
- Yutian Zou
- The State Laboratory of Membrane Biology, Department of Basic Medicine, School of Medicine, Tsinghua University, Beijing, China.,Department of Science, Brookwood High School, Snellville, Georgia
| | - Danhui Ma
- The State Laboratory of Membrane Biology, Department of Basic Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Yinyin Wang
- The State Laboratory of Membrane Biology, Department of Basic Medicine, School of Medicine, Tsinghua University, Beijing, China
| |
Collapse
|
126
|
Daniels DL, Riching KM, Urh M. Monitoring and deciphering protein degradation pathways inside cells. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 31:61-68. [PMID: 31200861 DOI: 10.1016/j.ddtec.2018.12.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 01/18/2023]
Abstract
A new series of therapeutic modalities resulting in degradation of target proteins, termed proteolysis targeting chimeras (PROTACs), hold significant therapeutic potential with possible prolonged pharmacodynamics, improved potency, and ability to target proteins previously thought of as "undruggable". PROTACs are heterobifunctional small molecules consisting of a target binding handle bridged via a chemical linker to an E3 ligase handle which recruit the E3 ligase and ubiquitin machinery to target proteins, resulting in subsequent ubiquitination and degradation of the target. With the generation of small molecule PROTAC compound libraries for drug discovery, it becomes essential to have sensitive screening technologies to rapidly profile activity and have assays which can clearly inform on performance at the various cellular steps required for PROTAC-mediated degradation. For PROTAC compounds, this has been particularly challenging using either biochemical or cellular assay approaches. Biochemical assays are highly informative for the first part of the degradation process, including optimization of compound binding to targets and interrogation of target:PROTAC:E3 ligase ternary complex formation, but struggle with the remaining steps; recruitment of ternary complex into larger active E3 ligase complexes, ubiquitination, and proteasomal degradation. On the other hand, cellular assays are excellent at determining if the PROTAC successfully degrades the target in its relevant setting but struggle as early development PROTAC compounds are often poorly cell-permeable given their high molecular weight. Additionally, if degradation is not observed in a cellular assay, it is difficult to deconvolute the reason why or at which step there was failure. In this review we will highlight the current approaches along with recent advances to overcome the challenges faced for cellular PROTAC screening, which will enable and advance drug discovery of therapeutic degradation compounds.
Collapse
Affiliation(s)
- Danette L Daniels
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA.
| | - Kristin M Riching
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA
| | - Marjeta Urh
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA
| |
Collapse
|
127
|
Kang CH, Lee DH, Lee CO, Du Ha J, Park CH, Hwang JY. Induced protein degradation of anaplastic lymphoma kinase (ALK) by proteolysis targeting chimera (PROTAC). Biochem Biophys Res Commun 2018; 505:542-547. [DOI: 10.1016/j.bbrc.2018.09.169] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 09/26/2018] [Indexed: 12/22/2022]
|
128
|
Li D, Bheemanaboina RRY, Battini N, Tangadanchu VKR, Fang XF, Zhou CH. Novel organophosphorus aminopyrimidines as unique structural DNA-targeting membrane active inhibitors towards drug-resistant methicillin-resistant Staphylococcus aureus. MEDCHEMCOMM 2018; 9:1529-1537. [PMID: 30288226 DOI: 10.1039/c8md00301g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/29/2018] [Indexed: 12/18/2022]
Abstract
A series of novel unique structural organophosphorus aminopyrimidines were developed as potential DNA-targeting membrane active inhibitors through an efficient one-pot procedure from aldehydes, phosphonate and aminopyrimidine. The biological assay revealed that some of the prepared compounds displayed antibacterial activities. In particular, imidazole derivative 2c exhibited more potent inhibitory activity against MRSA with an MIC value of 4 μg mL-1 in comparison with the clinical drugs chloromycin and norfloxacin. Experiments revealed that the active molecule 2c had the ability to rapidly kill the tested strains without obviously triggering the development of bacterial resistance, showed low toxicity to L929 cells and could disturb the cell membrane. The molecular docking study discovered that compound 2c could bind with DNA gyrase via hydrogen bonds and other weak interactions. Further exploration disclosed that the active molecule 2c could also effectively intercalate into MRSA DNA and form a steady 2c-DNA supramolecular complex, which might further block DNA replication to exert powerful antibacterial effects.
Collapse
Affiliation(s)
- Di Li
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Rammohan R Yadav Bheemanaboina
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Narsaiah Battini
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Vijai Kumar Reddy Tangadanchu
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Xian-Fu Fang
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry , Key Laboratory of Applied Chemistry of Chongqing Municipality , School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China . ; ; Tel: +86 23 68254967
| |
Collapse
|