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Coomar S, Mota P, Penson A, Schwaller J, Abdel-Wahab O, Gillingham D. Overlaid Transcriptional and Proteome Analyses Identify Mitotic Kinesins as Important Targets of Arylsulfonamide-Mediated RBM39 Degradation. Mol Cancer Res 2023; 21:768-778. [PMID: 37255411 PMCID: PMC10395616 DOI: 10.1158/1541-7786.mcr-22-0541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/16/2023] [Accepted: 05/09/2023] [Indexed: 05/14/2023]
Abstract
Certain arylsulfonamides (ArSulf) induce an interaction between the E3 ligase substrate adaptor DCAF15 and the critical splicing factor RBM39, ultimately causing its degradation. However, degradation of a splicing factor introduces complex pleiotropic effects that are difficult to untangle, since, aside from direct protein degradation, downstream transcriptional effects also influence the proteome. By overlaying transcriptional data and proteome datasets, we distinguish transcriptional from direct degradation effects, pinpointing those proteins most impacted by splicing changes. Using our workflow, we identify and validate the upregulation of the arginine-and-serine rich protein (RSRP1) and the downregulation of the key kinesin motor proteins KIF20A and KIF20B due to altered splicing in the absence of RBM39. We further show that kinesin downregulation is connected to the multinucleation phenotype observed upon RBM39 depletion by ArSulfs. Our approach should be helpful in the assessment of potential cancer drug candidates which target splicing factors. IMPLICATIONS Our approach provides a workflow for identifying and studying the most strongly modulated proteins when splicing is altered. The work also uncovers a splicing-based approach toward pharmacologic targeting of mitotic kinesins.
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Affiliation(s)
- Seemon Coomar
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Pedro Mota
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Alexander Penson
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jürg Schwaller
- Department of Biomedicine, University Children's Hospital (UKBB), University of Basel, Basel, Switzerland
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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2
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Lyu Z, Zhao Y, Buuh ZY, Gorman N, Goldman AR, Islam MS, Tang HY, Wang RE. Steric-Free Bioorthogonal Labeling of Acetylation Substrates Based on a Fluorine-Thiol Displacement Reaction. J Am Chem Soc 2021; 143:1341-1347. [PMID: 33433199 PMCID: PMC8300487 DOI: 10.1021/jacs.0c05605] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have developed a novel bioorthogonal reaction that can selectively displace fluorine substitutions alpha to amide bonds. This fluorine-thiol displacement reaction (FTDR) allows for fluorinated cofactors or precursors to be utilized as chemical reporters, hijacking acetyltransferase-mediated acetylation both in vitro and in live cells, which cannot be achieved with azide- or alkyne-based chemical reporters. The fluoroacetamide labels can be further converted to biotin or fluorophore tags using FTDR, enabling the general detection and imaging of acetyl substrates. This strategy may lead to a steric-free labeling platform for substrate proteins, expanding our chemical toolbox for functional annotation of post-translational modifications in a systematic manner.
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Affiliation(s)
- Zhigang Lyu
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Yue Zhao
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Zakey Yusuf Buuh
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Nicole Gorman
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Aaron R Goldman
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Md Shafiqul Islam
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
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3
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Bond AG, Testa A, Ciulli A. Stereoselective synthesis of allele-specific BET inhibitors. Org Biomol Chem 2020; 18:7533-7539. [PMID: 32756710 DOI: 10.1039/d0ob01165g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Developing stereoselective synthetic routes that are efficient and cost-effective allows easy access to biologically active molecules. Our previous syntheses of allele-selective bumped inhibitors of the Bromo and Extra-Terminal (BET) domain proteins, Brd2, Brd3, Brd4 and BrdT, required a wasteful, late-stage alkylation step and expensive chiral separation. To circumvent these limitations, we developed a route based on stereocontrolled alkylation of an N-Pf protected aspartic acid derivative that was used in a divergent, racemisation-free protocol to yield structurally diverse and enantiopure triazolodiazepines. With this approach, we synthesized bumped thienodiazepine-based BET inhibitor, ET-JQ1-OMe, in five steps and 99% ee without the need for chiral chromatography. Exquisite selectivity of ET-JQ1-OMe for Leu-Ala and Leu-Val mutants over wild-type bromodomain was established by isothermal titration calorimetry and X-ray crystallography. Our new approach provides unambiguous chemical evidence for the absolute stereochemistry of the active, allele-specific BET inhibitors and a viable route that will open wider access to this compound class.
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Affiliation(s)
- Adam G Bond
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK.
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4
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He Y, Koch R, Budamagunta V, Zhang P, Zhang X, Khan S, Thummuri D, Ortiz YT, Zhang X, Lv D, Wiegand JS, Li W, Palmer AC, Zheng G, Weinstock DM, Zhou D. DT2216-a Bcl-xL-specific degrader is highly active against Bcl-xL-dependent T cell lymphomas. J Hematol Oncol 2020; 13:95. [PMID: 32677976 PMCID: PMC7364785 DOI: 10.1186/s13045-020-00928-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Patients with advanced T cell lymphomas (TCLs) have limited therapeutic options and poor outcomes in part because their TCLs evade apoptosis through upregulation of anti-apoptotic Bcl-2 proteins. Subsets of TCL cell lines, patient-derived xenografts (PDXs), and primary patient samples depend on Bcl-xL for survival. However, small molecule Bcl-xL inhibitors such as ABT263 have failed during clinical development due to on-target and dose-limiting thrombocytopenia. METHODS We have developed DT2216, a proteolysis targeting chimera (PROTAC) targeting Bcl-xL for degradation via Von Hippel-Lindau (VHL) E3 ligase, and shown that it has better anti-tumor activity but is less toxic to platelets compared to ABT263. Here, we examined the therapeutic potential of DT2216 for TCLs via testing its anti-TCL activity in vitro using MTS assay, immunoblotting, and flow cytometry and anti-TCL activity in vivo using TCL cell xenograft and PDX model in mice. RESULTS The results showed that DT2216 selectively killed various Bcl-xL-dependent TCL cells including MyLa cells in vitro. In vivo, DT2216 alone was highly effective against MyLa TCL xenografts in mice without causing significant thrombocytopenia or other toxicity. Furthermore, DT2216 combined with ABT199 (a selective Bcl-2 inhibitor) synergistically reduced disease burden and improved survival in a TCL PDX mouse model dependent on both Bcl-2 and Bcl-xL. CONCLUSIONS These findings support the clinical testing of DT2216 in patients with Bcl-xL-dependent TCLs, both as a single agent and in rational combinations.
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Affiliation(s)
- Yonghan He
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Raphael Koch
- Department of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Vivekananda Budamagunta
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Peiyi Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Sajid Khan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Dinesh Thummuri
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Yuma T Ortiz
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Xin Zhang
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Dongwen Lv
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Janet S Wiegand
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Wen Li
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Adam C Palmer
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - David M Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Avenue, Dana 510B, Boston, MA, USA.
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA.
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5
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Ibrahim AFM, Shen L, Tatham MH, Dickerson D, Prescott AR, Abidi N, Xirodimas DP, Hay RT. Antibody RING-Mediated Destruction of Endogenous Proteins. Mol Cell 2020; 79:155-166.e9. [PMID: 32454028 PMCID: PMC7332993 DOI: 10.1016/j.molcel.2020.04.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/20/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023]
Abstract
To understand gene function, the encoding DNA or mRNA transcript can be manipulated and the consequences observed. However, these approaches do not have a direct effect on the protein product of the gene, which is either permanently abrogated or depleted at a rate defined by the half-life of the protein. We therefore developed a single-component system that could induce the rapid degradation of the specific endogenous protein itself. A construct combining the RING domain of ubiquitin E3 ligase RNF4 with a protein-specific camelid nanobody mediates target destruction by the ubiquitin proteasome system, a process we describe as antibody RING-mediated destruction (ARMeD). The technique is highly specific because we observed no off-target protein destruction. Furthermore, bacterially produced nanobody-RING fusion proteins electroporated into cells induce degradation of target within minutes. With increasing availability of protein-specific nanobodies, this method will allow rapid and specific degradation of a wide range of endogenous proteins.
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Affiliation(s)
- Adel F M Ibrahim
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Linnan Shen
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Michael H Tatham
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - David Dickerson
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Alan R Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Naima Abidi
- Cell Biology Research Centre of Montpellier, CNRS, UMR 5237, Montpellier, France
| | - Dimitris P Xirodimas
- Cell Biology Research Centre of Montpellier, CNRS, UMR 5237, Montpellier, France
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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6
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Abstract
The dynamic nature of histone post-translational modifications such as methylation or acetylation makes possible the alteration of disease associated epigenetic states through the manipulation of the associated epigenetic machinery. One approach is through small molecule perturbation. Chemical probes of epigenetic reader domains have been critical in improving our understanding of the biological consequences of modulating their targets, while also enabling the development of novel probe-based reagents. By appending a functional handle to a reader domain probe, a chemical toolbox of reagents can be created to facilitate chemiprecipitation of epigenetic complexes, evaluate probe selectivity, develop in vitro screening assays, visualize cellular target localization, enable target degradation and recruit epigenetic machinery to a site within the genome in a highly controlled fashion.
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7
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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: 339] [Impact Index Per Article: 67.8] [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.
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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
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8
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Khan S, Zhang X, Lv D, Zhang Q, He Y, Zhang P, Liu X, Thummuri D, Yuan Y, Wiegand JS, Pei J, Zhang W, Sharma A, McCurdy CR, Kuruvilla VM, Baran N, Ferrando AA, Kim YM, Rogojina A, Houghton PJ, Huang G, Hromas R, Konopleva M, Zheng G, Zhou D. A selective BCL-X L PROTAC degrader achieves safe and potent antitumor activity. Nat Med 2019; 25:1938-1947. [PMID: 31792461 PMCID: PMC6898785 DOI: 10.1038/s41591-019-0668-z] [Citation(s) in RCA: 324] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/28/2019] [Indexed: 12/20/2022]
Abstract
BCL-XL is a well-validated cancer target. However, the on-target and dose-limiting thrombocytopenia limits the use of BCL-XL inhibitors such as ABT263 as safe and effective anticancer agents. To reduce the toxicity of ABT263, we converted it into DT2216, a BCL-XL proteolysis targeting chimera (PROTAC), that targets BCL-XL to the Von Hippel-Lindau (VHL) E3 ligase for degradation. We found that DT2216 was more potent against various BCL-XL-dependent leukemia and cancer cells but significantly less toxic to platelets than ABT263 in vitro because VHL is poorly expressed in platelets. In vivo, DT2216 effectively inhibits the growth of several xenograft tumors as a single agent or in combination with other chemotherapeutic agents, without causing significant thrombocytopenia. These findings demonstrate the potential to use PROTAC technology to reduce on-target drug toxicities and rescue the therapeutic potential of previously undruggable targets. Furthermore, DT2216 may be developed as a safe first-in-class anticancer agent targeting BCL-XL.
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Affiliation(s)
- Sajid Khan
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Dongwen Lv
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Qi Zhang
- Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Yonghan He
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Peiyi Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Xingui Liu
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Dinesh Thummuri
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Janet S Wiegand
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Jing Pei
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Weizhou Zhang
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Abhisheak Sharma
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Vinitha M Kuruvilla
- Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Natalia Baran
- Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Adolfo A Ferrando
- Department of Pediatrics, Pathology, Cell Biology and Systems of Biology and Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Yong-Mi Kim
- Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Anna Rogojina
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Guangcun Huang
- Department of Medicine, the Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Robert Hromas
- Department of Medicine, the Long School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Marina Konopleva
- Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA.
| | - Daohong Zhou
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA.
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9
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Tovell H, Testa A, Maniaci C, Zhou H, Prescott AR, Macartney T, Ciulli A, Alessi DR. Rapid and Reversible Knockdown of Endogenously Tagged Endosomal Proteins via an Optimized HaloPROTAC Degrader. ACS Chem Biol 2019; 14:882-892. [PMID: 30978004 PMCID: PMC6528276 DOI: 10.1021/acschembio.8b01016] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Inducing
post-translational protein knockdown is an important approach
to probe biology and validate drug targets. An efficient strategy
to achieve this involves expression of a protein of interest fused
to an exogenous tag, allowing tag-directed chemical degraders to mediate
protein ubiquitylation and proteasomal degradation. Here, we combine
improved HaloPROTAC degrader probes with CRISPR/Cas9 genome editing
technology to trigger rapid degradation of endogenous target proteins.
Our optimized probe, HaloPROTAC-E, a chloroalkane conjugate of high-affinity
VHL binder VH298, induced reversible degradation of two endosomally
localized proteins, SGK3 and VPS34, with a DC50 of 3–10
nM. HaloPROTAC-E induced rapid (∼50% degradation after 30 min)
and complete (Dmax of ∼95% at 48
h) depletion of Halo-tagged SGK3, blocking downstream phosphorylation
of the SGK3 substrate NDRG1. HaloPROTAC-E more potently induced greater
steady state degradation of Halo tagged endogenous VPS34 than the
previously reported HaloPROTAC3 compound. Quantitative global proteomics
revealed that HaloPROTAC-E is remarkably selective inducing only degradation
of the Halo tagged endogenous VPS34 complex (VPS34, VPS15, Beclin1,
and ATG14) and no other proteins were significantly degraded. This
study exemplifies the combination of HaloPROTACs with CRISPR/Cas9
endogenous protein tagging as a useful method to induce rapid and
reversible degradation of endogenous proteins to interrogate their
function.
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Affiliation(s)
- Hannah Tovell
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Andrea Testa
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, U.K
| | - Chiara Maniaci
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, U.K
| | - Houjiang Zhou
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Alan R Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Thomas Macartney
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, U.K
| | - Dario R Alessi
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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10
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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: 164] [Impact Index Per Article: 32.8] [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.
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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
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11
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Islam K. The Bump-and-Hole Tactic: Expanding the Scope of Chemical Genetics. Cell Chem Biol 2018; 25:1171-1184. [PMID: 30078633 PMCID: PMC6195450 DOI: 10.1016/j.chembiol.2018.07.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/13/2018] [Accepted: 07/02/2018] [Indexed: 12/15/2022]
Abstract
Successful mapping of the human genome has sparked a widespread interest in deciphering functional information encoded in gene sequences. However, because of the high degree of conservation in sequences along with topological and biochemical similarities among members of a protein superfamily, uncovering physiological role of a particular protein has been a challenging task. Chemical genetic approaches have made significant contributions toward understanding protein function. One such effort, dubbed the bump-and-hole approach, has convincingly demonstrated that engineering at the protein-small molecule interface constitutes a powerful method for elucidating the function of a specific gene product. By manipulating the steric component of protein-ligand interactions in a complementary manner, an orthogonal system is developed to probe a specific enzyme-cofactor pair without interference from related members. This article outlines current efforts to expand the approach for diverse protein classes and their applications. Potential future innovations to address contemporary biological problems are highlighted as well.
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Affiliation(s)
- Kabirul Islam
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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12
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Sohtome Y, Sodeoka M. Development of Chaetocin and
S
‐Adenosylmethionine Analogues as Tools for Studying Protein Methylation. CHEM REC 2018; 18:1660-1671. [DOI: 10.1002/tcr.201800118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Yoshihiro Sohtome
- Synthetic Organic Chemistry LaboratoryRIKEN Cluster for Pioneering Research 2-1 Hirosawa, Wako Saitama Japan
- RIKEN Center for Sustainable Resource Science
- AMED-CREST, Japan Agency for Medical Research and Development
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry LaboratoryRIKEN Cluster for Pioneering Research 2-1 Hirosawa, Wako Saitama Japan
- RIKEN Center for Sustainable Resource Science
- AMED-CREST, Japan Agency for Medical Research and Development
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Steinebach C, Lindner S, Udeshi ND, Mani DC, Kehm H, Köpff S, Carr SA, Gütschow M, Krönke J. Homo-PROTACs for the Chemical Knockdown of Cereblon. ACS Chem Biol 2018; 13:2771-2782. [PMID: 30118587 DOI: 10.1021/acschembio.8b00693] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The immunomodulatory drugs (IMiDs) thalidomide, lenalidomide, and pomalidomide, all approved for the treatment of multiple myeloma, induce targeted ubiquitination and degradation of Ikaros (IKZF1) and Aiolos (IKZF3) via the cereblon (CRBN) E3 ubiquitin ligase. IMiD-based proteolysis-targeting chimeras (PROTACs) can efficiently recruit CRBN to a protein of interest, leading to its ubiquitination and proteasomal degradation. By linking two pomalidomide molecules, we designed homobifunctional, so-called homo-PROTACs and investigated their ability to induce self-directed ubiquitination and degradation. The homodimerized compound 15a was characterized as a highly potent and efficient CRBN degrader with only minimal effects on IKZF1 and IKZF3. The cellular selectivity of 15a for CRBN degradation was confirmed at the proteome level by quantitative mass spectrometry. Inactivation by compound 15a did not affect proliferation of different cell lines, prevented pomalidomide-induced degradation of IKZF1 and IKZF3, and antagonized the effects of pomalidomide on multiple myeloma cells. Homobifunctional CRBN degraders will be useful tools for future biomedical investigations of CRBN-related signaling and may help to further elucidate the molecular mechanism of thalidomide analogues.
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Affiliation(s)
- Christian Steinebach
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Stefanie Lindner
- Department of Internal Medicine III, University Hospital Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Namrata D. Udeshi
- Proteomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Deepak C. Mani
- Proteomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Hannes Kehm
- Department of Internal Medicine III, University Hospital Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Simon Köpff
- Department of Internal Medicine III, University Hospital Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Steven A. Carr
- Proteomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Jan Krönke
- Department of Internal Medicine III, University Hospital Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
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14
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Sviripa VM, Kril LM, Zhang W, Xie Y, Wyrebek P, Ponomareva L, Liu X, Yuan Y, Zhan CG, Watt DS, Liu C. Phenylethynyl-substituted Heterocycles Inhibit Cyclin D1 and Induce the Expression of Cyclin-dependent Kinase Inhibitor p21 Wif1/Cip1 in Colorectal Cancer Cells. MEDCHEMCOMM 2018. [PMID: 29527286 DOI: 10.1039/c7md00393e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fluorinated, phenylethynyl-substituted heterocycles that possessed either an N-methylamino or N,N-dimethylamino group attached to heterocycles including pyridines, indoles, 1H-indazoles, quinolines, and isoquinolines inhibited the proliferation of LS174T colon cancer cells in which the inhibition of cyclin D1 and induction of the cyclin-dependent kinase inhibitor-1 (i.e., p21Wif1/Cip1) served as a readout for antineoplastic activity at a cellular level. On a molecular level, these agents, particularly 4-((2,6-difluorophenyl)ethynyl)-N-methylisoquinolin-1-amine and 4-((2,6-difluorophenyl)ethynyl)-N,N-dimethylisoquinolin-1-amine, bound and inhibited the catalytic subunit of methionine S-adenosyltransferase-2 (MAT2A).
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Affiliation(s)
- Vitaliy M Sviripa
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596.,Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596
| | - Liliia M Kril
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596.,Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509
| | - Wen Zhang
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509.,Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093
| | - Yanqi Xie
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509.,Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093
| | - Przemyslaw Wyrebek
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596.,Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509
| | - Larissa Ponomareva
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596.,Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596
| | - Xifu Liu
- Epionc, Inc., P.O. Box 23436, Lexington, KY 40523
| | - Yaxia Yuan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596.,Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596.,Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky 40536-0596
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596.,Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596.,Molecular Modeling and Biopharmaceutical Center, College of Pharmacy, University of Kentucky 40536-0596
| | - David S Watt
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596.,Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596.,Epionc, Inc., P.O. Box 23436, Lexington, KY 40523.,Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509.,Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093
| | - Chunming Liu
- Epionc, Inc., P.O. Box 23436, Lexington, KY 40523.,Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509.,Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093
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Runcie AC, Zengerle M, Chan KH, Testa A, van Beurden L, Baud MGJ, Epemolu O, Ellis LCJ, Read KD, Coulthard V, Brien A, Ciulli A. Optimization of a "bump-and-hole" approach to allele-selective BET bromodomain inhibition. Chem Sci 2018; 9:2452-2468. [PMID: 29732121 PMCID: PMC5909127 DOI: 10.1039/c7sc02536j] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 01/23/2018] [Indexed: 12/27/2022] Open
Abstract
Allele-specific chemical genetics enables selective inhibition within families of highly-conserved proteins.
Allele-specific chemical genetics enables selective inhibition within families of highly-conserved proteins. The four BET (bromodomain & extra-terminal domain) proteins – BRD2, BRD3, BRD4 and BRDT bind acetylated chromatin via their bromodomains and regulate processes such as cell proliferation and inflammation. BET bromodomains are of particular interest, as they are attractive therapeutic targets but existing inhibitors are pan-selective. We previously established a bump-&-hole system for the BET bromodomains, pairing a leucine/alanine mutation with an ethyl-derived analogue of an established benzodiazepine scaffold. Here we optimize upon this system with the introduction of a more conservative and less disruptive leucine/valine mutation. Extensive structure–activity-relationships of diverse benzodiazepine analogues guided the development of potent, mutant-selective inhibitors with desirable physiochemical properties. The active enantiomer of our best compound – 9-ME-1 – shows ∼200 nM potency, >100-fold selectivity for the L/V mutant over wild-type and excellent DMPK properties. Through a variety of in vitro and cellular assays we validate the capabilities of our optimized system, and then utilize it to compare the relative importance of the first and second bromodomains to chromatin binding. These experiments confirm the primacy of the first bromodomain in all BET proteins, but also significant variation in the importance of the second bromodomain. We also show that, despite having a minor role in chromatin recognition, BRD4 BD2 is still essential for gene expression, likely through the recruitment of non-histone proteins. The disclosed inhibitor:mutant pair provides a powerful tool for future cellular and in vivo target validation studies.
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Affiliation(s)
- A C Runcie
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - M Zengerle
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - K-H Chan
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - A Testa
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - L van Beurden
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - M G J Baud
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - O Epemolu
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - L C J Ellis
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - K D Read
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - V Coulthard
- Reach Separations Ltd , BioCity Nottingham , Nottingham , UK
| | - A Brien
- Reach Separations Ltd , BioCity Nottingham , Nottingham , UK
| | - A Ciulli
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
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Gul S. Epigenetic assays for chemical biology and drug discovery. Clin Epigenetics 2017; 9:41. [PMID: 28439316 PMCID: PMC5399855 DOI: 10.1186/s13148-017-0342-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 04/12/2017] [Indexed: 12/27/2022] Open
Abstract
The implication of epigenetic abnormalities in many diseases and the approval of a number of compounds that modulate specific epigenetic targets in a therapeutically relevant manner in cancer specifically confirms that some of these targets are druggable by small molecules. Furthermore, a number of compounds are currently in clinical trials for other diseases including cardiovascular, neurological and metabolic disorders. Despite these advances, the approved treatments for cancer only extend progression-free survival for a relatively short time and being associated with significant side effects. The current clinical trials involving the next generation of epigenetic drugs may address the disadvantages of the currently approved epigenetic drugs. The identification of chemical starting points of many drugs often makes use of screening in vitro assays against libraries of synthetic or natural products. These assays can be biochemical (using purified protein) or cell-based (using for example, genetically modified, cancer cell lines or primary cells) and performed in microtiter plates, thus enabling a large number of samples to be tested. A considerable number of such assays are available to monitor epigenetic target activity, and this review provides an overview of drug discovery and chemical biology and describes assays that monitor activities of histone deacetylase, lysine-specific demethylase, histone methyltransferase, histone acetyltransferase and bromodomain. It is of critical importance that an appropriate assay is developed and comprehensively validated for a given drug target prior to screening in order to improve the probability of the compound progressing in the drug discovery value chain.
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Affiliation(s)
- Sheraz Gul
- Fraunhofer Institute for Molecular Biology and Applied Ecology - ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
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Abstract
INTRODUCTION Epigenetic regulators including writers, erasers, and readers of chromatin marks have been implicated in numerous diseases and are therefore subject of intense academic and pharmaceutical research. While several small-molecule inhibitors targeting writers or erasers are either approved drugs or are currently being evaluated in clinical trials, the targeting of epigenetic readers has lagged behind. Proof-of-principle that epigenetic readers are also relevant drug targets was provided by landmark discoveries of selective inhibitors targeting the BET family of acetyl-lysine readers. More recently, high affinity chemical probes for non-BET acetyl- and methyl-lysine reader domains have also been developed. Areas covered: This article covers recent advances with the identification and validation of inhibitors and chemical probes targeting epigenetic reader domains. Issues related to epigenetic reader druggability, quality requirements for chemical probes, interpretation of cellular action, unexpected cross-talk, and future challenges are also discussed. Expert opinion: Chemical probes provide a powerful means to unravel biological functions of epigenetic readers and evaluate their potential as drug targets. To yield meaningful results, potency, selectivity, and cellular target engagement of chemical probes need to be stringently validated. Future chemical probes will probably need to fulfil additional criteria such as strict target specificity or the targeting of readers within protein complexes.
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Affiliation(s)
- Holger Greschik
- a Urologische Klinik und Zentrale Klinische Forschung , Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg , Freiburg , Germany
| | - Roland Schüle
- a Urologische Klinik und Zentrale Klinische Forschung , Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg , Freiburg , Germany.,b Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg , Freiburg , Germany.,c BIOSS Centre of Biological Signalling Studies , Albert-Ludwigs-University Freiburg , Freiburg , Germany
| | - Thomas Günther
- a Urologische Klinik und Zentrale Klinische Forschung , Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg , Freiburg , Germany
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18
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Switching domains. Nat Chem Biol 2016; 12:659-60. [DOI: 10.1038/nchembio.2154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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