1
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Swinton M, Dubec M, McHugh D, Biglin E, Sanchez DF, Oliveira P, Price G, McWilliam A, van Herk M, Hoskin P, Buckley DL, Hudson A, Bristow RG, Choudhury A. Validation of Hypoxia Detection Sequences on the MR Linac. Int J Radiat Oncol Biol Phys 2023; 117:e723-e724. [PMID: 37786109 DOI: 10.1016/j.ijrobp.2023.06.2234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Magnetic resonance linear accelerator (MRL) systems permit acquisition of novel imaging at the time of radiotherapy. A validated MR hypoxia imaging biomarker could select patients for adaptive radiotherapy with hypoxia modification or dose escalation. The aims of this study were (1) to develop a protocol for quantitative hypoxia sensitive MRI (2) to validate these in prostate cancer (PCa) against pimonidazole-stained prostatectomy sections. MATERIALS/METHODS Blood oxygen level dependent (BOLD), intravoxel incoherent motion (IVIM), oxygen-enhanced (OE) and dynamic contrast enhanced (DCE) MRI were used. Sequences were developed on a diagnostic 1.5 T MR (MRD) and MRL with healthy volunteers and PCa patients. The Hyprogen trial includes men with localized PCa scheduled for prostatectomy. Imaging is acquired twice prior to surgery and oral pimonidazole is taken 8-16 hours before surgery. Whole prostate (WP) and dominant prostatic lesion (DIL) were outlined on T2-weighted (T2W) images and a 'normal prostate' (NP) volume created by subtracting DIL from WP. Contours were applied to parametric maps from the quantitative MRI, with median and IQR extracted. Patient-specific 3D-printed prostate molds were created from WP volumes and used to guide prostate whole organ dissection. RESULTS Three of 20 patients recruited to date. MRI data were acquired successfully. A personalized prostate mold was produced for each patient and facilitated dissection of the prostatectomy specimen in a matching plane to MRI to validate hypoxia detection of the MR protocol. Correlation with pimonidazole staining is underway. Imaging parameter median values for NP and DIL acquired on MRD and MRL for the first patient are shown (Table 1). The expected differences between NP and DIL for T1 and D are seen and median values for T2* are consistent with reported values in the literature. CONCLUSION The MR hypoxia protocol can be acquired safely and is well-tolerated on the MRL. Once validated against pimonidazole staining adaptive radiotherapy protocols will be developed to use this information.
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Affiliation(s)
- M Swinton
- Christie Hospital, Manchester, United Kingdom
| | - M Dubec
- University of Manchester, Manchester, United Kingdom
| | - D McHugh
- The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - E Biglin
- University of Manchester, Manchester, United Kingdom
| | - D F Sanchez
- The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - P Oliveira
- The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - G Price
- The University of Manchester, Manchester, United Kingdom
| | - A McWilliam
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - M van Herk
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - P Hoskin
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - D L Buckley
- Biomedical Imaging, University of Leeds, Leeds, United Kingdom
| | - A Hudson
- The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - R G Bristow
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - A Choudhury
- Department of Clinical Oncology, The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK, Manchester, United Kingdom
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2
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Pinch BJ, Buckley DL, Gleim S, Brittain SM, Tandeske L, D'Alessandro PL, Hauseman ZJ, Lipps J, Xu L, Harvey EP, Schirle M, Sprague ER, Forrester WC, Dovala D, McGregor LM, Thoma CR. A strategy to assess the cellular activity of E3 ligase components against neo-substrates using electrophilic probes. Cell Chem Biol 2021; 29:57-66.e6. [PMID: 34499862 DOI: 10.1016/j.chembiol.2021.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 06/17/2021] [Accepted: 08/20/2021] [Indexed: 01/12/2023]
Abstract
While there are hundreds of predicted E3 ligases, characterizing their applications for targeted protein degradation has proved challenging. Here, we report a chemical biology approach to evaluate the ability of modified recombinant E3 ligase components to support neo-substrate degradation. Bypassing the need for specific E3 ligase binders, we use maleimide-thiol chemistry for covalent functionalization followed by E3 electroporation (COFFEE) in live cells. We demonstrate that electroporated recombinant von Hippel-Lindau (VHL) protein, covalently functionalized at its ligandable cysteine with JQ1 or dasatinib, induces degradation of BRD4 or tyrosine kinases, respectively. Furthermore, by applying COFFEE to SPSB2, a Cullin-RING ligase 5 receptor, as well as to SKP1, the adaptor protein for Cullin-RING ligase 1 F box (SCF) complexes, we validate this method as a powerful approach to define the activity of previously uncharacterized ubiquitin ligase components, and provide further evidence that not only E3 ligase receptors but also adaptors can be directly hijacked for neo-substrate degradation.
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Affiliation(s)
- Benika J Pinch
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
| | - Dennis L Buckley
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Scott Gleim
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Scott M Brittain
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Laura Tandeske
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | | | | | - Jennifer Lipps
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Lei Xu
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Edward P Harvey
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | | | - Dustin Dovala
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA.
| | - Lynn M McGregor
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
| | - Claudio R Thoma
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
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3
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Shirasaki R, Matthews GM, Gandolfi S, de Matos Simoes R, Buckley DL, Raja Vora J, Sievers QL, Brüggenthies JB, Dashevsky O, Poarch H, Tang H, Bariteau MA, Sheffer M, Hu Y, Downey-Kopyscinski SL, Hengeveld PJ, Glassner BJ, Dhimolea E, Ott CJ, Zhang T, Kwiatkowski NP, Laubach JP, Schlossman RL, Richardson PG, Culhane AC, Groen RWJ, Fischer ES, Vazquez F, Tsherniak A, Hahn WC, Levy J, Auclair D, Licht JD, Keats JJ, Boise LH, Ebert BL, Bradner JE, Gray NS, Mitsiades CS. Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins. Cell Rep 2021; 34:108532. [PMID: 33406420 DOI: 10.1016/j.celrep.2020.108532] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 06/14/2019] [Accepted: 11/25/2020] [Indexed: 12/15/2022] Open
Abstract
Heterobifunctional proteolysis-targeting chimeric compounds leverage the activity of E3 ligases to induce degradation of target oncoproteins and exhibit potent preclinical antitumor activity. To dissect the mechanisms regulating tumor cell sensitivity to different classes of pharmacological "degraders" of oncoproteins, we performed genome-scale CRISPR-Cas9-based gene editing studies. We observed that myeloma cell resistance to degraders of different targets (BET bromodomain proteins, CDK9) and operating through CRBN (degronimids) or VHL is primarily mediated by prevention of, rather than adaptation to, breakdown of the target oncoprotein; and this involves loss of function of the cognate E3 ligase or interactors/regulators of the respective cullin-RING ligase (CRL) complex. The substantial gene-level differences for resistance mechanisms to CRBN- versus VHL-based degraders explains mechanistically the lack of cross-resistance with sequential administration of these two degrader classes. Development of degraders leveraging more diverse E3 ligases/CRLs may facilitate sequential/alternating versus combined uses of these agents toward potentially delaying or preventing resistance.
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Affiliation(s)
- Ryosuke Shirasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Geoffrey M Matthews
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara Gandolfi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Ricardo de Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseline Raja Vora
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Quinlan L Sievers
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Johanna B Brüggenthies
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Haley Poarch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Huihui Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Megan A Bariteau
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Yiguo Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Sondra L Downey-Kopyscinski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul J Hengeveld
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Brian J Glassner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tinghu Zhang
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicholas P Kwiatkowski
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob P Laubach
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Robert L Schlossman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Paul G Richardson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Richard W J Groen
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Eric S Fischer
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joan Levy
- Multiple Myeloma Research Foundation, Norwalk, CT, USA
| | | | - Jonathan D Licht
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | | | - Lawrence H Boise
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael S Gray
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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4
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Nabet B, Ferguson FM, Seong BKA, Kuljanin M, Leggett AL, Mohardt ML, Robichaud A, Conway AS, Buckley DL, Mancias JD, Bradner JE, Stegmaier K, Gray NS. Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules. Nat Commun 2020; 11:4687. [PMID: 32948771 PMCID: PMC7501296 DOI: 10.1038/s41467-020-18377-w] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
Chemical biology strategies for directly perturbing protein homeostasis including the degradation tag (dTAG) system provide temporal advantages over genetic approaches and improved selectivity over small molecule inhibitors. We describe dTAGV-1, an exclusively selective VHL-recruiting dTAG molecule, to rapidly degrade FKBP12F36V-tagged proteins. dTAGV-1 overcomes a limitation of previously reported CRBN-recruiting dTAG molecules to degrade recalcitrant oncogenes, supports combination degrader studies and facilitates investigations of protein function in cells and mice.
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Affiliation(s)
- Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bo Kyung A Seong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Miljan Kuljanin
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alan L Leggett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mikaela L Mohardt
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amanda Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amy S Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Joseph D Mancias
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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5
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Remillard D, Buckley DL, Seo HS, Ferguson FM, Dhe-Paganon S, Bradner JE, Gray NS. Dual Inhibition of TAF1 and BET Bromodomains from the BI-2536 Kinase Inhibitor Scaffold. ACS Med Chem Lett 2019; 10:1443-1449. [PMID: 31620231 DOI: 10.1021/acsmedchemlett.9b00243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/13/2019] [Indexed: 12/13/2022] Open
Abstract
Recent reports have highlighted the dual bromodomains of TAF1 (TAF1(1,2)) as synergistic with BET inhibition in cellular cancer models, engendering interest in TAF/BET polypharmacology. Here, we examine structure activity relationships within the BI-2536 PLK1 kinase inhibitor scaffold, previously reported to bind BRD4. We examine binding by this ligand to TAF1(2) and apply structure guided design strategies to discriminate binding to both the PLK1 kinase and BRD4(1) bromodomain while retaining activity on TAF1(2). Through this effort we discover potent dual inhibitors of TAF1(2)/BRD4(1), as well as biased derivatives showing marked TAF1 selectivity. We resolve X-ray crystallographic data sets to examine the mechanisms of the observed TAF1 selectivity and to provide a resource for further development of this scaffold.
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Affiliation(s)
- David Remillard
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
| | - Dennis L. Buckley
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
| | - Fleur M. Ferguson
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston Massachusetts 02115, United States
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
| | - James E. Bradner
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
| | - Nathanael S. Gray
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston Massachusetts 02115, United States
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6
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Wang J, Erazo T, Ferguson FM, Buckley DL, Gomez N, Muñoz-Guardiola P, Diéguez-Martínez N, Deng X, Hao M, Massefski W, Fedorov O, Offei-Addo NK, Park PM, Dai L, DiBona A, Becht K, Kim ND, McKeown MR, Roberts JM, Zhang J, Sim T, Alessi DR, Bradner JE, Lizcano JM, Blacklow SC, Qi J, Xu X, Gray NS. Structural and Atropisomeric Factors Governing the Selectivity of Pyrimido-benzodiazipinones as Inhibitors of Kinases and Bromodomains. ACS Chem Biol 2018; 13:2438-2448. [PMID: 30102854 PMCID: PMC6333101 DOI: 10.1021/acschembio.7b00638] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bromodomains have been pursued intensively over the past several years as emerging targets for the development of anticancer and anti-inflammatory agents. It has recently been shown that some kinase inhibitors are able to potently inhibit the bromodomains of BRD4. The clinical activities of PLK inhibitor BI-2536 and JAK2-FLT3 inhibitor TG101348 have been attributed to this unexpected polypharmacology, indicating that dual-kinase/bromodomain activity may be advantageous in a therapeutic context. However, for target validation and biological investigation, a more selective target profile is desired. Here, we report that benzo[e]pyrimido-[5,4- b]diazepine-6(11H)-ones, versatile ATP-site directed kinase pharmacophores utilized in the development of inhibitors of multiple kinases, including several previously reported kinase chemical probes, are also capable of exhibiting potent BRD4-dependent pharmacology. Using a dual kinase-bromodomain inhibitor of the kinase domains of ERK5 and LRRK2, and the bromodomain of BRD4 as a case study, we define the structure-activity relationships required to achieve dual kinase/BRD4 activity, as well as how to direct selectivity toward inhibition of either ERK5 or BRD4. This effort resulted in identification of one of the first reported kinase-selective chemical probes for ERK5 (JWG-071), a BET selective inhibitor with 1 μM BRD4 IC50 (JWG-115), and additional inhibitors with rationally designed polypharmacology (JWG-047, JWG-069). Co-crystallography of seven representative inhibitors with the first bromodomain of BRD4 demonstrate that distinct atropisomeric conformers recognize the kinase ATP-site and the BRD4 acetyl lysine binding site, conformational preferences supported by rigid docking studies.
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Affiliation(s)
- Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Tatiana Erazo
- Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina. Universitat Autònoma de Barcelona, E-08193 Barcelona, Spain
| | - Fleur M. Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis L. Buckley
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nestor Gomez
- Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina. Universitat Autònoma de Barcelona, E-08193 Barcelona, Spain
| | - Pau Muñoz-Guardiola
- Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina. Universitat Autònoma de Barcelona, E-08193 Barcelona, Spain
| | - Nora Diéguez-Martínez
- Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina. Universitat Autònoma de Barcelona, E-08193 Barcelona, Spain
| | - Xianming Deng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Mingfeng Hao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Walter Massefski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Oleg Fedorov
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | - Paul M. Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Lingling Dai
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Amy DiBona
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kelly Becht
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nam Doo Kim
- NDBio Therapeutics Inc., 32 Songdogwahak-ro, Yeonsu-gu, Incheon 21984, Republic of Korea
| | - Michael R. McKeown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Justin M. Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jinwei Zhang
- MRC Protein Phosphorylation and Ubiquitination Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - Taebo Sim
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul, Korea and KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Korea
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitination Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - James E. Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Jose M. Lizcano
- Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Facultat de Medicina. Universitat Autònoma de Barcelona, E-08193 Barcelona, Spain
| | - Stephen C. Blacklow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Xiang Xu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Corresponding Author,
| | - Nathanael S. Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Corresponding Author,
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7
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Liu S, Yosief HO, Dai L, Huang H, Dhawan G, Zhang X, Muthengi AM, Roberts J, Buckley DL, Perry JA, Wu L, Bradner JE, Qi J, Zhang W. Structure-Guided Design and Development of Potent and Selective Dual Bromodomain 4 (BRD4)/Polo-like Kinase 1 (PLK1) Inhibitors. J Med Chem 2018; 61:7785-7795. [PMID: 30125504 PMCID: PMC6309379 DOI: 10.1021/acs.jmedchem.8b00765] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The simultaneous inhibition of polo-like kinase 1 (PLK1) and BRD4 bromodomain by a single molecule could lead to the development of an effective therapeutic strategy for a variety of diseases in which PLK1 and BRD4 are implicated. Compound 23 has been found to be a potent dual kinase-bromodomain inhibitor (BRD4-BD1 IC50 = 28 nM, PLK1 IC50 = 40 nM). Compound 6 was found to be the most selective PLK1 inhibitor over BRD4 in our series (BRD4-BD1 IC50 = 2579 nM, PLK1 IC50 = 9.9 nM). Molecular docking studies with 23 and BRD4-BD1/PLK1 as well as with 6 corroborate the biochemical assay results.
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Affiliation(s)
- Shuai Liu
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | - Hailemichael O Yosief
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | - Lingling Dai
- Phase I Clinical Trial Center & Department of Clinical Pharmacology, Xiangya Hospital , Central South University , Changsha , Hunan 410008 , P.R. China
| | - He Huang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , United States
| | - Gagan Dhawan
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
- Department of Biomedical Science, Acharya Narendra Dev College , University of Delhi , New Delhi 110019 , India
| | - Xiaofeng Zhang
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | - Alex M Muthengi
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | | | | | | | | | - James E Bradner
- Novartis Institutes for Biomedical Research , Cambridge , Massachusetts 02139 , United States
| | - Jun Qi
- Department of Medicine , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Wei Zhang
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
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8
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Brunetti L, Gundry MC, Sorcini D, Guzman AG, Huang YH, Ramabadran R, Gionfriddo I, Mezzasoma F, Milano F, Nabet B, Buckley DL, Kornblau SM, Lin CY, Sportoletti P, Martelli MP, Falini B, Goodell MA. Mutant NPM1 Maintains the Leukemic State through HOX Expression. Cancer Cell 2018; 34:499-512.e9. [PMID: 30205049 PMCID: PMC6159911 DOI: 10.1016/j.ccell.2018.08.005] [Citation(s) in RCA: 185] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/14/2018] [Accepted: 08/04/2018] [Indexed: 01/16/2023]
Abstract
NPM1 is the most frequently mutated gene in cytogenetically normal acute myeloid leukemia (AML). In AML cells, NPM1 mutations result in abnormal cytoplasmic localization of the mutant protein (NPM1c); however, it is unknown whether NPM1c is required to maintain the leukemic state. Here, we show that loss of NPM1c from the cytoplasm, either through nuclear relocalization or targeted degradation, results in immediate downregulation of homeobox (HOX) genes followed by differentiation. Finally, we show that XPO1 inhibition relocalizes NPM1c to the nucleus, promotes differentiation of AML cells, and prolongs survival of Npm1-mutated leukemic mice. We describe an exquisite dependency of NPM1-mutant AML cells on NPM1c, providing the rationale for the use of nuclear export inhibitors in AML with mutated NPM1.
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MESH Headings
- Aged
- Animals
- Cell Differentiation/genetics
- Cell Line, Tumor
- Cell Nucleus/metabolism
- Cytoplasm/metabolism
- Down-Regulation
- Female
- Gene Expression Regulation, Leukemic
- Homeodomain Proteins/metabolism
- Humans
- Hydrazines/pharmacology
- Karyopherins/antagonists & inhibitors
- Karyopherins/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mutation
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Nucleophosmin
- Proteolysis
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/metabolism
- Triazoles/pharmacology
- Xenograft Model Antitumor Assays
- Exportin 1 Protein
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Affiliation(s)
- Lorenzo Brunetti
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX 77030, USA; Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, 06132 Perugia, Italy
| | - Michael C Gundry
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniele Sorcini
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, 06132 Perugia, Italy
| | - Anna G Guzman
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yung-Hsin Huang
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Raghav Ramabadran
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ilaria Gionfriddo
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, 06132 Perugia, Italy
| | - Federica Mezzasoma
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, 06132 Perugia, Italy
| | - Francesca Milano
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, 06132 Perugia, Italy
| | - Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Steven M Kornblau
- Department of Leukemia and Department of Stem Cell Transplantation and Cellular Therapy, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Paolo Sportoletti
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, 06132 Perugia, Italy
| | - Maria Paola Martelli
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, 06132 Perugia, Italy
| | - Brunangelo Falini
- Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, 06132 Perugia, Italy
| | - Margaret A Goodell
- Stem Cell and Regenerative Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Texas Children's Hospital and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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9
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Moser SC, Voerman JSA, Buckley DL, Winter GE, Schliehe C. Acute Pharmacologic Degradation of a Stable Antigen Enhances Its Direct Presentation on MHC Class I Molecules. Front Immunol 2018; 8:1920. [PMID: 29358938 PMCID: PMC5766668 DOI: 10.3389/fimmu.2017.01920] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/14/2017] [Indexed: 12/23/2022] Open
Abstract
Bifunctional degraders, also referred to as proteolysis-targeting chimeras (PROTACs), are a recently developed class of small molecules. They were designed to specifically target endogenous proteins for ubiquitin/proteasome-dependent degradation and to thereby interfere with pathological mechanisms of diseases, including cancer. In this study, we hypothesized that this process of acute pharmacologic protein degradation might increase the direct MHC class I presentation of degraded targets. By studying this question, we contribute to an ongoing discussion about the origin of peptides feeding the MHC class I presentation pathway. Two scenarios have been postulated: peptides can either be derived from homeostatic turnover of mature proteins and/or from short-lived defective ribosomal products (DRiPs), but currently, it is still unclear to what ratio and efficiency both pathways contribute to the overall MHC class I presentation. We therefore generated the intrinsically stable model antigen GFP-S8L-F12 that was susceptible to acute pharmacologic degradation via the previously described degradation tag (dTAG) system. Using different murine cell lines, we show here that the bifunctional molecule dTAG-7 induced rapid proteasome-dependent degradation of GFP-S8L-F12 and simultaneously increased its direct presentation on MHC class I molecules. Using the same model in a doxycycline-inducible setting, we could further show that stable, mature antigen was the major source of peptides presented, thereby excluding a dominant role of DRiPs in our system. This study is, to our knowledge, the first to investigate targeted pharmacologic protein degradation in the context of antigen presentation and our data point toward future applications by strategically combining therapies using bifunctional degraders with their stimulating effect on direct MHC class I presentation.
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Affiliation(s)
- Sarah C Moser
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jane S A Voerman
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Dennis L Buckley
- Department for Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christopher Schliehe
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
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10
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Weintraub AS, Li CH, Zamudio AV, Sigova AA, Hannett NM, Day DS, Abraham BJ, Cohen MA, Nabet B, Buckley DL, Guo YE, Hnisz D, Jaenisch R, Bradner JE, Gray NS, Young RA. YY1 Is a Structural Regulator of Enhancer-Promoter Loops. Cell 2017; 171:1573-1588.e28. [PMID: 29224777 DOI: 10.1016/j.cell.2017.11.008] [Citation(s) in RCA: 562] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/08/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
Abstract
There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not employ this structural protein. Here, we show that the ubiquitously expressed transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF. YY1 binds to active enhancers and promoter-proximal elements and forms dimers that facilitate the interaction of these DNA elements. Deletion of YY1 binding sites or depletion of YY1 protein disrupts enhancer-promoter looping and gene expression. We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.
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Affiliation(s)
- Abraham S Weintraub
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Alicia V Zamudio
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Alla A Sigova
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Daniel S Day
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Malkiel A Cohen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Behnam Nabet
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Yang Eric Guo
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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11
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Huang HT, Dobrovolsky D, Paulk J, Yang G, Weisberg EL, Doctor ZM, Buckley DL, Cho JH, Ko E, Jang J, Shi K, Choi HG, Griffin JD, Li Y, Treon SP, Fischer ES, Bradner JE, Tan L, Gray NS. A Chemoproteomic Approach to Query the Degradable Kinome Using a Multi-kinase Degrader. Cell Chem Biol 2017; 25:88-99.e6. [PMID: 29129717 DOI: 10.1016/j.chembiol.2017.10.005] [Citation(s) in RCA: 258] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/11/2017] [Accepted: 10/17/2017] [Indexed: 12/16/2022]
Abstract
Heterobifunctional molecules that recruit E3 ubiquitin ligases, such as cereblon, for targeted protein degradation represent an emerging pharmacological strategy. A major unanswered question is how generally applicable this strategy is to all protein targets. In this study, we designed a multi-kinase degrader by conjugating a highly promiscuous kinase inhibitor with a cereblon-binding ligand, and used quantitative proteomics to discover 28 kinases, including BTK, PTK2, PTK2B, FLT3, AURKA, AURKB, TEC, ULK1, ITK, and nine members of the CDK family, as degradable. This set of kinases is only a fraction of the intracellular targets bound by the degrader, demonstrating that successful degradation requires more than target engagement. The results guided us to develop selective degraders for FLT3 and BTK, with potentials to improve disease treatment. Together, this study demonstrates an efficient approach to triage a gene family of interest to identify readily degradable targets for further studies and pre-clinical developments.
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Affiliation(s)
- Hai-Tsang Huang
- 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
| | - Dennis Dobrovolsky
- 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
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Guang Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Ellen L Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Zainab M Doctor
- 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
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Joong-Heui Cho
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea
| | - Eunhwa Ko
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea
| | - Jaebong Jang
- 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
| | - Kun Shi
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hwan Geun Choi
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea
| | - James D Griffin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ying Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Steven P Treon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, 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
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Li Tan
- 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; Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.
| | - 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.
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12
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Huang HT, Seo HS, Zhang T, Wang Y, Jiang B, Li Q, Buckley DL, Nabet B, Roberts JM, Paulk J, Dastjerdi S, Winter GE, McLauchlan H, Moran J, Bradner JE, Eck MJ, Dhe-Paganon S, Zhao JJ, Gray NS. MELK is not necessary for the proliferation of basal-like breast cancer cells. eLife 2017; 6. [PMID: 28926338 PMCID: PMC5605198 DOI: 10.7554/elife.26693] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/18/2017] [Indexed: 01/22/2023] Open
Abstract
Thorough preclinical target validation is essential for the success of drug discovery efforts. In this study, we combined chemical and genetic perturbants, including the development of a novel selective maternal embryonic leucine zipper kinase (MELK) inhibitor HTH-01-091, CRISPR/Cas9-mediated MELK knockout, a novel chemical-induced protein degradation strategy, RNA interference and CRISPR interference to validate MELK as a therapeutic target in basal-like breast cancers (BBC). In common culture conditions, we found that small molecule inhibition, genetic deletion, or acute depletion of MELK did not significantly affect cellular growth. This discrepancy to previous findings illuminated selectivity issues of the widely used MELK inhibitor OTSSP167, and potential off-target effects of MELK-targeting short hairpins. The different genetic and chemical tools developed here allow for the identification and validation of any causal roles MELK may play in cancer biology, which will be required to guide future MELK drug discovery efforts. Furthermore, our study provides a general framework for preclinical target validation.
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Affiliation(s)
- Hai-Tsang Huang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Yubao Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Baishan Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Qing Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Behnam Nabet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Shiva Dastjerdi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Georg E Winter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Hilary McLauchlan
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jennifer Moran
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States.,Novartis Institutes for Biomedical Research, Cambridge, United States
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States
| | - Jean J Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
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13
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Winter GE, Mayer A, Buckley DL, Erb MA, Roderick JE, Vittori S, Reyes JM, di Iulio J, Souza A, Ott CJ, Roberts JM, Zeid R, Scott TG, Paulk J, Lachance K, Olson CM, Dastjerdi S, Bauer S, Lin CY, Gray NS, Kelliher MA, Churchman LS, Bradner JE. BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment. Mol Cell 2017; 67:5-18.e19. [PMID: 28673542 DOI: 10.1016/j.molcel.2017.06.004] [Citation(s) in RCA: 278] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/14/2017] [Accepted: 06/02/2017] [Indexed: 12/19/2022]
Abstract
Processive elongation of RNA Polymerase II from a proximal promoter paused state is a rate-limiting event in human gene control. A small number of regulatory factors influence transcription elongation on a global scale. Prior research using small-molecule BET bromodomain inhibitors, such as JQ1, linked BRD4 to context-specific elongation at a limited number of genes associated with massive enhancer regions. Here, the mechanistic characterization of an optimized chemical degrader of BET bromodomain proteins, dBET6, led to the unexpected identification of BET proteins as master regulators of global transcription elongation. In contrast to the selective effect of bromodomain inhibition on transcription, BET degradation prompts a collapse of global elongation that phenocopies CDK9 inhibition. Notably, BRD4 loss does not directly affect CDK9 localization. These studies, performed in translational models of T cell leukemia, establish a mechanism-based rationale for the development of BET bromodomain degradation as cancer therapy.
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Affiliation(s)
- Georg E Winter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andreas Mayer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Michael A Erb
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Justine E Roderick
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sarah Vittori
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jaime M Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Julia di Iulio
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda Souza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Rhamy Zeid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Thomas G Scott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kate Lachance
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Calla M Olson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Shiva Dastjerdi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sophie Bauer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Charles Y Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Michelle A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.
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14
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Remillard D, Buckley DL, Paulk J, Brien GL, Sonnett M, Seo HS, Dastjerdi S, Wühr M, Dhe-Paganon S, Armstrong SA, Bradner JE. Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands. Angew Chem Int Ed Engl 2017; 56:5738-5743. [PMID: 28418626 DOI: 10.1002/anie.201611281] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/24/2017] [Indexed: 12/12/2022]
Abstract
The bromodomain-containing protein BRD9, a subunit of the human BAF (SWI/SNF) nucleosome remodeling complex, has emerged as an attractive therapeutic target in cancer. Despite the development of chemical probes targeting the BRD9 bromodomain, there is a limited understanding of BRD9 function beyond acetyl-lysine recognition. We have therefore created the first BRD9-directed chemical degraders, through iterative design and testing of heterobifunctional ligands that bridge the BRD9 bromodomain and the cereblon E3 ubiquitin ligase complex. Degraders of BRD9 exhibit markedly enhanced potency compared to parental ligands (10- to 100-fold). Parallel study of degraders with divergent BRD9-binding chemotypes in models of acute myeloid leukemia resolves bromodomain polypharmacology in this emerging drug class. Together, these findings reveal the tractability of non-BET bromodomain containing proteins to chemical degradation, and highlight lead compound dBRD9 as a tool for the study of BRD9.
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Affiliation(s)
- David Remillard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gerard L Brien
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew Sonnett
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shiva Dastjerdi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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15
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Remillard D, Buckley DL, Paulk J, Brien GL, Sonnett M, Seo HS, Dastjerdi S, Wühr M, Dhe-Paganon S, Armstrong SA, Bradner JE. Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611281] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- David Remillard
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Dennis L. Buckley
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Joshiawa Paulk
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Gerard L. Brien
- Department of Pediatric Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Matthew Sonnett
- Department of Systems Biology; Harvard Medical School; Boston MA USA
- Lewis-Sigler Institute for Integrative Genomics; Princeton University; Princeton NJ USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology; Dana-Farber Cancer Institute; Boston MA USA
| | - Shiva Dastjerdi
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics; Princeton University; Princeton NJ USA
- Department of Molecular Biology; Princeton University; Princeton NJ USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology; Dana-Farber Cancer Institute; Boston MA USA
| | - Scott A. Armstrong
- Department of Pediatric Oncology; Dana-Farber Cancer Institute; Boston MA USA
| | - James E. Bradner
- Department of Medical Oncology; Dana-Farber Cancer Institute; Boston MA USA
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16
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Winter GE, Buckley DL, Bradner JE. Abstract IA31: Phthalimide conjugation as a strategy for targeted protein degradation. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.pmccavuln16-ia31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Ligand-induced target protein destabilization is an efficacious therapeutic strategy in cancer, but discovery in this field has historically been serendipitous given the lack of rational design principles. Building on the molecular logic of immunomodulatory drugs (“IMiDs”), we innovated a facile chemical solution for targeted protein degradation using bifunctional small molecules capable of recruiting the E3 ligase cereblon (CRBN). These bifunctional molecules induce immediate, and complete proteasomal degradation of their target proteins and thus represent a novel class of small molecule therapeutics with an entirely uncharted and unique molecular pharmacology.
Focusing our initial efforts on degraders of the BET family of proteins, we observed that they exhibit superior efficacy than BET inhibitors through unknown mechanisms. In order to dissect and mechanistically explain that differential molecular pharmacology, we used optimized small-molecule degraders and kinetic measures of chromatin structure and function to unveil an unrecognized, essential role for BRD4 in global control of transcriptional pause-release. Targeted BET degradation nucleates a collapse in the transcriptional core regulatory circuitry and thus enabled us to exploit transcriptional addictions in T-Cell acute lymphoblastic leukemia (T-ALL) that were intractable using competitive BET bromodomain inhibitors.
Citation Format: Georg E. Winter, Dennis L. Buckley, James E. Bradner. Phthalimide conjugation as a strategy for targeted protein degradation. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr IA31.
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17
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Koblan LW, Buckley DL, Ott CJ, Fitzgerald ME, Ember SWJ, Zhu JY, Liu S, Roberts JM, Remillard D, Vittori S, Zhang W, Schonbrunn E, Bradner JE. Assessment of Bromodomain Target Engagement by a Series of BI2536 Analogues with Miniaturized BET-BRET. ChemMedChem 2016; 11:2575-2581. [PMID: 27862999 DOI: 10.1002/cmdc.201600502] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 10/21/2016] [Indexed: 01/27/2023]
Abstract
Evaluating the engagement of a small molecule ligand with a protein target in cells provides useful information for chemical probe optimization and pharmaceutical development. While several techniques exist that can be performed in a low-throughput manner, systematic evaluation of large compound libraries remains a challenge. In-cell engagement measurements are especially useful when evaluating compound classes suspected to target multiple cellular factors. In this study we used a bioluminescent resonant energy transfer assay to assess bromodomain engagement by a compound series containing bromodomain- and kinase-biasing polypharmacophores based on the known dual BRD4 bromodomain/PLK1 kinase inhibitor BI2536. With this assay, we discovered several novel agents with bromodomain-selective specificity profiles and cellular activity. Thus, this platform aids in distinguishing molecules whose cellular activity is difficult to assess due to polypharmacologic effects.
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Affiliation(s)
- Luke W Koblan
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, 02142, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, 02142, USA
| | - Mark E Fitzgerald
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, 02142, USA
- C4 Therapeutics, Cambridge, MA, 02142, USA
| | - Stuart W J Ember
- Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, 33612, USA
- Reaction Biology Corporation, Malvern, PA, 19355, USA
| | - Jin-Yi Zhu
- Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Shuai Liu
- Department of Chemistry, University of Massachusetts-Boston, Boston, MA, 02125, USA
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David Remillard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sarah Vittori
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, 02142, USA
| | - Wei Zhang
- Department of Chemistry, University of Massachusetts-Boston, Boston, MA, 02125, USA
| | - Ernst Schonbrunn
- Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, 02142, USA
- Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA
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18
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Koblan LW, Buckley DL, Ott CJ, Fitzgerald ME, Ember SWJ, Zhu J, Liu S, Roberts JM, Remillard D, Vittori S, Zhang W, Schonbrunn E, Bradner JE. Back Cover: Assessment of Bromodomain Target Engagement by a Series of BI2536 Analogues with Miniaturized BET‐BRET (ChemMedChem 23/2016). ChemMedChem 2016. [DOI: 10.1002/cmdc.201600587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Luke W. Koblan
- Center for the Science of Therapeutics Broad Institute Cambridge MA 02142 USA
| | - Dennis L. Buckley
- Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Christopher J. Ott
- Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Center for the Science of Therapeutics Broad Institute Cambridge MA 02142 USA
| | - Mark E. Fitzgerald
- Center for the Science of Therapeutics Broad Institute Cambridge MA 02142 USA
- C4 Therapeutics Cambridge MA 02142 USA
| | - Stuart W. J. Ember
- Drug Discovery Department Moffitt Cancer Center Tampa FL 33612 USA
- Reaction Biology Corporation Malvern PA 19355 USA
| | - Jin‐Yi Zhu
- Drug Discovery Department Moffitt Cancer Center Tampa FL 33612 USA
| | - Shuai Liu
- Department of Chemistry University of Massachusetts-Boston Boston MA 02125 USA
| | - Justin M. Roberts
- Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA
| | - David Remillard
- Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA
| | - Sarah Vittori
- Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA
- Center for the Science of Therapeutics Broad Institute Cambridge MA 02142 USA
| | - Wei Zhang
- Department of Chemistry University of Massachusetts-Boston Boston MA 02125 USA
| | - Ernst Schonbrunn
- Drug Discovery Department Moffitt Cancer Center Tampa FL 33612 USA
| | - James E. Bradner
- Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Center for the Science of Therapeutics Broad Institute Cambridge MA 02142 USA
- Novartis Institutes for Biomedical Research Cambridge MA 02139 USA
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19
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Matthews GM, Hu Y, Sheffer M, Hengeveld PJ, Buckley DL, Bariteau MA, Poarch H, Bradner JE, Mitsiades CS. Abstract 4713: BET bromodomain degradation as a therapeutic strategy in drug-resistant multiple myeloma. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Multiple myeloma (MM) is an incurable malignancy with an unmet need for novel therapeutic modalities. Moreover, acquired or de novo resistance to established or novel therapeutics remains a major challenge in this, and other, neoplasias. BET Bromodomain inhibitors (BBIs), including JQ1, have potent anti-MM activity in vitro and in in vivo, but do not provide curative outcome and do not induce apoptosis in most cell types. We sought to investigate dBET, a class of BBIs that induce degradation of BET Bromodomains (BRDs) through CRBN-mediated ubiquitination and proteasomal degradation, in drug-resistant MM. Additionally, we posited that resistance to dBET treatment would emerge through genetic perturbations and wished to uncover potential mechanisms prior to its clinical utilization. To address this, we compared effects of optimized lead compound, dBET6, with JQ1 on a panel of MM cell lines, including clones resistant to JQ1 or bortezomib and assessed viability using CS-BLI/CTG assay and BRD/c-MYC expression by western blot. Using an open-ended unbiased genome-wide CRISPR (clustered regularly interspaced short palindromic repeats)-associated Cas9 approach, we examined whether we could uncover genes associated with resistance to dBET6. MM1.S cells were transduced with Cas9 and pooled lentiviral particles of the GeCKO library, consisting of 2 pooled sgRNA sub-libraries (∼120,000 sgRNAs; targeting ∼19,000 genes and ∼1800 miRNAs). Using this CRISPR/Cas9-based approach we sought to expedite the isolation of MM cells resistant to dBET6. We treated the pool of cells thrice with dBET (≥IC80), allowing regrowth between treatments and maintaining a coverage of 1000 cells/sgRNA. dBET6-resistant cells were processed to quantify sgRNA enrichment or depletion, using deep sequencing. We observed dBET6 to have significantly greater potency against MM cells than JQ1, or its combination with lenalidomide, and that MM1S.CRBN-/- cells were resistant to dBET6. Resistance to neither JQ1 nor Bortezomib conferred resistance to dBET6. We observed dBET6 to induce rapid (<4hrs) degradation of BRD2, BRD3 and BRD4 and complete absence of c-MYC protein, in contrast to JQ1 which caused dose-dependent down-regulation of c-MYC, and apparent upregulation of BRD4. As predicted, our CRISPR/Cas9 screen identified significant enrichment of sgRNAs targeting CRBN, as well as the Cullin-RING ligase (CRL) complex, known to play a critical role in E3 ubiquitin ligase activity. In summary, our data support the development of dBET for the treatment of drug-resistant MM. Additionally, our results demonstrate that loss of function of CRBN or the CRL complex induces dBET resistance by perturbing dBET-mediated BRD4 degradation. However, it is plausible that additional CRBN/CRL-independent mechanisms of dBET resistance exist that allow cells to survive despite complete degradation of BRDs and this will be a key question to be answered in future studies.
Citation Format: Geoffrey M. Matthews, Yiguo Hu, Michal Sheffer, Paul J. Hengeveld, Dennis L. Buckley, Megan A. Bariteau, Haley Poarch, James E. Bradner, Constantine S. Mitsiades. BET bromodomain degradation as a therapeutic strategy in drug-resistant multiple myeloma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4713.
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Affiliation(s)
| | - Yiguo Hu
- Dana Farber Cancer Institute, Boston, MA
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20
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Buckley DL, Raina K, Darricarrere N, Hines J, Gustafson JL, Smith IE, Miah AH, Harling JD, Crews CM. HaloPROTACS: Use of Small Molecule PROTACs to Induce Degradation of HaloTag Fusion Proteins. ACS Chem Biol 2015; 10:1831-7. [PMID: 26070106 DOI: 10.1021/acschembio.5b00442] [Citation(s) in RCA: 274] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Small molecule-induced protein degradation is an attractive strategy for the development of chemical probes. One method for inducing targeted protein degradation involves the use of PROTACs, heterobifunctional molecules that can recruit specific E3 ligases to a desired protein of interest. PROTACs have been successfully used to degrade numerous proteins in cells, but the peptidic E3 ligase ligands used in previous PROTACs have hindered their development into more mature chemical probes or therapeutics. We report the design of a novel class of PROTACs that incorporate small molecule VHL ligands to successfully degrade HaloTag7 fusion proteins. These HaloPROTACs will inspire the development of future PROTACs with more drug-like properties. Additionally, these HaloPROTACs are useful chemical genetic tools, due to their ability to chemically knock down widely used HaloTag7 fusion proteins in a general fashion.
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Affiliation(s)
| | | | | | | | | | - Ian E. Smith
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline, Stevenage, SG1 2NY, United Kingdom
| | - Afjal H. Miah
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline, Stevenage, SG1 2NY, United Kingdom
| | - John D. Harling
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline, Stevenage, SG1 2NY, United Kingdom
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21
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Bondeson DP, Mares A, Smith IED, Ko E, Campos S, Miah AH, Mulholland KE, Routly N, Buckley DL, Gustafson JL, Zinn N, Grandi P, Shimamura S, Bergamini G, Faelth-Savitski M, Bantscheff M, Cox C, Gordon DA, Willard RR, Flanagan JJ, Casillas LN, Votta BJ, den Besten W, Famm K, Kruidenier L, Carter PS, Harling JD, Churcher I, Crews CM. Catalytic in vivo protein knockdown by small-molecule PROTACs. Nat Chem Biol 2015; 11:611-7. [PMID: 26075522 PMCID: PMC4629852 DOI: 10.1038/nchembio.1858] [Citation(s) in RCA: 757] [Impact Index Per Article: 84.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/03/2015] [Indexed: 01/01/2023]
Abstract
The current predominant therapeutic paradigm is based on maximizing drug-receptor occupancy to achieve clinical benefit. This strategy, however, generally requires excessive drug concentrations to ensure sufficient occupancy, often leading to adverse side effects. Here, we describe major improvements to the proteolysis targeting chimeras (PROTACs) method, a chemical knockdown strategy in which a heterobifunctional molecule recruits a specific protein target to an E3 ubiquitin ligase, resulting in the target's ubiquitination and degradation. These compounds behave catalytically in their ability to induce the ubiquitination of super-stoichiometric quantities of proteins, providing efficacy that is not limited by equilibrium occupancy. We present two PROTACs that are capable of specifically reducing protein levels by >90% at nanomolar concentrations. In addition, mouse studies indicate that they provide broad tissue distribution and knockdown of the targeted protein in tumor xenografts. Together, these data demonstrate a protein knockdown system combining many of the favorable properties of small-molecule agents with the potent protein knockdown of RNAi and CRISPR.
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Affiliation(s)
- Daniel P Bondeson
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Alina Mares
- GSK Medicines Research Centre, Stevenage, UK
| | | | - Eunhwa Ko
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | | | | | | | | | - Dennis L Buckley
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Jeffrey L Gustafson
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Nico Zinn
- Cellzome, a GSK company, Heidelberg, Germany
| | | | | | | | | | | | - Carly Cox
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | | | | | | | - Linda N Casillas
- Pattern Recognition Receptor Discovery Performance Unit, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Bartholomew J Votta
- Pattern Recognition Receptor Discovery Performance Unit, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Willem den Besten
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | | | | | | | | | | | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Department of Pharmacology, Yale University, New Haven, Connecticut, USA
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22
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Gustafson JL, Neklesa TK, Cox CS, Roth AG, Buckley DL, Tae HS, Sundberg TB, Stagg DB, Hines J, McDonnell DP, Norris JD, Crews CM. Small-Molecule-Mediated Degradation of the Androgen Receptor through Hydrophobic Tagging. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503720] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Gustafson JL, Neklesa TK, Cox CS, Roth AG, Buckley DL, Tae HS, Sundberg TB, Stagg DB, Hines J, McDonnell DP, Norris JD, Crews CM. Small-Molecule-Mediated Degradation of the Androgen Receptor through Hydrophobic Tagging. Angew Chem Int Ed Engl 2015; 54:9659-62. [PMID: 26083457 DOI: 10.1002/anie.201503720] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Indexed: 11/07/2022]
Abstract
Androgen receptor (AR)-dependent transcription is a major driver of prostate tumor cell proliferation. Consequently, it is the target of several antitumor chemotherapeutic agents, including the AR antagonist MDV3100/enzalutamide. Recent studies have shown that a single AR mutation (F876L) converts MDV3100 action from an antagonist to an agonist. Here we describe the generation of a novel class of selective androgen receptor degraders (SARDs) to address this resistance mechanism. Molecules containing hydrophobic degrons linked to small-molecule AR ligands induce AR degradation, reduce expression of AR target genes and inhibit proliferation in androgen-dependent prostate cancer cell lines. These results suggest that selective AR degradation may be an effective therapeutic prostate tumor strategy in the context of AR mutations that confer resistance to second-generation AR antagonists.
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Affiliation(s)
- Jeffrey L Gustafson
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Taavi K Neklesa
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Carly S Cox
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Anke G Roth
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Dennis L Buckley
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Hyun Seop Tae
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Thomas B Sundberg
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - D Blake Stagg
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710 (USA)
| | - John Hines
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA)
| | - Donald P McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710 (USA)
| | - John D Norris
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710 (USA)
| | - Craig M Crews
- Departments of Molecular, Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, New Haven, CT 065111 (USA).
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24
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Winter GE, Buckley DL, Paulk J, Roberts JM, Souza A, Dhe-Paganon S, Bradner JE. DRUG DEVELOPMENT. Phthalimide conjugation as a strategy for in vivo target protein degradation. Science 2015; 348:1376-81. [PMID: 25999370 DOI: 10.1126/science.aab1433] [Citation(s) in RCA: 1078] [Impact Index Per Article: 119.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/06/2015] [Indexed: 01/23/2023]
Abstract
The development of effective pharmacological inhibitors of multidomain scaffold proteins, notably transcription factors, is a particularly challenging problem. In part, this is because many small-molecule antagonists disrupt the activity of only one domain in the target protein. We devised a chemical strategy that promotes ligand-dependent target protein degradation using as an example the transcriptional coactivator BRD4, a protein critical for cancer cell growth and survival. We appended a competitive antagonist of BET bromodomains to a phthalimide moiety to hijack the cereblon E3 ubiquitin ligase complex. The resultant compound, dBET1, induced highly selective cereblon-dependent BET protein degradation in vitro and in vivo and delayed leukemia progression in mice. A second series of probes resulted in selective degradation of the cytosolic protein FKBP12. This chemical strategy for controlling target protein stability may have implications for therapeutically targeting previously intractable proteins.
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Affiliation(s)
- Georg E Winter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Amanda Souza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA. Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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25
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Singel SM, Cornelius C, Zaganjor E, Batten K, Sarode VR, Buckley DL, Peng Y, John GB, Li HC, Sadeghi N, Wright WE, Lum L, Corson TW, Shay JW. KIF14 promotes AKT phosphorylation and contributes to chemoresistance in triple-negative breast cancer. Neoplasia 2015; 16:247-56, 256.e2. [PMID: 24784001 DOI: 10.1016/j.neo.2014.03.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 12/21/2022] Open
Abstract
Despite evidence that kinesin family member 14 (KIF14) can serve as a prognostic biomarker in various solid tumors, how it contributes to tumorigenesis remains unclear. We observed that experimental decrease in KIF14 expression increases docetaxel chemosensitivity in estrogen receptor-negative/progesterone receptor-negative/human epidermal growth factor receptor 2-negative, "triple-negative" breast cancers (TNBC). To investigate the oncogenic role of KIF14, we used noncancerous human mammary epithelial cells and ectopically expressed KIF14 and found increased proliferative capacity, increased anchorage-independent grown in vitro, and increased resistance to docetaxel but not to doxorubicin, carboplatin, or gemcitabine. Seventeen benign breast biopsies of BRCA1 or BRCA2 mutation carriers showed increased KIF14 mRNA expression by fluorescence in situ hybridization compared to controls with no known mutations in BRCA1 or BRCA2, suggesting increased KIF14 expression as a biomarker of high-risk breast tissue. Evaluation of 34 cases of locally advanced TNBC showed that KIF14 expression significantly correlates with chemotherapy-resistant breast cancer. KIF14 knockdown also correlates with decreased AKT phosphorylation and activity. Live-cell imaging confirmed an insulin-induced temporal colocalization of KIF14 and AKT at the plasma membrane, suggesting a potential role of KIF14 in promoting activation of AKT. An experimental small-molecule inhibitor of KIF14 was then used to evaluate the potential anticancer benefits of downregulating KIF14 activity. Inhibition of KIF14 shows a chemosensitizing effect and correlates with decreasing activation of AKT. Together, these findings show an early and critical role for KIF14 in the tumorigenic potential of TNBC, and therapeutic targeting of KIF14 is feasible and effective for TNBC.
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Affiliation(s)
- Stina M Singel
- Division of Hematology-Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Cell Biology University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Crystal Cornelius
- Department of Cell Biology University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elma Zaganjor
- Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Kimberly Batten
- Department of Cell Biology University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Venetia R Sarode
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Yan Peng
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - George B John
- Clinical Laboratory Services, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hsiao C Li
- Division of Hematology-Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Navid Sadeghi
- Division of Hematology-Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Woodring E Wright
- Department of Cell Biology University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lawrence Lum
- Department of Cell Biology University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Timothy W Corson
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jerry W Shay
- Department of Cell Biology University of Texas Southwestern Medical Center, Dallas, TX, USA.
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McKeown MR, Shaw DL, Fu H, Liu S, Xu X, Marineau JJ, Huang Y, Zhang X, Buckley DL, Kadam A, Zhang Z, Blacklow SC, Qi J, Zhang W, Bradner JE. Biased multicomponent reactions to develop novel bromodomain inhibitors. J Med Chem 2014; 57:9019-27. [PMID: 25314271 PMCID: PMC4234447 DOI: 10.1021/jm501120z] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BET bromodomain inhibition has contributed new insights into gene regulation and emerged as a promising therapeutic strategy in cancer. Structural analogy of early methyl-triazolo BET inhibitors has prompted a need for structurally dissimilar ligands as probes of bromodomain function. Using fluorous-tagged multicomponent reactions, we developed a focused chemical library of bromodomain inhibitors around a 3,5-dimethylisoxazole biasing element with micromolar biochemical IC50. Iterative synthesis and biochemical assessment allowed optimization of novel BET bromodomain inhibitors based on an imidazo[1,2-a]pyrazine scaffold. Lead compound 32 (UMB-32) binds BRD4 with a Kd of 550 nM and 724 nM cellular potency in BRD4-dependent lines. Additionally, compound 32 shows potency against TAF1, a bromodomain-containing transcription factor previously unapproached by discovery chemistry. Compound 32 was cocrystallized with BRD4, yielding a 1.56 Å resolution crystal structure. This research showcases new applications of fluorous and multicomponent chemical synthesis for the development of novel epigenetic inhibitors.
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Affiliation(s)
- Michael R McKeown
- Department of Medical Oncology, Dana-Farber Cancer Institute , 450 Brookline Avenue, Boston, Massachusetts 02215, United States
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Buckley DL, Crews CM. Small-molecule control of intracellular protein levels through modulation of the ubiquitin proteasome system. Angew Chem Int Ed Engl 2014; 53:2312-30. [PMID: 24459094 PMCID: PMC4348030 DOI: 10.1002/anie.201307761] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Indexed: 12/25/2022]
Abstract
Traditionally, biological probes and drugs have targeted the activities of proteins (such as enzymes and receptors) that can be readily controlled by small molecules. The remaining majority of the proteome has been deemed "undruggable". By using small-molecule modulators of the ubiquitin proteasome, protein levels, rather than protein activity, can be targeted instead, thus increasing the number of druggable targets. Whereas targeting of the proteasome itself can lead to a global increase in protein levels, the targeting of other components of the UPS (e.g., the E3 ubiquitin ligases) can lead to an increase in protein levels in a more targeted fashion. Alternatively, multiple strategies for inducing protein degradation with small-molecule probes are emerging. With the ability to induce and inhibit the degradation of targeted proteins, small-molecule modulators of the UPS have the potential to significantly expand the druggable portion of the proteome beyond traditional targets, such as enzymes and receptors.
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Affiliation(s)
- Dennis L. Buckley
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
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Buckley DL, Crews CM. Steuerung der intrazellulären Proteinmenge durch niedermolekulare Modulatoren des Ubiquitin-Proteasom-Systems. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307761] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Chapman SJ, Wah TM, Sourbron SP, Buckley DL. The effects of cryoablation on renal cell carcinoma perfusion and glomerular filtration rate measured using dynamic contrast-enhanced MRI: a feasibility study. Clin Radiol 2013; 68:887-94. [PMID: 23639366 DOI: 10.1016/j.crad.2013.03.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 03/14/2013] [Indexed: 11/25/2022]
Abstract
AIM To assess the effect of cryoablation on renal cell carcinoma (RCC) perfusion and single kidney (SK) glomerular filtration rate (GFR) using dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI). MATERIALS AND METHODS Eighteen patients undergoing percutaneous cryoablation of a solitary RCC between August 2010 and November 2011 were evaluated with DCE-MRI immediately before and 1 month post-cryoablation. DCE-MRI data were acquired with 2 s temporal resolution in a coronal plane during the first pass of a 0.1 mmol/kg bolus dose of Gd-DOTA. Perfusion of the RCC (in ml/min/100 ml tissue) was estimated using a maximum slope technique. An index of SK GFR (SK-GFRi) was assessed using data acquired every 30 s for the following 3 min in the axial plane and analysed using Rutland-Patlak plots. This was compared to the GFR estimated by creatinine clearance (eGFR). RESULTS Perfusion in the zone of ablation decreased significantly (p<0.001) from a mean of 98.0 ± 37.5 ml/min/100 ml pre-cryoablation to 11.6 ± 4.1 ml/min/100 ml post-cryoablation; a mean decrease of 88.2%. Functional analysis was performed in seventeen patients. eGFR was underestimated by SK-GFRi which decreased significantly in tumour-bearing (-31.7%, p = 0.011), but not in contralateral kidneys (-4.4%, p = 0.14). CONCLUSION It is feasible to measure RCC perfusion pre- and post-cryoablation using DCE-MRI. The significant decrease within the zone of ablation suggests that this technique may be useful for assessment of treatment response. Further work is required to address the underestimation of eGFR by SK-GFRi and to validate the perfusion findings.
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Affiliation(s)
- S J Chapman
- Division of Medical Physics, University of Leeds, Leeds, UK
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Van Molle I, Thomann A, Buckley DL, So EC, Lang S, Crews CM, Ciulli A. Dissecting fragment-based lead discovery at the von Hippel-Lindau protein:hypoxia inducible factor 1α protein-protein interface. ACTA ACUST UNITED AC 2013; 19:1300-12. [PMID: 23102223 DOI: 10.1016/j.chembiol.2012.08.015] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/10/2012] [Accepted: 08/16/2012] [Indexed: 01/06/2023]
Abstract
Fragment screening is widely used to identify attractive starting points for drug design. However, its potential and limitations to assess the tractability of often challenging protein:protein interfaces have been underexplored. Here, we address this question by means of a systematic deconstruction of lead-like inhibitors of the pVHL:HIF-1α interaction into their component fragments. Using biophysical techniques commonly employed for screening, we could only detect binding of fragments that violate the Rule of Three, are more complex than those typically screened against classical druggable targets, and occupy two adjacent binding subsites at the interface rather than just one. Analyses based on ligand and group lipophilicity efficiency of anchored fragments were applied to dissect the individual subsites and probe for binding hot spots. The implications of our findings for targeting protein interfaces by fragment-based approaches are discussed.
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Affiliation(s)
- Inge Van Molle
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
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Buckley DL, Gustafson JL, Van Molle I, Roth AG, Tae HS, Gareiss PC, Jorgensen WL, Ciulli A, Crews CM. Small-molecule inhibitors of the interaction between the E3 ligase VHL and HIF1α. Angew Chem Int Ed Engl 2012; 51:11463-7. [PMID: 23065727 DOI: 10.1002/anie.201206231] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Indexed: 01/03/2023]
Affiliation(s)
- Dennis L Buckley
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
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32
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Buckley DL, Gustafson JL, Van Molle I, Roth AG, Tae HS, Gareiss PC, Jorgensen WL, Ciulli A, Crews CM. Niedermolekulare Inhibitoren der Wechselwirkung zwischen der E3-Ligase VHL und HIF1α. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206231] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Leach MO, Morgan B, Tofts PS, Buckley DL, Huang W, Horsfield MA, Chenevert TL, Collins DJ, Jackson A, Lomas D, Whitcher B, Clarke L, Plummer R, Judson I, Jones R, Alonzi R, Brunner T, Koh DM, Murphy P, Waterton JC, Parker G, Graves MJ, Scheenen TWJ, Redpath TW, Orton M, Karczmar G, Huisman H, Barentsz J, Padhani A. Imaging vascular function for early stage clinical trials using dynamic contrast-enhanced magnetic resonance imaging. Eur Radiol 2012; 22:1451-64. [PMID: 22562143 DOI: 10.1007/s00330-012-2446-x] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 02/23/2012] [Accepted: 02/28/2012] [Indexed: 12/11/2022]
Abstract
Many therapeutic approaches to cancer affect the tumour vasculature, either indirectly or as a direct target. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) has become an important means of investigating this action, both pre-clinically and in early stage clinical trials. For such trials, it is essential that the measurement process (i.e. image acquisition and analysis) can be performed effectively and with consistency among contributing centres. As the technique continues to develop in order to provide potential improvements in sensitivity and physiological relevance, there is considerable scope for between-centre variation in techniques. A workshop was convened by the Imaging Committee of the Experimental Cancer Medicine Centres (ECMC) to review the current status of DCE-MRI and to provide recommendations on how the technique can best be used for early stage trials. This review and the consequent recommendations are summarised here. Key Points • Tumour vascular function is key to tumour development and treatment • Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) can assess tumour vascular function • Thus DCE-MRI with pharmacokinetic models can assess novel treatments • Many recent developments are advancing the accuracy of and information from DCE-MRI • Establishing common methodology across multiple centres is challenging and requires accepted guidelines.
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Affiliation(s)
- M O Leach
- Cancer Research UK and EPSRC Cancer Imaging Centre, Institute of Cancer Research & Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2, 5PT, UK.
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Buckley DL, Van Molle I, Gareiss PC, Tae HS, Michel J, Noblin DJ, Jorgensen WL, Ciulli A, Crews CM. Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1α interaction. J Am Chem Soc 2012; 134:4465-8. [PMID: 22369643 PMCID: PMC3448299 DOI: 10.1021/ja209924v] [Citation(s) in RCA: 319] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
E3 ubiquitin ligases, which bind protein targets, leading
to their
ubiquitination and subsequent degradation, are attractive drug targets
due to their exquisite substrate specificity. However, the development
of small-molecule inhibitors has proven extraordinarily challenging
as modulation of E3 ligase activities requires the targeting of protein–protein
interactions. Using rational design, we have generated the first small
molecule targeting the von Hippel–Lindau protein (VHL), the
substrate recognition subunit of an E3 ligase, and an important target
in cancer, chronic anemia, and ischemia. We have also obtained the
crystal structure of VHL bound to our most potent inhibitor, confirming
that the compound mimics the binding mode of the transcription factor
HIF-1α, a substrate of VHL. These results have the potential
to guide future development of improved lead compounds as therapeutics
for the treatment of chronic anemia and ischemia.
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Affiliation(s)
- Dennis L Buckley
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
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Abstract
The tracer-kinetic models developed in the early 1990s for dynamic contrast-enhanced MRI (DCE-MRI) have since become a standard in numerous applications. At the same time, the development of MRI hardware has led to increases in image quality and temporal resolution that reveal the limitations of the early models. This in turn has stimulated an interest in the development and application of a second generation of modelling approaches. They are designed to overcome these limitations and produce additional and more accurate information on tissue status. In particular, models of the second generation enable separate estimates of perfusion and capillary permeability rather than a single parameter K(trans) that represents a combination of the two. A variety of such models has been proposed in the literature, and development in the field has been constrained by a lack of transparency regarding terminology, notations and physiological assumptions. In this review, we provide an overview of these models in a manner that is both physically intuitive and mathematically rigourous. All are derived from common first principles, using concepts and notations from general tracer-kinetic theory. Explicit links to their historical origins are included to allow for a transfer of experience obtained in other fields (PET, SPECT, CT). A classification is presented that reveals the links between all models, and with the models of the first generation. Detailed formulae for all solutions are provided to facilitate implementation. Our aim is to encourage the application of these tools to DCE-MRI by offering researchers a clearer understanding of their assumptions and requirements.
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Affiliation(s)
- S P Sourbron
- Division of Medical Physics, University of Leeds, Leeds, West Yorkshire, UK
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Richardson OC, Scott MLJ, Tanner SF, Waterton JC, Buckley DL. Overcoming the low relaxivity of gadofosveset at high field with spin locking. Magn Reson Med 2011; 68:1234-8. [PMID: 22161901 PMCID: PMC3666098 DOI: 10.1002/mrm.23316] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 11/10/2011] [Accepted: 11/12/2011] [Indexed: 01/13/2023]
Abstract
The contrast agent gadofosveset, which binds reversibly to serum albumin, has a high longitudinal relaxivity at lower magnetic fields (≤3.0 T) but a much lower relaxivity at high fields. Spin locking is sensitive to macromolecular content; it is hypothesized that combining this technique with the albumin-binding properties of gadofosveset may enable increased relaxivity at high fields. In vitro measurements at 4.7 T found significantly higher spin-lock relaxation rates, R1ρ (1/T1ρ), when gadofosveset was serum albumin-bound than when unbound. R1ρ values for a nonbinding contrast agent (gadopentetate dimeglumine) in serum albumin were similar to those for unbound gadofosveset. R2 (1/T2) values were also significantly higher at 4.7 T for serum albumin-bound gadofosveset than for unbound. Spin locking at high field generates significantly higher relaxation rates for gadofosveset than conventional contrast agents and may provide a method for differentiating free and bound molecules at these field strengths.
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Affiliation(s)
- O C Richardson
- Division of Medical Physics, University of Leeds, Leeds, UK
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Buckley DL, Corson TW, Aberle N, Crews CM. HIV protease-mediated activation of sterically capped proteasome inhibitors and substrates. J Am Chem Soc 2011; 133:698-700. [PMID: 21186803 DOI: 10.1021/ja109377p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Strategies for selectively killing HIV-infected cells present an appealing alternative to traditional antiretroviral drugs. We show here the first example of an inactive “Trojan horse” molecule that releases a cytotoxic, small-molecule proteasome inhibitor upon cleavage by HIV-1 protease. As a proof-of-concept strategy, the protein avidin was used to block entry of the compound into the proteasome in the absence of HIV-1 protease. We demonstrate that this strategy is also feasible without requiring an exogenous protein; a polylysine dendrimer-containing molecule is unable to enter the proteasome until cleaved by HIV-1 protease. These results demonstrate that conditional proteasome inhibitors could prove useful in the development of new tools for chemical biology and future therapeutics.
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Affiliation(s)
- Dennis L Buckley
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
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Naish JH, McGrath DM, Bains LJ, Passera K, Roberts C, Watson Y, Cheung S, Taylor MB, Logue JP, Buckley DL, Tessier J, Young H, Waterton JC, Parker GJM. Comparison of dynamic contrast-enhanced MRI and dynamic contrast-enhanced CT biomarkers in bladder cancer. Magn Reson Med 2011; 66:219-26. [PMID: 21437971 DOI: 10.1002/mrm.22774] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 10/25/2010] [Accepted: 11/24/2010] [Indexed: 11/10/2022]
Abstract
Dynamic contrast-enhanced MRI (DCE-MRI) is frequently used to provide response biomarkers in clinical trials of novel cancer therapeutics but assessment of their physiological accuracy is difficult. DCE-CT provides an independent probe of similar pharmacokinetic processes and may be modeled in the same way as DCE-MRI to provide purportedly equivalent physiological parameters. In this study, DCE-MRI and DCE-CT were directly compared in subjects with primary bladder cancer to assess the degree to which the model parameters report modeled physiology rather than artefacts of the measurement technique and to determine the interchangeability of the techniques in a clinical trial setting. The biomarker K(trans) obtained by fitting an extended version of the Kety model voxelwise to both DCE-MRI and DCE-CT data was in excellent agreement (mean across subjects was 0.085 ± 0.030 min(-1) for DCE-MRI and 0.087 ± 0.033 min(-1) for DCE-CT, intermodality coefficient of variation 9%). The parameter v(p) derived from DCE-CT was significantly greater than that derived from DCE-MRI (0.018 ± 0.006 compared to 0.009 ± 0.008, P = 0.0007) and v(e) was in reasonable agreement only for low values. The study provides evidence that the biomarker K(trans) is a robust parameter indicative of the underlying physiology and relatively independent of the method of measurement.
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Affiliation(s)
- J H Naish
- Imaging Science and Biomedical Engineering, School of Cancer and Enabling Sciences, University of Manchester, Manchester, United Kingdom.
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Chrysochou C, Buckley DL, Kalra PA. Magnetic resonance imaging: advances in the investigation of atheromatous renovascular disease. J Nephrol 2008; 21:468-477. [PMID: 18651535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Prediction of renal functional outcome following revascularization procedures in atheromatous renovascular disease (ARVD) has remained a challenge. In considering the etiology of renal impairment, researchers have shifted their focus now from the influence of degree of renal artery stenosis (RAS) to the importance of intrinsic parenchymal damage caused by hypertension, atheroemboli, downstream cytokine and/or cholesterol crystal release, as well as indicators of tissue viability. Magnetic resonance (MR) imaging techniques and MR-based indices are able to provide a detailed assessment of the morphologic and functional aspects of the ARVD kidney. These indices look beyond "lumenology" and enable a better understanding of the parenchyma's physiology which may provide insight into predictors of outcome. This review summarizes the multipurpose benefits of MR in the assessment of ARVD.
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Affiliation(s)
- C Chrysochou
- Renal Department, Salford Royal Hospital NHS Foundation Trust, Salford, Manchester - UK.
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Cheung CM, Shurrab AE, Buckley DL, Hegarty J, Middleton RJ, Mamtora H, Kalra PA. MR-derived renal morphology and renal function in patients with atherosclerotic renovascular disease. Kidney Int 2006; 69:715-22. [PMID: 16395249 DOI: 10.1038/sj.ki.5000118] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Appropriate selection of patients with atherosclerotic renovascular disease (ARVD) for revascularization might be improved if accurate non-invasive investigations were used to assess severity of pre-existing parenchymal damage. The purpose of this study was to evaluate the associations between magnetic resonance imaging (MRI)-measured renal morphological parameters and single-kidney glomerular filtration rate (GFR) in ARVD. Three-dimensional (3D)-MRI was performed on 35 ARVD patients. Renal bipolar length (BL), parenchymal volume, parenchymal (PT), and cortical thicknesses (CT) were measured in 65 kidneys. Thirteen kidneys were supplied by normal vessels, 13 had insignificant (<50%) renal artery stenosis (RAS), 33 significant (>or=50%) RAS, and six complete vessel occlusion. All patients underwent radioisotopic measurement of single-kidney GFR (isoSK-GFR). Overall, 3D parameters such as parenchymal volume were better correlates of isoSK-GFR (r=0.86, P<0.001) than BL (r=0.78, P<0.001), PT (r=0.63, P<0.001) or CT (r=0.60, P<0.001). Kidneys with >or=50% RAS did show significant reduction in mean CT compared to those supplied by normal vessel (5.67+/-1.63 vs 7.28+/-1.80 mm, P=0.002; 22.1% reduction) and an even greater loss of parenchymal volume (120.65+/-47.15 vs 179.24+/-86.90 ml, P<0.001; 32.7% reduction) with no significant reduction in BL. In a proportion of >or=50% RAS kidneys, a disproportionately high parenchymal volume to isoSK-GFR was observed supporting a concept of 'hibernating parenchyma'. 3D parameters of parenchymal volume are stronger correlates of isoSK-GFR than two-dimensional measures of BL, PT or CT. 3D morphological evaluation together with isoSK-GFR might be useful in aiding patient selection for renal revascularization. Kidneys with increased parenchymal volume to SK-GFR might represent a subgroup with the potential to respond beneficially to angioplasty.
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Affiliation(s)
- C M Cheung
- Department of Renal Medicine, Hope Hospital, Salford, and Imaging Science and Biomedical Engineering, University of Manchester, UK.
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Harrer J, Parker GJM, Krings T, Haroon HA, Buckley DL, Roberts C, Noth J, Thron A, Jackson A. Assessment of microvascular characteristics of meningeomas with T1-weighted dynamic contrast-enhanced MRI. KLIN NEUROPHYSIOL 2006. [DOI: 10.1055/s-2006-939164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Jayson GC, Parker GJM, Mullamitha S, Valle JW, Saunders M, Broughton L, Lawrance J, Carrington B, Roberts C, Issa B, Buckley DL, Cheung S, Davies K, Watson Y, Zinkewich-Péotti K, Rolfe L, Jackson A. Blockade of platelet-derived growth factor receptor-beta by CDP860, a humanized, PEGylated di-Fab', leads to fluid accumulation and is associated with increased tumor vascularized volume. J Clin Oncol 2004; 23:973-81. [PMID: 15466784 DOI: 10.1200/jco.2005.01.032] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE CDP860 is an engineered Fab' fragment-polyethylene glycol conjugate, which binds to and blocks the activity of the beta-subunit of the platelet-derived growth factor receptor (PDGFR-beta). Studies in animals have suggested that PDGFR-beta inhibition reduces tumor interstitial fluid pressure, and thus increases the uptake of concomitantly administered drugs. The purpose of this study was to determine whether changes in tumor vascular parameters could be detected in humans, and to assess whether CDP860 would be likely to increase the uptake of a concurrently administered small molecule in future studies. PATIENTS AND METHODS Patients with advanced ovarian or colorectal cancer and good performance status received intravenous infusions of CDP860 on days 0 and 28. Patients had serial dynamic contrast-enhanced magnetic resonance imaging studies to measure changes in tumor vascular parameters. RESULTS Three of eight patients developed significant ascites, and seven of eight showed evidence of fluid retention. In some patients, the ratio of vascular volume to total tumor volume increased significantly (P < .001) within 24 hours following CDP860 administration, an effect suggestive of recruitment of previously non-functioning vessels. CONCLUSION These observations suggest that inhibition of PDGFR-beta might improve delivery of a concurrently administered therapy. However, in cancer patients, further exploration of the dosing regimen of CDP860 is required to dissociate adverse effects from beneficial effects. The findings challenge the view that inhibition of PDGF alone is beneficial, and confirm that effects of PDGFR kinase inhibition mediate, to some extent, the fluid retention observed in patients treated with mixed tyrosine kinase inhibitors.
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Affiliation(s)
- G C Jayson
- Cancer Research UK, Department of Medical Oncology, Christie Hospital, Manchester M20 4BX, United Kingdom.
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Harrer JU, Haroon HA, Buckley DL, Embleton K, Roberts C, Jackson A, Parker GJM. Beurteilung mikrovaskulärer Charakteristika von hochgradigen Gliomen mit Kontrastmittel-gestützter dynamischer MRT. Akt Neurol 2004. [DOI: 10.1055/s-2004-832963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abstract
This study examines multicomponent diffusion in isolated single neurons and discusses the implications of the results for macroscopic water diffusion in tissues. L7 Aplysia neurons were isolated and analyzed using a 600 MHz Bruker wide-bore instrument with a magnetic susceptibility-matched radiofrequency microcoil. Using a biexponential fit, the apparent diffusion coefficients (ADCs) from the cytoplasm (with relative fraction) were 0.48 +/- 0.14 x 10(-3) mm2 x s(-1) (61 +/- 11%) for the fast component, and 0.034 +/- 0.017 x 10(-3) mm2 x s(-1) (32 +/- 11%) for the slow component (N = 10). Diffusion in the nucleus appears to be primarily monoexponential, but with biexponential analysis it yields 1.31 +/- 0.32 x 10(-3) mm2 x s(-1) (89 +/- 6%) for the fast component and 0.057 +/- 0.073 x 10(-3) mm2 x s(-1) (11 +/- 6%) for the slow (N = 5). The slow component in the nucleus may be explained by cytoplasmic volume averaging. These data demonstrate that water diffusion in the cytoplasm of isolated single Aplysia neurons supports a multiexponential model. The ADCs are consistent with previous measurements in the cytoplasm of single neurons and with the slow ADC measurement in perfused brain slices. These distributions may explain the multiple compartments observed in tissues, greatly aiding the development of quantitative models of MRI in whole tissues.
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Affiliation(s)
- S C Grant
- Department of Bioengineering, University of Illinois-Chicago, Chicago, Illinois, USA.
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Abstract
Myocardial tissue slices were isolated from the left ventricular free wall (7 slices) and left ventricular papillary muscle (3 slices) of New Zealand White male rabbits (n = 4) and were subsequently superfused with a modified St. Thomas' Hospital cardioplegic solution at 19 degrees C. The diffusion-weighted images were obtained with a 600-MHz nuclear magnetic resonance spectrometer using diffusion gradient b-values that ranged from 166 to 6,408 s/mm(2); the apparent diffusion coefficient of water in the tissues were subsequently calculated. All of the tissue samples that were studied exhibited nonmonoexponential diffusion. Data from seven slices were mathematically fitted by a biexponential expression with a fast diffusion component of 0.72 +/- 0.07 x 10(-3) mm(2)/s, and a slow diffusion component of 0.060 +/- 0.033 x 10(-3) mm(2)/s. The fast component dominated the calculated apparent diffusion coefficient of the tissue, composed of 82 +/- 3% of the overall diffusion-dependent signal decay. Thus myocardial tissue exhibits characteristics consistent with multiple compartments of diffusion. This work has important implications for myocardial diffusion tensor imaging, as well as the changes in diffusion that have been reported following myocardial ischemia.
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Affiliation(s)
- J R Forder
- Department of Neuroscience, University of Florida, Gainesville 32611, USA.
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Abstract
Nonmonoexponential MR diffusion decay behavior has been observed at high diffusion-weighting strengths for cell aggregates and tissues, including the myocardium; however, implications for myocardial MR diffusion tensor imaging are largely unknown. In this study, a slow-exchange-limit, two-component diffusion tensor model was fitted to diffusion-weighted images obtained in isolated, perfused rat hearts. Results indicate that there are at least two distinct components of anisotropic diffusion, characterized by a "fast" component whose principal diffusivity is comparable to that of the perfusate, and a highly anisotropic "slow" component. It is speculated that the two components correspond to tissue compartments and have a general agreement with the orientations of anisotropy, or fiber orientations, in the myocardium. Moreover, consideration of previous studies of myocardial diffusion suggests that the presently observed fast component may likely be dominated by diffusion in the vascular space, whereas the slow component may include the intracellular and interstitial compartments. The implications of the results for myocardial fiber orientation mapping and limitations of the current two-component model used are also discussed.
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Affiliation(s)
- E W Hsu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708-0281, USA.
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Inglis BA, Bossart EL, Buckley DL, Wirth ED, Mareci TH. Visualization of neural tissue water compartments using biexponential diffusion tensor MRI. Magn Reson Med 2001; 45:580-7. [PMID: 11283985 DOI: 10.1002/mrm.1079] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The apparent diffusion tensor (ADT) imaging method was extended to account for multiple diffusion components. A biexponential ADT imaging experiment was used to obtain separate images of rapidly and slowly diffusing water fractions in excised rat spinal cord. The fast and slow component tensors were compared and found to exhibit similar gross features, such as fractional anisotropy, in both white and gray matter. However, there were also some important differences, which are consistent with the different structures occupying intracellular and extracellular spaces. Evidence supporting the assignment of the two tensor components to extracellular and intracellular water fractions is provided by an NMR spectroscopic investigation of homogeneous samples of brain tissue. Magn Reson Med 45:580-587, 2001.
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Affiliation(s)
- B A Inglis
- Department of Neuroscience, Center for Structural Biology, University of Florida Brain Institute, and the National High Magnetic Field Laboratory, University of Florida, Gainesville, Florida, USA.
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Shi J, Bui JD, Yang SH, He Z, Lucas TH, Buckley DL, Blackband SJ, King MA, Day AL, Simpkins JW. Estrogens decrease reperfusion-associated cortical ischemic damage: an MRI analysis in a transient focal ischemia model. Stroke 2001; 32:987-92. [PMID: 11283401 DOI: 10.1161/01.str.32.4.987] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND AND PURPOSE Early identification of irreversible cerebral ischemia is critical in defining strategies that influence neuronal survival after stroke. We used MRI to investigate the effects of 17beta-estradiol (E2) on the temporal evolution of focal ischemia. METHODS Female rats were ovariectomized and divided into 1 of 2 groups: ovariectomy alone (OVX; n=4) or ovariectomy with estrogen replacement (OVX+E2; n=3). Both groups were then subjected to 1-hour middle cerebral artery occlusion (MCAO), with the use of a standardized endovascular monofilament model, followed by reperfusion. Sequential diffusion-weighted (DWI) and T2-weighted (T2WI) MRI were obtained during and after the MCAO. In separate groups of animals (n=5 for OVX and OVX+E2), cerebral blood flow (CBF) was measured by laser-Doppler methods before, during, and after occlusion. RESULTS DWI detected similar lesion characteristics during MCAO in both groups. In the OVX group, lesion size did not change during reperfusion, but the signal intensity ratio increased early and stabilized during the latter stages. In contrast, DWI lesion size decreased during reperfusion in OVX+E2 rats by 50% to 60% (P<0.05), a size reduction almost exclusively limited to cortical regions. During MCAO, the signal intensity ratio in OVX+E2 rats was reduced compared with OVX rats. Reperfusion further attenuated the signal intensity ratio in cortical but not subcortical regions (P<0.05 versus OVX). T2WI revealed no lesions in either group during MCAO, but it detected lesion sizes similar to that of DWI during reperfusion. Furthermore, similar patterns and magnitudes of estrogen treatment-related decrease in lesion size were noted after reperfusion. T2WI demonstrated less intense signal intensity ratio changes in both groups compared with DWI. There were no differences in CBF between groups either during occlusion, early reperfusion, or 1 day after reperfusion. CONCLUSIONS This study strongly suggests that estrogens selectively protect cortical tissue from ischemic damage during MCAO and that this protection is exerted during both the occlusion and reperfusion phases of ischemia and does not involve an estrogen-related change in CBF.
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Affiliation(s)
- J Shi
- Departments of Pharmacodynamics, University of Florida Brain Institute, Tallahassee, Florida, USA
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Abstract
In this paper we briefly review the origins of NMR microscopy, and in the spirit of the Sir Peter Mansfield Symposium of which this presentation was a part, point out especially Sir Mansfield and his co-workers contributions in this area. We then review some recent studies applying magnetic resonance (MR) microscopy focusing on our own contributions in these regards, in particular with reference to imaging of single neurons and more recent microimaging studies on isolated perfused brain slices. Finally we briefly describe recent preliminary studies on the feasibility of spectroscopic experiments that may be performed at the single cell level, further illustrating the growing scope and potential of magnetic resonance imaging (MRI) in general as a tool for examining biological systems non-invasively.
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Affiliation(s)
- S J Blackband
- Center for Structural Biology at the University of Florida Brain Institute, Gainesville 32610, USA
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Tofts PS, Brix G, Buckley DL, Evelhoch JL, Henderson E, Knopp MV, Larsson HB, Lee TY, Mayr NA, Parker GJ, Port RE, Taylor J, Weisskoff RM. Estimating kinetic parameters from dynamic contrast-enhanced T(1)-weighted MRI of a diffusable tracer: standardized quantities and symbols. J Magn Reson Imaging 1999. [PMID: 10508281 DOI: 10.1002/(sici)1522-2586(199909)10:3<223:aid-jmri2>3.0.co;2-s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We describe a standard set of quantity names and symbols related to the estimation of kinetic parameters from dynamic contrast-enhanced T(1)-weighted magnetic resonance imaging data, using diffusable agents such as gadopentetate dimeglumine (Gd-DTPA). These include a) the volume transfer constant K(trans) (min(-1)); b) the volume of extravascular extracellular space (EES) per unit volume of tissue v(e) (0 < v(e) < 1); and c) the flux rate constant between EES and plasma k(ep) (min(-1)). The rate constant is the ratio of the transfer constant to the EES (k(ep) = K(trans)/v(e)). Under flow-limited conditions K(trans) equals the blood plasma flow per unit volume of tissue; under permeability-limited conditions K(trans) equals the permeability surface area product per unit volume of tissue. We relate these quantities to previously published work from our groups; our future publications will refer to these standardized terms, and we propose that these be adopted as international standards.
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Affiliation(s)
- P S Tofts
- Department of Clinical Neurology, Institute of Neurology, University College London, London WC1N 3BG, United Kingdom.
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