101
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Avgan N, Wang JI, Fernandez-Chamorro J, Weatheritt RJ. Multilayered control of exon acquisition permits the emergence of novel forms of regulatory control. Genome Biol 2019; 20:141. [PMID: 31315652 PMCID: PMC6637531 DOI: 10.1186/s13059-019-1757-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 07/09/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The long introns of mammals are pools of evolutionary potential due to the multiplicity of sequences that permit the acquisition of novel exons. However, the permissibility of genes to this type of acquisition and its influence on the evolution of cell regulation is poorly understood. RESULTS Here, we observe that human genes are highly permissive to the inclusion of novel exonic regions permitting the emergence of novel regulatory features. Our analysis reveals the potential for novel exon acquisition to occur in over 30% of evaluated human genes. Regulatory processes including the rate of splicing efficiency and RNA polymerase II (RNAPII) elongation control this process by modulating the "window of opportunity" for spliceosomal recognition. DNA damage alters this window promoting the inclusion of repeat-derived novel exons that reduce the ribosomal engagement of cell cycle genes. Finally, we demonstrate that the inclusion of novel exons is suppressed in hematological cancer samples and can be reversed by drugs modulating the rate of RNAPII elongation. CONCLUSION Our work demonstrates that the inclusion of repeat-associated novel intronic regions is a tightly controlled process capable of expanding the regulatory capacity of cells.
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Affiliation(s)
- Nesli Avgan
- EMBL Australia, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Juli I Wang
- EMBL Australia, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
| | | | - Robert J Weatheritt
- EMBL Australia, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia.
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102
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Abstract
Less than a decade ago, it was shown that bromodomains, acetyl lysine 'reader' modules found in proteins with varied functions, were highly tractable small-molecule targets. This is an unusual property for protein-protein or protein-peptide interaction domains, and it prompted a wave of chemical probe discovery to understand the biological potential of new agents that targeted bromodomains. The original examples, inhibitors of the bromodomain and extra-terminal (BET) class of bromodomains, showed enticing anti-inflammatory and anticancer activities, and several compounds have since advanced to human clinical trials. Here, we review the current state of BET inhibitor biology in relation to clinical development, and we discuss the next wave of bromodomain inhibitors with clinical potential in oncology and non-oncology indications. The lessons learned from BET inhibitor programmes should affect efforts to develop drugs that target non-BET bromodomains and other epigenetic readers.
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103
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Zhang L, Riley-Gillis B, Vijay P, Shen Y. Acquired Resistance to BET-PROTACs (Proteolysis-Targeting Chimeras) Caused by Genomic Alterations in Core Components of E3 Ligase Complexes. Mol Cancer Ther 2019; 18:1302-1311. [PMID: 31064868 DOI: 10.1158/1535-7163.mct-18-1129] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/28/2019] [Accepted: 05/02/2019] [Indexed: 11/16/2022]
Abstract
Proteolysis-targeting chimeras (PROTAC) are bifunctional molecules that hijack endogenous E3 ubiquitin ligases to induce ubiquitination and subsequent degradation of protein of interest. Recently, it has been shown that PROTACs with robust in vitro and in vivo activities and, in some cases, drug-like pharmaceutical properties can be generated using small-molecule ligands for the E3 ligases VHL and CRBN. These findings stoked tremendous enthusiasm on using PROTACs for therapeutics development. Innate and acquired drug resistance often underlies therapeutic failures, particularly for cancer therapy. With the PROTAC technology progressing rapidly toward therapeutic applications, it would be important to understand whether and how resistance to these novel agents may emerge. Using BET-PROTACs as a model system, we demonstrate that resistance to both VHL- and CRBN-based PROTACs can occur in cancer cells following chronic treatment. However, unlike what was often observed for many targeted therapeutics, resistance to BET-PROTACs did not result from secondary mutations that affect compound binding to the target. In contrast, acquired resistance to both VHL- and CRBN-based BET-PROTACs was primarily caused by genomic alterations that compromise core components of the relevant E3 ligase complexes.
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Affiliation(s)
- Lu Zhang
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois.
| | | | - Priyanka Vijay
- Genomic Research Center, AbbVie Inc., North Chicago, Illinois
| | - Yu Shen
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois.
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104
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RUNX1-targeted therapy for AML expressing somatic or germline mutation in RUNX1. Blood 2019; 134:59-73. [PMID: 31023702 DOI: 10.1182/blood.2018893982] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 04/16/2019] [Indexed: 12/22/2022] Open
Abstract
RUNX1 transcription factor regulates normal and malignant hematopoiesis. Somatic or germline mutant RUNX1 (mtRUNX1) is associated with poorer outcome in acute myeloid leukemia (AML). Knockdown or inhibition of RUNX1 induced more apoptosis of AML expressing mtRUNX1 versus wild-type RUNX1 and improved survival of mice engrafted with mtRUNX1-expressing AML. CRISPR/Cas9-mediated editing-out of RUNX1 enhancer (eR1) within its intragenic super-enhancer, or BET protein BRD4 depletion by short hairpin RNA, repressed RUNX1, inhibited cell growth, and induced cell lethality in AML cells expressing mtRUNX1. Moreover, treatment with BET protein inhibitor or degrader (BET-proteolysis targeting chimera) repressed RUNX1 and its targets, inducing apoptosis and improving survival of mice engrafted with AML expressing mtRUNX1. Library of Integrated Network-based Cellular Signatures 1000-connectivity mapping data sets queried with messenger RNA signature of RUNX1 knockdown identified novel expression-mimickers (EMs), which repressed RUNX1 and exerted in vitro and in vivo efficacy against AML cells expressing mtRUNX1. In addition, the EMs cinobufagin, anisomycin, and narciclasine induced more lethality in hematopoietic progenitor cells (HPCs) expressing germline mtRUNX1 from patients with AML compared with HPCs from patients with familial platelet disorder (FPD), or normal untransformed HPCs. These findings highlight novel therapeutic agents for AML expressing somatic or germline mtRUNX1.
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105
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Xi M, Chen Y, Yang H, Xu H, Du K, Wu C, Xu Y, Deng L, Luo X, Yu L, Wu Y, Gao X, Cai T, Chen B, Shen R, Sun H. Small molecule PROTACs in targeted therapy: An emerging strategy to induce protein degradation. Eur J Med Chem 2019; 174:159-180. [PMID: 31035238 DOI: 10.1016/j.ejmech.2019.04.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/13/2019] [Accepted: 04/13/2019] [Indexed: 01/01/2023]
Abstract
Inhibitors and nucleic acid based techniques were two main approaches to interfere with protein signaling and respective cascade in the past. Until recently, a new class of small molecules named proteolysis-targeting chimeras (PROTACs) have emerged. Each contains a target warhead, a linker and an E3 ligand. These bifunctional molecules recruit E3 ligases and target specific proteins for degradation via the ubiquitin (Ub) proteasome system (UPS). The degradation provides several advantages over inhibition in potency, selectivity and drug resistance. Thus, a variety of small molecule PROTACs have been discovered so far. In this review, we summarize the biological mechanism, advantages and recent progress of PROTACs, trying to offer an outlook in development of drugs targeting degradation in future.
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Affiliation(s)
- Meiyang Xi
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yi Chen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Hongyu Yang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China
| | - Huiting Xu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Kui Du
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Chunlei Wu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yanfei Xu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Liping Deng
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Xiang Luo
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Lemao Yu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yonghua Wu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Xiaozhong Gao
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Tao Cai
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Bin Chen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Runpu Shen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China.
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China.
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106
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Targeted protein degradation: elements of PROTAC design. Curr Opin Chem Biol 2019; 50:111-119. [PMID: 31004963 DOI: 10.1016/j.cbpa.2019.02.022] [Citation(s) in RCA: 346] [Impact Index Per Article: 69.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 12/26/2022]
Abstract
Targeted protein degradation using Proteolysis Targeting Chimeras (PROTACs) has emerged as a novel therapeutic modality in drug discovery. PROTACs mediate the degradation of select proteins of interest (POIs) by hijacking the activity of E3 ubiquitin ligases for POI ubiquitination and subsequent degradation by the 26S proteasome. This hijacking mechanism has been used to degrade various types of disease-relevant POIs. In this review, we aim to highlight the recent advances in targeted protein degradation and describe the challenges that need to be addressed in order to efficiently develop potent PROTACs.
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107
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Yang CY, Qin C, Bai L, Wang S. Small-molecule PROTAC degraders of the Bromodomain and Extra Terminal (BET) proteins - A review. DRUG DISCOVERY TODAY. TECHNOLOGIES 2019; 31:43-51. [PMID: 31200858 DOI: 10.1016/j.ddtec.2019.04.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 05/22/2023]
Abstract
The PROteolysis TArgeting Chimeric (PROTAC) concept has provided an opportunity for the discovery and development of a completely new type of therapy involving induction of protein degradation. The BET proteins, comprised of BRD2, BRD3, BRD4 and the testis-specific BRDT protein, are epigenetic readers and master transcription coactivators. Extremely potent and efficacious small-molecule PROTAC degraders of the BET proteins, based on available, potent and selective BET inhibitors, have been reported. BET degraders differ from BET inhibitors in their cellular potency, phenotypic effects, pharmacokinetic properties and toxicity profiles. Herein, we provide a review of BET degraders and the differential outcome observed in the cellular and animal models for BET degraders in comparison to BET inhibitors.
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Affiliation(s)
- Chao-Yie Yang
- The Rogel Cancer Center, Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Chong Qin
- The Rogel Cancer Center, Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Longchuan Bai
- The Rogel Cancer Center, Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Shaomeng Wang
- The Rogel Cancer Center, Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States.
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108
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Selective degradation of CDK6 by a palbociclib based PROTAC. Bioorg Med Chem Lett 2019; 29:1375-1379. [PMID: 30935795 DOI: 10.1016/j.bmcl.2019.03.035] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 12/28/2022]
Abstract
Development of selective kinase inhibitors that target the ATP binding site continues to be a challenge largely due to similar binding pockets. Palbociclib is a cyclin-dependent kinase inhibitor that targets the ATP binding site of CDK4 and CDK6 with similar potency. The enzymatic function associated with the kinase can be effectively probed using kinase inhibitors however the kinase-independent functions cannot. Herein, we report a palbociclib based PROTAC that selectively degrades CDK6 while sparing the homolog CDK4. We used competition studies to characterize the binding and mechanism of CDK6 degradation.
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109
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Watt GF, Scott-Stevens P, Gaohua L. Targeted protein degradation in vivo with Proteolysis Targeting Chimeras: Current status and future considerations. DRUG DISCOVERY TODAY. TECHNOLOGIES 2019; 31:69-80. [PMID: 31200862 DOI: 10.1016/j.ddtec.2019.02.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/21/2019] [Indexed: 02/08/2023]
Abstract
Proteolysis Targeting Chimeras (PROTACs) are a rapidly expanding new therapeutic modality inducing selective protein degradation and offering the potential of a differentiated pharmacological profile across multiple therapeutic areas. As the repertoire of protein targets and E3 ligases available for incorporation into PROTACs continues to grow, understanding the drug- and system-dependent parameters for PROTACs will be critical for achieving tissue/cell specific pharmacology. The review discusses the current knowledge and future direction of in vivo PROTAC study evaluation. The importance of establishing the quantitative relationship between loss of protein target and biological function in vivo, coupled with building mechanistic PK/PD and ultimately PBPK/PD models, is emphasised with the aim to aid translation from preclinical to clinical space.
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Affiliation(s)
- Gillian F Watt
- Protein Degradation Discovery Performance Unit, Future Pipelines Discovery, GlaxoSmithKline, Medicines Research Centre, Stevenage SG1 2NY, UK.
| | - Paul Scott-Stevens
- Protein Degradation Discovery Performance Unit, Future Pipelines Discovery, GlaxoSmithKline, Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Lu Gaohua
- Drug Design and Selection - SMTB, R&D Platform Technologies Sciences,GlaxoSmithKline, Medicines Research Centre, Stevenage SG1 2NY, UK
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110
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Veggiani G, Gerpe MCR, Sidhu SS, Zhang W. Emerging drug development technologies targeting ubiquitination for cancer therapeutics. Pharmacol Ther 2019; 199:139-154. [PMID: 30851297 PMCID: PMC7112620 DOI: 10.1016/j.pharmthera.2019.03.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Development of effective cancer therapeutic strategies relies on our ability to interfere with cellular processes that are dysregulated in tumors. Given the essential role of the ubiquitin proteasome system (UPS) in regulating a myriad of cellular processes, it is not surprising that malfunction of UPS components is implicated in numerous human diseases, including many types of cancer. The clinical success of proteasome inhibitors in treating multiple myeloma has further stimulated enthusiasm for targeting UPS proteins for pharmacological intervention in cancer treatment, particularly in the precision medicine era. Unfortunately, despite tremendous efforts, the paucity of potent and selective UPS inhibitors has severely hampered attempts to exploit the UPS for therapeutic benefits. To tackle this problem, many groups have been working on technology advancement to rapidly and effectively screen for potent and specific UPS modulators as intracellular probes or early-phase therapeutic agents. Here, we review several emerging technologies for developing chemical- and protein-based molecules to manipulate UPS enzymatic activity, with the aim of providing an overview of strategies available to target ubiquitination for cancer therapy.
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Affiliation(s)
- Gianluca Veggiani
- The Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - María Carla Rosales Gerpe
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E., Guelph, Ontario N1G2W1, Canada
| | - Sachdev S Sidhu
- The Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada.
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E., Guelph, Ontario N1G2W1, Canada.
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111
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Kim SA, Go A, Jo SH, Park SJ, Jeon YU, Kim JE, Lee HK, Park CH, Lee CO, Park SG, Kim P, Park BC, Cho SY, Kim S, Ha JD, Kim JH, Hwang JY. A novel cereblon modulator for targeted protein degradation. Eur J Med Chem 2019; 166:65-74. [DOI: 10.1016/j.ejmech.2019.01.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/19/2018] [Accepted: 01/10/2019] [Indexed: 01/01/2023]
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112
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Piya S, Mu H, Bhattacharya S, Lorenzi PL, Davis RE, McQueen T, Ruvolo V, Baran N, Wang Z, Qian Y, Crews CM, Konopleva M, Ishizawa J, You MJ, Kantarjian H, Andreeff M, Borthakur G. BETP degradation simultaneously targets acute myelogenous leukemia stem cells and the microenvironment. J Clin Invest 2019; 129:1878-1894. [PMID: 30829648 DOI: 10.1172/jci120654] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Anti-leukemic effect of BET/BRD4 (BETP) protein inhibition has been largely attributed to transcriptional downregulation of cellular anabolic/anti-apoptotic processes but its effect on bone marrow microenvironment, a sanctuary favoring persistence of leukemia stem/progenitor cells, is unexplored. Sustained degradation of BETP with small-molecule BET proteolysis-targeting chimera (PROTAC), ARV-825, resulted in marked downregulation of surface CXCR4 and CD44, key proteins in leukemia-microenvironment interaction, in AML cells. Abrogation of surface CXCR4 expression impaired SDF-1α directed migration and was mediated through transcriptional down-regulation of PIM1 kinase that in turn phosphorylates CXCR4 and facilitates its surface localization. Down-regulation of CD44/CD44v8-10 impaired cystine uptake, lowered intracellular reduced glutathione and increased oxidative stress. More importantly, BETP degradation markedly decreased CD34+CD38-CD90-CD45RA+ leukemic stem cell population and alone or in combination with Cytarabine, prolonged survival in mouse model of human leukemia including AML-PDX. Gene expression profiling and single cell proteomics confirmed down regulation of the gene signatures associated with 'stemness' in AML and Wnt/β-catenin, Myc pathways. Hence, BETP degradation by ARV-825 simultaneously targets cell intrinsic signaling, stromal interactions and metabolism in AML.
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Affiliation(s)
- Sujan Piya
- Section of Molecular Hematology and Therapy.,Department of Leukemia
| | - Hong Mu
- Section of Molecular Hematology and Therapy.,Department of Leukemia
| | | | | | - R Eric Davis
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Teresa McQueen
- Section of Molecular Hematology and Therapy.,Department of Leukemia
| | - Vivian Ruvolo
- Section of Molecular Hematology and Therapy.,Department of Leukemia
| | - Natalia Baran
- Section of Molecular Hematology and Therapy.,Department of Leukemia
| | - Zhiqiang Wang
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yimin Qian
- Arvinas Inc., New Haven, Connecticut, USA
| | - Craig M Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | | | | | - M James You
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Michael Andreeff
- Section of Molecular Hematology and Therapy.,Department of Leukemia
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113
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Bewersdorf JP, Shallis R, Stahl M, Zeidan AM. Epigenetic therapy combinations in acute myeloid leukemia: what are the options? Ther Adv Hematol 2019; 10:2040620718816698. [PMID: 30719265 PMCID: PMC6348528 DOI: 10.1177/2040620718816698] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/08/2018] [Indexed: 01/01/2023] Open
Abstract
Epigenetics refers to the regulation of gene expression mainly by changes in DNA methylation and modifications of histone proteins without altering the actual DNA sequence. While epigenetic modifications are essential for normal cell differentiation, several driver mutations in leukemic pathogenesis have been identified in genes that affect epigenetic processes, such as DNA methylation and histone acetylation. Several therapeutic options to target epigenetic alterations in acute myeloid leukemia (AML) have been successfully tested in preclinical studies and various drugs have already been approved for use in clinical practice. Among these already approved therapeutics are hypomethylating agents (azacitidine and decitabine) and isocitrate dehydrogenase inhibitors (ivosidenib, enasidenib). Other agents such as bromodomain-containing epigenetic reader proteins and histone methylation (e.g. DOT1L) inhibitors are currently in advanced clinical testing. As several epigenetic therapies have only limited efficacy when used as single agents, combination therapies that target AML pathogenesis at different levels and exploit synergistic mechanisms are also in clinical trials. Combinations of either epigenetic therapies with conventional chemotherapy, different forms of epigenetic therapies, or epigenetic therapies with immunotherapy are showing promising early results. In this review we summarize the underlying pathophysiology and rationale for epigenetically-based combination therapies, review current preclinical and clinical data and discuss the future directions of epigenetic therapy combinations in AML.
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Affiliation(s)
- Jan Philipp Bewersdorf
- Department of Internal Medicine, Section of Hematology, Yale University School of Medicine, New Haven, CT, USA
| | - Rory Shallis
- Department of Internal Medicine, Section of Hematology, Yale University School of Medicine, New Haven, CT, USA
| | - Maximilian Stahl
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amer M Zeidan
- Department of Internal Medicine, Section of Hematology, Yale University School of Medicine, 333 Cedar Street, PO Box 208028, New Haven, CT 06520-8055, USA
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114
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Lim SL, Damnernsawad A, Shyamsunder P, Chng WJ, Han BC, Xu L, Pan J, Pravin DP, Alkan S, Tyner JW, Koeffler HP. Proteolysis targeting chimeric molecules as therapy for multiple myeloma: efficacy, biomarker and drug combinations. Haematologica 2019; 104:1209-1220. [PMID: 30606790 PMCID: PMC6545861 DOI: 10.3324/haematol.2018.201483] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/02/2019] [Indexed: 12/31/2022] Open
Abstract
Proteolysis targeting chimeric molecule ARV 825 causes ubiquitination of bromodomains resulting in their efficient degradation by proteasome activity. Bromodomain degradation down-regulates MYC transcription contributing to growth inhibition of various human cancers. We examined the therapeutic potential of ARV 825 against multiple myeloma (MM) cells both in vitro and in vivo In a dose-dependent manner, ARV 825 inhibited proliferation of 13 human MM cell lines and three fresh patient samples, and was associated with cell cycle arrest and apoptosis. ARV 825 rapidly and efficiently degraded BRD 2 and BRD 4. Sensitivity of MM cells to ARV 825 was positively correlated with cereblon levels. RNA sequencing analysis showed important genes such as CCR1, RGS, MYB and MYC were down-regulated by ARV 825. A total of 170 small molecule inhibitors were screened for synergy with ARV 825. Combination of ARV 825 with inhibitor of either dual PI3K/mTOR, CRM1, VEGFR, PDGFRα/b, FLT3, IGF-1R, protein kinase C, CBP-EP300 or JAK1/2 showed synergistic activity. Importantly, ARV 825 significantly inhibited the growth of MM xenografts and improved mice survival. Taken together, our results, in conjunction with recently published findings, provide a rationale for investigating the efficacy of ARV 825 for MM, use of cereblon as a biomarker for therapy of MM patients, and the combination of ARV 825 with small molecule inhibitors to improve the outcome of MM patients.
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Affiliation(s)
- Su Lin Lim
- Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Alisa Damnernsawad
- Division of Hematology and Medical Oncology, Oregon Health and Science University Knight Cancer Institute, Portland, OR, USA
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jian Pan
- Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Dakle Pushkar Pravin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Serhan Alkan
- Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Jeffrey W Tyner
- Division of Hematology and Medical Oncology, Oregon Health and Science University Knight Cancer Institute, Portland, OR, USA
| | - H Phillip Koeffler
- Cedars Sinai Medical Center, Los Angeles, CA, USA.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
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115
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Zou Y, Ma D, Wang Y. The PROTAC technology in drug development. Cell Biochem Funct 2019; 37:21-30. [PMID: 30604499 PMCID: PMC6590639 DOI: 10.1002/cbf.3369] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/28/2022]
Abstract
Currently, a new technology termed PROTAC, proteolysis targeting chimera, has been developed for inducing the protein degradation by a targeting molecule. This technology takes advantage of a moiety of targeted protein and a moiety of recognizing E3 ubiquitin ligase and produces a hybrid molecule to specifically knock down a targeted protein. During the first decade, three pedigreed groups worked on the development of this technology. To date, this technology has been extended by different groups, aiming to develop new drugs against different diseases including cancers. This review summarizes the contributions of the groups for the development of PROTAC. SIGNIFICANCE OF THE STUDY: This review summarized the development of the PROTAC technology for readers and also presented the author's opinions on the application of the technology in tumor therapy.
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Affiliation(s)
- Yutian Zou
- The State Laboratory of Membrane Biology, Department of Basic Medicine, School of Medicine, Tsinghua University, Beijing, China.,Department of Science, Brookwood High School, Snellville, Georgia
| | - Danhui Ma
- The State Laboratory of Membrane Biology, Department of Basic Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Yinyin Wang
- The State Laboratory of Membrane Biology, Department of Basic Medicine, School of Medicine, Tsinghua University, Beijing, China
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116
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117
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Targeting nuclear β-catenin as therapy for post-myeloproliferative neoplasm secondary AML. Leukemia 2018; 33:1373-1386. [PMID: 30575820 DOI: 10.1038/s41375-018-0334-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/23/2018] [Accepted: 10/16/2018] [Indexed: 01/14/2023]
Abstract
Transformation of post-myeloproliferative neoplasms into secondary (s) AML exhibit poor clinical outcome. In addition to increased JAK-STAT and PI3K-AKT signaling, post-MPN sAML blast progenitor cells (BPCs) demonstrate increased nuclear β-catenin levels and TCF7L2 (TCF4) transcriptional activity. Knockdown of β-catenin or treatment with BC2059 that disrupts binding of β-catenin to TBL1X (TBL1) depleted nuclear β-catenin levels. This induced apoptosis of not only JAKi-sensitive but also JAKi-persister/resistant post-MPN sAML BPCs, associated with attenuation of TCF4 transcriptional targets MYC, BCL-2, and Survivin. Co-targeting of β-catenin and JAK1/2 inhibitor ruxolitinib (rux) synergistically induced lethality in post-MPN sAML BPCs and improved survival of mice engrafted with human sAML BPCs. Notably, co-treatment with BET protein degrader ARV-771 and BC2059 also synergistically induced apoptosis and improved survival of mice engrafted with JAKi-sensitive or JAKi-persister/resistant post-MPN sAML cells. These preclinical findings highlight potentially promising anti-post-MPN sAML activity of the combination of β-catenin and BETP antagonists against post-MPN sAML BPCs.
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118
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Jensen SM, Potts GK, Ready DB, Patterson MJ. Specific MHC-I Peptides Are Induced Using PROTACs. Front Immunol 2018; 9:2697. [PMID: 30524438 PMCID: PMC6262898 DOI: 10.3389/fimmu.2018.02697] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/01/2018] [Indexed: 01/10/2023] Open
Abstract
Peptides presented by the class-I major histocompatibility complex (MHC-I) are important targets for immunotherapy. The identification of these peptide targets greatly facilitates the generation of T-cell-based therapeutics. Herein, we report the capability of proteolysis targeting chimera (PROTAC) compounds to induce the presentation of specific MHC class-I peptides derived from endogenous cellular proteins. Using LC-MS/MS, we identified several BET-derived MHC-I peptides induced by treatment with three BET-directed PROTAC compounds. To understand our ability to tune this process, we measured the relative rate of presentation of these peptides under varying treatment conditions using label-free mass spectrometry quantification. We found that the rate of peptide presentation reflected the rate of protein degradation, indicating a direct relationship between PROTAC treatment and peptide presentation. We additionally analyzed the effect of PROTAC treatment on the entire immunopeptidome and found many new peptides that were displayed in a PROTAC-specific fashion: we determined that these identifications map to the BET pathway, as well as, potential off-target or unique-to-PROTAC pathways. This work represents the first evidence of the use of PROTAC compounds to induce the presentation of MHC-I peptides from endogenous cellular proteins, highlighting the capability of PROTAC compounds for the discovery and generation of new targets for immunotherapy.
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Affiliation(s)
- Stephanie M Jensen
- Discovery Chemistry and Technology, AbbVie North Chicago, IL, United States
| | - Gregory K Potts
- Discovery Chemistry and Technology, AbbVie North Chicago, IL, United States
| | - Damien B Ready
- Discovery Chemistry and Technology, AbbVie North Chicago, IL, United States
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119
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Duan Y, Guan Y, Qin W, Zhai X, Yu B, Liu H. Targeting Brd4 for cancer therapy: inhibitors and degraders. MEDCHEMCOMM 2018; 9:1779-1802. [PMID: 30542529 PMCID: PMC6238758 DOI: 10.1039/c8md00198g] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/03/2018] [Indexed: 12/24/2022]
Abstract
Bromodomain-containing protein 4 (Brd4) plays an important role in mediating the expression of genes involved in cancers and non-cancer diseases such as inflammatory diseases and acute heart failure. Inactivating Brd4 or downregulating its expression inhibits cancer development, leading to the current interest in Brd4 as a promising anticancer drug target. Numerous Brd4 inhibitors have been studied in recent years and some of them are currently in various phases of clinical trials. Recently, selective degradation of target proteins by small bifunctional molecules (PROTACs) has emerged as an attractive drug discovery approach owing to the advantages it could offer over traditional small-molecule inhibitors. A number of Brd4 degraders have been reported and showed more efficient anticancer activities than just protein inhibition. In this review, we will discuss recent findings in the discovery and development of small-molecule inhibitors and degraders that target Brd4 as a potential anticancer agent.
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Affiliation(s)
- Yingchao Duan
- School of Pharmacy , Xinxiang Medical University , Xinxiang , Henan 453003 , China
| | - Yuanyuan Guan
- School of Pharmacy , Xinxiang Medical University , Xinxiang , Henan 453003 , China
| | - Wenping Qin
- School of Pharmacy , Xinxiang Medical University , Xinxiang , Henan 453003 , China
| | - Xiaoyu Zhai
- School of Pharmacy , Xinxiang Medical University , Xinxiang , Henan 453003 , China
| | - Bin Yu
- Key Laboratory of Advanced Pharmaceutical Technology , Ministry of Education of China , Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety , Institute of Drug Discovery and Development , School of Pharmaceutical Sciences , Zhengzhou University , 100 Kexue Avenue , Zhengzhou , Henan 450001 , China . ;
| | - Hongmin Liu
- Key Laboratory of Advanced Pharmaceutical Technology , Ministry of Education of China , Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety , Institute of Drug Discovery and Development , School of Pharmaceutical Sciences , Zhengzhou University , 100 Kexue Avenue , Zhengzhou , Henan 450001 , China . ;
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120
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An S, Fu L. Small-molecule PROTACs: An emerging and promising approach for the development of targeted therapy drugs. EBioMedicine 2018; 36:553-562. [PMID: 30224312 PMCID: PMC6197674 DOI: 10.1016/j.ebiom.2018.09.005] [Citation(s) in RCA: 211] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/27/2018] [Accepted: 09/05/2018] [Indexed: 12/29/2022] Open
Abstract
There are several challenges towards the development and clinical use of small molecule inhibitors, which are currently the main type of targeted therapies towards intracellular proteins. PROteolysis-TArgeting Chimeras (PROTACs) exploit the intracellular ubiquitin-proteasome system to selectively degrade target proteins. Recently, small-molecule PROTACs with high potency have been frequently reported. In this review, we summarize the emerging characteristics of small-molecule PROTACs, such as inducing a rapid, profound and sustained degradation, inducing a robust inhibition of downstream signals, displaying enhanced target selectivity, and overcoming resistance to small molecule inhibitors. In tumor xenografts, small-molecule PROTACs can significantly attenuate tumor progression. In addition, we also introduce recent developments of the PROTAC technology such as homo-PROTACs. The outstanding advantages over traditional small-molecule drugs and the promising preclinical data suggest that small-molecule PROTAC technology has the potential to greatly promote the development of targeted therapy drugs.
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Affiliation(s)
- Sainan An
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Liwu Fu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China.
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121
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Ebine K, Kumar K, Pham TN, Shields MA, Collier KA, Shang M, DeCant BT, Urrutia R, Hwang RF, Grimaldo S, Principe DR, Grippo PJ, Bentrem DJ, Munshi HG. Interplay between interferon regulatory factor 1 and BRD4 in the regulation of PD-L1 in pancreatic stellate cells. Sci Rep 2018; 8:13225. [PMID: 30185888 PMCID: PMC6125340 DOI: 10.1038/s41598-018-31658-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/21/2018] [Indexed: 01/18/2023] Open
Abstract
The fibrotic reaction is a characteristic feature of human pancreatic ductal adenocarcinoma (PDAC) tumors. It is associated with activation and proliferation of pancreatic stellate cells (PSCs), which are key regulators of fibrosis in vivo. While there is increasing interest in the regulation of PD-L1 expression in cancer and immune cells, the expression and regulation of PD-L1 in other stromal cells, such as PSCs, has not been fully evaluated. Here we show that PSCs in vitro express higher PD-L1 mRNA and protein levels compared to the levels present in PDAC cells. We show that inhibitors targeting bromodomain and extra-terminal (BET) proteins and BRD4 knockdown decrease interferon-γ (IFN-γ)-induced PD-L1 expression in PSCs. We also show that c-MYC, one of the well-established targets of BET inhibitors, does not mediate IFN-γ-regulated PD-L1 expression in PSCs. Instead we show that interferon regulatory factor 1 (IRF1) mediates IFN-γ-induced PD-L1 expression in PSCs. Finally, while we show that BET inhibitors do not regulate IFN-γ-induced IRF1 expression in PSCs, BET inhibitors decrease binding of IRF1 and BRD4 to the PD-L1 promoter. Together, these results demonstrate the interplay between IRF1 and BRD4 in the regulation of PD-L1 in PSCs.
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Affiliation(s)
- Kazumi Ebine
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Krishan Kumar
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- The Robert H. Lurie Comprehensive Cancer Center, Chicago, IL, USA.
| | - Thao N Pham
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Mario A Shields
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring, NY, USA
| | - Katharine A Collier
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Meng Shang
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Brian T DeCant
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Raul Urrutia
- Laboratory of Epigenetics and Chromatin Dynamics, Division of Gastroenterology and Hepatology, Department of Internal Medicine, Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rosa F Hwang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sam Grimaldo
- Department of Medicine, University of Illinois, Chicago, IL, USA
| | | | - Paul J Grippo
- Department of Medicine, University of Illinois, Chicago, IL, USA
| | - David J Bentrem
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
- The Robert H. Lurie Comprehensive Cancer Center, Chicago, IL, USA
| | - Hidayatullah G Munshi
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Jesse Brown VA Medical Center, Chicago, IL, USA.
- The Robert H. Lurie Comprehensive Cancer Center, Chicago, IL, USA.
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122
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Itoh Y. Chemical Protein Degradation Approach and its Application to Epigenetic Targets. CHEM REC 2018; 18:1681-1700. [PMID: 29893461 DOI: 10.1002/tcr.201800032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/24/2018] [Indexed: 12/17/2022]
Abstract
In addition to traditional drugs, such as enzyme inhibitors, receptor agonists/antagonists, and protein-protein interaction inhibitors as well as genetic technology, such as RNA interference and the CRISPR/Cas9 system, protein knockdown approaches using proteolysis-targeting chimeras (PROTACs) have attracted much attention. PROTACs, which induce selective degradation of their target protein via the ubiquitin-proteasome system, are useful for the down-regulation of various proteins, including disease-related proteins and epigenetic proteins. Recent reports have shown that chemical protein knockdown is possible not only in cells, but also in vivo and this approach is expected to be used as the therapeutic strategy for several diseases. Thus, this approach may be a significant technique to complement traditional drugs and genetic ablation and will be more widely used for drug discovery and chemical biology studies in the future. In this personal account, a history of chemical protein knockdown is introduced, and its features, recent progress in the epigenetics field, and future outlooks are discussed.
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Affiliation(s)
- Yukihiro Itoh
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
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123
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Ishida S, Akiyama H, Umezawa Y, Okada K, Nogami A, Oshikawa G, Nagao T, Miura O. Mechanisms for mTORC1 activation and synergistic induction of apoptosis by ruxolitinib and BH3 mimetics or autophagy inhibitors in JAK2-V617F-expressing leukemic cells including newly established PVTL-2. Oncotarget 2018; 9:26834-26851. [PMID: 29928488 PMCID: PMC6003557 DOI: 10.18632/oncotarget.25515] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/13/2018] [Indexed: 11/25/2022] Open
Abstract
The activated JAK2-V617F mutant is very frequently found in myeloproliferative neoplasms (MPNs), and its inhibitor ruxolitinib has been in clinical use, albeit with limited efficacies. Here, we examine the signaling mechanisms from JAK2-V617F and responses to ruxolitinib in JAK2-V617F-positive leukemic cell lines, including PVTL-2, newly established from a patient with post-MPN secondary acute myeloid leukemia, and the widely used model cell line HEL. We have found that ruxolitinib downregulated the mTORC1/S6K/4EBP1 pathway at least partly through inhibition of the STAT5/Pim-2 pathway with concomitant downregulation of c-Myc, MCL-1, and BCL-xL as well as induction of autophagy in these cells. Ruxolitinib very efficiently inhibited proliferation but only modestly induced apoptosis. However, inhibition of BCL-xL/BCL-2 by the BH3 mimetics ABT-737 and navitoclax or BCL-xL by A-1331852 induced caspase-dependent apoptosis involving activation of Bak and Bax synergistically with ruxolitinib in HEL cells. On the other hand, the putative pan-BH3 mimetic obatoclax as well as chloroquine and bafilomycin A1 inhibited autophagy at its late stage and induced apoptosis in PVTL-2 cells synergistically with ruxolitinib. The present study suggests that autophagy as well as the anti-apoptotic BCL-2 family members, regulated at least partly by the mTORC1 pathway downstream of STAT5/Pim-2, protects JAK2-V617F-positive leukemic cells from ruxolitinib-induced apoptosis depending on cell types and may contribute to development of new strategies against JAK2-V617F-positive neoplasms.
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Affiliation(s)
- Shinya Ishida
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroki Akiyama
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshihiro Umezawa
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keigo Okada
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ayako Nogami
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Gaku Oshikawa
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Toshikage Nagao
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Osamu Miura
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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125
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Huang F, Shao W, Fujinaga K, Peterlin BM. Bromodomain-containing protein 4-independent transcriptional activation by autoimmune regulator (AIRE) and NF-κB. J Biol Chem 2018; 293:4993-5004. [PMID: 29463681 PMCID: PMC5892592 DOI: 10.1074/jbc.ra117.001518] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 02/13/2018] [Indexed: 11/06/2022] Open
Abstract
Autoimmune regulator (AIRE) and nuclear factor-κB (NF-κB) are transcription factors (TFs) that direct the expression of individual genes and gene clusters. Bromodomain-containing protein 4 (BRD4) is an epigenetic regulator that recognizes and binds to acetylated histones. BRD4 also has been reported to promote interactions between the positive transcription elongation factor b (P-TEFb) and AIRE or P-TEFb and NF-κB subunit p65. Here, we report that AIRE and p65 bind to P-TEFb independently of BRD4. JQ1, a compound that disrupts interactions between BRD4 and acetylated proteins, does not decrease transcriptional activities of AIRE or p65. Moreover, siRNA-mediated inactivation of BRD4 alone or in combination with JQ1 had no effects on AIRE- and NF-κB-targeted genes on plasmids and in chromatin and on interactions between P-TEFb and AIRE or NF-κB. Finally, ChIP experiments revealed that recruitment of P-TEFb to AIRE or p65 to transcription complexes was independent of BRD4. We conclude that direct interactions between AIRE, NF-κB, and P-TEFb result in efficient transcription of their target genes.
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Affiliation(s)
- Fang Huang
- From the Departments of Medicine, Microbiology, and Immunology, University of California, San Francisco, California 94143
| | - Wei Shao
- From the Departments of Medicine, Microbiology, and Immunology, University of California, San Francisco, California 94143
| | - Koh Fujinaga
- From the Departments of Medicine, Microbiology, and Immunology, University of California, San Francisco, California 94143
| | - B Matija Peterlin
- From the Departments of Medicine, Microbiology, and Immunology, University of California, San Francisco, California 94143
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126
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Robb CM, Contreras JI, Kour S, Taylor MA, Abid M, Sonawane YA, Zahid M, Murry DJ, Natarajan A, Rana S. Chemically induced degradation of CDK9 by a proteolysis targeting chimera (PROTAC). Chem Commun (Camb) 2018. [PMID: 28636052 DOI: 10.1039/c7cc03879h] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9), a member of the cyclin-dependent protein kinase (CDK) family, is involved in transcriptional elongation of several target genes. CDK9 is ubiquitously expressed and has been shown to contribute to a variety of malignancies such as pancreatic, prostate and breast cancers. Here we report the development of a heterobifunctional small molecule proteolysis targeting chimera (PROTAC) capable of cereblon (CRBN) mediated proteasomal degradation of CDK9. In HCT116 cells, it selectively degrades CDK9 while sparing other CDK family members. This is the first example of a PROTAC that selectively degrades CDK9.
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Affiliation(s)
- Caroline M Robb
- Eppley Institute for Research in Cancer and Allied Diseases, Omaha, Nebraska 68022, USA.
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127
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Coleman KG, Crews CM. Proteolysis-Targeting Chimeras: Harnessing the Ubiquitin-Proteasome System to Induce Degradation of Specific Target Proteins. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2018. [DOI: 10.1146/annurev-cancerbio-030617-050430] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Craig M. Crews
- Department of Molecular, Cellular, and Developmental Biology; Department of Chemistry; and Department of Pharmacology, Yale University, New Haven, Connecticut 06511, USA
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128
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Gu S, Cui D, Chen X, Xiong X, Zhao Y. PROTACs: An Emerging Targeting Technique for Protein Degradation in Drug Discovery. Bioessays 2018; 40:e1700247. [PMID: 29473971 DOI: 10.1002/bies.201700247] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 01/20/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Shanshan Gu
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine; 310003 Hangzhou China
- Institute of Translational Medicine, Zhejiang University School of Medicine; Hangzhou China
| | - Danrui Cui
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine; 310003 Hangzhou China
- Institute of Translational Medicine, Zhejiang University School of Medicine; Hangzhou China
| | - Xiaoyu Chen
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine; 310003 Hangzhou China
- Institute of Translational Medicine, Zhejiang University School of Medicine; Hangzhou China
| | - Xiufang Xiong
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine; 310003 Hangzhou China
- Institute of Translational Medicine, Zhejiang University School of Medicine; Hangzhou China
| | - Yongchao Zhao
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, First Affiliated Hospital, Zhejiang University School of Medicine; 310003 Hangzhou China
- Institute of Translational Medicine, Zhejiang University School of Medicine; Hangzhou China
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129
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Akuffo AA, Alontaga AY, Metcalf R, Beatty MS, Becker A, McDaniel JM, Hesterberg RS, Goodheart WE, Gunawan S, Ayaz M, Yang Y, Karim MR, Orobello ME, Daniel K, Guida W, Yoder JA, Rajadhyaksha AM, Schönbrunn E, Lawrence HR, Lawrence NJ, Epling-Burnette PK. Ligand-mediated protein degradation reveals functional conservation among sequence variants of the CUL4-type E3 ligase substrate receptor cereblon. J Biol Chem 2018; 293:6187-6200. [PMID: 29449372 DOI: 10.1074/jbc.m117.816868] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/15/2018] [Indexed: 12/13/2022] Open
Abstract
Upon binding to thalidomide and other immunomodulatory drugs, the E3 ligase substrate receptor cereblon (CRBN) promotes proteosomal destruction by engaging the DDB1-CUL4A-Roc1-RBX1 E3 ubiquitin ligase in human cells but not in mouse cells, suggesting that sequence variations in CRBN may cause its inactivation. Therapeutically, CRBN engagers have the potential for broad applications in cancer and immune therapy by specifically reducing protein expression through targeted ubiquitin-mediated degradation. To examine the effects of defined sequence changes on CRBN's activity, we performed a comprehensive study using complementary theoretical, biophysical, and biological assays aimed at understanding CRBN's nonprimate sequence variations. With a series of recombinant thalidomide-binding domain (TBD) proteins, we show that CRBN sequence variants retain their drug-binding properties to both classical immunomodulatory drugs and dBET1, a chemical compound and targeting ligand designed to degrade bromodomain-containing 4 (BRD4) via a CRBN-dependent mechanism. We further show that dBET1 stimulates CRBN's E3 ubiquitin-conjugating function and degrades BRD4 in both mouse and human cells. This insight paves the way for studies of CRBN-dependent proteasome-targeting molecules in nonprimate models and provides a new understanding of CRBN's substrate-recruiting function.
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Affiliation(s)
- Afua A Akuffo
- From the Department of Immunology.,the Cancer Biology Ph.D. Program, University of South Florida, Tampa, Florida 33612
| | | | | | | | | | | | - Rebecca S Hesterberg
- From the Department of Immunology.,the Cancer Biology Ph.D. Program, University of South Florida, Tampa, Florida 33612
| | | | - Steven Gunawan
- the Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Muhammad Ayaz
- the Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | | | - Md Rezaul Karim
- the Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | | | | | | | - Jeffrey A Yoder
- the Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 27607, and
| | - Anjali M Rajadhyaksha
- Pediatric Neurology, Pediatrics, Brain and Mind Research Institute, Graduate Program in Neuroscience, Weill Cornell Medicine, Molecular and Developmental Neuroscience Laboratory, New York, New York 10065
| | - Ernst Schönbrunn
- the Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | | | - Nicholas J Lawrence
- the Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
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130
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Sun B, Fiskus W, Qian Y, Rajapakshe K, Raina K, Coleman KG, Crew AP, Shen A, Saenz DT, Mill CP, Nowak AJ, Jain N, Zhang L, Wang M, Khoury JD, Coarfa C, Crews CM, Bhalla KN. BET protein proteolysis targeting chimera (PROTAC) exerts potent lethal activity against mantle cell lymphoma cells. Leukemia 2018; 32:343-352. [PMID: 28663582 DOI: 10.1038/leu.2017.207] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/12/2017] [Accepted: 06/19/2017] [Indexed: 11/09/2022]
Abstract
Bromodomain extraterminal protein (BETP) inhibitors transcriptionally repress oncoproteins and nuclear factor-κB (NF-κB) target genes that undermines the growth and survival of mantle cell lymphoma (MCL) cells. However, BET bromodomain inhibitor (BETi) treatment causes accumulation of BETPs, associated with reversible binding and incomplete inhibition of BRD4 that potentially compromises the activity of BETi in MCL cells. Unlike BETi, BET-PROTACs (proteolysis-targeting chimera) ARV-825 and ARV-771 (Arvinas, Inc.) recruit and utilize an E3-ubiquitin ligase to effectively degrade BETPs in MCL cells. BET-PROTACs induce more apoptosis than BETi of MCL cells, including those resistant to ibrutinib. BET-PROTAC treatment induced more perturbations in the mRNA and protein expressions than BETi, with depletion of c-Myc, CDK4, cyclin D1 and the NF-κB transcriptional targets Bcl-xL, XIAP and BTK, while inducing the levels of HEXIM1, NOXA and CDKN1A/p21. Treatment with ARV-771, which possesses superior pharmacological properties compared with ARV-825, inhibited the in vivo growth and induced greater survival improvement than the BETi OTX015 of immune-depleted mice engrafted with MCL cells. Cotreatment of ARV-771 with ibrutinib or the BCL2 antagonist venetoclax or CDK4/6 inhibitor palbociclib synergistically induced apoptosis of MCL cells. These studies highlight promising and superior preclinical activity of BET-PROTAC than BETi, requiring further in vivo evaluation of BET-PROTAC as a therapy for ibrutinib-sensitive or -resistant MCL.
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Affiliation(s)
- B Sun
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - W Fiskus
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Y Qian
- Arvinas LLC, New Haven, CT, USA
| | - K Rajapakshe
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - K Raina
- Arvinas LLC, New Haven, CT, USA
| | | | | | - A Shen
- Arvinas LLC, New Haven, CT, USA
| | - D T Saenz
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C P Mill
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - A J Nowak
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - N Jain
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Zhang
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M Wang
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J D Khoury
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - C M Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - K N Bhalla
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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131
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Churcher I. Protac-Induced Protein Degradation in Drug Discovery: Breaking the Rules or Just Making New Ones? J Med Chem 2018; 61:444-452. [PMID: 29144739 DOI: 10.1021/acs.jmedchem.7b01272] [Citation(s) in RCA: 298] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Targeted protein degradation, using bifunctional small molecules (Protacs) to remove specific proteins from within cells, has emerged as a novel drug discovery strategy with the potential to offer therapeutic interventions not achievable with existing approaches. In this Perspective, the brief history of the field is surveyed from a drug discovery perspective with a focus on the key advances in knowledge which have led to the definition and exemplification of protein degradation concepts and their resulting applications to medicine discovery. The approach has the potential to bring disruptive change to drug discovery; the many potential advantages and outstanding challenges which lie ahead of this technology are discussed.
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Affiliation(s)
- Ian Churcher
- BenevolentBio , 40 Churchway, London NW1 1LW, U.K
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132
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Bose P, Gotlib J, Harrison CN, Verstovsek S. SOHO State-of-the-Art Update and Next Questions: MPN. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2018; 18:1-12. [PMID: 29277359 PMCID: PMC5915302 DOI: 10.1016/j.clml.2017.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 11/27/2017] [Indexed: 12/28/2022]
Abstract
The discovery of the activating Janus kinase (JAK)2V617F mutation in 2005 in most patients with the classic Philadelphia chromosome-negative myeloproliferative neoplasms (MPN) spurred intense interest in research into these disorders, culminating in the identification of activating mutations in MPL in 2006 and indels in the gene encoding calreticulin (CALR) in 2013, thus providing additional mechanistic explanations for the universal activation of JAK-signal transducer and activator of transcription (JAK-STAT) observed in these conditions, and the success of the JAK1/2 inhibitor ruxolitinib, which first received regulatory approval in 2011. The field has continued to advance rapidly since then, and the past 2 years have witnessed important changes to the classification of MPN and diagnostic criteria for polycythemia vera (PV), novel insights into the mechanisms of bone marrow fibrosis in primary myelofibrosis (PMF), increasing appreciation of the biologic differences between essential thrombocythemia (ET), prefibrotic and overt PMF, and between primary and post-PV/ET myelofibrosis (MF). Additionally, the mechanisms through which mutant CALR drives JAK-STAT pathway activation and oncogenic transformation are now better understood. Although mastocytosis is no longer included under the broad heading of MPN in the 2016 revision to the World Health Organization classification, an important milestone in mastocytosis research was reached in 2017 with the regulatory approval of midostaurin for patients with advanced systemic mastocytosis (AdvSM). In this article, we review the major recent developments in the areas of PV, ET, and MF, and also briefly summarize the literature on midostaurin and other KIT inhibitors for patients with AdvSM.
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Affiliation(s)
- Prithviraj Bose
- Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX.
| | - Jason Gotlib
- Department of Medicine - Hematology, Stanford University, Palo Alto, CA
| | | | - Srdan Verstovsek
- Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX
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133
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Stathis A, Bertoni F. BET Proteins as Targets for Anticancer Treatment. Cancer Discov 2017; 8:24-36. [PMID: 29263030 DOI: 10.1158/2159-8290.cd-17-0605] [Citation(s) in RCA: 315] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/14/2017] [Accepted: 10/11/2017] [Indexed: 11/16/2022]
Affiliation(s)
| | - Francesco Bertoni
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Università della Svizzera italiana, Istituto Oncologico di Ricerca, Bellinzona, Switzerland
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134
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Lei H, Wang W, Wu Y. Targeting oncoproteins for degradation by small molecules in myeloid leukemia. Leuk Lymphoma 2017; 59:2297-2304. [DOI: 10.1080/10428194.2017.1403600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hu Lei
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Weiwei Wang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Yingli Wu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
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135
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Integrated functional and mass spectrometry-based flow cytometric phenotyping to describe the immune microenvironment in acute myeloid leukemia. J Immunol Methods 2017; 453:44-52. [PMID: 29175391 DOI: 10.1016/j.jim.2017.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/21/2017] [Accepted: 11/21/2017] [Indexed: 12/15/2022]
Abstract
A hallmark of the development of cancer is its ability to avoid detection and elimination by the immune system. There are many identified mechanisms of this immune evasion that can be measured both phenotypically and functionally. Functional studies directly show the ability of the tumor microenvironment to suppress immune responses, typically measured as lymphocyte proliferation, cytokine production or killing ability. While a direct measurement of function is ideal, these assays require ex vivo activation which may not accurately mimic in vivo conditions. Phenotypic assays can directly measure the distribution and activation of immune cell types rapidly after isolation, preserving the conditions present in the patient. While conventional flow cytometry is a rapid and well established assay, it currently allows for measurement of only 12-14 parameters. Mass spectrometry-based flow cytometry, or CyTOF, offers the ability to measure 3-fold more parameters than conventional optical-based modalities providing an advantage in depth of analysis that can be crucial for precious human samples. The goal of this report is to describe the system our group has developed to measure both the phenotype and function of immune cells in the bone marrow of patients with acute myeloid leukemia. We hope to explain our system in the context of previous studies aimed at measuring immune status in tumors and to inform the reader as to some experimental approaches our group has found useful in developing the basic data required to rationally pursue immune-based therapies for patients with cancer.
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136
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137
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Schapira M, Tyers M, Torrent M, Arrowsmith CH. WD40 repeat domain proteins: a novel target class? Nat Rev Drug Discov 2017; 16:773-786. [PMID: 29026209 PMCID: PMC5975957 DOI: 10.1038/nrd.2017.179] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antagonism of protein-protein interactions (PPIs) with small molecules is becoming more feasible as a therapeutic approach. Successful PPI inhibitors tend to target proteins containing deep peptide-binding grooves or pockets rather than the more common large, flat protein interaction surfaces. Here, we review one of the most abundant PPI domains in the human proteome, the WD40 repeat (WDR) domain, which has a central peptide-binding pocket and is a member of the β-propeller domain-containing protein family. Recently, two WDR domain-containing proteins, WDR5 and EED, as well as other β-propeller domains have been successfully targeted by potent, specific, cell-active, drug-like chemical probes. Could WDR domains be a novel target class for drug discovery? Although the research is at an early stage and therefore not clinically validated, cautious optimism is justified, as WDR domain-containing proteins are involved in multiple disease-associated pathways. The druggability and structural diversity of WDR domain binding pockets suggest that understanding how to target this prevalent domain class will open up areas of disease biology that have so far resisted drug discovery efforts.
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Affiliation(s)
- Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Mount Sinai Hospital, The Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - Maricel Torrent
- Discovery Research, AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, 101 College St., Toronto, ON M5G 1L7, Canada
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138
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Affiliation(s)
- George M. Burslem
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
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139
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Crew AP, Raina K, Dong H, Qian Y, Wang J, Vigil D, Serebrenik YV, Hamman BD, Morgan A, Ferraro C, Siu K, Neklesa TK, Winkler JD, Coleman KG, Crews CM. Identification and Characterization of Von Hippel-Lindau-Recruiting Proteolysis Targeting Chimeras (PROTACs) of TANK-Binding Kinase 1. J Med Chem 2017; 61:583-598. [PMID: 28692295 DOI: 10.1021/acs.jmedchem.7b00635] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that recruit an E3 ligase to a target protein to facilitate ubiquitination and subsequent degradation of that protein. While the field of targeted degraders is still relatively young, the potential for this modality to become a differentiated and therapeutic reality is strong, such that both academic and pharmaceutical institutions are now entering this interesting area of research. In this article, we describe a broadly applicable process for identifying degrader hits based on the serine/threonine kinase TANK-binding kinase 1 (TBK1) and have generalized the key structural elements associated with degradation activities. Compound 3i is a potent hit (TBK1 DC50 = 12 nM, Dmax = 96%) with excellent selectivity against a related kinase IKKε, which was further used as a chemical tool to assess TBK1 as a target in mutant K-Ras cancer cells.
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Affiliation(s)
- Andrew P Crew
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Kanak Raina
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Hanqing Dong
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Yimin Qian
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Jing Wang
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Dominico Vigil
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
| | | | - Brian D Hamman
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Alicia Morgan
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Caterina Ferraro
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Kam Siu
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Taavi K Neklesa
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
| | - James D Winkler
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Kevin G Coleman
- Arvinas LLC , 5 Science Park, New Haven, Connecticut 06511, United States
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140
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Abstract
Traditional pharmaceutical drug discovery is almost exclusively focused on directly controlling protein activity to cure diseases. Modulators of protein activity, especially inhibitors, are developed and applied at high concentration to achieve maximal effects. Thereby, reduced bioavailability and off-target effects can hamper compound efficacy. Nucleic acid-based strategies that control protein function by affecting expression have emerged as an alternative. However, metabolic stability and broad bioavailability represent development hurdles that remain to be overcome for these approaches. More recently, utilizing the cell's own protein destruction machinery for selective degradation of essential drivers of human disorders has opened up a new and exciting area of drug discovery. Small-molecule-induced proteolysis of selected substrates offers the potential of reaching beyond the limitations of the current pharmaceutical paradigm to expand the druggable target space.
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Affiliation(s)
- Philipp M Cromm
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06511, USA.
| | - Craig M Crews
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06511, USA; Department of Chemistry, Yale University, New Haven, CT 06511, USA; Department of Pharmacology, Yale University, New Haven, CT 06511, USA.
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141
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Braun T, Gardin C. Investigational BET bromodomain protein inhibitors in early stage clinical trials for acute myelogenous leukemia (AML). Expert Opin Investig Drugs 2017; 26:803-811. [PMID: 28541716 DOI: 10.1080/13543784.2017.1335711] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Acute myelogenous leukemia (AML) is a heterogeneous group of malignancies driven by genetic mutations and deregulated epigenetic control. Relapse/refractory disease remains frequent in younger patients and even more so in older patients, including treatment with epigenetic drugs in this age group, mainly with hypomethylating agents. New treatment strategies are urgently needed. The recent discovery that epigenetic readers of the bromodomain (BRD) and extraterminal (BET) protein family, are crucial for AML maintenance by transcription of oncogenic c-MYC lead to rapid development of BET inhibitors entering clinical trials. Areas covered: We provide a critical overview using main sources for the use of BET inhibitors in AML treatment. Limits of this treatment approach including resistance mechanisms and future directions including development of new generation BET inhibitors and combination strategies with other drugs are detailed. Expert opinion: BET inhibitors were expected to overcome limits of conventional treatment in patients as impressive in vitro data emerged recently in well-characterized AML subsets, including those associated with poor risk characteristics in the clinic. Nevertheless single activity of BET inhibitors appears to be modest and resistance mechanisms were already identified. BET inhibitors with alternative mechanisms of action and/or combination strategies with epigenetic drugs should be tested.
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Affiliation(s)
- Thorsten Braun
- a Hematology Department , Avicenne Hospital-Assistance Publique Hôpitaux de Paris (AP-HP), University Paris XIII , Bobigny , France.,b Laboratoire de Transfert des Leucémies , Institut Universitaire d'Hématologie, University Paris VII , Paris , France
| | - Claude Gardin
- a Hematology Department , Avicenne Hospital-Assistance Publique Hôpitaux de Paris (AP-HP), University Paris XIII , Bobigny , France.,b Laboratoire de Transfert des Leucémies , Institut Universitaire d'Hématologie, University Paris VII , Paris , France
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142
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Field SD, Arkin J, Li J, Jones LH. Selective Downregulation of JAK2 and JAK3 by an ATP-Competitive pan-JAK Inhibitor. ACS Chem Biol 2017; 12:1183-1187. [PMID: 28318222 DOI: 10.1021/acschembio.7b00116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
PF-956980 has been used previously as a JAK3-selective chemical probe in numerous cell-based experiments. Here, we report that not only is PF-956980 a pan-JAK ATP-competitive inhibitor but it also causes selective reduction of endogenous JAK2 and JAK3 protein levels in human primary immune cells (in a time-dependent manner), leaving the other JAK family members (JAK1 and TYK2) unchanged. We found that PF-956980 selectively downregulated JAK2 and JAK3 mRNA, corresponding to changes observed at the protein level. This work highlights therapeutic opportunities for the development of pharmacological inhibitors that also modulate the expression of their cognate binding proteins.
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Affiliation(s)
- S. Denise Field
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Jacob Arkin
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Jing Li
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Lyn H. Jones
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
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143
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Ember SW, Lambert QT, Berndt N, Gunawan S, Ayaz M, Tauro M, Zhu JY, Cranfill PJ, Greninger P, Lynch CC, Benes CH, Lawrence HR, Reuther GW, Lawrence NJ, Schönbrunn E. Potent Dual BET Bromodomain-Kinase Inhibitors as Value-Added Multitargeted Chemical Probes and Cancer Therapeutics. Mol Cancer Ther 2017; 16:1054-1067. [PMID: 28336808 DOI: 10.1158/1535-7163.mct-16-0568-t] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/01/2016] [Accepted: 03/02/2017] [Indexed: 12/22/2022]
Abstract
Synergistic action of kinase and BET bromodomain inhibitors in cell killing has been reported for a variety of cancers. Using the chemical scaffold of the JAK2 inhibitor TG101348, we developed and characterized single agents which potently and simultaneously inhibit BRD4 and a specific set of oncogenic tyrosine kinases including JAK2, FLT3, RET, and ROS1. Lead compounds showed on-target inhibition in several blood cancer cell lines and were highly efficacious at inhibiting the growth of hematopoietic progenitor cells from patients with myeloproliferative neoplasm. Screening across 931 cancer cell lines revealed differential growth inhibitory potential with highest activity against bone and blood cancers and greatly enhanced activity over the single BET inhibitor JQ1. Gene drug sensitivity analyses and drug combination studies indicate synergism of BRD4 and kinase inhibition as a plausible reason for the superior potency in cell killing. Combined, our findings indicate promising potential of these agents as novel chemical probes and cancer therapeutics. Mol Cancer Ther; 16(6); 1054-67. ©2017 AACR.
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Affiliation(s)
- Stuart W Ember
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida
| | - Que T Lambert
- Tumor Biology Department, Moffitt Cancer Center, Tampa, Florida
| | - Norbert Berndt
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida
| | - Steven Gunawan
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida
| | - Muhammad Ayaz
- Chemical Biology Core, Moffitt Cancer Center, Tampa, Florida
| | - Marilena Tauro
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jin-Yi Zhu
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida
| | - Paula J Cranfill
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida
| | - Patricia Greninger
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Conor C Lynch
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Harshani R Lawrence
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida.,Chemical Biology Core, Moffitt Cancer Center, Tampa, Florida
| | - Gary W Reuther
- Tumor Biology Department, Moffitt Cancer Center, Tampa, Florida
| | | | - Ernst Schönbrunn
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida.
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