1
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Shuai W, Xiao H, Yang P, Zhang Y, Bu F, Wu Y, Sun Q, Wang G, Ouyang L. Structure-Guided Discovery and Preclinical Assessment of Novel (Thiophen-3-yl)aminopyrimidine Derivatives as Potent ERK1/2 Inhibitors. J Med Chem 2024; 67:6425-6455. [PMID: 38613499 DOI: 10.1021/acs.jmedchem.3c02392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2024]
Abstract
The RAS-RAF-MEK-ERK signaling cascade is abnormally activated in various tumors, playing a crucial role in mediating tumor progression. As the key component at the terminal stage of this cascade, ERK1/2 emerges as a potential antitumor target and offers a promising therapeutic strategy for tumors harboring BRAF or RAS mutations. Here, we identified 36c with a (thiophen-3-yl)aminopyrimidine scaffold as a potent ERK1/2 inhibitor through structure-guided optimization for hit 18. In preclinical studies, 36c showed powerful ERK1/2 inhibitory activities (ERK1/2 IC50 = 0.11/0.08 nM) and potent antitumor efficacy both in vitro and in vivo against triple-negative breast cancer and colorectal cancer models harboring BRAF and RAS mutations. 36c could directly inhibit ERK1/2, significantly block the phosphorylation expression of their downstream substrates p90RSK and c-Myc, and induce cell apoptosis and incomplete autophagy-related cell death. Taken together, this work provides a promising ERK1/2 lead compound for multiple tumor-treatment drug discovery.
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Affiliation(s)
- Wen Shuai
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Huan Xiao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Panpan Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Yiwen Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Faqian Bu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Yongya Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Qiu Sun
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Guan Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Liang Ouyang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu 610212, Sichuan, China
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2
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Bakulina O, Sapegin A, Bunev AS, Krasavin M. Synthetic approaches to constructing proteolysis targeting chimeras (PROTACs). MENDELEEV COMMUNICATIONS 2022. [DOI: 10.1016/j.mencom.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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3
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Torres-García D, van de Plassche MAT, van Boven E, van Leeuwen T, Groenewold MGJ, Sarris AJC, Klein L, Overkleeft HS, van Kasteren SI. Methyltetrazine as a small live-cell compatible bioorthogonal handle for imaging enzyme activities in situ. RSC Chem Biol 2022; 3:1325-1330. [DOI: 10.1039/d2cb00120a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022] Open
Abstract
Bioorthogonal chemistry combines well with activity-based protein profiling, as it allows for the introduction of detection tags without significantly influencing the physiochemical and biological functions of the probe.
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Affiliation(s)
- Diana Torres-García
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Merel A. T. van de Plassche
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Emma van Boven
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Tyrza van Leeuwen
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Mirjam G. J. Groenewold
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexi J. C. Sarris
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Luuk Klein
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Sander I. van Kasteren
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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4
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Yao T, Xu X, Huang R. Recent Advances about the Applications of Click Reaction in Chemical Proteomics. Molecules 2021; 26:5368. [PMID: 34500797 PMCID: PMC8434046 DOI: 10.3390/molecules26175368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/17/2022] Open
Abstract
Despite significant advances in biological and analytical approaches, a comprehensive portrait of the proteome and its dynamic interactions and modifications remains a challenging goal. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to elucidate protein composition, distribution, and relevant physiological and pharmacological functions. Click chemistry focuses on the development of new combinatorial chemical methods for carbon heteroatom bond (C-X-C) synthesis, which have been utilized extensively in the field of chemical proteomics. Click reactions have various advantages including high yield, harmless by-products, and simple reaction conditions, upon which the molecular diversity can be easily and effectively obtained. This paper reviews the application of click chemistry in proteomics from four aspects: (1) activity-based protein profiling, (2) enzyme-inhibitors screening, (3) protein labeling and modifications, and (4) hybrid monolithic column in proteomic analysis.
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Affiliation(s)
- Tingting Yao
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China;
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaowei Xu
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
| | - Rong Huang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China;
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5
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Verhelst SHL, Bonger KM, Willems LI. Bioorthogonal Reactions in Activity-Based Protein Profiling. Molecules 2020; 25:E5994. [PMID: 33352858 PMCID: PMC7765892 DOI: 10.3390/molecules25245994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/27/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase our understanding of physiological and pathological processes, to identify novel drug targets, to evaluate selectivity of drugs, and to image probe targets in cells. Bioorthogonal chemistry has substantially contributed to the field of ABPP, as it allows the introduction of tags, which may be bulky or have unfavorable physicochemical properties, at a late stage in the experiment. In this review, we give an overview of the bioorthogonal reactions that have been implemented in ABPP, provide examples of applications of bioorthogonal chemistry in ABPP, and share some thoughts on future directions.
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Affiliation(s)
- Steven H. L. Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Herestr. 49, Box 802, 3000 Leuven, Belgium
- AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Kimberly M. Bonger
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Lianne I. Willems
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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6
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Prevet H, Collins I. Labelled chemical probes for demonstrating direct target engagement in living systems. Future Med Chem 2019; 11:1195-1224. [PMID: 31280668 DOI: 10.4155/fmc-2018-0370] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024] Open
Abstract
Demonstrating target engagement in living systems can help drive successful drug discovery. Target engagement and occupancy studies in cells confirm direct binding of a ligand to its intended target protein and provide the binding affinity. Combined with biomarkers to measure the functional consequences of target engagement, these experiments can increase confidence in the relationship between in vitro pharmacology and observed biological effects. In this review, we focus on chemically and radioactively labelled probes as key reagents for performing such experiments. Using recent examples, we examine how the labelled probes have been employed in combination with unlabelled ligands to quantify target engagement in cells and in animals. Finally, we consider future developments of this emerging methodology.
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Affiliation(s)
- Hugues Prevet
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
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7
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Lebraud H, Surova O, Courtin A, O'Reilly M, Valenzano CR, Nordlund P, Heightman TD. Quantitation of ERK1/2 inhibitor cellular target occupancies with a reversible slow off-rate probe. Chem Sci 2018; 9:8608-8618. [PMID: 30568786 PMCID: PMC6253716 DOI: 10.1039/c8sc02754d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/15/2018] [Indexed: 11/21/2022] Open
Abstract
Target engagement is a key concept in drug discovery and its direct measurement can provide a quantitative understanding of drug efficacy and/or toxicity. Failure to demonstrate target occupancy in relevant cells and tissues has been recognised as a contributing factor to the low success rate of clinical drug development. Several techniques are emerging to quantify target engagement in cells; however, in situ measurements remain challenging, mainly due to technical limitations. Here, we report the development of a non-covalent clickable probe, based on SCH772984, a slow off-rate ERK1/2 inhibitor, which enabled efficient pull down of ERK1/2 protein via click reaction with tetrazine tagged agarose beads. This was used in a competition setting to measure relative target occupancy by selected ERK1/2 inhibitors. As a reference we used the cellular thermal shift assay, a label-free biophysical assay relying solely on ligand-induced thermodynamic stabilization of proteins. To validate the EC50 values measured by both methods, the results were compared with IC50 data for the phosphorylation of RSK, a downstream substrate of ERK1/2 used as a functional biomarker of ERK1/2 inhibition. We showed that a slow off-rate reversible probe can be used to efficiently pull down cellular proteins, significantly extending the potential of the approach beyond the need for covalent or photoaffinity warheads.
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Affiliation(s)
- Honorine Lebraud
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| | - Olga Surova
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
- Department of Oncology-Pathology , Karolinska Institute , CCK R8:01 , Karolinska Hospital , 171 76 Stockholm , Sweden
| | - Aurélie Courtin
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| | - Marc O'Reilly
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| | - Chiara R Valenzano
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| | - Pär Nordlund
- Department of Oncology-Pathology , Karolinska Institute , CCK R8:01 , Karolinska Hospital , 171 76 Stockholm , Sweden
| | - Tom D Heightman
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
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8
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Kidger AM, Sipthorp J, Cook SJ. ERK1/2 inhibitors: New weapons to inhibit the RAS-regulated RAF-MEK1/2-ERK1/2 pathway. Pharmacol Ther 2018; 187:45-60. [PMID: 29454854 DOI: 10.1016/j.pharmthera.2018.02.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The RAS-regulated RAF-MEK1/2-ERK1/2 signalling pathway is de-regulated in a variety of cancers due to mutations in receptor tyrosine kinases (RTKs), negative regulators of RAS (such as NF1) and core pathway components themselves (RAS, BRAF, CRAF, MEK1 or MEK2). This has driven the development of a variety of pharmaceutical agents to inhibit RAF-MEK1/2-ERK1/2 signalling in cancer and both RAF and MEK inhibitors are now approved and used in the clinic. There is now much interest in targeting at the level of ERK1/2 for a variety of reasons. First, since the pathway is linear from RAF-to-MEK-to-ERK then ERK1/2 are validated as targets per se. Second, innate resistance to RAF or MEK inhibitors involves relief of negative feedback and pathway re-activation with all signalling going through ERK1/2, validating the use of ERK inhibitors with RAF or MEK inhibitors as an up-front combination. Third, long-term acquired resistance to RAF or MEK inhibitors involves a variety of mechanisms (KRAS or BRAF amplification, MEK mutation, etc.) which re-instate ERK activity, validating the use of ERK inhibitors to forestall acquired resistance to RAF or MEK inhibitors. The first potent highly selective ERK1/2 inhibitors have now been developed and are entering clinical trials. They have one of three discrete mechanisms of action - catalytic, "dual mechanism" or covalent - which could have profound consequences for how cells respond and adapt. In this review we describe the validation of ERK1/2 as anti-cancer drug targets, consider the mechanism of action of new ERK1/2 inhibitors and how this may impact on their efficacy, anticipate factors that will determine how tumour cells respond and adapt to ERK1/2 inhibitors and consider ERK1/2 inhibitor drug combinations.
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Affiliation(s)
- Andrew M Kidger
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, England, United Kingdom.
| | - James Sipthorp
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, England, United Kingdom
| | - Simon J Cook
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, England, United Kingdom.
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9
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Shin M, Franks CE, Hsu KL. Isoform-selective activity-based profiling of ERK signaling. Chem Sci 2018; 9:2419-2431. [PMID: 29732117 PMCID: PMC5909473 DOI: 10.1039/c8sc00043c] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/28/2018] [Indexed: 12/25/2022] Open
Abstract
Extracellular signal-regulated kinases (ERKs) mediate downstream signaling of RAS-RAF-MEK as key regulators of the mitogen-activated protein kinase (MAPK) pathway. Activation of ERK signaling is a hallmark of cancer and upstream MAPK proteins have been extensively pursued as drug targets for cancer therapies. However, the rapid rise of resistance to clinical RAF and MEK inhibitors has prompted interest in targeting ERK (ERK1 and ERK2 isoforms) directly for cancer therapy. Current methods for evaluating activity of inhibitors against ERK isoforms are based primarily on analysis of recombinant proteins. Strategies to directly and independently profile native ERK1 and ERK2 activity would greatly complement current cell biological tools used to probe and target ERK function. Here, we present a quantitative chemoproteomic strategy that utilizes active-site directed probes to directly quantify native ERK activity in an isoform-specific fashion. We exploit a single isoleucine/leucine difference in ERK substrate binding sites to enable activity-based profiling of ERK1 versus ERK2 across a variety of cell types, tissues, and species. We used our chemoproteomic strategy to determine potency and selectivity of academic (VX-11e) and clinical (Ulixertinib) ERK inhibitors. Correlation of potency estimates by chemoproteomics with anti-proliferative activity of VX-11e and Ulixertinib revealed that >90% inactivation of both native ERK1 and ERK2 is needed to mediate cellular activity of inhibitors. Our findings introduce one of the first assays capable of independent evaluation of native ERK1 and ERK2 activity to advance drug discovery of oncogenic MAPK pathways.
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Affiliation(s)
- Myungsun Shin
- Department of Chemistry , University of Virginia , McCormick Road, P.O. Box 400319 , Charlottesville , Virginia 22904 , USA . ; Tel: +1-434-297-4864
| | - Caroline E Franks
- Department of Chemistry , University of Virginia , McCormick Road, P.O. Box 400319 , Charlottesville , Virginia 22904 , USA . ; Tel: +1-434-297-4864
| | - Ku-Lung Hsu
- Department of Chemistry , University of Virginia , McCormick Road, P.O. Box 400319 , Charlottesville , Virginia 22904 , USA . ; Tel: +1-434-297-4864
- Department of Pharmacology , University of Virginia , McCormick Road, P.O. Box 400319 , Charlottesville , Virginia 22908 , USA
- University of Virginia Cancer Center , University of Virginia , Charlottesville , VA 22903 , USA
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10
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Berard A, Kroeker A, McQueen P, Coombs KM. Methods and approaches to disease mechanisms using systems kinomics. Synth Syst Biotechnol 2018; 3:34-43. [PMID: 29911197 PMCID: PMC5884222 DOI: 10.1016/j.synbio.2017.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Accepted: 12/13/2017] [Indexed: 02/06/2023] Open
Abstract
All cellular functions, ranging from regular cell maintenance and homeostasis, specialized functions specific to cellular types, or generating responses due to external stimulus, are mediated by proteins within the cell. Regulation of these proteins allows the cell to alter its behavior under different circumstances. A major mechanism of protein regulation is utilizing protein kinases and phosphatases; enzymes that catalyze the transfer of phosphates between substrates [1]. Proteins involved in phosphate signaling are well studied and include kinases and phosphatases that catalyze opposing reactions regulating both structure and function of the cell. Kinomics is the study of kinases, phosphatases and their targets, and has been used to study the functional changes in numerous diseases and infectious diseases with aims to delineate the cellular functions affected. Identifying the phosphate signaling pathways changed by certain diseases or infections can lead to novel therapeutic targets. However, a daunting 518 putative protein kinase genes have been identified [2], indicating that this protein family is very large and complex. Identifying which enzymes are specific to a particular disease can be a laborious task. In this review, we will provide information on large-scale systems biology methodologies that allow global screening of the kinome to more efficiently identify which kinase pathways are pertinent for further study.
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Affiliation(s)
- Alicia Berard
- Department of Medical Microbiology, University of Manitoba, Winnipeg, R3E 0J9, Canada
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | | | - Peter McQueen
- Department of Medical Microbiology, University of Manitoba, Winnipeg, R3E 0J9, Canada
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Kevin M. Coombs
- Department of Medical Microbiology, University of Manitoba, Winnipeg, R3E 0J9, Canada
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11
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Protein degradation: a validated therapeutic strategy with exciting prospects. Essays Biochem 2017; 61:517-527. [PMID: 28970340 DOI: 10.1042/ebc20170030] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/10/2017] [Accepted: 09/15/2017] [Indexed: 01/19/2023]
Abstract
In a time of unprecedented challenges in developing potent, selective and well-tolerated protein inhibitors as therapeutics, drug hunters are increasingly seeking alternative modalities to modulate pharmacological targets. Selective inhibitors are achievable for only a fraction of the proteome, and are not guaranteed to elicit the desired response in patients, especially when pursuing targets identified through genetic knockdown. Targeted protein degradation holds the potential to expand the range of proteins that can be effectively modulated. Drugs inducing protein degradation through misfolding or by modulating cereblon (CRBN) substrate recognition are already approved for treatment of cancer patients. The last decade has seen the development of proteolysis targeting chimeras (PROTACs), small molecules that elicit proteasomal degradation by causing protein polyubiquitination. These have been used to degrade a range of disease-relevant proteins in cells, and some show promising efficacy in preclinical animal models, although their clinical efficacy and tolerability is yet to be proven. This review introduces current strategies for protein degradation with an emphasis on PROTACs and the role of click chemistry in PROTAC research through the formation of libraries of preclicked PROTACs or in-cell click-formed PROTACs (CLIPTACs).
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12
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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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13
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Sipthorp J, Lebraud H, Gilley R, Kidger AM, Okkenhaug H, Saba-El-Leil M, Meloche S, Caunt CJ, Cook SJ, Heightman TD. Visualization of Endogenous ERK1/2 in Cells with a Bioorthogonal Covalent Probe. Bioconjug Chem 2017; 28:1677-1683. [PMID: 28449575 DOI: 10.1021/acs.bioconjchem.7b00152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The RAS-RAF-MEK-ERK pathway has been intensively studied in oncology, with RAS known to be mutated in ∼30% of all human cancers. The recent emergence of ERK1/2 inhibitors and their ongoing clinical investigation demands a better understanding of ERK1/2 behavior following small-molecule inhibition. Although fluorescent fusion proteins and fluorescent antibodies are well-established methods of visualizing proteins, we show that ERK1/2 can be visualized via a less-invasive approach based on a two-step process using inverse electron demand Diels-Alder cycloaddition. Our previously reported trans-cyclooctene-tagged covalent ERK1/2 inhibitor was used in a series of imaging experiments following a click reaction with a tetrazine-tagged fluorescent dye. Although limitations were encountered with this approach, endogenous ERK1/2 was successfully imaged in cells, and "on-target" staining was confirmed by over-expressing DUSP5, a nuclear ERK1/2 phosphatase that anchors ERK1/2 in the nucleus.
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Affiliation(s)
- James Sipthorp
- Signalling Laboratory, The Babraham Institute , Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Honorine Lebraud
- Astex Pharmaceuticals , 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Rebecca Gilley
- Signalling Laboratory, The Babraham Institute , Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Andrew M Kidger
- Signalling Laboratory, The Babraham Institute , Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Hanneke Okkenhaug
- Signalling Laboratory, The Babraham Institute , Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Marc Saba-El-Leil
- Institute of Research in Immunology and Cancer and Department of Pharmacology, Université de Montréal , Montréal, Québec, Canada H3C 3J7
| | - Sylvain Meloche
- Institute of Research in Immunology and Cancer and Department of Pharmacology, Université de Montréal , Montréal, Québec, Canada H3C 3J7
| | - Christopher J Caunt
- Department of Biology and Biochemistry, University of Bath , Claverton Down, Bath BA2 7AY, U.K
| | - Simon J Cook
- Signalling Laboratory, The Babraham Institute , Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Tom D Heightman
- Astex Pharmaceuticals , 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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14
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Zhao Z, Liu Q, Bliven S, Xie L, Bourne PE. Determining Cysteines Available for Covalent Inhibition Across the Human Kinome. J Med Chem 2017; 60:2879-2889. [PMID: 28326775 PMCID: PMC5493210 DOI: 10.1021/acs.jmedchem.6b01815] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Covalently bound protein kinase inhibitors have been frequently designed to target noncatalytic cysteines at the ATP binding site. Thus, it is important to know if a given cysteine can form a covalent bond. Here we combine a function-site interaction fingerprint method and DFT calculations to determine the potential of cysteines to form a covalent interaction with an inhibitor. By harnessing the human structural kinome, a comprehensive structure-based binding site cysteine data set was assembled. The orientation of the cysteine thiol group indicates which cysteines can potentially form covalent bonds. These covalent inhibitor easy-available cysteines are located within five regions: P-loop, roof of pocket, front pocket, catalytic-2 of the catalytic loop, and DFG-3 close to the DFG peptide. In an independent test set these cysteines covered 95% of covalent kinase inhibitors. This study provides new insights into cysteine reactivity and preference which is important for the prospective development of covalent kinase inhibitors.
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Affiliation(s)
- Zheng Zhao
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20892, USA
| | - Qingsong Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui230031, China
| | - Spencer Bliven
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20892, USA
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, NY 10065, USA
- The Graduate Center, The City University of New York, NY 10016, USA
| | - Philip E. Bourne
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20892, USA
- Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA
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Lebraud H, Wright DJ, Johnson CN, Heightman TD. Protein Degradation by In-Cell Self-Assembly of Proteolysis Targeting Chimeras. ACS CENTRAL SCIENCE 2016; 2:927-934. [PMID: 28058282 PMCID: PMC5200928 DOI: 10.1021/acscentsci.6b00280] [Citation(s) in RCA: 240] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 05/03/2023]
Abstract
Selective degradation of proteins by proteolysis targeting chimeras (PROTACs) offers a promising potential alternative to protein inhibition for therapeutic intervention. Current PROTAC molecules incorporate a ligand for the target protein, a linker, and an E3 ubiquitin ligase recruiting group, which bring together target protein and ubiquitinating machinery. Such hetero-bifunctional molecules require significant linker optimization and possess high molecular weight, which can limit cellular permeation, solubility, and other drug-like properties. We show here that the hetero-bifunctional molecule can be formed intracellularly by bio-orthogonal click combination of two smaller precursors. We designed a tetrazine tagged thalidomide derivative which reacts rapidly with a trans-cyclo-octene tagged ligand of the target protein in cells to form a cereblon E3 ligase recruiting PROTAC molecule. The in-cell click-formed proteolysis targeting chimeras (CLIPTACs) were successfully used to degrade two key oncology targets, BRD4 and ERK1/2. ERK1/2 degradation was achieved using a CLIPTAC based on a covalent inhibitor. We expect this approach to be readily extendable to other inhibitor-protein systems because the tagged E3 ligase recruiter is capable of undergoing the click reaction with a suitably tagged ligand of any protein of interest to elicit its degradation.
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