1
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Chakraborty S, Ahler E, Simon JJ, Fang L, Potter ZE, Sitko KA, Stephany JJ, Guttman M, Fowler DM, Maly DJ. Profiling of drug resistance in Src kinase at scale uncovers a regulatory network coupling autoinhibition and catalytic domain dynamics. Cell Chem Biol 2024; 31:207-220.e11. [PMID: 37683649 PMCID: PMC10902203 DOI: 10.1016/j.chembiol.2023.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/03/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023]
Abstract
Kinase inhibitors are effective cancer therapies, but resistance often limits clinical efficacy. Despite the cataloging of numerous resistance mutations, our understanding of kinase inhibitor resistance is still incomplete. Here, we comprehensively profiled the resistance of ∼3,500 Src tyrosine kinase mutants to four different ATP-competitive inhibitors. We found that ATP-competitive inhibitor resistance mutations are distributed throughout Src's catalytic domain. In addition to inhibitor contact residues, residues that participate in regulating Src's phosphotransferase activity were prone to the development of resistance. Unexpectedly, we found that a resistance-prone cluster of residues located on the top face of the N-terminal lobe of Src's catalytic domain contributes to autoinhibition by reducing catalytic domain dynamics, and mutations in this cluster led to resistance by lowering inhibitor affinity and promoting kinase hyperactivation. Together, our studies demonstrate how drug resistance profiling can be used to define potential resistance pathways and uncover new mechanisms of kinase regulation.
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Affiliation(s)
- Sujata Chakraborty
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Ethan Ahler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Jessica J Simon
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Linglan Fang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Zachary E Potter
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Katherine A Sitko
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jason J Stephany
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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2
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Agius MP, Ko K, Johnson TK, Phadke S, Soellner MB. Conformation-tunable ATP-competitive kinase inhibitors. Chem Commun (Camb) 2022; 58:3541-3544. [PMID: 35195624 DOI: 10.1039/d1cc06893h] [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: 11/21/2022]
Abstract
Small molecule kinase inhibitors have shown immense clinical utility for diverse indications. While >60 kinase inhibitors have been approved (and many more in clinical trials), it remains unclear whether the clinical efficacy of a kinase inhibitor is solely dependent on enzymatic inhibition, or whether non-catalytic functions play a role in the efficacy of some kinase inhibitors. Here, we designed and synthesized a series of pyrazolopyrimidine kinase inhibitors that modulate the global kinase conformation of c-Src kinase. Expanding upon our findings from the pyrazolopyrimidine inhibitor series, we designed, synthesized, and evaluated three pair of conformation-selective kinase inhibitors, each with a unique hinge-binding scaffold. We profiled each pair of kinase inhibitors across 468 kinases and identified 38 kinases that could be studied using these pair of conformation-selective inhibitors. We also explore the binding of conformation-selective kinase inhibitors to mutant kinases of EGFR, FLT3, and KIT. Together, these studies yield important insight into the design of conformation-tunable kinase inhibitors and provide a toolset of compounds to study the role of protein conformation on kinase signaling.
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Affiliation(s)
- Michael P Agius
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Kristin Ko
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Taylor K Johnson
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Sameer Phadke
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
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3
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Cheng S, Yang GJ, Wang W, Ma DL, Leung CH. Discovery of a tetrahydroisoquinoline-based CDK9-cyclin T1 protein–protein interaction inhibitor as an anti-proliferative and anti-migration agent against triple-negative breast cancer cells. Genes Dis 2021; 9:1674-1688. [PMID: 36157485 PMCID: PMC9485199 DOI: 10.1016/j.gendis.2021.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 12/30/2022] Open
Affiliation(s)
- Shasha Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, PR China
| | - Guan-Jun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, PR China
| | - Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, PR China
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, PR China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, PR China
- Corresponding author.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, PR China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao SAR, PR China
- Corresponding author.
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4
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Joseph RE, Amatya N, Fulton DB, Engen JR, Wales TE, Andreotti A. Differential impact of BTK active site inhibitors on the conformational state of full-length BTK. eLife 2020; 9:60470. [PMID: 33226337 PMCID: PMC7834017 DOI: 10.7554/elife.60470] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/20/2020] [Indexed: 12/30/2022] Open
Abstract
Bruton’s tyrosine kinase (BTK) is targeted in the treatment of B-cell disorders including leukemias and lymphomas. Currently approved BTK inhibitors, including Ibrutinib, a first-in-class covalent inhibitor of BTK, bind directly to the kinase active site. While effective at blocking the catalytic activity of BTK, consequences of drug binding on the global conformation of full-length BTK are unknown. Here, we uncover a range of conformational effects in full-length BTK induced by a panel of active site inhibitors, including large-scale shifts in the conformational equilibria of the regulatory domains. Additionally, we find that a remote Ibrutinib resistance mutation, T316A in the BTK SH2 domain, drives spurious BTK activity by destabilizing the compact autoinhibitory conformation of full-length BTK, shifting the conformational ensemble away from the autoinhibited form. Future development of BTK inhibitors will need to consider long-range allosteric consequences of inhibitor binding, including the emerging application of these BTK inhibitors in treating COVID-19. Treatments for blood cancers, such as leukemia and lymphoma, rely heavily on chemotherapy, using drugs that target a vulnerable aspect of the cancer cells. B-cells, a type of white blood cell that produces antibodies, require a protein called Bruton’s tyrosine kinase, or BTK for short, to survive. The drug ibrutinib (Imbruvica) is used to treat B-cell cancers by blocking BTK. The BTK protein consists of several regions. One of them, known as the kinase domain, is responsible for its activity as an enzyme (which allows it to modify other proteins by adding a ‘tag’ known as a phosphate group). The other regions of BTK, known as regulatory modules, control this activity. In BTK’s inactive form, the regulatory modules attach to the kinase domain, blocking the regulatory modules from interacting with other proteins. When BTK is activated, it changes its conformation so the regulatory regions detach and become available for interactions with other proteins, at the same time exposing the active kinase domain. Ibrutinib and other BTK drugs in development bind to the kinase domain to block its activity. However, it is not known how this binding affects the regulatory modules. Previous efforts to study how drugs bind to BTK have used a version of the protein that only had the kinase domain, instead of the full-length protein. Now, Joseph et al. have studied full-length BTK and how it binds to five different drugs. The results reveal that ibrutinib and another drug called dasatinib both indirectly disrupt the normal position of the regulatory domains pushing BTK toward a conformation that resembles the activated state. By contrast, the three other compounds studied do not affect the inactive structure. Joseph et al. also examined a mutation in BTK that confers resistance against ibrutinib. This mutation increases the activity of BTK by disrupting the inactive structure, leading to B cells surviving better. Understanding how drug resistance mechanisms can work will lead to better drug treatment strategies for cancer. BTK is also a target in other diseases such as allergies or asthma and even COVID-19. If interactions between partner proteins and the regulatory domain are important in these diseases, then they may be better treated with drugs that maintain the regulatory modules in their inactive state. This research will help to design drugs that are better able to control BTK activity.
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Affiliation(s)
- Raji E Joseph
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - Neha Amatya
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - D Bruce Fulton
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
| | - Amy Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, United States
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5
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Potter ZE, Lau HT, Chakraborty S, Fang L, Guttman M, Ong SE, Fowler DM, Maly DJ. Parallel Chemoselective Profiling for Mapping Protein Structure. Cell Chem Biol 2020; 27:1084-1096.e4. [PMID: 32649906 PMCID: PMC7484201 DOI: 10.1016/j.chembiol.2020.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/27/2020] [Accepted: 06/19/2020] [Indexed: 01/01/2023]
Abstract
Solution-based structural techniques complement high-resolution structural data by providing insight into the oft-missed links between protein structure and dynamics. Here, we present Parallel Chemoselective Profiling, a solution-based structural method for characterizing protein structure and dynamics. Our method utilizes deep mutational scanning saturation mutagenesis data to install amino acid residues with specific chemistries at defined positions on the solvent-exposed surface of a protein. Differences in the extent of labeling of installed mutant residues are quantified using targeted mass spectrometry, reporting on each residue's local environment and structural dynamics. Using our method, we studied how conformation-selective, ATP-competitive inhibitors affect the local and global structure and dynamics of full-length Src kinase. Our results highlight how parallel chemoselective profiling can be used to study a dynamic multi-domain protein, and suggest that our method will be a useful addition to the relatively small toolkit of existing protein footprinting techniques.
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Affiliation(s)
- Zachary E Potter
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Ho-Tak Lau
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Sujata Chakraborty
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Linglan Fang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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6
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Fang L, Vilas-Boas J, Chakraborty S, Potter ZE, Register AC, Seeliger MA, Maly DJ. How ATP-Competitive Inhibitors Allosterically Modulate Tyrosine Kinases That Contain a Src-like Regulatory Architecture. ACS Chem Biol 2020; 15:2005-2016. [PMID: 32479050 DOI: 10.1021/acschembio.0c00429] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Small molecule kinase inhibitors that stabilize distinct ATP binding site conformations can differentially modulate the global conformation of Src-family kinases (SFKs). However, it is unclear which specific ATP binding site contacts are responsible for modulating the global conformation of SFKs and whether these inhibitor-mediated allosteric effects generalize to other tyrosine kinases. Here, we describe the development of chemical probes that allow us to deconvolute which features in the ATP binding site are responsible for the allosteric modulation of the global conformation of Src. We find that the ability of an inhibitor to modulate the global conformation of Src's regulatory domain-catalytic domain module relies mainly on the influence it has on the conformation of a structural element called helix αC. Furthermore, by developing a set of orthogonal probes that target a drug-sensitized Src variant, we show that stabilizing Src's helix αC in an active conformation is sufficient to promote a Src-mediated, phosphotransferase-independent alteration in cell morphology. Finally, we report that ATP-competitive, conformation-selective inhibitors can influence the global conformation of tyrosine kinases beyond the SFKs, suggesting that the allosteric networks we observe in Src are conserved in kinases that have a similar regulatory architecture. Our study highlights that an ATP-competitive inhibitor's interactions with helix αC can have a major influence on the global conformation of some tyrosine kinases.
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Affiliation(s)
| | - Jessica Vilas-Boas
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
| | | | | | | | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
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7
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Leroux AE, Biondi RM. Renaissance of Allostery to Disrupt Protein Kinase Interactions. Trends Biochem Sci 2019; 45:27-41. [PMID: 31690482 DOI: 10.1016/j.tibs.2019.09.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022]
Abstract
Protein-protein interactions often regulate the activity of protein kinases by allosterically modulating the conformation of the ATP-binding site. Bidirectional allostery implies that reverse modulation (i.e., from the ATP-binding site to the interaction and regulatory sites) must also be possible. Here, we review both the allosteric regulation of protein kinases and recent work describing how compounds binding at the ATP-binding site can promote or inhibit protein kinase interactions at regulatory sites via the reverse mechanism. Notably, the pharmaceutical industry has been developing compounds that bind to the ATP-binding site of protein kinases and potently disrupt protein-protein interactions between target protein kinases and their regulatory interacting partners. Learning to modulate allosteric processes will facilitate the development of protein-protein interaction modulators.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina; Department of Internal Medicine I, University Hospital, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; DKTK German Cancer Consortium (DKTK), Frankfurt, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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8
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Agius MP, Ko KS, Johnson TK, Kwarcinski FE, Phadke S, Lachacz EJ, Soellner MB. Selective Proteolysis to Study the Global Conformation and Regulatory Mechanisms of c-Src Kinase. ACS Chem Biol 2019; 14:1556-1563. [PMID: 31287657 PMCID: PMC7254491 DOI: 10.1021/acschembio.9b00306] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein kinase pathways are traditionally mapped by monitoring downstream phosphorylation. Meanwhile, the noncatalytic functions of protein kinases remain under-appreciated as critical components of kinase signaling. c-Src is a protein kinase known to have noncatalytic signaling function important in healthy and disease cell signaling. Large conformational changes in the regulatory domains regulate c-Src's noncatalytic functions. Herein, we demonstrate that changes in the global conformation of c-Src can be monitored using a selective proteolysis methodology. Further, we use this methodology to investigate changes in the global conformation of several clinical and nonclinical mutations of c-Src. Significantly, we identify a novel activating mutation observed clinically, W121R, that can escape down-regulation mechanisms. Our methodology can be expanded to monitor the global conformation of other tyrosine kinases, including c-Abl, and represents an important tool toward the elucidation of the noncatalytic functions of protein kinases.
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Affiliation(s)
- Michael P. Agius
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI
| | - Kristin S. Ko
- Department of Chemistry, University of Michigan, Ann Arbor, MI
| | - Taylor K. Johnson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI
| | | | - Sameer Phadke
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Eric J. Lachacz
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Matthew B. Soellner
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department of Chemistry, University of Michigan, Ann Arbor, MI
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9
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Fang L, Chakraborty S, Dieter EM, Potter ZE, Lombard CK, Maly DJ. Chemoproteomic Method for Profiling Inhibitor-Bound Kinase Complexes. J Am Chem Soc 2019; 141:11912-11922. [PMID: 31274292 DOI: 10.1021/jacs.9b02963] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Small molecule inhibitors often only block a subset of the cellular functions of their protein targets. In many cases, how inhibiting only a portion of a multifunctional protein's functions affects the state of the cell is not well-understood. Therefore, tools that allow the systematic characterization of the cellular interactions that inhibitor-bound proteins make would be of great utility, especially for multifunctional proteins. Here, we describe a chemoproteomic strategy for interrogating the cellular localization and interactomes of inhibitor-bound kinases. By developing a set of orthogonal inhibitors that contain a trans-cyclooctene (TCO) click handle, we are able to enrich and characterize the proteins complexed to a drug-sensitized variant of the multidomain kinase Src. We show that Src's cellular interactions are highly influenced by the intermolecular accessibility of its regulatory domains, which can be allosterically modulated through its ATP-binding site. Furthermore, we find that the signaling status of the cell also has a large effect on Src's interactome. Finally, we demonstrate that our TCO-conjugated probes can be used as a part of a proximity ligation assay to study Src's localization and interactions in situ. Together, our chemoproteomic strategy represents a comprehensive method for studying the localization and interactomes of inhibitor-bound kinases and, potentially, other druggable protein targets.
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10
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Chakraborty S, Inukai T, Fang L, Golkowski M, Maly DJ. Targeting Dynamic ATP-Binding Site Features Allows Discrimination between Highly Homologous Protein Kinases. ACS Chem Biol 2019; 14:1249-1259. [PMID: 31038916 DOI: 10.1021/acschembio.9b00214] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
ATP-competitive inhibitors that demonstrate exquisite selectivity for specific members of the human kinome have been developed. Despite this success, the identification of highly selective inhibitors is still very challenging, and it is often not possible to rationally engineer selectivity between the ATP-binding sites of kinases, especially among closely related family members. Src-family kinases (SFKs) are a highly homologous family of eight multidomain, nonreceptor tyrosine kinases that play general and specialized roles in numerous cellular processes. The high sequence and functional similarities between SFK members make it hard to rationalize how selectivity can be gained with inhibitors that target the ATP-binding site. Here, we describe the development of a series of inhibitors that are highly selective for the ATP-binding sites of the SFKs Lyn and Hck over other SFKs. By biochemically characterizing how these selective ATP-competitive inhibitors allosterically influence the global conformation of SFKs, we demonstrate that they most likely interact with a binding pocket created by the movement of the conformationally flexible helix αC in the ATP-binding site. With a series of sequence swap experiments, we show that sensitivity to this class of selective inhibitors is due to the identity of residues that control the conformational flexibility of helix αC rather than any specific ATP-binding site interactions. Thus, the ATP-binding sites of highly homologous kinases can be discriminated by targeting heterogeneity within conformationally flexible regions.
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Affiliation(s)
| | - Takayuki Inukai
- Medicinal Chemistry Research Laboratories, Ono Pharmaceutical Company, Ltd., 3-1-1 Sakurai, Shimamoto, Mishima, Osaka 618-8585, Japan
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11
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A Combined Approach Reveals a Regulatory Mechanism Coupling Src's Kinase Activity, Localization, and Phosphotransferase-Independent Functions. Mol Cell 2019; 74:393-408.e20. [PMID: 30956043 DOI: 10.1016/j.molcel.2019.02.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 11/20/2018] [Accepted: 01/31/2019] [Indexed: 02/06/2023]
Abstract
Multiple layers of regulation modulate the activity and localization of protein kinases. However, many details of kinase regulation remain incompletely understood. Here, we apply saturation mutagenesis and a chemical genetic method for allosterically modulating kinase global conformation to Src kinase, providing insight into known regulatory mechanisms and revealing a previously undiscovered interaction between Src's SH4 and catalytic domains. Abrogation of this interaction increased phosphotransferase activity, promoted membrane association, and provoked phosphotransferase-independent alterations in cell morphology. Thus, Src's SH4 domain serves as an intramolecular regulator coupling catalytic activity, global conformation, and localization, as well as mediating a phosphotransferase-independent function. Sequence conservation suggests that the SH4 domain regulatory interaction exists in other Src-family kinases. Our combined approach's ability to reveal a regulatory mechanism in one of the best-studied kinases suggests that it could be applied broadly to provide insight into kinase structure, regulation, and function.
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12
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Koudelková L, Pataki AC, Tolde O, Pavlik V, Nobis M, Gemperle J, Anderson K, Brábek J, Rosel D. Novel FRET-Based Src Biosensor Reveals Mechanisms of Src Activation and Its Dynamics in Focal Adhesions. Cell Chem Biol 2019; 26:255-268.e4. [DOI: 10.1016/j.chembiol.2018.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/12/2018] [Accepted: 10/26/2018] [Indexed: 10/27/2022]
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13
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Lombard CK, Davis AL, Inukai T, Maly DJ. Allosteric Modulation of JNK Docking Site Interactions with ATP-Competitive Inhibitors. Biochemistry 2018; 57:5897-5909. [PMID: 30211540 DOI: 10.1021/acs.biochem.8b00776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The c-Jun N-terminal kinases (JNKs) play a wide variety of roles in cellular signaling processes, dictating important, and even divergent, cellular fates. These essential kinases possess docking surfaces distal to their active sites that interact with diverse binding partners, including upstream activators, downstream substrates, and protein scaffolds. Prior studies have suggested that the interactions of certain protein-binding partners with one such JNK docking surface, termed the D-recruitment site (DRS), can allosterically influence the conformational state of the ATP-binding pocket of JNKs. To further explore the allosteric relationship between the ATP-binding pockets and DRSs of JNKs, we investigated how the interactions of the scaffolding protein JIP1, as well as the upstream activators MKK4 and MKK7, are allosterically influenced by the ATP-binding site occupancy of the JNKs. We show that the affinity of the JNKs for JIP1 can be divergently modulated with ATP-competitive inhibitors, with a >50-fold difference in dissociation constant observed between the lowest- and highest-affinity JNK1-inhibitor complexes. Furthermore, we found that we could promote or attenuate phosphorylation of JNK1's activation loop by MKK4 and MKK7, by varying the ATP-binding site occupancy. Given that JIP1, MKK4, and MKK7 all interact with JNK DRSs, these results demonstrate that there is functional allostery between the ATP-binding sites and DRSs of these kinases. Furthermore, our studies suggest that ATP-competitive inhibitors can allosterically influence the intracellular binding partners of the JNKs.
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Affiliation(s)
- Chloe K Lombard
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States
| | - Audrey L Davis
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States
| | - Takayuki Inukai
- Medicinal Chemistry Research Laboratories , Ono Pharmaceutical Company, Ltd. , 3-1-1 Sakurai , Shimamoto, Mishima, Osaka 618-8585 , Japan
| | - Dustin J Maly
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States.,Department of Biochemistry , University of Washington , Seattle , Washington 98117 , United States
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14
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Register AC, Chakraborty S, Maly DJ. Allosteric Modulation of Src Family Kinases with ATP-Competitive Inhibitors. Methods Mol Biol 2018; 1636:79-89. [PMID: 28730474 DOI: 10.1007/978-1-4939-7154-1_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Src family kinases (SFKs) are an important family of tyrosine kinases that are allosterically regulated by their SH2 and SH3 domains. Engagement of SFK SH2 and SH3 domains with their intramolecular ligands leads to reduced kinase activity by stabilizing an inactive ATP-binding site conformation. Disruption of these intramolecular interactions stabilizes a more active ATP-binding site conformation and restores SFK activity. Interestingly, this allosteric relationship is bidirectional in that ATP-competitive ligands that stabilize distinct active site conformations can divergently modulate the abilities of the regulatory SH2 and SH3 domains to participate in intermolecular interactions. Here, we describe a series of assays that profile the bidirectional relationship between the ATP-binding sites and regulatory domains of SFKs. These methods can be used to discover ATP-competitive inhibitors that are selective for distinct ATP-binding site conformations of SFKs and for characterizing the effects that ATP-competitive inhibitors of SFKs have on domains that are distal to their site of interaction.
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Affiliation(s)
- Ames C Register
- Departments of Chemistry and Biochemistry, University of Washington, 36 Bagley Hall, Box 351700, Seattle, WA, 98195-1700, USA
| | - Sujata Chakraborty
- Departments of Chemistry and Biochemistry, University of Washington, 36 Bagley Hall, Box 351700, Seattle, WA, 98195-1700, USA
| | - Dustin J Maly
- Departments of Chemistry and Biochemistry, University of Washington, 36 Bagley Hall, Box 351700, Seattle, WA, 98195-1700, USA.
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15
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Survey of solution dynamics in Src kinase reveals allosteric cross talk between the ligand binding and regulatory sites. Nat Commun 2017; 8:2160. [PMID: 29255153 PMCID: PMC5735167 DOI: 10.1038/s41467-017-02240-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/15/2017] [Indexed: 11/09/2022] Open
Abstract
The catalytic domain of protein tyrosine kinases can interconvert between active and inactive conformations in response to regulatory inputs. We recently demonstrated that Src kinase features an allosteric network that couples substrate-binding sites. However, the extent of conformational and dynamic changes that are propagated throughout the kinase domain remains poorly understood. Here, we monitor by NMR the effect of conformationally selective inhibitors on kinase backbone dynamics. We find that inhibitor binding and activation loop autophosphorylation induces dynamic changes across the entire kinase. We identify a highly conserved amino acid, Gly449, that is necessary for Src activation. Finally, we show for the first time how the SH3–SH2 domains perturb the dynamics of the kinase domain in the context of the full length protein. We provide experimental support for long-range communication in Src kinase that leads to the relative stabilization of active or inactive conformations and modulation of substrate affinity. Src is a prototypical signaling non-receptor protein tyrosine kinase that interconverts between distinct conformations. Here the authors use variants of the kinase-inhibitor dasatinib to define three specific conformational states of the Src kinase and shed insight on the effect of conformation-specific inhibitors on Src dynamics.
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Feldman HC, Tong M, Wang L, Meza-Acevedo R, Gobillot TA, Lebedev I, Gliedt MJ, Hari SB, Mitra AK, Backes BJ, Papa FR, Seeliger MA, Maly DJ. Structural and Functional Analysis of the Allosteric Inhibition of IRE1α with ATP-Competitive Ligands. ACS Chem Biol 2016; 11:2195-205. [PMID: 27227314 DOI: 10.1021/acschembio.5b00940] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The accumulation of unfolded proteins under endoplasmic reticulum (ER) stress leads to the activation of the multidomain protein sensor IRE1α as part of the unfolded protein response (UPR). Clustering of IRE1α lumenal domains in the presence of unfolded proteins promotes kinase trans-autophosphorylation in the cytosol and subsequent RNase domain activation. Interestingly, there is an allosteric relationship between the kinase and RNase domains of IRE1α, which allows ATP-competitive inhibitors to modulate the activity of the RNase domain. Here, we use kinase inhibitors to study how ATP-binding site conformation affects the activity of the RNase domain of IRE1α. We find that diverse ATP-competitive inhibitors of IRE1α promote dimerization and activation of RNase activity despite blocking kinase autophosphorylation. In contrast, a subset of ATP-competitive ligands, which we call KIRAs, allosterically inactivate the RNase domain through the kinase domain by stabilizing monomeric IRE1α. Further insight into how ATP-competitive inhibitors are able to divergently modulate the RNase domain through the kinase domain was gained by obtaining the first structure of apo human IRE1α in the RNase active back-to-back dimer conformation. Comparison of this structure with other existing structures of IRE1α and integration of our extensive structure activity relationship (SAR) data has led us to formulate a model to rationalize how ATP-binding site ligands are able to control the IRE1α oligomeric state and subsequent RNase domain activity.
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Affiliation(s)
- Hannah C. Feldman
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
| | - Michael Tong
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York, United States
| | - Likun Wang
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Diabetes
Center, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
- California
Institute for Quantitative Biosciences, University of California−San Francisco, San Francisco, California, United States
| | - Rosa Meza-Acevedo
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Diabetes
Center, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
- California
Institute for Quantitative Biosciences, University of California−San Francisco, San Francisco, California, United States
| | - Theodore A. Gobillot
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
| | - Ivan Lebedev
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York, United States
| | - Micah J. Gliedt
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
| | - Sanjay B. Hari
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
| | - Arinjay K. Mitra
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
| | - Bradley J. Backes
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
| | - Feroz R. Papa
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Diabetes
Center, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
- California
Institute for Quantitative Biosciences, University of California−San Francisco, San Francisco, California, United States
| | - Markus A. Seeliger
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington, United States
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Mapp AK, Pricer R, Sturlis S. Targeting transcription is no longer a quixotic quest. Nat Chem Biol 2016; 11:891-4. [PMID: 26575226 DOI: 10.1038/nchembio.1962] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Anna K Mapp
- Life Sciences Institute and the Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Rachel Pricer
- Life Sciences Institute and the Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Steven Sturlis
- Life Sciences Institute and the Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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Beck JR, Lawrence A, Tung AS, Harris EN, Stains CI. Interrogating Endogenous Protein Phosphatase Activity with Rationally Designed Chemosensors. ACS Chem Biol 2016; 11:284-90. [PMID: 26580981 DOI: 10.1021/acschembio.5b00506] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We introduce a versatile approach for repurposing protein kinase chemosensors, containing the phosphorylation-sensitive sulfonamido-oxine fluorophore termed Sox, for the specific determination of endogenous protein phosphatase activity from whole cell lysates and tissue homogenates. As a demonstration of this approach, we design and evaluate a direct chemosensor for protein tyrosine phosphatase-1B (PTP1B), an established signaling node in human disease. The optimal sensor design is capable of detecting as little as 6 pM (12 pg) full-length recombinant PTP1B and is remarkably selective for PTP1B among a panel of highly homologous tyrosine phosphatases. Coupling this robust activity probe with the specificity of antibodies allowed for the temporal analysis of endogenous PTP1B activity dynamics in lysates generated from HepG2 cells after stimulation with insulin. Lastly, we leveraged this assay format to profile PTP1B activity perturbations in a rat model of nonalcoholic fatty liver disease (NAFLD), providing direct evidence for elevated PTP1B catalytic activity in this disease state. Given the modular nature of this assay, we anticipate that this approach will have broad utility in monitoring phosphatase activity dynamics in human disease states.
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Affiliation(s)
- Jon R. Beck
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Antoneal Lawrence
- Department
of Chemistry, Lincoln University, Lincoln University, Pennsylvania 19352, United States
| | - Amar S. Tung
- Department
of Chemistry, Lincoln University, Lincoln University, Pennsylvania 19352, United States
| | - Edward N. Harris
- Department
of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Cliff I. Stains
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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Di Michele M, Stes E, Vandermarliere E, Arora R, Astorga-Wells J, Vandenbussche J, van Heerde E, Zubarev R, Bonnet P, Linders JTM, Jacoby E, Brehmer D, Martens L, Gevaert K. Limited Proteolysis Combined with Stable Isotope Labeling Reveals Conformational Changes in Protein (Pseudo)kinases upon Binding Small Molecules. J Proteome Res 2015; 14:4179-93. [PMID: 26293246 DOI: 10.1021/acs.jproteome.5b00282] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Likely due to conformational rearrangements, small molecule inhibitors may stabilize the active conformation of protein kinases and paradoxically promote tumorigenesis. We combined limited proteolysis with stable isotope labeling MS to monitor protein conformational changes upon binding of small molecules. Applying this method to the human serine/threonine kinase B-Raf, frequently mutated in cancer, we found that binding of ATP or its nonhydrolyzable analogue AMP-PNP, but not ADP, stabilized the structure of both B-Raf(WT) and B-Raf(V600E). The ATP-competitive type I B-Raf inhibitor vemurafenib and the type II inhibitor sorafenib stabilized the kinase domain (KD) but had distinct effects on the Ras-binding domain. Stabilization of the B-Raf(WT) KD was confirmed by hydrogen/deuterium exchange MS and molecular dynamics simulations. Our results are further supported by cellular assays in which we assessed cell viability and phosphorylation profiles in cells expressing B-Raf(WT) or B-Raf(V600E) in response to vemurafenib or sorafenib. Our data indicate that an overall stabilization of the B-Raf structure by specific inhibitors activates MAPK signaling and increases cell survival, helping to explain clinical treatment failure. We also applied our method to monitor conformational changes upon nucleotide binding of the pseudokinase KSR1, which holds high potential for inhibition in human diseases.
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Affiliation(s)
- Michela Di Michele
- Department of Medical Protein Research, VIB , A. Baertsoenkaai 3, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Elisabeth Stes
- Department of Medical Protein Research, VIB , A. Baertsoenkaai 3, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Elien Vandermarliere
- Department of Medical Protein Research, VIB , A. Baertsoenkaai 3, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Rohit Arora
- Institut de Chimie Organique et Analytique (ICOA), UMR 7311 CNRS-Université d'Orléans , Pôle de chimie, Rue de Chartres, 45100 Orléans, France
| | | | - Jonathan Vandenbussche
- Department of Medical Protein Research, VIB , A. Baertsoenkaai 3, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Erika van Heerde
- Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Roman Zubarev
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Scheelelaberatoriet Scheeles väg 2, SE-171 77 Stockholm, Sweden
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), UMR 7311 CNRS-Université d'Orléans , Pôle de chimie, Rue de Chartres, 45100 Orléans, France
| | - Joannes T M Linders
- Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Edgar Jacoby
- Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Dirk Brehmer
- Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Lennart Martens
- Department of Medical Protein Research, VIB , A. Baertsoenkaai 3, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB , A. Baertsoenkaai 3, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University , A. Baertsoenkaai 3, 9000 Ghent, Belgium
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Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway. Sci Rep 2015; 5:8026. [PMID: 25619172 PMCID: PMC4306142 DOI: 10.1038/srep08026] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 01/02/2015] [Indexed: 02/04/2023] Open
Abstract
A novel four-step pathway identified recently in mycobacteria channels trehalose to glycogen synthesis and is also likely involved in the biosynthesis of two other crucial polymers: intracellular methylglucose lipopolysaccharides and exposed capsular glucan. The structures of three of the intervening enzymes - GlgB, GlgE, and TreS - were recently reported, providing the first templates for rational drug design. Here we describe the structural characterization of the fourth enzyme of the pathway, mycobacterial maltokinase (Mak), uncovering a eukaryotic-like kinase (ELK) fold, similar to methylthioribose kinases and aminoglycoside phosphotransferases. The 1.15 Å structure of Mak in complex with a non-hydrolysable ATP analog reveals subtle structural rearrangements upon nucleotide binding in the cleft between the N- and the C-terminal lobes. Remarkably, this new family of ELKs has a novel N-terminal domain topologically resembling the cystatin family of protease inhibitors. By interfacing with and restraining the mobility of the phosphate-binding region of the N-terminal lobe, Mak's unusual N-terminal domain might regulate its phosphotransfer activity and represents the most likely anchoring point for TreS, the upstream enzyme in the pathway. By completing the gallery of atomic-detail models of an essential pathway, this structure opens new avenues for the rational design of alternative anti-tubercular compounds.
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Register AC, Leonard SE, Maly DJ. SH2-catalytic domain linker heterogeneity influences allosteric coupling across the SFK family. Biochemistry 2014; 53:6910-23. [PMID: 25302671 PMCID: PMC4230323 DOI: 10.1021/bi5008194] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Src-family
kinases (SFKs) make up a family of nine homologous multidomain
tyrosine kinases whose misregulation is responsible for human disease
(cancer, diabetes, inflammation, etc.). Despite overall sequence homology
and identical domain architecture, differences in SH3 and SH2 regulatory
domain accessibility and ability to allosterically autoinhibit the
ATP-binding site have been observed for the prototypical SFKs Src
and Hck. Biochemical and structural studies indicate that the SH2-catalytic
domain (SH2-CD) linker, the intramolecular binding epitope for SFK
SH3 domains, is responsible for allosterically coupling SH3 domain
engagement to autoinhibition of the ATP-binding site through the conformation
of the αC helix. As a relatively unconserved region between
SFK family members, SH2-CD linker sequence variability across the
SFK family is likely a source of nonredundant cellular functions between
individual SFKs via its effect on the availability of SH3 and SH2
domains for intermolecular interactions and post-translational modification.
Using a combination of SFKs engineered with enhanced or weakened regulatory
domain intramolecular interactions and conformation-selective inhibitors
that report αC helix conformation, this study explores how SH2-CD
sequence heterogeneity affects allosteric coupling across the SFK
family by examining Lyn, Fyn1, and Fyn2. Analyses of Fyn1 and Fyn2,
isoforms that are identical but for a 50-residue sequence spanning
the SH2-CD linker, demonstrate that SH2-CD linker sequence differences
can have profound effects on allosteric coupling between otherwise
identical kinases. Most notably, a dampened allosteric connection
between the SH3 domain and αC helix leads to greater autoinhibitory
phosphorylation by Csk, illustrating the complex effects of SH2-CD
linker sequence on cellular function.
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Affiliation(s)
- A C Register
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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