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Golkowski M, Lius A, Sapre T, Lau HT, Moreno T, Maly DJ, Ong SE. Multiplexed kinase interactome profiling quantifies cellular network activity and plasticity. Mol Cell 2023; 83:803-818.e8. [PMID: 36736316 PMCID: PMC10072906 DOI: 10.1016/j.molcel.2023.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/07/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Dynamic changes in protein-protein interaction (PPI) networks underlie all physiological cellular functions and drive devastating human diseases. Profiling PPI networks can, therefore, provide critical insight into disease mechanisms and identify new drug targets. Kinases are regulatory nodes in many PPI networks; yet, facile methods to systematically study kinase interactome dynamics are lacking. We describe kinobead competition and correlation analysis (kiCCA), a quantitative mass spectrometry-based chemoproteomic method for rapid and highly multiplexed profiling of endogenous kinase interactomes. Using kiCCA, we identified 1,154 PPIs of 238 kinases across 18 diverse cancer lines, quantifying context-dependent kinase interactome changes linked to cancer type, plasticity, and signaling states, thereby assembling an extensive knowledgebase for cell signaling research. We discovered drug target candidates, including an endocytic adapter-associated kinase (AAK1) complex that promotes cancer cell epithelial-mesenchymal plasticity and drug resistance. Our data demonstrate the importance of kinase interactome dynamics for cellular signaling in health and disease.
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Affiliation(s)
- Martin Golkowski
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
| | - Andrea Lius
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Tanmay Sapre
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Ho-Tak Lau
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Taylor Moreno
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
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Mensa-Wilmot K. How Physiologic Targets Can Be Distinguished from Drug-Binding Proteins. Mol Pharmacol 2021; 100:1-6. [PMID: 33941662 DOI: 10.1124/molpharm.120.000186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 04/09/2021] [Indexed: 01/04/2023] Open
Abstract
In clinical trials, some drugs owe their effectiveness to off-target activity. This and other observations raise a possibility that many studies identifying targets of drugs are incomplete. If off-target proteins are pharmacologically important, it will be worthwhile to identify them early in the development process to gain a better understanding of the molecular basis of drug action. Herein, we outline a multidisciplinary strategy for systematic identification of physiologic targets of drugs in cells. A drug-binding protein whose genetic disruption yields very similar molecular effects as treatment of cells with the drug may be defined as a physiologic target of the drug. For a drug developed with a rational approach, it is desirable to verify experimentally that a protein used for hit optimization in vitro remains the sole polypeptide recognized by the drug in a cell. SIGNIFICANCE STATEMENT: A body of evidence indicates that inactivation of many drug-binding proteins may not cause the pharmacological effects triggered by the drugs. A multidisciplinary cell-based approach can be of great value in identifying the physiologic targets of drugs, including those developed with target-based strategies.
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Affiliation(s)
- Kojo Mensa-Wilmot
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia
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Golkowski M, Lau HT, Chan M, Kenerson H, Vidadala VN, Shoemaker A, Maly DJ, Yeung RS, Gujral TS, Ong SE. Pharmacoproteomics Identifies Kinase Pathways that Drive the Epithelial-Mesenchymal Transition and Drug Resistance in Hepatocellular Carcinoma. Cell Syst 2020; 11:196-207.e7. [PMID: 32755597 DOI: 10.1016/j.cels.2020.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/30/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is a complex and deadly disease lacking druggable genetic mutations. The limited efficacy of systemic treatments for advanced HCC implies that predictive biomarkers and drug targets are urgently needed. Most HCC drugs target protein kinases, indicating that kinase-dependent signaling networks drive HCC progression. To identify HCC signaling networks that determine responses to kinase inhibitors (KIs), we apply a pharmacoproteomics approach integrating kinome activity in 17 HCC cell lines with their responses to 299 KIs, resulting in a comprehensive dataset of pathway-based drug response signatures. By profiling patient HCC samples, we identify signatures of clinical HCC drug responses in individual tumors. Our analyses reveal kinase networks promoting the epithelial-mesenchymal transition (EMT) and drug resistance, including a FZD2-AXL-NUAK1/2 signaling module, whose inhibition reverses the EMT and sensitizes HCC cells to drugs. Our approach identifies cancer drug targets and molecular signatures of drug response for personalized oncology.
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Affiliation(s)
- Martin Golkowski
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Ho-Tak Lau
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Marina Chan
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Heidi Kenerson
- Department of Surgery, University of Washington, Seattle, WA 98195, USA
| | | | - Anna Shoemaker
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Raymond S Yeung
- Department of Surgery, University of Washington, Seattle, WA 98195, USA
| | - Taranjit S Gujral
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
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Golkowski M, Vidadala VN, Lau HT, Shoemaker A, Shimizu-Albergine M, Beavo J, Maly DJ, Ong SE. Kinobead/LC-MS Phosphokinome Profiling Enables Rapid Analyses of Kinase-Dependent Cell Signaling Networks. J Proteome Res 2020; 19:1235-1247. [PMID: 32037842 DOI: 10.1021/acs.jproteome.9b00742] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Kinase-catalyzed protein phosphorylation is fundamental to eukaryotic signal transduction, regulating most cellular processes. Kinases are frequently dysregulated in cancer, inflammation, and degenerative diseases, and because they can be inhibited with small molecules, they became important drug targets. Accordingly, analytical approaches that determine kinase activation states are critically important to understand kinase-dependent signal transduction and to identify novel drug targets and predictive biomarkers. Multiplexed inhibitor beads (MIBs or kinobeads) efficiently enrich kinases from cell lysates for liquid chromatography-mass spectrometry (LC-MS) analysis. When combined with phosphopeptide enrichment, kinobead/LC-MS can also quantify the phosphorylation state of kinases, which determines their activation state. However, an efficient kinobead/LC-MS kinase phospho-profiling protocol that allows routine analyses of cell lines and tissues has not yet been developed. Here, we present a facile workflow that quantifies the global phosphorylation state of kinases with unprecedented sensitivity. We also found that our kinobead/LC-MS protocol can measure changes in kinase complex composition and show how these changes can indicate kinase activity. We demonstrate the utility of our approach in specifying kinase signaling pathways that control the acute steroidogenic response in Leydig cells; this analysis establishes the first comprehensive framework for the post-translational control of steroid biosynthesis.
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Affiliation(s)
- Martin Golkowski
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | | | - Ho-Tak Lau
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - Anna Shoemaker
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - Masami Shimizu-Albergine
- University of Washington Medicine Diabetes Institute, University of Washington, Seattle, Washington 98109, United States
| | - Joseph Beavo
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
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Vidadala RSR, Golkowski M, Hulverson MA, Choi R, McCloskey MC, Whitman GR, Huang W, Arnold SLM, Barrett LK, Fan E, Merritt EA, Van Voorhis WC, Ojo KK, Maly DJ. 7 H-Pyrrolo[2,3- d]pyrimidin-4-amine-Based Inhibitors of Calcium-Dependent Protein Kinase 1 Have Distinct Inhibitory and Oral Pharmacokinetic Characteristics Compared with 1 H-Pyrazolo[3,4- d]pyrimidin-4-amine-Based Inhibitors. ACS Infect Dis 2018. [PMID: 29522315 DOI: 10.1021/acsinfecdis.7b00224] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Selective inhibitors of Cryptosporidium calcium-dependent protein kinase 1 ( CpCDPK1) based on the 1 H-pyrazolo[3,4- d]pyrimidin-4-amine (pyrazolopyrimidine, PP) scaffold are effective in both in vitro and in vivo models of cryptosporidiosis. However, the search for distinct safety and pharmacokinetic (PK) properties has motivated our exploration of alternative scaffolds. Here, we describe a series of 7 H-pyrrolo[2,3- d]pyrimidin-4-amine (pyrrolopyrimidine, PrP)-based analogs of PP CpCDPK1 inhibitors. Most of the PrP-based inhibitors described potently inhibit the CpCDPK1 enzyme, demonstrate no toxicity against mammalian cells, and block proliferation of the C. parvum parasite in the low micromolar range. Interestingly, certain substituents that show reduced CpCDPK1 potency when displayed from a PP scaffold provided notably enhanced efficacy in the context of a PrP scaffold. PK studies on these paired compounds show that some PrP analogs have distinct physiochemical properties compared with their PP counterparts. These results demonstrate that inhibitors based on a PrP scaffold are distinct therapeutic alternatives to previously developed PP inhibitors.
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Affiliation(s)
- Rama S. R. Vidadala
- Department of Chemistry, University of Washington, 36 Bagley Hall, Box 351700, Seattle, Washington 98195, United States
| | - Martin Golkowski
- Department of Pharmacology, University of Washington, 1959 NE Pacific Street, Box 357280, Seattle, Washington 98195, United States
| | - Matthew A. Hulverson
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Ryan Choi
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Molly C. McCloskey
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Grant R. Whitman
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Wenlin Huang
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195, United States
| | - Samuel L. M. Arnold
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Lynn K. Barrett
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Erkang Fan
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195, United States
| | - Ethan A. Merritt
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195, United States
| | - Wesley C. Van Voorhis
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Kayode K. Ojo
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Dustin J. Maly
- Department of Chemistry, University of Washington, 36 Bagley Hall, Box 351700, Seattle, Washington 98195, United States
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