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Ratto A, Honek JF. Oxocarbon Acids and their Derivatives in Biological and Medicinal Chemistry. Curr Med Chem 2024; 31:1172-1213. [PMID: 36915986 DOI: 10.2174/0929867330666230313141452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 03/15/2023]
Abstract
The biological and medicinal chemistry of the oxocarbon acids 2,3- dihydroxycycloprop-2-en-1-one (deltic acid), 3,4-dihydroxycyclobut-3-ene-1,2-dione (squaric acid), 4,5-dihydroxy-4-cyclopentene-1,2,3-trione (croconic acid), 5,6-dihydroxycyclohex- 5-ene-1,2,3,4-tetrone (rhodizonic acid) and their derivatives is reviewed and their key chemical properties and reactions are discussed. Applications of these compounds as potential bioisosteres in biological and medicinal chemistry are examined. Reviewed areas include cell imaging, bioconjugation reactions, antiviral, antibacterial, anticancer, enzyme inhibition, and receptor pharmacology.
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Affiliation(s)
- Amanda Ratto
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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2
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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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3
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ATP-competitive partial antagonists of the IRE1α RNase segregate outputs of the UPR. Nat Chem Biol 2021; 17:1148-1156. [PMID: 34556859 PMCID: PMC8551014 DOI: 10.1038/s41589-021-00852-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 07/01/2021] [Indexed: 01/21/2023]
Abstract
The unfolded protein response (UPR) homeostatically matches endoplasmic reticulum (ER) protein-folding capacity to cellular secretory needs. However, under high or chronic ER stress, the UPR triggers apoptosis. This cell fate dichotomy is promoted by differential activation of the ER transmembrane kinase/endoribonuclease (RNase) IRE1α. We previously found that the RNase of IRE1α can be either fully activated or inactivated by ATP-competitive kinase inhibitors. Here we developed kinase inhibitors, partial antagonists of IRE1α RNase (PAIRs), that partially antagonize the IRE1α RNase at full occupancy. Biochemical and structural studies show that PAIRs promote partial RNase antagonism by intermediately displacing the helix αC in the IRE1α kinase domain. In insulin-producing β-cells, PAIRs permit adaptive splicing of Xbp1 mRNA while quelling destructive ER mRNA endonucleolytic decay and apoptosis. By preserving Xbp1 mRNA splicing, PAIRs allow B cells to differentiate into immunoglobulin-producing plasma cells. Thus, an intermediate RNase-inhibitory 'sweet spot', achieved by PAIR-bound IRE1α, captures a desirable conformation for drugging this master UPR sensor/effector.
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Agnew-Francis KA, Williams CM. Squaramides as Bioisosteres in Contemporary Drug Design. Chem Rev 2020; 120:11616-11650. [DOI: 10.1021/acs.chemrev.0c00416] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kylie A. Agnew-Francis
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
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5
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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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6
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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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Feldman HC, Vidadala VN, Potter ZE, Papa FR, Backes BJ, Maly DJ. Development of a Chemical Toolset for Studying the Paralog-Specific Function of IRE1. ACS Chem Biol 2019; 14:2595-2605. [PMID: 31609569 PMCID: PMC6925334 DOI: 10.1021/acschembio.9b00482] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The dual kinase endoribonuclease IRE1 is a master regulator of cell fate decisions in cells experiencing endoplasmic reticulum (ER) stress. In mammalian cells, there are two paralogs of IRE1: IRE1α and IRE1β. While IRE1α has been extensively studied, much less is understood about IRE1β and its role in signaling. In addition, whether the regulation of IRE1β's enzymatic activities varies compared to IRE1α is not known. Here, we show that the RNase domain of IRE1β is enzymatically active and capable of cleaving an XBP1 RNA mini-substrate in vitro. Using ATP-competitive inhibitors, we find that, like IRE1α, there is an allosteric relationship between the kinase and RNase domains of IRE1β. This allowed us to develop a novel toolset of both paralog specific and dual-IRE1α/β kinase inhibitors that attenuate RNase activity (KIRAs). Using sequence alignments of IRE1α and IRE1β, we propose a model for paralog-selective inhibition through interactions with nonconserved residues that differentiate the ATP-binding pockets of IRE1α and IRE1β.
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Affiliation(s)
- Hannah C. Feldman
- Department of Chemistry, University of Washington, Seattle, Washington, United States
| | | | - Zachary E. Potter
- Department of Chemistry, University of Washington, Seattle, Washington, United States
| | - Feroz R. Papa
- 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
- Department of Pathology, University of California−San Francisco, San Francisco, California, United States
- Diabetes 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
| | - 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
| | - 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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Reinecke M, Heinzlmeir S, Wilhelm M, Médard G, Klaeger S, Kuster B. Kinobeads: A Chemical Proteomic Approach for Kinase Inhibitor Selectivity Profiling and Target Discovery. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/9783527818242.ch4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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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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Zhu JN, Wang WK, Jin ZH, Wang QK, Zhao SY. Pyrrolo[3,4- c]pyrazole Synthesis via Copper(Ι) Chloride-Catalyzed Oxidative Coupling of Hydrazones to Maleimides. Org Lett 2019; 21:5046-5050. [PMID: 31247786 DOI: 10.1021/acs.orglett.9b01641] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A variety of pyrrolo[3,4- c]pyrazole derivatives from readily available aldehyde hydrazones and maleimides via direct oxidative coupling under radical cascade reaction have been reported. This method offers satisfactory chemical yields and good functional group compatibility. Moreover, this practical approach is catalyzed by CuCl utilizing air as the oxidant and some control experiments were performed to elaborate the mechanism.
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Affiliation(s)
- Jia-Nan Zhu
- College of Chemistry, Chemical Engineering and Biotechnology , Donghua University , Shanghai 201620 , People's Republic of China
| | - Wen-Kang Wang
- College of Chemistry, Chemical Engineering and Biotechnology , Donghua University , Shanghai 201620 , People's Republic of China
| | - Ze-Hui Jin
- College of Chemistry, Chemical Engineering and Biotechnology , Donghua University , Shanghai 201620 , People's Republic of China
| | - Qian-Kun Wang
- College of Chemistry, Chemical Engineering and Biotechnology , Donghua University , Shanghai 201620 , People's Republic of China
| | - Sheng-Yin Zhao
- College of Chemistry, Chemical Engineering and Biotechnology , Donghua University , Shanghai 201620 , People's Republic of China
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