1
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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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2
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Abstract
The epigenetic modifications of histones are versatile marks that are intimately connected to development and disease pathogenesis including human cancers. In this review, we will discuss the many different types of histone modifications and the biological processes with which they are involved. Specifically, we review the enzymatic machineries and modifications that are involved in cancer development and progression, and how to apply currently available small molecule inhibitors for histone modifiers as tool compounds to study the functional significance of histone modifications and their clinical implications.
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Affiliation(s)
- Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Simpson Querrey 7th Floor 303 E. Superior Street, Chicago, IL 60611 USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Simpson Querrey 7th Floor 303 E. Superior Street, Chicago, IL 60611 USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
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3
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Cermakova K, Hodges HC. Next-Generation Drugs and Probes for Chromatin Biology: From Targeted Protein Degradation to Phase Separation. Molecules 2018; 23:molecules23081958. [PMID: 30082609 PMCID: PMC6102721 DOI: 10.3390/molecules23081958] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/01/2018] [Accepted: 08/01/2018] [Indexed: 12/31/2022] Open
Abstract
Chromatin regulation is a critical aspect of nuclear function. Recent advances have provided detailed information about dynamic three-dimensional organization of chromatin and its regulatory factors. Mechanisms crucial for normal nuclear function and epigenetic control include compartmentalization of biochemical reactions by liquid-phase separated condensates and signal-dependent regulation of protein stability. Synthetic control of these phenomena by small molecules provides deep insight into essential activities such as histone modification, BAF (SWI/SNF) and PBAF remodeling, Polycomb repression, enhancer looping by cohesin and CTCF, as well as many other processes that contribute to transcription. As a result, a complete understanding of the spatiotemporal mechanisms that underlie chromatin regulation increasingly requires the use of fast-acting drugs and chemical probes. Here, we provide a comprehensive review of next-generation chemical biology tools to interrogate the chromatin regulatory landscape, including selective PROTAC E3 ubiquitin ligase degraders, degrons, fluorescent ligands, dimerizers, inhibitors, and other drugs. These small molecules provide important insights into the mechanisms that govern gene regulation, DNA repair, development, and diseases like cancer.
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Affiliation(s)
- Katerina Cermakova
- Department of Molecular & Cellular Biology, Center for Precision Environmental Health, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - H Courtney Hodges
- Department of Molecular & Cellular Biology, Center for Precision Environmental Health, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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4
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Abbina S, Siren EMJ, Moon H, Kizhakkedathu JN. Surface Engineering for Cell-Based Therapies: Techniques for Manipulating Mammalian Cell Surfaces. ACS Biomater Sci Eng 2017; 4:3658-3677. [DOI: 10.1021/acsbiomaterials.7b00514] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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5
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Murrey HE, Judkins JC, Am Ende CW, Ballard TE, Fang Y, Riccardi K, Di L, Guilmette ER, Schwartz JW, Fox JM, Johnson DS. Systematic Evaluation of Bioorthogonal Reactions in Live Cells with Clickable HaloTag Ligands: Implications for Intracellular Imaging. J Am Chem Soc 2015; 137:11461-75. [PMID: 26270632 PMCID: PMC4572613 DOI: 10.1021/jacs.5b06847] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Bioorthogonal
reactions, including the strain-promoted azide–alkyne
cycloaddition (SPAAC) and inverse electron demand Diels–Alder
(iEDDA) reactions, have become increasingly popular for live-cell
imaging applications. However, the stability and reactivity of reagents
has never been systematically explored in the context of a living
cell. Here we report a universal, organelle-targetable system based
on HaloTag protein technology for directly comparing bioorthogonal
reagent reactivity, specificity, and stability using clickable HaloTag
ligands in various subcellular compartments. This system enabled a
detailed comparison of the bioorthogonal reactions in live cells and
informed the selection of optimal reagents and conditions for live-cell
imaging studies. We found that the reaction of sTCO with monosubstituted
tetrazines is the fastest reaction in cells; however, both reagents
have stability issues. To address this, we introduced a new variant
of sTCO, Ag-sTCO, which has much improved stability and can be used
directly in cells for rapid bioorthogonal reactions with tetrazines.
Utilization of Ag complexes of conformationally strained trans-cyclooctenes should greatly expand their usefulness especially when
paired with less reactive, more stable tetrazines.
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Affiliation(s)
- Heather E Murrey
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Joshua C Judkins
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Christopher W Am Ende
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - T Eric Ballard
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States.,Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development , Groton, Connecticut 06340, United States
| | - Yinzhi Fang
- Brown Laboratories, Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - Keith Riccardi
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development , Groton, Connecticut 06340, United States
| | - Li Di
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development , Groton, Connecticut 06340, United States
| | - Edward R Guilmette
- Neuroscience and Pain Research Unit, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Joel W Schwartz
- Neuroscience and Pain Research Unit, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Joseph M Fox
- Brown Laboratories, Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - Douglas S Johnson
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
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6
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Abstract
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Exploration of protein function and
interaction is critical for
discovering links among genomics, proteomics, and disease state; yet,
the immense complexity of proteomics found in biological systems currently
limits our investigational capacity. Although affinity and autofluorescent
tags are widely employed for protein analysis, these methods have
been met with limited success because they lack specificity and require
multiple fusion tags and genetic constructs. As an alternative approach,
the innovative HaloTag protein fusion platform allows protein function
and interaction to be comprehensively analyzed using a single genetic
construct with multiple capabilities. This is accomplished using a
simplified process, in which a variable HaloTag ligand binds rapidly
to the HaloTag protein (usually linked to the protein of interest)
with high affinity and specificity. In this review, we examine all
current applications of the HaloTag technology platform for biomedical
applications, such as the study of protein isolation and purification,
protein function, protein–protein and protein–DNA interactions,
biological assays, in vitro cellular imaging, and in vivo molecular imaging. In addition, novel uses of the
HaloTag platform are briefly discussed along with potential future
applications.
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Affiliation(s)
- Christopher G England
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Haiming Luo
- ‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weibo Cai
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,§University of Wisconsin Carbone Cancer Center, Madison, Wisconsin 53705, United States
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7
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Pulsipher A, Griffin ME, Stone SE, Hsieh-Wilson LC. Long-Lived Engineering of Glycans to Direct Stem Cell Fate. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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8
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Pulsipher A, Griffin ME, Stone SE, Hsieh-Wilson LC. Long-lived engineering of glycans to direct stem cell fate. Angew Chem Int Ed Engl 2014; 54:1466-70. [PMID: 25476911 DOI: 10.1002/anie.201409258] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/11/2014] [Indexed: 12/23/2022]
Abstract
Glycans mediate many critical, long-term biological processes, such as stem cell differentiation. However, few methods are available for the sustained remodeling of cells with specific glycan structures. A new strategy that enables the long-lived presentation of defined glycosaminoglycans on cell surfaces using HaloTag proteins (HTPs) as anchors is reported. By controlling the sulfation patterns of heparan sulfate (HS) on pluripotent embryonic stem cell (ESC) membranes, it is demonstrated that specific glycans cause ESCs to undergo accelerated exit from self-renewal and differentiation into neuronal cell types. Thus, the stable display of glycans on HTP scaffolds provides a powerful, versatile means to direct key signaling events and biological outcomes such as stem cell fate.
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Affiliation(s)
- Abigail Pulsipher
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125 (USA)
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9
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Leonard SE, Register AC, Krishnamurty R, Brighty GJ, Maly DJ. Divergent modulation of Src-family kinase regulatory interactions with ATP-competitive inhibitors. ACS Chem Biol 2014; 9:1894-905. [PMID: 24946274 PMCID: PMC4136698 DOI: 10.1021/cb500371g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Multidomain protein kinases, central
controllers of signal transduction,
use regulatory domains to modulate catalytic activity in a complex
cellular environment. Additionally, these domains regulate noncatalytic
functions, including cellular localization and protein–protein
interactions. Src-family kinases (SFKs) are promising therapeutic
targets for a number of diseases and are an excellent model for studying
the regulation of multidomain kinases. Here, we demonstrate that the
regulatory domains of the SFKs Src and Hck are divergently affected
by ligands that stabilize two distinct inactive ATP-binding site conformations.
Conformation-selective, ATP-competitive inhibitors differentially
modulate the ability of the SH3 and SH2 domains of Src and Hck to
engage in intermolecular interactions and the ability of the kinase–inhibitor
complex to undergo post-translational modification by effector enzymes.
This surprising divergence in regulatory domain behavior by two classes
of inhibitors that each stabilize inactive ATP-binding site conformations
is found to occur through perturbation or stabilization of the αC
helix. These studies provide insight into how conformation-selective,
ATP-competitive inhibitors can be designed to modulate domain interactions
and post-translational modifications distal to the ATP-binding site
of kinases.
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Affiliation(s)
- Stephen E. Leonard
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - A. C. Register
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ratika Krishnamurty
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gabriel J. Brighty
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
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10
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Miyazaki A, Asanuma M, Dodo K, Egami H, Sodeoka M. A "catch-and-release" protocol for alkyne-tagged molecules based on a resin-bound cobalt complex for peptide enrichment in aqueous media. Chemistry 2014; 20:8116-28. [PMID: 24788842 DOI: 10.1002/chem.201400056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Indexed: 01/09/2023]
Abstract
The development of new and mild protocols for the specific enrichment of biomolecules is of significant interest from the perspective of chemical biology. A cobalt-phosphine complex immobilised on a solid-phase resin has been found to selectively bind to a propargyl carbamate tag, that is, "catch", under dilute aqueous conditions (pH 7) at 4 °C. Upon acidic treatment of the resulting resin-bound alkyne-cobalt complex, the Nicholas reaction was induced to "release" the alkyne-tagged molecule from the resin as a free amine. Model studies revealed that selective enrichment of the alkyne-tagged molecule could be achieved with high efficiency at 4 °C. The proof-of-concept was applied to an alkyne-tagged amino acid and dipeptide. Studies using an alkyne-tagged dipeptide proved that this protocol is compatible with various amino acids bearing a range of functionalities in the side-chain. In addition, selective enrichment and detection of an amine derived from the "catch and release" of an alkyne-tagged dipeptide in the presence of various peptides has been accomplished under highly dilute conditions, as determined by mass spectrometry.
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Affiliation(s)
- Ayako Miyazaki
- Sodeoka Live Cell Chemistry Project, ERATO, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan) and Synthetic Organic Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Current address: Institute of Transformative, Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan)
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11
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Preston GW, Radford SE, Ashcroft AE, Wilson AJ. Analysis of amyloid nanostructures using photo-cross-linking: in situ comparison of three widely used photo-cross-linkers. ACS Chem Biol 2014; 9:761-8. [PMID: 24372480 PMCID: PMC3964826 DOI: 10.1021/cb400731s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Photoinduced cross-linking (PIC) has become a powerful tool in chemical biology for the identification and mapping of stable or transient interactions between biomacromolecules and their (unknown) ligands. However, the value of PIC for in vitro and in vivo structural proteomics can be realized only if cross-linking reports accurately on biomacromolecule secondary, tertiary, and quaternary structures with residue-specific resolution. Progress in this area requires rigorous and comparative studies of PIC reagents, but despite widespread use of PIC, these have rarely been performed. The use of PIC to report reliably on noncovalent structure is therefore limited, and its potentials have yet to be fully realized. In the present study, we compared the abilities of three probes, phenyl trifluoromethyldiazirine (TFMD), benzophenone (BP), and phenylazide (PA), to record structural information within a biomolecular complex. For this purpose, we employed a self-assembled amyloid-like peptide nanostructure as a tightly and specifically packed model environment in which to photolyze the reagents. Information about PIC products was gathered using mass spectrometry and ion mobility spectrometry, and the data were interpreted using a mechanism-oriented approach. While all three PIC groups appeared to generate information within the packed peptide environment, the data highlight technical limitations of BP and PA. On the other hand, TFMD displayed accuracy and generated straightforward results. Thus TFMD, with its robust and rapid photochemistry, was shown to be an ideal probe for cross-linking of peptide nanostructures. The implications of our findings for detailed analyses of complex systems, including those that are transiently populated, are discussed.
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Affiliation(s)
- George W. Preston
- School
of Chemistry, ‡Astbury Centre for Structural Molecular Biology, and §School of Molecular and Cellular Biology,
Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Sheena E. Radford
- School
of Chemistry, ‡Astbury Centre for Structural Molecular Biology, and §School of Molecular and Cellular Biology,
Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Alison. E. Ashcroft
- School
of Chemistry, ‡Astbury Centre for Structural Molecular Biology, and §School of Molecular and Cellular Biology,
Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Andrew J. Wilson
- School
of Chemistry, ‡Astbury Centre for Structural Molecular Biology, and §School of Molecular and Cellular Biology,
Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
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12
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Hari SB, Merritt EA, Maly DJ. Sequence determinants of a specific inactive protein kinase conformation. ACTA ACUST UNITED AC 2014; 20:806-15. [PMID: 23790491 DOI: 10.1016/j.chembiol.2013.05.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/18/2013] [Accepted: 05/09/2013] [Indexed: 02/07/2023]
Abstract
Only a small percentage of protein kinases have been shown to adopt a distinct inactive ATP-binding site conformation, called the Asp-Phe-Gly-out (DFG-out) conformation. Given the high degree of homology within this enzyme family, we sought to understand the basis of this disparity on a sequence level. We identified two residue positions that sensitize mitogen-activated protein kinases (MAPKs) to inhibitors that stabilize the DFG-out inactive conformation. After characterizing the structure and dynamics of an inhibitor-sensitive MAPK mutant, we demonstrated the generality of this strategy by sensitizing a kinase (apoptosis signal-regulating kinase 1) not in the MAPK family to several DFG-out stabilizing ligands, using the same residue positions. The use of specific inactive conformations may aid the study of noncatalytic roles of protein kinases, such as binding partner interactions and scaffolding effects.
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Affiliation(s)
- Sanjay B Hari
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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13
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Golkowski M, Brigham JL, Perera GK, Romano GE, Maly DJ, Ong SE. Rapid profiling of protein kinase inhibitors by quantitative proteomics. MEDCHEMCOMM 2014; 5:363-369. [PMID: 24648882 DOI: 10.1039/c3md00315a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ability to determine structure-activity relationships (SAR) and identify cellular targets from cell lysates and tissues is of great utility for kinase inhibitor drug discovery. We describe a streamlined mass spectrometry-based chemoproteomics workflow to examine the SAR and target profiles of a small library of kinase inhibitors that consists of the drug dasatinib and a panel of general type II inhibitors. By combining a simplified affinity enrichment and on-bead protein digestion workflow with quantitative proteomics, we achieved sensitive and specific enrichment of target kinases using our small molecule probes. We applied the affinity matrices in competition experiments with soluble probes in HeLa cell lysates using less than 1 mg of protein per experiment. Each pull-down experiment was analyzed in a single nano LC-MS run. Stringent selection criteria for target identification were applied to deduce 28 protein targets for dasatinib and 31 protein targets for our general type II kinase inhibitor in HeLa cell lysate. Additional kinase and protein targets were identified with the general type II inhibitor analogs, with small structural changes leading to divergent target profiles. We observed surprisingly high sequence coverage on some proteins, enabling further analyses of phosphorylation sites for several target kinases without additional sample processing. Our rapid workflow profiled cellular targets for six small molecules within a week, demonstrating that an unbiased proteomics screen of cellular targets yields valuable SAR information and may be incorporated at an early stage in kinase inhibitor development.
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Affiliation(s)
- Martin Golkowski
- Department of Pharmacology, University of Washington, Seattle, Washington, USA
| | - Jennifer L Brigham
- Division of Chemistry, University of Washington, Seattle, Washington, USA
| | - Gayani K Perera
- Division of Chemistry, University of Washington, Seattle, Washington, USA
| | - Guillermo E Romano
- Division of Chemistry, University of Washington, Seattle, Washington, USA
| | - Dustin J Maly
- Division of Chemistry, University of Washington, Seattle, Washington, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, Washington, USA
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14
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An H, Statsyuk AV. Development of activity-based probes for ubiquitin and ubiquitin-like protein signaling pathways. J Am Chem Soc 2013; 135:16948-62. [PMID: 24138456 DOI: 10.1021/ja4099643] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ubiquitin and ubiquitin-like (UBL) proteins regulate a vast variety of cellular functions. Some UBL proteins are present in all cell types, while others are expressed only in certain cells or under certain environmental conditions. This highlights the central role of UBL systems in regulation of ubiquitous as well as specific cellular functions. UBL proteins share little amino acid sequence identity to each other, yet they share similar 3D shapes, which is exemplified by the β-grasp fold. Central to UBL protein signaling pathways are UBL protein-activating E1 enzymes that activate the C-terminus of UBL proteins for subsequent conjugation to the protein substrates. Due to their critical roles in biology, E1 enzymes have been recognized as emerging drug targets to treat human diseases. In spite of their biological significance, however, methods to discover UBL proteins and to monitor the intracellular activity of E1 enzymes are lacking. Thus, there is a critical need for methods to evaluate the intracellular mechanisms of action of E1 enzyme inhibitors. Here we describe the development of a mechanism-based small-molecule probe, ABP1, that can be used to discover and to detect active UBL proteins, and to monitor the intracellular activity of E1 enzymes inside intact cells. The developed probe can also be used to profile the selectivity of E1 enzyme-targeting drugs in vitro and inside intact cells.
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Affiliation(s)
- Heeseon An
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, Chemistry of Life Processes Institute, Northwestern University , Silverman Hall, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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15
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Auld D, Lea W, Davis MI, Simeonov A. Literature Search and Review. Assay Drug Dev Technol 2013. [DOI: 10.1089/adt.2013.1106.lr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Doug Auld
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
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