1
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Goyal P, Tao AJ, Mumby EJ, English JG, Ferguson FM. Measuring Ligand-bound Protein Complexes with Proximity Labeling: A Practical Guide. Chembiochem 2024:e202400073. [PMID: 38457625 DOI: 10.1002/cbic.202400073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
Identifying the drug-target interactome of small molecule therapeutics is essential for understanding the full pharmacological effects of a compound. These therapies often induce changes within the cellular proteome, leading to unexpected consequences such as changes in the targets complexation state or off-target interactions between the compound and additional proteins. Currently, unbiased target-ID approaches are being used to embark on this task. Here we provide an overview of the strengths and limitations of these methods, and a practical step-by-step protocol for using the BioTAC system to assist with drug target and interactome ID.
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Affiliation(s)
- Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Andrew J Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth J Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Justin G English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Fleur M Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
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2
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Tao AJ, Jiang J, Gadbois GE, Goyal P, Boyle BT, Mumby EJ, Myers SA, English JG, Ferguson FM. A biotin targeting chimera (BioTAC) system to map small molecule interactomes in situ. Nat Commun 2023; 14:8016. [PMID: 38049406 PMCID: PMC10695998 DOI: 10.1038/s41467-023-43507-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/12/2023] [Indexed: 12/06/2023] Open
Abstract
Understanding how small molecules bind to specific protein complexes in living cells is critical to understanding their mechanism-of-action. Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules would provide advantages over target-focused approaches, including the ability to detect previously unknown ligand targets and complexes. However, there are few current methods for unbiased profiling of small molecule interactomes. To address this, we envisioned a technology that would combine the sensitivity and live-cell compatibility of proximity labelling coupled to mass spectrometry, with the specificity and unbiased nature of chemoproteomics. In this manuscript, we describe the BioTAC system, a small-molecule guided proximity labelling platform that can rapidly identify both direct and complexed small molecule binding proteins. We benchmark the system against µMap, photoaffinity labelling, affinity purification coupled to mass spectrometry and proximity labelling coupled to mass spectrometry datasets. We also apply the BioTAC system to provide interactome maps of Trametinib and analogues. The BioTAC system overcomes a limitation of current approaches and supports identification of both inhibitor bound and molecular glue bound complexes.
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Affiliation(s)
- Andrew J Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gillian E Gadbois
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bridget T Boyle
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth J Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Justin G English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
| | - Fleur M Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
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3
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Tao AJ, Jiang J, Gadbois GE, Goyal P, Boyle BT, Mumby EJ, Myers SA, English JG, Ferguson FM. A Biotin Targeting Chimera (BioTAC) System to Map Small Molecule Interactomes in situ. bioRxiv 2023:2023.08.21.554211. [PMID: 37662262 PMCID: PMC10473607 DOI: 10.1101/2023.08.21.554211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules provide advantages over target-focused approaches, including the ability to detect previously unknown targets, and the inclusion of chemical off-compete controls leading to high-confidence identifications. We describe the BioTAC system, a small-molecule guided proximity labelling platform, to rapidly identify both direct and complexed small molecule binding proteins. The BioTAC system overcomes a limitation of current approaches, and supports identification of both inhibitor bound and molecular glue bound complexes.
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Affiliation(s)
- Andrew J. Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Gillian E. Gadbois
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Bridget T. Boyle
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth J. Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Justin G. English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Fleur M. Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
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4
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Olsen RH, English JG. Advancements in G protein-coupled receptor biosensors to study GPCR-G protein coupling. Br J Pharmacol 2023; 180:1433-1443. [PMID: 36166832 PMCID: PMC10511148 DOI: 10.1111/bph.15962] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022] Open
Abstract
Enzymatic and cellular signalling biosensors are used to decipher the activities of complex biological systems. Biosensors for monitoring G protein-coupled receptors (GPCRs), the most drugged class of proteins in the human body, are plentiful and vary in utility, form and function. Their applications have continually expanded our understanding of this important protein class. Here, we briefly summarize a subset of this field with accelerating importance: transducer biosensors measuring receptor-coupling and selectivity, with an emphasis on sensors measuring receptor association and activation of heterotrimeric signalling complexes.
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Affiliation(s)
| | - Justin G. English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132 USA
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5
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Zahm AM, Owens WS, Himes SR, Rondem KE, Fallon BS, Gormick AN, Bloom JS, Kosuri S, Chan H, English JG. Discovery and Validation of Context-Dependent Synthetic Mammalian Promoters. bioRxiv 2023:2023.05.11.539703. [PMID: 37214829 PMCID: PMC10197685 DOI: 10.1101/2023.05.11.539703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cellular transcription enables cells to adapt to various stimuli and maintain homeostasis. Transcription factors bind to transcription response elements (TREs) in gene promoters, initiating transcription. Synthetic promoters, derived from natural TREs, can be engineered to control exogenous gene expression using endogenous transcription machinery. This technology has found extensive use in biological research for applications including reporter gene assays, biomarker development, and programming synthetic circuits in living cells. However, a reliable and precise method for selecting minimally-sized synthetic promoters with desired background, amplitude, and stimulation response profiles has been elusive. In this study, we introduce a massively parallel reporter assay library containing 6184 synthetic promoters, each less than 250 bp in length. This comprehensive library allows for rapid identification of promoters with optimal transcriptional output parameters across multiple cell lines and stimuli. We showcase this library's utility to identify promoters activated in unique cell types, and in response to metabolites, mitogens, cellular toxins, and agonism of both aminergic and non-aminergic GPCRs. We further show these promoters can be used in luciferase reporter assays, eliciting 50-100 fold dynamic ranges in response to stimuli. Our platform is effective, easily implemented, and provides a solution for selecting short-length promoters with precise performance for a multitude of applications.
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Affiliation(s)
- Adam M. Zahm
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Samuel R. Himes
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kathleen E. Rondem
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Braden S. Fallon
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Alexa N. Gormick
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | | | | | - Justin G. English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
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6
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Fallon BS, English JG. Ion-ing out the genetic variants of Kir2.1. eLife 2022; 11:80718. [PMID: 35816168 PMCID: PMC9273208 DOI: 10.7554/elife.80718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Deep mutational scanning provides new insights into how mutations alter the expression and activity of the potassium ion channel Kir2.1, which is associated with many diseases.
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Affiliation(s)
- Braden S Fallon
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Justin G English
- Department of Biochemistry, University of Utah, Salt Lake City, United States
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7
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Cao C, Kang HJ, Singh I, Chen H, Zhang C, Ye W, Hayes BW, Liu J, Gumpper RH, Bender BJ, Slocum ST, Krumm BE, Lansu K, McCorvy JD, Kroeze WK, English JG, DiBerto JF, Olsen RHJ, Huang XP, Zhang S, Liu Y, Kim K, Karpiak J, Jan LY, Abraham SN, Jin J, Shoichet BK, Fay JF, Roth BL. Structure, function and pharmacology of human itch GPCRs. Nature 2021; 600:170-175. [PMID: 34789874 PMCID: PMC9150435 DOI: 10.1038/s41586-021-04126-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/08/2021] [Indexed: 11/09/2022]
Abstract
The MRGPRX family of receptors (MRGPRX1-4) is a family of mas-related G-protein-coupled receptors that have evolved relatively recently1. Of these, MRGPRX2 and MRGPRX4 are key physiological and pathological mediators of itch and related mast cell-mediated hypersensitivity reactions2-5. MRGPRX2 couples to both Gi and Gq in mast cells6. Here we describe agonist-stabilized structures of MRGPRX2 coupled to Gi1 and Gq in ternary complexes with the endogenous peptide cortistatin-14 and with a synthetic agonist probe, respectively, and the development of potent antagonist probes for MRGPRX2. We also describe a specific MRGPRX4 agonist and the structure of this agonist in a complex with MRGPRX4 and Gq. Together, these findings should accelerate the structure-guided discovery of therapeutic agents for pain, itch and mast cell-mediated hypersensitivity.
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MESH Headings
- Cryoelectron Microscopy
- Drug Inverse Agonism
- GTP-Binding Protein alpha Subunits, Gi-Go/chemistry
- GTP-Binding Protein alpha Subunits, Gi-Go/metabolism
- GTP-Binding Protein alpha Subunits, Gi-Go/ultrastructure
- GTP-Binding Protein alpha Subunits, Gq-G11/chemistry
- GTP-Binding Protein alpha Subunits, Gq-G11/metabolism
- GTP-Binding Protein alpha Subunits, Gq-G11/ultrastructure
- Humans
- Models, Molecular
- Nerve Tissue Proteins/antagonists & inhibitors
- Nerve Tissue Proteins/chemistry
- Nerve Tissue Proteins/metabolism
- Nerve Tissue Proteins/ultrastructure
- Pruritus/metabolism
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/antagonists & inhibitors
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Receptors, G-Protein-Coupled/ultrastructure
- Receptors, Neuropeptide/antagonists & inhibitors
- Receptors, Neuropeptide/chemistry
- Receptors, Neuropeptide/metabolism
- Receptors, Neuropeptide/ultrastructure
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Affiliation(s)
- Can Cao
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Hye Jin Kang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Isha Singh
- Department of Pharmaceutical Sciences, University of California San Francisco, School of Medicine, San Francisco, CA, USA
| | - He Chen
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chengwei Zhang
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wenlei Ye
- Department of Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Byron W Hayes
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Jing Liu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan H Gumpper
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Brian J Bender
- Department of Pharmaceutical Sciences, University of California San Francisco, School of Medicine, San Francisco, CA, USA
| | - Samuel T Slocum
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Brian E Krumm
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Katherine Lansu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - John D McCorvy
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Wesley K Kroeze
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Justin G English
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jeffrey F DiBerto
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Reid H J Olsen
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Shicheng Zhang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Yongfeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Kuglae Kim
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Joel Karpiak
- Department of Pharmaceutical Sciences, University of California San Francisco, School of Medicine, San Francisco, CA, USA
| | - Lily Y Jan
- Department of Physiology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Soman N Abraham
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
- Program in Emerging Infectious Diseases, Duke-National University of Singapore, Singapore, Singapore
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian K Shoichet
- Department of Pharmaceutical Sciences, University of California San Francisco, School of Medicine, San Francisco, CA, USA.
| | - Jonathan F Fay
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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8
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Nagai Y, Miyakawa N, Takuwa H, Hori Y, Oyama K, Ji B, Takahashi M, Huang XP, Slocum ST, DiBerto JF, Xiong Y, Urushihata T, Hirabayashi T, Fujimoto A, Mimura K, English JG, Liu J, Inoue KI, Kumata K, Seki C, Ono M, Shimojo M, Zhang MR, Tomita Y, Nakahara J, Suhara T, Takada M, Higuchi M, Jin J, Roth BL, Minamimoto T. Deschloroclozapine, a potent and selective chemogenetic actuator enables rapid neuronal and behavioral modulations in mice and monkeys. Nat Neurosci 2020; 23:1157-1167. [PMID: 32632286 DOI: 10.1038/s41593-020-0661-3] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/27/2020] [Indexed: 11/10/2022]
Abstract
The chemogenetic technology designer receptors exclusively activated by designer drugs (DREADDs) afford remotely reversible control of cellular signaling, neuronal activity and behavior. Although the combination of muscarinic-based DREADDs with clozapine-N-oxide (CNO) has been widely used, sluggish kinetics, metabolic liabilities and potential off-target effects of CNO represent areas for improvement. Here, we provide a new high-affinity and selective agonist deschloroclozapine (DCZ) for muscarinic-based DREADDs. Positron emission tomography revealed that DCZ selectively bound to and occupied DREADDs in both mice and monkeys. Systemic delivery of low doses of DCZ (1 or 3 μg per kg) enhanced neuronal activity via hM3Dq within minutes in mice and monkeys. Intramuscular injections of DCZ (100 μg per kg) reversibly induced spatial working memory deficits in monkeys expressing hM4Di in the prefrontal cortex. DCZ represents a potent, selective, metabolically stable and fast-acting DREADD agonist with utility in both mice and nonhuman primates for a variety of applications.
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Affiliation(s)
- Yuji Nagai
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Naohisa Miyakawa
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Hiroyuki Takuwa
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Yukiko Hori
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Kei Oyama
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Bin Ji
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Manami Takahashi
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel T Slocum
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jeffrey F DiBerto
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Takuya Urushihata
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Toshiyuki Hirabayashi
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Atsushi Fujimoto
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Koki Mimura
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Justin G English
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jing Liu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ken-Ichi Inoue
- Systems Neuroscience Section, Primate Research Institute, Kyoto University, Inuyama, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Katsushi Kumata
- Department of Radiopharmaceuticals Development, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Chie Seki
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Maiko Ono
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Masafumi Shimojo
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Ming-Rong Zhang
- Department of Radiopharmaceuticals Development, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Yutaka Tomita
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
| | - Jin Nakahara
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
| | - Tetsuya Suhara
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Masahiko Takada
- Systems Neuroscience Section, Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Makoto Higuchi
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), Department of Pharmacology, University of North Carolina at Chapel Hill Medical School, Chapel Hill, NC, USA.
| | - Takafumi Minamimoto
- Department of Functional Brain Imaging, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan.
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9
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Olsen RHJ, DiBerto JF, English JG, Glaudin AM, Krumm BE, Slocum ST, Che T, Gavin AC, McCorvy JD, Roth BL, Strachan RT. TRUPATH, an open-source biosensor platform for interrogating the GPCR transducerome. Nat Chem Biol 2020; 16:841-849. [PMID: 32367019 PMCID: PMC7648517 DOI: 10.1038/s41589-020-0535-8] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 03/30/2020] [Indexed: 12/18/2022]
Abstract
G-protein-coupled receptors (GPCRs) remain major drug targets, despite our incomplete understanding of how they signal through 16 non-visual G-protein signal transducers (collectively named the transducerome) to exert their actions. To address this gap, we have developed an open-source suite of 14 optimized bioluminescence resonance energy transfer (BRET) Gαβγ biosensors (named TRUPATH) to interrogate the transducerome with single pathway resolution in cells. Generated through exhaustive protein engineering and empirical testing, the TRUPATH suite of Gαβγ biosensors includes the first Gα15 and GαGustducin probes. In head-to-head studies, TRUPATH biosensors outperformed first-generation sensors at multiple GPCRs and in different cell lines. Benchmarking studies with TRUPATH biosensors recapitulated previously documented signaling bias and revealed new coupling preferences for prototypic and understudied GPCRs with potential in vivo relevance. To enable a greater understanding of GPCR molecular pharmacology by the scientific community, we have made TRUPATH biosensors easily accessible as a kit through Addgene.
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Affiliation(s)
- Reid H J Olsen
- Department of Pharmacology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jeffrey F DiBerto
- Department of Pharmacology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Justin G English
- Department of Pharmacology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Alexis M Glaudin
- Department of Pharmacology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Brian E Krumm
- Department of Pharmacology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Samuel T Slocum
- Department of Pharmacology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Tao Che
- Department of Pharmacology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Ariana C Gavin
- Department of Pharmacology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - John D McCorvy
- Department of Pharmacology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
| | - Ryan T Strachan
- Department of Pharmacology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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English JG, Olsen RHJ, Lansu K, Patel M, White K, Cockrell AS, Singh D, Strachan RT, Wacker D, Roth BL. VEGAS as a Platform for Facile Directed Evolution in Mammalian Cells. Cell 2019; 178:1030. [PMID: 31398329 DOI: 10.1016/j.cell.2019.07.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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English JG, Olsen RHJ, Lansu K, Patel M, White K, Cockrell AS, Singh D, Strachan RT, Wacker D, Roth BL. VEGAS as a Platform for Facile Directed Evolution in Mammalian Cells. Cell 2019; 178:748-761.e17. [PMID: 31280962 DOI: 10.1016/j.cell.2019.05.051] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/06/2019] [Accepted: 05/23/2019] [Indexed: 02/08/2023]
Abstract
Directed evolution, artificial selection toward designed objectives, is routinely used to develop new molecular tools and therapeutics. Successful directed molecular evolution campaigns repeatedly test diverse sequences with a designed selective pressure. Unicellular organisms and their viral pathogens are exceptional for this purpose and have been used for decades. However, many desirable targets of directed evolution perform poorly or unnaturally in unicellular backgrounds. Here, we present a system for facile directed evolution in mammalian cells. Using the RNA alphavirus Sindbis as a vector for heredity and diversity, we achieved 24-h selection cycles surpassing 10-3 mutations per base. Selection is achieved through genetically actuated sequences internal to the host cell, thus the system's name: viral evolution of genetically actuating sequences, or "VEGAS." Using VEGAS, we evolve transcription factors, GPCRs, and allosteric nanobodies toward functional signaling endpoints each in less than 1 weeks' time.
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Affiliation(s)
- Justin G English
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Reid H J Olsen
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Katherine Lansu
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Michael Patel
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Karoline White
- Department of Biology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Adam S Cockrell
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Darshan Singh
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Ryan T Strachan
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Daniel Wacker
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA.
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Abstract
Neurologic disorders are frequently a result of inappropriate electrical and/or chemical signaling of neurons and glia. Ultimate remediation would necessitate reprogramming these signals. Historically, correcting neuronal and glial signaling is accomplished via drug therapy/administration, although they frequently fail to effectively and fully treat the underlying disorder. Developments in basic research have produced several new classes of potential therapeutics to directly and precisely control neuron activity at the single-cell level. We review one such technology, Designer Receptors Exclusively Activated by Designer Drugs, and suggest its potential as a powerful tool for augmenting neuronal and glial signaling and activity for basic and translational applications.
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Affiliation(s)
- Justin G English
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill
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English JG, Shellhammer JP, Malahe M, McCarter PC, Elston TC, Dohlman HG. MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast. Sci Signal 2015; 8:ra5. [PMID: 25587192 DOI: 10.1126/scisignal.2005774] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Signaling pathways can behave as switches or rheostats, generating binary or graded responses to a given cell stimulus. We evaluated whether a single signaling pathway can simultaneously encode a switch and a rheostat. We found that the kinase Hog1 mediated a bifurcated cellular response: Activation and commitment to adaptation to osmotic stress are switchlike, whereas protein induction and the resolution of this commitment are graded. Through experimentation, bioinformatics analysis, and computational modeling, we determined that graded recovery is encoded through feedback phosphorylation and a gene induction program that is both temporally staggered and variable across the population. This switch-to-rheostat signaling mechanism represents a versatile stress adaptation system, wherein a broad range of inputs generate an "all-in" response that is later tuned to allow graded recovery of individual cells over time.
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Affiliation(s)
- Justin G English
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - James P Shellhammer
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael Malahe
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Patrick C McCarter
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy C Elston
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Henrik G Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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