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Giancola JB, Grimm JB, Jun JV, Petri YD, Lavis LD, Raines RT. Evaluation of the Cytosolic Uptake of HaloTag Using a pH-Sensitive Dye. ACS Chem Biol 2024; 19:908-915. [PMID: 38525961 PMCID: PMC11186736 DOI: 10.1021/acschembio.3c00713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
The efficient cytosolic delivery of proteins is critical for advancing novel therapeutic strategies. Current delivery methods are severely limited by endosomal entrapment, and detection methods lack sophistication in tracking the fate of delivered protein cargo. HaloTag, a commonly used protein in chemical biology and a challenging delivery target, is an exceptional model system for understanding and exploiting cellular delivery. Here, we employed a combinatorial strategy to direct HaloTag to the cytosol. We established the use of Virginia Orange, a pH-sensitive fluorophore, and Janelia Fluor 585, a similar but pH-agnostic fluorophore, in a fluorogenic assay to ascertain protein localization within human cells. Using this assay, we investigated HaloTag delivery upon modification with cell-penetrating peptides, carboxyl group esterification, and cotreatment with an endosomolytic agent. We found efficacious cytosolic entry with two distinct delivery methods. This study expands the toolkit for detecting the cytosolic access of proteins and highlights that multiple intracellular delivery strategies can be used synergistically to effect cytosolic access. Moreover, HaloTag is poised to serve as a platform for the delivery of varied cargo into human cells.
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Affiliation(s)
- JoLynn B. Giancola
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn VA 20147, United States
| | - Joomyung V. Jun
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yana D. Petri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn VA 20147, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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McCullough BS, Barrios AM. Fluorogenic probes for imaging cellular phosphatase activity. Curr Opin Chem Biol 2020; 57:34-40. [PMID: 32470893 PMCID: PMC7483602 DOI: 10.1016/j.cbpa.2020.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/26/2020] [Accepted: 04/08/2020] [Indexed: 11/23/2022]
Abstract
The ability to visualize enzyme activity in a cell, tissue, or living organism can greatly enhance our understanding of the biological roles of that enzyme. While many aspects of cellular signaling are controlled by reversible protein phosphorylation, our understanding of the biological roles of the protein phosphatases involved is limited. Here, we provide an overview of progress toward the development of fluorescent probes that can be used to visualize the activity of protein phosphatases. Significant advances include the development of probes with visible and near-infrared (near-IR) excitation and emission profiles, which provides greater tissue and whole-animal imaging capabilities. In addition, the development of peptide-based probes has provided some selectivity for a phosphatase of interest. Key challenges involve the difficulty of achieving sufficient selectivity for an individual member of a phosphatase enzyme family and the necessity of fully validating the best probes before they can be adopted widely.
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Affiliation(s)
- Brandon S McCullough
- Department of Medicinal Chemistry, University of Utah College of Pharmacy, Salt Lake City, UT 84112-0581, USA
| | - Amy M Barrios
- Department of Medicinal Chemistry, University of Utah College of Pharmacy, Salt Lake City, UT 84112-0581, USA.
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3
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Srinivasan B, Kantae V, Robinson J. Resurrecting the phoenix: When an assay fails. Med Res Rev 2020; 40:1776-1793. [DOI: 10.1002/med.21670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/18/2020] [Accepted: 03/27/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Bharath Srinivasan
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Vasudev Kantae
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - James Robinson
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca Cambridge UK
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4
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Ma ES, Barrios AM. Rational design of a SHP-2 targeted, fluorogenic peptide substrate. Bioorg Med Chem Lett 2019; 29:2452-2454. [PMID: 31351693 DOI: 10.1016/j.bmcl.2019.07.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/19/2019] [Accepted: 07/20/2019] [Indexed: 10/26/2022]
Abstract
Protein tyrosine phosphatase (PTP) targeted, peptide based chemical probes are valuable tools for studying this important family of enzymes, despite the inherent difficulty of developing peptides targeted towards an individual PTP. Here, we have taken a rational approach to designing a SHP-2 targeted, fluorogenic peptide substrate based on information about the potential biological substrates of SHP-2. The fluorogenic, phosphotyrosine mimetic phosphocoumaryl aminopropionic acid (pCAP) provides a facile readout for monitoring PTP activity. By optimizing the amino acids surrounding the pCAP residue, we obtained a substrate with the sequence Ac-DDPI-pCAP-DVLD-NH2 and optimized kinetic parameters (kcat = 0.059 ± 0.008 s-1, Km = 220 ± 50 µM, kcat/Km of 270 M-1s-1). In comparison, the phosphorylated coumarin moiety alone is an exceedingly poor substrate for SHP-2, with a kcat value of 0.0038 ± 0.0003 s-1, a Km value of 1100 ± 100 µM and a kcat/Km of 3 M-1s-1. Furthermore, this optimized peptide has selectivity for SHP-2 over HePTP, MEG1 and PTPµ. The data presented here demonstrate that PTP-targeted peptide substrates can be obtained by optimizing the sequence of a pCAP containing peptide.
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Affiliation(s)
- Elena S Ma
- University of Utah College of Pharmacy, Department of Medicinal Chemistry, Salt Lake City, UT 84112, United States
| | - Amy M Barrios
- University of Utah College of Pharmacy, Department of Medicinal Chemistry, Salt Lake City, UT 84112, United States.
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5
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Shi J, Ruijtenbeek R, Pieters RJ. Demystifying O-GlcNAcylation: hints from peptide substrates. Glycobiology 2019; 28:814-824. [PMID: 29635275 DOI: 10.1093/glycob/cwy031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
O-GlcNAcylation, analogous to phosphorylation, is an essential post-translational modification of proteins at Ser/Thr residues with a single β-N-acetylglucosamine moiety. This dynamic protein modification regulates many fundamental cellular processes and its deregulation has been linked to chronic diseases such as cancer, diabetes and neurodegenerative disorders. Reversible attachment and removal of O-GlcNAc is governed only by O-GlcNAc transferase and O-GlcNAcase, respectively. Peptide substrates, derived from natural O-GlcNAcylation targets, function in the catalytic cores of these two enzymes by maintaining interactions between enzyme and substrate, which makes them ideal models for the study of O-GlcNAcylation and deglycosylation. These peptides provide valuable tools for a deeper understanding of O-GlcNAc processing enzymes. By taking advantage of peptide chemistry, recent progress in the study of activity and regulatory mechanisms of these two enzymes has advanced our understanding of their fundamental specificities as well as their potential as therapeutic targets. Hence, this review summarizes the recent achievements on this modification studied at the peptide level, focusing on enzyme activity, enzyme specificity, direct function, site-specific antibodies and peptide substrate-inspired inhibitors.
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Affiliation(s)
- Jie Shi
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands
| | - Rob Ruijtenbeek
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands.,PamGene International BV, HH's-Hertogenbosch, The Netherlands
| | - Roland J Pieters
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, TB Utrecht, The Netherlands
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6
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Casey GR, Stains CI. Interrogating Protein Phosphatases with Chemical Activity Probes. Chemistry 2018; 24:7810-7824. [PMID: 29338103 PMCID: PMC5986605 DOI: 10.1002/chem.201705194] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Indexed: 12/30/2022]
Abstract
Protein phosphatases, while long overlooked, have recently become appreciated as drivers of both normal- and disease-associated signaling events. As a result, the spotlight is now turning torwards this enzyme family and efforts geared towards the development of modern chemical tools for studying these enzymes are well underway. This Minireview focuses on the evolution of chemical activity probes, both optical and covalent, for the study of protein phosphatases. Small-molecule probes, global monitoring of phosphatase activity through the use of covalent modifiers, and targeted fluorescence-based activity probes are discussed. We conclude with an overview of open questions in the field and highlight the potential impact of chemical tools for studying protein phosphatases.
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Affiliation(s)
- Garrett R Casey
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Cliff I Stains
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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McCullough BS, Barrios AM. Facile, Fluorogenic Assay for Protein Histidine Phosphatase Activity. Biochemistry 2018; 57:2584-2589. [DOI: 10.1021/acs.biochem.8b00278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Brandon S. McCullough
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Amy M. Barrios
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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Biswas S, McCullough BS, Ma ES, LaJoie D, Russell CW, Garrett Brown D, Round JL, Ullman KS, Mulvey MA, Barrios AM. Dual colorimetric and fluorogenic probes for visualizing tyrosine phosphatase activity. Chem Commun (Camb) 2017; 53:2233-2236. [DOI: 10.1039/c6cc09204g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two resorufin-based substrates were developed, providing sensitive fluorogenic readouts for PTP activityin vitroand in living cells.
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Affiliation(s)
- Suvendu Biswas
- Department of Medicinal Chemistry
- University of Utah College of Pharmacy
- Salt Lake City
- USA
| | - Brandon S. McCullough
- Department of Medicinal Chemistry
- University of Utah College of Pharmacy
- Salt Lake City
- USA
| | - Elena S. Ma
- Department of Medicinal Chemistry
- University of Utah College of Pharmacy
- Salt Lake City
- USA
| | - Dollie LaJoie
- Department of Oncological Sciences
- University of Utah School of Medicine
- Salt Lake City
- USA
| | - Colin W. Russell
- Department of Pathology
- University of Utah School of Medicine
- Salt Lake City
- USA
| | - D. Garrett Brown
- Department of Pathology
- University of Utah School of Medicine
- Salt Lake City
- USA
| | - June L. Round
- Department of Pathology
- University of Utah School of Medicine
- Salt Lake City
- USA
| | - Katharine S. Ullman
- Department of Oncological Sciences
- University of Utah School of Medicine
- Salt Lake City
- USA
| | - Matthew A. Mulvey
- Department of Pathology
- University of Utah School of Medicine
- Salt Lake City
- USA
| | - Amy M. Barrios
- Department of Medicinal Chemistry
- University of Utah College of Pharmacy
- Salt Lake City
- USA
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T-helper signals restore B-cell receptor signaling in autoreactive anergic B cells by upregulating CD45 phosphatase activity. J Allergy Clin Immunol 2016; 138:839-851.e8. [DOI: 10.1016/j.jaci.2016.01.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 12/08/2015] [Accepted: 01/29/2016] [Indexed: 12/25/2022]
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Stanford SM, Ahmed V, Barrios AM, Bottini N. Cellular biochemistry methods for investigating protein tyrosine phosphatases. Antioxid Redox Signal 2014; 20:2160-78. [PMID: 24294920 PMCID: PMC3995294 DOI: 10.1089/ars.2013.5731] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SIGNIFICANCE The protein tyrosine phosphatases (PTPs) are a family of proteins that play critical roles in cellular signaling and influence many aspects of human health and disease. Although a wealth of information has been collected about PTPs since their discovery, many questions regarding their regulation and function still remain. CRITICAL ISSUES Of particular importance are the elucidation of the biological substrates of individual PTPs and understanding of the chemical and biological basis for temporal and spatial resolution of PTP activity within a cell. RECENT ADVANCES Drawing from recent advances in both biology and chemistry, innovative approaches have been developed to study the intracellular biochemistry and physiology of PTPs. We provide a summary of PTP-tailored techniques and approaches, emphasizing methodologies to study PTP activity within a cellular context. We first provide a discussion of methods for identifying PTP substrates, including substrate-trapping mutants and synthetic peptide libraries for substrate selectivity profiling. We next provide an overview of approaches for monitoring intracellular PTP activity, including a discussion of mechanistic-based probes, gel-based assays, substrates that can be used intracellularly, and assays tied to cell growth. Finally, we review approaches used for monitoring PTP oxidation, a key regulatory pathway for these enzymes, discussing the biotin switch method and variants of this approach, along with affinity trapping techniques and probes designed to detect PTP oxidation. FUTURE DIRECTIONS Further development of approaches to investigate the intracellular PTP activity and functions will provide specific insight into their mechanisms of action and control of diverse signaling pathways.
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Affiliation(s)
- Stephanie M Stanford
- 1 Division of Cellular Biology, La Jolla Institute for Allergy and Immunology , La Jolla, California
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