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Wang H, Gaston R, Ahmed KT, Dudley GB, Barrios AM. Derivatives of the Fungal Natural Product Illudalic Acid Inhibit the Activity of Protein Histidine Phosphatase PHPT1. ChemMedChem 2023; 18:e202300187. [PMID: 37267298 PMCID: PMC10443188 DOI: 10.1002/cmdc.202300187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/04/2023]
Abstract
PHPT1 is a protein histidine phosphatase that has been implicated in several disease pathways, but the chemical tools necessary to study the biological roles of this enzyme and investigate its utility as a therapeutic target have yet to be developed. To this end, the discovery of PHPT1 inhibitors is an area of significant interest. Here, we report an investigation of illudalic acid and illudalic acid analog-based inhibition of PHPT1 activity. Four of the seven analogs investigated had IC50 values below 5 μM, with the most potent compound (IA1-8H2) exhibiting an IC50 value of 3.4±0.7 μM. Interestingly, these compounds appear to be non-covalent, non-competitive inhibitors of PHPT1 activity, in contrast to other recently reported PHPT1 inhibitors. Mutating the three cysteine residues to alanine has no effect on inhibition, indicating that cysteine is not critical for interactions between inhibitor and enzyme.
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Affiliation(s)
- Hanfei Wang
- Department of Medicinal Chemistry, University of Utah College of Pharmacy, Salt Lake City, UT 84112
| | - Robert Gaston
- Department of Chemistry, West Virginia University, Morgantown, WV 26506
| | - Kh Tanvir Ahmed
- Department of Chemistry, West Virginia University, Morgantown, WV 26506
| | - Gregory B. Dudley
- Department of Chemistry, West Virginia University, Morgantown, WV 26506
| | - Amy M. Barrios
- Department of Medicinal Chemistry, University of Utah College of Pharmacy, Salt Lake City, UT 84112
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Lim S. A Review of the Bacterial Phosphoproteomes of Beneficial Microbes. Microorganisms 2023; 11:microorganisms11040931. [PMID: 37110354 PMCID: PMC10145908 DOI: 10.3390/microorganisms11040931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
The number and variety of protein post-translational modifications (PTMs) found and characterized in bacteria over the past ten years have increased dramatically. Compared to eukaryotic proteins, most post-translational protein changes in bacteria affect relatively few proteins because the majority of modified proteins exhibit substoichiometric modification levels, which makes structural and functional analyses challenging. In addition, the number of modified enzymes in bacterial species differs widely, and degrees of proteome modification depend on environmental conditions. Nevertheless, evidence suggests that protein PTMs play essential roles in various cellular processes, including nitrogen metabolism, protein synthesis and turnover, the cell cycle, dormancy, spore germination, sporulation, persistence, and virulence. Additional investigations on protein post-translational changes will undoubtedly close knowledge gaps in bacterial physiology and create new means of treating infectious diseases. Here, we describe the role of the post-translation phosphorylation of major bacterial proteins and review the progress of research on phosphorylated proteins depending on bacterial species.
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Affiliation(s)
- Sooa Lim
- Department of Pharmaceutical Engineering, Hoseo University, Asan-si 31499, Republic of Korea
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3
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Hajdusits B, Suskiewicz MJ, Hundt N, Meinhart A, Kurzbauer R, Leodolter J, Kukura P, Clausen T. McsB forms a gated kinase chamber to mark aberrant bacterial proteins for degradation. eLife 2021; 10:63505. [PMID: 34328418 PMCID: PMC8370763 DOI: 10.7554/elife.63505] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 07/29/2021] [Indexed: 01/04/2023] Open
Abstract
In Gram-positive bacteria, the McsB protein arginine kinase is central to protein quality control, labeling aberrant molecules for degradation by the ClpCP protease. Despite its importance for stress response and pathogenicity, it is still elusive how the bacterial degradation labeling is regulated. Here, we delineate the mechanism how McsB targets aberrant proteins during stress conditions. Structural data reveal a self-compartmentalized kinase, in which the active sites are sequestered in a molecular cage. The ‘closed’ octamer interconverts with other oligomers in a phosphorylation-dependent manner and, unlike these ‘open’ forms, preferentially labels unfolded proteins. In vivo data show that heat-shock triggers accumulation of higher order oligomers, of which the octameric McsB is essential for surviving stress situations. The interconversion of open and closed oligomers represents a distinct regulatory mechanism of a degradation labeler, allowing the McsB kinase to adapt its potentially dangerous enzyme function to the needs of the bacterial cell.
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Affiliation(s)
- Bence Hajdusits
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Marcin J Suskiewicz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Nikolas Hundt
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Anton Meinhart
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.,Medical University of Vienna, Vienna, Austria
| | - Robert Kurzbauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Julia Leodolter
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.,Medical University of Vienna, Vienna, Austria
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4
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Ahn S, Jung H, Kee JM. Quest for the Crypto-phosphoproteome. Chembiochem 2020; 22:319-325. [PMID: 33094900 DOI: 10.1002/cbic.202000583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/14/2020] [Indexed: 11/05/2022]
Abstract
Protein phosphorylation is one of the most studied post-translational modifications (PTMs). Despite the remarkable advances in phosphoproteomics, a chemically less-stable subset of the phosphosites, which we call the crypto-phosphoproteome, has remained underexplored due to technological challenges. In this Viewpoint, we briefly summarize the current understanding of these elusive protein phosphorylations and identify the missing pieces for future studies.
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Affiliation(s)
- Seungmin Ahn
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Hoyoung Jung
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Jung-Min Kee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
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Casey GR, Stains CI. A fluorescent probe for monitoring PTP-PEST enzymatic activity. Analyst 2020; 145:6713-6718. [PMID: 32812952 DOI: 10.1039/d0an00993h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Phosphatase non-receptor type 12 (PTPN12 or PTP-PEST) is a critical regulator of cell migration, acting as a tumor suppressor in cancer. Decreases in PTP-PEST expression correlate with aggressive phenotypes in hepatocellular carcinoma (HCC). Despite the importance of PTP-PEST in cellular signaling, methods to directly monitor its enzymatic activity are lacking. Herein, we report the design, synthesis, and optimization of a probe to directly monitor PTP-PEST enzymatic activity via a fluorescent readout. This activity sensor, termed pPEST1tide, is capable of detecting as little as 0.2 nM recombinant PTP-PEST. In addition, we demonstrate that this probe can selectively report on PTP-PEST activity using a panel of potential off-target enzymes. In the long-term, this activity probe could be utilized to identify small molecule modulators of PTP-PEST activity as well as provide a prognostic readout for HCC.
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Affiliation(s)
- Garrett R Casey
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
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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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Sun Y, Zhang Y, Zhang H, Liu M, Liu Y. Integrating Highly Efficient Recognition and Signal Transition of g-C3N4 Embellished Ti3C2 MXene Hybrid Nanosheets for Electrogenerated Chemiluminescence Analysis of Protein Kinase Activity. Anal Chem 2020; 92:10668-10676. [DOI: 10.1021/acs.analchem.0c01776] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yan Sun
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education, China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P. R. China
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology of Ministry of Education, Tsinghua University, Beijing 100084, P. R. China
| | - Yimeng Zhang
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology of Ministry of Education, Tsinghua University, Beijing 100084, P. R. China
| | - HuiXin Zhang
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology of Ministry of Education, Tsinghua University, Beijing 100084, P. R. China
| | - Meiling Liu
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education, China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P. R. China
| | - Yang Liu
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology of Ministry of Education, Tsinghua University, Beijing 100084, P. R. China
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