1
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Escobar EE, Yang W, Lanzillotti MB, Juetten KJ, Shields S, Siegel D, Zhang YJ, Brodbelt JS. Tracking Inhibition of Human Small C-Terminal Domain Phosphatase 1 Using 193 nm Ultraviolet Photodissociation Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1330-1341. [PMID: 38662915 PMCID: PMC11384422 DOI: 10.1021/jasms.4c00098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Working in tandem with kinases via a dynamic interplay of phosphorylation and dephosphorylation of proteins, phosphatases regulate many cellular processes and thus represent compelling therapeutic targets. Here we leverage ultraviolet photodissociation to shed light on the binding characteristics of two covalent phosphatase inhibitors, T65 and rabeprazole, and their respective interactions with the human small C-terminal domain phosphatase 1 (SCP1) and its single-point mutant C181A, in which a nonreactive alanine replaces one key reactive cysteine. Top-down MS/MS analysis is used to localize the binding of T65 and rabeprazole on the two proteins and estimate the relative reactivities of each cysteine residue.
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Affiliation(s)
| | | | | | | | | | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive 0741, La Jolla, California 92093, United States
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2
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Kobayashi T, Yamazaki K, Shinada J, Mizunuma M, Furukawa K, Chuman Y. Identification of Inhibitors of the Disease-Associated Protein Phosphatase Scp1 Using Antibody Mimetic Molecules. Int J Mol Sci 2024; 25:3737. [PMID: 38612548 PMCID: PMC11011526 DOI: 10.3390/ijms25073737] [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: 02/28/2024] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Protein phosphorylation is a prevalent translational modification, and its dysregulation has been implicated in various diseases, including cancer. Despite its significance, there is a lack of specific inhibitors of the FCP/SCP-type Ser/Thr protein phosphatase Scp1, characterized by high specificity and affinity. In this study, we focused on adnectin, an antibody-mimetic protein, aiming to identify Scp1-specific binding molecules with a broad binding surface that target the substrate-recognition site of Scp1. Biopanning of Scp1 was performed using an adnectin-presenting phage library with a randomized FG loop. We succeeded in identifying FG-1Adn, which showed high affinity and specificity for Scp1. Ala scanning analysis of the Scp1-binding sequence in relation to the FG-1 peptide revealed that hydrophobic residues, including aromatic amino acids, play important roles in Scp1 recognition. Furthermore, FG-1Adn was found to co-localize with Scp1 in cells, especially on the plasma membrane. In addition, Western blotting analysis showed that FG-1Adn increased the phosphorylation level of the target protein of Scp1 in cells, indicating that FG-1Adn can inhibit the function of Scp1. These results suggest that FG-1Adn can be used as a specific inhibitor of Scp1.
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Affiliation(s)
| | | | | | | | | | - Yoshiro Chuman
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan; (T.K.); (K.Y.); (J.S.); (M.M.); (K.F.)
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3
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Glycolytic flux control by drugging phosphoglycolate phosphatase. Nat Commun 2022; 13:6845. [PMID: 36369173 PMCID: PMC9652372 DOI: 10.1038/s41467-022-34228-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
Targeting the intrinsic metabolism of immune or tumor cells is a therapeutic strategy in autoimmunity, chronic inflammation or cancer. Metabolite repair enzymes may represent an alternative target class for selective metabolic inhibition, but pharmacological tools to test this concept are needed. Here, we demonstrate that phosphoglycolate phosphatase (PGP), a prototypical metabolite repair enzyme in glycolysis, is a pharmacologically actionable target. Using a combination of small molecule screening, protein crystallography, molecular dynamics simulations and NMR metabolomics, we discover and analyze a compound (CP1) that inhibits PGP with high selectivity and submicromolar potency. CP1 locks the phosphatase in a catalytically inactive conformation, dampens glycolytic flux, and phenocopies effects of cellular PGP-deficiency. This study provides key insights into effective and precise PGP targeting, at the same time validating an allosteric approach to control glycolysis that could advance discoveries of innovative therapeutic candidates.
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4
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Medellin B, Yang W, Konduri S, Dong J, Irani S, Wu H, Matthews WL, Zhang ZY, Siegel D, Zhang Y. Targeted Covalent Inhibition of Small CTD Phosphatase 1 to Promote the Degradation of the REST Transcription Factor in Human Cells. J Med Chem 2022; 65:507-519. [PMID: 34931516 PMCID: PMC8826594 DOI: 10.1021/acs.jmedchem.1c01655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The repressor element-1 silencing transcription factor (REST) represses neuronal gene expression, whose dysregulation is implicated in brain tumors and neurological diseases. A high level of REST protein drives the tumor growth in some glioblastoma cells. While transcription factors like REST are challenging targets for small-molecule inhibitors, the inactivation of a regulatory protein, small CTD phosphatase 1 (SCP1), promotes REST degradation and reduces transcriptional activity. This study rationally designed a series of α,β-unsaturated sulfones to serve as potent and selective covalent inhibitors against SCP1. The compounds inactivate SCP1 via covalent modification of Cys181 located at the active site entrance. Cellular studies showed that the inhibitors inactivate SCP1 in a time- and dose-dependent manner with an EC50 ∼1.5 μM, reducing REST protein levels and activating specific REST-suppressed genes. These compounds represent a promising line of small-molecule inhibitors as a novel lead for glioblastoma whose growth is driven by REST transcription activity.
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Affiliation(s)
| | | | - Srihari Konduri
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Jiajun Dong
- Department of Medicinal Chemistry and Molecular Pharmacology and Department of Chemistry, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Seema Irani
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Haoyi Wu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Wendy L. Matthews
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology and Department of Chemistry, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Dionico Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Yan Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, United States
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5
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Thielen N, Neefjes M, Wiegertjes R, van den Akker G, Vitters E, van Beuningen H, Blaney Davidson E, Koenders M, van Lent P, van de Loo F, van Caam A, van der Kraan P. Osteoarthritis-Related Inflammation Blocks TGF-β's Protective Effect on Chondrocyte Hypertrophy via (de)Phosphorylation of the SMAD2/3 Linker Region. Int J Mol Sci 2021; 22:ijms22158124. [PMID: 34360888 PMCID: PMC8347103 DOI: 10.3390/ijms22158124] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 01/13/2023] Open
Abstract
Osteoarthritis (OA) is a degenerative joint disease characterized by irreversible cartilage damage, inflammation and altered chondrocyte phenotype. Transforming growth factor-β (TGF-β) signaling via SMAD2/3 is crucial for blocking hypertrophy. The post-translational modifications of these SMAD proteins in the linker domain regulate their function and these can be triggered by inflammation through the activation of kinases or phosphatases. Therefore, we investigated if OA-related inflammation affects TGF-β signaling via SMAD2/3 linker-modifications in chondrocytes. We found that both Interleukin (IL)-1β and OA-synovium conditioned medium negated SMAD2/3 transcriptional activity in chondrocytes. This inhibition of TGF-β signaling was enhanced if SMAD3 could not be phosphorylated on Ser213 in the linker region and the inhibition by IL-1β was less if the SMAD3 linker could not be phosphorylated at Ser204. Our study shows evidence that inflammation inhibits SMAD2/3 signaling in chondrocytes via SMAD linker (de)-phosphorylation. The involvement of linker region modifications may represent a new therapeutic target for OA.
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Affiliation(s)
- Nathalie Thielen
- Department of Experimental Rheumatology, Radboud University Medical Center, 6500 MD Nijmegen, The Netherlands; (N.T.); (M.N.); (R.W.); (E.V.); (H.v.B.); (E.B.D.); (M.K.); (P.v.L.); (F.v.d.L.); (A.v.C.)
| | - Margot Neefjes
- Department of Experimental Rheumatology, Radboud University Medical Center, 6500 MD Nijmegen, The Netherlands; (N.T.); (M.N.); (R.W.); (E.V.); (H.v.B.); (E.B.D.); (M.K.); (P.v.L.); (F.v.d.L.); (A.v.C.)
| | - Renske Wiegertjes
- Department of Experimental Rheumatology, Radboud University Medical Center, 6500 MD Nijmegen, The Netherlands; (N.T.); (M.N.); (R.W.); (E.V.); (H.v.B.); (E.B.D.); (M.K.); (P.v.L.); (F.v.d.L.); (A.v.C.)
| | - Guus van den Akker
- Department of Orthopedic Surgery, Maastricht University, 6200 MD Maastricht, The Netherlands;
| | - Elly Vitters
- Department of Experimental Rheumatology, Radboud University Medical Center, 6500 MD Nijmegen, The Netherlands; (N.T.); (M.N.); (R.W.); (E.V.); (H.v.B.); (E.B.D.); (M.K.); (P.v.L.); (F.v.d.L.); (A.v.C.)
| | - Henk van Beuningen
- Department of Experimental Rheumatology, Radboud University Medical Center, 6500 MD Nijmegen, The Netherlands; (N.T.); (M.N.); (R.W.); (E.V.); (H.v.B.); (E.B.D.); (M.K.); (P.v.L.); (F.v.d.L.); (A.v.C.)
| | - Esmeralda Blaney Davidson
- Department of Experimental Rheumatology, Radboud University Medical Center, 6500 MD Nijmegen, The Netherlands; (N.T.); (M.N.); (R.W.); (E.V.); (H.v.B.); (E.B.D.); (M.K.); (P.v.L.); (F.v.d.L.); (A.v.C.)
| | - Marije Koenders
- Department of Experimental Rheumatology, Radboud University Medical Center, 6500 MD Nijmegen, The Netherlands; (N.T.); (M.N.); (R.W.); (E.V.); (H.v.B.); (E.B.D.); (M.K.); (P.v.L.); (F.v.d.L.); (A.v.C.)
| | - Peter van Lent
- Department of Experimental Rheumatology, Radboud University Medical Center, 6500 MD Nijmegen, The Netherlands; (N.T.); (M.N.); (R.W.); (E.V.); (H.v.B.); (E.B.D.); (M.K.); (P.v.L.); (F.v.d.L.); (A.v.C.)
| | - Fons van de Loo
- Department of Experimental Rheumatology, Radboud University Medical Center, 6500 MD Nijmegen, The Netherlands; (N.T.); (M.N.); (R.W.); (E.V.); (H.v.B.); (E.B.D.); (M.K.); (P.v.L.); (F.v.d.L.); (A.v.C.)
| | - Arjan van Caam
- Department of Experimental Rheumatology, Radboud University Medical Center, 6500 MD Nijmegen, The Netherlands; (N.T.); (M.N.); (R.W.); (E.V.); (H.v.B.); (E.B.D.); (M.K.); (P.v.L.); (F.v.d.L.); (A.v.C.)
| | - Peter van der Kraan
- Department of Experimental Rheumatology, Radboud University Medical Center, 6500 MD Nijmegen, The Netherlands; (N.T.); (M.N.); (R.W.); (E.V.); (H.v.B.); (E.B.D.); (M.K.); (P.v.L.); (F.v.d.L.); (A.v.C.)
- Correspondence:
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6
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Methods for Identification of Substrates/Inhibitors of FCP/SCP Type Protein Ser/Thr Phosphatases. Processes (Basel) 2020. [DOI: 10.3390/pr8121598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Protein phosphorylation is the most widespread type of post-translational modification and is properly controlled by protein kinases and phosphatases. Regarding the phosphorylation of serine (Ser) and threonine (Thr) residues, relatively few protein Ser/Thr phosphatases control the specific dephosphorylation of numerous substrates, in contrast with Ser/Thr kinases. Recently, protein Ser/Thr phosphatases were reported to have rigid substrate recognition and exert various biological functions. Therefore, identification of targeted proteins by individual protein Ser/Thr phosphatases is crucial to clarify their own biological functions. However, to date, information on the development of methods for identification of the substrates of protein Ser/Thr phosphatases remains scarce. In turn, substrate-trapping mutants are powerful tools to search the individual substrates of protein tyrosine (Tyr) phosphatases. This review focuses on the development of novel methods for the identification of Ser/Thr phosphatases, especially small C-terminal domain phosphatase 1 (Scp1), using peptide-displayed phage library with AlF4−/BeF3−, and discusses the identification of putative inhibitors.
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7
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Matsuoka H, Ando K, Swayze EJ, Unan EC, Mathew J, Hu Q, Tsuda Y, Nakashima Y, Saeki H, Oki E, Bharti AK, Mori M. CTDSP1 inhibitor rabeprazole regulates DNA-PKcs dependent topoisomerase I degradation and irinotecan drug resistance in colorectal cancer. PLoS One 2020; 15:e0228002. [PMID: 32764831 PMCID: PMC7413750 DOI: 10.1371/journal.pone.0228002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022] Open
Abstract
Irinotecan specifically targets topoisomerase I (topoI), and is used to treat various solid tumors, but only 13–32% of patients respond to the therapy. Now, it is understood that the rapid rate of topoI degradation in response to irinotecan causes irinotecan resistance. We have published that the deregulated DNA-PKcs kinase cascade ensures rapid degradation of topoI and is at the core of the drug resistance mechanism of topoI inhibitors, including irinotecan. We also identified CTD small phosphatase 1 (CTDSP1) (a nuclear phosphatase) as a primary upstream regulator of DNA-PKcs in response to topoI inhibitors. Previous reports showed that rabeprazole, a proton pump inhibitor (PPI) inhibits CTDSP1 activity. The purpose of this study was to confirm the effects of rabeprazole on CTDSP1 activity and its impact on irinotecan-based therapy in colon cancer. Using differentially expressing CTDSP1 cells, we demonstrated that CTDSP1 contributes to the irinotecan sensitivity by preventing topoI degradation. Retrospective analysis of patients receiving irinotecan with or without rabeprazole has shown the effects of CTDSP1 on irinotecan response. These results indicate that CTDSP1 promotes sensitivity to irinotecan and rabeprazole prevents this effect, resulting in drug resistance. To ensure the best chance at effective treatment, rabeprazole may not be a suitable PPI for cancer patients treated with irinotecan.
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Affiliation(s)
- Hiroya Matsuoka
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka City, Fukuoka, Japan
| | - Koji Ando
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka City, Fukuoka, Japan
- * E-mail:
| | - Emma J. Swayze
- Division of Hematology and Medical Oncology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Elizabeth C. Unan
- Division of Hematology and Medical Oncology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Joseph Mathew
- Division of Hematology and Medical Oncology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Quingjiang Hu
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka City, Fukuoka, Japan
| | - Yasuo Tsuda
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka City, Fukuoka, Japan
| | - Yuichiro Nakashima
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka City, Fukuoka, Japan
| | - Hiroshi Saeki
- Department of General Surgical Science, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka City, Fukuoka, Japan
| | - Ajit K. Bharti
- Division of Hematology and Medical Oncology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Masaki Mori
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka City, Fukuoka, Japan
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8
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Rallabandi HR, Lee D, Sung J, Kim YJ. Peripheral Inhibition of Small C‐Terminal Domain Phosphatase 1 With Napthoquinone Analogs. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Harikrishna Reddy Rallabandi
- Department of Medicinal Biosciences and Nanotechnology Research CenterKonkuk University Chungju 27478 Republic of Korea
| | - Dongsun Lee
- Department of Medicinal Biosciences and Nanotechnology Research CenterKonkuk University Chungju 27478 Republic of Korea
| | - Jinmo Sung
- Department of Medicinal Biosciences and Nanotechnology Research CenterKonkuk University Chungju 27478 Republic of Korea
| | - Young Jun Kim
- Department of Medicinal Biosciences and Nanotechnology Research CenterKonkuk University Chungju 27478 Republic of Korea
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9
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Rallabandi HR, Ganesan P, Kim YJ. Targeting the C-Terminal Domain Small Phosphatase 1. Life (Basel) 2020; 10:life10050057. [PMID: 32397221 PMCID: PMC7281111 DOI: 10.3390/life10050057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
The human C-terminal domain small phosphatase 1 (CTDSP1/SCP1) is a protein phosphatase with a conserved catalytic site of DXDXT/V. CTDSP1’s major activity has been identified as dephosphorylation of the 5th Ser residue of the tandem heptad repeat of the RNA polymerase II C-terminal domain (RNAP II CTD). It is also implicated in various pivotal biological activities, such as acting as a driving factor in repressor element 1 (RE-1)-silencing transcription factor (REST) complex, which silences the neuronal genes in non-neuronal cells, G1/S phase transition, and osteoblast differentiation. Recent findings have denoted that negative regulation of CTDSP1 results in suppression of cancer invasion in neuroglioma cells. Several researchers have focused on the development of regulating materials of CTDSP1, due to the significant roles it has in various biological activities. In this review, we focused on this emerging target and explored the biological significance, challenges, and opportunities in targeting CTDSP1 from a drug designing perspective.
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10
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Identification of a Specific Inhibitor of Human Scp1 Phosphatase Using the Phosphorylation Mimic Phage Display Method. Catalysts 2019. [DOI: 10.3390/catal9100842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Protein phosphatases are divided into tyrosine (Tyr) phosphatases and serine/threonine (Ser/Thr) phosphatases. While substrate trapping mutants are frequently used to identify substrates of Tyr phosphatases, a rapid and simple method to identify Ser/Thr phosphatase substrates is yet to be developed. The TFIIF-associating component of RNA polymerase II C-terminal domain (CTD) phosphatase/small CTD phosphatase (FCP/SCP) phosphatase family is one of the three types of Ser/Thr protein phosphatases. Defects in these phosphatases are correlated with the occurrence of various diseases such as cancer and neuropathy. Recently, we developed phosphorylation mimic phage display (PMPD) method with AlF4−, a methodology to identify substrates for FCP/SCP type Ser/Thr phosphatase Scp1. Here, we report a PMPD method using BeF3− to identify novel substrate peptides bound to Scp1. After screening peptide phages, we identified peptides that bound to Scp1 in a BeF3−-dependent manner. Synthetic phosphopeptide BeM12-1, the sequence of which was isolated at the highest frequency, directly bound to Scp1. The binding was inhibited by adding BeF3−, indicating that the peptide binds to the active center of catalytic site in Scp1. The phosphorylated BeM12-1 worked as a competitive inhibitor of Scp1. Thus, PMPD method may be applicable for the identification of novel substrates and inhibitors of the FCP/SCP phosphatase family.
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11
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Burkholder NT, Mayfield JE, Yu X, Irani S, Arce DK, Jiang F, Matthews WL, Xue Y, Zhang YJ. Phosphatase activity of small C-terminal domain phosphatase 1 (SCP1) controls the stability of the key neuronal regulator RE1-silencing transcription factor (REST). J Biol Chem 2018; 293:16851-16861. [PMID: 30217818 DOI: 10.1074/jbc.ra118.004722] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/20/2018] [Indexed: 02/03/2023] Open
Abstract
The RE1-silencing transcription factor (REST) is the major scaffold protein for assembly of neuronal gene silencing complexes that suppress gene transcription through regulating the surrounding chromatin structure. REST represses neuronal gene expression in stem cells and non-neuronal cells, but it is minimally expressed in neuronal cells to ensure proper neuronal development. Dysregulation of REST function has been implicated in several cancers and neurological diseases. Modulating REST gene silencing is challenging because cellular and developmental differences can affect its activity. We therefore considered the possibility of modulating REST activity through its regulatory proteins. The human small C-terminal domain phosphatase 1 (SCP1) regulates the phosphorylation state of REST at sites that function as REST degradation checkpoints. Using kinetic analysis and direct visualization with X-ray crystallography, we show that SCP1 dephosphorylates two degron phosphosites of REST with a clear preference for phosphoserine 861 (pSer-861). Furthermore, we show that SCP1 stabilizes REST protein levels, which sustains REST's gene silencing function in HEK293 cells. In summary, our findings strongly suggest that REST is a bona fide substrate for SCP1 in vivo and that SCP1 phosphatase activity protects REST against degradation. These observations indicate that targeting REST via its regulatory protein SCP1 can modulate its activity and alter signaling in this essential developmental pathway.
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Affiliation(s)
| | | | - Xiaohua Yu
- the Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and
| | | | | | - Faqin Jiang
- the School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | | | - Yuanchao Xue
- the Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and
| | - Yan Jessie Zhang
- From the Departments of Molecular Biosciences and .,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712
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12
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Sun S, Liu S, Zhang Z, Zeng W, Sun C, Tao T, Lin X, Feng XH. Phosphatase UBLCP1 controls proteasome assembly. Open Biol 2018; 7:rsob.170042. [PMID: 28539385 PMCID: PMC5451543 DOI: 10.1098/rsob.170042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/20/2017] [Indexed: 12/26/2022] Open
Abstract
Ubiquitin-like domain-containing C-terminal domain phosphatase 1 (UBLCP1), an FCP/SCP phosphatase family member, was identified as the first proteasome phosphatase. UBLCP1 binds to proteasome subunit Rpn1 and dephosphorylates the proteasome in vitro. However, it is still unclear which proteasome subunit(s) are the bona fide substrate(s) of UBLCP1 and the precise mechanism for proteasome regulation remains elusive. Here, we show that UBLCP1 selectively binds to the 19S regulatory particle (RP) through its interaction with Rpn1, but not the 20S core particle (CP) or the 26S proteasome holoenzyme. In the RP, UBLCP1 dephosphorylates the subunit Rpt1, impairs its ATPase activity, and consequently disrupts the 26S proteasome assembly, yet it has no effects on the RP assembly from precursor complexes. The Rpn1-binding and phosphatase activities of UBLCP1 are essential for its function on Rpt1 dephosphorylation and proteasome activity both in vivo and in vitro. Our study establishes the essential role of the UBLCP1/Rpn1/Rpt1 complex in regulating proteasome assembly.
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Affiliation(s)
- Shuangwu Sun
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Sisi Liu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Zhengmao Zhang
- Michael E. DeBakey, Department of Surgery, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Wang Zeng
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Chuang Sun
- Michael E. DeBakey, Department of Surgery, Houston, TX, USA
| | - Tao Tao
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Xia Lin
- Michael E. DeBakey, Department of Surgery, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Xin-Hua Feng
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China .,Michael E. DeBakey, Department of Surgery, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
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13
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Morrison LJ, Chai W, Rosenberg JA, Henkelman G, Brodbelt JS. Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry. Phys Chem Chem Phys 2018; 19:20057-20074. [PMID: 28722742 DOI: 10.1039/c7cp04073c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.
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14
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Park H, Lee HS, Ku B, Lee SR, Kim SJ. Two-track virtual screening approach to identify both competitive and allosteric inhibitors of human small C-terminal domain phosphatase 1. J Comput Aided Mol Des 2017; 31:743-753. [PMID: 28653253 DOI: 10.1007/s10822-017-0037-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/20/2017] [Indexed: 11/29/2022]
Abstract
Despite a wealth of persuasive evidence for the involvement of human small C-terminal domain phosphatase 1 (Scp1) in the impairment of neuronal differentiation and in Huntington's disease, small-molecule inhibitors of Scp1 have been rarely reported so far. This study aims to the discovery of both competitive and allosteric Scp1 inhibitors through the two-track virtual screening procedure. By virtue of the improvement of the scoring function by implementing a new molecular solvation energy term and by reoptimizing the atomic charges for the active-site Mg2+ ion cluster, we have been able to identify three allosteric and five competitive Scp1 inhibitors with low-micromolar inhibitory activity. Consistent with the results of kinetic studies on the inhibitory mechanisms, the allosteric inhibitors appear to be accommodated in the peripheral binding pocket through the hydrophobic interactions with the nonpolar residues whereas the competitive ones bind tightly in the active site with a direct coordination to the central Mg2+ ion. Some structural modifications to improve the biochemical potency of the newly identified inhibitors are proposed based on the binding modes estimated with docking simulations.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul, 05006, South Korea.
| | - Hye Seon Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Cheongwon-gu, Cheongju, 28116, South Korea
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea.
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15
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Abstract
Phosphatases play key roles in normal physiology and diseases. Studying phosphatases has been both essential and challenging, and the application of conventional genetic and biochemical methods has led to crucial but still limited understanding of their mechanisms, substrates, and exclusive functions within highly intricate networks. With the advances in technologies such as cellular imaging and molecular and chemical biology in terms of sensitive tools and methods, the phosphatase field has thrived in the past years and has set new insights for cell signaling studies and for therapeutic development. In this review, we give an overview of the existing interdisciplinary tools for phosphatases, give examples on how they have been applied to increase our understanding of these enzymes, and suggest how they-and other tools yet barely used in the phosphatase field-might be adapted to address future questions and challenges.
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Affiliation(s)
- Sara Fahs
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
| | - Pablo Lujan
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
| | - Maja Köhn
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
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16
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Park H, Lee HS, Kim SJ. Virtual Screening with Docking Simulations and Biochemical Evaluation of VHY Phosphatase Inhibitors. Chem Pharm Bull (Tokyo) 2016; 63:807-11. [PMID: 26423037 DOI: 10.1248/cpb.c15-00431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although VH1-related member Y (VHY) phosphatase is responsible for the pathogenesis of neuroinflammatory diseases, no small-molecule inhibitor of VHY has been reported so far. Here we first report eight VHY inhibitors identified from molecular docking-based virtual screening and subsequent enzyme inhibition assays. These inhibitors exhibit good biochemical potencies against VHY, with associated IC50 values ranging from 1 to 9 µM. Because all these inhibitors were also screened in silico for having desirable physicochemical properties as a drug candidate, they deserve further investigation by structure-activity relationship studies to develop new medicines for the treatment of neuroinflammatory diseases. The structural features of VHY-inhibitor interactions relevant to the micromolar-level inhibitory activity are addressed in detail.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University
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17
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Mayfield JE, Burkholder NT, Zhang YJ. Dephosphorylating eukaryotic RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:372-87. [PMID: 26779935 DOI: 10.1016/j.bbapap.2016.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/11/2016] [Accepted: 01/14/2016] [Indexed: 12/20/2022]
Abstract
The phosphorylation state of the C-terminal domain of RNA polymerase II is required for the temporal and spatial recruitment of various factors that mediate transcription and RNA processing throughout the transcriptional cycle. Therefore, changes in CTD phosphorylation by site-specific kinases/phosphatases are critical for the accurate transmission of information during transcription. Unlike kinases, CTD phosphatases have been traditionally neglected as they are thought to act as passive negative regulators that remove all phosphate marks at the conclusion of transcription. This over-simplified view has been disputed in recent years and new data assert the active and regulatory role phosphatases play in transcription. We now know that CTD phosphatases ensure the proper transition between different stages of transcription, balance the distribution of phosphorylation for accurate termination and re-initiation, and prevent inappropriate expression of certain genes. In this review, we focus on the specific roles of CTD phosphatases in regulating transcription. In particular, we emphasize how specificity and timing of dephosphorylation are achieved for these phosphatases and consider the various regulatory factors that affect these dynamics.
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Affiliation(s)
- Joshua E Mayfield
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Nathaniel T Burkholder
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yan Jessie Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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18
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Knobloch G, Jabari N, Stadlbauer S, Schindelin H, Köhn M, Gohla A. Synthesis of hydrolysis-resistant pyridoxal 5′-phosphate analogs and their biochemical and X-ray crystallographic characterization with the pyridoxal phosphatase chronophin. Bioorg Med Chem 2015; 23:2819-27. [DOI: 10.1016/j.bmc.2015.02.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 12/12/2022]
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19
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Panoramic view of a superfamily of phosphatases through substrate profiling. Proc Natl Acad Sci U S A 2015; 112:E1974-83. [PMID: 25848029 DOI: 10.1073/pnas.1423570112] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Large-scale activity profiling of enzyme superfamilies provides information about cellular functions as well as the intrinsic binding capabilities of conserved folds. Herein, the functional space of the ubiquitous haloalkanoate dehalogenase superfamily (HADSF) was revealed by screening a customized substrate library against >200 enzymes from representative prokaryotic species, enabling inferred annotation of ∼35% of the HADSF. An extremely high level of substrate ambiguity was revealed, with the majority of HADSF enzymes using more than five substrates. Substrate profiling allowed assignment of function to previously unannotated enzymes with known structure, uncovered potential new pathways, and identified iso-functional orthologs from evolutionarily distant taxonomic groups. Intriguingly, the HADSF subfamily having the least structural elaboration of the Rossmann fold catalytic domain was the most specific, consistent with the concept that domain insertions drive the evolution of new functions and that the broad specificity observed in HADSF may be a relic of this process.
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20
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He Y, Guo X, Yu ZH, Wu L, Gunawan AM, Zhang Y, Dixon JE, Zhang ZY. A potent and selective inhibitor for the UBLCP1 proteasome phosphatase. Bioorg Med Chem 2015; 23:2798-809. [PMID: 25907364 DOI: 10.1016/j.bmc.2015.03.066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 11/17/2022]
Abstract
The ubiquitin-like domain-containing C-terminal domain phosphatase 1 (UBLCP1) has been implicated as a negative regulator of the proteasome, a key mediator in the ubiquitin-dependent protein degradation. Small molecule inhibitors that block UBLCP1 activity would be valuable as research tools and potential therapeutics for human diseases caused by the cellular accumulation of misfold/damaged proteins. We report a salicylic acid fragment-based library approach aimed at targeting both the phosphatase active site and its adjacent binding pocket for enhanced affinity and selectivity. Screening of the focused libraries led to the identification of the first potent and selective UBLCP1 inhibitor 13. Compound 13 exhibits an IC50 of 1.0μM for UBLCP1 and greater than 5-fold selectivity against a large panel of protein phosphatases from several distinct families. Importantly, the inhibitor possesses efficacious cellular activity and is capable of inhibiting UBLCP1 function in cells, which in turn up-regulates nuclear proteasome activity. These studies set the groundwork for further developing compound 13 into chemical probes or potential therapeutic agents targeting the UBLCP1 phosphatase.
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Affiliation(s)
- Yantao He
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Xing Guo
- Department of Pharmacology, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Zhi-Hong Yu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Li Wu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Andrea M Gunawan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Yan Zhang
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Jack E Dixon
- Department of Pharmacology, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Zhong-Yin Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA.
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21
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Lindh M, Svensson F, Schaal W, Zhang J, Sköld C, Brandt P, Karlén A. Toward a Benchmarking Data Set Able to Evaluate Ligand- and Structure-based Virtual Screening Using Public HTS Data. J Chem Inf Model 2015; 55:343-53. [DOI: 10.1021/ci5005465] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Martin Lindh
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| | - Fredrik Svensson
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| | - Wesley Schaal
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| | - Jin Zhang
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| | - Christian Sköld
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| | - Peter Brandt
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
| | - Anders Karlén
- Organic Pharmaceutical Chemistry,
Department of Medicinal Chemistry, Uppsala University, Biomedical
Centre, Box 574, SE- 751 23 Uppsala, Sweden
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22
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Krueger AB, Drasin DJ, Lea WA, Patrick AN, Patnaik S, Backos DS, Matheson CJ, Hu X, Barnaeva E, Holliday MJ, Blevins MA, Robin TP, Eisenmesser EZ, Ferrer M, Simeonov A, Southall N, Reigan P, Marugan J, Ford HL, Zhao R. Allosteric inhibitors of the Eya2 phosphatase are selective and inhibit Eya2-mediated cell migration. J Biol Chem 2014; 289:16349-61. [PMID: 24755226 DOI: 10.1074/jbc.m114.566729] [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] [Indexed: 11/06/2022] Open
Abstract
Eya proteins are essential co-activators of the Six family of transcription factors and contain a unique tyrosine phosphatase domain belonging to the haloacid dehalogenase family of phosphatases. The phosphatase activity of Eya is important for the transcription of a subset of Six1-target genes, and also directs cells to the repair rather than apoptosis pathway upon DNA damage. Furthermore, Eya phosphatase activity has been shown to mediate transformation, invasion, migration, and metastasis of breast cancer cells, making it a potential new drug target for breast cancer. We have previously identified a class of N-arylidenebenzohydrazide compounds that specifically inhibit the Eya2 phosphatase. Herein, we demonstrate that these compounds are reversible inhibitors that selectively inhibit the phosphatase activity of Eya2, but not Eya3. Our mutagenesis results suggest that this class of compounds does not bind to the active site and the binding does not require the coordination with Mg(2+). Moreover, these compounds likely bind within a site on the opposite face of the active site, and function as allosteric inhibitors. We also demonstrate that this class of compounds inhibits Eya2 phosphatase-mediated cell migration, setting the foundation for these molecules to be developed into chemical probes for understanding the specific function of the Eya2 phosphatase and to serve as a prototype for the development of Eya2 phosphatase specific anti-cancer drugs.
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Affiliation(s)
- Aaron B Krueger
- From the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - David J Drasin
- the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Wendy A Lea
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Aaron N Patrick
- the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Samarjit Patnaik
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Donald S Backos
- the Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, Colorado 80045
| | - Christopher J Matheson
- the Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, Colorado 80045
| | - Xin Hu
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Elena Barnaeva
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Michael J Holliday
- From the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Melanie A Blevins
- From the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Tyler P Robin
- the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Elan Z Eisenmesser
- From the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Marc Ferrer
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Anton Simeonov
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Noel Southall
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Philip Reigan
- the Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, Colorado 80045
| | - Juan Marugan
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Heide L Ford
- the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045,
| | - Rui Zhao
- From the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045,
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23
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Cross-talk of phosphorylation and prolyl isomerization of the C-terminal domain of RNA Polymerase II. Molecules 2014; 19:1481-511. [PMID: 24473209 PMCID: PMC4350670 DOI: 10.3390/molecules19021481] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/06/2014] [Accepted: 01/21/2014] [Indexed: 12/04/2022] Open
Abstract
Post-translational modifications of the heptad repeat sequences in the C-terminal domain (CTD) of RNA polymerase II (Pol II) are well recognized for their roles in coordinating transcription with other nuclear processes that impinge upon transcription by the Pol II machinery; and this is primarily achieved through CTD interactions with the various nuclear factors. The identification of novel modifications on new regulatory sites of the CTD suggests that, instead of an independent action for all modifications on CTD, a combinatorial effect is in operation. In this review we focus on two well-characterized modifications of the CTD, namely serine phosphorylation and prolyl isomerization, and discuss the complex interplay between the enzymes modifying their respective regulatory sites. We summarize the current understanding of how the prolyl isomerization state of the CTD dictates the specificity of writers (CTD kinases), erasers (CTD phosphatases) and readers (CTD binding proteins) and how that correlates to transcription status. Subtle changes in prolyl isomerization states cannot be detected at the primary sequence level, we describe the methods that have been utilized to investigate this mode of regulation. Finally, a general model of how prolyl isomerization regulates the phosphorylation state of CTD, and therefore transcription-coupled processes, is proposed.
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24
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Zhang M, Yogesha SD, Mayfield JE, Gill GN, Zhang Y. Viewing serine/threonine protein phosphatases through the eyes of drug designers. FEBS J 2013; 280:4739-60. [PMID: 23937612 DOI: 10.1111/febs.12481] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 07/03/2013] [Accepted: 08/02/2013] [Indexed: 01/04/2023]
Abstract
Protein phosphatases, as the counterpart to protein kinases, are essential for homeostatic balance of cell signaling. Small chemical compounds that modulate the specific activity of phosphatases can be powerful tools to elucidate the biological functions of these enzymes. More importantly, many phosphatases are central players in the development of pathological pathways where inactivation can reverse or delay the onset of human diseases. Therefore, potent inhibitors for such phosphatases can be of great therapeutic benefit. In contrast to the seemingly identical enzymatic mechanism and structural characterization of eukaryotic protein kinases, protein phosphatases evolved from diverse ancestors, resulting in different domain architectures, reaction mechanisms and active site properties. In this review, we discuss for each family of serine/threonine protein phosphatases their involvement in biological processes and corresponding strategies for small chemical intervention. Recent advances in modern drug discovery technologies have markedly facilitated the identification of selective inhibitors for some members of the phosphatase family. Furthermore, the rapid growth in knowledge about structure-activity relationships related to possible new drug targets has aided the discovery of natural product inhibitors for the phosphatase family. This review summarizes the current state of investigation of the small molecules that regulate the function of serine/threonine phosphatases, the challenges presented and also strategies to overcome these obstacles.
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Affiliation(s)
- Mengmeng Zhang
- Department of Chemistry and Biochemistry, University of Texas at Austin, TX, USA
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25
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Park H, Yu KR, Ku B, Kim BY, Kim SJ. Identification of novel PTPRQ phosphatase inhibitors based on the virtual screening with docking simulations. Theor Biol Med Model 2013; 10:49. [PMID: 23981594 PMCID: PMC3765866 DOI: 10.1186/1742-4682-10-49] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/23/2013] [Indexed: 02/05/2023] Open
Abstract
Protein tyrosine phosphatase receptor type Q (PTPRQ) is an unusual PTP that has intrinsic dephosphorylating activity for various phosphatidyl inositides instead of phospho-tyrosine substrates. Although PTPRQ was known to be involved in the pathogenesis of obesity, no small-molecule inhibitor has been reported so far. Here we report six novel PTPRQ inhibitors identified with computer-aided drug design protocol involving the virtual screening with docking simulations and enzyme inhibition assay. These inhibitors exhibit moderate potencies against PTPRQ with the associated IC50 values ranging from 29 to 86 μM. Because the newly discovered inhibitors were also computationally screened for having desirable physicochemical properties as a drug candidate, they deserve consideration for further development by structure-activity relationship studies to optimize the antiobestic activities. Structural features relevant to the stabilization of the inhibitors in the active site of PTPRQ are addressed in detail.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 98 Kunja-Dong, Kwangjin-Ku, Seoul 143-747, Korea.
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26
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Discovery of novel protein tyrosine phosphatase sigma inhibitors through the virtual screening with modified scoring function. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0713-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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27
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De Munter S, Köhn M, Bollen M. Challenges and opportunities in the development of protein phosphatase-directed therapeutics. ACS Chem Biol 2013; 8:36-45. [PMID: 23214403 DOI: 10.1021/cb300597g] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein phosphatases have both protective and promoting roles in the etiology of diseases. A prominent example is the existence of oncogenic as well as tumor-suppressing protein phosphatases. A few protein phosphatase activity modulators are already applied in therapies. These were however not developed in target-directed approaches, and the recent discovery of phosphatase involvement followed their application in therapy. Nevertheless, these examples demonstrate that small molecules can be generated that modulate the activity of protein phosphatases and are beneficial for the treatment of protein phosphorylation diseases. We describe here strategies for the development of activators and inhibitors of protein phosphatases and clarify some long-standing misconceptions concerning the druggability of these enzymes. Recent developments suggest that it is feasible to design potent and selective protein phosphatase modulators with a therapeutic potential.
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Affiliation(s)
- Sofie De Munter
- Laboratory of Biosignaling & Therapeutics, Department of Cellular and Molecular Medicine, University of Leuven, Leuven, Belgium
| | - Maja Köhn
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg,
Germany
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, Department of Cellular and Molecular Medicine, University of Leuven, Leuven, Belgium
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28
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Park H, Jeon JY, Ryu SE. Virtual Screening and Biochemical Evaluation of Mitogen-activated Protein Kinase Phosphatase 4 Inhibitors. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.11.3772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 728] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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30
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Discovery of potent inhibitors of receptor protein tyrosine phosphatase sigma through the structure-based virtual screening. Bioorg Med Chem Lett 2012; 22:6333-7. [DOI: 10.1016/j.bmcl.2012.08.081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 08/09/2012] [Accepted: 08/22/2012] [Indexed: 11/22/2022]
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31
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Zhang M, Wang XJ, Chen X, Bowman ME, Luo Y, Noel JP, Ellington AD, Etzkorn FA, Zhang Y. Structural and kinetic analysis of prolyl-isomerization/phosphorylation cross-talk in the CTD code. ACS Chem Biol 2012; 7:1462-70. [PMID: 22670809 DOI: 10.1021/cb3000887] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The C-terminal domain (CTD) of eukaryotic RNA polymerase II is an essential regulator for RNA polymerase II-mediated transcription. It is composed of multiple repeats of a consensus sequence Tyr(1)Ser(2)Pro(3)Thr(4)Ser(5)Pro(6)Ser(7). CTD regulation of transcription is mediated by both phosphorylation of the serines and prolyl isomerization of the two prolines. Interestingly, the phosphorylation sites are typically close to prolines, and thus the conformation of the adjacent proline could impact the specificity of the corresponding kinases and phosphatases. Experimental evidence of cross-talk between these two regulatory mechanisms has been elusive. Pin1 is a highly conserved phosphorylation-specific peptidyl-prolyl isomerase (PPIase) that recognizes the phospho-Ser/Thr (pSer/Thr)-Pro motif with CTD as one of its primary substrates in vivo. In the present study, we provide structural snapshots and kinetic evidence that support the concept of cross-talk between prolyl isomerization and phosphorylation. We determined the structures of Pin1 bound with two substrate isosteres that mimic peptides containing pSer/Thr-Pro motifs in cis or trans conformations. The results unequivocally demonstrate the utility of both cis- and trans-locked alkene isosteres as close geometric mimics of peptides bound to a protein target. Building on this result, we identified a specific case in which Pin1 differentially affects the rate of dephosphorylation catalyzed by two phosphatases (Scp1 and Ssu72) that target the same serine residue in the CTD heptad repeat but have different preferences for the isomerization state of the adjacent proline residue. These data exemplify for the first time how modulation of proline isomerization can kinetically impact signal transduction in transcription regulation.
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Affiliation(s)
- Mengmeng Zhang
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Xiaodong J. Wang
- Department of Chemistry, Virginia Tech, MC 0212, Blacksburg, Virginia 24061,
United States
| | - Xi Chen
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Marianne E. Bowman
- Jack Skirball Chemical Biology
and Protein Laboratory, The Salk Institute, 10010 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Yonghua Luo
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Joseph P. Noel
- Jack Skirball Chemical Biology
and Protein Laboratory, The Salk Institute, 10010 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Andrew D. Ellington
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Felicia A. Etzkorn
- Department of Chemistry, Virginia Tech, MC 0212, Blacksburg, Virginia 24061,
United States
| | - Yan Zhang
- Department
of Chemistry and
Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
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Seifried A, Schultz J, Gohla A. Human HAD phosphatases: structure, mechanism, and roles in health and disease. FEBS J 2012; 280:549-71. [PMID: 22607316 DOI: 10.1111/j.1742-4658.2012.08633.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Phosphatases of the haloacid dehalogenase (HAD) superfamily of hydrolases are an ancient and very large class of enzymes that have evolved to dephosphorylate a wide range of low- and high molecular weight substrates with often exquisite specificities. HAD phosphatases constitute approximately one-fifth of all human phosphatase catalytic subunits. While the overall sequence similarity between HAD phosphatases is generally very low, family members can be identified based on the presence of a characteristic Rossmann-like fold and the active site sequence DxDx(V/T). HAD phosphatases employ an aspartate residue as a nucleophile in a magnesium-dependent phosphoaspartyl transferase reaction. Although there is genetic evidence demonstrating a causal involvement of some HAD phosphatases in diseases such as cancer, cardiovascular, metabolic and neurological disorders, the physiological roles of many of these enzymes are still poorly understood. In this review, we discuss the structure and evolution of human HAD phosphatases, and summarize their known functions in health and disease.
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Affiliation(s)
- Annegrit Seifried
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
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UBLCP1 is a 26S proteasome phosphatase that regulates nuclear proteasome activity. Proc Natl Acad Sci U S A 2011; 108:18649-54. [PMID: 21949367 DOI: 10.1073/pnas.1113170108] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Protein degradation by the 26S proteasome is a fundamental process involved in a broad range of cellular activities, yet how proteasome activity is regulated remains poorly understood. We report here that ubiquitin-like domain-containing C-terminal domain phosphatase 1 (UBLCP1) is a 26S proteasome phosphatase that regulates nuclear proteasome activity. UBLCP1 directly interacts with the proteasome via its UBL domain and is exclusively localized in the nucleus. UBLCP1 dephosphorylates the 26S proteasome and inhibits proteasome activity in vitro. Knockdown of UBLCP1 in cells promotes 26S proteasome assembly and selectively enhances nuclear proteasome activity. Our results describe the first identified proteasome-specific phosphatase and uncover a unique mechanism for phosphoregulation of the proteasome.
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