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Ahanin EF, Sager RA, Backe SJ, Dunn DM, Dushukyan N, Blanden AR, Mate NA, Suzuki T, Anderson T, Roy M, Oberoi J, Prodromou C, Nsouli I, Daneshvar M, Bratslavsky G, Woodford MR, Bourboulia D, Chisholm JD, Mollapour M. Catalytic inhibitor of Protein Phosphatase 5 activates the extrinsic apoptotic pathway by disrupting complex II in kidney cancer. Cell Chem Biol 2023; 30:1223-1234.e12. [PMID: 37527661 PMCID: PMC10592443 DOI: 10.1016/j.chembiol.2023.06.026] [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: 03/08/2023] [Revised: 05/11/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023]
Abstract
Serine/threonine protein phosphatase-5 (PP5) is involved in tumor progression and survival, making it an attractive therapeutic target. Specific inhibition of protein phosphatases has remained challenging because of their conserved catalytic sites. PP5 contains its regulatory domains within a single polypeptide chain, making it a more desirable target. Here we used an in silico approach to screen and develop a selective inhibitor of PP5. Compound P053 is a competitive inhibitor of PP5 that binds to its catalytic domain and causes apoptosis in renal cancer. We further demonstrated that PP5 interacts with FADD, RIPK1, and caspase 8, components of the extrinsic apoptotic pathway complex II. Specifically, PP5 dephosphorylates and inactivates the death effector protein FADD, preserving complex II integrity and regulating extrinsic apoptosis. Our data suggests that PP5 promotes renal cancer survival by suppressing the extrinsic apoptotic pathway. Pharmacologic inhibition of PP5 activates this pathway, presenting a viable therapeutic strategy for renal cancer.
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Affiliation(s)
- Elham F Ahanin
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Rebecca A Sager
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Diana M Dunn
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Natela Dushukyan
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Adam R Blanden
- Department of Neurology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Nilamber A Mate
- Department of Chemistry, Syracuse University, Syracuse, NY 13210, USA
| | - Tamie Suzuki
- Department of Chemistry, Syracuse University, Syracuse, NY 13210, USA
| | - Tyler Anderson
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; College of Health Professions, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Merin Roy
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Jasmeen Oberoi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Chrisostomos Prodromou
- School of Life Sciences, Biochemistry and Biomedicine, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Imad Nsouli
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Michael Daneshvar
- Department of Urology, University of California, California, Irvine, CA 92868, USA
| | - Gennady Bratslavsky
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
| | - John D Chisholm
- Department of Chemistry, Syracuse University, Syracuse, NY 13210, USA.
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
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2
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Shuhaibar LC, Kaci N, Egbert JR, Horville T, Loisay L, Vigone G, Uliasz TF, Dambroise E, Swingle MR, Honkanen RE, Biosse Duplan M, Jaffe LA, Legeai-Mallet L. Phosphatase inhibition by LB-100 enhances BMN-111 stimulation of bone growth. JCI Insight 2021; 6:141426. [PMID: 33986191 PMCID: PMC8262325 DOI: 10.1172/jci.insight.141426] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/25/2021] [Indexed: 12/16/2022] Open
Abstract
Activating mutations in fibroblast growth factor receptor 3 (FGFR3) and inactivating mutations in the natriuretic peptide receptor 2 (NPR2) guanylyl cyclase both result in decreased production of cyclic GMP in chondrocytes and severe short stature, causing achondroplasia (ACH) and acromesomelic dysplasia, type Maroteaux, respectively. Previously, we showed that an NPR2 agonist BMN-111 (vosoritide) increases bone growth in mice mimicking ACH (Fgfr3Y367C/+). Here, because FGFR3 signaling decreases NPR2 activity by dephosphorylating the NPR2 protein, we tested whether a phosphatase inhibitor (LB-100) could enhance BMN-111–stimulated bone growth in ACH. Measurements of cGMP production in chondrocytes of living tibias, and of NPR2 phosphorylation in primary chondrocytes, showed that LB-100 counteracted FGF-induced dephosphorylation and inactivation of NPR2. In ex vivo experiments with Fgfr3Y367C/+ mice, the combination of BMN-111 and LB-100 increased bone length and cartilage area, restored chondrocyte terminal differentiation, and increased the proliferative growth plate area, more than BMN-111 alone. The combination treatment also reduced the abnormal elevation of MAP kinase activity in the growth plate of Fgfr3Y367C/+ mice and improved the skull base anomalies. Our results provide a proof of concept that a phosphatase inhibitor could be used together with an NPR2 agonist to enhance cGMP production as a therapy for ACH.
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Affiliation(s)
- Leia C Shuhaibar
- Department of Cell Biology, University of Connecticut Health Center, Farmington Connecticut, USA
| | - Nabil Kaci
- Université de Paris, Imagine Institute, Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, F‑75015, Paris, France.,Inovarion, F-75005 Paris, France
| | - Jeremy R Egbert
- Department of Cell Biology, University of Connecticut Health Center, Farmington Connecticut, USA
| | - Thibault Horville
- Université de Paris, Imagine Institute, Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, F‑75015, Paris, France
| | - Léa Loisay
- Université de Paris, Imagine Institute, Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, F‑75015, Paris, France
| | - Giulia Vigone
- Department of Cell Biology, University of Connecticut Health Center, Farmington Connecticut, USA
| | - Tracy F Uliasz
- Department of Cell Biology, University of Connecticut Health Center, Farmington Connecticut, USA
| | - Emilie Dambroise
- Université de Paris, Imagine Institute, Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, F‑75015, Paris, France
| | - Mark R Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile Alabama, USA
| | - Richard E Honkanen
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile Alabama, USA
| | - Martin Biosse Duplan
- Université de Paris, Imagine Institute, Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, F‑75015, Paris, France.,Service de Médecine Bucco-Dentaire, Hôpital Bretonneau, AP-HP, Paris, France
| | - Laurinda A Jaffe
- Department of Cell Biology, University of Connecticut Health Center, Farmington Connecticut, USA
| | - Laurence Legeai-Mallet
- Université de Paris, Imagine Institute, Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, F‑75015, Paris, France
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3
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Papke CM, Smolen KA, Swingle MR, Cressey L, Heng RA, Toporsian M, Deng L, Hagen J, Shen Y, Chung WK, Kettenbach AN, Honkanen RE. A disorder-related variant (E420K) of a PP2A-regulatory subunit (PPP2R5D) causes constitutively active AKT-mTOR signaling and uncoordinated cell growth. J Biol Chem 2021; 296:100313. [PMID: 33482199 PMCID: PMC7952134 DOI: 10.1016/j.jbc.2021.100313] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 02/08/2023] Open
Abstract
Functional genomic approaches have facilitated the discovery of rare genetic disorders and improved efforts to decipher their underlying etiology. PPP2R5D-related disorder is an early childhood onset condition characterized by intellectual disability, hypotonia, autism-spectrum disorder, macrocephaly, and dysmorphic features. The disorder is caused by de novo single nucleotide changes in PPP2R5D, which generate heterozygous dominant missense variants. PPP2R5D is known to encode a B'-type (B'56δ) regulatory subunit of a PP2A-serine/threonine phosphatase. To help elucidate the molecular mechanisms altered in PPP2R5D-related disorder, we used a CRISPR-single-base editor to generate HEK-293 cells in which a single transition (c.1258G>A) was introduced into one allele, precisely recapitulating a clinically relevant E420K variant. Unbiased quantitative proteomic and phosphoproteomic analyses of endogenously expressed proteins revealed heterozygous-dominant changes in kinase/phosphatase signaling. These data combined with orthogonal validation studies revealed a previously unrecognized interaction of PPP2R5D with AKT in human cells, leading to constitutively active AKT-mTOR signaling, increased cell size, and uncoordinated cellular growth in E420K-variant cells. Rapamycin reduced cell size and dose-dependently reduced RPS6 phosphorylation in E420K-variant cells, suggesting that inhibition of mTOR1 can suppress both the observed RPS6 hyperphosphorylation and increased cell size. Together, our findings provide a deeper understanding of PPP2R5D and insight into how the E420K-variant alters signaling networks influenced by PPP2R5D. Our comprehensive approach, which combines precise genome editing, isobaric tandem mass tag labeling of peptides generated from endogenously expressed proteins, and concurrent liquid chromatography-mass spectrometry (LC-MS3), also provides a roadmap that can be used to rapidly explore the etiologies of additional genetic disorders.
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Affiliation(s)
- Cinta M Papke
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Kali A Smolen
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Mark R Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Lauren Cressey
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Richard A Heng
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Mourad Toporsian
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Liyong Deng
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Jacob Hagen
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA; Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA.
| | - Richard E Honkanen
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA.
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Sager RA, Dushukyan N, Woodford M, Mollapour M. Structure and function of the co-chaperone protein phosphatase 5 in cancer. Cell Stress Chaperones 2020; 25:383-394. [PMID: 32239474 PMCID: PMC7193036 DOI: 10.1007/s12192-020-01091-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/04/2020] [Accepted: 03/12/2020] [Indexed: 12/12/2022] Open
Abstract
Protein phosphatase 5 (PP5) is a serine/threonine protein phosphatase that regulates many cellular functions including steroid hormone signaling, stress response, proliferation, apoptosis, and DNA repair. PP5 is also a co-chaperone of the heat shock protein 90 molecular chaperone machinery that assists in regulation of cellular signaling pathways essential for cell survival and growth. PP5 plays a significant role in survival and propagation of multiple cancers, which makes it a promising target for cancer therapy. Though there are several naturally occurring PP5 inhibitors, none is specific for PP5. Here, we review the roles of PP5 in cancer progression and survival and discuss the unique features of the PP5 structure that differentiate it from other phosphoprotein phosphatase (PPP) family members and make it an attractive therapeutic target.
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Affiliation(s)
- Rebecca A Sager
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- College of Medicine, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Natela Dushukyan
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Mark Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
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5
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Clausse V, Tao D, Debnath S, Fang Y, Tagad HD, Wang Y, Sun H, LeClair CA, Mazur SJ, Lane K, Shi ZD, Vasalatiy O, Eells R, Baker LK, Henderson MJ, Webb MR, Shen M, Hall MD, Appella E, Appella DH, Coussens NP. Physiologically relevant orthogonal assays for the discovery of small-molecule modulators of WIP1 phosphatase in high-throughput screens. J Biol Chem 2019; 294:17654-17668. [PMID: 31481464 PMCID: PMC6873202 DOI: 10.1074/jbc.ra119.010201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/30/2019] [Indexed: 01/07/2023] Open
Abstract
WT P53-Induced Phosphatase 1 (WIP1) is a member of the magnesium-dependent serine/threonine protein phosphatase (PPM) family and is induced by P53 in response to DNA damage. In several human cancers, the WIP1 protein is overexpressed, which is generally associated with a worse prognosis. Although WIP1 is an attractive therapeutic target, no potent, selective, and bioactive small-molecule modulator with favorable pharmacokinetics has been reported. Phosphatase enzymes are among the most challenging targets for small molecules because of the difficulty of achieving both modulator selectivity and bioavailability. Another major obstacle has been the availability of robust and physiologically relevant phosphatase assays that are suitable for high-throughput screening. Here, we describe orthogonal biochemical WIP1 activity assays that utilize phosphopeptides from native WIP1 substrates. We optimized an MS assay to quantify the enzymatically dephosphorylated peptide reaction product in a 384-well format. Additionally, a red-shifted fluorescence assay was optimized in a 1,536-well format to enable real-time WIP1 activity measurements through the detection of the orthogonal reaction product, Pi. We validated these two optimized assays by quantitative high-throughput screening against the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection and used secondary assays to confirm and evaluate inhibitors identified in the primary screen. Five inhibitors were further tested with an orthogonal WIP1 activity assay and surface plasmon resonance binding studies. Our results validate the application of miniaturized physiologically relevant and orthogonal WIP1 activity assays to discover small-molecule modulators from high-throughput screens.
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Affiliation(s)
- Victor Clausse
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Subrata Debnath
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Harichandra D Tagad
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Hongmao Sun
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Sharlyn J Mazur
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Kelly Lane
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Zhen-Dan Shi
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Olga Vasalatiy
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Rebecca Eells
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Lynn K Baker
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Martin R Webb
- Francis Crick Institute, 1 Midland Road, London NW1 AT, United Kingdom
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Ettore Appella
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Nathan P Coussens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
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6
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Swingle MR, Honkanen RE. Inhibitors of Serine/Threonine Protein Phosphatases: Biochemical and Structural Studies Provide Insight for Further Development. Curr Med Chem 2019; 26:2634-2660. [PMID: 29737249 PMCID: PMC10013172 DOI: 10.2174/0929867325666180508095242] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/05/2018] [Accepted: 03/29/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND The reversible phosphorylation of proteins regulates many key functions in eukaryotic cells. Phosphorylation is catalyzed by protein kinases, with the majority of phosphorylation occurring on side chains of serine and threonine residues. The phosphomonoesters generated by protein kinases are hydrolyzed by protein phosphatases. In the absence of a phosphatase, the half-time for the hydrolysis of alkyl phosphate dianions at 25º C is over 1 trillion years; knon ~2 x 10-20 sec-1. Therefore, ser/thr phosphatases are critical for processes controlled by reversible phosphorylation. METHODS This review is based on the literature searched in available databases. We compare the catalytic mechanism of PPP-family phosphatases (PPPases) and the interactions of inhibitors that target these enzymes. RESULTS PPPases are metal-dependent hydrolases that enhance the rate of hydrolysis ([kcat/kM]/knon ) by a factor of ~1021, placing them among the most powerful known catalysts on earth. Biochemical and structural studies indicate that the remarkable catalytic proficiencies of PPPases are achieved by 10 conserved amino acids, DXH(X)~26DXXDR(X)~20- 26NH(X)~50H(X)~25-45R(X)~30-40H. Six act as metal-coordinating residues. Four position and orient the substrate phosphate. Together, two metal ions and the 10 catalytic residues position the phosphoryl group and an activated bridging water/hydroxide nucleophile for an inline attack upon the substrate phosphorous atom. The PPPases are conserved among species, and many structurally diverse natural toxins co-evolved to target these enzymes. CONCLUSION Although the catalytic site is conserved, opportunities for the development of selective inhibitors of this important group of metalloenzymes exist.
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Affiliation(s)
- Mark R Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile AL 36688, United States
| | - Richard E Honkanen
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile AL 36688, United States
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7
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Hong TJ, Park K, Choi EW, Hahn JS. Ro 90-7501 inhibits PP5 through a novel, TPR-dependent mechanism. Biochem Biophys Res Commun 2017; 482:215-220. [DOI: 10.1016/j.bbrc.2016.11.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 11/08/2016] [Indexed: 01/03/2023]
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8
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Swingle M, Volmar CH, Saldanha SA, Chase P, Eberhart C, Salter EA, D'Arcy B, Schroeder CE, Golden JE, Wierzbicki A, Hodder P, Honkanen RE. An Ultra-High-Throughput Screen for Catalytic Inhibitors of Serine/Threonine Protein Phosphatases Types 1 and 5 (PP1C and PP5C). SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2017; 22:21-31. [PMID: 27628691 PMCID: PMC8041090 DOI: 10.1177/1087057116668852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Although there has been substantial success in the development of specific inhibitors for protein kinases, little progress has been made in the identification of specific inhibitors for their protein phosphatase counterparts. Inhibitors of PP1 and PP5 are desired as probes for research and to test their potential for drug development. We developed and miniaturized (1536-well plate format) nearly identical homogeneous, fluorescence intensity (FLINT) enzymatic assays to detect inhibitors of PP1 or PP5. The assays were used in an ultra-high-throughput screening (uHTS) campaign, testing >315,000 small-molecule compounds. Both assays demonstrated robust performance, with a Z' of 0.92 ± 0.03 and 0.95 ± 0.01 for the PP1 and PP5 assays, respectively. Screening the same library with both assays aided the identification of class inhibitors and assay artifacts. Confirmation screening and hit prioritization assays used [32P/33P]-radiolabel protein substrates, revealing excellent agreement between the FLINT and radiolabel assays. This screening campaign led to the discovery of four novel unrelated small-molecule inhibitors of PP1 and ~30 related small-molecule inhibitors of PP5. The results suggest that this uHTS approach is suitable for identifying selective chemical probes that inhibit PP1 or PP5 activity, and it is likely that similar assays can be developed for other PPP-family phosphatases.
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Affiliation(s)
| | - Claude-Henry Volmar
- 2 Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
- 3 Center for Therapeutic Innovation and Department of Psychiatry, University of Miami Miller School of Medicine, Miami, FL, USA
| | - S Adrian Saldanha
- 2 Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
- 4 Forma Therapeutics, Watertown, MA, USA
| | - Peter Chase
- 2 Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
- 5 BMS, Lawrenceville, NJ, USA
| | - Christina Eberhart
- 2 Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
| | | | | | - Chad E Schroeder
- 6 University of Kansas Specialized Chemistry Center, Lawrence, KS, USA
| | - Jennifer E Golden
- 6 University of Kansas Specialized Chemistry Center, Lawrence, KS, USA
| | | | - Peter Hodder
- 2 Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
- 7 Amgen, Thousand Oaks, CA, USA
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9
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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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10
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Chattopadhyay D, Swingle MR, Salter EA, Wood E, D'Arcy B, Zivanov C, Abney K, Musiyenko A, Rusin SF, Kettenbach A, Yet L, Schroeder CE, Golden JE, Dunham WH, Gingras AC, Banerjee S, Forbes D, Wierzbicki A, Honkanen RE. Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C. Biochem Pharmacol 2016; 109:14-26. [PMID: 27002182 DOI: 10.1016/j.bcp.2016.03.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/15/2016] [Indexed: 12/24/2022]
Abstract
Cantharidin is a natural toxin and an active constituent in a traditional Chinese medicine used to treat tumors. Cantharidin acts as a semi-selective inhibitor of PPP-family ser/thr protein phosphatases. Despite sharing a common catalytic mechanism and marked structural similarity with PP1C, PP2AC and PP5C, human PP4C was found to be insensitive to the inhibitory activity of cantharidin. To explore the molecular basis for this selectivity, we synthesized and tested novel C5/C6-derivatives designed from quantum-based modeling of the interactions revealed in the co-crystal structures of PP5C in complex with cantharidin. Structure-activity relationship studies and analysis of high-resolution (1.25Å) PP5C-inhibitor co-crystal structures reveal close contacts between the inhibitor bridgehead oxygen and both a catalytic metal ion and a non-catalytic phenylalanine residue, the latter of which is substituted by tryptophan in PP4C. Quantum chemistry calculations predicted that steric clashes with the bulkier tryptophan side chain in PP4C would force all cantharidin-based inhibitors into an unfavorable binding mode, disrupting the strong coordination of active site metal ions observed in the PP5C co-crystal structures, thereby rendering PP4C insensitive to the inhibitors. This prediction was confirmed by inhibition studies employing native human PP4C. Mutation of PP5C (F446W) and PP1C (F257W), to mimic the PP4C active site, resulted in markedly suppressed sensitivity to cantharidin. These observations provide insight into the structural basis for the natural selectivity of cantharidin and provide an avenue for PP4C deselection. The novel crystal structures also provide insight into interactions that provide increased selectivity of the C5/C6 modifications for PP5C versus other PPP-family phosphatases.
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Affiliation(s)
| | - Mark R Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Edward A Salter
- Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA
| | - Eric Wood
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA; Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA
| | - Brandon D'Arcy
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Catherine Zivanov
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA; Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA
| | - Kevin Abney
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Alla Musiyenko
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Scott F Rusin
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Arminja Kettenbach
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Larry Yet
- Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA
| | - Chad E Schroeder
- Department of Medicinal Chemistry, University of Kansas Specialized Chemistry Center, Lawrence, KS 66047, USA
| | - Jennifer E Golden
- Department of Medicinal Chemistry, University of Kansas Specialized Chemistry Center, Lawrence, KS 66047, USA
| | - Wade H Dunham
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Anne-Claude Gingras
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Surajit Banerjee
- Northeastern Collaborative Access Team (NE-CAT) Cornell University, Lemont, IL, USA
| | - David Forbes
- Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA
| | - Andrzej Wierzbicki
- Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA
| | - Richard E Honkanen
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA.
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Klumpp M. Non-stoichiometric inhibition in integrated lead finding - a literature review. Expert Opin Drug Discov 2015; 11:149-62. [PMID: 26653534 DOI: 10.1517/17460441.2016.1128892] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Non-stoichiometric inhibition summarizes different mechanisms by which low-molecular weight compounds can reproducibly inhibit high-throughput screening (HTS) and other lead finding assays without binding to a structurally defined site on their molecular target. This disqualifies such molecules from optimization by medicinal chemistry, and therefore their rapid elimination from screening hit lists is essential for productive and effective drug discovery. AREAS COVERED This review covers recent literature that either investigates the various mechanisms behind non-stoichiometric inhibition or suggests assays and readouts to identify them. In addition, combination of the various methods to distill promising molecules out of raw primary hit lists step-by-step is considered. Emerging technologies to demonstrate target engagement in cells are also discussed. EXPERT OPINION Over the last few years, awareness of non-stoichiometric inhibitors within screening libraries and HTS hit lists has considerably increased, not only in the pharmaceutical industry but also in the academic drug discovery community. This has resulted in a variety of methods to detect and handle such compounds. These range from in silico approaches to flag suspicious compounds, and counterassays to measure non-stoichiometric inhibition, to biophysical methods that positively demonstrate stoichiometric binding. In addition, novel technologies to verify target engagement within cells are becoming available. While still a time- and resource-consuming nuisance, non-stoichiometric inhibitors therefore do not fundamentally jeopardize the discovery of low molecular weight lead and drug candidates. Rather, they should be viewed as a manageable issue that with appropriate expertise can be overcome through integration of the above-mentioned approaches.
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Affiliation(s)
- Martin Klumpp
- a Novartis Institute of Biomedical Research Basel, Novartis Pharma AG , Basel , Switzerland
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