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Gannam ZTK, Jamali H, Kweon OS, Herrington J, Shillingford SR, Papini C, Gentzel E, Lolis E, Bennett AM, Ellman JA, Anderson KS. Defining the structure-activity relationship for a novel class of allosteric MKP5 inhibitors. Eur J Med Chem 2022; 243:114712. [PMID: 36116232 PMCID: PMC9830533 DOI: 10.1016/j.ejmech.2022.114712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 01/13/2023]
Abstract
Mitogen-activated protein kinase (MAPK) phosphatase 5 (MKP5) is responsible for regulating the activity of the stress-responsive MAPKs and has been put forth as a potential therapeutic target for a number of diseases, including dystrophic muscle disease a fatal rare disease which has neither a treatment nor cure. In previous work, we identified Compound 1 (3,3-dimethyl-1-((9-(methylthio)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl)thio)butan-2-one) as the lead compound of a novel class of MKP5 inhibitors. In this work, we explore the structure-activity relationship for inhibition of MKP5 through modifications to the scaffold and functional groups present in 1. A series of derivative compounds was designed, synthesized, and evaluated for inhibition of MKP5. In addition, the X-ray crystal structures of six enzyme-inhibitor complexes were solved, further elucidating the necessary requirements for MKP5 inhibition. We found that the parallel-displaced π-π interaction between the inhibitor three-ring core and Tyr435 is critical for modulating potency, and that modifications to the core and functionalization at the C-9 position are essential for ensuring proper positioning of the core for this interaction. These results lay the foundation from which more potent MKP5 allosteric inhibitors can be developed for potential therapeutics towards the treatment of dystrophic muscle disease.
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Affiliation(s)
- Zira T K Gannam
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Haya Jamali
- Department of Chemistry, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Oh Sang Kweon
- Department of Chemistry, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - James Herrington
- Yale Center for Molecular Discovery, Yale University School of Medicine, New Haven, CT, 06520, USA
| | | | - Christina Papini
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Erik Gentzel
- Department of Chemistry, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Elias Lolis
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Anton M Bennett
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA; Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Jonathan A Ellman
- Department of Chemistry, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06520, USA.
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Saburina IN, Kosheleva NV, Kopylov AT, Lipina TV, Krasina ME, Zurina IM, Gorkun AA, Girina SS, Pulin AA, Kaysheva AL, Morozov SG. Proteomic and electron microscopy study of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells in three-dimensional culture. Proteomics 2021; 22:e2000304. [PMID: 34674377 DOI: 10.1002/pmic.202000304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 08/24/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022]
Abstract
Myocyte differentiation is featured by adaptation processes, including mitochondria repopulation and cytoskeleton re-organization. The difference between monolayer and spheroid cultured cells at the proteomic level is uncertain. We cultivated alveolar mucosa multipotent mesenchymal stromal cells in spheroids in a myogenic way for the proper conditioning of ECM architecture and cell morphology, which induced spontaneous myogenic differentiation of cells within spheroids. Electron microscopy analysis was used for the morphometry of mitochondria biogenesis, and proteomic was used complementary to unveil events underlying differences between two-dimensional/three-dimensional myoblasts differentiation. The prevalence of elongated mitochondria with an average area of 0.097 μm2 was attributed to monolayer cells 7 days after the passage. The population of small mitochondria with a round shape and area of 0.049 μm2 (p < 0.05) was observed in spheroid cells cultured under three-dimensional conditions. Cells in spheroids were quantitatively enriched in proteins of mitochondria biogenesis (DNM1L, IDH2, SSBP1), respiratory chain (ACO2, ATP5I, COX5A), extracellular proteins (COL12A1, COL6A1, COL6A2), and cytoskeleton (MYL6, MYL12B, MYH10). Most of the Rab-related transducers were inhibited in spheroid culture. The proteomic assay demonstrated delicate mechanisms of mitochondria autophagy and repopulation, cytoskeleton assembling, and biogenesis. Differences in the ultrastructure of mitochondria indicate active biogenesis under three-dimensional conditions.
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Affiliation(s)
- Irina N Saburina
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation
| | - Nastasia V Kosheleva
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation.,Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation.,World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov University, Moscow, Russia
| | - Arthur T Kopylov
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation.,World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov University, Moscow, Russia.,Department of Proteomic Research, Institute of Biomedical Chemistry, Moscow, Russian Federation
| | - Tatiana V Lipina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Marina E Krasina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Irina M Zurina
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation.,Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Anastasiya A Gorkun
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation.,Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Svetlana S Girina
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation
| | - Andrey A Pulin
- Pirogov National Medical Surgical Center, Moscow, Russian Federation
| | - Anna L Kaysheva
- Department of Proteomic Research, Institute of Biomedical Chemistry, Moscow, Russian Federation
| | - Sergey G Morozov
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation
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Affinity capture in bottom-up protein analysis - Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers. Anal Chim Acta 2021; 1182:338714. [PMID: 34602193 DOI: 10.1016/j.aca.2021.338714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022]
Abstract
Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.
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Seternes OM, Kidger AM, Keyse SM. Dual-specificity MAP kinase phosphatases in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:124-143. [PMID: 30401534 PMCID: PMC6227380 DOI: 10.1016/j.bbamcr.2018.09.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/15/2018] [Accepted: 09/06/2018] [Indexed: 02/07/2023]
Abstract
It is well established that a family of dual-specificity MAP kinase phosphatases (MKPs) play key roles in the regulated dephosphorylation and inactivation of MAP kinase isoforms in mammalian cells and tissues. MKPs provide a mechanism of spatiotemporal feedback control of these key signalling pathways, but can also mediate crosstalk between distinct MAP kinase cascades and facilitate interactions between MAP kinase pathways and other key signalling modules. As our knowledge of the regulation, substrate specificity and catalytic mechanisms of MKPs has matured, more recent work using genetic models has revealed key physiological functions for MKPs and also uncovered potentially important roles in regulating the pathophysiological outcome of signalling with relevance to human diseases. These include cancer, diabetes, inflammatory and neurodegenerative disorders. It is hoped that this understanding will reveal novel therapeutic targets and biomarkers for disease, thus contributing to more effective diagnosis and treatment for these debilitating and often fatal conditions. A comprehensive review of the dual-specificity MAP kinase Phosphatases (MKPs) Focus is on MKPs in the regulation of MAPK signalling in health and disease. Covers roles of MKPs in inflammation, obesity/diabetes, cancer and neurodegeneration
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Affiliation(s)
- Ole-Morten Seternes
- Department of Pharmacy, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Andrew M Kidger
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, England, UK.
| | - Stephen M Keyse
- Stress Response Laboratory, Jacqui Wood Cancer Centre, James Arrot Drive, Ninewells Hospital & Medical School, Dundee DD1 9SY, UK.
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Min K, Lawan A, Bennett AM. Loss of MKP-5 promotes myofiber survival by activating STAT3/Bcl-2 signaling during regenerative myogenesis. Skelet Muscle 2017; 7:21. [PMID: 29047406 PMCID: PMC5648478 DOI: 10.1186/s13395-017-0137-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/25/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The mitogen-activated protein kinases (MAPKs) have been shown to be involved in regulating myofiber survival. In skeletal muscle, p38 MAPK and JNK are negatively regulated by MAPK phosphatase-5 (MKP-5). During muscle regeneration, MKP-5 is downregulated, thereby promoting p38 MAPK/JNK signaling, and subsequent repair of damaged muscle. Mice lacking MKP-5 expression exhibit enhanced regenerative myogenesis. However, the effect of MKP-5 on myofiber survival during regeneration is unclear. METHODS To investigate whether MKP-5 is involved in myofiber survival, skeletal muscle injury was induced by cardiotoxin injection, and the effects on apoptosis were assessed by TUNEL assay in wild type and MKP-5-deficient mice. The contribution of MKP-5 to apoptotic signaling and its link to this pathway through mitochondrial function were determined in regenerating skeletal muscle of MKP-5-deficient mice. RESULTS We found that loss of MKP-5 in skeletal muscle resulted in improved myofiber survival. In response to skeletal muscle injury, loss of MKP-5 decreased activation of the mitochondrial apoptotic pathway involving the signal transducer and activator of transcription 3 (STAT3) and increased expression of the anti-apoptotic transcription factor Bcl-2. Skeletal muscle of MKP-5-deficient mice also exhibited an improved anti-oxidant capacity as a result of increased expression of catalase further contributing to myofiber survival by attenuating oxidative damage. CONCLUSIONS Taken together, these findings suggest that MKP-5 coordinates skeletal muscle regeneration by regulating mitochondria-mediated apoptosis. MKP-5 negatively regulates apoptotic signaling, and during regeneration, MKP-5 downregulation contributes to the restoration of myofiber survival. Finally, these results suggest that MKP-5 inhibition may serve as an important therapeutic target for the preservation of skeletal muscle survival in degenerative muscle diseases.
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Affiliation(s)
- Kisuk Min
- Department of Pharmacology, Yale University, New Haven, CT, 06520, USA
| | - Ahmed Lawan
- Department of Pharmacology, Yale University, New Haven, CT, 06520, USA
| | - Anton M Bennett
- Department of Pharmacology, Yale University, New Haven, CT, 06520, USA. .,Program in Integrative Cell Signaling and Neurobiology of Metabolism, Yale University, New Haven, CT, 06520, USA.
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