1
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Torres Robles J, Lou HJ, Shi G, Pan PL, Turk BE. Linear motif specificity in signaling through p38α and ERK2 mitogen-activated protein kinases. Proc Natl Acad Sci U S A 2023; 120:e2316599120. [PMID: 37988460 PMCID: PMC10691213 DOI: 10.1073/pnas.2316599120] [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: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades are essential for eukaryotic cells to integrate and respond to diverse stimuli. Maintaining specificity in signaling through MAPK networks is key to coupling distinct inputs to appropriate cellular responses. Docking sites-short linear motifs found in MAPK substrates, regulators, and scaffolds-can promote signaling specificity through selective interactions, but how they do so remains unresolved. Here, we screened a proteomic library for sequences interacting with the MAPKs extracellular signal-regulated kinase 2 (ERK2) and p38α, identifying selective and promiscuous docking motifs. Sequences specific for p38α had high net charge and lysine content, and selective binding depended on a pair of acidic residues unique to the p38α docking interface. Finally, we validated a set of full-length proteins harboring docking sites selected in our screens to be authentic MAPK interactors and substrates. This study identifies features that help define MAPK signaling networks and explains how specific docking motifs promote signaling integrity.
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Affiliation(s)
- Jaylissa Torres Robles
- Department of Chemistry, Yale University, New Haven, CT06520
- Department of Pharmacology, Yale School of Medicine, New Haven, CT06520
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT06520
| | - Guangda Shi
- Department of Pharmacology, Yale School of Medicine, New Haven, CT06520
| | | | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT06520
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2
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Postiglione AE, Adams LL, Ekhator ES, Odelade AE, Patwardhan S, Chaudhari M, Pardue AS, Kumari A, LeFever WA, Tornow OP, Kaoud TS, Neiswinger J, Jeong JS, Parsonage D, Nelson KJ, Kc DB, Furdui CM, Zhu H, Wommack AJ, Dalby KN, Dong M, Poole LB, Keyes JD, Newman RH. Hydrogen peroxide-dependent oxidation of ERK2 within its D-recruitment site alters its substrate selection. iScience 2023; 26:107817. [PMID: 37744034 PMCID: PMC10514464 DOI: 10.1016/j.isci.2023.107817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/11/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Extracellular signal-regulated kinases 1 and 2 (ERK1/2) are dysregulated in many pervasive diseases. Recently, we discovered that ERK1/2 is oxidized by signal-generated hydrogen peroxide in various cell types. Since the putative sites of oxidation lie within or near ERK1/2's ligand-binding surfaces, we investigated how oxidation of ERK2 regulates interactions with the model substrates Sub-D and Sub-F. These studies revealed that ERK2 undergoes sulfenylation at C159 on its D-recruitment site surface and that this modification modulates ERK2 activity differentially between substrates. Integrated biochemical, computational, and mutational analyses suggest a plausible mechanism for peroxide-dependent changes in ERK2-substrate interactions. Interestingly, oxidation decreased ERK2's affinity for some D-site ligands while increasing its affinity for others. Finally, oxidation by signal-generated peroxide enhanced ERK1/2's ability to phosphorylate ribosomal S6 kinase A1 (RSK1) in HeLa cells. Together, these studies lay the foundation for examining crosstalk between redox- and phosphorylation-dependent signaling at the level of kinase-substrate selection.
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Affiliation(s)
- Anthony E. Postiglione
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Biology, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Laquaundra L. Adams
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Ese S. Ekhator
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Anuoluwapo E. Odelade
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Supriya Patwardhan
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Meenal Chaudhari
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Computational Data Science and Engineering, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Mathematics and Computer Science, University of Virginia at Wise, Wise, VA 24293, USA
| | - Avery S. Pardue
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Anjali Kumari
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - William A. LeFever
- Department of Chemistry, High Point University, High Point, NC 27268, USA
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Olivia P. Tornow
- Department of Chemistry, High Point University, High Point, NC 27268, USA
| | - Tamer S. Kaoud
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Johnathan Neiswinger
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biology, Belhaven University, Jackson, MS 39202, USA
| | - Jun Seop Jeong
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Kimberly J. Nelson
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Dukka B. Kc
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Cristina M. Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew J. Wommack
- Department of Chemistry, High Point University, High Point, NC 27268, USA
| | - Kevin N. Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ming Dong
- Department of Chemistry, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Jeremiah D. Keyes
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
- Department of Biology, Penn State University Behrend, Erie, PA 16563, USA
- Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
| | - Robert H. Newman
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
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3
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Sammons RM, Cho EJ, Dalby KN. Identification and biochemical characterization of small molecule inhibitors of ERK2 that target the D-recruitment site. Methods Enzymol 2023; 690:445-499. [PMID: 37858538 PMCID: PMC10950554 DOI: 10.1016/bs.mie.2023.06.016] [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] [Indexed: 10/21/2023]
Abstract
Extracellular signal-regulated kinase (ERK) is the culmination of a mitogen-activated protein kinase cascade that regulates cellular processes like proliferation, migration, and survival. Consequently, abnormal ERK signaling often plays a role in the tumorigenesis and metastasis of numerous cancers. ERK inhibition is a sought-after treatment for cancers, especially since clinically approved drugs that target signaling upstream of ERK often induce acquired resistance. Furthermore, the ERK2 isoform may have a differential role in various cancers from the other canonical isoform, ERK1. We demonstrate that small molecules can inhibit ERK2 catalytic and noncatalytic functions by binding to the D-recruitment site (DRS), a protein-protein interaction site distal to the enzyme active site. Using a fluorescence anisotropy-based high-throughput screening, we identify compounds that bind to the DRS and exhibit dose-dependent inhibition of ERK2 activity and ERK2 phosphorylation. We characterize the dose-dependent potency of ERK2 inhibitors using fluorescence anisotropy-based binding assays, fluorescence-based ERK2 substrate phosphorylation assays, and in vitro ERK2 activation assays. In our example, the binding of a DRS inhibitor can be prevented by mutating the DRS residue Cys-159 to serine, indicating that this residue is essential for the interaction. Resulting inhibitors from this process can be assessed in cellular and in vivo experiments for inhibition of ERK signaling and can be evaluated as potential cancer drugs.
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Affiliation(s)
- R M Sammons
- Targeted Therapeutic Drug Discovery and Development Program, The University of Texas at Austin, Austin, TX, United States
| | - E J Cho
- Targeted Therapeutic Drug Discovery and Development Program, The University of Texas at Austin, Austin, TX, United States
| | - K N Dalby
- Targeted Therapeutic Drug Discovery and Development Program, The University of Texas at Austin, Austin, TX, United States; Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, United States.
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4
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Pan X, Pei J, Wang A, Shuai W, Feng L, Bu F, Zhu Y, Zhang L, Wang G, Ouyang L. Development of small molecule extracellular signal-regulated kinases (ERKs) inhibitors for cancer therapy. Acta Pharm Sin B 2022; 12:2171-2192. [PMID: 35646548 PMCID: PMC9136582 DOI: 10.1016/j.apsb.2021.12.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 01/09/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway is widely activated by a variety of extracellular stimuli, and its dysregulation is associated with the proliferation, invasion, and migration of cancer cells. ERK1/2 is located at the distal end of this pathway and rarely undergoes mutations, making it an attractive target for anticancer drug development. Currently, an increasing number of ERK1/2 inhibitors have been designed and synthesized for antitumor therapy, among which representative compounds have entered clinical trials. When ERK1/2 signal transduction is eliminated, ERK5 may provide a bypass route to rescue proliferation, and weaken the potency of ERK1/2 inhibitors. Therefore, drug research targeting ERK5 or based on the compensatory mechanism of ERK5 for ERK1/2 opens up a new way for oncotherapy. This review provides an overview of the physiological and biological functions of ERKs, focuses on the structure-activity relationships of small molecule inhibitors targeting ERKs, with a view to providing guidance for future drug design and optimization, and discusses the potential therapeutic strategies to overcome drug resistance.
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Affiliation(s)
- Xiaoli Pan
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Junping Pei
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Aoxue Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Wen Shuai
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lu Feng
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Faqian Bu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yumeng Zhu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
- Corresponding authors. Tel./fax: +86 28 85503817.
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
- Corresponding authors. Tel./fax: +86 28 85503817.
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
- Corresponding authors. Tel./fax: +86 28 85503817.
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5
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Garcia Michel LR, Keirns CD, Ahlbrecht BC, Barr DA. Calculating Transfer Entropy from Variance-Covariance Matrices Provides Insight into Allosteric Communication in ERK2. J Chem Theory Comput 2021; 17:3168-3177. [PMID: 33929855 DOI: 10.1021/acs.jctc.1c00004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We develop an approach by which reliable estimates of the transfer entropy can be obtained from the variance-covariance matrix of atomic fluctuations, which converges quickly and retains sensitivity to the full chemical profile of the biomolecular system. We validate our method on ERK2, a well-studied kinase involved in the MAPK signaling cascade for which considerable computational, experimental, and mutation data are available. We present the results of transfer entropy analysis on data obtained from molecular dynamics simulations of wild-type active and inactive ERK2, along with mutants Q103A, I84A, L73P, and G83A. We show that our method is systematically consistent within the context of other approaches for calculating transfer entropy, and we provide a method for interpreting networks of interconnected residues in the protein from a perspective of allosteric coupling. We introduce new insights about possible allosteric activity of the extreme N-terminal region of the kinase, and we describe evidence that suggests that activation may occur by different paths or routes in different mutants. Our results highlight systematic advantages and disadvantages of each method for calculating transfer entropy and show the important role of transfer entropy analysis for understanding allosteric behavior in biomolecular systems.
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Affiliation(s)
- Luisa R Garcia Michel
- Department of Chemistry, University of Mary, Bismarck, North Dakota 58504, United States
| | - Clara D Keirns
- Department of Chemistry, University of Mary, Bismarck, North Dakota 58504, United States
| | - Benjamin C Ahlbrecht
- Department of Chemistry, University of Mary, Bismarck, North Dakota 58504, United States
| | - Daniel A Barr
- Department of Chemistry, University of Mary, Bismarck, North Dakota 58504, United States
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6
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ERK signalling: a master regulator of cell behaviour, life and fate. Nat Rev Mol Cell Biol 2020; 21:607-632. [PMID: 32576977 DOI: 10.1038/s41580-020-0255-7] [Citation(s) in RCA: 472] [Impact Index Per Article: 118.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2020] [Indexed: 12/13/2022]
Abstract
The proteins extracellular signal-regulated kinase 1 (ERK1) and ERK2 are the downstream components of a phosphorelay pathway that conveys growth and mitogenic signals largely channelled by the small RAS GTPases. By phosphorylating widely diverse substrates, ERK proteins govern a variety of evolutionarily conserved cellular processes in metazoans, the dysregulation of which contributes to the cause of distinct human diseases. The mechanisms underlying the regulation of ERK1 and ERK2, their mode of action and their impact on the development and homeostasis of various organisms have been the focus of much attention for nearly three decades. In this Review, we discuss the current understanding of this important class of kinases. We begin with a brief overview of the structure, regulation, substrate recognition and subcellular localization of ERK1 and ERK2. We then systematically discuss how ERK signalling regulates six fundamental cellular processes in response to extracellular cues. These processes are cell proliferation, cell survival, cell growth, cell metabolism, cell migration and cell differentiation.
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7
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Kaoud TS, Johnson WH, Ebelt ND, Piserchio A, Zamora-Olivares D, Van Ravenstein SX, Pridgen JR, Edupuganti R, Sammons R, Cano M, Warthaka M, Harger M, Tavares CDJ, Park J, Radwan MF, Ren P, Anslyn EV, Tsai KY, Ghose R, Dalby KN. Modulating multi-functional ERK complexes by covalent targeting of a recruitment site in vivo. Nat Commun 2019; 10:5232. [PMID: 31745079 PMCID: PMC6863825 DOI: 10.1038/s41467-019-12996-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 10/10/2019] [Indexed: 12/31/2022] Open
Abstract
Recently, the targeting of ERK with ATP-competitive inhibitors has emerged as a potential clinical strategy to overcome acquired resistance to BRAF and MEK inhibitor combination therapies. In this study, we investigate an alternative strategy of targeting the D-recruitment site (DRS) of ERK. The DRS is a conserved region that lies distal to the active site and mediates ERK-protein interactions. We demonstrate that the small molecule BI-78D3 binds to the DRS of ERK2 and forms a covalent adduct with a conserved cysteine residue (C159) within the pocket and disrupts signaling in vivo. BI-78D3 does not covalently modify p38MAPK, JNK or ERK5. BI-78D3 promotes apoptosis in BRAF inhibitor-naive and resistant melanoma cells containing a BRAF V600E mutation. These studies provide the basis for designing modulators of protein-protein interactions involving ERK, with the potential to impact ERK signaling dynamics and to induce cell cycle arrest and apoptosis in ERK-dependent cancers.
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Affiliation(s)
- Tamer S Kaoud
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - William H Johnson
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Nancy D Ebelt
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
| | | | - Sabrina X Van Ravenstein
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jacey R Pridgen
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ramakrishna Edupuganti
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Rachel Sammons
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Micael Cano
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Mangalika Warthaka
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Matthew Harger
- Biomedical Engineering Department, The University of Texas at Austin, Austin, TX, USA
| | - Clint D J Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jihyun Park
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mohamed F Radwan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Pengyu Ren
- Biomedical Engineering Department, The University of Texas at Austin, Austin, TX, USA
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA.,Graduate Programs in Biochemistry, Chemistry and Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA.
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8
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Taylor CA, Cormier KW, Keenan SE, Earnest S, Stippec S, Wichaidit C, Juang YC, Wang J, Shvartsman SY, Goldsmith EJ, Cobb MH. Functional divergence caused by mutations in an energetic hotspot in ERK2. Proc Natl Acad Sci U S A 2019; 116:15514-15523. [PMID: 31296562 PMCID: PMC6681740 DOI: 10.1073/pnas.1905015116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The most frequent extracellular signal-regulated kinase 2 (ERK2) mutation occurring in cancers is E322K (E-K). ERK2 E-K reverses a buried charge in the ERK2 common docking (CD) site, a region that binds activators, inhibitors, and substrates. Little is known about the cellular consequences associated with this mutation, other than apparent increases in tumor resistance to pathway inhibitors. ERK2 E-K, like the mutation of the preceding aspartate (ERK2 D321N [D-N]) known as the sevenmaker mutation, causes increased activity in cells and evades inactivation by dual-specificity phosphatases. As opposed to findings in cancer cells, in developmental assays in Drosophila, only ERK2 D-N displays a significant gain of function, revealing mutation-specific phenotypes. The crystal structure of ERK2 D-N is indistinguishable from that of wild-type protein, yet this mutant displays increased thermal stability. In contrast, the crystal structure of ERK2 E-K reveals profound structural changes, including disorder in the CD site and exposure of the activation loop phosphorylation sites, which likely account for the decreased thermal stability of the protein. These contiguous mutations in the CD site of ERK2 are both required for docking interactions but lead to unpredictably different functional outcomes. Our results suggest that the CD site is in an energetically strained configuration, and this helps drive conformational changes at distal sites on ERK2 during docking interactions.
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Affiliation(s)
- Clinton A Taylor
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Kevin W Cormier
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Shannon E Keenan
- Department of Chemical and Biological Engineering, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Svetlana Earnest
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Steve Stippec
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Chonlarat Wichaidit
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Yu-Chi Juang
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Junmei Wang
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390
| | - Stanislav Y Shvartsman
- Department of Chemical and Biological Engineering, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | | | - Melanie H Cobb
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390;
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9
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Sammons RM, Perry NA, Li Y, Cho EJ, Piserchio A, Zamora-Olivares DP, Ghose R, Kaoud TS, Debevec G, Bartholomeusz C, Gurevich VV, Iverson TM, Giulianotti M, Houghten RA, Dalby KN. A Novel Class of Common Docking Domain Inhibitors That Prevent ERK2 Activation and Substrate Phosphorylation. ACS Chem Biol 2019; 14:1183-1194. [PMID: 31058487 DOI: 10.1021/acschembio.9b00093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Extracellular signal-regulated kinases (ERK1/2) are mitogen-activated protein kinases (MAPKs) that play a pro-tumorigenic role in numerous cancers. ERK1/2 possess two protein-docking sites that are distinct from the active site: the D-recruitment site (DRS) and the F-recruitment site. These docking sites facilitate substrate recognition, intracellular localization, signaling specificity, and protein complex assembly. Targeting these sites on ERK in a therapeutic context may overcome many problems associated with traditional ATP-competitive inhibitors. Here, we identified a new class of inhibitors that target the ERK DRS by screening a synthetic combinatorial library of more than 30 million compounds. The screen detects the competitive displacement of a fluorescent peptide from the DRS of ERK2. The top molecular scaffold from the screen was optimized for structure-activity relationship by positional scanning of different functional groups. This resulted in 10 compounds with similar binding affinities and a shared core structure consisting of a tertiary amine hub with three functionalized cyclic guanidino branches. Compound 2507-1 inhibited ERK2 from phosphorylating a DRS-targeting substrate and prevented the phosphorylation of ERK2 by a constitutively active MEK1 (MAPK/ERK kinase 1) mutant. Interaction between an analogue, 2507-8, and the ERK2 DRS was confirmed by nuclear magnetic resonance and X-ray crystallography. 2507-8 forms critical interactions at the common docking domain residue Asp319 via an arginine-like moiety that is shared by all 10 hits, suggesting a common binding mode. The structural and biochemical insights reported here provide the basis for developing new ERK inhibitors that are not ATP-competitive but instead function by disrupting critical protein-protein interactions.
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Affiliation(s)
| | | | - Yangmei Li
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, United States
- Department of Drug Discovery & Biomedical Sciences, University of South Carolina, Columbia, South Carolina 29208, United States
| | | | - Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | | | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | - Tamer S. Kaoud
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | - Ginamarie Debevec
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, United States
| | | | | | | | - Marc Giulianotti
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, United States
| | - Richard A. Houghten
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, United States
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10
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Sammons RM, Ghose R, Tsai KY, Dalby KN. Targeting ERK beyond the boundaries of the kinase active site in melanoma. Mol Carcinog 2019; 58:1551-1570. [PMID: 31190430 DOI: 10.1002/mc.23047] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/14/2022]
Abstract
Extracellular signal-regulated kinase 1/2 (ERK1/2) constitute a point of convergence for complex signaling events that regulate essential cellular processes, including proliferation and survival. As such, dysregulation of the ERK signaling pathway is prevalent in many cancers. In the case of BRAF-V600E mutant melanoma, ERK inhibition has emerged as a viable clinical approach to abrogate signaling through the ERK pathway, even in cases where MEK and Raf inhibitor treatments fail to induce tumor regression due to resistance mechanisms. Several ERK inhibitors that target the active site of ERK have reached clinical trials, however, many critical ERK interactions occur at other potentially druggable sites on the protein. Here we discuss the role of ERK signaling in cell fate, in driving melanoma, and in resistance mechanisms to current BRAF-V600E melanoma treatments. We explore targeting ERK via a distinct site of protein-protein interaction, known as the D-recruitment site (DRS), as an alternative or supplementary mode of ERK pathway inhibition in BRAF-V600E melanoma. Targeting the DRS with inhibitors in melanoma has the potential to not only disrupt the catalytic apparatus of ERK but also its noncatalytic functions, which have significant impacts on spatiotemporal signaling dynamics and cell fate.
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Affiliation(s)
- Rachel M Sammons
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York
| | - Kenneth Y Tsai
- Departments of Anatomic Pathology and Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas.,Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
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11
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Ghose R. Nature of the Pre-Chemistry Ensemble in Mitogen-Activated Protein Kinases. J Mol Biol 2018; 431:145-157. [PMID: 30562484 DOI: 10.1016/j.jmb.2018.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
Abstract
In spite of the availability of a significant amount of structural detail on docking interactions involving mitogen-activated protein kinases (MAPKs) and their substrates, the mechanism by which the disordered phospho-acceptor on the substrate transiently interacts with the kinase catalytic elements and is phosphorylated, often with high efficiency, remains poorly understood. Here, this dynamic interaction is analyzed in the context of available biophysical and biochemical data for ERK2, an archetypal MAPK. A hypothesis about the nature of the ternary complex involving a MAPK, its substrate, and ATP immediately prior to the chemical step (the pre-chemistry complex) is proposed. It is postulated that the solution ensemble (the pre-chemistry ensemble) representing the pre-chemistry complex comprises several conformations that are linked by dynamics on multiple timescales. These individual conformations possess different intrinsic abilities to proceed through the chemical step. The overall rate of chemistry is therefore related to the microscopic nature of the pre-chemistry ensemble, its constituent conformational microstates, and their intrinsic abilities to yield a phosphorylated product. While characterizing these microstates within the pre-chemistry ensemble in atomic or near-atomic detail is an extremely challenging proposition, recent developments in hybrid methodologies that employ computational approaches driven by experimental data appear to provide the most promising path forward toward achieving this goal.
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Affiliation(s)
- Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA; Graduate Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016, USA; Graduate Program in Physics, The Graduate Center of CUNY, New York, NY 10016, USA
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12
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Abstract
NMR spectroscopy and other solution methods are increasingly being used to obtain novel insights into the mechanisms by which MAPK regulatory proteins bind and direct the activity of MAPKs. Here, we describe how interactions between the MAPK p38α and its regulatory proteins are studied using NMR spectroscopy, isothermal titration calorimetry, and small angle X-ray scattering (SAXS).
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Affiliation(s)
- Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI, 02912, USA. .,Department of Chemistry, Brown University, Providence, RI, 02912, USA.
| | - Rebecca Page
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
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13
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Keyes JD, Parsonage D, Yammani RD, Rogers LC, Kesty C, Furdui CM, Nelson KJ, Poole LB. Endogenous, regulatory cysteine sulfenylation of ERK kinases in response to proliferative signals. Free Radic Biol Med 2017; 112:534-543. [PMID: 28843779 PMCID: PMC5623068 DOI: 10.1016/j.freeradbiomed.2017.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/11/2017] [Accepted: 08/22/2017] [Indexed: 01/04/2023]
Abstract
ERK-dependent signaling is key to many pathways through which extracellular signals are transduced into cell-fate decisions. One conundrum is the way in which disparate signals induce specific responses through a common, ERK-dependent kinase cascade. While studies have revealed intricate ways of controlling ERK signaling through spatiotemporal localization and phosphorylation dynamics, additional modes of ERK regulation undoubtedly remain to be discovered. We hypothesized that fine-tuning of ERK signaling could occur by cysteine oxidation. We report that ERK is actively and directly oxidized by signal-generated H2O2 during proliferative signaling, and that ERK oxidation occurs downstream of a variety of receptor classes tested in four cell lines. Furthermore, within the tested cell lines and proliferative signals, we observed that both activation loop-phosphorylated and non-phosphorylated ERK undergo sulfenylation in cells and that dynamics of ERK sulfenylation is dependent on the cell growth conditions prior to stimulation. We also tested the effect of endogenous ERK oxidation on kinase activity and report that phosphotransfer reactions are reversibly inhibited by oxidation by as much as 80-90%, underscoring the importance of considering this additional modification when assessing ERK activation in response to extracellular signals.
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Affiliation(s)
- Jeremiah D Keyes
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Molecular Signaling, Wake Forest University, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, USA
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, USA
| | - Rama D Yammani
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, USA
| | - LeAnn C Rogers
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Molecular Signaling, Wake Forest University, USA
| | - Chelsea Kesty
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Molecular Signaling, Wake Forest University, USA
| | - Cristina M Furdui
- Center for Molecular Signaling, Wake Forest University, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, USA; Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Kimberly J Nelson
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Molecular Signaling, Wake Forest University, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, USA
| | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Molecular Signaling, Wake Forest University, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, USA.
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14
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Local destabilization, rigid body, and fuzzy docking facilitate the phosphorylation of the transcription factor Ets-1 by the mitogen-activated protein kinase ERK2. Proc Natl Acad Sci U S A 2017; 114:E6287-E6296. [PMID: 28716922 DOI: 10.1073/pnas.1702973114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mitogen-activated protein (MAP) kinase substrates are believed to require consensus docking motifs (D-site, F-site) to engage and facilitate efficient site-specific phosphorylation at specific serine/threonine-proline sequences by their cognate kinases. In contrast to other MAP kinase substrates, the transcription factor Ets-1 has no canonical docking motifs, yet it is efficiently phosphorylated by the MAP kinase ERK2 at a consensus threonine site (T38). Using NMR methodology, we demonstrate that this phosphorylation is enabled by a unique bipartite mode of ERK2 engagement by Ets-1 and involves two suboptimal noncanonical docking interactions instead of a single canonical docking motif. The N terminus of Ets-1 interacts with a part of the ERK2 D-recruitment site that normally accommodates the hydrophobic sidechains of a canonical D-site, retaining a significant degree of disorder in its ERK2-bound state. In contrast, the C-terminal region of Ets-1, including its Pointed (PNT) domain, engages in a largely rigid body interaction with a section of the ERK2 F-recruitment site through a binding mode that deviates significantly from that of a canonical F-site. This latter interaction is notable for the destabilization of a flexible helix that bridges the phospho-acceptor site to the rigid PNT domain. These two spatially distinct, individually weak docking interactions facilitate the highly specific recognition of ERK2 by Ets-1, and enable the optimal localization of its dynamic phospho-acceptor T38 at the kinase active site to enable efficient phosphorylation.
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15
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NMR Characterization of Information Flow and Allosteric Communities in the MAP Kinase p38γ. Sci Rep 2016; 6:28655. [PMID: 27353957 PMCID: PMC4926091 DOI: 10.1038/srep28655] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/07/2016] [Indexed: 02/01/2023] Open
Abstract
The intramolecular network structure of a protein provides valuable insights into allosteric sites and communication pathways. However, a straightforward method to comprehensively map and characterize these pathways is not currently available. Here we present an approach to characterize intramolecular network structure using NMR chemical shift perturbations. We apply the method to the mitogen activated protein kinase (MAPK) p38γ. p38γ contains allosteric sites that are conserved among eukaryotic kinases as well as unique to the MAPK family. How these regulatory sites communicate with catalytic residues is not well understood. Using our method, we observe and characterize for the first time information flux between regulatory sites through a conserved kinase infrastructure. This network is accessed, reinforced, and broken in various states of p38γ, reflecting the functional state of the protein. We demonstrate that the approach detects critical junctions in the network corresponding to biologically significant allosteric sites and pathways.
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16
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Boulton S, Melacini G. Advances in NMR Methods To Map Allosteric Sites: From Models to Translation. Chem Rev 2016; 116:6267-304. [PMID: 27111288 DOI: 10.1021/acs.chemrev.5b00718] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The last five years have witnessed major developments in the understanding of the allosteric phenomenon, broadly defined as coupling between remote molecular sites. Such advances have been driven not only by new theoretical models and pharmacological applications of allostery, but also by progress in the experimental approaches designed to map allosteric sites and transitions. Among these techniques, NMR spectroscopy has played a major role given its unique near-atomic resolution and sensitivity to the dynamics that underlie allosteric couplings. Here, we highlight recent progress in the NMR methods tailored to investigate allostery with the goal of offering an overview of which NMR approaches are best suited for which allosterically relevant questions. The picture of the allosteric "NMR toolbox" is provided starting from one of the simplest models of allostery (i.e., the four-state thermodynamic cycle) and continuing to more complex multistate mechanisms. We also review how such an "NMR toolbox" has assisted the elucidation of the allosteric molecular basis for disease-related mutations and the discovery of novel leads for allosteric drugs. From this overview, it is clear that NMR plays a central role not only in experimentally validating transformative theories of allostery, but also in tapping the full translational potential of allosteric systems.
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Affiliation(s)
- Stephen Boulton
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
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17
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Neumann TS, Span EA, Kalous KS, Bongard R, Gastonguay A, Lepley MA, Kutty RG, Nayak J, Bohl C, Lange RG, Sarker MI, Talipov MR, Rathore R, Ramchandran R, Sem DS. Identification of inhibitors that target dual-specificity phosphatase 5 provide new insights into the binding requirements for the two phosphate pockets. BMC BIOCHEMISTRY 2015; 16:19. [PMID: 26286528 PMCID: PMC4545774 DOI: 10.1186/s12858-015-0048-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/04/2015] [Indexed: 12/02/2022]
Abstract
BACKGROUND Dual-specificity phosphatase-5 (DUSP5) plays a central role in vascular development and disease. We present a p-nitrophenol phosphate (pNPP) based enzymatic assay to screen for inhibitors of the phosphatase domain of DUSP5. METHODS pNPP is a mimic of the phosphorylated tyrosine on the ERK2 substrate (pERK2) and binds the DUSP5 phosphatase domain with a Km of 7.6 ± 0.4 mM. Docking followed by inhibitor verification using the pNPP assay identified a series of polysulfonated aromatic inhibitors that occupy the DUSP5 active site in the region that is likely occupied by the dual-phosphorylated ERK2 substrate tripeptide (pThr-Glu-pTyr). Secondary assays were performed with full length DUSP5 with ERK2 as substrate. RESULTS The most potent inhibitor has a naphthalene trisulfonate (NTS) core. A search for similar compounds in a drug database identified suramin, a dimerized form of NTS. While suramin appears to be a potent and competitive inhibitor (25 ± 5 μM), binding to the DUSP5 phosphatase domain more tightly than the monomeric ligands of which it is comprised, it also aggregates. Further ligand-based screening, based on a pharmacophore derived from the 7 Å separation of sulfonates on inhibitors and on sulfates present in the DUSP5 crystal structure, identified a disulfonated and phenolic naphthalene inhibitor (CSD (3) _2320) with IC₅₀ of 33 μM that is similar to NTS and does not aggregate. CONCLUSIONS The new DUSP5 inhibitors we identify in this study typically have sulfonates 7 Å apart, likely positioning them where the two phosphates of the substrate peptide (pThr-Glu-pTyr) bind, with one inhibitor also positioning a phenolic hydroxyl where the water nucleophile may reside. Polysulfonated aromatic compounds do not commonly appear in drugs and have a tendency to aggregate. One FDA-approved polysulfonated drug, suramin, inhibits DUSP5 and also aggregates. Docking and modeling studies presented herein identify polysulfonated aromatic inhibitors that do not aggregate, and provide insights to guide future design of mimics of the dual-phosphate loops of the ERK substrates for DUSPs.
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Affiliation(s)
- Terrence S Neumann
- Department of Chemistry and Biochemistry, Texas Wesleyan University, 1201 Wesleyan Ave., Fort Worth, TX, 76105, USA.
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA.
| | - Elise A Span
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA.
| | - Kelsey S Kalous
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA.
| | - Robert Bongard
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA.
| | - Adam Gastonguay
- Department of Pediatrics, Department of Obstetrics and Gynecology, Medical College of Wisconsin, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, Milwaukee, WI 53226, USA.
| | - Michael A Lepley
- Department of Pediatrics, Department of Obstetrics and Gynecology, Medical College of Wisconsin, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, Milwaukee, WI 53226, USA.
| | - Raman G Kutty
- Department of Pediatrics, Department of Obstetrics and Gynecology, Medical College of Wisconsin, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, Milwaukee, WI 53226, USA.
| | - Jaladhi Nayak
- Department of Pediatrics, Department of Obstetrics and Gynecology, Medical College of Wisconsin, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, Milwaukee, WI 53226, USA.
| | - Chris Bohl
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA
| | - Rachel G Lange
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA
| | - Majher I Sarker
- Department of Chemistry, Wehr Chemistry Building, P.O. Box 1881, 535 N. 14th Street, Milwaukee, WI 53201, USA.
| | - Marat R Talipov
- Department of Chemistry, Wehr Chemistry Building, P.O. Box 1881, 535 N. 14th Street, Milwaukee, WI 53201, USA.
| | - Rajendra Rathore
- Department of Chemistry, Wehr Chemistry Building, P.O. Box 1881, 535 N. 14th Street, Milwaukee, WI 53201, USA.
| | - Ramani Ramchandran
- Department of Pediatrics, Department of Obstetrics and Gynecology, Medical College of Wisconsin, Children's Research Institute (CRI) Developmental Vascular Biology Program, Translational and Biomedical Research Center, Milwaukee, WI 53226, USA.
| | - Daniel S Sem
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences, and School of Pharmacy, Concordia University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI 53097, USA.
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18
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Xiao Y, Warner LR, Latham MP, Ahn NG, Pardi A. Structure-Based Assignment of Ile, Leu, and Val Methyl Groups in the Active and Inactive Forms of the Mitogen-Activated Protein Kinase Extracellular Signal-Regulated Kinase 2. Biochemistry 2015; 54:4307-19. [PMID: 26132046 DOI: 10.1021/acs.biochem.5b00506] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Resonance assignments are the first step in most NMR studies of protein structure, function, and dynamics. Standard protein assignment methods employ through-bond backbone experiments on uniformly (13)C/(15)N-labeled proteins. For larger proteins, this through-bond assignment procedure often breaks down due to rapid relaxation and spectral overlap. The challenges involved in studies of larger proteins led to efficient methods for (13)C labeling of side chain methyl groups, which have favorable relaxation properties and high signal-to-noise. These methyls are often still assigned by linking them to the previously assigned backbone, thus limiting the applications for larger proteins. Here, a structure-based procedure is described for assignment of (13)C(1)H3-labeled methyls by comparing distance information obtained from three-dimensional methyl-methyl nuclear Overhauser effect (NOE) spectroscopy with the X-ray structure. The Ile, Leu, or Val (ILV) methyl type is determined by through-bond experiments, and the methyl-methyl NOE data are analyzed in combination with the known structure. A hierarchical approach was employed that maps the largest observed "NOE-methyl cluster" onto the structure. The combination of identification of ILV methyl type with mapping of the NOE-methyl clusters greatly simplifies the assignment process. This method was applied to the inactive and active forms of the 42-kDa ILV (13)C(1)H3-methyl labeled extracellular signal-regulated kinase 2 (ERK2), leading to assignment of 60% of the methyls, including 90% of Ile residues. A series of ILV to Ala mutants were analyzed, which helped confirm the assignments. These assignments were used to probe the local and long-range effects of ligand binding to inactive and active ERK2.
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Affiliation(s)
- Yao Xiao
- †Department of Chemistry and Biochemistry and ‡BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Lisa R Warner
- †Department of Chemistry and Biochemistry and ‡BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Michael P Latham
- †Department of Chemistry and Biochemistry and ‡BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Natalie G Ahn
- †Department of Chemistry and Biochemistry and ‡BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Arthur Pardi
- †Department of Chemistry and Biochemistry and ‡BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80309, United States
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19
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Structural and Dynamic Features of F-recruitment Site Driven Substrate Phosphorylation by ERK2. Sci Rep 2015; 5:11127. [PMID: 26054059 PMCID: PMC4459106 DOI: 10.1038/srep11127] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/18/2015] [Indexed: 02/07/2023] Open
Abstract
The F-recruitment site (FRS) of active ERK2 binds F-site (Phe-x-Phe-Pro) sequences found downstream of the Ser/Thr phospho-acceptor on cellular substrates. Here we apply NMR methods to analyze the interaction between active ERK2 (ppERK2), and a 13-residue F-site-bearing peptide substrate derived from its cellular target, the transcription factor Elk-1. Our results provide detailed insight into previously elusive structural and dynamic features of FRS/F-site interactions and FRS-driven substrate phosphorylation. We show that substrate F-site engagement significantly quenches slow dynamics involving the ppERK2 activation-loop and the FRS. We also demonstrate that the F-site phenylalanines make critical contacts with ppERK2, in contrast to the proline whose cis-trans isomerization has no significant effect on F-site recognition by the kinase FRS. Our results support a mechanism where phosphorylation of the disordered N-terminal phospho-acceptor is facilitated by its increased productive encounters with the ppERK2 active site due to docking of the proximal F-site at the kinase FRS.
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20
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Warthaka M, Adelmann CH, Kaoud TS, Edupuganti R, Yan C, Johnson WH, Ferguson S, Tavares CD, Pence LJ, Anslyn EV, Ren P, Tsai KY, Dalby KN. Quantification of a Pharmacodynamic ERK End Point in Melanoma Cell Lysates: Toward Personalized Precision Medicine. ACS Med Chem Lett 2015; 6:47-52. [PMID: 25589929 DOI: 10.1021/ml500198b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 10/17/2014] [Indexed: 01/26/2023] Open
Abstract
Protein kinases are mutated or otherwise rendered constitutively active in numerous cancers where they are attractive therapeutic targets with well over a dozen kinase inhibitors now being used in therapy. While fluorescent sensors have capacity to measure changes in kinase activity, surprisingly they have not been utilized for biomarker studies. A first-generation peptide sensor for ERK based on the Sox fluorophore is described. This sensor called ERK-sensor-D1 possesses high activity toward ERK and more than 10-fold discrimination over other MAPKs. The sensor can rapidly quantify ERK activity in cell lysates and monitor ERK pathway engagement by BRAF and MEK inhibitors in cultured melanoma cell lines. The dynamic range of the sensor assay allows ERK activities that have potential for profound clinical consequences to be rapidly distinguished.
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Affiliation(s)
| | - Charles H. Adelmann
- Department
of Immunology and Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Tamer S. Kaoud
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | | | | | | | | | | | - Lindy J. Pence
- Department
of Immunology and Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | | | | | - Kenneth Y. Tsai
- Department
of Immunology and Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
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21
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Zhang R, Li J, Wu WJ. Relative Chemical Shifts for Obtaining Accurate Chemical Shifts of Hydrogen Atoms in CH Groups. CHINESE J CHEM PHYS 2014. [DOI: 10.1063/1674-0068/27/02/240-242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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22
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Peti W, Page R. Molecular basis of MAP kinase regulation. Protein Sci 2013; 22:1698-710. [PMID: 24115095 DOI: 10.1002/pro.2374] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 12/11/2022]
Abstract
Mitogen-activated protein kinases (MAPKs; ERK1/2, p38, JNK, and ERK5) have evolved to transduce environmental and developmental signals (growth factors, stress) into adaptive and programmed responses (differentiation, inflammation, apoptosis). Almost 20 years ago, it was discovered that MAPKs contain a docking site in the C-terminal lobe that binds a conserved 13-16 amino acid sequence known as the D- or KIM-motif (kinase interaction motif). Recent crystal structures of MAPK:KIM-peptide complexes are leading to a precise understanding of how KIM sequences contribute to MAPK selectivity. In addition, new crystal and especially NMR studies are revealing how residues outside the canonical KIM motif interact with specific MAPKs and contribute further to MAPK selectivity and signaling pathway fidelity. In this review, we focus on these recent studies, with an emphasis on the use of NMR spectroscopy, isothermal titration calorimetry and small angle X-ray scattering to investigate these processes.
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Affiliation(s)
- Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, 02912; Department of Chemistry, Brown University, Providence, Rhode Island, 02912
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23
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Kumar GS, Zettl H, Page R, Peti W. Structural basis for the regulation of the mitogen-activated protein (MAP) kinase p38α by the dual specificity phosphatase 16 MAP kinase binding domain in solution. J Biol Chem 2013; 288:28347-56. [PMID: 23926106 PMCID: PMC3784751 DOI: 10.1074/jbc.m113.499178] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/01/2013] [Indexed: 12/11/2022] Open
Abstract
Mitogen-activated protein kinases (MAPKs) fulfill essential biological functions and are key pharmaceutical targets. Regulation of MAPKs is achieved via a plethora of regulatory proteins including activating MAPKKs and an abundance of deactivating phosphatases. Although all regulatory proteins use an identical interaction site on MAPKs, the common docking and hydrophobic pocket, they use distinct kinase interaction motif (KIM or D-motif) sequences that are present in linear, peptide-like, or well folded protein domains. It has been recently shown that a KIM-containing MAPK-specific dual specificity phosphatase DUSP10 uses a unique binding mode to interact with p38α. Here we describe the interaction of the MAPK binding domain of DUSP16 with p38α and show that despite belonging to the same dual specificity phosphatase (DUSP) family, its interaction mode differs from that of DUSP10. Indeed, the DUSP16 MAPK binding domain uses an additional helix, α-helix 4, to further engage p38α. This leads to an additional interaction surface on p38α. Together, these structural and energetic differences in p38α engagement highlight the fine-tuning necessary to achieve MAPK specificity and regulation among multiple regulatory proteins.
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Affiliation(s)
| | - Heiko Zettl
- From the Departments of Molecular Pharmacology, Physiology and Biotechnology
| | - Rebecca Page
- Molecular Biology, Cell Biology, and Biochemistry, and
| | - Wolfgang Peti
- From the Departments of Molecular Pharmacology, Physiology and Biotechnology
- Chemistry, Brown University, Providence, Rhode Island 02912
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24
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Dioletis E, Dingley AJ, Driscoll PC. Structural and functional characterization of the recombinant death domain from death-associated protein kinase. PLoS One 2013; 8:e70095. [PMID: 23922916 PMCID: PMC3726526 DOI: 10.1371/journal.pone.0070095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/20/2013] [Indexed: 11/18/2022] Open
Abstract
Death-associated protein kinase (DAPk) is a calcium/calmodulin-regulated Ser/Thr-protein kinase that functions at an important point of integration for cell death signaling pathways. DAPk has a structurally unique multi-domain architecture, including a C-terminally positioned death domain (DD) that is a positive regulator of DAPk activity. In this study, recombinant DAPk-DD was observed to aggregate readily and could not be prepared in sufficient yield for structural analysis. However, DAPk-DD could be obtained as a soluble protein in the form of a translational fusion protein with the B1 domain of streptococcal protein G. In contrast to other DDs that adopt the canonical six amphipathic α-helices arranged in a compact fold, the DAPk-DD was found to possess surprisingly low regular secondary structure content and an absence of a stable globular fold, as determined by circular dichroism (CD), NMR spectroscopy and a temperature-dependent fluorescence assay. Furthermore, we measured the in vitro interaction between extracellular-regulated kinase-2 (ERK2) and various recombinant DAPk-DD constructs. Despite the low level of structural order, the recombinant DAPk-DD retained the ability to interact with ERK2 in a 1∶1 ratio with a K d in the low micromolar range. Only the full-length DAPk-DD could bind ERK2, indicating that the apparent 'D-motif' located in the putative sixth helix of DAPk-DD is not sufficient for ERK2 recognition. CD analysis revealed that binding of DAPk-DD to ERK2 is not accompanied by a significant change in secondary structure. Taken together our data argue that the DAPk-DD, when expressed in isolation, does not adopt a classical DD fold, yet in this state retains the capacity to interact with at least one of its binding partners. The lack of a stable globular structure for the DAPk-DD may reflect either that its folding would be supported by interactions absent in our experimental set-up, or a limitation in the structural bioinformatics assignment of the three-dimensional structure.
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Affiliation(s)
- Evangelos Dioletis
- Research Department of Structural & Molecular Biology, University College London, London, United Kingdom
| | - Andrew J. Dingley
- School of Chemical Sciences and School of Biological Science, The University of Auckland, Auckland, New Zealand
- ICS-6 (Structural biochemistry), Research Center Jülich, Jülich, Germany
| | - Paul C. Driscoll
- Division of Molecular Structure, Medical Research Council National Institute for Medical Research, London, United Kingdom
- * E-mail:
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25
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Ghose R. A measured approach: determining the PLCγ1 docking site on Itk using a biochemical ruler. J Mol Biol 2013; 425:679-82. [PMID: 23266656 DOI: 10.1016/j.jmb.2012.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Ranajeet Ghose
- Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.
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26
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Glatz G, Gógl G, Alexa A, Reményi A. Structural mechanism for the specific assembly and activation of the extracellular signal regulated kinase 5 (ERK5) module. J Biol Chem 2013; 288:8596-8609. [PMID: 23382384 PMCID: PMC3605678 DOI: 10.1074/jbc.m113.452235] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) activation depends on a linear binding motif found in all MAPK kinases (MKK). In addition, the PB1 (Phox and Bem1) domain of MKK5 is required for extracellular signal regulated kinase 5 (ERK5) activation. We present the crystal structure of ERK5 in complex with an MKK5 construct comprised of the PB1 domain and the linear binding motif. We show that ERK5 has distinct protein-protein interaction surfaces compared with ERK2, which is the closest ERK5 paralog. The two MAPKs have characteristically different physiological functions and their distinct protein-protein interaction surface topography enables them to bind different sets of activators and substrates. Structural and biochemical characterization revealed that the MKK5 PB1 domain cooperates with the MAPK binding linear motif to achieve substrate specific binding, and it also enables co-recruitment of the upstream activating enzyme and the downstream substrate into one signaling competent complex. Studies on present day MAPKs and MKKs hint on the way protein kinase networks may evolve. In particular, they suggest how paralogous enzymes with similar catalytic properties could acquire novel signaling roles by merely changing the way they make physical links to other proteins.
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Affiliation(s)
- Gábor Glatz
- Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Gergő Gógl
- Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Anita Alexa
- Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Attila Reményi
- Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary.
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27
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Lau DKW, Okon M, McIntosh LP. The PNT domain from Drosophila pointed-P2 contains a dynamic N-terminal helix preceded by a disordered phosphoacceptor sequence. Protein Sci 2012; 21:1716-25. [PMID: 22936607 DOI: 10.1002/pro.2151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/22/2012] [Accepted: 08/27/2012] [Indexed: 11/06/2022]
Abstract
Pointed-P2, the Drosophila ortholog of human ETS1 and ETS2, is a transcription factor involved in Ras/MAP kinase-regulated gene expression. In addition to a DNA-binding ETS domain, Pointed-P2 contains a PNT (or SAM) domain that serves as a docking module to enhance phosphorylation of an adjacent phosphoacceptor threonine by the ERK2 MAP kinase Rolled. Using NMR chemical shift, ¹⁵N relaxation, and amide hydrogen exchange measurements, we demonstrate that the Pointed-P2 PNT domain contains a dynamic N-terminal helix H0 appended to a core conserved five-helix bundle diagnostic of the SAM domain fold. Neither the secondary structure nor dynamics of the PNT domain is perturbed significantly upon in vitro ERK2 phosphorylation of three threonine residues in a disordered sequence immediately preceding this domain. These data thus confirm that the Drosophila Pointed-P2 PNT domain and phosphoacceptors are highly similar to those of the well-characterized human ETS1 transcription factor. NMR-monitored titrations also revealed that the phosphoacceptors and helix H0, as well as region of the core helical bundle identified previously by mutational analyses as a kinase docking site, are selectively perturbed upon ERK2 binding by Pointed-P2. Based on a homology model derived from the ETS1 PNT domain, helix H0 is predicted to partially occlude the docking interface. Therefore, this dynamic helix must be displaced to allow both docking of the kinase, as well as binding of Mae, a Drosophila protein that negatively regulates Pointed-P2 by competing with the kinase for its docking site.
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Affiliation(s)
- Desmond K W Lau
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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28
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Piserchio A, Francis DM, Koveal D, Dalby KN, Page R, Peti W, Ghose R. Docking interactions of hematopoietic tyrosine phosphatase with MAP kinases ERK2 and p38α. Biochemistry 2012; 51:8047-9. [PMID: 23030599 DOI: 10.1021/bi3012725] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hematopoietic tyrosine phosphatase (HePTP) regulates orthogonal MAP kinase signaling cascades by dephosphorylating both extracellular signal-regulated kinase (ERK) and p38. HePTP recognizes a docking site (D-recruitment site, DRS) on its targets using a conserved N-terminal sequence motif (D-motif). Using solution nuclear magnetic resonance spectroscopy and isothermal titration calorimetry, we compare, for the first time, the docking interactions of HePTP with ERK2 and p38α. Our results demonstrate that ERK2-HePTP interactions primarily involve the D-motif, while a contiguous region called the kinase specificity motif also plays a key role in p38α-HePTP interactions. D-Motif-DRS interactions for the two kinases, while similar overall, do show some specific differences.
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Affiliation(s)
- Andrea Piserchio
- Department of Chemistry, The City College of New York, New York, NY 10031, USA
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29
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Schnieders MJ, Kaoud TS, Yan C, Dalby KN, Ren P. Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases. Curr Pharm Des 2012; 18:1173-85. [PMID: 22316156 DOI: 10.2174/138161212799436368] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 12/06/2011] [Indexed: 12/22/2022]
Abstract
Due to their role in cellular signaling mitogen activated protein (MAP) kinases represent targets of pharmaceutical interest. However, the majority of known MAP kinase inhibitors compete with cellular ATP and target an ATP binding pocket that is highly conserved in the 500 plus representatives of the human protein kinase family. Here we review progress toward the development of non-ATP competitive MAP kinase inhibitors for the extracellular signal regulated kinases (ERK1/2), the c-jun N-terminal kinases (JNK1/2/3) and the p38 MAPKs (α, β, γ, and δ). Special emphasis is placed on the role of computational methods in the drug discovery process for MAP kinases. Topics include recent advances in X-ray crystallography theory that improve the MAP kinase structures essential to structurebased drug discovery, the use of molecular dynamics to understand the conformational heterogeneity of the activation loop and inhibitors discovered by virtual screening. The impact of an advanced polarizable force field such as AMOEBA used in conjunction with sophisticated kinetic and thermodynamic simulation methods is also discussed.
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Affiliation(s)
- Michael J Schnieders
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA.
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30
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ERK1/2 MAP kinases: structure, function, and regulation. Pharmacol Res 2012; 66:105-43. [PMID: 22569528 DOI: 10.1016/j.phrs.2012.04.005] [Citation(s) in RCA: 1090] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 11/21/2022]
Abstract
ERK1 and ERK2 are related protein-serine/threonine kinases that participate in the Ras-Raf-MEK-ERK signal transduction cascade. This cascade participates in the regulation of a large variety of processes including cell adhesion, cell cycle progression, cell migration, cell survival, differentiation, metabolism, proliferation, and transcription. MEK1/2 catalyze the phosphorylation of human ERK1/2 at Tyr204/187 and then Thr202/185. The phosphorylation of both tyrosine and threonine is required for enzyme activation. Whereas the Raf kinase and MEK families have narrow substrate specificity, ERK1/2 catalyze the phosphorylation of hundreds of cytoplasmic and nuclear substrates including regulatory molecules and transcription factors. ERK1/2 are proline-directed kinases that preferentially catalyze the phosphorylation of substrates containing a Pro-Xxx-Ser/Thr-Pro sequence. Besides this primary structure requirement, many ERK1/2 substrates possess a D-docking site, an F-docking site, or both. A variety of scaffold proteins including KSR1/2, IQGAP1, MP1, β-Arrestin1/2 participate in the regulation of the ERK1/2 MAP kinase cascade. The regulatory dephosphorylation of ERK1/2 is mediated by protein-tyrosine specific phosphatases, protein-serine/threonine phosphatases, and dual specificity phosphatases. The combination of kinases and phosphatases make the overall process reversible. The ERK1/2 catalyzed phosphorylation of nuclear transcription factors including those of Ets, Elk, and c-Fos represents an important function and requires the translocation of ERK1/2 into the nucleus by active and passive processes involving the nuclear pore. These transcription factors participate in the immediate early gene response. The activity of the Ras-Raf-MEK-ERK cascade is increased in about one-third of all human cancers, and inhibition of components of this cascade by targeted inhibitors represents an important anti-tumor strategy. Thus far, however, only inhibition of mutant B-Raf (Val600Glu) has been found to be therapeutically efficacious.
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31
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Francis DM, Różycki B, Koveal D, Hummer G, Page R, Peti W. Structural basis of p38α regulation by hematopoietic tyrosine phosphatase. Nat Chem Biol 2011; 7:916-24. [PMID: 22057126 DOI: 10.1038/nchembio.707] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 08/30/2011] [Indexed: 12/14/2022]
Abstract
MAP kinases regulate essential cellular events, including cell growth, differentiation and inflammation. The solution structure of a complete MAPK-MAPK-regulatory protein complex, p38α-HePTP, was determined, enabling a comprehensive investigation of the molecular basis of specificity and fidelity in MAPK regulation. Structure determination was achieved by combining NMR spectroscopy and small-angle X-ray scattering data with a new ensemble calculation-refinement procedure. We identified 25 residues outside of the HePTP kinase interaction motif necessary for p38α recognition. The complex adopts an extended conformation in solution and rarely samples the conformation necessary for kinase deactivation. Complex formation also does not affect the N-terminal lobe, the activation loop of p38α or the catalytic domain of HePTP. Together, these results show how the downstream tyrosine phosphatase HePTP regulates p38α and provide for fundamentally new insights into MAPK regulation and specificity.
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Affiliation(s)
- Dana M Francis
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, USA
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Lee S, Warthaka M, Yan C, Kaoud TS, Ren P, Dalby KN. Examining docking interactions on ERK2 with modular peptide substrates. Biochemistry 2011; 50:9500-10. [PMID: 21955038 DOI: 10.1021/bi201103b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
ERK2 primarily recognizes substrates through two recruitment sites, which lie outside the active site cleft of the kinase. These recruitment sites bind modular-docking sequences called docking sites and are potentially attractive sites for the development of non-ATP competitive inhibitors. The D-recruitment site (DRS) and the F-recruitment site (FRS) bind D-sites and F-sites, respectively. For example, peptides that target the FRS have been proposed to inhibit all ERK2 activity (Galanis, A., Yang, S. H., and Sharrocks, A. D. (2001) J. Biol. Chem. 276, 965-973); however, it has not been established whether this inhibition is steric or allosteric in origin. To facilitate inhibitor design and to examine potential coupling of recruitment sites to other ligand recognition sites within ERK2, energetic coupling within ERK2 was investigated using two new modular peptide substrates for ERK2. Modeling shows that one peptide (Sub-D) recognizes the DRS, while the other peptide (Sub-F) binds the FRS. A steady-state kinetic analysis reveals little evidence of thermodynamic linkage between the peptide substrate and ATP. Both peptides are phosphorylated through a random-order sequential mechanism with a k(cat)/K(m) comparable to Ets-1, a bona fide ERK2 substrate. Occupancy of the FRS with a peptide containing a modular docking sequence has no effect on the intrinsic ability of ERK2 to phosphorylate Sub-D. Occupancy of the DRS with a peptide containing a modular docking sequence has a slight effect (1.3 ± 0.1-fold increase in k(cat)) on the intrinsic ability of ERK2 to phosphorylate Sub-F. These data suggest that while docking interactions at the DRS and the FRS are energetically uncoupled, the DRS can exhibit weak communication to the active site. In addition, they suggest that peptides bound to the FRS inhibit the phosphorylation of protein substrates through a steric mechanism. The modeling and kinetic data suggest that the recruitment of ERK2 to cellular locations via its DRS may facilitate the formation of F-site selective ERK2 signaling complexes, while recruitment via the FRS will likely inhibit ERK2 through a steric mechanism of inhibition. Such recruitment may serve as an additional level of ERK2 regulation.
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Affiliation(s)
- Sunbae Lee
- Division of Medicinal Chemistry, University of Texas at Austin, Texas 78712, United States
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