1
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Gomez-Soler M, Olson EJ, de la Torre ER, Zhao C, Lamberto I, Flood DT, Danho W, Lechtenberg BC, Riedl SJ, Dawson PE, Pasquale EB. Lipidation and PEGylation Strategies to Prolong the in Vivo Half-Life of a Nanomolar EphA4 Receptor Antagonist. Eur J Med Chem 2023; 262:115876. [PMID: 38523699 PMCID: PMC10959496 DOI: 10.1016/j.ejmech.2023.115876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
The EphA4 receptor tyrosine kinase plays a role in neurodegenerative diseases, inhibition of nerve regeneration, cancer progression and other diseases. Therefore, EphA4 inhibition has potential therapeutic value. Selective EphA4 kinase inhibitors are not available, but we identified peptide antagonists that inhibit ephrin ligand binding to EphA4 with high specificity. One of these peptides is the cyclic APY-d3 (βAPYCVYRβASWSC-NH2), which inhibits ephrin-A5 ligand binding to EphA4 with low nanomolar binding affinity and is highly protease resistant. Here we describe modifications of APY-d3 that yield two different key derivatives with greatly increased half-lives in the mouse circulation, the lipidated APY-d3-laur8 and the PEGylated APY-d3-PEG4. These two derivatives inhibit ligand induced EphA4 activation in cells with sub-micromolar potency. Since they retain high potency and specificity for EphA4, lipidated and PEGylated APY-d3 derivatives represent new tools for discriminating EphA4 activities in vivo and for preclinical testing of EphA4 inhibition in animal disease models.
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Affiliation(s)
- Maricel Gomez-Soler
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Erika J. Olson
- Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Elena Rubio de la Torre
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Chunxia Zhao
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Ilaria Lamberto
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Dillon T. Flood
- Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Waleed Danho
- Del Mar, California 92014, United States
- Deceased
| | - Bernhard C. Lechtenberg
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Stefan J. Riedl
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Elena B. Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
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2
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Yang J, Weisberg EL, Liu X, Magin RS, Chan WC, Hu B, Schauer NJ, Zhang S, Lamberto I, Doherty L, Meng C, Sattler M, Cabal-Hierro L, Winer E, Stone R, Marto JA, Griffin JD, Buhrlage SJ. Small molecule inhibition of deubiquitinating enzyme JOSD1 as a novel targeted therapy for leukemias with mutant JAK2. Leukemia 2021; 36:210-220. [PMID: 34326465 DOI: 10.1038/s41375-021-01336-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/14/2021] [Accepted: 06/22/2021] [Indexed: 01/30/2023]
Abstract
Mutations in the Janus Kinase 2 (JAK2) gene resulting in constitutive kinase activation represent the most common genetic event in myeloproliferative neoplasms (MPN), a group of diseases involving overproduction of one or more kinds of blood cells, including red cells, white cells, and platelets. JAK2 kinase inhibitors, such as ruxolitinib, provide clinical benefit, but inhibition of wild-type (wt) JAK2 limits their clinical utility due to toxicity to normal cells, and small molecule inhibition of mutated JAK2 kinase activity can lead to drug resistance. Here, we present a strategy to target mutated JAK2 for degradation, using the cell's intracellular degradation machinery, while sparing non-mutated JAK2. We employed a chemical genetics screen, followed by extensive selectivity profiling and genetic studies, to identify the deubiquitinase (DUB), JOSD1, as a novel regulator of mutant JAK2. JOSD1 interacts with and stabilizes JAK2-V617F, and inactivation of the DUB leads to JAK2-V617F protein degradation by increasing its ubiquitination levels, thereby shortening its protein half-life. Moreover, targeting of JOSD1 leads to the death of JAK2-V617F-positive primary acute myeloid leukemia (AML) cells. These studies provide a novel therapeutic approach to achieving selective targeting of mutated JAK2 signaling in MPN.
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Affiliation(s)
- Jing Yang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ellen L Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Xiaoxi Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Robert S Magin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Wai Cheung Chan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bin Hu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nathan J Schauer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shengzhe Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ilaria Lamberto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Laura Doherty
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Chengcheng Meng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martin Sattler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Lucia Cabal-Hierro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Eric Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Richard Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - James D Griffin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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3
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Pan Y, Lu S, Lei L, Lamberto I, Wang Y, Pasquale EB, Wang Y. Genetically Encoded FRET Biosensor for Visualizing EphA4 Activity in Different Compartments of the Plasma Membrane. ACS Sens 2019; 4:294-300. [PMID: 30608127 DOI: 10.1021/acssensors.8b00465] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The EphA4 receptor tyrosine kinase is well-known for its pivotal role in development, cancer progression, and neurological disorders. However, how EphA4 kinase activity is regulated in time and space still remains unclear. To visualize EphA4 activity in different membrane microdomains, we developed a sensitive EphA4 biosensor based on Förster resonance energy transfer (FRET), and targeted it in or outside raft-like microdomains in the plasma membrane. We showed that our biosensor can produce a robust and specific FRET response upon EphA4 activation, both in vitro and in live cells. Interestingly, we observed stronger FRET responses for the non-raft targeting biosensor than for the raft targeting biosensor, suggesting that stronger EphA4 activation may occur in non-raft regions. Further investigations revealed the importance of the actin cytoskeleton in suppressing EphA4 activity in raft-like microdomains. Therefore, our FRET-based EphA4 biosensor could serve as a powerful tool to visualize and investigate EphA4 activation and signaling in specific subcellular compartments of single live cells.
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Affiliation(s)
| | | | | | - Ilaria Lamberto
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States,
| | - Yi Wang
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Champaign, Illinois 61820, United States
| | - Elena B. Pasquale
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States,
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4
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Buhrlage S, Weisberg E, Lamberto I, Yang J, Schauer N, Sattler M, Nonami A, Christie A, Weinstock D, Ritorto S, DeCesare V, Trost M, Stone R, Gray N, Griffin J. Abstract PR04: Degradation of leukemia oncogenes: A novel approach to therapy of leukemia. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.hemmal17-pr04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
AML is a heterogeneous group of malignancies with significant variability in phenotype and mechanisms of leukemogenesis. Despite our increased understanding of the genetic abnormalities that drive AML, very few targeted therapeutic agents have yet been developed. The prevailing approach to drugging oncoproteins is direct targeting of the mutant protein with a small molecule or antibody. Unfortunately, this strategy has not proven particularly fruitful in the case of AML as many mutant driver proteins are “undruggable” and the targetable enzymes (i.e., oncogenic FLT3) rapidly acquire resistance to inhibitors in the clinic. We are pursuing a novel and innovative approach that focuses on promoting degradation of AML oncoproteins through small-molecule inhibition of the cellular machinery that regulates turnover. Many oncoproteins are tagged for degradation by the proteasome or lysosome by post-translational addition of polyubiquitin chains. The process is, however, highly dynamic and reversible by deubiquitylating enzymes (DUBs), which cleave ubiquitin from substrate proteins. A subset of AML mutant drivers, including RAS, FLT3, and PML-RARα, have been found to undergo ubiquitin-mediated degradation; however, the DUB enzymes stabilizing them are unknown.
In order to identify novel targets and compounds that regulate protein homeostasis of leukemic oncoproteins, we employed whole-cell phenotypic screens of most reported small-molecule DUB inhibitors, annotated for inhibitory activity across a broad panel of DUBS, using oncogene-dependent and control cell lines followed by hit validation and target deconvolution. Using this approach, we identified inhibitors, and candidate DUBs, involved in regulation of protein levels of mutant FLT3, mutant JAK2, mutant KRAS, and PML-RARα;. Follow-up work that focused on FLT3-ITD identified USP10 as a DUB that stabilizes the oncoprotein via removal of a degradative ubiquitin tag. Furthermore, we show that pharmacologic inhibition of USP10 promotes degradation of FLT3-ITD but not wild-type (wt) FLT3, leads to selective killing of oncogenic FLT3-expressing AML cells in vitro and in vivo, and overrides resistance to FLT3 kinase inhibitors caused by tyrosine kinase domain (TKD) mutations and other mechanisms. Our studies hence validate USP10 as a therapeutic target for FLT3 mutant-positive AML. Building on this work, we executed a medicinal chemistry optimization effort that has yielded USP10 inhibitors with improved potency, and selectivity and mechanism studies have yielded insights into the origin of specificity for mutant versus wt FLT3. Furthermore, we have validated multiple DUB inhibitors that promote selective degradation of V617F JAK2 and intriguingly, identified compounds efficacious, in terms of inhibition of proliferation, across multiple genetic backgrounds. To the best of our knowledge, this is the first identification of a novel DUB substrate using a DUB-targeting small-molecule library screen and the first demonstration of stabilization of a mutant driver oncoprotein in AML by a DUB enzyme.
DUB inhibitors have the potential to eliminate oncoproteins, but it is early yet in the field. The first DUB inhibitor clinical trial is starting this year for multiple myeloma. Our work establishing the therapeutic potential of DUB inhibitors for oncogenes including PML-RARα; and constitutively activated FLT3, JAK2, and RAS, as well as potentially other oncoprotein-driven AML patient populations, will lay the groundwork for development of first-in-class drugs for AML.
This abstract is also being presented as Poster 10.
Citation Format: Sara Buhrlage, Ellen Weisberg, Ilaria Lamberto, Jing Yang, Nathan Schauer, Martin Sattler, Atushi Nonami, Amanda Christie, David Weinstock, Stella Ritorto, Virginia DeCesare, Matthias Trost, Richard Stone, Nathanael Gray, James Griffin. Degradation of leukemia oncogenes: A novel approach to therapy of leukemia [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr PR04.
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Affiliation(s)
| | | | | | - Jing Yang
- 1Dana-Farber Cancer Institute, Boston, MA,
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5
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Lamberto I, Liu X, Seo HS, Schauer NJ, Iacob RE, Hu W, Das D, Mikhailova T, Weisberg EL, Engen JR, Anderson KC, Chauhan D, Dhe-Paganon S, Buhrlage SJ. Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7. Cell Chem Biol 2017; 24:1490-1500.e11. [PMID: 29056421 DOI: 10.1016/j.chembiol.2017.09.003] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/09/2017] [Accepted: 09/05/2017] [Indexed: 01/30/2023]
Abstract
Deubiquitinating enzymes (DUBs) have garnered significant attention as drug targets in the last 5-10 years. The excitement stems in large part from the powerful ability of DUB inhibitors to promote degradation of oncogenic proteins, especially proteins that are challenging to directly target but which are stabilized by DUB family members. Highly optimized and well-characterized DUB inhibitors have thus become highly sought after tools. Most reported DUB inhibitors, however, are polypharmacological agents possessing weak (micromolar) potency toward their primary target, limiting their utility in target validation and mechanism studies. Due to a lack of high-resolution DUB⋅small-molecule ligand complex structures, no structure-guided optimization efforts have been reported for a mammalian DUB. Here, we report a small-molecule⋅ubiquitin-specific protease (USP) family DUB co-structure and rapid design of potent and selective inhibitors of USP7 guided by the structure. Interestingly, the compounds are non-covalent active-site inhibitors.
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Affiliation(s)
- Ilaria Lamberto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xiaoxi Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nathan J Schauer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Wanyi Hu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deepika Das
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tatiana Mikhailova
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen L Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dharminder Chauhan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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6
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Ficarro SB, Browne CM, Card JD, Alexander WM, Zhang T, Park E, McNally R, Dhe-Paganon S, Seo HS, Lamberto I, Eck MJ, Buhrlage SJ, Gray NS, Marto JA. Leveraging Gas-Phase Fragmentation Pathways for Improved Identification and Selective Detection of Targets Modified by Covalent Probes. Anal Chem 2016; 88:12248-12254. [PMID: 28193034 DOI: 10.1021/acs.analchem.6b03394] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The recent approval of covalent inhibitors for multiple clinical indications has reignited enthusiasm for this class of drugs. As interest in covalent drugs has increased, so too has the need for analytical platforms that can leverage their mechanism-of-action to characterize modified protein targets. Here we describe novel gas phase dissociation pathways which yield predictable fragment ions during MS/MS of inhibitor-modified peptides. We find that these dissociation pathways are common to numerous cysteine-directed probes as well as the covalent drugs, Ibrutinib and Neratinib. We leverage the predictable nature of these fragment ions to improve the confidence of peptide sequence assignment in proteomic analyses and explore their potential use in selective mass spectrometry-based assays.
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Affiliation(s)
- Scott B Ficarro
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Christopher M Browne
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | | | - William M Alexander
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Tinghu Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Eunyoung Park
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Randall McNally
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Sirano Dhe-Paganon
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Hyuk-Soo Seo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Ilaria Lamberto
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Michael J Eck
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Sara J Buhrlage
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Jarrod A Marto
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School , Boston, Massachusetts 02115, United States
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7
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Olson EJ, Lechtenberg BC, Zhao C, de la Torre ER, Lamberto I, Riedl SJ, Dawson PE, Pasquale EB. Modifications of a Nanomolar Cyclic Peptide Antagonist for the EphA4 Receptor To Achieve High Plasma Stability. ACS Med Chem Lett 2016; 7:841-6. [PMID: 27660688 DOI: 10.1021/acsmedchemlett.6b00132] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/25/2016] [Indexed: 01/08/2023] Open
Abstract
EphA4 is a receptor tyrosine kinase with a critical role in repulsive axon guidance and synaptic function. However, aberrant EphA4 activity can inhibit neural repair after injury and exacerbate neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and Alzheimer's. We previously identified the cyclic peptide APY-d2 (APYCVYRβASWSC-nh2, containing a disulfide bond) as a potent and selective EphA4 antagonist. However, APY-d2 lacks sufficient plasma stability to be useful for EphA4 inhibition in vivo through peripheral administration. Using structure-activity relationship studies, we show that protecting the peptide N-terminus from proteolytic degradation dramatically increases the persistence of the active peptide in plasma and that a positively charged peptide N-terminus is essential for high EphA4 binding affinity. Among several improved APY-d2 derivatives, the cyclic peptides APY-d3 (βAPYCVYRβASWSC-nh2) and APY-d4 (βAPYCVYRβAEWEC-nh2) combine high stability in plasma and cerebrospinal fluid with slightly enhanced potency. These properties make them valuable research tools and leads toward development of therapeutics for neurological diseases.
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Affiliation(s)
- Erika J. Olson
- Departments
of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Bernhard C. Lechtenberg
- Cancer
Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Chunxia Zhao
- Cancer
Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Elena Rubio de la Torre
- Cancer
Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Ilaria Lamberto
- Cancer
Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Stefan J. Riedl
- Cancer
Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Departments
of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Elena B. Pasquale
- Cancer
Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
- Pathology
Department, University of California, San Diego, La Jolla, California 92093, United States
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8
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Barquilla A, Lamberto I, Noberini R, Heynen-Genel S, Brill LM, Pasquale EB. Protein kinase A can block EphA2 receptor-mediated cell repulsion by increasing EphA2 S897 phosphorylation. Mol Biol Cell 2016; 27:2757-70. [PMID: 27385333 PMCID: PMC5007095 DOI: 10.1091/mbc.e16-01-0048] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/24/2016] [Indexed: 12/18/2022] Open
Abstract
The EphA2 receptor plays multiple roles in cancer through two distinct signaling mechanisms. In a novel cross-talk, the β2-adrenoceptor/cAMP/PKA axis can promote EphA2 pro-oncogenic, ligand-independent signaling, blocking cell repulsion induced by ligand-dependent signaling. PKA emerges as a third kinase, besides AKT and RSK, that can regulate EphA2. The EphA2 receptor tyrosine kinase plays key roles in tissue homeostasis and disease processes such as cancer, pathological angiogenesis, and inflammation through two distinct signaling mechanisms. EphA2 “canonical” signaling involves ephrin-A ligand binding, tyrosine autophosphorylation, and kinase activity; EphA2 “noncanonical” signaling involves phosphorylation of serine 897 (S897) by AKT and RSK kinases. To identify small molecules counteracting EphA2 canonical signaling, we developed a high-content screening platform measuring inhibition of ephrin-A1–induced PC3 prostate cancer cell retraction. Surprisingly, most hits from a screened collection of pharmacologically active compounds are agents that elevate intracellular cAMP by activating G protein–coupled receptors such as the β2-adrenoceptor. We found that cAMP promotes phosphorylation of S897 by protein kinase A (PKA) as well as increases the phosphorylation of several nearby serine/threonine residues, which constitute a phosphorylation hotspot. Whereas EphA2 canonical and noncanonical signaling have been viewed as mutually exclusive, we show that S897 phosphorylation by PKA can coexist with EphA2 tyrosine phosphorylation and block cell retraction induced by EphA2 kinase activity. Our findings reveal a novel paradigm in EphA2 function involving the interplay of canonical and noncanonical signaling and highlight the ability of the β2-adrenoceptor/cAMP/PKA axis to rewire EphA2 signaling in a subset of cancer cells.
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Affiliation(s)
- Antonio Barquilla
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Ilaria Lamberto
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Roberta Noberini
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Susanne Heynen-Genel
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Laurence M Brill
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 Pathology Department, University of California, San Diego, La Jolla, CA 92093
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9
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Forse GJ, Uson ML, Nasertorabi F, Kolatkar A, Lamberto I, Pasquale EB, Kuhn P. Distinctive Structure of the EphA3/Ephrin-A5 Complex Reveals a Dual Mode of Eph Receptor Interaction for Ephrin-A5. PLoS One 2015; 10:e0127081. [PMID: 25993310 PMCID: PMC4439037 DOI: 10.1371/journal.pone.0127081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/11/2015] [Indexed: 11/19/2022] Open
Abstract
The Eph receptor tyrosine kinase/ephrin ligand system regulates a wide spectrum of physiological processes, while its dysregulation has been implicated in cancer progression. The human EphA3 receptor is widely upregulated in the tumor microenvironment and is highly expressed in some types of cancer cells. Furthermore, EphA3 is among the most highly mutated genes in lung cancer and it is also frequently mutated in other cancers. We report the structure of the ligand-binding domain of the EphA3 receptor in complex with its preferred ligand, ephrin-A5. The structure of the complex reveals a pronounced tilt of the ephrin-A5 ligand compared to its orientation when bound to the EphA2 and EphB2 receptors and similar to its orientation when bound to EphA4. This tilt brings an additional area of ephrin-A5 into contact with regions of EphA3 outside the ephrin-binding pocket thereby enlarging the size of the interface, which is consistent with the high binding affinity of ephrin-A5 for EphA3. This large variation in the tilt of ephrin-A5 bound to different Eph receptors has not been previously observed for other ephrins.
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Affiliation(s)
- Garry Jason Forse
- Dornsife College of Letters, Arts and Sciences, University of Southern California, 3430 S. Vermont Ave., Suite 105 (110), MC3301, Los Angeles, CA, 90089–3301, United States of America
| | - Maria Loressa Uson
- Dornsife College of Letters, Arts and Sciences, University of Southern California, 3430 S. Vermont Ave., Suite 105 (110), MC3301, Los Angeles, CA, 90089–3301, United States of America
| | - Fariborz Nasertorabi
- Dornsife College of Letters, Arts and Sciences, University of Southern California, 3430 S. Vermont Ave., Suite 105 (110), MC3301, Los Angeles, CA, 90089–3301, United States of America
| | - Anand Kolatkar
- Dornsife College of Letters, Arts and Sciences, University of Southern California, 3430 S. Vermont Ave., Suite 105 (110), MC3301, Los Angeles, CA, 90089–3301, United States of America
| | - Ilaria Lamberto
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California, 92037, United States of America
| | - Elena Bianca Pasquale
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California, 92037, United States of America
- Department of Pathology, University of California San Diego, La Jolla, California, 92093, United States of America
| | - Peter Kuhn
- Dornsife College of Letters, Arts and Sciences, University of Southern California, 3430 S. Vermont Ave., Suite 105 (110), MC3301, Los Angeles, CA, 90089–3301, United States of America
- * E-mail:
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10
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Lamberto I, Lechtenberg BC, Olson EJ, Mace PD, Dawson PE, Riedl SJ, Pasquale EB. Development and structural analysis of a nanomolar cyclic peptide antagonist for the EphA4 receptor. ACS Chem Biol 2014; 9:2787-95. [PMID: 25268696 PMCID: PMC4273976 DOI: 10.1021/cb500677x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The EphA4 receptor is highly expressed in the nervous system, and recent findings suggest that its signaling activity hinders neural repair and exacerbates certain neurodegenerative processes. EphA4 has also been implicated in cancer progression. Thus, EphA4 inhibitors represent potential therapeutic leads and useful research tools to elucidate the role of EphA4 in physiology and disease. Here, we report the structure of a cyclic peptide antagonist, APY, in complex with the EphA4 ligand-binding domain (LBD), which represents the first structure of a cyclic peptide bound to a receptor tyrosine kinase. The structure shows that the dodecameric APY efficiently occupies the ephrin ligand-binding pocket of EphA4 and promotes a "closed" conformation of the surrounding loops. Structure-guided relaxation of the strained APY β-turn and amidation of the C terminus to allow an additional intrapeptide hydrogen bond yielded APY-βAla8.am, an improved APY derivative that binds to EphA4 with nanomolar affinity. APY-βAla8.am potently inhibits ephrin-induced EphA4 activation in cells and EphA4-dependent neuronal growth cone collapse, while retaining high selectivity for EphA4. The two crystal structures of APY and APY-βAla8.am bound to EphA4, in conjunction with secondary phage display screens, highlighted peptide residues that are essential for EphA4 binding as well as residues that can be modified. Thus, the APY scaffold represents an exciting prototype, particularly since cyclic peptides have potentially favorable metabolic stability and are emerging as an important class of molecules for disruption of protein-protein interactions.
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Affiliation(s)
- Ilaria Lamberto
- Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Bernhard C. Lechtenberg
- Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Erika J. Olson
- Department
of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Peter D. Mace
- Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Department
of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Stefan J. Riedl
- Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Elena B. Pasquale
- Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
- Pathology
Department, University of California San Diego, La Jolla, California 92093, United States
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11
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Duggineni S, Mitra S, Lamberto I, Han X, Xu Y, An J, Pasquale EB, Huang Z. Design and Synthesis of Potent Bivalent Peptide Agonists Targeting the EphA2 Receptor. ACS Med Chem Lett 2013; 4. [PMID: 24167659 DOI: 10.1021/ml3004523] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Designing potent and selective peptides and small molecules that target Eph receptor tyrosine kinases remains a challenge and new strategies are needed for developing novel and potent ligands for these receptors. In this study, we performed a structure-activity relationship study of a previously identified 12 amino acid-long peptide, SWL, by alanine scanning to identify residues important for receptor binding. To further enhance and optimize the receptor binding affinity of the SWL peptide, we applied the concept of bivalent ligand design to synthesize several SWL-derived dimeric peptides as novel ligands capable of binding simultaneously to two EphA2 receptor molecules. The dimeric peptides possess higher receptor binding affinity than the original monomeric SWL peptide, consistent with bivalent binding. The most potent dimeric peptide, a SWL dimer with a 6 carbon linker, has about 13 fold increased potency compared to SWL. Furthermore, similar to SWL, the dimeric peptide is an agonist and can promote EphA2 tyrosine phosphorylation (activation) in cultured cells.
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Affiliation(s)
- Srinivas Duggineni
- SUNY Upstate Cancer Research Institute,
Department of Pharmacology, State University of New York, Syracuse,
New York 13210, United States
| | - Sayantan Mitra
- Sanford-Burnham Medical Research Institute,
La Jolla, California 92037, United States
| | - Ilaria Lamberto
- Sanford-Burnham Medical Research Institute,
La Jolla, California 92037, United States
| | - Xiaofeng Han
- SUNY Upstate Cancer Research Institute,
Department of Pharmacology, State University of New York, Syracuse,
New York 13210, United States
| | - Yan Xu
- SUNY Upstate Cancer Research Institute,
Department of Pharmacology, State University of New York, Syracuse,
New York 13210, United States
| | - Jing An
- SUNY Upstate Cancer Research Institute,
Department of Pharmacology, State University of New York, Syracuse,
New York 13210, United States
| | - Elena B. Pasquale
- Sanford-Burnham Medical Research Institute,
La Jolla, California 92037, United States
- Department of Pathology, University
of California, San Diego, California 92093, United States
| | - Ziwei Huang
- SUNY Upstate Cancer Research Institute,
Department of Pharmacology, State University of New York, Syracuse,
New York 13210, United States
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12
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Noberini R, Lamberto I, Pasquale EB. Targeting Eph receptors with peptides and small molecules: progress and challenges. Semin Cell Dev Biol 2011; 23:51-7. [PMID: 22044885 DOI: 10.1016/j.semcdb.2011.10.023] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 10/17/2011] [Indexed: 11/18/2022]
Abstract
The Eph receptors are a large family of receptor tyrosine kinases. Their kinase activity and downstream signaling ability are stimulated by the binding of cell surface-associated ligands, the ephrins. The ensuing signals are bidirectional because the ephrins can also transduce signals (known as reverse signals) following their interaction with Eph receptors. The ephrin-binding pocket in the extracellular N-terminal domain of the Eph receptors and the ATP-binding pocket in the intracellular kinase domain represent potential binding sites for peptides and small molecules. Indeed, a number of peptides and chemical compounds that target Eph receptors and inhibit ephrin binding or kinase activity have been identified. These molecules show promise as probes to study Eph receptor/ephrin biology, as lead compounds for drug development, and as targeting agents to deliver drugs or imaging agents to tumors. Current challenges are to find (1) small molecules that inhibit Eph receptor-ephrin interactions with high binding affinity and good lead-like properties and (2) selective kinase inhibitors that preferentially target the Eph receptor family or subsets of Eph receptors. Strategies that could also be explored include targeting additional Eph receptor interfaces and the ephrin ligands.
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Affiliation(s)
- Roberta Noberini
- Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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13
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Lamberto I, Percudani R, Gatti R, Folli C, Petrucco S. Conserved alternative splicing of Arabidopsis transthyretin-like determines protein localization and S-allantoin synthesis in peroxisomes. Plant Cell 2010; 22:1564-74. [PMID: 20511299 PMCID: PMC2899872 DOI: 10.1105/tpc.109.070102] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 04/14/2010] [Accepted: 05/10/2010] [Indexed: 05/19/2023]
Abstract
S-allantoin, a major ureide compound, is produced in plant peroxisomes from oxidized purines. Sequence evidence suggested that the Transthyretin-like (TTL) protein, which interacts with brassinosteroid receptors, may act as a bifunctional enzyme in the synthesis of S-allantoin. Here, we show that recombinant TTL from Arabidopsis thaliana catalyzes two enzymatic reactions leading to the stereoselective formation of S-allantoin, hydrolysis of hydroxyisourate through a C-terminal Urah domain, and decarboxylation of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline through an N-terminal Urad domain. We found that two different mRNAs are produced from the TTL gene through alternative use of two splice acceptor sites. The corresponding proteins differ in the presence (TTL(1-)) and the absence (TTL(2-)) of a rare internal peroxisomal targeting signal (PTS2). The two proteins have similar catalytic activity in vitro but different in vivo localization: TTL(1-) localizes in peroxisomes, whereas TTL(2-) localizes in the cytosol. Similar splice variants are present in monocots and dicots. TTL originated in green algae through a Urad-Urah fusion, which entrapped an N-terminal PTS2 between the two domains. The presence of this gene in all Viridiplantae indicates that S-allantoin biosynthesis has general significance in plant nitrogen metabolism, while conservation of alternative splicing suggests that this mechanism has general implications in the regulation of the ureide pathway in flowering plants.
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Affiliation(s)
- Ilaria Lamberto
- Dipartimento di Biochimica e Biologia Molecolare, Università di Parma, 43124 Parma, Italy
| | - Riccardo Percudani
- Dipartimento di Biochimica e Biologia Molecolare, Università di Parma, 43124 Parma, Italy
- Address correspondence to
| | - Rita Gatti
- Dipartimento di Medicina Sperimentale, Sezione di Istologia, Università di Parma, 43125 Parma, Italy
| | - Claudia Folli
- Dipartimento di Biochimica e Biologia Molecolare, Università di Parma, 43124 Parma, Italy
| | - Stefania Petrucco
- Dipartimento di Biochimica e Biologia Molecolare, Università di Parma, 43124 Parma, Italy
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Serventi F, Ramazzina I, Lamberto I, Puggioni V, Gatti R, Percudani R. Chemical basis of nitrogen recovery through the ureide pathway: formation and hydrolysis of S-ureidoglycine in plants and bacteria. ACS Chem Biol 2010; 5:203-14. [PMID: 20038185 DOI: 10.1021/cb900248n] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While some organisms, including humans, eliminate oxidized purines to get rid of excess nitrogen, for many others the recovery of the purine ring nitrogen is vital. In the so-called ureide pathway, nitrogen is released as ammonia from allantoate through a series of reactions starting with allantoate amidohydrolase (AAH), a manganese-dependent enzyme found in plants and bacteria. We report NMR evidence that the true product of the AAH reaction is S-ureidoglycine, a nonstandard alpha-amino acid that spontaneously releases ammonia in vitro. Using gene proximity and logical genome analysis, we identified a candidate gene (ylbA) for S-ureidoglycine metabolism. The proteins encoded by Escherichia coli and Arabidopsis thaliana genes catalyze the manganese-dependent release of ammonia through hydrolysis of S-ureidoglycine. Hydrolysis then inverts the configuration and yields S-ureidoglycolate. S-Ureidoglycine aminohydrolase (UGHY) is cytosolic in bacteria, whereas in plants it is localized, like allantoate amidohydrolase, in the endoplasmic reticulum. These findings strengthen the basis for the known sensitivity of the ureide pathway to Mn availability and suggest a further rationale for the active transport of Mn in the endoplasmic reticulum of plant cells.
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Affiliation(s)
| | | | | | | | - Rita Gatti
- Dipartimento di Medicina Sperimentale, Sezione di Istologia, Università di Parma, 43100 Parma, Italy
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