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Suciu RM, Luvaga IK, Hazeen A, Weerasooriya C, Richardson SK, Firestone AJ, Shannon K, Howell AR, Cravatt BF. Chemical proteomic analysis of palmostatin beta-lactone analogs that affect N-Ras palmitoylation. Bioorg Med Chem Lett 2021; 53:128414. [PMID: 34666187 DOI: 10.1016/j.bmcl.2021.128414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Received: 09/01/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 11/18/2022]
Abstract
S-Palmitoylation is a reversible post-translational lipid modification that regulates protein trafficking and signaling. The enzymatic depalmitoylation of proteins is inhibited by the beta-lactones Palmostatin M and B, which have been found to target several serine hydrolases. In efforts to better understand the mechanism of action of Palmostatin M, we describe herein the synthesis, chemical proteomic analysis, and functional characterization of analogs of this compound. We identify Palmostatin M analogs that maintain inhibitory activity in N-Ras depalmitoylation assays while displaying complementary reactivity across the serine hydrolase class as measured by activity-based protein profiling. Active Palmostatin M analogs inhibit the recently characterized ABHD17 subfamily of depalmitoylating enzymes, while sparing other candidate depalmitoylases such as LYPLA1 and LYPLA2. These findings improve our understanding of the structure-activity relationship of Palmostatin M and refine the set of serine hydrolase targets relevant to the compound's effects on N-Ras palmitoylation dynamics.
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Affiliation(s)
- Radu M Suciu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Irungu K Luvaga
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - Akram Hazeen
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | | | | | - Ari J Firestone
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Kevin Shannon
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Amy R Howell
- Department of Chemistry, University of Connecticut, Storrs, CT, USA.
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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2
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Lin Z, Wang X, Bustin KA, Shishikura K, McKnight NR, He L, Suciu RM, Hu K, Han X, Ahmadi M, Olson EJ, Parsons WH, Matthews ML. Activity-Based Hydrazine Probes for Protein Profiling of Electrophilic Functionality in Therapeutic Targets. ACS Cent Sci 2021; 7:1524-1534. [PMID: 34584954 PMCID: PMC8461768 DOI: 10.1021/acscentsci.1c00616] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Indexed: 05/08/2023]
Abstract
Most known probes for activity-based protein profiling (ABPP) use electrophilic groups that tag a single type of nucleophilic amino acid to identify cases in which its hyper-reactivity underpins function. Much important biochemistry derives from electrophilic enzyme cofactors, transient intermediates, and labile regulatory modifications, but ABPP probes for such species are underdeveloped. Here, we describe a versatile class of probes for this less charted hemisphere of the proteome. The use of an electron-rich hydrazine as the common chemical modifier enables covalent targeting of multiple, pharmacologically important classes of enzymes bearing diverse organic and inorganic cofactors. Probe attachment occurs by both polar and radicaloid mechanisms, can be blocked by molecules that occupy the active sites, and depends on the proper poise of the active site for turnover. These traits will enable the probes to be used to identify specific inhibitors of individual members of these multiple enzyme classes, making them uniquely versatile among known ABPP probes.
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Affiliation(s)
- Zongtao Lin
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Xie Wang
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Katelyn A. Bustin
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kyosuke Shishikura
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Nate R. McKnight
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lin He
- Zenagem,
LLC, Fountain Valley, California 92708, United States
| | - Radu M. Suciu
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Kai Hu
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Xian Han
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
| | - Mina Ahmadi
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Erika J. Olson
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - William H. Parsons
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Megan L. Matthews
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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3
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Mizrak D, Bayin NS, Yuan J, Liu Z, Suciu RM, Niphakis MJ, Ngo N, Lum KM, Cravatt BF, Joyner AL, Sims PA. Single-Cell Profiling and SCOPE-Seq Reveal Lineage Dynamics of Adult Ventricular-Subventricular Zone Neurogenesis and NOTUM as a Key Regulator. Cell Rep 2021; 31:107805. [PMID: 32579931 PMCID: PMC7396151 DOI: 10.1016/j.celrep.2020.107805] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 05/13/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
In the adult ventricular-subventricular zone (V-SVZ), neural stem cells (NSCs) generate new olfactory bulb (OB) neurons and glia throughout life. To map adult neuronal lineage progression, we profiled >56,000 V-SVZ and OB cells by single-cell RNA sequencing (scRNA-seq). Our analyses reveal the molecular diversity of OB neurons, including fate-mapped neurons, lineage progression dynamics, and an NSC intermediate enriched for Notum, which encodes a secreted WNT antagonist. SCOPE-seq technology, which links live-cell imaging with scRNA-seq, uncovers cell-size transitions during NSC differentiation and preferential NOTUM binding to proliferating neuronal precursors. Consistently, application of NOTUM protein in slice cultures and pharmacological inhibition of NOTUM in slice cultures and in vivo demonstrated that NOTUM negatively regulates V-SVZ proliferation. Timely, context-dependent neurogenesis demands adaptive signaling among neighboring progenitors. Our findings highlight a critical regulatory state during NSC activation marked by NOTUM, which attenuates WNT-stimulated proliferation in NSC progeny.
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Affiliation(s)
- Dogukan Mizrak
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - N Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Jinzhou Yuan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zhouzerui Liu
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Radu M Suciu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Micah J Niphakis
- Lundbeck La Jolla Research Center, Inc., 10835 Road to the Cure, Suite 250, San Diego, CA 92121, USA
| | - Nhi Ngo
- Lundbeck La Jolla Research Center, Inc., 10835 Road to the Cure, Suite 250, San Diego, CA 92121, USA
| | - Kenneth M Lum
- Lundbeck La Jolla Research Center, Inc., 10835 Road to the Cure, Suite 250, San Diego, CA 92121, USA
| | - Benjamin F Cravatt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA; Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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4
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Litwin K, Crowley VM, Suciu RM, Boger DL, Cravatt BF. Chemical proteomic identification of functional cysteines with atypical electrophile reactivities. Tetrahedron Lett 2021; 67. [PMID: 33776155 DOI: 10.1016/j.tetlet.2021.152861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/19/2022]
Abstract
Cysteine-directed covalent ligands have emerged as a versatile category of chemical probes and drugs that leverage thiol nucleophilicity to form permanent adducts with proteins of interest. Understanding the scope of cysteines that can be targeted by covalent ligands, as well as the types of electrophiles that engage these residues, represent important challenges for fully realizing the potential of cysteine-directed chemical probe discovery. Although chemical proteomic strategies have begun to address these important questions, only a limited number of electrophilic chemotypes have been explored to date. Here, we describe a diverse set of candidate electrophiles appended to a common core 6-methoxy-1,2,3,4-tetrahydroquinoline fragment and evaluate their global cysteine reactivity profiles in human cancer cell proteomes. This work uncovered atypical reactivity patterns for a discrete set of cysteines, including residues involved in enzymatic catalysis and located in proximity to protein-protein interactions. These findings thus point to potentially preferred electrophilic groups for site-selectively targeting functional cysteines in the human proteome.
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Affiliation(s)
- Kevin Litwin
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92307, United States
| | - Vincent M Crowley
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92307, United States
| | - Radu M Suciu
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92307, United States
| | - Dale L Boger
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92307, United States
| | - Benjamin F Cravatt
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92307, United States
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5
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Vinogradova EV, Zhang X, Remillard D, Lazar DC, Suciu RM, Wang Y, Bianco G, Yamashita Y, Crowley VM, Schafroth MA, Yokoyama M, Konrad DB, Lum KM, Simon GM, Kemper EK, Lazear MR, Yin S, Blewett MM, Dix MM, Nguyen N, Shokhirev MN, Chin EN, Lairson LL, Melillo B, Schreiber SL, Forli S, Teijaro JR, Cravatt BF. An Activity-Guided Map of Electrophile-Cysteine Interactions in Primary Human T Cells. Cell 2020; 182:1009-1026.e29. [PMID: 32730809 DOI: 10.1016/j.cell.2020.07.001] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [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] [Received: 10/18/2019] [Revised: 05/14/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022]
Abstract
Electrophilic compounds originating from nature or chemical synthesis have profound effects on immune cells. These compounds are thought to act by cysteine modification to alter the functions of immune-relevant proteins; however, our understanding of electrophile-sensitive cysteines in the human immune proteome remains limited. Here, we present a global map of cysteines in primary human T cells that are susceptible to covalent modification by electrophilic small molecules. More than 3,000 covalently liganded cysteines were found on functionally and structurally diverse proteins, including many that play fundamental roles in immunology. We further show that electrophilic compounds can impair T cell activation by distinct mechanisms involving the direct functional perturbation and/or degradation of proteins. Our findings reveal a rich content of ligandable cysteines in human T cells and point to electrophilic small molecules as a fertile source for chemical probes and ultimately therapeutics that modulate immunological processes and their associated disorders.
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Affiliation(s)
| | - Xiaoyu Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Remillard
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel C Lazar
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Radu M Suciu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yujia Wang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Giulia Bianco
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Yamashita
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Medicinal Chemistry Research Laboratories, New Drug Research Division, Otsuka Pharmaceutical Co., Ltd., 463-10 Kawauchi-cho, Tokushima 771-0192, Japan
| | - Vincent M Crowley
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael A Schafroth
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Minoru Yokoyama
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David B Konrad
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kenneth M Lum
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel M Simon
- Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA 92121, USA
| | - Esther K Kemper
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael R Lazear
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sifei Yin
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Megan M Blewett
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Melissa M Dix
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nhan Nguyen
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Emily N Chin
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Luke L Lairson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02138, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Teijaro
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
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6
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Zambetti NA, Firestone AJ, Remsberg JR, Huang BJ, Wong JC, Long AM, Predovic M, Suciu RM, Inguva A, Kogan SC, Haigis KM, Cravatt BF, Shannon K. Genetic disruption of N-RasG12D palmitoylation perturbs hematopoiesis and prevents myeloid transformation in mice. Blood 2020; 135:1772-1782. [PMID: 32219446 PMCID: PMC7225687 DOI: 10.1182/blood.2019003530] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 10/01/2019] [Accepted: 02/26/2020] [Indexed: 02/08/2023] Open
Abstract
Oncogenic RAS mutations pose substantial challenges for rational drug discovery. Sequence variations within the hypervariable region of Ras isoforms underlie differential posttranslational modification and subcellular trafficking, potentially resulting in selective vulnerabilities. Specifically, inhibiting the palmitoylation/depalmitoylation cycle is an appealing strategy for treating NRAS mutant cancers, particularly as normal tissues would retain K-Ras4b function for physiologic signaling. The role of endogenous N-RasG12D palmitoylation in signal transduction, hematopoietic differentiation, and myeloid transformation is unknown, and addressing these key questions will inform efforts to develop mechanism-based therapies. To evaluate the palmitoylation/depalmitoylation cycle as a candidate drug target in an in vivo disease-relevant model system, we introduced a C181S mutation into a conditional NrasG12D "knock-in" allele. The C181S second-site amino acid substitution abrogated myeloid transformation by NrasG12D, which was associated with mislocalization of the nonpalmitoylated N-Ras mutant protein, reduced Raf/MEK/ERK signaling, and alterations in hematopoietic stem and progenitor populations. Furthermore, hematologic malignancies arising in NrasG12D/G12D,C181S compound heterozygous mice invariably acquired revertant mutations that restored cysteine 181. Together, these studies validate the palmitoylation cycle as a promising therapeutic target in NRAS mutant cancers.
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Affiliation(s)
- Noemi A Zambetti
- Department of Pediatrics
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Ari J Firestone
- Department of Pediatrics
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | | | - Benjamin J Huang
- Department of Pediatrics
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Jasmine C Wong
- Department of Pediatrics
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | | | | | - Radu M Suciu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA
| | | | - Scott C Kogan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA
| | - Kevin M Haigis
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Boston, MA; and
- Department of Medicine, Harvard University Medical School, Boston, MA
| | | | - Kevin Shannon
- Department of Pediatrics
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
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7
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Zambetti NA, Firestone AJ, Wong JC, Long AM, Inguva A, Remsberg JR, Suciu RM, Cravatt BF, Haigis KM, Shannon K. Abstract A25: In vivo evidence validating the palmitoylation/depalmitoylation cycle as a therapeutic target in NRAS mutant hematologic cancers. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-a25] [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
A dynamic cycle of palmitoylation and depalmitoylation stably localizes N-Ras, but not K-Ras-4b, at the plasma membrane. This selective dependency suggests that targeting palmitoylation could inhibit the growth of NRAS-mutant cancers while leaving normal cells unaffected, due to their intact K-Ras-4b function. We sought to clarify the dependency of oncogenic N-Ras signaling on palmitoylation in a model relevant to human cancer. We used the lox-STOP-lox (LSL) knock-in system (Haigis et al., Nat Genet 2008) to express an NrasG12D oncogene at physiologic levels, and generated a second site mutation abrogating the palmitoylation site (C181S). We then compared Mx1-Cre; NrasLSL-G12D,C181S/LSL-G12D,C181S to Mx1-Cre; NrasWT/WT and Mx1-Cre; NrasLSL-G12D/LSL-G12D (hereafter G12D,C181S, WT, and G12D, respectively). We injected mice with poly(I:C) at weaning to excise the LSL cassette in hematopoietic cells. As reported (Wang et al., Blood 2011; Xu et al., Cancer Disc 2013), G12D mice died early (119-267 days, n=14) from an aggressive myeloproliferative disorder (MPD). In contrast, no mortality was observed in the G12D,C181S and WT cohorts until 18-19 months of age (p=3x10-6 by Kaplan-Meier analysis). Pathologic analysis of 6-month-old mice showed that key features of MPD were fully rescued in the G12D,C181S cohort. Specifically, whereas white blood cell (WBC) counts and spleen sizes were in the normal range in G12D,C181S and WT mice, G12D mice had profound leukocytosis (median WBC count: 52.19 k/μL), splenomegaly (median spleen weight: 0.884 g), and myeloid expansion (n=6). Biochemical analysis revealed that N-RasG12D,C181S accumulated in the GTP-bound conformation, but mostly localized in the cytosol, and failed to hyperactivate the MAPK pathway. We next generated NrasG12D,C181S/G12D compound heterozygous mice to investigate potential interactions between oncogenic NrasG12D alleles with and without the C181S mutation in vivo. Over half of these mice developed hematologic disease and died prematurely, although later than homozygous G12D mutant mice (median survivals: 429 and 225 days; n = 22 and 14, respectively). Common findings in moribund mice were splenomegaly, expansion of myeloid cells, and different degrees of leukocytosis and anemia. Importantly, genetic analysis from diseased mice revealed reduced frequency or absence of the NrasG12D,C181S allele (allelic burden 0-30%) due to secondary somatic genetic events. This observation supports the existence of high selective pressure to overcome growth-suppressive properties of unpalmitoylated N-Ras during leukemogenesis. In conclusion, these studies provide strong genetic evidence validating palmitoylation as a therapeutic target in NRAS mutant hematologic malignancies and establish a novel model for addressing this question in other cancers.
Citation Format: Noemi A. Zambetti, Ari J. Firestone, Jasmine C. Wong, Amanda M. Long, Anagha Inguva, Jarrett R. Remsberg, Radu M. Suciu, Benjamin F. Cravatt, Kevin M. Haigis, Kevin Shannon. In vivo evidence validating the palmitoylation/depalmitoylation cycle as a therapeutic target in NRAS mutant hematologic cancers [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A25.
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Affiliation(s)
- Noemi A. Zambetti
- 1Department of Pediatrics, University of California San Francisco, San Francisco, CA,
| | - Ari J. Firestone
- 1Department of Pediatrics, University of California San Francisco, San Francisco, CA,
| | - Jasmine C. Wong
- 1Department of Pediatrics, University of California San Francisco, San Francisco, CA,
| | - Amanda M. Long
- 1Department of Pediatrics, University of California San Francisco, San Francisco, CA,
| | - Anagha Inguva
- 1Department of Pediatrics, University of California San Francisco, San Francisco, CA,
| | - Jarrett R. Remsberg
- 2Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA,
| | - Radu M. Suciu
- 2Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA,
| | - Benjamin F. Cravatt
- 2Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA,
| | - Kevin M. Haigis
- 3Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard University Medical School, Boston, MA
| | - Kevin Shannon
- 1Department of Pediatrics, University of California San Francisco, San Francisco, CA,
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8
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Zambaldo C, Vinogradova EV, Qi X, Iaconelli J, Suciu RM, Koh M, Senkane K, Chadwick SR, Sanchez BB, Chen JS, Chatterjee AK, Liu P, Schultz PG, Cravatt BF, Bollong MJ. 2-Sulfonylpyridines as Tunable, Cysteine-Reactive Electrophiles. J Am Chem Soc 2020; 142:8972-8979. [PMID: 32302104 DOI: 10.1021/jacs.0c02721] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The emerging use of covalent ligands as chemical probes and drugs would benefit from an expanded repertoire of cysteine-reactive electrophiles for efficient and diverse targeting of the proteome. Here we use the endogenous electrophile sensor of mammalian cells, the KEAP1-NRF2 pathway, to discover cysteine-reactive electrophilic fragments from a reporter-based screen for NRF2 activation. This strategy identified a series of 2-sulfonylpyridines that selectively react with biological thiols via nucleophilic aromatic substitution (SNAr). By tuning the electrophilicity and appended recognition elements, we demonstrate the potential of the 2-sulfonylpyridine reactive group with the discovery of a selective covalent modifier of adenosine deaminase (ADA). Targeting a cysteine distal to the active site, this molecule attenuates the enzymatic activity of ADA and inhibits proliferation of lymphocytic cells. This study introduces a modular and tunable SNAr-based reactive group for targeting reactive cysteines in the human proteome and illustrates the pharmacological utility of this electrophilic series.
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Affiliation(s)
- Claudio Zambaldo
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Ekaterina V Vinogradova
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Xiaotian Qi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jonathan Iaconelli
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Radu M Suciu
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Minseob Koh
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Kristine Senkane
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Stormi R Chadwick
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Brittany B Sanchez
- Automated Synthesis Facility, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jason S Chen
- Automated Synthesis Facility, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Arnab K Chatterjee
- California Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Michael J Bollong
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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9
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Yamashita Y, Vinogradova EV, Zhang X, Suciu RM, Cravatt BF. A Chemical Proteomic Probe for the Mitochondrial Pyruvate Carrier Complex. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yu Yamashita
- Department of Chemistry The Scripps Research Institute La Jolla CA 92037 USA
- Medicinal Chemistry Research Laboratories New Drug Research Division Otsuka Pharmaceutical Co., Ltd. 463-10 Kawauchi-cho Tokushima 771-0192 Japan
| | | | - Xiaoyu Zhang
- Department of Chemistry The Scripps Research Institute La Jolla CA 92037 USA
| | - Radu M. Suciu
- Department of Chemistry The Scripps Research Institute La Jolla CA 92037 USA
| | - Benjamin F. Cravatt
- Department of Chemistry The Scripps Research Institute La Jolla CA 92037 USA
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10
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Yamashita Y, Vinogradova EV, Zhang X, Suciu RM, Cravatt BF. A Chemical Proteomic Probe for the Mitochondrial Pyruvate Carrier Complex. Angew Chem Int Ed Engl 2020; 59:3896-3899. [PMID: 31863675 DOI: 10.1002/anie.201914391] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 11/11/2019] [Revised: 12/02/2019] [Indexed: 01/24/2023]
Abstract
Target engagement assays are crucial for establishing the mechanism-of-action of small molecules in living systems. Integral membrane transporters can present a challenging protein class for assessing cellular engagement by small molecules. The chemical proteomic discovery of alpha-chloroacetamide (αCA) compounds that covalently modify cysteine-54 (C54) of the MPC2 subunit of the mitochondrial pyruvate carrier (MPC) is presented. This finding is used to create an alkyne-modified αCA, YY4-yne, that serves as a cellular engagement probe for MPC2 in click chemistry-enabled western blotting or global mass spectrometry-based proteomic experiments. Studies with YY4-yne revealed that UK-5099, an alpha-cyanocinnamate inhibitor of the MPC complex, engages MPC2 with remarkable selectivity in human cells. These findings support a model where UK-5099 inhibits the MPC complex by binding to C54 of MPC2 in a covalent reversible manner that can be quantified in cells using the YY4-yne probe.
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Affiliation(s)
- Yu Yamashita
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Medicinal Chemistry Research Laboratories, New Drug Research Division, Otsuka Pharmaceutical Co., Ltd., 463-10 Kawauchi-cho, Tokushima, 771-0192, Japan
| | | | - Xiaoyu Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Radu M Suciu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
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11
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Pentinmikko N, Iqbal S, Mana M, Andersson S, Cognetta AB, Suciu RM, Roper J, Luopajärvi K, Markelin E, Gopalakrishnan S, Smolander OP, Naranjo S, Saarinen T, Juuti A, Pietiläinen K, Auvinen P, Ristimäki A, Gupta N, Tammela T, Jacks T, Sabatini DM, Cravatt BF, Yilmaz ÖH, Katajisto P. Notum produced by Paneth cells attenuates regeneration of aged intestinal epithelium. Nature 2019; 571:398-402. [PMID: 31292548 DOI: 10.1038/s41586-019-1383-0] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/10/2019] [Indexed: 12/12/2022]
Abstract
A decline in stem cell function impairs tissue regeneration during ageing, but the role of the stem-cell-supporting niche in ageing is not well understood. The small intestine is maintained by actively cycling intestinal stem cells that are regulated by the Paneth cell niche1,2. Here we show that the regenerative potential of human and mouse intestinal epithelium diminishes with age owing to defects in both stem cells and their niche. The functional decline was caused by a decrease in stemness-maintaining Wnt signalling due to production of Notum, an extracellular Wnt inhibitor, in aged Paneth cells. Mechanistically, high activity of mammalian target of rapamycin complex 1 (mTORC1) in aged Paneth cells inhibits activity of peroxisome proliferator activated receptor α (PPAR-α)3, and lowered PPAR-α activity increased Notum expression. Genetic targeting of Notum or Wnt supplementation restored function of aged intestinal organoids. Moreover, pharmacological inhibition of Notum in mice enhanced the regenerative capacity of aged stem cells and promoted recovery from chemotherapy-induced damage. Our results reveal a role of the stem cell niche in ageing and demonstrate that targeting of Notum can promote regeneration of aged tissues.
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Affiliation(s)
- Nalle Pentinmikko
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sharif Iqbal
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Miyeko Mana
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA, USA
| | - Simon Andersson
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Armand B Cognetta
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Radu M Suciu
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jatin Roper
- Department of Medicine, Division of Gastroenterology, Duke University, Durham, NC, USA
| | - Kalle Luopajärvi
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Eino Markelin
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | | | | | - Santiago Naranjo
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA, USA
| | - Tuure Saarinen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.,Abdominal Center, Department of Gastrointestinal Surgery, Helsinki University Hospital, Helsinki, Finland
| | - Anne Juuti
- Abdominal Center, Department of Gastrointestinal Surgery, Helsinki University Hospital, Helsinki, Finland
| | - Kirsi Pietiläinen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ari Ristimäki
- Department of Pathology, Research Programs Unit and HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Nitin Gupta
- Atlanta Gastroenterology Associates, Atlanta, GA, USA
| | - Tuomas Tammela
- Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tyler Jacks
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA, USA.,Howard Hughes Medical Institute, MIT, Cambridge, MA, USA
| | - David M Sabatini
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA, USA.,Howard Hughes Medical Institute, MIT, Cambridge, MA, USA.,Whitehead Institute for Biomedical Research, Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA, USA
| | - Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ömer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology, MIT, Cambridge, MA, USA
| | - Pekka Katajisto
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland. .,Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland. .,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
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12
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Senkane K, Vinogradova EV, Suciu RM, Crowley VM, Zaro BW, Bradshaw JM, Brameld KA, Cravatt BF. The Proteome‐Wide Potential for Reversible Covalency at Cysteine. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Kristine Senkane
- Department of ChemistryThe Scripps Research Institute La Jolla CA 92037 USA
| | | | - Radu M. Suciu
- Department of ChemistryThe Scripps Research Institute La Jolla CA 92037 USA
| | - Vincent M. Crowley
- Department of ChemistryThe Scripps Research Institute La Jolla CA 92037 USA
| | - Balyn W. Zaro
- Department of ChemistryThe Scripps Research Institute La Jolla CA 92037 USA
| | | | - Ken A. Brameld
- Principia Biopharma 220 E. Grand Avenue South San Francisco CA 94080 USA
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13
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Senkane K, Vinogradova EV, Suciu RM, Crowley VM, Zaro BW, Bradshaw JM, Brameld KA, Cravatt BF. The Proteome-Wide Potential for Reversible Covalency at Cysteine. Angew Chem Int Ed Engl 2019; 58:11385-11389. [PMID: 31222866 DOI: 10.1002/anie.201905829] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 05/10/2019] [Indexed: 01/06/2023]
Abstract
Reversible covalency, achieved with, for instance, highly electron-deficient olefins, offers a compelling strategy to design chemical probes and drugs that benefit from the sustained target engagement afforded by irreversible compounds, while avoiding permanent protein modification. Reversible covalency has mainly been evaluated for cysteine residues in individual kinases and the broader potential for this strategy to engage cysteines across the proteome remains unexplored. Herein, we describe a mass-spectrometry-based platform that integrates gel filtration with activity-based protein profiling to assess cysteine residues across the human proteome for both irreversible and reversible interactions with small-molecule electrophiles. Using this method, we identify numerous cysteine residues from diverse protein classes that are reversibly engaged by cyanoacrylamide fragment electrophiles, revealing the broad potential for reversible covalency as a strategy for chemical-probe discovery.
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Affiliation(s)
- Kristine Senkane
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | | | - Radu M Suciu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Vincent M Crowley
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Balyn W Zaro
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - J Michael Bradshaw
- Principia Biopharma, 220 E. Grand Avenue, South San Francisco, CA, 94080, USA
| | - Ken A Brameld
- Principia Biopharma, 220 E. Grand Avenue, South San Francisco, CA, 94080, USA
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
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14
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Zaro BW, Vinogradova EV, Lazar DC, Blewett MM, Suciu RM, Takaya J, Studer S, de la Torre JC, Casanova JL, Cravatt BF, Teijaro JR. Dimethyl Fumarate Disrupts Human Innate Immune Signaling by Targeting the IRAK4-MyD88 Complex. J Immunol 2019; 202:2737-2746. [PMID: 30885957 DOI: 10.4049/jimmunol.1801627] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/26/2019] [Indexed: 12/14/2022]
Abstract
Dimethyl fumarate (DMF) is a prescribed treatment for multiple sclerosis and has also been used to treat psoriasis. The electrophilicity of DMF suggests that its immunosuppressive activity is related to the covalent modification of cysteine residues in the human proteome. Nonetheless, our understanding of the proteins modified by DMF in human immune cells and the functional consequences of these reactions remains incomplete. In this study, we report that DMF inhibits human plasmacytoid dendritic cell function through a mechanism of action that is independent of the major electrophile sensor NRF2. Using chemical proteomics, we instead identify cysteine 13 of the innate immune kinase IRAK4 as a principal cellular target of DMF. We show that DMF blocks IRAK4-MyD88 interactions and IRAK4-mediated cytokine production in a cysteine 13-dependent manner. Our studies thus identify a proteomic hotspot for DMF action that constitutes a druggable protein-protein interface crucial for initiating innate immune responses.
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Affiliation(s)
- Balyn W Zaro
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | | | - Daniel C Lazar
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037; and
| | - Megan M Blewett
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Radu M Suciu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Junichiro Takaya
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Sean Studer
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037; and
| | - Juan Carlos de la Torre
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037; and
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037;
| | - John R Teijaro
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037; and
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15
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Gao DW, Vinogradova EV, Nimmagadda SK, Medina JM, Xiao Y, Suciu RM, Cravatt BF, Engle KM. Direct Access to Versatile Electrophiles via Catalytic Oxidative Cyanation of Alkenes. J Am Chem Soc 2018; 140:8069-8073. [PMID: 29894184 DOI: 10.1021/jacs.8b03704] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nucleophilic attack on carbon-based electrophiles is a central reactivity paradigm in chemistry and biology. The steric and electronic properties of the electrophile dictate its reactivity with different nucleophiles of interest, allowing the opportunity to fine-tune electrophiles for use as coupling partners in multistep organic synthesis or for covalent modification of proteins in drug discovery. Reactions that directly transform inexpensive chemical feedstocks into versatile carbon electrophiles would therefore be highly enabling. Herein, we report the catalytic, regioselective oxidative cyanation of conjugated and nonconjugated alkenes using a homogeneous copper catalyst and a bystanding N-F oxidant to furnish branched alkenyl nitriles that are difficult to prepare using existing methods. We show that the alkenyl nitrile products serve as electrophilic reaction partners for both organic synthesis and the chemical proteomic discovery of covalent protein ligands.
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Affiliation(s)
- De-Wei Gao
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Ekaterina V Vinogradova
- Department of Molecular Medicine , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Sri Krishna Nimmagadda
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Jose M Medina
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Yiyang Xiao
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Radu M Suciu
- Department of Molecular Medicine , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Benjamin F Cravatt
- Department of Molecular Medicine , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Keary M Engle
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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16
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Suciu RM, Cognetta AB, Potter ZE, Cravatt BF. Selective Irreversible Inhibitors of the Wnt-Deacylating Enzyme NOTUM Developed by Activity-Based Protein Profiling. ACS Med Chem Lett 2018; 9:563-568. [PMID: 29937983 PMCID: PMC6004566 DOI: 10.1021/acsmedchemlett.8b00191] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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] [Received: 04/25/2018] [Accepted: 05/17/2018] [Indexed: 02/07/2023] Open
Abstract
![]()
Wnt
proteins are secreted morphogens that play critical roles in
embryonic development and tissue remodeling in adult organisms. Aberrant
Wnt signaling contributes to diseases such as cancer. Wnts are modified
by an unusual O-fatty acylation event (O-linked palmitoleoylation of a conserved serine) that is required
for binding to Frizzled receptors. O-Palmitoleoylation
of Wnts is introduced by the porcupine (PORCN) acyltransferase and
removed by the serine hydrolase NOTUM. PORCN inhibitors are under
development for oncology, while NOTUM inhibitors have potential for
treating degenerative diseases. Here, we describe the use of activity-based
protein profiling (ABPP) to discover and advance a class of N-hydroxyhydantoin (NHH) carbamates that potently and selectively
inhibit NOTUM. An optimized NHH carbamate inhibitor, ABC99, preserves
Wnt-mediated cell signaling in the presence of NOTUM and was also
converted into an ABPP probe for visualizing NOTUM in native biological
systems.
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Affiliation(s)
- Radu M. Suciu
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Armand B. Cognetta
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Zachary E. Potter
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
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17
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Horning BD, Suciu RM, Ghadiri DA, Ulanovskaya OA, Matthews ML, Lum KM, Backus KM, Brown SJ, Rosen H, Cravatt BF. Chemical Proteomic Profiling of Human Methyltransferases. J Am Chem Soc 2016; 138:13335-13343. [PMID: 27689866 DOI: 10.1021/jacs.6b07830] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Methylation is a fundamental mechanism used in Nature to modify the structure and function of biomolecules, including proteins, DNA, RNA, and metabolites. Methyl groups are predominantly installed into biomolecules by a large and diverse class of S-adenosyl methionine (SAM)-dependent methyltransferases (MTs), of which there are ∼200 known or putative members in the human proteome. Deregulated MT activity contributes to numerous diseases, including cancer, and several MT inhibitors are in clinical development. Nonetheless, a large fraction of the human MT family remains poorly characterized, underscoring the need for new technologies to characterize MTs and their inhibitors in native biological systems. Here, we describe a suite of S-adenosyl homocysteine (SAH) photoreactive probes and their application in chemical proteomic experiments to profile and enrich a large number of MTs (>50) from human cancer cell lysates with remarkable specificity over other classes of proteins. We further demonstrate that the SAH probes can enrich MT-associated proteins and be used to screen for and assess the selectivity of MT inhibitors, leading to the discovery of a covalent inhibitor of nicotinamide N-methyltransferase (NNMT), an enzyme implicated in cancer and metabolic disorders. The chemical proteomics probes and methods for their utilization reported herein should prove of value for the functional characterization of MTs, MT complexes, and MT inhibitors in mammalian biology and disease.
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Affiliation(s)
- Benjamin D Horning
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Radu M Suciu
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Darian A Ghadiri
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Olesya A Ulanovskaya
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Megan L Matthews
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Kenneth M Lum
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Keriann M Backus
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Steven J Brown
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Hugh Rosen
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
| | - Benjamin F Cravatt
- Departments of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92307, United States
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18
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Suciu RM, Aydin E, Chen BE. GeneDig: a web application for accessing genomic and bioinformatics knowledge. BMC Bioinformatics 2015; 16:67. [PMID: 25888373 PMCID: PMC4349619 DOI: 10.1186/s12859-015-0497-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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] [Received: 09/18/2014] [Accepted: 02/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With the exponential increase and widespread availability of genomic, transcriptomic, and proteomic data, accessing these '-omics' data is becoming increasingly difficult. The current resources for accessing and analyzing these data have been created to perform highly specific functions intended for specialists, and thus typically emphasize functionality over user experience. RESULTS We have developed a web-based application, GeneDig.org, that allows any general user access to genomic information with ease and efficiency. GeneDig allows for searching and browsing genes and genomes, while a dynamic navigator displays genomic, RNA, and protein information simultaneously for co-navigation. We demonstrate that our application allows more than five times faster and efficient access to genomic information than any currently available methods. CONCLUSION We have developed GeneDig as a platform for bioinformatics integration focused on usability as its central design. This platform will introduce genomic navigation to broader audiences while aiding the bioinformatics analyses performed in everyday biology research.
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Affiliation(s)
- Radu M Suciu
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal General Hospital, 1650 Cedar Ave, L7-224, Montréal, H3G 1A4, , Québec, Canada.
| | - Emir Aydin
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal General Hospital, 1650 Cedar Ave, L7-224, Montréal, H3G 1A4, , Québec, Canada.
| | - Brian E Chen
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal General Hospital, 1650 Cedar Ave, L7-224, Montréal, H3G 1A4, , Québec, Canada. .,Departments of Medicine and Neurology & Neurosurgery, McGill University, Montréal, Québec, Canada.
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