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Babbe H, Sundberg TB, Tichenor M, Seierstad M, Bacani G, Berstler J, Chai W, Chang L, Chung DM, Coe K, Collins B, Finley M, Guletsky A, Lemke CT, Mak PA, Mathur A, Mercado-Marin EV, Metkar S, Raymond DD, Rives ML, Rizzolio M, Shaffer PL, Smith R, Smith J, Steele R, Steffens H, Suarez J, Tian G, Majewski N, Volak LP, Wei J, Desai PT, Ong LL, Koudriakova T, Goldberg SD, Hirst G, Kaushik VK, Ort T, Seth N, Graham DB, Plevy S, Venable JD, Xavier RJ, Towne JE. Identification of highly selective SIK1/2 inhibitors that modulate innate immune activation and suppress intestinal inflammation. Proc Natl Acad Sci U S A 2024; 121:e2307086120. [PMID: 38147543 PMCID: PMC10769863 DOI: 10.1073/pnas.2307086120] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/07/2023] [Indexed: 12/28/2023] Open
Abstract
The salt-inducible kinases (SIK) 1-3 are key regulators of pro- versus anti-inflammatory cytokine responses during innate immune activation. The lack of highly SIK-family or SIK isoform-selective inhibitors suitable for repeat, oral dosing has limited the study of the optimal SIK isoform selectivity profile for suppressing inflammation in vivo. To overcome this challenge, we devised a structure-based design strategy for developing potent SIK inhibitors that are highly selective against other kinases by engaging two differentiating features of the SIK catalytic site. This effort resulted in SIK1/2-selective probes that inhibit key intracellular proximal signaling events including reducing phosphorylation of the SIK substrate cAMP response element binding protein (CREB) regulated transcription coactivator 3 (CRTC3) as detected with an internally generated phospho-Ser329-CRTC3-specific antibody. These inhibitors also suppress production of pro-inflammatory cytokines while inducing anti-inflammatory interleukin-10 in activated human and murine myeloid cells and in mice following a lipopolysaccharide challenge. Oral dosing of these compounds ameliorates disease in a murine colitis model. These findings define an approach to generate highly selective SIK1/2 inhibitors and establish that targeting these isoforms may be a useful strategy to suppress pathological inflammation.
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Affiliation(s)
- Holger Babbe
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Thomas B. Sundberg
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | - Mark Tichenor
- Janssen Research and Development, LLC., San Diego, CA92121
| | - Mark Seierstad
- Janssen Research and Development, LLC., San Diego, CA92121
| | - Genesis Bacani
- Janssen Research and Development, LLC., San Diego, CA92121
| | - James Berstler
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | - Wenying Chai
- Janssen Research and Development, LLC., San Diego, CA92121
| | - Leon Chang
- Janssen Research and Development, LLC., San Diego, CA92121
| | | | - Kevin Coe
- Janssen Research and Development, LLC., San Diego, CA92121
| | | | - Michael Finley
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Alexander Guletsky
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | - Christopher T. Lemke
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | - Puiying A. Mak
- Janssen Research and Development, LLC., San Diego, CA92121
| | - Ashok Mathur
- Janssen Research and Development, LLC., Spring House, PA19477
| | | | - Shailesh Metkar
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | - Donald D. Raymond
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | | | | | - Paul L. Shaffer
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Russell Smith
- Janssen Research and Development, LLC., San Diego, CA92121
| | | | - Ruth Steele
- Janssen Research and Development, LLC., Spring House, PA19477
| | | | - Javier Suarez
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Gaochao Tian
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Nathan Majewski
- Janssen Research and Development, LLC., Spring House, PA19477
| | | | - Jianmei Wei
- Janssen Research and Development, LLC., San Diego, CA92121
| | - Prerak T. Desai
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Luvena L. Ong
- Janssen Research and Development, LLC., Spring House, PA19477
| | | | | | - Gavin Hirst
- Janssen Research and Development, LLC., San Diego, CA92121
| | - Virendar K. Kaushik
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | - Tatiana Ort
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Nilufer Seth
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Daniel B. Graham
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA02142
| | - Scott Plevy
- Janssen Research and Development, LLC., Spring House, PA19477
| | | | - Ramnik J. Xavier
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA02142
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Grell TA, Mason M, Thompson AA, Gómez-Tamayo JC, Riley D, Wagner MV, Steele R, Ortiz-Meoz RF, Wadia J, Shaffer PL, Tresadern G, Sharma S, Yu X. Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer. Heliyon 2022; 8:e12392. [PMID: 36590518 PMCID: PMC9801130 DOI: 10.1016/j.heliyon.2022.e12392] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/07/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent studies have implicated the third and least well-characterized isoform, mitochondrial NADP+-dependent malic enzyme 3 (ME3), as a therapeutic target for pancreatic cancers. Here, we utilized an integrated structure approach to determine the structures of ME3 in various ligand-binding states at near-atomic resolutions. ME3 is captured in the open form existing as a stable tetramer and its dynamic Domain C is critical for activity. Catalytic assay results reveal that ME3 is a non-allosteric enzyme and does not require modulators for activity while structural analysis suggests that the inner stability of ME3 Domain A relative to ME2 disables allostery in ME3. With structural information available for all three malic enzymes, the foundation has been laid to understand the structural and biochemical differences of these enzymes and could aid in the development of specific malic enzyme small molecule drugs.
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Affiliation(s)
- Tsehai A.J. Grell
- Structural and Protein Sciences, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Mark Mason
- Structural and Protein Sciences, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Aaron A. Thompson
- Structural and Protein Sciences, Janssen Research and Development, LLC, San Diego, California 92121, United States
| | | | - Daniel Riley
- Lead Discovery and Molecular Pharmacology, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Michelle V. Wagner
- Emerging Science Initiative, Janssen Research and Development, LLC, San Diego, California 92121, United States
| | - Ruth Steele
- Structural and Protein Sciences, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Rodrigo F. Ortiz-Meoz
- Lead Discovery and Molecular Pharmacology, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Jay Wadia
- Emerging Science Initiative, Janssen Research and Development, LLC, San Diego, California 92121, United States
| | - Paul L. Shaffer
- Structural and Protein Sciences, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Gary Tresadern
- Computational Chemistry, Janssen Research and Development, LLC, Beerse, B2340, Belgium
| | - Sujata Sharma
- Structural and Protein Sciences, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States,Structural and Protein Sciences, Janssen Research and Development, LLC, San Diego, California 92121, United States,Corresponding author.
| | - Xiaodi Yu
- Structural and Protein Sciences, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States,Corresponding author.
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3
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Simard JR, Michelsen K, Wang Y, Yang C, Youngblood B, Grubinska B, Taborn K, Gillie DJ, Cook K, Chung K, Long AM, Hall BE, Shaffer PL, Foti RS, Gingras J. Modulation of Ligand-Gated Glycine Receptors Via Functional Monoclonal Antibodies. J Pharmacol Exp Ther 2022; 383:56-69. [PMID: 35926871 DOI: 10.1124/jpet.121.001026] [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] [Received: 11/17/2021] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 12/15/2022] Open
Abstract
Ion channels are targets of considerable therapeutic interest to address a wide variety of neurologic indications, including pain perception. Current pharmacological strategies have focused mostly on small molecule approaches that can be limited by selectivity requirements within members of a channel family or superfamily. Therapeutic antibodies have been proposed, designed, and characterized to alleviate this selectivity limitation; however, there are no Food and Drug Administration-approved therapeutic antibody-based drugs targeting ion channels on the market to date. Here, in an effort to identify novel classes of engineered ion channel modulators for potential neurologic therapeutic applications, we report the generation and characterization of six (EC50 < 25nM) Cys-loop receptor family monoclonal antibodies with modulatory function against rat and human glycine receptor alpha 1 (GlyRα1) and/or GlyRα3. These antibodies have activating (i.e., positive modulator) or inhibiting (i.e., negative modulator) profiles. Moreover, GlyRα3 selectivity was successfully achieved for two of the three positive modulators identified. When dosed intravenously, the antibodies achieved sufficient brain exposure to cover their calculated in vitro EC50 values. When compared head-to-head at identical exposures, the GlyRα3-selective antibody showed a more desirable safety profile over the nonselective antibody, thus demonstrating, for the first time, an advantage for GlyRα3-selectivity. Our data show that ligand-gated ion channels of the glycine receptor family within the central nervous system can be functionally modulated by engineered biologics in a dose-dependent manner and that, despite high protein homology between the alpha subunits, selectivity can be achieved within this receptor family, resulting in future therapeutic candidates with more desirable drug safety profiles. SIGNIFICANCE STATEMENT: This study presents immunization and multiplatform screening approaches to generate a diverse library of functional antibodies (agonist, potentiator, or inhibitory) raised against human glycine receptors (GlyRs). This study also demonstrates the feasibility of acquiring alpha subunit selectivity, a desirable therapeutic profile. When tested in vivo, these tool molecules demonstrated an increased safety profile in favor of GlyRα3-selectivity. These are the first reported functional GlyR antibodies that may open new avenues to treating central nervous system diseases with subunit selective biologics.
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Affiliation(s)
- Jeffrey R Simard
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Klaus Michelsen
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Yan Wang
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Chunhua Yang
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Beth Youngblood
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Barbara Grubinska
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Kristin Taborn
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Daniel J Gillie
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Kevin Cook
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Kyu Chung
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Alexander M Long
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Brian E Hall
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Paul L Shaffer
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Robert S Foti
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
| | - Jacinthe Gingras
- Departments of Neuroscience (J.R.S., C.Y., B.Y. B.G., K.T., D.J.G., J.G.), Molecular Engineering (K.M., A.M.L., P.L.S.), Protein Technologies (Y.W., B.E.H.), and Pharmacokinetics and Drug Metabolism (R.S.F.), Amgen Research, Cambridge, Massachusetts; and Department of Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California (K.Co., K.Ch.)
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4
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Huang X, Chen H, Shaffer PL. Crystal Structures of Human GlyRα3 Bound to Ivermectin. Structure 2017; 25:945-950.e2. [PMID: 28479061 DOI: 10.1016/j.str.2017.04.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [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: 12/20/2016] [Revised: 01/31/2017] [Accepted: 04/14/2017] [Indexed: 11/30/2022]
Abstract
Ivermectin acts as a positive allosteric modulator of several Cys-loop receptors including the glutamate-gated chloride channels (GluCls), γ-aminobutyric acid receptors (GABAARs), glycine receptors (GlyRs), and neuronal α7-nicotinic receptors (α7 nAChRs). The crystal structure of Caenorhabditis elegans GluCl complexed with ivermectin revealed the details of its ivermectin binding site. Although the electron microscopy structure of zebrafish GlyRα1 complexed with ivermectin demonstrated a similar binding orientation, detailed structural information on the ivermectin binding and pore opening for Cys-loop receptors in vertebrates has been elusive. Here we present the crystal structures of human GlyRα3 in complex with ivermectin at 2.85 and 3.08 Å resolution. Our structures allow us to explore in detail the molecular recognition of ivermectin by GlyRs, GABAARs, and α7 nAChRs. Comparisons with previous structures reveal how the ivermectin binding expands the ion channel pore. Our results hold promise in structure-based design of GlyR modulators for the treatment of neuropathic pain.
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Affiliation(s)
- Xin Huang
- Department of Molecular Structure and Characterization, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA.
| | - Hao Chen
- Department of Protein Technologies, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA
| | - Paul L Shaffer
- Department of Molecular Structure and Characterization, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA.
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5
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Bregman H, Simard JR, Andrews KL, Ayube S, Chen H, Gunaydin H, Guzman-Perez A, Hu J, Huang L, Huang X, Krolikowski PH, Lehto SG, Lewis RT, Michelsen K, Pegman P, Plant MH, Shaffer PL, Teffera Y, Yi S, Zhang M, Gingras J, DiMauro EF. The Discovery and Hit-to-Lead Optimization of Tricyclic Sulfonamides as Potent and Efficacious Potentiators of Glycine Receptors. J Med Chem 2016; 60:1105-1125. [PMID: 28001399 DOI: 10.1021/acs.jmedchem.6b01496] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Current pain therapeutics suffer from undesirable psychotropic and sedative side effects, as well as abuse potential. Glycine receptors (GlyRs) are inhibitory ligand-gated ion channels expressed in nerves of the spinal dorsal horn, where their activation is believed to reduce transmission of painful stimuli. Herein, we describe the identification and hit-to-lead optimization of a novel class of tricyclic sulfonamides as allosteric GlyR potentiators. Initial optimization of high-throughput screening (HTS) hit 1 led to the identification of 3, which demonstrated ex vivo potentiation of glycine-activated current in mouse dorsal horn neurons from spinal cord slices. Further improvement of potency and pharmacokinetics produced in vivo proof-of-concept tool molecule 20 (AM-1488), which reversed tactile allodynia in a mouse spared-nerve injury (SNI) model. Additional structural optimization provided highly potent potentiator 32 (AM-3607), which was cocrystallized with human GlyRα3cryst to afford the first described potentiator-bound X-ray cocrystal structure within this class of ligand-gated ion channels (LGICs).
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Affiliation(s)
| | - Jeffrey R Simard
- Department of Neuroscience, Amgen Inc. , One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | | | | | | | | | | | | | | | | | | | - Sonya G Lehto
- Department of Neuroscience, Amgen Inc. , One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | | | | | | | | | | | | | | | - Maosheng Zhang
- Department of Neuroscience, Amgen Inc. , One Amgen Center Drive, Thousand Oaks, California 91320, United States
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Smith AL, Andrews KL, Beckmann H, Bellon SF, Beltran PJ, Booker S, Chen H, Chung YA, D’Angelo ND, Dao J, Dellamaggiore KR, Jaeckel P, Kendall R, Labitzke K, Long AM, Materna-Reichelt S, Mitchell P, Norman MH, Powers D, Rose M, Shaffer PL, Wu MM, Lipford JR. Discovery of 1H-Pyrazol-3(2H)-ones as Potent and Selective Inhibitors of Protein Kinase R-like Endoplasmic Reticulum Kinase (PERK). J Med Chem 2015; 58:1426-41. [DOI: 10.1021/jm5017494] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - Holger Beckmann
- Amgen Research GmbH, Josef-Engert-Straße
11, D-93053 Regensburg, Germany
| | | | | | | | | | | | | | | | | | - Peter Jaeckel
- Amgen Research GmbH, Josef-Engert-Straße
11, D-93053 Regensburg, Germany
| | | | - Katja Labitzke
- Amgen Research GmbH, Josef-Engert-Straße
11, D-93053 Regensburg, Germany
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7
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Peterson EA, Boezio AA, Andrews PS, Boezio CM, Bush TL, Cheng AC, Choquette D, Coats JR, Colletti AE, Copeland KW, DuPont M, Graceffa R, Grubinska B, Kim JL, Lewis RT, Liu J, Mullady EL, Potashman MH, Romero K, Shaffer PL, Stanton MK, Stellwagen JC, Teffera Y, Yi S, Cai T, La DS. Discovery and optimization of potent and selective imidazopyridine and imidazopyridazine mTOR inhibitors. Bioorg Med Chem Lett 2012; 22:4967-74. [PMID: 22765895 DOI: 10.1016/j.bmcl.2012.06.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 06/06/2012] [Accepted: 06/11/2012] [Indexed: 12/18/2022]
Abstract
mTOR is a critical regulator of cellular signaling downstream of multiple growth factors. The mTOR/PI3K/AKT pathway is frequently mutated in human cancers and is thus an important oncology target. Herein we report the evolution of our program to discover ATP-competitive mTOR inhibitors that demonstrate improved pharmacokinetic properties and selectivity compared to our previous leads. Through targeted SAR and structure-guided design, new imidazopyridine and imidazopyridazine scaffolds were identified that demonstrated superior inhibition of mTOR in cellular assays, selectivity over the closely related PIKK family and improved in vivo clearance over our previously reported benzimidazole series.
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Affiliation(s)
- Emily A Peterson
- Medicinal Chemistry, Amgen Inc., 360 Binney St., Cambridge, MA 02142, USA.
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8
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Abstract
Amino acid, polyamine, and organocation (APC) transporters are secondary transporters that play essential roles in nutrient uptake, neurotransmitter recycling, ionic homeostasis, and regulation of cell volume. Here, we present the crystal structure of apo-ApcT, a proton-coupled broad-specificity amino acid transporter, at 2.35 angstrom resolution. The structure contains 12 transmembrane helices, with the first 10 consisting of an inverted structural repeat of 5 transmembrane helices like the leucine transporter LeuT. The ApcT structure reveals an inward-facing, apo state and an amine moiety of lysine-158 located in a position equivalent to the sodium ion site Na2 of LeuT. We propose that lysine-158 is central to proton-coupled transport and that the amine group serves the same functional role as the Na2 ion in LeuT, thus demonstrating common principles among proton- and sodium-coupled transporters.
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Affiliation(s)
- Paul L Shaffer
- Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA
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9
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Shaffer PL, McDonnell DP, Gewirth DT. Characterization of transcriptional activation and DNA-binding functions in the hinge region of the vitamin D receptor. Biochemistry 2005; 44:2678-85. [PMID: 15709781 DOI: 10.1021/bi0477182] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [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] [Indexed: 11/28/2022]
Abstract
The vitamin D receptor (VDR) is a ligand-responsive transcription factor that forms active, heterodimeric complexes with the 9-cis retinoic acid receptor (RXR) on vitamin D response elements (VDREs). Both proteins consist of an N-terminal DNA-binding domain, a C-terminal ligand-binding domain, and an intervening hinge region. The length requirements of the hinge for both transcriptional regulation and DNA binding have not been studied to date for any member of the steroid hormone superfamily. We have generated a series of internal deletion mutants of the VDR hinge and found that deletion of as few as five amino acids from the C-terminus of the hinge significantly reduces transcriptional activation in vivo. Replacing deleted residues in the C-terminus of the hinge with alanines restored activity, indicating that this section of the hinge acts as a sequence-independent spacer. The hinge region of VDR forms a long helix, and the geometric consequences of this structure may explain the requirement of the hinge region for transcriptional activity. Interestingly, all of the deletion mutants, even those that do not activate transcription, bind VDREs with equal and high affinity, indicating that the defect in these mutants is not their ability to bind VDREs. In contrast to VDR, constructs of RXR containing deletions of up to 14 amino acids in the hinge region exhibit near wild-type transcriptional activity. The ability to delete more of the RXR hinge may be related to the additional plasticity required by its role as the common heterodimer partner for nuclear receptors on differing DNA elements.
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Affiliation(s)
- Paul L Shaffer
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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Immormino RM, Dollins DE, Shaffer PL, Soldano KL, Walker MA, Gewirth DT. Ligand-induced conformational shift in the N-terminal domain of GRP94, an Hsp90 chaperone. J Biol Chem 2004; 279:46162-71. [PMID: 15292259 DOI: 10.1074/jbc.m405253200] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
GRP94 is the endoplasmic reticulum paralog of cytoplasmic Hsp90. Models of Hsp90 action posit an ATP-dependent conformational switch in the N-terminal ligand regulatory domain of the chaperone. However, crystal structures of the isolated N-domain of Hsp90 in complex with a variety of ligands have yet to demonstrate such a conformational change. We have determined the structure of the N-domain of GRP94 in complex with ATP, ADP, and AMP. Compared with the N-ethylcarboxamidoadenosine and radicicol-bound forms, these structures reveal a large conformational rearrangement in the protein. The nucleotide-bound form exposes new surfaces that interact to form a biochemically plausible dimer that is reminiscent of those seen in structures of MutL and DNA gyrase. Weak ATP binding and a conformational change in response to ligand identity are distinctive mechanistic features of GRP94 and suggest a model for how GRP94 functions in the absence of co-chaperones and ATP hydrolysis.
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Affiliation(s)
- Robert M Immormino
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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Abstract
The Vitamin D receptor (VDR) is a ligand-responsive transcription factor that forms homo- or heterodimers on response elements composed of two hexameric half-sites separated by three base pairs of spacer DNA. Binding of 1alpha,25-dihydroxyvitamin D(3) to the full-length VDR causes destabilization of the VDR homodimer and formation of a heterodimeric complex with the 9-cis retinoic acid receptor (RXR). VDR and RXR DNA-binding domains (DBDs) do not mimic this behavior, however: VDR DBD homodimers are formed exclusively, even in the presence of excess RXR DBD. Exploiting the asymmetry of the heterodimer and our knowledge of the homodimeric DBD interface, we have engineered VDR mutants that disfavor the homodimeric complex and allow for the formation of heterodimeric DBD complexes with RXR on DR3 elements. One of these complexes has been crystallized and its structure determined. However, the polarity of the proteins relative to the DNA is non-physiological due to crystal packing between symmetry-related VDR DBD protomers. This reveals a flattened energy landscape that appears to rely on elements outside of the core DBD for response element discrimination in the heterodimer.
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Affiliation(s)
- Paul L Shaffer
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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Shaffer PL, Jivan A, Dollins DE, Claessens F, Gewirth DT. Structural basis of androgen receptor binding to selective androgen response elements. Proc Natl Acad Sci U S A 2004; 101:4758-63. [PMID: 15037741 PMCID: PMC387321 DOI: 10.1073/pnas.0401123101] [Citation(s) in RCA: 254] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Steroid receptors bind as dimers to a degenerate set of response elements containing inverted repeats of a hexameric half-site separated by 3 bp of spacer (IR3). Naturally occurring selective androgen response elements have recently been identified that resemble direct repeats of the hexameric half-site (ADR3). The 3D crystal structure of the androgen receptor (AR) DNA-binding domain bound to a selective ADR3 reveals an unexpected head-to-head arrangement of the two protomers rather than the expected head-to-tail arrangement seen in nuclear receptors bound to response elements of similar geometry. Compared with the glucocorticoid receptor, the DNA-binding domain dimer interface of the AR has additional interactions that stabilize the AR dimer and increase the affinity for nonconsensus response elements. This increased interfacial stability compared with the other steroid receptors may account for the selective binding of AR to ADR3 response elements.
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Affiliation(s)
- Paul L Shaffer
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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Abstract
The vitamin D receptor (VDR) is a member of the steroid and nuclear hormone receptor superfamily of eukaryotic transcription factors and binds target DNA, or response elements, as a homodimer or heterodimer with the 9-cis retinoid X receptor (RXR). In this chapter, we survey the current understanding of VDR-DNA interactions, emphasizing recent structural insights. We highlight the stereochemical interactions that dictate DNA binding and hexameric half-site sequence affinity as well as the protein-protein interactions that account for preferential binding to a direct repeat of half-sites with three base pairs of spacer DNA (DR3). In addition, we review alternative response element arrangements other than those with DR3. Finally, the chapter discusses the VDR DNA binding domain (DBD) and suggests that it violates classical canons because it does not heterodimerize with the RXR DBD. This unique behavior of VDR is considered in light of recent results demonstrating the formation of VDR DBD-DNA and DR3 DBD-DNA complexes with RXR using a mutant VDR protomer.
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Affiliation(s)
- Paul L Shaffer
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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Abstract
The vitamin D receptor (VDR) forms homo- or heterodimers on response elements composed of two hexameric half-sites separated by 3 bp of spacer DNA. We describe here the crystal structures at 2.7-2.8 A resolution of the VDR DNA-binding region (DBD) in complex with response elements from three different promoters: osteopontin (SPP), canonical DR3 and osteocalcin (OC). These structures reveal the chemical basis for the increased affinity of VDR for the SPP response element, and for the poor stability of the VDR-OC complex, relative to the canonical DR3 response element. The homodimeric protein-protein interface is stabilized by van der Waals interactions and is predominantly non-polar. An extensive alpha-helix at the C-terminal end of the VDR DBD resembles that found in the thyroid hormone receptor (TR), and suggests a mechanism by which VDR and TR discriminate among response elements. Selective structure-based mutations in the asymmetric homodimeric interface result in a VDR DBD protein that is defective in homodimerization but now forms heterodimers with the 9-cis retinoic acid receptor (RXR) DBD.
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Affiliation(s)
| | - Daniel T. Gewirth
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
Corresponding author e-mail:
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