1
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Inghardt T, Antonsson T, Ericsson C, Hovdal D, Johannesson P, Johansson C, Jurva U, Kajanus J, Kull B, Michaëlsson E, Pettersen A, Sjögren T, Sörensen H, Westerlund K, Lindstedt EL. Discovery of AZD4831, a Mechanism-Based Irreversible Inhibitor of Myeloperoxidase, As a Potential Treatment for Heart Failure with Preserved Ejection Fraction. J Med Chem 2022; 65:11485-11496. [PMID: 36005476 PMCID: PMC9469207 DOI: 10.1021/acs.jmedchem.1c02141] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myeloperoxidase is a promising therapeutic target for treatment of patients suffering from heart failure with preserved ejection fraction (HFpEF). We aimed to discover a covalent myeloperoxidase inhibitor with high selectivity for myeloperoxidase over thyroid peroxidase, limited penetration of the blood-brain barrier, and pharmacokinetics suitable for once-daily oral administration at low dose. Structure-activity relationship, biophysical, and structural studies led to prioritization of four compounds for in-depth safety and pharmacokinetic studies in animal models. One compound (AZD4831) progressed to clinical studies on grounds of high potency (IC50, 1.5 nM in vitro) and selectivity (>450-fold vs thyroid peroxidase in vitro), the mechanism of irreversible inhibition, and the safety profile. Following phase 1 studies in healthy volunteers and a phase 2a study in patients with HFpEF, a phase 2b/3 efficacy study of AZD4831 in patients with HFpEF started in 2021.
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Affiliation(s)
- Tord Inghardt
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Thomas Antonsson
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Cecilia Ericsson
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Daniel Hovdal
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Petra Johannesson
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Carina Johansson
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Ulrik Jurva
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Johan Kajanus
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Bengt Kull
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Erik Michaëlsson
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Anna Pettersen
- Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Tove Sjögren
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Henrik Sörensen
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Kristina Westerlund
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
| | - Eva-Lotte Lindstedt
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Gothenburg, Sweden
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2
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Myeloperoxidase: A versatile mediator of endothelial dysfunction and therapeutic target during cardiovascular disease. Pharmacol Ther 2020; 221:107711. [PMID: 33137376 DOI: 10.1016/j.pharmthera.2020.107711] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023]
Abstract
Myeloperoxidase (MPO) is a prominent mammalian heme peroxidase and a fundamental component of the innate immune response against microbial pathogens. In recent times, MPO has received considerable attention as a key oxidative enzyme capable of impairing the bioactivity of nitric oxide (NO) and promoting endothelial dysfunction; a clinically relevant event that manifests throughout the development of inflammatory cardiovascular disease. Increasing evidence indicates that during cardiovascular disease, MPO is released intravascularly by activated leukocytes resulting in its transport and sequestration within the vascular endothelium. At this site, MPO catalyzes various oxidative reactions that are capable of promoting vascular inflammation and impairing NO bioactivity and endothelial function. In particular, MPO catalyzes the production of the potent oxidant hypochlorous acid (HOCl) and the catalytic consumption of NO via the enzyme's NO oxidase activity. An emerging paradigm is the ability of MPO to also influence endothelial function via non-catalytic, cytokine-like activities. In this review article we discuss the implications of our increasing knowledge of the versatility of MPO's actions as a mediator of cardiovascular disease and endothelial dysfunction for the development of new pharmacological agents capable of effectively combating MPO's pathogenic activities. More specifically, we will (i) discuss the various transport mechanisms by which MPO accumulates into the endothelium of inflamed or diseased arteries, (ii) detail the clinical and basic scientific evidence identifying MPO as a significant cause of endothelial dysfunction and cardiovascular disease, (iii) provide an up-to-date coverage on the different oxidative mechanisms by which MPO can impair endothelial function during cardiovascular disease including an evaluation of the contributions of MPO-catalyzed HOCl production and NO oxidation, and (iv) outline the novel non-enzymatic mechanisms of MPO and their potential contribution to endothelial dysfunction. Finally, we deliver a detailed appraisal of the different pharmacological strategies available for targeting the catalytic and non-catalytic modes-of-action of MPO in order to protect against endothelial dysfunction in cardiovascular disease.
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3
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Patnaik A, Axford L, Deng L, Cohick E, Ren X, Loi S, Kecman S, Hollis-Symynkywicz M, Harrison TJ, Papillon JPN, Dales N, Hamann LG, Lee L, Regard JB, Marcinkeviciene J, Marro ML, Patterson AW. Discovery of a novel indole pharmacophore for the irreversible inhibition of myeloperoxidase (MPO). Bioorg Med Chem 2020; 28:115548. [PMID: 32503688 DOI: 10.1016/j.bmc.2020.115548] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/01/2020] [Accepted: 05/05/2020] [Indexed: 12/23/2022]
Abstract
Myeloperoxidase (MPO) activity and subsequent generation of hypochlorous acid has been associated with the killing of host-invading microorganisms (e.g. bacteria, viruses, and fungi). However, during oxidative stress, high MPO activity can damage host tissue and is linked to several chronic inflammatory conditions. Herein, we describe the development of a novel biaryl, indole-pyrazole series of irreversible mechanism-based inhibitors of MPO. Derived from an indole-containing high-throughput screen hit, optimization efforts resulted in potent and selective 6-substituted indoles with good oral bioavailability and in vivo activity.
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Affiliation(s)
- Anup Patnaik
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States.
| | - Laura Axford
- Cardiovascular and Metabolic Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Lin Deng
- PK Sciences, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Evan Cohick
- Cardiovascular and Metabolic Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Xianglin Ren
- Cardiovascular and Metabolic Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Sally Loi
- Cardiovascular and Metabolic Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Sam Kecman
- Cardiovascular and Metabolic Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Micah Hollis-Symynkywicz
- Cardiovascular and Metabolic Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Tyler J Harrison
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Julien P N Papillon
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Natalie Dales
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Lawrence G Hamann
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Lac Lee
- Cardiovascular and Metabolic Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Jean B Regard
- Cardiovascular and Metabolic Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Jovita Marcinkeviciene
- Cardiovascular and Metabolic Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Martin L Marro
- Cardiovascular and Metabolic Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States
| | - Andrew W Patterson
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States.
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4
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Marro ML, Patterson AW, Lee L, Deng L, Reynolds A, Ren X, Axford L, Patnaik A, Hollis-Symynkywicz M, Casson N, Custeau D, Ames L, Loi S, Zhang L, Honda T, Blank J, Harrison TJ, Papillon JPN, Hamann LG, Marcinkeviciene J, Regard JB. Discovery of 1-((6-Aminopyridin-3-yl)Methyl)-3-(4-Bromophenyl)Urea as a Potent, Irreversible Myeloperoxidase Inhibitor. J Pharmacol Exp Ther 2018; 367:147-154. [DOI: 10.1124/jpet.118.248435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 08/01/2018] [Indexed: 11/22/2022] Open
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5
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Myeloperoxidase in the inflamed colon: A novel target for treating inflammatory bowel disease. Arch Biochem Biophys 2018; 645:61-71. [DOI: 10.1016/j.abb.2018.03.012] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 12/17/2022]
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6
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Forbes LV, Kettle AJ. A multi-substrate assay for finding physiologically effective inhibitors of myeloperoxidase. Anal Biochem 2018; 544:13-21. [DOI: 10.1016/j.ab.2017.12.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 12/23/2022]
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7
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Maiocchi SL, Morris JC, Rees MD, Thomas SR. Regulation of the nitric oxide oxidase activity of myeloperoxidase by pharmacological agents. Biochem Pharmacol 2017; 135:90-115. [PMID: 28344126 DOI: 10.1016/j.bcp.2017.03.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/22/2017] [Indexed: 01/10/2023]
Abstract
The leukocyte-derived heme enzyme myeloperoxidase (MPO) is released extracellularly during inflammation and impairs nitric oxide (NO) bioavailability by directly oxidizing NO or producing NO-consuming substrate radicals. Here, structurally diverse pharmacological agents with activities as MPO substrates/inhibitors or antioxidants were screened for their effects on MPO NO oxidase activity in human plasma and physiological model systems containing endogenous MPO substrates/antioxidants (tyrosine, urate, ascorbate). Hydrazide-based irreversible/reversible MPO inhibitors (4-ABAH, isoniazid) or the sickle cell anaemia drug, hydroxyurea, all promoted MPO NO oxidase activity. This involved the capacity of NO to antagonize MPO inhibition by hydrazide-derived radicals and/or the ability of drug-derived radicals to stimulate MPO turnover thereby increasing NO consumption by MPO redox intermediates or NO-consuming radicals. In contrast, the mechanism-based irreversible MPO inhibitor 2-thioxanthine, potently inhibited MPO turnover and NO consumption. Although the phenolics acetaminophen and resveratrol initially increased MPO turnover and NO consumption, they limited the overall extent of NO loss by rapidly depleting H2O2 and promoting the formation of ascorbyl radicals, which inefficiently consume NO. The vitamin E analogue trolox inhibited MPO NO oxidase activity in ascorbate-depleted fluids by scavenging NO-consuming tyrosyl and urate radicals. Tempol and related nitroxides decreased NO consumption in ascorbate-replete fluids by scavenging MPO-derived ascorbyl radicals. Indoles or apocynin yielded marginal effects. Kinetic analyses rationalized differences in drug activities and identified criteria for the improved inhibition of MPO NO oxidase activity. This study reveals that widely used agents have important implications for MPO NO oxidase activity under physiological conditions, highlighting new pharmacological strategies for preserving NO bioavailability during inflammation.
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Affiliation(s)
- Sophie L Maiocchi
- Mechanisms of Disease & Translational Research, Department of Pathology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia; School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jonathan C Morris
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Martin D Rees
- Mechanisms of Disease & Translational Research, Department of Pathology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Shane R Thomas
- Mechanisms of Disease & Translational Research, Department of Pathology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
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8
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Talib J, Maghzal GJ, Cheng D, Stocker R. Detailed protocol to assess in vivo and ex vivo myeloperoxidase activity in mouse models of vascular inflammation and disease using hydroethidine. Free Radic Biol Med 2016; 97:124-135. [PMID: 27184954 DOI: 10.1016/j.freeradbiomed.2016.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/30/2016] [Accepted: 05/06/2016] [Indexed: 12/20/2022]
Abstract
Myeloperoxidase (MPO) activity contributes to arterial inflammation, vascular dysfunction and disease, including atherosclerosis. Current assessment of MPO activity in biological systems in vivo utilizes 3-chlorotyrosine (3-Cl-Tyr) as a biomarker of hypochlorous acid (HOCl) and other chlorinating species. However, 3-Cl-Tyr is formed in low yield and is subject to further metabolism. Recently, we reported a method to selectively assess MPO-activity in vivo by measuring the conversion of hydroethidine to 2-chloroethidium (2-Cl-E(+)) by liquid chromatography with tandem mass spectrometry (LC-MS/MS) (J. Biol. Chem., 289, 2014, pp. 5580-5595). The hydroethidine-based method has greater sensitivity for MPO activity than measurement of 3-Cl-Tyr. The current methods paper provides a detailed protocol to determine in vivo and ex vivo MPO activity in arteries from mouse models of vascular inflammation and disease by utilizing the conversion of hydroethidine to 2-Cl-E(+). Procedures for the synthesis of standards, preparation of tissue homogenates and the generation of 2-Cl-E(+) are also provided in detail, as are the conditions for LC-MS/MS detection of 2-Cl-E(+).
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Affiliation(s)
- Jihan Talib
- Vascular Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Ghassan J Maghzal
- Vascular Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - David Cheng
- Vascular Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Roland Stocker
- Vascular Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia; School of Medical Sciences, University of New South Wales, Sydney, Australia.
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9
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Arbelo-Lopez HD, Simakov NA, Smith JC, Lopez-Garriga J, Wymore T. Homolytic Cleavage of Both Heme-Bound Hydrogen Peroxide and Hydrogen Sulfide Leads to the Formation of Sulfheme. J Phys Chem B 2016; 120:7319-31. [DOI: 10.1021/acs.jpcb.6b02839] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Hector D. Arbelo-Lopez
- Chemistry
Department, University of Puerto Rico, Mayagüez Campus, Mayagüez 00681, Puerto Rico
| | - Nikolay A. Simakov
- Center
for Computational Research, University of Buffalo, Buffalo, New York 14203, United States
| | - Jeremy C. Smith
- UT/ORNL
Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Juan Lopez-Garriga
- Chemistry
Department, University of Puerto Rico, Mayagüez Campus, Mayagüez 00681, Puerto Rico
| | - Troy Wymore
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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10
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Dong JQ, Varma MV, Wolford A, Ryder T, Di L, Feng B, Terra SG, Sagawa K, Kalgutkar AS. Pharmacokinetics and Disposition of the Thiouracil Derivative PF-06282999, an Orally Bioavailable, Irreversible Inactivator of Myeloperoxidase Enzyme, Across Animals and Humans. Drug Metab Dispos 2015; 44:209-19. [DOI: 10.1124/dmd.115.067868] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/23/2015] [Indexed: 11/22/2022] Open
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11
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Ruggeri RB, Buckbinder L, Bagley SW, Carpino PA, Conn EL, Dowling MS, Fernando DP, Jiao W, Kung DW, Orr STM, Qi Y, Rocke BN, Smith A, Warmus JS, Zhang Y, Bowles D, Widlicka DW, Eng H, Ryder T, Sharma R, Wolford A, Okerberg C, Walters K, Maurer TS, Zhang Y, Bonin PD, Spath SN, Xing G, Hepworth D, Ahn K, Kalgutkar AS. Discovery of 2-(6-(5-Chloro-2-methoxyphenyl)-4-oxo-2-thioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamide (PF-06282999): A Highly Selective Mechanism-Based Myeloperoxidase Inhibitor for the Treatment of Cardiovascular Diseases. J Med Chem 2015; 58:8513-28. [DOI: 10.1021/acs.jmedchem.5b00963] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Roger B. Ruggeri
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Leonard Buckbinder
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Scott W. Bagley
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Philip A. Carpino
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Edward L. Conn
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Matthew S. Dowling
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Dilinie P. Fernando
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Wenhua Jiao
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Daniel W. Kung
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Suvi T. M. Orr
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Yingmei Qi
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Benjamin N. Rocke
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Aaron Smith
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Joseph S. Warmus
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Yan Zhang
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Daniel Bowles
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Daniel W. Widlicka
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Heather Eng
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Tim Ryder
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Raman Sharma
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Angela Wolford
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Carlin Okerberg
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Karen Walters
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Tristan S. Maurer
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Yanwei Zhang
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Paul D. Bonin
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Samantha N. Spath
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Gang Xing
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - David Hepworth
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Kay Ahn
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
| | - Amit S. Kalgutkar
- Worldwide Research
and Development, Pfizer,
Inc., Groton, Connecticut 06340, United States
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12
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Fox NK, Brenner SE, Chandonia JM. The value of protein structure classification information-Surveying the scientific literature. Proteins 2015; 83:2025-38. [PMID: 26313554 PMCID: PMC4609302 DOI: 10.1002/prot.24915] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/06/2015] [Accepted: 08/18/2015] [Indexed: 11/08/2022]
Abstract
The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP-extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012-2013 that cite SCOP, 439 actually use data from the resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non-SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings.
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Affiliation(s)
- Naomi K Fox
- Lawrence Berkeley National Laboratory, Physical Biosciences Division, Berkeley, California, 94720
| | - Steven E Brenner
- Lawrence Berkeley National Laboratory, Physical Biosciences Division, Berkeley, California, 94720.,Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720
| | - John-Marc Chandonia
- Lawrence Berkeley National Laboratory, Physical Biosciences Division, Berkeley, California, 94720
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13
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Biela A, Coste F, Culard F, Guerin M, Goffinont S, Gasteiger K, Cieśla J, Winczura A, Kazimierczuk Z, Gasparutto D, Carell T, Tudek B, Castaing B. Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization. Nucleic Acids Res 2014; 42:10748-61. [PMID: 25143530 PMCID: PMC4176347 DOI: 10.1093/nar/gku613] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the recent discovery of synthetic lethal relationships between DNA glycosylases and other pathways highlights the potential of DNA glycosylase inhibitors for future medicinal chemistry development in cancer therapy. By combining biochemical and structural approaches, the physical target of 2-thioxanthine (2TX), an uncompetitive inhibitor of Fpg, was identified. 2TX interacts with the zinc finger (ZnF) DNA binding domain of the enzyme. This explains why the zincless hNEIL1 enzyme is resistant to 2TX. Crystal structures of the enzyme bound to DNA in the presence of 2TX demonstrate that the inhibitor chemically reacts with cysteine thiolates of ZnF and induces the loss of zinc. The molecular mechanism by which 2TX inhibits Fpg may be generalized to all prokaryote and eukaryote ZnF-containing Fpg/Nei-DNA glycosylases. Cell experiments show that 2TX can operate in cellulo on the human Fpg/Nei DNA glycosylases. The atomic elucidation of the determinants for the interaction of 2TX to Fpg provides the foundation for the future design and synthesis of new inhibitors with high efficiency and selectivity.
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Affiliation(s)
- Artur Biela
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Franck Coste
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France
| | - Françoise Culard
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France
| | - Martine Guerin
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France
| | - Stéphane Goffinont
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France
| | - Karola Gasteiger
- Department of Chemistry, Ludwig-Maximilians-Universität (LMU), Butenandtstr. 5-13 (Haus F), München D-81377, Germany
| | - Jarosław Cieśla
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Alicja Winczura
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Zygmunt Kazimierczuk
- Institute of Chemistry, Warsaw University of Life Sciences, 159C Nowoursynowska St., 02-787 Warsaw, Poland
| | - Didier Gasparutto
- Laboratoire Lésions des Acides Nucléiques, SCIB/UMR E3 CEA-UJF, INAC, CEA, Grenoble, France
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität (LMU), Butenandtstr. 5-13 (Haus F), München D-81377, Germany
| | - Barbara Tudek
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland Institute of Genetics and Biotechnology, Warsaw University, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France
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Cardiac phosphoproteomics during remote ischemic preconditioning: a role for the sarcomeric Z-disk proteins. BIOMED RESEARCH INTERNATIONAL 2014; 2014:767812. [PMID: 24795895 PMCID: PMC3985148 DOI: 10.1155/2014/767812] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 02/20/2014] [Accepted: 02/21/2014] [Indexed: 01/26/2023]
Abstract
Remote ischemic preconditioning (RIPC) induced by brief ischemia/reperfusion cycles of remote organ (e.g., limb) is cardioprotective. The myocardial cellular changes during RIPC responsible for this phenomenon are not currently known. The aim of this work was to identify the activation by phosphorylation of cardiac proteins following RIPC. To achieve our aim we used isobaric tandem mass tagging (TMT) and reverse phase nanoliquid chromatography tandem spectrometry using a Linear Trap Quadropole (LTQ) Orbitrap Velos mass spectrometer.
Male C57/Bl6 mice were anesthetized by an intraperitoneal injection of Tribromoethanol. A cuff was placed around the hind limb and inflated at 200 mmHg to prevent blood flow as confirmed by Laser Doppler Flowmetry. RIPC was induced by 4 cycles of 5 min of limb ischemia followed by 5 min of reperfusion. Hearts were extracted for phosphoproteomics. We identified approximately 30 phosphoproteins that were differentially expressed in response to RIPC protocol. The levels of several phosphoproteins in the Z-disk of the sarcomere including phospho-myozenin-2 were significantly higher than control. This study describes and validates a novel approach to monitor the changes in the cardiac phosphoproteome following the cardioprotective intervention of RIPC and prior to index ischemia. The increased level of phosphorylated sarcomeric proteins suggests they may have a role in cardiac signaling during RIPC.
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15
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Ward J, Spath SN, Pabst B, Carpino PA, Ruggeri RB, Xing G, Speers AE, Cravatt BF, Ahn K. Mechanistic characterization of a 2-thioxanthine myeloperoxidase inhibitor and selectivity assessment utilizing click chemistry--activity-based protein profiling. Biochemistry 2013; 52:9187-201. [PMID: 24320749 DOI: 10.1021/bi401354d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myeloperoxidase (MPO) is a heme peroxidase that catalyzes the production of hypochlorous acid. Despite a high level of interest in MPO as a therapeutic target, there have been limited reports about MPO inhibitors that are suitable for evaluating MPO in pharmacological studies. 2-Thioxanthine, 3-(2-ethoxypropyl)-2-thioxo-2,3-dihydro-1H-purin-6(9H)-one (A), has recently been reported to inhibit MPO by covalently modifying the heme prosthetic group. Here we report a detailed mechanistic characterization demonstrating that A possesses all the distinguishing features of a mechanism-based inactivator. A is a time-dependent MPO inhibitor and displays saturable inactivation kinetics consistent with a two-step mechanism of inactivation and a potency (k(inact)/K(I) ratio) of 8450 ± 780 M⁻¹ s⁻¹. MPO inactivation by A is dependent on MPO catalysis and is protected by substrate. A reduces MPO compound I to compound II with a second-order rate constant of (0.801 ± 0.056) × 10⁶ M⁻¹ s⁻¹, and its irreversible inactivation of MPO occurs prior to release of the activated inhibitory species. Despite its relatively high selectivity against a broad panel of more than 100 individual targets, including enzymes, receptors, transporters, and ion channels, we demonstrate that A labels multiple other protein targets in the presence of MPO. By synthesizing an alkyne analogue of A and utilizing click chemistry-activity-based protein profiling, we present that the MPO-activated inhibitory species can diffuse away to covalently modify other proteins, as reflected by the relatively high partition ratio of A, which we determined to be 15.6. This study highlights critical methods that can guide the discovery and development of next-generation MPO inhibitors.
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Affiliation(s)
- Jessica Ward
- Cardiovascular and Metabolic Diseases Research Unit and ‡Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
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16
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Unexpected mucin-type O-glycosylation and host-specific N-glycosylation of human recombinant interleukin-17A expressed in a human kidney cell line. Protein Expr Purif 2013; 87:27-34. [DOI: 10.1016/j.pep.2012.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/23/2012] [Accepted: 09/24/2012] [Indexed: 11/30/2022]
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17
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Recent advances in cardiovascular proteomics. J Proteomics 2012; 81:3-14. [PMID: 23153792 DOI: 10.1016/j.jprot.2012.10.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 10/10/2012] [Accepted: 10/31/2012] [Indexed: 01/08/2023]
Abstract
Cardiovascular diseases (CVDs) are the major source of global morbidity and death and more people die annually from CVDs than from any other cause. These diseases can occur quickly, as seen in acute myocardial infarction (AMI), or progress slowly over years as with chronic heart failure. Advances in mass spectrometry detection and analysis, together with improved isolation and enrichment techniques allowing for the separation of organelles and membrane proteins, now allow for the indepth analysis of the cardiac proteome. Here we outline current insights that have been provided through cardiovascular proteomics, and discuss studies that have developed innovative technologies which permit the examination of the protein complement in specific organelles including exosomes and secreted proteins. We highlight these foundational studies and illustrate how they are providing the technologies and tools which are now being applied to further study cardiovascular disease; provide new diagnostic markers and potentially new methods of cardiac patient management with identification of novel drug targets. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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