151
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Tallman KR, Levine SR, Beatty KE. Small-Molecule Probes Reveal Esterases with Persistent Activity in Dormant and Reactivating Mycobacterium tuberculosis. ACS Infect Dis 2016; 2:936-944. [PMID: 27690385 DOI: 10.1021/acsinfecdis.6b00135] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is the deadliest bacterial pathogen in the world. An estimated one-third of humans harbor Mtb in a dormant state. These asymptomatic, latent infections impede tuberculosis eradication due to the long-term potential for reactivation. Dormant Mtb has reduced enzymatic activity, but hydrolases that remain active facilitate pathogen survival. We targeted Mtb esterases, a diverse set of enzymes in the serine hydrolase family, and studied their activities using both activity-based probes (ABPs) and fluorogenic esterase substrates. These small-molecule probes revealed functional esterases in active, dormant, and reactivating cultures. Using ABPs, we identified five esterases that remained active in dormant Mtb, including LipM (Rv2284), LipN (Rv2970c), CaeA (Rv2224c), Rv0183, and Rv1683. Three of these, CaeA, Rv0183, and Rv1683, were catalytically active in all three culture conditions. Fluorogenic probes additionally revealed LipH (Rv1399c), Culp1 (Rv1984c), and Rv3036c esterase activity in dormant and active cultures. Esterases with persistent activity are potential diagnostic biomarkers or therapeutic targets for Mtb-infected individuals with latent or active tuberculosis.
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Affiliation(s)
- Katie R. Tallman
- Program in Chemical Biology and Department of Biomedical Engineering, Oregon Health & Science University, Mail Code CL3B, 2730 S.W. Moody Avenue, Portland, Oregon 97201, United States
| | - Samantha R. Levine
- Program in Chemical Biology and Department of Biomedical Engineering, Oregon Health & Science University, Mail Code CL3B, 2730 S.W. Moody Avenue, Portland, Oregon 97201, United States
| | - Kimberly E. Beatty
- Program in Chemical Biology and Department of Biomedical Engineering, Oregon Health & Science University, Mail Code CL3B, 2730 S.W. Moody Avenue, Portland, Oregon 97201, United States
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152
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Zahov S, Garzinsky D, Hanekamp W, Lehr M. 1-Heteroarylpropan-2-ones as inhibitors of fatty acid amide hydrolase: Studies on structure-activity relationships and metabolic stability. Bioorg Med Chem 2016; 25:825-837. [PMID: 27989417 DOI: 10.1016/j.bmc.2016.11.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/09/2016] [Accepted: 11/13/2016] [Indexed: 10/20/2022]
Abstract
The serine hydrolase fatty acid amide hydrolase (FAAH) catalyzes the degradation of the endocannabinoid anandamide, which possesses analgesic and anti-inflammatory effects. A new series of 1-heteroarylpropan-2-ones was synthesized and evaluated for FAAH inhibition. Structure-activity relationship studies revealed that 1H-benzotriazol-1-yl, 1H-7-azabenzotriazol-1-yl, 1H-tetrazol-1-yl and 2H-tetrazol-2-yl substituents have the highest impact on inhibitory potency. Furthermore, attempts were made to increase the limited metabolic stability of the ketone functionality of these compounds towards metabolic reduction by introduction of shielding alkyl substituents in proximity of this serine reactive group.
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Affiliation(s)
- Stefan Zahov
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstrasse 48, D-48149 Münster, Germany
| | - David Garzinsky
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstrasse 48, D-48149 Münster, Germany
| | - Walburga Hanekamp
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstrasse 48, D-48149 Münster, Germany
| | - Matthias Lehr
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstrasse 48, D-48149 Münster, Germany.
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153
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Mahatmanto T. Review seed biopharmaceutical cyclic peptides: From discovery to applications. Biopolymers 2016; 104:804-14. [PMID: 26385189 DOI: 10.1002/bip.22741] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/17/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Mini-proteins (or peptides) with disulfide bond/s and a cyclic backbone offer exciting opportunities for applications in medicine, as these ribosomally synthesized and posttranslationally modified peptides are exceptionally stable and amenable to grafting epitopes with desirable activities. Here I discuss important aspects of the discovery and applications of disulfide-bonded cyclic peptides from seeds, i.e., the trypsin inhibitor cyclotides and the preproalbumin with sunflower trypsin inhibitor-derived peptides, focusing on bioanalytical methods for and insights generated from their discovery as well as their potential use as engineering scaffolds for peptide-based drug design. The recent discovery of their precursors and processing enzymes could potentially enable in planta production of designer disulfide-bonded cyclic peptides, preferably in edible seeds, and address the demand for new biopharmaceutical peptides in a cost-effective manner.
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Affiliation(s)
- Tunjung Mahatmanto
- Department of Agricultural Product Technology, Faculty of Agricultural Technology, Brawijaya University, Malang, East Java, 65145, Indonesia
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154
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Palumbo R, Gogliettino M, Cocca E, Iannitti R, Sandomenico A, Ruvo M, Balestrieri M, Rossi M, Palmieri G. APEH Inhibition Affects Osteosarcoma Cell Viability via Downregulation of the Proteasome. Int J Mol Sci 2016; 17:ijms17101614. [PMID: 27669226 PMCID: PMC5085647 DOI: 10.3390/ijms17101614] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/08/2016] [Accepted: 09/19/2016] [Indexed: 01/13/2023] Open
Abstract
The proteasome is a multienzymatic complex that controls the half-life of the majority of intracellular proteins, including those involved in apoptosis and cell-cycle progression. Recently, proteasome inhibition has been shown to be an effective anticancer strategy, although its downregulation is often accompanied by severe undesired side effects. We previously reported that the inhibition of acylpeptide hydrolase (APEH) by the peptide SsCEI 4 can significantly affect the proteasome activity in A375 melanoma or Caco-2 adenocarcinoma cell lines, thus shedding new light on therapeutic strategies based on downstream regulation of proteasome functions. In this work, we investigated the functional correlation between APEH and proteasome in a panel of cancer cell lines, and evaluated the cell proliferation upon SsCEI 4-treatments. Results revealed that SsCEI 4 triggered a proliferative arrest specifically in osteosarcoma U2OS cells via downregulation of the APEH–proteasome system, with the accumulation of the typical hallmarks of proteasome: NF-κB, p21Waf1, and polyubiquitinylated proteins. We found that the SsCEI 4 anti-proliferative effect involved a senescence-like growth arrest without noticeable cytotoxicity. These findings represent an important step toward understanding the mechanism(s) underlying the APEH-mediated downregulation of proteasome in order to design new molecules able to efficiently regulate the proteasome system for alternative therapeutic strategies.
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Affiliation(s)
- Rosanna Palumbo
- Institute of Biostructure and Bioimaging, National Research Council (CNR-IBB), Napoli 80134, Italy.
| | - Marta Gogliettino
- Institute of Biosciences and BioResources, National Research Council (CNR-IBBR), Napoli 80131, Italy.
| | - Ennio Cocca
- Institute of Biosciences and BioResources, National Research Council (CNR-IBBR), Napoli 80131, Italy.
| | - Roberta Iannitti
- Institute of Biostructure and Bioimaging, National Research Council (CNR-IBB), Napoli 80134, Italy.
| | - Annamaria Sandomenico
- Institute of Biostructure and Bioimaging, National Research Council (CNR-IBB), Napoli 80134, Italy.
| | - Menotti Ruvo
- Institute of Biostructure and Bioimaging, National Research Council (CNR-IBB), Napoli 80134, Italy.
| | - Marco Balestrieri
- Institute of Biosciences and BioResources, National Research Council (CNR-IBBR), Napoli 80131, Italy.
| | - Mosè Rossi
- Institute of Biosciences and BioResources, National Research Council (CNR-IBBR), Napoli 80131, Italy.
| | - Gianna Palmieri
- Institute of Biosciences and BioResources, National Research Council (CNR-IBBR), Napoli 80131, Italy.
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155
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Ahn K, Boehm M, Brown MF, Calloway J, Che Y, Chen J, Fennell KF, Geoghegan KF, Gilbert AM, Gutierrez JA, Kalgutkar AS, Lanba A, Limberakis C, Magee TV, O’Doherty I, Oliver R, Pabst B, Pandit J, Parris K, Pfefferkorn JA, Rolph TP, Patel R, Schuff B, Shanmugasundaram V, Starr JT, Varghese AH, Vera NB, Vernochet C, Yan J. Discovery of a Selective Covalent Inhibitor of Lysophospholipase-like 1 (LYPLAL1) as a Tool to Evaluate the Role of this Serine Hydrolase in Metabolism. ACS Chem Biol 2016; 11:2529-40. [PMID: 27391855 DOI: 10.1021/acschembio.6b00266] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Lysophospholipase-like 1 (LYPLAL1) is an uncharacterized metabolic serine hydrolase. Human genome-wide association studies link variants of the gene encoding this enzyme to fat distribution, waist-to-hip ratio, and nonalcoholic fatty liver disease. We describe the discovery of potent and selective covalent small-molecule inhibitors of LYPLAL1 and their use to investigate its role in hepatic metabolism. In hepatocytes, selective inhibition of LYPLAL1 increased glucose production supporting the inference that LYPLAL1 is a significant actor in hepatic metabolism. The results provide an example of how a selective chemical tool can contribute to evaluating a hypothetical target for therapeutic intervention, even in the absence of complete biochemical characterization.
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Affiliation(s)
- Kay Ahn
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Markus Boehm
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Matthew F. Brown
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jessica Calloway
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ye Che
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jinshan Chen
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Kimberly F. Fennell
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Kieran F. Geoghegan
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Adam M. Gilbert
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jemy A. Gutierrez
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Amit S. Kalgutkar
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Adhiraj Lanba
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Chris Limberakis
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Thomas V. Magee
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Inish O’Doherty
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Robert Oliver
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Brandon Pabst
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jayvardhan Pandit
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Kevin Parris
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jeffrey A. Pfefferkorn
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Timothy P. Rolph
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Rushi Patel
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Brandon Schuff
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Veerabahu Shanmugasundaram
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jeremy T. Starr
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Alison H. Varghese
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Nicholas B. Vera
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Cecile Vernochet
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jiangli Yan
- Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research
Unit, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
- Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
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156
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Targeting biomolecules with reversible covalent chemistry. Curr Opin Chem Biol 2016; 34:110-116. [PMID: 27599186 DOI: 10.1016/j.cbpa.2016.08.011] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 08/13/2016] [Accepted: 08/18/2016] [Indexed: 02/08/2023]
Abstract
Interaction of biomolecules typically proceeds in a highly selective and reversible manner, for which covalent bond formation has been largely avoided due to the potential difficulty of dissociation. However, employing reversible covalent warheads in drug design has given rise to covalent enzyme inhibitors that serve as powerful therapeutics, as well as molecular probes with exquisite target selectivity. This review article summarizes the recent advances in the development of reversible covalent chemistry for biological and medicinal applications. Specifically, we document the chemical strategies that allow for reversible modification of the three major classes of nucleophiles in biology: thiols, alcohols and amines. Emphasis is given to the chemical mechanisms that underlie the development of these reversible covalent reactions and their utilization in biology.
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157
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Roberts AM, Ward CC, Nomura DK. Activity-based protein profiling for mapping and pharmacologically interrogating proteome-wide ligandable hotspots. Curr Opin Biotechnol 2016; 43:25-33. [PMID: 27568596 DOI: 10.1016/j.copbio.2016.08.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/04/2016] [Accepted: 08/11/2016] [Indexed: 11/19/2022]
Abstract
Despite the completion of human genome sequencing efforts nearly 15 years ago that brought with it the promise of genome-based discoveries that would cure human diseases, most protein targets that control human diseases have remained largely untranslated, in-part because they represent difficult protein targets to drug. In addition, many of these protein targets lack screening assays or accessible binding pockets, making the development of small-molecule modulators very challenging. Here, we discuss modern methods for activity-based protein profiling-based chemoproteomic strategies to map 'ligandable' hotspots in proteomes using activity and reactivity-based chemical probes to allow for pharmacological interrogation of these previously difficult targets. We will showcase several recent examples of how these technologies have been used to develop highly selective small-molecule inhibitors against disease-related protein targets.
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Affiliation(s)
- Allison M Roberts
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Carl C Ward
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, United States.
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158
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Abstract
In this issue of Cell Chemical Biology, Ortega et al. (2016) present a study utilizing a click-chemistry-enabled fluorophosphonate for activity-based identification of serine hydrolases, pinpointing a range of proteins including previously annotated hypotheticals. The application of this technology on both actively replicating and non-replicating Mycobacterium tuberculosis gives us a glimpse of its serine hydrolytic landscape during different stages of metabolic activity.
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Affiliation(s)
- Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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159
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Baillie TA. Targeted Covalent Inhibitors for Drug Design. Angew Chem Int Ed Engl 2016; 55:13408-13421. [DOI: 10.1002/anie.201601091] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Thomas A. Baillie
- Department of Medicinal Chemistry, School of Pharmacy; University of Washington; Box 357610 Seattle WA 98195-7610 USA
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160
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Affiliation(s)
- Thomas A. Baillie
- Department of Medicinal Chemistry, School of Pharmacy; University of Washington; Box 357610 Seattle WA 98195-7610 USA
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161
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Navia-Paldanius D, Patel JZ, López Navarro M, Jakupović H, Goffart S, Pasonen-Seppänen S, Nevalainen TJ, Jääskeläinen T, Laitinen T, Laitinen JT, Savinainen JR. Chemoproteomic, biochemical and pharmacological approaches in the discovery of inhibitors targeting human α/β-hydrolase domain containing 11 (ABHD11). Eur J Pharm Sci 2016; 93:253-63. [PMID: 27544863 DOI: 10.1016/j.ejps.2016.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/28/2016] [Accepted: 08/16/2016] [Indexed: 10/21/2022]
Abstract
ABHD11 (α/β-hydrolase domain containing 11) is a non-annotated enzyme belonging to the family of metabolic serine hydrolases (mSHs). Its natural substrates and products are unknown. Using competitive activity-based protein profiling (ABPP) to identify novel inhibitors of human (h)ABHD11, three compounds from our chemical library exhibited low nanomolar potency towards hABHD11. Competitive ABPP of various proteomes revealed fatty acid amide hydrolase (FAAH) as the sole off-target among the mSHs. Our fluorescent activity assays designed for natural lipase substrates revealed no activity of hABHD11 towards mono- or diacylglycerols. A broader profiling using para-nitrophenyl (pNP)-linked substrates indicated no amidase/protease, phosphatase, sulfatase, phospholipase C or phosphodiesterase activity. Instead, hABHD11 readily utilized para-nitrophenyl butyrate (pNPC4), indicating lipase/esterase-type activity that could be exploited in inhibitor discovery. Additionally, a homology model was created based on the crystal structure of bacterial esterase YbfF. In contrast to YbfF, which reportedly hydrolyze long-chain acyl-CoA, hABHD11 did not utilize oleoyl-CoA or arachidonoyl-CoA. In conclusion, the present study reports the discovery of potent hABHD11 inhibitors with good selectivity among mSHs. We developed substrate-based activity assays for hABHD11 that could be further exploited in inhibitor discovery and created the first homology-based hABHD11 model, offering initial insights into the active site of this poorly characterized enzyme.
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Affiliation(s)
- Dina Navia-Paldanius
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland.
| | - Jayendra Z Patel
- School of Pharmacy, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Miriam López Navarro
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Hermina Jakupović
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Steffi Goffart
- Department of Biology, University of Eastern Finland, P.O Box 111, 80101 Joensuu, Finland
| | - Sanna Pasonen-Seppänen
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Tapio J Nevalainen
- School of Pharmacy, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Tiina Jääskeläinen
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland; Institute of Dentistry, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Tuomo Laitinen
- School of Pharmacy, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Jarmo T Laitinen
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Juha R Savinainen
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
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162
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Ruivo EFP, Gonçalves LM, Carvalho LAR, Guedes RC, Hofbauer S, Brito JA, Archer M, Moreira R, Lucas SD. Clickable 4-Oxo-β-lactam-Based Selective Probing for Human Neutrophil Elastase Related Proteomes. ChemMedChem 2016; 11:2037-42. [DOI: 10.1002/cmdc.201600258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/28/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Eduardo F. P. Ruivo
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Lídia M. Gonçalves
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Luís A. R. Carvalho
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Stefan Hofbauer
- Instituto de Tecnologia Química e Biológica-António Xavier; Universidade Nova de Lisboa; Avenida da República 2780-157 Oeiras Portugal
- Department for Structural and Computational Biology; Max F. Perutz Laboratories; University of Vienna; 1030 Vienna Austria
| | - José A. Brito
- Instituto de Tecnologia Química e Biológica-António Xavier; Universidade Nova de Lisboa; Avenida da República 2780-157 Oeiras Portugal
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica-António Xavier; Universidade Nova de Lisboa; Avenida da República 2780-157 Oeiras Portugal
| | - Rui Moreira
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Susana D. Lucas
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
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163
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Mechanism-Guided Discovery of an Esterase Scaffold with Promiscuous Amidase Activity. Catalysts 2016. [DOI: 10.3390/catal6060090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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164
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Komatsu T, Virdee S. ICBS and ECBS Chemical Biology Meeting 2015 - Let Them Come to Berlin! ACS Chem Biol 2016; 11:1159-66. [PMID: 27198933 DOI: 10.1021/acschembio.6b00268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Toru Komatsu
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- JST PRESTO, Tokyo, Japan
| | - Satpal Virdee
- MRC
Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
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165
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Abstract
In this issue of Chemistry & Biology, Cognetta et al. (2015) describe new pharmacological tools, including N-hydroxyhydantoin-containing carbamate inhibitors and an activity-based probe, for palmitoyl protein thioesterase 1 and alpha, beta-hydrolase domain-4 that expand the toolkit for the serine hydrolases.
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166
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Panlilio LV, Thorndike EB, Nikas SP, Alapafuja SO, Bandiera T, Cravatt BF, Makriyannis A, Piomelli D, Goldberg SR, Justinova Z. Effects of fatty acid amide hydrolase (FAAH) inhibitors on working memory in rats. Psychopharmacology (Berl) 2016; 233:1879-88. [PMID: 26558620 PMCID: PMC4846548 DOI: 10.1007/s00213-015-4140-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 10/29/2015] [Indexed: 11/24/2022]
Abstract
RATIONALE Manipulations of the endocannabinoid system could potentially produce therapeutic effects with minimal risk of adverse cannabis-like side effects. Inhibitors of fatty acid amide hydrolase (FAAH) increase endogenous levels of the cannabinoid-receptor agonist, anandamide, and show promise for treating a wide range of disorders. However, their effects on learning and memory have not been fully characterized. OBJECTIVES We determined the effects of five structurally different FAAH inhibitors in an animal model of working memory known to be sensitive to impairment by delta-9 tetrahydrocannabinol (THC). METHODS A delayed nonmatching-to-position procedure was used in rats. Illuminated nosepoke holes were used to provide sample cues (left versus right) and record responses (correct versus incorrect) after delays ranging from 0 to 28 s. Various test drugs were given acutely up to two times per week before daily sessions. RESULTS One FAAH inhibitor, AM3506 (3 mg/kg), decreased accuracy in the memory task. Four other FAAH inhibitors (URB597, URB694, PF-04457845, and ARN14633) and a monoacylglycerol lipase inhibitor (JZL184, which blocks the degradation of the endocannabinoid 2-arachidonoylglycerol) had no effect. Testing of AM3506 in combination with antagonists for receptors known to be affected by anandamide and other fatty acid amides indicated that the impairment induced by AM3506 was mediated by cannabinoid CB1 receptors, and not by alpha-type peroxisome proliferator-activated receptors (PPAR-alpha) or vanilloid transient receptor potential cation channels (TRPV1). CONCLUSIONS FAAH inhibitors differ with respect to their potential for memory impairment, abuse liability, and probably other cannabis-like effects, and they should be evaluated individually for specific therapeutic and adverse effects.
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Affiliation(s)
- Leigh V. Panlilio
- Preclinical Pharmacology Section, Behavioral Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Eric B. Thorndike
- Preclinical Pharmacology Section, Behavioral Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Spyros P. Nikas
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | | | - Tiziano Bandiera
- Drug Discovery and Development, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA; Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Alexandros Makriyannis
- Center for Drug Discovery, Department of Pharmaceutical Sciences and Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Daniele Piomelli
- Drug Discovery and Development, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Anatomy and Neurobiology, University of California Irvine, Irvine, California, USA
| | - Steven R. Goldberg
- Preclinical Pharmacology Section, Behavioral Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Zuzana Justinova
- Preclinical Pharmacology Section, Behavioral Neuroscience Research Branch, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
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167
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Sarma BK, Liu X, Kodadek T. Identification of selective covalent inhibitors of platelet activating factor acetylhydrolase 1B2 from the screening of an oxadiazolone-capped peptoid-azapeptoid hybrid library. Bioorg Med Chem 2016; 24:3953-3963. [PMID: 27160052 DOI: 10.1016/j.bmc.2016.04.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/21/2022]
Abstract
A potent and selective inhibitor of platelet-activating factor acetylhydrolase 1B2 (PAFAH1B2) is described. The compound was derived by improvement of a modest affinity primary hit isolated from the screening of a bead-displayed peptoid-azapeptoid hybrid library tethered to an oxadiazolone 'warhead'. The oxadiazolone moiety of the inhibitors was found to react covalently with the active site serine residue of PAFAH1B2. This screening strategy may be useful for the identification of many selective, covalent inhibitors of serine hydrolases.
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Affiliation(s)
- Bani Kanta Sarma
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh-201314, India
| | - Xiaodan Liu
- Departments of Chemistry, Scripps Research Institute, Scripps Florida, 130 Scripps Way, #3A2, Jupiter, Fl 33458, USA
| | - Thomas Kodadek
- Departments of Chemistry, Scripps Research Institute, Scripps Florida, 130 Scripps Way, #3A2, Jupiter, Fl 33458, USA
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168
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Cerny MA. Prevalence of Non-Cytochrome P450-Mediated Metabolism in Food and Drug Administration-Approved Oral and Intravenous Drugs: 2006-2015. Drug Metab Dispos 2016; 44:1246-52. [DOI: 10.1124/dmd.116.070763] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 04/14/2016] [Indexed: 01/04/2023] Open
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169
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Chen ZJ, Tian Z, Kallio K, Oleson AL, Ji A, Borchardt D, Jiang DE, Remington SJ, Ai HW. The N-B Interaction through a Water Bridge: Understanding the Chemoselectivity of a Fluorescent Protein Based Probe for Peroxynitrite. J Am Chem Soc 2016; 138:4900-7. [PMID: 27019313 PMCID: PMC4958459 DOI: 10.1021/jacs.6b01285] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Boronic acid and esters have been extensively utilized for molecular recognition and chemical sensing. We recently reported a genetically encoded peroxynitrite (ONOO(-))-specific fluorescent sensor, pnGFP, based on the incorporation of a boronic acid moiety into a circularly permuted green fluorescent protein (cpGFP) followed by directed protein evolution. Different from typical arylboronic acids and esters, the chromophore of pnGFP is unreactive to millimolar concentrations of hydrogen peroxide (H2O2). The focus of this study is to explore the mechanism for the observed unusual chemoselectivity of pnGFP toward peroxynitrite over hydrogen peroxide by using site-directed mutagenesis, X-ray crystallography, (11)B NMR, and computational analysis. Our data collectively support that a His residue on the protein scaffold polarizes a water molecule to induce the formation of an sp(3)-hybridized boron in the chromophore, thereby tuning the reactivity of pnGFP with various reactive oxygen and nitrogen species (ROS/RNS). Our study demonstrates the first example of tunable boron chemistry in a folded nonnative protein, which offers wide implications in designing selective chemical probes.
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Affiliation(s)
- Zhi-jie Chen
- Department of Chemistry, University of California at Riverside, 501 Big Springs Road, Riverside, CA 92521, United States of America
| | - Ziqi Tian
- Department of Chemistry, University of California at Riverside, 501 Big Springs Road, Riverside, CA 92521, United States of America
| | - Karen Kallio
- Department of Physics and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, United States of America
| | - April L Oleson
- Department of Physics and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, United States of America
| | - Ao Ji
- Department of Chemistry, University of California at Riverside, 501 Big Springs Road, Riverside, CA 92521, United States of America
| | - Dan Borchardt
- Department of Chemistry, University of California at Riverside, 501 Big Springs Road, Riverside, CA 92521, United States of America
| | - De-en Jiang
- Department of Chemistry, University of California at Riverside, 501 Big Springs Road, Riverside, CA 92521, United States of America
| | - S. James Remington
- Department of Physics and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, United States of America
,Corresponding Authors: ,
| | - Hui-wang Ai
- Department of Chemistry, University of California at Riverside, 501 Big Springs Road, Riverside, CA 92521, United States of America
,Corresponding Authors: ,
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170
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Synthesis, molecular docking and biological evaluation of N,N-disubstituted 2-aminothiazolines as a new class of butyrylcholinesterase and carboxylesterase inhibitors. Bioorg Med Chem 2016; 24:1050-62. [DOI: 10.1016/j.bmc.2016.01.031] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/04/2016] [Accepted: 01/17/2016] [Indexed: 11/21/2022]
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171
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Doler C, Schweiger M, Zimmermann R, Breinbauer R. Chemical Genetic Approaches for the Investigation of Neutral Lipid Metabolism. Chembiochem 2016; 17:358-77. [DOI: 10.1002/cbic.201500501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Carina Doler
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Martina Schweiger
- Institute of Molecular Biosciences; University of Graz; Heinrichstrasse 31/II 8010 Graz Austria
| | - Robert Zimmermann
- Institute of Molecular Biosciences; University of Graz; Heinrichstrasse 31/II 8010 Graz Austria
| | - Rolf Breinbauer
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
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172
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Ortega C, Anderson LN, Frando A, Sadler NC, Brown RW, Smith RD, Wright AT, Grundner C. Systematic Survey of Serine Hydrolase Activity in Mycobacterium tuberculosis Defines Changes Associated with Persistence. Cell Chem Biol 2016; 23:290-298. [PMID: 26853625 DOI: 10.1016/j.chembiol.2016.01.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/23/2015] [Accepted: 10/03/2015] [Indexed: 01/17/2023]
Abstract
The transition from replication to non-replication underlies much of Mycobacterium tuberculosis (Mtb) pathogenesis, as non- or slowly replicating Mtb are responsible for persistence and poor treatment outcomes. Therapeutic targeting of non-replicating populations is a priority for tuberculosis treatment, but few drug targets in non-replicating Mtb are currently known. Here, we directly measured the activity of the highly diverse and druggable serine hydrolases (SHs) during active replication and non-replication using activity-based proteomics. We predict SH activity for 78 proteins, including 27 proteins with unknown function, and identify 37 SHs that remain active in the absence of replication, providing a set of candidate persistence targets. Non-replication was associated with major shifts in SH activity. These activity changes were largely independent of SH abundance, indicating extensive post-translational regulation of SHs. By probing a large cross-section of druggable Mtb enzyme space during replication and non-replication, we identify new SHs and suggest new persistence targets.
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Affiliation(s)
- Corrie Ortega
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA 98109, USA
| | - Lindsey N Anderson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Andrew Frando
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Natalie C Sadler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Robert W Brown
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA 98109, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Aaron T Wright
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Christoph Grundner
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA.
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173
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Kowada T, Maeda H, Kikuchi K. BODIPY-based probes for the fluorescence imaging of biomolecules in living cells. Chem Soc Rev 2016; 44:4953-72. [PMID: 25801415 DOI: 10.1039/c5cs00030k] [Citation(s) in RCA: 866] [Impact Index Per Article: 108.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fluorescence imaging techniques have been widely used to visualize biological molecules and phenomena. In particular, several studies on the development of small-molecule fluorescent probes have been carried out, because their fluorescence properties can be easily tuned by synthetic chemical modification. For this reason, various fluorescent probes have been developed for targeting biological components, such as proteins, peptides, amino acids, and ions, to the interior and exterior of cells. In this review, we cover advances in the development of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY)-based fluorescent probes for biological studies over the past decade.
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Affiliation(s)
- Toshiyuki Kowada
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, Japan.
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174
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Morera E, Di Marzo V, Monti L, Allarà M, Schiano Moriello A, Nalli M, Ortar G, De Petrocellis L. Arylboronic acids as dual-action FAAH and TRPV1 ligands. Bioorg Med Chem Lett 2016; 26:1401-5. [PMID: 26850005 DOI: 10.1016/j.bmcl.2016.01.071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 01/22/2016] [Accepted: 01/23/2016] [Indexed: 12/17/2022]
Abstract
A series of 31 arylboronic acids designed on the basis of the pharmacophore model for a variety of TRPV1 antagonists was prepared and tested on FAAH and TRPV1 channel. Four of them, that is, compounds 3c, 4a, 5a,b acted as dual FAAH/TRPV1 blockers with IC50 values between 0.56 and 8.11μM whereas ten others (compounds 1c,f-i, 2c-f, 4b) inhibited FAAH and activated/desensitized TRPV1.
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Affiliation(s)
- Enrico Morera
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, piazzale Aldo Moro 5, 00185 Roma, Italy.
| | - Vincenzo Di Marzo
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy
| | - Ludovica Monti
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Marco Allarà
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy
| | - Aniello Schiano Moriello
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy
| | - Marianna Nalli
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Giorgio Ortar
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Luciano De Petrocellis
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy.
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175
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Waldner BJ, Fuchs JE, Huber RG, von Grafenstein S, Schauperl M, Kramer C, Liedl KR. Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases. J Phys Chem B 2016; 120:299-308. [PMID: 26709959 PMCID: PMC4724848 DOI: 10.1021/acs.jpcb.5b10637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Members of the same protease family
show different substrate specificity,
even if they share identical folds, depending on the physiological
processes they are part of. Here, we investigate the key factors for
subpocket and global specificity of factor Xa, elastase, and granzyme
B which despite all being serine proteases and sharing the chymotrypsin-fold
show distinct substrate specificity profiles. We determined subpocket
interaction potentials with GRID for static X-ray structures and an in silico generated ensemble of conformations. Subpocket
interaction potentials determined for static X-ray structures turned
out to be insufficient to explain serine protease specificity for
all subpockets. Therefore, we generated conformational ensembles using
molecular dynamics simulations. We identified representative binding
site conformations using distance-based hierarchical agglomerative
clustering and determined subpocket interaction potentials for each
representative conformation of the binding site. Considering the differences
in subpocket interaction potentials for these representative conformations
as well as their abundance allowed us to quantitatively explain subpocket
specificity for the nonprime side for all three example proteases
on a molecular level. The methods to identify key regions determining
subpocket specificity introduced in this study are directly applicable
to other serine proteases, and the results provide starting points
for new strategies in rational drug design.
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Affiliation(s)
- Birgit J Waldner
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Julian E Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.,Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Roland G Huber
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.,Bioinformatics Institute (BII), Agency of Science, Technology and Research (A* STAR) , 30 Biopolis Street, Matrix#07-01, 138671 Singapore
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Michael Schauperl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Christian Kramer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
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176
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Chen B, Ge SS, Zhao YC, Chen C, Yang S. Activity-based protein profiling: an efficient approach to study serine hydrolases and their inhibitors in mammals and microbes. RSC Adv 2016. [DOI: 10.1039/c6ra20006k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
This review focuses on the identification of serine hydrolases and their inhibitors in mammals and microbes with activity-based protein profiling (ABPP).
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Affiliation(s)
- Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Sha-Sha Ge
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Yuan-Chao Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Chong Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
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177
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Martin BP, Vasilieva E, Dupureur CM, Spilling CD. Synthesis and comparison of the biological activity of monocyclic phosphonate, difluorophosphonate and phosphate analogs of the natural AChE inhibitor cyclophostin. Bioorg Med Chem 2015; 23:7529-34. [DOI: 10.1016/j.bmc.2015.10.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/20/2015] [Accepted: 10/29/2015] [Indexed: 12/15/2022]
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178
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de Veer SJ, Wang CK, Harris JM, Craik DJ, Swedberg JE. Improving the Selectivity of Engineered Protease Inhibitors: Optimizing the P2 Prime Residue Using a Versatile Cyclic Peptide Library. J Med Chem 2015; 58:8257-68. [PMID: 26393374 DOI: 10.1021/acs.jmedchem.5b01148] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Standard mechanism inhibitors are attractive design templates for engineering reversible serine protease inhibitors. When optimizing interactions between the inhibitor and target protease, many studies focus on the nonprimed segment of the inhibitor's binding loop (encompassing the contact β-strand). However, there are currently few methods for screening residues on the primed segment. Here, we designed a synthetic inhibitor library (based on sunflower trypsin inhibitor-1) for characterizing the P2' specificity of various serine proteases. Screening the library against 13 different proteases revealed unique P2' preferences for trypsin, chymotrypsin, matriptase, plasmin, thrombin, four kallikrein-related peptidases, and several clotting factors. Using this information to modify existing engineered inhibitors yielded new variants that showed considerably improved selectivity, reaching up to 7000-fold selectivity over certain off-target proteases. Our study demonstrates the importance of the P2' residue in standard mechanism inhibition and unveils a new approach for screening P2' substitutions that will benefit future inhibitor engineering studies.
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Affiliation(s)
- Simon J de Veer
- Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane, Queensland QLD 4059, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland , 306 Carmody Road, Building 80, Queensland Bioscience Presinct, Brisbane, Queensland, QLD 4072, Australia
| | - Jonathan M Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane, Queensland QLD 4059, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland , 306 Carmody Road, Building 80, Queensland Bioscience Presinct, Brisbane, Queensland, QLD 4072, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland , 306 Carmody Road, Building 80, Queensland Bioscience Presinct, Brisbane, Queensland, QLD 4072, Australia
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179
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Lodola A, Castelli R, Mor M, Rivara S. Fatty acid amide hydrolase inhibitors: a patent review (2009-2014). Expert Opin Ther Pat 2015; 25:1247-66. [PMID: 26413912 DOI: 10.1517/13543776.2015.1067683] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Fatty acid amide hydrolase (FAAH) is a key enzyme responsible for the degradation of the endocannabinoid anandamide. FAAH inactivation is emerging as a strategy to treat several CNS and peripheral diseases, including inflammation and pain. The search for effective FAAH inhibitors has thus become a key focus in present drug discovery. AREAS COVERED Patents and patent applications published from 2009 to 2014 in which novel chemical classes are claimed to inhibit FAAH. EXPERT OPINION FAAH is a promising target for treating many disease conditions including pain, inflammation and mood disorders. In the last few years, remarkable efforts have been made to develop new FAAH inhibitors (either reversible and irreversible) characterized by excellent potency and selectivity, to complete the arsenal of tools for modulating FAAH activity. The failure of PF-04457845 in a Phase II study on osteoarthritis pain has not flattened the interest in FAAH inhibitors. New clinical trials on 'classical' FAAH inhibitors are now ongoing, and new strategies based on compounds with peculiar in vivo distribution (e.g., peripheral) or with multiple pharmacological activities (e.g., FAAH and COX) are under investigation and could boost the therapeutic potential of this class in the next future.
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Affiliation(s)
- Alessio Lodola
- a 1 Università degli Studi di Parma, Dipartimento di Farmacia , Parco Area delle Scienze 27/A, Parma, Italy
| | - Riccardo Castelli
- b 2 Università degli Studi di Parma, Dipartimento di Farmacia , Parco Area delle Scienze 27/A, Parma, Italy
| | - Marco Mor
- c 3 Università degli Studi di Parma, Dipartimento di Farmacia , Parco Area delle Scienze 27/A, Parma, Italy +39 0521 905059 ; +39 0521 905006 ;
| | - Silvia Rivara
- a 1 Università degli Studi di Parma, Dipartimento di Farmacia , Parco Area delle Scienze 27/A, Parma, Italy
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180
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Xu H, Majmudar JD, Davda D, Ghanakota P, Kim KH, Carlson HA, Showalter HD, Martin BR, Amidon GL. Substrate-Competitive Activity-Based Profiling of Ester Prodrug Activating Enzymes. Mol Pharm 2015; 12:3399-407. [PMID: 26262434 DOI: 10.1021/acs.molpharmaceut.5b00414] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the mechanistic basis of prodrug delivery and activation is critical for establishing species-specific prodrug sensitivities necessary for evaluating preclinical animal models and potential drug-drug interactions. Despite significant adoption of prodrug methodologies for enhanced pharmacokinetics, functional annotation of prodrug activating enzymes is laborious and often unaddressed. Activity-based protein profiling (ABPP) describes an emerging chemoproteomic approach to assay active site occupancy within a mechanistically similar enzyme class in native proteomes. The serine hydrolase enzyme family is broadly reactive with reporter-linked fluorophosphonates, which have shown to provide a mechanism-based covalent labeling strategy to assay the activation state and active site occupancy of cellular serine amidases, esterases, and thioesterases. Here we describe a modified ABPP approach using direct substrate competition to identify activating enzymes for an ethyl ester prodrug, the influenza neuraminidase inhibitor oseltamivir. Substrate-competitive ABPP analysis identified carboxylesterase 1 (CES1) as an oseltamivir-activating enzyme in intestinal cell homogenates. Saturating concentrations of oseltamivir lead to a four-fold reduction in the observed rate constant for CES1 inactivation by fluorophosphonates. WWL50, a reported carbamate inhibitor of mouse CES1, blocked oseltamivir hydrolysis activity in human cell homogenates, confirming CES1 is the primary prodrug activating enzyme for oseltamivir in human liver and intestinal cell lines. The related carbamate inhibitor WWL79 inhibited mouse but not human CES1, providing a series of probes for analyzing prodrug activation mechanisms in different preclinical models. Overall, we present a substrate-competitive activity-based profiling approach for broadly surveying candidate prodrug hydrolyzing enzymes and outline the kinetic parameters for activating enzyme discovery, ester prodrug design, and preclinical development of ester prodrugs.
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Affiliation(s)
- Hao Xu
- Department of Medicinal Chemistry, College of Pharmacy, ‡Department of Pharmaceutical Sciences, College of Pharmacy, §Department of Chemistry, and ⊥Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jaimeen D Majmudar
- Department of Medicinal Chemistry, College of Pharmacy, ‡Department of Pharmaceutical Sciences, College of Pharmacy, §Department of Chemistry, and ⊥Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Dahvid Davda
- Department of Medicinal Chemistry, College of Pharmacy, ‡Department of Pharmaceutical Sciences, College of Pharmacy, §Department of Chemistry, and ⊥Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Phani Ghanakota
- Department of Medicinal Chemistry, College of Pharmacy, ‡Department of Pharmaceutical Sciences, College of Pharmacy, §Department of Chemistry, and ⊥Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Ki H Kim
- Department of Medicinal Chemistry, College of Pharmacy, ‡Department of Pharmaceutical Sciences, College of Pharmacy, §Department of Chemistry, and ⊥Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, ‡Department of Pharmaceutical Sciences, College of Pharmacy, §Department of Chemistry, and ⊥Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Hollis D Showalter
- Department of Medicinal Chemistry, College of Pharmacy, ‡Department of Pharmaceutical Sciences, College of Pharmacy, §Department of Chemistry, and ⊥Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Brent R Martin
- Department of Medicinal Chemistry, College of Pharmacy, ‡Department of Pharmaceutical Sciences, College of Pharmacy, §Department of Chemistry, and ⊥Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Gordon L Amidon
- Department of Medicinal Chemistry, College of Pharmacy, ‡Department of Pharmaceutical Sciences, College of Pharmacy, §Department of Chemistry, and ⊥Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States
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181
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Capello M, Lee M, Wang H, Babel I, Katz MH, Fleming JB, Maitra A, Wang H, Tian W, Taguchi A, Hanash SM. Carboxylesterase 2 as a Determinant of Response to Irinotecan and Neoadjuvant FOLFIRINOX Therapy in Pancreatic Ductal Adenocarcinoma. J Natl Cancer Inst 2015. [DOI: 10.1093/jnci/djv132\] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
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182
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Kohnz RA, Mulvihill MM, Chang JW, Hsu KL, Sorrentino A, Cravatt BF, Bandyopadhyay S, Goga A, Nomura DK. Activity-Based Protein Profiling of Oncogene-Driven Changes in Metabolism Reveals Broad Dysregulation of PAFAH1B2 and 1B3 in Cancer. ACS Chem Biol 2015; 10:1624-30. [PMID: 25945974 DOI: 10.1021/acschembio.5b00053] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Targeting dysregulated metabolic pathways is a promising therapeutic strategy for eradicating cancer. Understanding how frequently altered oncogenes regulate metabolic enzyme targets would be useful in identifying both broad-spectrum and targeted metabolic therapies for cancer. Here, we used activity-based protein profiling to identify serine hydrolase activities that were consistently upregulated by various human oncogenes. Through this profiling effort, we found oncogenic regulatory mechanisms for several cancer-relevant serine hydrolases and discovered that platelet activating factor acetylhydrolase 1B2 and 1B3 (PAFAH1B2 and PAFAH1B3) activities were consistently upregulated by several oncogenes, alongside previously discovered cancer-relevant hydrolases fatty acid synthase and monoacylglycerol lipase. While we previously showed that PAFAH1B2 and 1B3 were important in breast cancer, our most recent profiling studies have revealed that these enzymes may be dysregulated broadly across many types of cancers. Here, we find that pharmacological blockade of both enzymes impairs cancer pathogenicity across multiple different types of cancer cells, including breast, ovarian, melanoma, and prostate cancer. We also show that pharmacological blockade of PAFAH1B2 and 1B3 causes unique changes in lipid metabolism, including heightened levels of tumor-suppressing lipids. Our results reveal oncogenic regulatory mechanisms of several cancer-relevant serine hydrolases using activity-based protein profiling, and we show that PAFAH1B2 and 1B3 are important in maintaining cancer pathogenicity across a wide spectrum of cancer types.
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Affiliation(s)
- Rebecca A. Kohnz
- Program in Metabolic Biology, Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
| | - Melinda M. Mulvihill
- Program in Metabolic Biology, Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
| | - Jae Won Chang
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Rd. SR107, La Jolla, California 92037, United States
| | - Ku-Lung Hsu
- Department
of Chemistry, University of Virginia, McCormick Road,
P.O. Box 400319, Charlottesville, Virginia 22904-4319, United States
| | | | - Benjamin F. Cravatt
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Rd. SR107, La Jolla, California 92037, United States
| | | | - Andrei Goga
- University of California, San Francisco Helen Diller Family Comprehensive Cancer Center, Box 0128, San Francisco, California 94143, United States
| | - Daniel K. Nomura
- Program in Metabolic Biology, Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
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183
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Sundermann T, Hanekamp W, Lehr M. Structure-activity relationship studies on 1-heteroaryl-3-phenoxypropan-2-ones acting as inhibitors of cytosolic phospholipase A2α and fatty acid amide hydrolase: replacement of the activated ketone group by other serine traps. J Enzyme Inhib Med Chem 2015; 31:653-63. [PMID: 26153239 DOI: 10.3109/14756366.2015.1057721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cytosolic phospholipase A2α (cPLA2α) and fatty acid amide hydrolase (FAAH) are serine hydrolases. cPLA2α is involved in the generation of pro-inflammatory lipid mediators, FAAH terminates the anti-inflammatory effects of endocannabinoids. Therefore, inhibitors of these enzymes may represent new drug candidates for the treatment of inflammation. We have reported that certain 1-heteroarylpropan-2-ones are potent inhibitors of cPLA2α and FAAH. The serine reactive ketone group of these compounds, which is crucial for enzyme inhibition, is readily metabolized resulting in inactive alcohol derivatives. In order to obtain metabolically more stable inhibitors, we replaced this moiety by α-ketoheterocyle, cyanamide and nitrile serine traps. Investigations on activity and metabolic stability of these substances revealed that in all cases an increased metabolic stability was accompanied by a loss of inhibitory potency against cPLA2α and FAAH, respectively.
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Affiliation(s)
- Tom Sundermann
- a Department of Chemistry and Pharmacy , Institute of Pharmaceutical and Medicinal Chemistry, University of Münster , Münster , Germany
| | - Walburga Hanekamp
- a Department of Chemistry and Pharmacy , Institute of Pharmaceutical and Medicinal Chemistry, University of Münster , Münster , Germany
| | - Matthias Lehr
- a Department of Chemistry and Pharmacy , Institute of Pharmaceutical and Medicinal Chemistry, University of Münster , Münster , Germany
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184
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Cognetta AB, Niphakis MJ, Lee HC, Martini ML, Hulce JJ, Cravatt BF. Selective N-Hydroxyhydantoin Carbamate Inhibitors of Mammalian Serine Hydrolases. ACTA ACUST UNITED AC 2015; 22:928-37. [PMID: 26120000 DOI: 10.1016/j.chembiol.2015.05.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/18/2015] [Accepted: 05/30/2015] [Indexed: 01/12/2023]
Abstract
Serine hydrolase inhibitors, which facilitate enzyme function assignment and are used to treat a range of human disorders, often act by an irreversible mechanism that involves covalent modification of the serine hydrolase catalytic nucleophile. The portion of mammalian serine hydrolases for which selective inhibitors have been developed, however, remains small. Here, we show that N-hydroxyhydantoin (NHH) carbamates are a versatile class of irreversible serine hydrolase inhibitors that can be modified on both the staying (carbamylating) and leaving (NHH) groups to optimize potency and selectivity. Synthesis of a small library of NHH carbamates and screening by competitive activity-based protein profiling furnished selective, in vivo-active inhibitors and tailored activity-based probes for multiple mammalian serine hydrolases, including palmitoyl protein thioesterase 1, mutations of which cause the human disease infantile neuronal ceroid lipofuscinosis.
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Affiliation(s)
- Armand B Cognetta
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Micah J Niphakis
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hyeon-Cheol Lee
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael L Martini
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan J Hulce
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Benjamin F Cravatt
- Department of Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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185
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Capello M, Lee M, Wang H, Babel I, Katz MH, Fleming JB, Maitra A, Wang H, Tian W, Taguchi A, Hanash SM. Carboxylesterase 2 as a Determinant of Response to Irinotecan and Neoadjuvant FOLFIRINOX Therapy in Pancreatic Ductal Adenocarcinoma. J Natl Cancer Inst 2015; 107:djv132. [PMID: 26025324 DOI: 10.1093/jnci/djv132] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Serine hydrolases (SHs) are among the largest classes of enzymes in humans and play crucial role in many pathophysiological processes of cancer. We have undertaken a comprehensive proteomic analysis to assess the differential expression and cellular localization of SHs, which uncovered distinctive expression of Carboxylesterase 2 (CES2), the most efficient carboxyl esterase in activating the prodrug irinotecan into SN-38, in pancreatic ductal adenocarcinoma (PDAC). We therefore assessed the extent of heterogeneity in CES2 expression in PDAC and its potential relevance to irinotecan based therapy. METHODS CES2 expression in PDAC and paired nontumor tissues was evaluated by immunohistochemistry. CES2 activity was assessed by monitoring the hydrolysis of the substrate p-NPA and correlated with irinotecan IC50 values by means of Pearson's correlation. Kaplan-Meier and Cox regression analyses were applied to assess the association between overall survival and CES2 expression in patients who underwent neoadjuvant FOLFIRINOX treatment. All statistical tests were two-sided. RESULTS Statistically significant overexpression of CES2, both at the mRNA and protein levels, was observed in PDAC compared with paired nontumor tissue (P < .001), with 48 of 118 (40.7%) tumors exhibiting high CES2 expression. CES2 activity in 11 PDAC cell lines was inversely correlated with irinotecan IC50 values (R = -0.68, P = .02). High CES2 expression in tumor tissue was associated with longer overall survival in resectable and borderline resectable patients who underwent neoadjuvant FOLFIRINOX treatment (hazard ratio = 0.14, 95% confidence interval = 0.04 to 0.51, P = .02). CONCLUSION Our findings suggest that CES2 expression and activity, by mediating the intratumoral activation of irinotecan, is a contributor to FOLFIRINOX sensitivity in pancreatic cancer and CES2 assessment may define a subset of patients likely to respond to irinotecan based therapy.
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Affiliation(s)
- Michela Capello
- : Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX (MC, HW, SMH); Fred Hutchinson Cancer Research Center, Seattle, WA (ML, IB); Departments of Surgical Oncology (MHK, JBF), Pathology (AM, HW, WT), and Translational Molecular Pathology (AM, HW, AT, SMH), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Minhee Lee
- : Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX (MC, HW, SMH); Fred Hutchinson Cancer Research Center, Seattle, WA (ML, IB); Departments of Surgical Oncology (MHK, JBF), Pathology (AM, HW, WT), and Translational Molecular Pathology (AM, HW, AT, SMH), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hong Wang
- : Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX (MC, HW, SMH); Fred Hutchinson Cancer Research Center, Seattle, WA (ML, IB); Departments of Surgical Oncology (MHK, JBF), Pathology (AM, HW, WT), and Translational Molecular Pathology (AM, HW, AT, SMH), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ingrid Babel
- : Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX (MC, HW, SMH); Fred Hutchinson Cancer Research Center, Seattle, WA (ML, IB); Departments of Surgical Oncology (MHK, JBF), Pathology (AM, HW, WT), and Translational Molecular Pathology (AM, HW, AT, SMH), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Matthew H Katz
- : Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX (MC, HW, SMH); Fred Hutchinson Cancer Research Center, Seattle, WA (ML, IB); Departments of Surgical Oncology (MHK, JBF), Pathology (AM, HW, WT), and Translational Molecular Pathology (AM, HW, AT, SMH), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jason B Fleming
- : Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX (MC, HW, SMH); Fred Hutchinson Cancer Research Center, Seattle, WA (ML, IB); Departments of Surgical Oncology (MHK, JBF), Pathology (AM, HW, WT), and Translational Molecular Pathology (AM, HW, AT, SMH), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Anirban Maitra
- : Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX (MC, HW, SMH); Fred Hutchinson Cancer Research Center, Seattle, WA (ML, IB); Departments of Surgical Oncology (MHK, JBF), Pathology (AM, HW, WT), and Translational Molecular Pathology (AM, HW, AT, SMH), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Huamin Wang
- : Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX (MC, HW, SMH); Fred Hutchinson Cancer Research Center, Seattle, WA (ML, IB); Departments of Surgical Oncology (MHK, JBF), Pathology (AM, HW, WT), and Translational Molecular Pathology (AM, HW, AT, SMH), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Weihua Tian
- : Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX (MC, HW, SMH); Fred Hutchinson Cancer Research Center, Seattle, WA (ML, IB); Departments of Surgical Oncology (MHK, JBF), Pathology (AM, HW, WT), and Translational Molecular Pathology (AM, HW, AT, SMH), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ayumu Taguchi
- : Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX (MC, HW, SMH); Fred Hutchinson Cancer Research Center, Seattle, WA (ML, IB); Departments of Surgical Oncology (MHK, JBF), Pathology (AM, HW, WT), and Translational Molecular Pathology (AM, HW, AT, SMH), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Samir M Hanash
- : Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX (MC, HW, SMH); Fred Hutchinson Cancer Research Center, Seattle, WA (ML, IB); Departments of Surgical Oncology (MHK, JBF), Pathology (AM, HW, WT), and Translational Molecular Pathology (AM, HW, AT, SMH), The University of Texas MD Anderson Cancer Center, Houston, TX.
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186
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Abstract
Eukaryotic and prokaryotic organisms possess huge numbers of uncharacterized enzymes. Selective inhibitors offer powerful probes for assigning functions to enzymes in native biological systems. Here, we discuss how the chemical proteomic platform activity-based protein profiling (ABPP) can be implemented to discover selective and in vivo-active inhibitors for enzymes. We further describe how these inhibitors have been used to delineate the biochemical and cellular functions of enzymes, leading to the discovery of metabolic and signaling pathways that make important contributions to human physiology and disease. These studies demonstrate the value of selective chemical probes as drivers of biological inquiry.
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Affiliation(s)
- Micah J Niphakis
- The Skaggs Institute for Chemical Biology and the Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037;
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187
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Hunerdosse DM, Morris PJ, Miyamoto DK, Fisher KJ, Bateman LA, Ghazaleh JR, Zhong S, Nomura DK. Chemical genetics screening reveals KIAA1363 as a cytokine-lowering target. ACS Chem Biol 2014; 9:2905-13. [PMID: 25343321 PMCID: PMC4273974 DOI: 10.1021/cb500717g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Inflammation is a hallmark of many human diseases, including pain, arthritis, atherosclerosis, obesity and diabetes, cancer, and neurodegenerative diseases. Although there are several successfully marketed small molecules anti-inflammatory drugs such as cyclooxygenase inhibitors and glucocorticoids, many of these compounds are also associated with various adverse cardiovascular or immunosuppressive side effects. Thus, identifying novel anti-inflammatory small molecules and their targets is critical for developing safer and more effective next-generation treatment strategies for inflammatory diseases. Here, we have conducted a chemical genetics screen to identify small molecules that suppress the release of the inflammatory cytokine TNFα from stimulated macrophages. We have used an enzyme class-directed chemical library for our screening efforts to facilitate subsequent target identification using activity-based protein profiling (ABPP). Using this strategy, we have found that KIAA1363 is a novel target for lowering key pro-inflammatory cytokines through affecting key ether lipid metabolism pathways. Our study highlights the application of combining chemical genetics with chemoproteomic and metabolomic approaches toward identifying and characterizing anti-inflammatory smal molecules and their targets.
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Affiliation(s)
- Devon M. Hunerdosse
- Program in Metabolic Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Patrick J. Morris
- Program in Metabolic Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - David K. Miyamoto
- Program in Metabolic Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Karl J. Fisher
- Program in Metabolic Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Leslie A. Bateman
- Program in Metabolic Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jonathan R. Ghazaleh
- Program in Metabolic Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Sharon Zhong
- Program in Metabolic Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Daniel K. Nomura
- Program in Metabolic Biology, University of California, Berkeley, Berkeley, California 94720, United States
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188
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Delorme V, Raux B, Puppo R, Leclaire J, Cavalier JF, Marc S, Kamarajugadda PK, Buono G, Fotiadu F, Canaan S, Carrière F. Supported inhibitor for fishing lipases in complex biological media and mass spectrometry identification. Biochimie 2014; 107 Pt A:124-34. [DOI: 10.1016/j.biochi.2014.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/16/2014] [Indexed: 12/24/2022]
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189
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Mahatmanto T, Mylne JS, Poth AG, Swedberg JE, Kaas Q, Schaefer H, Craik DJ. The evolution of Momordica cyclic peptides. Mol Biol Evol 2014; 32:392-405. [PMID: 25376175 DOI: 10.1093/molbev/msu307] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cyclic proteins have evolved for millions of years across all kingdoms of life to confer structural stability over their acyclic counterparts while maintaining intrinsic functional properties. Here, we show that cyclic miniproteins (or peptides) from Momordica (Cucurbitaceae) seeds evolved in species that diverged from an African ancestor around 19 Ma. The ability to achieve head-to-tail cyclization of Momordica cyclic peptides appears to have been acquired through a series of mutations in their acyclic precursor coding sequences following recent and independent gene expansion event(s). Evolutionary analysis of Momordica cyclic peptides reveals sites that are under selection, highlighting residues that are presumably constrained for maintaining their function as potent trypsin inhibitors. Molecular dynamics of Momordica cyclic peptides in complex with trypsin reveals site-specific residues involved in target binding. In a broader context, this study provides a basis for selecting Momordica species to further investigate the biosynthesis of the cyclic peptides and for constructing libraries that may be screened against evolutionarily related serine proteases implicated in human diseases.
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Affiliation(s)
- Tunjung Mahatmanto
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Joshua S Mylne
- The University of Western Australia, School of Chemistry and Biochemistry & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Perth, WA, Australia
| | - Aaron G Poth
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Hanno Schaefer
- Plant Biodiversity Research, Technische Universität München, Freising, Germany
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
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190
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Kohnz RA, Nomura DK. Chemical approaches to therapeutically target the metabolism and signaling of the endocannabinoid 2-AG and eicosanoids. Chem Soc Rev 2014; 43:6859-69. [PMID: 24676249 PMCID: PMC4159426 DOI: 10.1039/c4cs00047a] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The endocannabinoid system, most popularly known as the target of the psychoactive component of marijuana, Δ(9)-tetrahydrocannabinol (THC), is a signaling network that modulates a diverse range of physiological processes including nociception, behavior, cognitive function, appetite, metabolism, motor control, memory formation, and inflammation. While THC and its derivatives have garnered notoriety in the eyes of the public, the endocannabinoid system consists of two endogenous signaling lipids, 2-arachidonoylglycerol (2-AG) and N-arachidonoylethanolamine (anandamide), which activate cannabinoid receptors CB1 and CB2 in the nervous system and peripheral tissues. This review will focus on the recent efforts to chemically manipulate 2-AG signaling through the development of inhibitors of the 2-AG-synthesizing enzyme diacylglycerol lipase (DAGL) or the 2-AG-degrading enzyme monoacylglycerol lipase (MAGL), and assessing the therapeutic potential of DAGL and MAGL inhibitors in pain, inflammation, degenerative diseases, tissue injury, and cancer.
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Affiliation(s)
- Rebecca A Kohnz
- Program in Metabolic Biology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA.
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191
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Otrubova K, Srinivasan V, Boger DL. Discovery libraries targeting the major enzyme classes: the serine hydrolases. Bioorg Med Chem Lett 2014; 24:3807-13. [PMID: 25037918 PMCID: PMC4130767 DOI: 10.1016/j.bmcl.2014.06.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 11/19/2022]
Abstract
Two libraries of modestly reactive ureas containing either electron-deficient acyl anilines or acyl pyrazoles were prepared and are reported as screening libraries for candidate serine hydrolase inhibitors. Within each library is a small but powerful subset of compounds that serve as a chemotype fragment screening library capable of subsequent structural diversification. Elaboration of the pyrazole-based ureas provided remarkably potent irreversible inhibitors of fatty acid amide hydrolase (FAAH, apparent Ki=100-200 pM) complementary to those previously disclosed enlisting electron-deficient aniline-based ureas.
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Affiliation(s)
- Katerina Otrubova
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla CA 92037, United States
| | - Venkat Srinivasan
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla CA 92037, United States
| | - Dale L Boger
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla CA 92037, United States.
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192
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Bachovchin DA, Koblan LW, Wu W, Liu Y, Li Y, Zhao P, Woznica I, Shu Y, Lai JH, Poplawski SE, Kiritsy CP, Healey SE, DiMare M, Sanford DG, Munford RS, Bachovchin WW, Golub TR. A high-throughput, multiplexed assay for superfamily-wide profiling of enzyme activity. Nat Chem Biol 2014; 10:656-63. [PMID: 24997602 PMCID: PMC5953424 DOI: 10.1038/nchembio.1578] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 05/29/2014] [Indexed: 12/12/2022]
Abstract
The selectivity of an enzyme inhibitor is a key determinant of its usefulness as a tool compound or its safety as a drug. Yet selectivity is never assessed comprehensively in the early stages of the drug discovery process, and only rarely in the later stages, because technical limitations prohibit doing otherwise. Here, we report EnPlex, an efficient, high-throughput method for simultaneously assessing inhibitor potency and specificity, and pilot its application to 96 serine hydrolases. EnPlex analysis of widely used serine hydrolase inhibitors revealed numerous previously unrecognized off-target interactions, some of which may help to explain previously confounding adverse effects. In addition, EnPlex screening of a hydrolase-directed library of boronic acid- and nitrile-containing compounds provided structure-activity relationships in both potency and selectivity dimensions from which lead candidates could be more effectively prioritized. Follow-up of a series of dipeptidyl peptidase 4 inhibitors showed that EnPlex indeed predicted efficacy and safety in animal models. These results demonstrate the feasibility and value of high-throughput, superfamily-wide selectivity profiling and suggest that such profiling can be incorporated into the earliest stages of drug discovery.
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Affiliation(s)
| | - Luke W. Koblan
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Wengen Wu
- Department of Biochemistry, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | - Yuxin Liu
- Department of Biochemistry, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | - Youhua Li
- Department of Biochemistry, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | - Peng Zhao
- Department of Biochemistry, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | - Iwona Woznica
- Department of Biochemistry, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | - Ying Shu
- Department of Biochemistry, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | - Jack H. Lai
- Department of Biochemistry, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | - Sarah E. Poplawski
- Department of Biochemistry, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | | | - Sarah E. Healey
- Department of Biochemistry, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | - Matthew DiMare
- Department of Biochemistry, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | - David G. Sanford
- Department of Biochemistry, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
| | - Robert S. Munford
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - William W. Bachovchin
- Department of Biochemistry, Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA
- Arisaph Pharmaceuticals, 100 High Street, Boston, MA 02110, USA
| | - Todd R. Golub
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115 USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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193
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Muelbaier M, Drewes G. Drug selectivity: Running in the family. Nat Chem Biol 2014; 10:608-9. [PMID: 24997603 DOI: 10.1038/nchembio.1585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marcel Muelbaier
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
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194
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Furman J, Kang M, Choi S, Cao Y, Wold ED, Sun SB, Smider V, Schultz PG, Kim CH. A genetically encoded aza-Michael acceptor for covalent cross-linking of protein-receptor complexes. J Am Chem Soc 2014; 136:8411-7. [PMID: 24846839 PMCID: PMC4227728 DOI: 10.1021/ja502851h] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Indexed: 12/31/2022]
Abstract
Selective covalent bond formation at a protein-protein interface potentially can be achieved by genetically introducing into a protein an appropriately "tuned" electrophilic unnatural amino acid that reacts with a native nucleophilic residue in its cognate receptor upon complex formation. We have evolved orthogonal aminoacyl-tRNA synthetase/tRNACUA pairs that genetically encode three aza-Michael acceptor amino acids, N(ε)-acryloyl-(S)-lysine (AcrK, 1), p-acrylamido-(S)-phenylalanine (AcrF, 2), and p-vinylsulfonamido-(S)-phenylalanine (VSF, 3), in response to the amber stop codon in Escherichia coli. Using an αErbB2 Fab-ErbB2 antibody-receptor pair as an example, we demonstrate covalent bond formation between an αErbB2-VSF mutant and a specific surface lysine ε-amino group of ErbB2, leading to near quantitative cross-linking to either purified ErbB2 in vitro or to native cellular ErbB2 at physiological pH. This efficient biocompatible reaction may be useful for creating novel cell biological probes, diagnostics, or therapeutics that selectively and irreversibly bind a target protein in vitro or in living cells.
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Affiliation(s)
- Jennifer
L. Furman
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Mingchao Kang
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- California
Institute for Biomedical Research, 11119 North Torrey Pines Road Suite 100, La
Jolla, California 92037, United States
| | - Seihyun Choi
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yu Cao
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Erik D. Wold
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sophie B. Sun
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- California
Institute for Biomedical Research, 11119 North Torrey Pines Road Suite 100, La
Jolla, California 92037, United States
| | - Vaughn
V. Smider
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G. Schultz
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- California
Institute for Biomedical Research, 11119 North Torrey Pines Road Suite 100, La
Jolla, California 92037, United States
| | - Chan Hyuk Kim
- California
Institute for Biomedical Research, 11119 North Torrey Pines Road Suite 100, La
Jolla, California 92037, United States
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195
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Morris PJ, Medina-Cleghorn D, Heslin A, King SM, Orr J, Mulvihill MM, Krauss RM, Nomura DK. Organophosphorus flame retardants inhibit specific liver carboxylesterases and cause serum hypertriglyceridemia. ACS Chem Biol 2014; 9:1097-103. [PMID: 24597639 PMCID: PMC4027947 DOI: 10.1021/cb500014r] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Humans are prevalently exposed to organophosphorus flame retardants (OPFRs) contained in consumer products and electronics, though their toxicological effects and mechanisms remain poorly understood. We show here that OPFRs inhibit specific liver carboxylesterases (Ces) and cause altered hepatic lipid metabolism. Ablation of the OPFR target Ces1g has been previously linked to dyslipidemia in mice. Consistent with OPFR inhibition of Ces1g, we also observe OPFR-induced serum hypertriglyceridemia in mice. Our findings suggest novel toxicities that may arise from OPFR exposure and highlight the utility of chemoproteomic and metabolomic platforms in the toxicological characterization of environmental chemicals.
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Affiliation(s)
- Patrick J. Morris
- Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
| | - Daniel Medina-Cleghorn
- Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
| | - Ann Heslin
- Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
| | - Sarah M. King
- Children’s Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, California 94609, United States
| | - Joseph Orr
- Children’s Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, California 94609, United States
| | - Melinda M. Mulvihill
- Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
| | - Ronald M. Krauss
- Children’s Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, California 94609, United States
| | - Daniel K. Nomura
- Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
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196
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Shokhen M, Hirsch M, Khazanov N, Ozeri R, Perlman N, Traube T, Vijayakumar S, Albeck A. From Catalytic Mechanism to Rational Design of Reversible Covalent Inhibitors of Serine and Cysteine Hydrolases. Isr J Chem 2014. [DOI: 10.1002/ijch.201300144] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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197
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Naffin-Olivos JL, Georgieva M, Goldfarb N, Madan-Lala R, Dong L, Bizzell E, Valinetz E, Brandt GS, Yu S, Shabashvili DE, Ringe D, Dunn BM, Petsko GA, Rengarajan J. Mycobacterium tuberculosis Hip1 modulates macrophage responses through proteolysis of GroEL2. PLoS Pathog 2014; 10:e1004132. [PMID: 24830429 PMCID: PMC4022732 DOI: 10.1371/journal.ppat.1004132] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 04/03/2014] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) employs multiple strategies to evade host immune responses and persist within macrophages. We have previously shown that the cell envelope-associated Mtb serine hydrolase, Hip1, prevents robust macrophage activation and dampens host pro-inflammatory responses, allowing Mtb to delay immune detection and accelerate disease progression. We now provide key mechanistic insights into the molecular and biochemical basis of Hip1 function. We establish that Hip1 is a serine protease with activity against protein and peptide substrates. Further, we show that the Mtb GroEL2 protein is a direct substrate of Hip1 protease activity. Cleavage of GroEL2 is specifically inhibited by serine protease inhibitors. We mapped the cleavage site within the N-terminus of GroEL2 and confirmed that this site is required for proteolysis of GroEL2 during Mtb growth. Interestingly, we discovered that Hip1-mediated cleavage of GroEL2 converts the protein from a multimeric to a monomeric form. Moreover, ectopic expression of cleaved GroEL2 monomers into the hip1 mutant complemented the hyperinflammatory phenotype of the hip1 mutant and restored wild type levels of cytokine responses in infected macrophages. Our studies point to Hip1-dependent proteolysis as a novel regulatory mechanism that helps Mtb respond rapidly to changing host immune environments during infection. These findings position Hip1 as an attractive target for inhibition for developing immunomodulatory therapeutics against Mtb.
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Affiliation(s)
- Jacqueline L. Naffin-Olivos
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Maria Georgieva
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Nathan Goldfarb
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - Ranjna Madan-Lala
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Lauren Dong
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Erica Bizzell
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Ethan Valinetz
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Gabriel S. Brandt
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- Franklin and Marshall College, Lancaster, Pennsylvania, United States of America
| | - Sarah Yu
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - Daniil E. Shabashvili
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - Dagmar Ringe
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Ben M. Dunn
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - Gregory A. Petsko
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jyothi Rengarajan
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
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198
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Hunerdosse D, Nomura DK. Activity-based proteomic and metabolomic approaches for understanding metabolism. Curr Opin Biotechnol 2014; 28:116-26. [PMID: 24594637 DOI: 10.1016/j.copbio.2014.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/30/2014] [Accepted: 02/03/2014] [Indexed: 12/20/2022]
Abstract
There are an increasing number of human pathologies that have been associated with altered metabolism, including obesity, diabetes, atherosclerosis, cancer, and neurodegenerative diseases. Most attention on metabolism has been focused on well-understood metabolic pathways and has largely ignored most of the biochemical pathways that operate in (patho)physiological settings, in part because of the vast landscape of uncharacterized and undiscovered metabolic pathways. One technology that has arisen to meet this challenge is activity-based protein profiling (ABPP) that uses activity-based chemical probes to broadly assess the functional states of both characterized and uncharacterized enzymes. This review will focus on how ABPP, coupled with inhibitor discovery platforms and functional metabolomic technologies, have led to discoveries that have expanded our knowledge of metabolism in health and disease.
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Affiliation(s)
- Devon Hunerdosse
- Program in Metabolic Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Daniel K Nomura
- Program in Metabolic Biology, University of California, Berkeley, Berkeley, CA 94720, United States.
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199
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Davda D, Martin BR. Acyl protein thioesterase inhibitors as probes of dynamic S-palmitoylation. MEDCHEMCOMM 2014; 5:268-276. [PMID: 25558349 PMCID: PMC4280026 DOI: 10.1039/c3md00333g] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein palmitoylation describes the hydrophobic post-translational modification of cysteine residues in certain proteins, and is required for the spatial organization and composition of cellular membrane environments. Certain palmitoylated proteins are processed by acyl protein thioesterase (APT) enzymes, which catalyze thioester hydrolysis of palmitoylated cysteine residues. Inhibiting APT enzymes disrupts Ras trafficking and attenuates oncogenic growth signaling, highlighting these enzymes as potential therapeutic targets. As members of the serine hydrolase enzyme family, APT enzymes can be assayed by fluorophosphonate activity-based protein profiling (ABPP) methods, allowing rapid profiling of inhibitor selectivity and potency. In this review, we discuss recent progress in the development of potent and selective inhibitors to APT enzymes, including both competitive and non-competitive chemotypes. These examples highlight how ABPP methods integrate with medicinal chemistry for the discovery and optimization of inhibitors in complex proteomes.
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Affiliation(s)
- Dahvid Davda
- Program in Chemical Biology, University of Michigan, 930. N. University Ave., Ann Arbor, MI 48109, USA
| | - Brent R. Martin
- Program in Chemical Biology, University of Michigan, 930. N. University Ave., Ann Arbor, MI 48109, USA
- Department of Chemistry, University of Michigan, 930. N. University Ave., Ann Arbor, MI 48109, USA
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200
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Traube T, Shokhen M, Albeck A. A new method for filtering of reactive "warheads" of transition-state analog protease inhibitors. Eur J Med Chem 2014; 77:134-8. [PMID: 24631732 DOI: 10.1016/j.ejmech.2014.02.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 02/27/2014] [Indexed: 10/25/2022]
Abstract
In light of the major contribution of the reactive warhead to the binding energy trend in reversible covalent transition-state analog inhibitors of serine and cysteine hydrolases, would it be possible to rationally design and quickly filter such warheads, especially for large-scale screening? The previously defined W1 and W2 covalent descriptors quantitatively account for the energetic effect of the covalent bonds reorganization, accompanying enzyme-inhibitor covalent binding. The quantum mechanically calculated W1 and W2 reflect the warhead binding energy by modeling of the enzyme-inhibitor reaction core. Here, we demonstrate the use of these descriptors for warhead filtering, and examine its scope and limitations. The W1 and W2 descriptors provide a tool for rational design of various warheads as universal building blocks of real inhibitors without the requirement of 3D structural information about the target enzyme or QSAR studies. These warheads could then be used as hit structural templates in the subsequent optimization of inhibitors recognition sites.
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Affiliation(s)
- Tamar Traube
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
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