101
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Larsen EM, Stephens DC, Clarke NH, Johnson RJ. Ester-prodrugs of ethambutol control its antibacterial activity and provide rapid screening for mycobacterial hydrolase activity. Bioorg Med Chem Lett 2017; 27:4544-4547. [PMID: 28882482 DOI: 10.1016/j.bmcl.2017.08.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/24/2017] [Accepted: 08/27/2017] [Indexed: 10/19/2022]
Abstract
M. tuberculosis contains an unusually high number of serine hydrolases by proteome percentage compared to other common bacteria or humans. This letter describes a method to probe the global substrate specificity of mycobacterial serine hydrolases with ester-protected prodrugs of ethambutol, a first-line antibiotic treatment for TB. These compounds were synthesized directly from ethambutol using a selective o-acylation to yield products in high yield and purity with minimal workup. A library of derivatives was screened against M. smegmatis, a non-infectious model for M. tuberculosis, which displayed significantly lowered biological activity compared to ethambutol. Incubation with a general serine hydrolase reactivated each derivative to near-ethambutol levels, demonstrating that esterification of ethambutol should provide a simple screen for mycobacterial hydrolase activity.
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Affiliation(s)
- Erik M Larsen
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208, USA
| | - Dominique C Stephens
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208, USA
| | - Nathan H Clarke
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208, USA
| | - R Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave., Indianapolis, IN 46208, USA.
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102
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Jones LH. Understanding the chemically-reactive proteome. MOLECULAR BIOSYSTEMS 2017; 12:1728-30. [PMID: 26726011 DOI: 10.1039/c5mb00760g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The reactivity of amino acid residues in proteins is context-dependent and difficult to predict. Chemical biology can be used to understand the chemical modifications of proteins to help elucidate the nature of the reactive proteome. The resulting insights can be applied to pharmacoproteomics, target identification and molecular pathology.
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Affiliation(s)
- Lyn H Jones
- Worldwide Medicinal Chemistry, Pfizer, 610 Main Street, Cambridge MA, 02139, USA.
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103
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Abstract
The Ras proteins are well-known drivers of many cancers and thus represent attractive targets for the development of anticancer therapeutics. Inhibitors that disrupt the association of the Ras proteins with membranes by blocking the addition of the farnesyl lipid moiety to the Ras C-terminus failed in clinical trials. Here, we explore the possibility of targeting a second lipid modification, S-acylation, commonly referred to as palmitoylation, as a strategy to disrupt the membrane interaction of specific Ras isoforms. We review the enzymes involved in adding and removing palmitate from Ras and discuss their potential roles in regulating Ras tumorigenesis. In addition, we examine other proteins that affect Ras protein localization and may serve as future drug targets.
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104
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Maccarrone M. Metabolism of the Endocannabinoid Anandamide: Open Questions after 25 Years. Front Mol Neurosci 2017; 10:166. [PMID: 28611591 PMCID: PMC5447297 DOI: 10.3389/fnmol.2017.00166] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/12/2017] [Indexed: 02/06/2023] Open
Abstract
Cannabis extracts have been used for centuries, but its main active principle ∆9-tetrahydrocannabinol (THC) was identified about 50 years ago. Yet, it is only 25 years ago that the first endogenous ligand of the same receptors engaged by the cannabis agents was discovered. This “endocannabinoid (eCB)” was identified as N-arachidonoylethanolamine (or anandamide (AEA)), and was shown to have several receptors, metabolic enzymes and transporters that altogether drive its biological activity. Here I report on the latest advances about AEA metabolism, with the aim of focusing open questions still awaiting an answer for a deeper understanding of AEA activity, and for translating AEA-based drugs into novel therapeutics for human diseases.
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Affiliation(s)
- Mauro Maccarrone
- Department of Medicine, Campus Bio-Medico University of RomeRome, Italy.,European Center for Brain Research, IRCCS Santa Lucia FoundationRome, Italy
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105
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Activity-based protein profiling as a robust method for enzyme identification and screening in extremophilic Archaea. Nat Commun 2017; 8:15352. [PMID: 28480883 PMCID: PMC5424146 DOI: 10.1038/ncomms15352] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/13/2017] [Indexed: 02/07/2023] Open
Abstract
Archaea are characterized by a unique life style in often environmental extremes but their thorough investigation is currently hampered by a limited set of suitable in vivo research methodologies. Here, we demonstrate that in vivo activity-based protein profiling (ABPP) may be used to sensitively detect either native or heterogeneously expressed active enzymes in living archaea even under these extreme conditions. In combination with the development of a genetically engineered archaeal screening strain, ABPP can furthermore be used in functional enzyme screenings from (meta)genome samples. We anticipate that our ABPP approach may therefore find application in basic archaeal research but also in the discovery of novel enzymes from (meta)genome libraries. Activity-based protein profiling (ABPP) is a chemical proteomics method to profile activity states of enzymes under physiological conditions. Here the authors show that ABPP can be applied to archaeal serine hydrolases in the model organism Sulfolobus acidocaldarius and can be used to identify novel putative serine hydrolases.
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106
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Wieczorek R, Adamala K, Gasperi T, Polticelli F, Stano P. Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine. Life (Basel) 2017; 7:E19. [PMID: 28397774 PMCID: PMC5492141 DOI: 10.3390/life7020019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and so, instead, small molecule catalysis (organocatalysis) may have occurred. The best candidates for the role of primitive organocatalysts are amino acids and short random peptides, which are believed to have been available in an early period on Earth. In this review, we discuss the occurrence of primordial organocatalysts in the form of peptides, in particular commenting on reports about seryl-histidine dipeptide, which have recently been investigated. Starting from this specific case, we also mention a peptide fragment condensation scenario, as well as other potential roles of peptides in primordial times. The review actually aims to stimulate further investigation on an unexplored field of research, namely one that specifically looks at the catalytic activity of small random peptides with respect to reactions relevant to prebiotic chemistry and early chemical evolution.
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Affiliation(s)
- Rafal Wieczorek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Katarzyna Adamala
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Tecla Gasperi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.
| | - Fabio Polticelli
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.
- National Institute of Nuclear Physics, Roma Tre Section, Via della Vasca Navale 84, 00146 Rome, Italy.
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Campus Ecotekne (S.P. 6 Lecce-Monteroni), 73100 Lecce, Italy.
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107
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Wittouck S, van Noort V. Correlated duplications and losses in the evolution of palmitoylation writer and eraser families. BMC Evol Biol 2017; 17:83. [PMID: 28320309 PMCID: PMC5359973 DOI: 10.1186/s12862-017-0932-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 03/09/2017] [Indexed: 12/27/2022] Open
Abstract
Background Protein post-translational modifications (PTMs) change protein properties. Each PTM type is associated with domain families that apply the modification (writers), remove the modification (erasers) and bind to the modified sites (readers) together called toolkit domains. The evolutionary origin and diversification remains largely understudied, except for tyrosine phosphorylation. Protein palmitoylation entails the addition of a palmitoyl fatty acid to a cysteine residue. This PTM functions as a membrane anchor and is involved in a range of cellular processes. One writer family and two erasers families are known for protein palmitoylation. Results In this work we unravel the evolutionary history of these writer and eraser families. We constructed a high-quality profile hidden Markov model (HMM) of each family, searched for protein family members in fully sequenced genomes and subsequently constructed phylogenetic distributions of the families. We constructed Maximum Likelihood phylogenetic trees and using gene tree rearrangement and tree reconciliation inferred their evolutionary histories in terms of duplication and loss events. We identified lineages where the families expanded or contracted and found that the evolutionary histories of the families are correlated. The results show that the erasers were invented first, before the origin of the eukaryotes. The writers first arose in the eukaryotic ancestor. The writers and erasers show co-expansions in several eukaryotic ancestral lineages. These expansions often seem to be followed by contractions in some or all of the lineages further in evolution. Conclusions A general pattern of correlated evolution appears between writer and eraser domains. These co-evolution patterns could be used in new methods for interaction prediction based on phylogenies. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0932-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stijn Wittouck
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.
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108
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Abstract
Two avenues to understanding gene function are complementary and often overlapping: experimental work and computational prediction. While experimental annotation generally produces high-quality annotations, it is low throughput. Conversely, computational annotations have broad coverage, but the quality of annotations may be variable, and therefore evaluating the quality of computational annotations is a critical concern.In this chapter, we provide an overview of strategies to evaluate the quality of computational annotations. First, we discuss why evaluating quality in this setting is not trivial. We highlight the various issues that threaten to bias the evaluation of computational annotations, most of which stem from the incompleteness of biological databases. Second, we discuss solutions that address these issues, for example, targeted selection of new experimental annotations and leveraging the existing experimental annotations.
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Affiliation(s)
- Nives Škunca
- Department of Computer Science, ETH Zurich, Universitätstrasse 19, 8092, Zurich, Switzerland.
- SIB Swiss Institute of Bioinformatics, Universitätstr. 19, 8092, Zurich, Switzerland.
- University College London, Street Gower St, WC1E 6BT, London, UK.
| | | | - Martin Steffen
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
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109
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Dai ZR, Feng L, Jin Q, Cheng H, Li Y, Ning J, Yu Y, Ge GB, Cui JN, Yang L. A practical strategy to design and develop an isoform-specific fluorescent probe for a target enzyme: CYP1A1 as a case study. Chem Sci 2016; 8:2795-2803. [PMID: 28553516 PMCID: PMC5426458 DOI: 10.1039/c6sc03970g] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/16/2016] [Indexed: 12/21/2022] Open
Abstract
The development of isoform-specific probe(s) for a target enzyme with multiple homologs is always challenging. Herein, a practical strategy was used to design and develop an isoform-specific probe for CYP1A1, a key cytochrome P450 isoenzyme involved in xenobiotic metabolism and bioactivation. On the basis of the subtle differences in 3D structure and substrate preference between CYP1A1 and its homolog CYP1A2, we proposed that it was possible to design a CYP1A1-specific probe via local modification of the reaction site on known CYP1A substrates. To validate this hypothesis, 4-hydroxy-1,8-naphthalimide (HN) was selected as the basic fluorophore due to its excellent optical properties, while a series of O-alkylated HN derivatives were prepared to evaluate their specificity towards CYP1A1. Our results revealed that the introduction of a chloroethyl to HN could get the best isoform selectivity towards CYP1A1 over other CYPs including CYP1A2. The newly developed probe NBCeN exhibited excellent specificity, high sensitivity, and a ratiometric fluorescence response following CYP1A1-catalyzed O-dechloroethylation. NBCeN was successfully used to real-time monitor the activity of CYP1A1 in complex biological samples and to rapidly screen CYP1A1 modulators in living systems. NBCeN could also be used for two-photon imaging of intracellular CYP1A1 in living cells and tissues with high ratiometric imaging resolution and deep tissue penetration. All these findings demonstrated that local modification of non-specific substrates was a practical strategy to develop an isoform-specific probe for a target isoenzyme, while NBCeN could serve as a specific imaging tool to explore the biological functions of CYP1A1 in complex biological systems.
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Affiliation(s)
- Zi-Ru Dai
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ; .,Graduate School of Chinese Academy of Sciences , Beijing , China
| | - Lei Feng
- State Key Laboratory of Fine Chemicals , Dalian University of Technology , Dalian , China
| | - Qiang Jin
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ; .,Graduate School of Chinese Academy of Sciences , Beijing , China
| | - Hailing Cheng
- Cancer Institute , The Second Hospital of Dalian Medical University , Dalian , China
| | - Yan Li
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ;
| | - Jing Ning
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ;
| | - Yang Yu
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ;
| | - Guang-Bo Ge
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ; .,State Key Laboratory of Fine Chemicals , Dalian University of Technology , Dalian , China
| | - Jing-Nan Cui
- State Key Laboratory of Fine Chemicals , Dalian University of Technology , Dalian , China
| | - Ling Yang
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , China . ;
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110
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Mindrebo JT, Nartey CM, Seto Y, Burkart MD, Noel JP. Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom. Curr Opin Struct Biol 2016; 41:233-246. [PMID: 27662376 PMCID: PMC5687975 DOI: 10.1016/j.sbi.2016.08.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 12/13/2022]
Abstract
The alpha/beta hydrolase (ABH) superfamily is a widespread and functionally malleable protein fold recognized for its diverse biochemical activities across all three domains of life. ABH enzymes possess unexpected catalytic activity in the green plant lineage through selective alterations in active site architecture and chemistry. Furthermore, the ABH fold serves as the core structure for phytohormone and ligand receptors in the gibberellin, strigolactone, and karrikin signaling pathways in plants. Despite recent discoveries, the ABH family is sparsely characterized in plants, a sessile kingdom known to evolve complex and specialized chemical adaptations as survival responses to widely varying biotic and abiotic ecologies. This review calls attention to the ABH superfamily in the plant kingdom to highlight the functional adaptability of the ABH fold.
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Affiliation(s)
- Jeffrey T Mindrebo
- Department of Chemistry and Biochemistry, The University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Charisse M Nartey
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yoshiya Seto
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, The University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Joseph P Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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111
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Kory N, Grond S, Kamat SS, Li Z, Krahmer N, Chitraju C, Zhou P, Fröhlich F, Semova I, Ejsing C, Zechner R, Cravatt BF, Farese RV, Walther TC. Mice lacking lipid droplet-associated hydrolase, a gene linked to human prostate cancer, have normal cholesterol ester metabolism. J Lipid Res 2016; 58:226-235. [PMID: 27836991 DOI: 10.1194/jlr.m072538] [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: 10/11/2016] [Revised: 11/03/2016] [Indexed: 01/22/2023] Open
Abstract
Variations in the gene LDAH (C2ORF43), which encodes lipid droplet-associated hydrolase (LDAH), are among few loci associated with human prostate cancer. Homologs of LDAH have been identified as proteins of lipid droplets (LDs). LDs are cellular organelles that store neutral lipids, such as triacylglycerols and sterol esters, as precursors for membrane components and as reservoirs of metabolic energy. LDAH is reported to hydrolyze cholesterol esters and to be important in macrophage cholesterol ester metabolism. Here, we confirm that LDAH is localized to LDs in several model systems. We generated a murine model in which Ldah is disrupted but found no evidence for a major function of LDAH in cholesterol ester or triacylglycerol metabolism in vivo, nor a role in energy or glucose metabolism. Our data suggest that LDAH is not a major cholesterol ester hydrolase, and an alternative metabolic function may be responsible for its possible effect on development of prostate cancer.
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Affiliation(s)
- Nora Kory
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Susanne Grond
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Siddhesh S Kamat
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA.,Skaggs Institute for Chemical Biology Scripps Research Institute, La Jolla, CA
| | - Zhihuan Li
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Natalie Krahmer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Chandramohan Chitraju
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Ping Zhou
- Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA
| | - Florian Fröhlich
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Ivana Semova
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Christer Ejsing
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Rudolf Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Benjamin F Cravatt
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA.,Skaggs Institute for Chemical Biology Scripps Research Institute, La Jolla, CA
| | - Robert V Farese
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA .,Department of Cell Biology, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Tobias C Walther
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA .,Department of Cell Biology, Harvard Medical School, Boston, MA.,Broad Institute of MIT and Harvard, Cambridge, MA.,Howard Hughes Medical Institute, Boston, MA
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112
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Molecular design of N,N-disubstituted 2-aminothiazolines as selective carboxylesterase inhibitors. Russ Chem Bull 2016. [DOI: 10.1007/s11172-016-1339-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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113
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Eleftheriadis N, Thee SA, Zwinderman MRH, Leus NGJ, Dekker FJ. Activity-Based Probes for 15-Lipoxygenase-1. Angew Chem Int Ed Engl 2016; 55:12300-5. [PMID: 27612308 PMCID: PMC5218545 DOI: 10.1002/anie.201606876] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Indexed: 12/12/2022]
Abstract
Human 15-lipoxygenase-1 (15-LOX-1) plays an important role in several inflammatory lung diseases, such as asthma, COPD, and chronic bronchitis, as well as various CNS diseases, such as Alzheimer's disease, Parkinson's disease, and stroke. Activity-based probes of 15-LOX-1 are required to explore the role of this enzyme further and to enable drug discovery. In this study, we developed a 15-LOX-1 activity-based probe for the efficient activity-based labeling of recombinant 15-LOX-1. 15-LOX-1-dependent labeling in cell lysates and tissue samples was also possible. To mimic the natural substrate of the enzyme, we designed activity-based probes that covalently bind to the active enzyme and include a terminal alkene as a chemical reporter for the bioorthogonal linkage of a detectable functionality through an oxidative Heck reaction. The activity-based labeling of 15-LOX-1 should enable the investigation and identification of this enzyme in complex biological samples, thus opening up completely new opportunities for drug discovery.
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Affiliation(s)
- Nikolaos Eleftheriadis
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Stephanie A Thee
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Martijn R H Zwinderman
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niek G J Leus
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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114
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Eleftheriadis N, Thee SA, Zwinderman MRH, Leus NGJ, Dekker FJ. Activity-Based Probes for 15-Lipoxygenase-1. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Nikolaos Eleftheriadis
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Stephanie A. Thee
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Martijn R. H. Zwinderman
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Niek G. J. Leus
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology; Groningen Research Institute of Pharmacy; University of Groningen; Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
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115
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Saxena C. Identification of protein binding partners of small molecules using label-free methods. Expert Opin Drug Discov 2016; 11:1017-25. [DOI: 10.1080/17460441.2016.1227316] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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116
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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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117
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Daneri-Castro SN, Chandrasekar B, Grosse-Holz FM, van der Hoorn RAL, Roberts TH. Activity-based protein profiling of hydrolytic enzymes induced by gibberellic acid in isolated aleurone layers of malting barley. FEBS Lett 2016; 590:2956-62. [DOI: 10.1002/1873-3468.12320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/14/2016] [Accepted: 07/16/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Sergio N. Daneri-Castro
- Faculty of Agriculture and Environment; Plant Breeding Institute; University of Sydney; Eveleigh Australia
| | | | | | | | - Thomas H. Roberts
- Faculty of Agriculture and Environment; Plant Breeding Institute; University of Sydney; Eveleigh Australia
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118
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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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Hatzios SK, Abel S, Martell J, Hubbard T, Sasabe J, Munera D, Clark L, Bachovchin DA, Qadri F, Ryan ET, Davis BM, Weerapana E, Waldor MK. Chemoproteomic profiling of host and pathogen enzymes active in cholera. Nat Chem Biol 2016; 12:268-274. [PMID: 26900865 PMCID: PMC4765928 DOI: 10.1038/nchembio.2025] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 12/31/2015] [Indexed: 12/15/2022]
Abstract
Activity-based protein profiling (ABPP) is a chemoproteomic tool for detecting active enzymes in complex biological systems. We used ABPP to identify secreted bacterial and host serine hydrolases that are active in animals infected with the cholera pathogen Vibrio cholerae. Four V. cholerae proteases were consistently active in infected rabbits, and one, VC0157 (renamed IvaP), was also active in human choleric stool. Inactivation of IvaP influenced the activity of other secreted V. cholerae and rabbit enzymes in vivo, and genetic disruption of all four proteases increased the abundance of intelectin, an intestinal lectin, and its binding to V. cholerae in infected rabbits. Intelectin also bound to other enteric bacterial pathogens, suggesting that it may constitute a previously unrecognized mechanism of bacterial surveillance in the intestine that is inhibited by pathogen-secreted proteases. Our work demonstrates the power of activity-based proteomics to reveal host-pathogen enzymatic dialog in an animal model of infection.
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Affiliation(s)
- Stavroula K. Hatzios
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Sören Abel
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Department of Pharmacy, University of Tromsø (UiT), The Arctic University of Norway, Tromsø, Norway
| | | | - Troy Hubbard
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Jumpei Sasabe
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Diana Munera
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Lars Clark
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Brigid M. Davis
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | | | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
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120
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Target identification of covalently binding drugs by activity-based protein profiling (ABPP). Bioorg Med Chem 2016; 24:3291-303. [PMID: 27085673 DOI: 10.1016/j.bmc.2016.03.050] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 03/25/2016] [Accepted: 03/26/2016] [Indexed: 12/12/2022]
Abstract
The characterization of the target proteins of drug molecules has become an important goal in understanding its mode of action and origin of side effects due to off-target binding. This is especially important for covalently binding drugs usually containing electrophilic moieties, which potentially can react with nucleophilic residues found in many proteins. This review gives a comprehensive overview of the use of activity-based protein profiling (ABPP) as an efficient tool for the target identification of covalently binding drugs.
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121
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Parsons WH, Kolar MJ, Kamat SS, Cognetta AB, Hulce JJ, Saez E, Kahn BB, Saghatelian A, Cravatt BF. AIG1 and ADTRP are atypical integral membrane hydrolases that degrade bioactive FAHFAs. Nat Chem Biol 2016; 12:367-372. [PMID: 27018888 PMCID: PMC4837090 DOI: 10.1038/nchembio.2051] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 02/05/2016] [Indexed: 12/04/2022]
Abstract
Enzyme classes may contain outlier members that share mechanistic, but not sequence or structural relatedness with more common representatives. The functional annotation of such exceptional proteins can be challenging. Here, we use activity-based profiling to discover that the poorly characterized multipass transmembrane proteins AIG1 and ADTRP are atypical hydrolytic enzymes that depend on conserved threonine and histidine residues for catalysis. Both AIG1 and ADTRP hydrolyze bioactive fatty-acid esters of hydroxy-fatty acids (FAHFAs), but not other major classes of lipids. We discover multiple cell-active, covalent inhibitors of AIG1 and show that these agents block FAHFA hydrolysis in mammalian cells. These results indicate that AIG1 and ADTRP are founding members of an evolutionarily conserved class of transmembrane threonine hydrolases involved in bioactive lipid metabolism. More generally, our findings demonstrate how chemical proteomics can excavate potential cases of convergent/parallel protein evolution that defy conventional sequence- and structure-based predictions.
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Affiliation(s)
- William H Parsons
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Matthew J Kolar
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, La Jolla, California 92037, United States
| | - Siddhesh S Kamat
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Armand B Cognetta
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Jonathan J Hulce
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Enrique Saez
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Barbara B Kahn
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Alan Saghatelian
- Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, La Jolla, California 92037, United States
| | - Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037
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122
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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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123
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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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Viader A, Ogasawara D, Joslyn CM, Sanchez-Alavez M, Mori S, Nguyen W, Conti B, Cravatt BF. A chemical proteomic atlas of brain serine hydrolases identifies cell type-specific pathways regulating neuroinflammation. eLife 2016; 5:e12345. [PMID: 26779719 PMCID: PMC4737654 DOI: 10.7554/elife.12345] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/13/2015] [Indexed: 12/19/2022] Open
Abstract
Metabolic specialization among major brain cell types is central to nervous system function and determined in large part by the cellular distribution of enzymes. Serine hydrolases are a diverse enzyme class that plays fundamental roles in CNS metabolism and signaling. Here, we perform an activity-based proteomic analysis of primary mouse neurons, astrocytes, and microglia to furnish a global portrait of the cellular anatomy of serine hydrolases in the brain. We uncover compelling evidence for the cellular compartmentalization of key chemical transmission pathways, including the functional segregation of endocannabinoid (eCB) biosynthetic enzymes diacylglycerol lipase-alpha (DAGLα) and –beta (DAGLβ) to neurons and microglia, respectively. Disruption of DAGLβ perturbed eCB-eicosanoid crosstalk specifically in microglia and suppressed neuroinflammatory events in vivo independently of broader effects on eCB content. Mapping the cellular distribution of metabolic enzymes thus identifies pathways for regulating specialized inflammatory responses in the brain while avoiding global alterations in CNS function. DOI:http://dx.doi.org/10.7554/eLife.12345.001 The brain is made up of many types of cells. These include the neurons that transmit messages throughout the nervous system, and microglia, which act as the first line of the brain’s immune defense. The activity of both neurons and microglia can be influenced by molecules called endocannabinoids that bind to proteins on the cells’ surface. For example, endocannabinoids affect how a neuron responds to messages sent to it from a neighbouring neuron, and help microglia to regulate the inflammation of brain tissue. Enzymes called serine hydrolases play important roles in several different signaling processes in the brain, including those involving endocannabinoids. Viader et al. have now studied the activities of these enzymes – including two called DAGLα and DAGLβ – in the mouse brain using a technique called activity-based protein profiling. This revealed that DAGLα plays an important role in controlling how neurons respond to endocannabinoids, while DAGLβ performs the equivalent role in microglia. When Viader et al. shut down DAGLβ activity, this only affected endocannabinoid signaling in microglia. This also had the effect of reducing inflammation in the brain, without affecting how endocannabinoids signal in neurons. These results suggest that inhibitors of DAGLβ could offer a way to suppress inflammation in the brain, which may contribute to neuropsychiatric and neurodegenerative diseases, while preserving the normal pathways that neurons use to communicate with one another. DOI:http://dx.doi.org/10.7554/eLife.12345.002
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Affiliation(s)
- Andreu Viader
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Daisuke Ogasawara
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Christopher M Joslyn
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Manuel Sanchez-Alavez
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Simone Mori
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - William Nguyen
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Bruno Conti
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
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125
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Carland F, Defries A, Cutler S, Nelson T. Novel Vein Patterns in Arabidopsis Induced by Small Molecules. PLANT PHYSIOLOGY 2016; 170:338-53. [PMID: 26574596 PMCID: PMC4704596 DOI: 10.1104/pp.15.01540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/03/2015] [Indexed: 05/03/2023]
Abstract
The critical role of veins in transporting water, nutrients, and signals suggests that some key regulators of vein formation may be genetically redundant and, thus, undetectable by forward genetic screens. To identify such regulators, we screened more than 5000 structurally diverse small molecules for compounds that alter Arabidopsis (Arabidopsis thaliana) leaf vein patterns. Many compound-induced phenotypes were observed, including vein networks with an open reticulum; decreased or increased vein number and thickness; and misaligned, misshapen, or nonpolar vascular cells. Further characterization of several individual active compounds suggests that their targets include hormone cross talk, hormone-dependent transcription, and PIN-FORMED trafficking.
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Affiliation(s)
- Francine Carland
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520 (F.C., T.N.);Bloomfield Industries, Inc., Staten Island, New York 10314 (A.D.); andDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, California 92507 (S.C.)
| | - Andrew Defries
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520 (F.C., T.N.);Bloomfield Industries, Inc., Staten Island, New York 10314 (A.D.); andDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, California 92507 (S.C.)
| | - Sean Cutler
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520 (F.C., T.N.);Bloomfield Industries, Inc., Staten Island, New York 10314 (A.D.); andDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, California 92507 (S.C.)
| | - Timothy Nelson
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520 (F.C., T.N.);Bloomfield Industries, Inc., Staten Island, New York 10314 (A.D.); andDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, California 92507 (S.C.)
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126
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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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127
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Lin DTS, Conibear E. ABHD17 proteins are novel protein depalmitoylases that regulate N-Ras palmitate turnover and subcellular localization. eLife 2015; 4:e11306. [PMID: 26701913 PMCID: PMC4755737 DOI: 10.7554/elife.11306] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/21/2015] [Indexed: 12/22/2022] Open
Abstract
Dynamic changes in protein S-palmitoylation are critical for regulating protein localization and signaling. Only two enzymes - the acyl-protein thioesterases APT1 and APT2 – are known to catalyze palmitate removal from cytosolic cysteine residues. It is unclear if these enzymes act constitutively on all palmitoylated proteins, or if additional depalmitoylases exist. Using a dual pulse-chase strategy comparing palmitate and protein half-lives, we found knockdown or inhibition of APT1 and APT2 blocked depalmitoylation of Huntingtin, but did not affect palmitate turnover on postsynaptic density protein 95 (PSD95) or N-Ras. We used activity profiling to identify novel serine hydrolase targets of the APT1/2 inhibitor Palmostatin B, and discovered that a family of uncharacterized ABHD17 proteins can accelerate palmitate turnover on PSD95 and N-Ras. ABHD17 catalytic activity is required for N-Ras depalmitoylation and re-localization to internal cellular membranes. Our findings indicate that the family of depalmitoylation enzymes may be substantially broader than previously believed. DOI:http://dx.doi.org/10.7554/eLife.11306.001 Proteins play important roles in many processes in cells. Some of these proteins can be modified by the addition of a molecule called palmitate. This process, termed “palmitoylation”, helps direct these proteins to the compartments within the cell where they are needed to carry out their roles. One target of palmitoylation is N-Ras, which is a protein that can promote the development of cancer. We understand quite a lot about how palmitate is added to proteins, but much less about how it is removed. So far, researchers have only identified two enzymes – known as APT1 and APT2 – that can remove palmitate from proteins, but it is possible that there are others. Identifying other “depalmitoylase” enzymes could help us find ways to block the removal of palmitate from N-Ras, which could lead to new treatments for some cancers. Lin and Conibear used several biochemical techniques to search for depalmitoylase enzymes in human cells. The experiments reveal that although APT1 and APT2 are important for removing palmitate from some proteins, they are not needed to remove palmitate from N-Ras. Instead, Lin and Conibear found that an enzyme called ABHD17 removes palmitate from N-Ras. The next step following on from this work will be to find out what other proteins ABHD17 acts on in cells. A longer-term challenge will be to develop specific chemicals that inhibit ABHD17 activity and test if they are able to reduce the growth of cancer cells. DOI:http://dx.doi.org/10.7554/eLife.11306.002
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Affiliation(s)
- David Tse Shen Lin
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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129
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Doyle SK, Pop MS, Evans HL, Koehler AN. Advances in discovering small molecules to probe protein function in a systems context. Curr Opin Chem Biol 2015; 30:28-36. [PMID: 26615565 DOI: 10.1016/j.cbpa.2015.10.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/30/2015] [Accepted: 10/30/2015] [Indexed: 12/15/2022]
Abstract
High throughput screening (HTS) has historically been used for drug discovery almost exclusively by the pharmaceutical industry. Due to a significant decrease in costs associated with establishing a high throughput facility and an exponential interest in discovering probes of development and disease associated biomolecules, HTS core facilities have become an integral part of most academic and non-profit research institutions over the past decade. This major shift has led to the development of new HTS methodologies extending beyond the capabilities and target classes used in classical drug discovery approaches such as traditional enzymatic activity-based screens. In this brief review we describe some of the most interesting developments in HTS technologies and methods for chemical probe discovery.
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Affiliation(s)
- Shelby K Doyle
- David H. Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marius S Pop
- David H. Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helen L Evans
- David H. Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Angela N Koehler
- David H. Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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131
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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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Garrett CK, Broadwell LJ, Hayne CK, Neher SB. Modulation of the Activity of Mycobacterium tuberculosis LipY by Its PE Domain. PLoS One 2015; 10:e0135447. [PMID: 26270534 PMCID: PMC4536007 DOI: 10.1371/journal.pone.0135447] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/22/2015] [Indexed: 01/11/2023] Open
Abstract
Mycobacterium tuberculosis harbors over 160 genes encoding PE/PPE proteins, several of which have roles in the pathogen’s virulence. A number of PE/PPE proteins are secreted via Type VII secretion systems known as the ESX secretion systems. One PE protein, LipY, has a triglyceride lipase domain in addition to its PE domain. LipY can regulate intracellular triglyceride levels and is also exported to the cell wall by one of the ESX family members, ESX-5. Upon export, LipY’s PE domain is removed by proteolytic cleavage. Studies using cells and crude extracts suggest that LipY’s PE domain not only directs its secretion by ESX-5, but also functions to inhibit its enzymatic activity. Here, we attempt to further elucidate the role of LipY’s PE domain in the regulation of its enzymatic activity. First, we established an improved purification method for several LipY variants using detergent micelles. We then used enzymatic assays to confirm that the PE domain down-regulates LipY activity. The PE domain must be attached to LipY in order to effectively inhibit it. Finally, we determined that full length LipY and the mature lipase lacking the PE domain (LipYΔPE) have similar melting temperatures. Based on our improved purification strategy and activity-based approach, we concluded that LipY’s PE domain down-regulates its enzymatic activity but does not impact the thermal stability of the enzyme.
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Affiliation(s)
- Christopher K. Garrett
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Lindsey J. Broadwell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Cassandra K. Hayne
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Saskia B. Neher
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- * E-mail:
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Yang LL, Yang X, Li GB, Fan KG, Yin PF, Chen XG. An integrated molecular docking and rescoring method for predicting the sensitivity spectrum of various serine hydrolases to organophosphorus pesticides. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2015; 96:2184-92. [PMID: 26172068 DOI: 10.1002/jsfa.7335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 06/11/2015] [Accepted: 07/06/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Ling-Ling Yang
- School of Food and Bioengineering; Xihua University; Sichuan 610039 China
| | - Xiao Yang
- School of Food and Bioengineering; Xihua University; Sichuan 610039 China
| | - Guo-Bo Li
- School of Food and Bioengineering; Xihua University; Sichuan 610039 China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital; Sichuan University; Sichuan 610041 China
| | - Kai-Ge Fan
- School of Food and Bioengineering; Xihua University; Sichuan 610039 China
| | - Peng-Fei Yin
- School of Food and Bioengineering; Xihua University; Sichuan 610039 China
| | - Xiang-Gui Chen
- School of Food and Bioengineering; Xihua University; Sichuan 610039 China
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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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135
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Lindsey ML, Mayr M, Gomes AV, Delles C, Arrell DK, Murphy AM, Lange RA, Costello CE, Jin YF, Laskowitz DT, Sam F, Terzic A, Van Eyk J, Srinivas PR. Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association. Circulation 2015. [PMID: 26195497 DOI: 10.1161/cir.0000000000000226] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The year 2014 marked the 20th anniversary of the coining of the term proteomics. The purpose of this scientific statement is to summarize advances over this period that have catalyzed our capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the current status of the field. Key successes that have energized the field are delineated; opportunities for proteomics to drive basic science research, facilitate clinical translation, and establish diagnostic and therapeutic healthcare algorithms are discussed; and challenges that remain to be solved before proteomic technologies can be readily translated from scientific discoveries to meaningful advances in cardiovascular care are addressed. Proteomics is the result of disruptive technologies, namely, mass spectrometry and database searching, which drove protein analysis from 1 protein at a time to protein mixture analyses that enable large-scale analysis of proteins and facilitate paradigm shifts in biological concepts that address important clinical questions. Over the past 20 years, the field of proteomics has matured, yet it is still developing rapidly. The scope of this statement will extend beyond the reaches of a typical review article and offer guidance on the use of next-generation proteomics for future scientific discovery in the basic research laboratory and clinical settings.
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136
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Antifungal activity of berberine hydrochloride and palmatine hydrochloride against Microsporum canis -induced dermatitis in rabbits and underlying mechanism. Altern Ther Health Med 2015; 15:177. [PMID: 26054937 PMCID: PMC4460627 DOI: 10.1186/s12906-015-0680-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 05/20/2015] [Indexed: 02/06/2023]
Abstract
Background Phellodendron amurense, exhibits antifungal activity mainly by bioactive components including berberine hydrochloride and palmatine hydrochloride. This study was conducted to evaluate the antifungal effects of berberine hydrochloride, palmatine hydrochloride, and a mixture of both substances against Microsporum canis in vivo and in vitro. Methods The minimal inhibitory concentrations (MICs) of monomers and clotrimazole were determined using 1.5 % tryptic soy agar. The effects of these drugs on Microsporum canis growth was detected by determining dry weight. Transmission electron microscopy (TEM) was performed to observe the effect of chemicals on cell ultrastructure. Differential mRNA expressions of eight genes of M. canis treated with berberine or palmatine or their combination at different time points were determined by real-time PCR. NADH enzyme concentration was also detected. Clinical evaluation via in-vivo antifungal assay was also performed. Skin histology PAS staining was also carried out. Results Results showed that MICs of berberine, palmatine and clotrimazole were 1, 1, and 0.015 mg/mL, respectively. No significant difference was observed among the growth curves of the three groups before 18 h was reached. TEM showed that these drugs could destroy the cell membrane and organelles of M. canis at different time points. After 30 h of incubation, relative mRNA expressions of the genes in the combined group were significantly higher than those in the other groups including the clotrimazole group (P < 0.05); Palmatine initially induced the mRNA up-regulation of PGAL4, FSH1, PQ-LRP, NADH1 and NDR in M. canis; by contrast, berberine maintained a high expression level of these genes to shorten fungal life cycle and eradicate M. canis. Clinical results showed that combined treatment was more effective than single administration of each monomer or clotrimazole. Hence, berberine mixed with palmatine significantly elicited antifungal activities and could be used to treat M. canis in rabbits. Conclusion These results provide a comprehensive view of the mechanism of berberine and palmatine in anti-M. canis activity.
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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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138
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Chang JW, Zuhl AM, Speers AE, Niessen S, Brown SJ, Mulvihill MM, Fan YC, Spicer TP, Southern M, Scampavia L, Fernandez-Vega V, Dix MM, Cameron MD, Hodder PS, Rosen H, Nomura DK, Kwon O, Hsu KL, Cravatt BF. Selective inhibitor of platelet-activating factor acetylhydrolases 1b2 and 1b3 that impairs cancer cell survival. ACS Chem Biol 2015; 10:925-32. [PMID: 25602368 DOI: 10.1021/cb500893q] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Platelet-activating factor acetylhydrolases (PAFAHs) 1b2 and 1b3 are poorly characterized serine hydrolases that form a complex with a noncatalytic protein (1b1) to regulate brain development, spermatogenesis, and cancer pathogenesis. Determining physiological substrates and biochemical functions for the PAFAH1b complex would benefit from selective chemical probes that can perturb its activity in living systems. Here, we report a class of tetrahydropyridine reversible inhibitors of PAFAH1b2/3 discovered using a fluorescence polarization-activity-based protein profiling (fluopol-ABPP) screen of the NIH 300,000+ compound library. The most potent of these agents, P11, exhibited IC50 values of ∼40 and 900 nM for PAFAH1b2 and 1b3, respectively. We confirm selective inhibition of PAFAH1b2/3 in cancer cells by P11 using an ABPP protocol adapted for in situ analysis of reversible inhibitors and show that this compound impairs tumor cell survival, supporting a role for PAFAH1b2/3 in cancer.
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Affiliation(s)
| | | | | | | | | | - Melinda M. Mulvihill
- Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
| | - Yi Chiao Fan
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | | | | | | | | | | | | | | | | | - Daniel K. Nomura
- Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, California 94720, United States
| | - Ohyun Kwon
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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139
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Hett EC, Xu H, Geoghegan KF, Gopalsamy A, Kyne RE, Menard CA, Narayanan A, Parikh MD, Liu S, Roberts L, Robinson RP, Tones MA, Jones LH. Rational targeting of active-site tyrosine residues using sulfonyl fluoride probes. ACS Chem Biol 2015; 10:1094-8. [PMID: 25571984 DOI: 10.1021/cb5009475] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This work describes the first rational targeting of tyrosine residues in a protein binding site by small-molecule covalent probes. Specific tyrosine residues in the active site of the mRNA-decapping scavenger enzyme DcpS were modified using reactive sulfonyl fluoride covalent inhibitors. Structure-based molecular design was used to create an alkyne-tagged probe bearing the sulfonyl fluoride warhead, thus enabling the efficient capture of the protein from a complex proteome. Use of the probe in competition experiments with a diaminoquinazoline DcpS inhibitor permitted the quantification of intracellular target occupancy. As a result, diaminoquinazoline upregulators of survival motor neuron protein that are used for the treatment of spinal muscular atrophy were confirmed as inhibitors of DcpS in human primary cells. This work illustrates the utility of sulfonyl fluoride probes designed to react with specific tyrosine residues of a protein and augments the chemical biology toolkit by these probes uses in target validation and molecular pharmacology.
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Affiliation(s)
- Erik C. Hett
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Hua Xu
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Kieran F. Geoghegan
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ariamala Gopalsamy
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Robert E. Kyne
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Carol A. Menard
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Arjun Narayanan
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mihir D. Parikh
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Shenping Liu
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Lee Roberts
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ralph P. Robinson
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Michael A. Tones
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Lyn H. Jones
- Worldwide
Medicinal Chemistry and ‡Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
- Structural Biology and Biophysics, Worldwide Medicinal Chemistry, ∥Worldwide Medicinal
Chemistry, and ⊥Primary Pharmacology Group, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
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140
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Yang P, Liu K. Activity-based protein profiling: recent advances in probe development and applications. Chembiochem 2015; 16:712-24. [PMID: 25652106 DOI: 10.1002/cbic.201402582] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 11/08/2022]
Abstract
The completion of the human genome sequencing project has provided a wealth of new information regarding the genomic blueprint of the cell. Although, to date, there are roughly 20,000 genes in the human genome, the functions of only a handful of proteins are clear. The major challenge lies in translating genomic information into an understanding of their cellular functions. The recently developed activity-based protein profiling (ABPP) is an unconventional approach that is complementary for gene expression analysis and an ideal utensil in decoding this overflow of genomic information. This approach makes use of synthetic small molecules that covalently modify a set of related proteins and subsequently facilitates identification of the target protein, enabling rapid biochemical analysis and inhibitor discovery. This tutorial review introduces recent advances in the field of ABPP and its applications.
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Affiliation(s)
- Pengyu Yang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 (USA)
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141
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Shannon DA, Weerapana E. Covalent protein modification: the current landscape of residue-specific electrophiles. Curr Opin Chem Biol 2015; 24:18-26. [DOI: 10.1016/j.cbpa.2014.10.021] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 10/24/2014] [Accepted: 10/27/2014] [Indexed: 12/11/2022]
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142
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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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143
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Affiliation(s)
- Evan W Miller
- Department of Chemistry, at University of California-Berkeley, Berkeley, California, USA
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144
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Immunomodulatory lysophosphatidylserines are regulated by ABHD16A and ABHD12 interplay. Nat Chem Biol 2015; 11:164-71. [PMID: 25580854 PMCID: PMC4301979 DOI: 10.1038/nchembio.1721] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 11/04/2014] [Indexed: 01/25/2023]
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145
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Carvalho LAR, Ruivo EFP, Lucas SD, Moreira R. Activity-based probes as molecular tools for biomarker discovery. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00417e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Activity-based protein profiling has emerged as an exceptional tool for biomarker discovery and validation.
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Affiliation(s)
- L. A. R. Carvalho
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa. Av. Prof. Gama Pinto
- 1649-003 Lisboa
- Portugal
| | - E. F. P. Ruivo
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa. Av. Prof. Gama Pinto
- 1649-003 Lisboa
- Portugal
| | - S. D. Lucas
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa. Av. Prof. Gama Pinto
- 1649-003 Lisboa
- Portugal
| | - R. Moreira
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa. Av. Prof. Gama Pinto
- 1649-003 Lisboa
- Portugal
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146
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McDonald RI, Guilinger JP, Mukherji S, Curtis EA, Lee WI, Liu DR. Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling. Nat Chem Biol 2014; 10:1049-54. [PMID: 25306441 PMCID: PMC4232462 DOI: 10.1038/nchembio.1655] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 08/21/2014] [Indexed: 02/08/2023]
Abstract
Probes that form covalent bonds with RNA molecules on the basis of their chemical reactivity would advance our ability to study the transcriptome. We developed a set of electrophilic activity-based RNA probes designed to react with unusually nucleophilic RNAs. We used these probes to identify reactive genome-encoded RNAs, resulting in the discovery of a 42-nt catalytic RNA from an archaebacterium that reacts with a 2,3-disubstituted epoxide at N7 of a specific guanosine. Detailed characterization of the catalytic RNA revealed the structural requirements for reactivity. We developed this catalytic RNA into a general tool to selectively conjugate a small molecule to an RNA of interest. This strategy enabled up to 500-fold enrichment of target RNA from total mammalian RNA or from cell lysate. We demonstrated the utility of this approach by selectively capturing proteins in yeast cell lysate that bind the ASH1 mRNA.
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Affiliation(s)
- Richard I. McDonald
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
| | - John P. Guilinger
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
| | - Shankar Mukherji
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, Harvard University, 52 Oxford St., Cambridge, MA 02138, USA
| | - Edward A. Curtis
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
| | - Won I. Lee
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
| | - David R. Liu
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
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147
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Kucharova V, Wiker HG. Proteogenomics in microbiology: taking the right turn at the junction of genomics and proteomics. Proteomics 2014; 14:2360-675. [PMID: 25263021 DOI: 10.1002/pmic.201400168] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/18/2014] [Accepted: 09/23/2014] [Indexed: 12/14/2022]
Abstract
High-accuracy and high-throughput proteomic methods have completely changed the way we can identify and characterize proteins. MS-based proteomics can now provide a unique supplement to genomic data and add a new level of information to the interpretation of genomic sequences. Proteomics-driven genome annotation has become especially relevant in microbiology where genomes are sequenced on a daily basis and limitations of an in silico driven annotation process are well recognized. In this review paper, we outline different strategies on how one can design a proteogenomic experiment, for example on genome-sequenced (synonymous proteogenomics) versus unsequenced organisms (ortho-proteogenomics) or with the aid of other "omic" data such as RNA-seq. We touch upon many challenges that are encountered during a typical proteogenomic study, mostly concerning bioinformatics methods and downstream data analysis, but also related to creation and use of sequence databases. A large list of proteogenomic case studies of different microorganisms is provided to illustrate the mapping of MS/MS-derived peptide spectra to genomic DNA sequences. These investigations have led to accurate determination of translational initiation sites, pointed out eventual read-throughs or programmed frameshifts, detected signal peptide processing or other protein maturation events, removed questionable annotation assignments, and provided evidence for predicted hypothetical proteins.
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Affiliation(s)
- Veronika Kucharova
- Department of Clinical Science, The Gade Research Group for Infection and Immunity, University of Bergen, Norway
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148
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Analysis of protein-protein interactions in MCF-7 and MDA-MB-231 cell lines using phthalic acid chemical probes. Int J Mol Sci 2014; 15:20770-88. [PMID: 25402641 PMCID: PMC4264195 DOI: 10.3390/ijms151120770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 10/16/2014] [Accepted: 10/27/2014] [Indexed: 01/20/2023] Open
Abstract
Phthalates are a class of plasticizers that have been characterized as endocrine disrupters, and are associated with genital diseases, cardiotoxicity, hepatotoxicity, and nephrotoxicity in the GeneOntology gene/protein database. In this study, we synthesized phthalic acid chemical probes and demonstrated differing protein–protein interactions between MCF-7 cells and MDA-MB-231 breast cancer cell lines. Phthalic acid chemical probes were synthesized using silicon dioxide particle carriers, which were modified using the silanized linker 3-aminopropyl triethoxyslane (APTES). Incubation with cell lysates from breast cancer cell lines revealed interactions between phthalic acid and cellular proteins in MCF-7 and MDA-MB-231 cells. Subsequent proteomics analyses indicated 22 phthalic acid-binding proteins in both cell types, including heat shock cognate 71-kDa protein, ATP synthase subunit beta, and heat shock protein HSP 90-beta. In addition, 21 MCF-7-specific and 32 MDA-MB-231 specific phthalic acid-binding proteins were identified, including related proteasome proteins, heat shock 70-kDa protein, and NADPH dehydrogenase and ribosomal correlated proteins, ras-related proteins, and members of the heat shock protein family, respectively.
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149
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BioGPS descriptors for rational engineering of enzyme promiscuity and structure based bioinformatic analysis. PLoS One 2014; 9:e109354. [PMID: 25353170 PMCID: PMC4212942 DOI: 10.1371/journal.pone.0109354] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/27/2014] [Indexed: 11/20/2022] Open
Abstract
A new bioinformatic methodology was developed founded on the Unsupervised Pattern Cognition Analysis of GRID-based BioGPS descriptors (Global Positioning System in Biological Space). The procedure relies entirely on three-dimensional structure analysis of enzymes and does not stem from sequence or structure alignment. The BioGPS descriptors account for chemical, geometrical and physical-chemical features of enzymes and are able to describe comprehensively the active site of enzymes in terms of “pre-organized environment” able to stabilize the transition state of a given reaction. The efficiency of this new bioinformatic strategy was demonstrated by the consistent clustering of four different Ser hydrolases classes, which are characterized by the same active site organization but able to catalyze different reactions. The method was validated by considering, as a case study, the engineering of amidase activity into the scaffold of a lipase. The BioGPS tool predicted correctly the properties of lipase variants, as demonstrated by the projection of mutants inside the BioGPS “roadmap”.
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150
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Tse J, Wang Y, Zengeya T, Rozners E, Tan-Wilson A. Peptide nucleic acid probe for protein affinity purification based on biotin-streptavidin interaction and peptide nucleic acid strand hybridization. Anal Biochem 2014; 470:34-40. [PMID: 25447466 DOI: 10.1016/j.ab.2014.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/06/2014] [Accepted: 10/09/2014] [Indexed: 01/25/2023]
Abstract
We describe a new method for protein affinity purification that capitalizes on the high affinity of streptavidin for biotin but does not require dissociation of the biotin-streptavidin complex for protein retrieval. Conventional reagents place both the selectively reacting group (the "warhead") and the biotin on the same molecule. We place the warhead and the biotin on separate molecules, each linked to a short strand of peptide nucleic acid (PNA), synthetic polymers that use the same bases as DNA but attached to a backbone that is resistant to attack by proteases and nucleases. As in DNA, PNA strands with complementary base sequences hybridize. In conditions that favor PNA duplex formation, the warhead strand (carrying the tagged protein) and the biotin strand form a complex that is held onto immobilized streptavidin. As in DNA, the PNA duplex dissociates at moderately elevated temperature; therefore, retrieval of the tagged protein is accomplished by a brief exposure to heat. Using iodoacetate as the warhead, 8-base PNA strands, biotin, and streptavidin-coated magnetic beads, we demonstrate retrieval of the cysteine protease papain. We were also able to use our iodoacetyl-PNA:PNA-biotin probe for retrieval and identification of a thiol reductase and a glutathione transferase from soybean seedling cotyledons.
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Affiliation(s)
- Jenny Tse
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Yuanyuan Wang
- Department of Biological Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Thomas Zengeya
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Eriks Rozners
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Anna Tan-Wilson
- Department of Biological Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA.
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