ABSTRACT
Isobaric labeling empowers proteome-wide expression measurements simultaneously across multiple samples. Here an expanded set of 16 isobaric reagents based on an isobutyl-proline immonium ion reporter structure (TMTpro) is presented. These reagents have similar characteristics to existing tandem mass tag reagents but with increased fragmentation efficiency and signal. In a proteome-scale example dataset, we compared eight common cell lines with and without Torin1 treatment with three replicates, quantifying more than 8,800 proteins (mean of 7.5 peptides per protein) per replicate with an analysis time of only 1.1 h per proteome. Finally, we modified the thermal stability assay to examine proteome-wide melting shifts after treatment with DMSO, 1 or 20 µM staurosporine with five replicates. This assay identified and dose-stratified staurosporine binding to 228 cellular kinases in just one, 18-h experiment. TMTpro reagents allow complex experimental designs-all with essentially no missing values across the 16 samples and no loss in quantitative integrity.
Subject(s)
Peptides/chemistry , Proteome/chemistry , Proteomics/methods , Tandem Mass Spectrometry/methods , Cell Line , Humans , Isotope LabelingABSTRACT
Cross-linking mass spectrometry (XL-MS) is an attractive method for the proteome-wide characterization of protein structures and interactions. Currently, the depth of inâ vivo XL-MS studies is lagging behind the established applications to cell lysates, because cross-linking reagents that can penetrate intact cells and strategies to enrich cross-linked peptides lack efficiency. To tackle these limitations, we have developed a phosphonate-containing cross-linker, tBu-PhoX, that efficiently permeates various biological membranes and can be robustly enriched using routine immobilized metal ion affinity chromatography. We have established a tBu-PhoX-based inâ vivo XL-MS approach that enables cross-links in intact human cells to be identified in high numbers with substantially reduced analysis time. Collectively, the developed cross-linker and XL-MS approach pave the way for the comprehensive XL-MS characterization of living systems.
Subject(s)
Proteome , Chromatography, Affinity , Cross-Linking Reagents/chemistry , Humans , Imidazoles , Mass Spectrometry/methodsABSTRACT
Only a small fraction of vitamin B12-requiring organisms are able to synthesize B12 de novo, making it a common commodity in microbial communities. Initially recognized as an enzyme cofactor of a few enzymes, recent studies have revealed additional B12-binding enzymes and regulatory roles for B12 Here we report the development and use of a B12-based chemical probe to identify B12-binding proteins in a nonphototrophic B12-producing bacterium. Two unexpected discoveries resulted from this study. First, we identified a light-sensing B12-binding transcriptional regulator and demonstrated that it controls folate and ubiquinone biosynthesis. Second, our probe captured proteins involved in folate, methionine, and ubiquinone metabolism, suggesting that it may play a role as an allosteric effector of these processes. These metabolic processes produce precursors for synthesis of DNA, RNA, and protein. Thereby, B12 likely modulates growth, and by limiting its availability to auxotrophs, B12-producing organisms may facilitate coordination of community metabolism.
Subject(s)
Folic Acid/metabolism , Halomonas/metabolism , Methionine/metabolism , Ubiquinone/metabolism , Vitamin B 12/metabolism , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Base Sequence , Biochemical Phenomena/radiation effects , Gammaproteobacteria/genetics , Gammaproteobacteria/metabolism , Halomonas/genetics , Protein Binding/radiation effects , Sequence Homology, Amino Acid , Sequence Homology, Nucleic Acid , Ultraviolet Rays , Vitamin B 12/chemistryABSTRACT
Cytochrome P450s are oxidative metabolic enzymes that play critical roles in the biotransformation of endogenous compounds and xenobiotics. The expression and activity of P450 enzymes varies considerably throughout human development; the deficit in our understanding of these dynamics limits our ability to predict environmental and pharmaceutical exposure effects. In an effort to develop a more comprehensive understanding of the ontogeny of P450 enzymes, we employed a multi-omic characterization of P450 transcript expression, protein abundance, and functional activity. Modified mechanism-based inhibitors of P450s were used as chemical probes for isolating active P450 proteoforms in human hepatic microsomes with developmental stages ranging from early gestation to late adult. High-resolution liquid chromatography-mass spectrometry was used to identify and quantify probe-labeled P450s, allowing for a functional profile of P450 ontogeny. Total protein abundance profiles and P450 rRNA was also measured, and our results reveal life-stage-dependent variability in P450 expression, abundance, and activity throughout human development and frequent discordant relationships between expression and activity. We have significantly expanded the knowledge of P450 ontogeny, particularly at the level of individual P450 activity. We anticipate that these results will be useful for enabling predictive therapeutic dosing, and for avoiding potentially adverse and harmful reactions during maturation from both therapeutic drugs and environmental xenobiotics.
Subject(s)
Aging/metabolism , Cytochrome P-450 Enzyme System/metabolism , Liver/enzymology , Adolescent , Adult , Age Factors , Aging/genetics , Child , Child, Preschool , Chromatography, High Pressure Liquid , Cytochrome P-450 Enzyme System/genetics , Gene Expression Regulation, Developmental , Gene Expression Regulation, Enzymologic , Genomics/methods , Gestational Age , Humans , Infant , Infant, Newborn , Isoenzymes , Mass Spectrometry , Microsomes, Liver/enzymology , Proteomics/methods , RNA, Messenger/genetics , RNA, Messenger/metabolism , Substrate SpecificityABSTRACT
A high-throughput screening campaign was conducted to identify small molecules with the ability to inhibit the interaction between the vitamin D receptor (VDR) and steroid receptor coactivator 2. These inhibitors represent novel molecular probes for modulating gene regulation mediated by VDR. Peroxisome proliferator-activated receptor (PPAR) δ agonist GW0742 was among the identified VDR-coactivator inhibitors and has been characterized herein as a pan nuclear receptor antagonist at concentrations of > 12.1 µM. The highest antagonist activity for GW0742 was found for VDR and the androgen receptor. Surprisingly, GW0742 behaved as a PPAR agonist and antagonist, activating transcription at lower concentrations and inhibiting this effect at higher concentrations. A unique spectroscopic property of GW0742 was identified as well. In the presence of rhodamine-derived molecules, GW0742 increased the fluorescence intensity and level of fluorescence polarization at an excitation wavelength of 595 nm and an emission wavelength of 615 nm in a dose-dependent manner. The GW0742-inhibited NR-coactivator binding resulted in a reduced level of expression of five different NR target genes in LNCaP cells in the presence of agonist. Especially VDR target genes CYP24A1, IGFBP-3, and TRPV6 were negatively regulated by GW0742. GW0742 is the first VDR ligand inhibitor lacking the secosteroid structure of VDR ligand antagonists. Nevertheless, the VDR-meditated downstream process of cell differentiation was antagonized by GW0742 in HL-60 cells that were pretreated with the endogenous VDR agonist 1,25-dihydroxyvitamin D3.
Subject(s)
Cell Nucleus/metabolism , Nuclear Receptor Coactivator 2/chemistry , PPAR delta/agonists , Receptors, Calcitriol/chemistry , Thiazoles/pharmacology , Cell Line, Tumor , DNA/chemistry , Dose-Response Relationship, Drug , HEK293 Cells , HL-60 Cells , Humans , Inhibitory Concentration 50 , Ligands , Protein Binding , Rhodamines/chemistry , Spectrophotometry/methodsABSTRACT
The first ratiometric fluorescent reporter was designed for the detection of cardiac troponin I (cTnI), a key protein elicited during cardiac muscle cell death. In designing this abiotic fluorescent probe, docking simulation studies were performed to predict the probe/protein interactions along the solvent exposed regions of cTnI. Simple cuvette titration experiments in aqueous buffered solution indicate remarkable selectivity for cardiac troponin in the clinically relevant nM region versus skeletal troponin.
Subject(s)
Fluorescent Dyes/chemistry , Myocytes, Smooth Muscle/chemistry , Troponin I/chemistry , Biomarkers/blood , Biomarkers/chemistry , Fluorescent Dyes/chemical synthesis , Humans , Models, Molecular , Molecular Structure , Myocytes, Smooth Muscle/metabolism , Troponin I/bloodABSTRACT
A 3 x 3 matrix of disubstituted N-aryl-1,8-naphthalimides was synthesized for the evaluation and discovery of dual fluorescence (DF). The matrix elements included for this study were based on a predictive model that is proposed as a seesaw balanced photophysical model. This model serves as a guide to optimize the dual fluorescence emission from N-phenyl-1,8-naphthalimides by appropriate placement of substituent groups at both the 4-position of the N-arene as well as the 4'-position of the naphthalene ring. Steady-state fluorescence studies under a variety of solvents indicate that four of the nine dyes in the matrix are dual fluorescent. To provide a more quantitative description of the model, cyclic voltammetry experiments were used to calculate HOMO/LUMO energies of the aromatic components that comprise these DF dyes and give evidence in support for potential mixing of S1 and S2 excited states. Given the difficulties in predicting excited state properties such as molecular fluorescence, this ratio of four out of nine "hits" for discovering DF signifies proof of principle for this proposed model and should provide a rational basis for the synthesis of future DF 1,8-naphthalimide systems.
Subject(s)
Fluorescent Dyes/chemistry , Naphthalimides/chemistry , Absorption , Color , Electrons , Models, Molecular , Molecular Conformation , Spectrometry, FluorescenceABSTRACT
Two highly water-soluble monoboronic acid probes that display the more desirable off-on fluorescence response were synthesized based on 4-sulfo-1,8-naphthalic anhydride and a remarkable sensitivity for glucose rather than fructose and galactose was also observed.
Subject(s)
Boronic Acids/chemistry , Glucose/analysis , Naphthalenes/analysis , Water/chemistry , Boronic Acids/chemical synthesis , Naphthalimides/chemistry , Sensitivity and Specificity , SolubilityABSTRACT
Three isomers of hydroxy substituted N-aryl-1, 8-naphthalimides based on N-aryl naphthalic anhydride fluorophore have been synthesized. The decrease in fluorescence intensity from ortho to para substitution of hydroxy group on N-aryl reveals that para substituted isomer undergoes ESEC (Excited State with Extended Conjugation) mechanism which is proved by low quantum yield and appearance of dual emission. The ortho isomer, however, has high quantum yield and no tautomer emission, indicating ESIPT (Excited State Intramolecular Proton Transfer) mechanism is not operating. Similarly, all these isomers show strong fluorescence quenching in presence of strong H-bonding solvents like DMSO and pyridine, but there was neither the shift of emission bands nor the appearance of new bands for proton transfer to these solvents. Thus, it also indicates the absence of excited state proton transfer mechanism. Both the ortho isomer, and to a greater degree the meta isomer, showed larger quenching constants (Kapp) with pyridine than DMSO. This trend opposes the hydrogen-bond affinity for these solvents with phenol and points to a 2-point recognition interaction. In addition, a naphthalimide derivative using 2-aminoimidazole was prepared and examined for optimal positioning of a six-membered ring hydrogen bond pattern. No dual fluorescence was observed for this compound either.
Subject(s)
Fluorescence , Fluorescent Dyes/chemistry , Naphthalimides/chemistry , Fluorescent Dyes/chemical synthesis , Isomerism , Molecular Structure , Naphthalimides/chemical synthesis , Quantum TheoryABSTRACT
We describe the parallel synthesis of novel analogs of GW0742, a peroxisome proliferator-activated receptor δ (PPARδ) agonist. For that purpose, modified reaction conditions were applied, such as a solid-phase palladium-catalyzed Suzuki coupling. In addition, tetrazole-based compounds were generated as a bioisostere for carboxylic acid-containing ligand GW0742. The new compounds were investigated for their ability to activate PPARδ mediated transcription and their cross-reactivity with the vitamin D receptor (VDR), another member of the nuclear receptor superfamily. We identified many potent PPARδ agonists that were less toxic than GW0742, where â¼65 of the compounds synthesized exhibited partial PPARδ activity (23-98%) with EC50 values ranging from 0.007-18.2 µM. Some ligands, such as compound 32, were more potent inhibitors of VDR-mediated transcription with significantly reduced PPARδ activity than GW0742, however, none of the ligands were completely selective for VDR inhibition over PPARδ activation of transcription.
Subject(s)
PPAR delta/chemistry , Receptors, Calcitriol/antagonists & inhibitors , Tetrazoles/chemistry , Thiazoles/chemistry , Cell Survival/drug effects , Drug Design , HEK293 Cells , High-Throughput Screening Assays , Humans , Ligands , Molecular Docking Simulation , PPAR delta/agonists , PPAR delta/genetics , Receptors, Calcitriol/chemistry , Receptors, Calcitriol/metabolism , Small Molecule Libraries , Structure-Activity Relationship , Tetrazoles/chemical synthesis , Thiazoles/chemical synthesis , Transcription, GeneticABSTRACT
The development of renewable biofuels is a global priority, but success will require novel technologies that greatly improve our understanding of microbial systems biology. An approach with great promise in enabling functional characterization of microbes is activity-based protein profiling (ABPP), which employs chemical probes to directly measure enzyme function in discrete enzyme classes in vivo and/or in vitro, thereby facilitating the rapid discovery of new biocatalysts and enabling much improved biofuel production platforms. We review general design strategies in ABPP, and highlight recent advances that are or could be pivotal to biofuels processes including applications of ABPP to cellulosic bioethanol, biodiesel, and phototrophic production of hydrocarbons. We also examine the key challenges and opportunities of ABPP in renewable biofuels research. The integration of ABPP with molecular and systems biology approaches will shed new insight on the catalytic and regulatory mechanisms of functional enzymes and their synergistic effects in the field of biofuels production.
ABSTRACT
AIM: To investigate the in vivo effects of 3-indolylmethanamines 31B and PS121912 in treating ovarian cancer and leukemia, respectively. MATERIALS AND METHODS: Terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) and western blotting were applied to demonstrate the induction of apoptosis. Xenografted mice were investigated to show the antitumor effects of 3-indolylmethanamines. (13)C-Nuclear magnetic resource (NMR) and western blotting were used to demonstrate inhibition of glucose metabolism. RESULTS: 31B inhibited ovarian cancer cell proliferation and activated caspase-3, cleaved poly (ADP-ribose) polymerase 1 (PARP1), and phosphorylated mitogen-activated protein kinases (MAPK), JUN N-terminal kinase/stress-activated protein kinase (JNK/SAPK) and p38. 31B reduced ovarian cancer xenograft tumor growth and PS121912 inhibited the growth of HL-60-derived xenografts without any sign of toxicity. Compound 31B inhibited de novo glycolysis and lipogenesis mediated by the reduction of fatty acid synthase and lactate dehydrogenase-A expression. CONCLUSION: 3-Indolylmethanamines represent a new class of antitumor agents. We have shown for the first time the in vivo anticancer effects of 3-indolylmethanamines 31B and PS121912.
Subject(s)
Amines/chemistry , Aniline Compounds/pharmacology , Antineoplastic Agents/pharmacology , Apoptosis/drug effects , Hydrocarbons, Aromatic/pharmacology , Indoles/chemistry , Ovarian Neoplasms/drug therapy , Animals , Blotting, Western , Cell Proliferation/drug effects , Female , Flow Cytometry , Humans , Indoles/pharmacology , Magnetic Resonance Spectroscopy , Mice , Mice, Nude , Ovarian Neoplasms/metabolism , Ovarian Neoplasms/pathology , Tumor Cells, Cultured , Xenograft Model Antitumor AssaysABSTRACT
Herein we describe the evaluation of GW0742 analogs in respect to their ability to modulate transcription mediated by the vitamin D receptor (VDR) and the peroxisome proliferator activated receptor (PPAR) δ. The GW0742 analog bearing a carboxylic ester functionality in place of the carboxylic acid was partially activating both nuclear receptors at low concentration and inhibited transcription at higher compound concentrations. The GW0742 alcohol derivative was more active than the ester in respect to VDR but less active in regard to PPARδ. Importantly, the alcohol derivative was significantly more toxic than the corresponding acid and ester.
ABSTRACT
Nuclear receptor coregulators are master regulators of transcription and selectively interact with the vitamin D receptor (VDR) to modulate cell differentiation, cell proliferation and calcium homeostasis. Herein, we report the syntheses and evaluation of highly potent and selective VDR-coactivator inhibitors based on a recently identified 3-indolylmethanamine scaffold. The most active compound, PS121912, selectively inhibited VDR-mediated transcription among eight other nuclear receptors tested. PS121912 is also selectively disrupting the binding between VDR and the third nuclear receptor interaction domain of the coactivator SRC2. Genetic studies revealed that PS121912 behaves like a VDR antagonist by repressing 1,25-(OH)2D3 activated gene transcription. In addition, PS121912 induced apoptosis in HL-60.
ABSTRACT
Herein, we described the development of two virtual screens to identify new vitamin D receptor (VDR) antagonists among nuclear receptor (NR) ligands. Therefore, a database of 14330 nuclear receptor ligands and their NR affinities was assembled using the online available "Binding Database". Two different virtual screens were carried out in conjunction with a reported VDR crystal structure applying a stringent and less stringent pharmacophore model to filter docked NR ligand conformations. The pharmacophore models were based on the spatial orientation of the hydroxyl functionalities of VDR's natural ligands 1,25(OH2)D3 and 25(OH2)D3. The first virtual screen identified 32 NR ligands with a calculate free energy of VDR binding of more than -6.0 kJ/mol. All but nordihydroguaiaretic acid (NDGA) are VDR ligands, which inhibited the interaction between VDR and coactivator peptide SRC2-3 with an IC50 value of 15.8 µM. The second screen identified 162 NR ligands with a calculate free energy of VDR binding of more than -6.0 kJ/mol. More than half of these ligands were developed to bind VDR followed by ERα/ß ligands (26%), TRα/ß ligands (7%) and LxRα/ß ligands (7%). The binding between VDR and ERα ligand H6036 as well as TRα/ß ligand triiodothyronine and a homoserine analog thereof was confirmed by fluorescence polarization.
ABSTRACT
Testing small molecules for their ability to modify cysteine residues of proteins in the early stages of drug discovery is expected to accelerate our ability to develop more selective drugs with lesser side effects. In addition, this approach also enables the rapid evaluation of the mode of binding of new drug candidates with respect to thiol reactivity and metabolism by glutathione. Herein, we describe the development of a fluorescence-based high-throughput assay that allows the identification of thiol-reactive compounds. A thiol-containing fluorescent probe, MSTI, was synthesized and used to evaluate small molecules from the Library of Pharmacologically Active Compounds (LOPAC) collection of bioactive molecules. LOPAC compounds that are known to react with sulfur nucleophiles were identified with this assay, for example, irreversible protease inhibitors, nitric oxide-releasing compounds, and proton-pump inhibitors. The results confirm that both electrophilic and redox reactive compounds can be quickly identified in a high-throughput manner, enabling the assessment of screening libraries with respect to thiol-reactive compounds.
Subject(s)
Drug Evaluation, Preclinical/methods , Fluorescent Dyes/chemistry , High-Throughput Screening Assays/methods , Small Molecule Libraries/pharmacology , Sulfhydryl Compounds/chemistry , Drug Discovery/methods , Fluorescence , Glutathione/metabolism , Nitric Oxide/metabolism , Oxidation-Reduction/drug effects , Protease Inhibitors/pharmacology , Proton Pump Inhibitors/pharmacologyABSTRACT
The vitamin D receptor (VDR) is a nuclear hormone receptor that regulates cell proliferation, cell differentiation, and calcium homeostasis. The receptor is activated by vitamin D analogues that induce the disruption of VDR-corepressor binding and promote VDR-coactivator interactions. The interactions between VDR and coregulators are essential for VDR-mediated transcription. Small molecule inhibition of VDR-coregulator binding represents an alternative method to the traditional ligand-based approach in order to modulate the expression of VDR target genes. A high throughput fluorescence polarization screen that quantifies the inhibition of binding between VDR and a fluorescently labeled steroid receptor coactivator 2 peptide was applied to discover the new small molecule VDR-coactivator inhibitors, 3-indolylmethanamines. Structure-activity relationship studies with 3-indolylmethanamine analogues were used to determine their mode of VDR-binding and to produce the first VDR-selective and irreversible VDR-coactivator inhibitors with the ability to regulate the transcription of the human VDR target gene TRPV6.
Subject(s)
Indoles/chemical synthesis , Methylamines/chemical synthesis , Nuclear Receptor Coactivators/antagonists & inhibitors , Receptors, Calcitriol/antagonists & inhibitors , Cell Line , High-Throughput Screening Assays , Humans , Indoles/chemistry , Indoles/pharmacology , Membranes, Artificial , Methylamines/chemistry , Methylamines/pharmacology , Nuclear Receptor Coactivator 2/antagonists & inhibitors , Nuclear Receptor Coactivator 2/metabolism , Nuclear Receptor Coactivator 3/antagonists & inhibitors , Nuclear Receptor Coactivator 3/metabolism , Nuclear Receptor Coactivators/metabolism , Permeability , Protein Binding , Receptors, Calcitriol/metabolism , Solubility , Structure-Activity Relationship , TRPV Cation Channels/genetics , Transcription, Genetic/drug effectsABSTRACT
A ten element matrix of 5- and 6-substituted-(2,3)-naphthalimides was prepared for the appropriate placement of substituents necessary to promote dual fluorescence (DF). As prescribed by our balanced seesaw photophysical model this matrix yielded nine new DF dyes out of a possible ten compounds. From this set of nine DF dyes, 4-fluoronaphthalic amide (37) was selected as a probe for ratiometric detection of DNA and demonstration of panchromatic emission.
Subject(s)
DNA/analysis , Fluorescent Dyes/chemistry , Naphthalimides/chemistry , DNA/chemistry , LightABSTRACT
The synthesis and photophysical characterization of a new white-light fluorophore is described. The optimization of excitation wavelengths allows the naphthalimide (NI) dyes to display blue, green or white light emission depending on the excitation wavelength.
ABSTRACT
The 3 x 3 matrix elements included for the evaluation of dual fluorescence are based on a predictive model described as a 'seesaw balanced' photophysical model.