2008 6th IEEE International Conference on Industrial Informatics, 2008
Abstract Although it is widely believed that software quality will be improved by the use of auto... more Abstract Although it is widely believed that software quality will be improved by the use of automated testing, automation is still not well-off in industry today. There are quite a few issues of traditional software test automation mode, for example, high cost, knowledge ...
Toxicological sciences : an official journal of the Society of Toxicology, 2014
The dysregulation of phosphatidylinositol 3-kinase (PI3K)-dependent pathways is implicated in sev... more The dysregulation of phosphatidylinositol 3-kinase (PI3K)-dependent pathways is implicated in several human cancers making it an attractive target for small molecule PI3K inhibitors. A series of potent pyridyltriazine-containing inhibitors of class Ia PI3Ks were synthesized and a subset of compounds was evaluated in exploratory repeat-dose rat toxicology studies. Daily oral dosing of compound 1: in Sprague Dawley rats for four consecutive days was associated with hepatobiliary toxicity that included biliary epithelial hyperplasia and hypertrophy, periductular edema, biliary stasis, and acute peribiliary inflammatory infiltrates. These histological changes were associated with clinical pathology changes that included increased serum liver enzymes, total bile acids, and bilirubin. The predominant clearance pathway of 1: was shown in vitro and in a bile-duct cannulated rat (14)C-ADME study to be P450-mediated oxidative metabolism. An O-demethylated pyridine metabolite, M3: , was identi...
Journal of Pharmaceutical and Biomedical Analysis, 2011
An LC-MS/MS method using pre-column derivatization with phenylisothiocyanate (PITC) was developed... more An LC-MS/MS method using pre-column derivatization with phenylisothiocyanate (PITC) was developed to quantify glycine in human cerebrospinal fluid (CSF) and applied to the determination of glycine in human samples collected during clinical testing. The calibration curve range for the assay was 50-10,000 ng/mL and ¹³C₂¹⁵N-glycine was used as an internal standard. Artificial CSF was used as a surrogate matrix for standards due to the presence of endogenous glycine in human CSF and this approach was validated with additional experiments involving either standard addition, or stable labeled glycine as an alternate calibration standard for endogenous glycine. Interday bias (% RE) and precision (% CV) were -4.2 and 12.3% at the LLOQ, and less than ±0.9 and 8.3% for higher concentrations, respectively. Glycine was stable in artificial CSF for at least 5h at room temperature, 55 days at -70 °C (-60 to -80 °C range), and through three freeze-thaw cycles.
An assessment of 2,4-dinitrophenylhydrazine (DNPH)-detectable protein-based carbonyls is one of t... more An assessment of 2,4-dinitrophenylhydrazine (DNPH)-detectable protein-based carbonyls is one of the most common assays used to quantify oxidative stress in vitro and in vivo. In this study, we compared, for the lipid-binding protein beta-lactoglobulin, the extent to which carbonyl reactivity could be introduced by adventitious metal-catalyzed oxidation (MCO) in the absence and presence of a polyunsaturated lipid or by treatment with various individual bifunctional lipid oxidation products capable of introducing carbonyls into proteins by adduction to nucleophilic side chains. With metal ions and either O2/reductant or H2O2 as the terminal oxidant, the maximal level of DNPH-detectable carbonyl generation obtainable in several hours was 0.1-0.2 mol carbonyl per mol protein monomer, with Cu(II) being more effective than Fe(II). Exposure instead to bifunctional lipoxidation-derived aldehydes (1-2 mM) generated in some cases in excess of 1 mol carbonyl per mol protein. The rank order of carbonyl incorporation reactivity was acrolein > 4-oxo-2-nonenal > 4-hydroxy-2-nonenal > 2,4-decadienal > malondialdehyde. Protein cross-linking ability followed a somewhat different rank order. Parallel studies on reductively methylated beta-lactoglobulin revealed that His and Cys residues are intrinsically more responsible than Lys residues for carbonyl appearance and that the availability of Lys residues accounts for the reduction of carbonyl content at later time (presumably reflecting cross-linking chemistry) that occurs for acrolein and 4-oxo-2-nonenal. Overall, these results suggest that DNPH reactivity observed physiologically on nonmetalloproteins may arise more from the attachment of lipid-derived products of oxidative stress than from adventitious MCO of side chains. Additional studies carried out to clarify the potential use of DNPH derivatization to tag peptide-based carbonyls for mass spectrometric analysis revealed that DNPH derivatization can reverse under the conditions used for proteolysis.
A 2-aminothiazole derivative 1 was developed as a potential inhibitor of the oncology target AKT,... more A 2-aminothiazole derivative 1 was developed as a potential inhibitor of the oncology target AKT, a serine/threonine kinase. When incubated in rat and human liver microsomes in the presence of NADPH, 1 underwent significant metabolic activation on its 2-aminothiazole ring, leading to substantial covalent protein binding. Upon addition of glutathione, covalent binding was reduced significantly, and multiple glutathione adducts were detected. Novel metabolites from the in vitro incubates were characterized by LC-MS and NMR to discern the mechanism of bioactivation. An in silico model was developed based on the proposed mechanism and was employed to predict bioactivation in 23 structural analogues. The predictions were confirmed empirically for the bioactivation liability, in vitro, by LC-MS methods screening for glutathione incorporation. New compounds were identified with a low propensity for bioactivation.
Sensitive and selective liquid chromatography-mass spectrometry (LC-MS) analysis is a powerful an... more Sensitive and selective liquid chromatography-mass spectrometry (LC-MS) analysis is a powerful and essential tool for metabolite identification in drug discovery and development. An MS(2) (or tandem, MS/MS) mass spectrum is acquired from the fragmentation of a precursor ion by multiple methods including information-dependent acquisition (IDA), SWATH (sequential window acquisition of all theoretical fragment-ion spectra), and MS(All) (also called MS(E)) techniques. We compared these three techniques in their capabilities to produce comprehensive MS(2) data by assessing both metabolite MS(2) acquisition hit rate and the quality of MS(2) spectra. Rat liver microsomal incubations from eight test compounds were analyzed with four methods (IDA, MMDF (multiple mass defect filters)-IDA, SWATH, or MS(All)) using an ultrahigh-performance liquid chromatography-qudrupole time-of-flight mass spectrometry (UHPLC-Q-TOF MS) platform. A combined total of 227 drug-related materials (DRM) were detected from all eight test article incubations, and among those, 5% and 4% of DRM were not triggered for MS(2) acquisition with IDA and MMDF-IDA methods, respectively. When the same samples were spiked to an equal volume of blank rat urine (urine sample), the DRM without MS(2) acquisition increased to 29% and 18%, correspondingly. In contrast, 100% of DRM in both matrixes were subjected to MS(2) acquisition with either the SWATH or MS(All) method. However, the quality of the acquired MS(2) spectra decreased in the order of IDA, SWATH, and MS(All) methods. An average of 10, 9, and 6 out of 10 most abundant ions in MS(2) spectra were the real product ions of DRM detected in microsomal samples from IDA, SWATH, and MS(All) methods, respectively. The corresponding numbers declined to 9, 6, and 3 in the urine samples. Overall, IDA-based methods acquired qualitatively better MS(2) spectra but with a lower MS(2) acquisition hit rate than the other two methods. SWATH outperformed the MS(All) method given its better quality of MS(2) spectra with an identical MS(2) acquisition hit rate.
2008 6th IEEE International Conference on Industrial Informatics, 2008
Abstract Although it is widely believed that software quality will be improved by the use of auto... more Abstract Although it is widely believed that software quality will be improved by the use of automated testing, automation is still not well-off in industry today. There are quite a few issues of traditional software test automation mode, for example, high cost, knowledge ...
Toxicological sciences : an official journal of the Society of Toxicology, 2014
The dysregulation of phosphatidylinositol 3-kinase (PI3K)-dependent pathways is implicated in sev... more The dysregulation of phosphatidylinositol 3-kinase (PI3K)-dependent pathways is implicated in several human cancers making it an attractive target for small molecule PI3K inhibitors. A series of potent pyridyltriazine-containing inhibitors of class Ia PI3Ks were synthesized and a subset of compounds was evaluated in exploratory repeat-dose rat toxicology studies. Daily oral dosing of compound 1: in Sprague Dawley rats for four consecutive days was associated with hepatobiliary toxicity that included biliary epithelial hyperplasia and hypertrophy, periductular edema, biliary stasis, and acute peribiliary inflammatory infiltrates. These histological changes were associated with clinical pathology changes that included increased serum liver enzymes, total bile acids, and bilirubin. The predominant clearance pathway of 1: was shown in vitro and in a bile-duct cannulated rat (14)C-ADME study to be P450-mediated oxidative metabolism. An O-demethylated pyridine metabolite, M3: , was identi...
Journal of Pharmaceutical and Biomedical Analysis, 2011
An LC-MS/MS method using pre-column derivatization with phenylisothiocyanate (PITC) was developed... more An LC-MS/MS method using pre-column derivatization with phenylisothiocyanate (PITC) was developed to quantify glycine in human cerebrospinal fluid (CSF) and applied to the determination of glycine in human samples collected during clinical testing. The calibration curve range for the assay was 50-10,000 ng/mL and ¹³C₂¹⁵N-glycine was used as an internal standard. Artificial CSF was used as a surrogate matrix for standards due to the presence of endogenous glycine in human CSF and this approach was validated with additional experiments involving either standard addition, or stable labeled glycine as an alternate calibration standard for endogenous glycine. Interday bias (% RE) and precision (% CV) were -4.2 and 12.3% at the LLOQ, and less than ±0.9 and 8.3% for higher concentrations, respectively. Glycine was stable in artificial CSF for at least 5h at room temperature, 55 days at -70 °C (-60 to -80 °C range), and through three freeze-thaw cycles.
An assessment of 2,4-dinitrophenylhydrazine (DNPH)-detectable protein-based carbonyls is one of t... more An assessment of 2,4-dinitrophenylhydrazine (DNPH)-detectable protein-based carbonyls is one of the most common assays used to quantify oxidative stress in vitro and in vivo. In this study, we compared, for the lipid-binding protein beta-lactoglobulin, the extent to which carbonyl reactivity could be introduced by adventitious metal-catalyzed oxidation (MCO) in the absence and presence of a polyunsaturated lipid or by treatment with various individual bifunctional lipid oxidation products capable of introducing carbonyls into proteins by adduction to nucleophilic side chains. With metal ions and either O2/reductant or H2O2 as the terminal oxidant, the maximal level of DNPH-detectable carbonyl generation obtainable in several hours was 0.1-0.2 mol carbonyl per mol protein monomer, with Cu(II) being more effective than Fe(II). Exposure instead to bifunctional lipoxidation-derived aldehydes (1-2 mM) generated in some cases in excess of 1 mol carbonyl per mol protein. The rank order of carbonyl incorporation reactivity was acrolein > 4-oxo-2-nonenal > 4-hydroxy-2-nonenal > 2,4-decadienal > malondialdehyde. Protein cross-linking ability followed a somewhat different rank order. Parallel studies on reductively methylated beta-lactoglobulin revealed that His and Cys residues are intrinsically more responsible than Lys residues for carbonyl appearance and that the availability of Lys residues accounts for the reduction of carbonyl content at later time (presumably reflecting cross-linking chemistry) that occurs for acrolein and 4-oxo-2-nonenal. Overall, these results suggest that DNPH reactivity observed physiologically on nonmetalloproteins may arise more from the attachment of lipid-derived products of oxidative stress than from adventitious MCO of side chains. Additional studies carried out to clarify the potential use of DNPH derivatization to tag peptide-based carbonyls for mass spectrometric analysis revealed that DNPH derivatization can reverse under the conditions used for proteolysis.
A 2-aminothiazole derivative 1 was developed as a potential inhibitor of the oncology target AKT,... more A 2-aminothiazole derivative 1 was developed as a potential inhibitor of the oncology target AKT, a serine/threonine kinase. When incubated in rat and human liver microsomes in the presence of NADPH, 1 underwent significant metabolic activation on its 2-aminothiazole ring, leading to substantial covalent protein binding. Upon addition of glutathione, covalent binding was reduced significantly, and multiple glutathione adducts were detected. Novel metabolites from the in vitro incubates were characterized by LC-MS and NMR to discern the mechanism of bioactivation. An in silico model was developed based on the proposed mechanism and was employed to predict bioactivation in 23 structural analogues. The predictions were confirmed empirically for the bioactivation liability, in vitro, by LC-MS methods screening for glutathione incorporation. New compounds were identified with a low propensity for bioactivation.
Sensitive and selective liquid chromatography-mass spectrometry (LC-MS) analysis is a powerful an... more Sensitive and selective liquid chromatography-mass spectrometry (LC-MS) analysis is a powerful and essential tool for metabolite identification in drug discovery and development. An MS(2) (or tandem, MS/MS) mass spectrum is acquired from the fragmentation of a precursor ion by multiple methods including information-dependent acquisition (IDA), SWATH (sequential window acquisition of all theoretical fragment-ion spectra), and MS(All) (also called MS(E)) techniques. We compared these three techniques in their capabilities to produce comprehensive MS(2) data by assessing both metabolite MS(2) acquisition hit rate and the quality of MS(2) spectra. Rat liver microsomal incubations from eight test compounds were analyzed with four methods (IDA, MMDF (multiple mass defect filters)-IDA, SWATH, or MS(All)) using an ultrahigh-performance liquid chromatography-qudrupole time-of-flight mass spectrometry (UHPLC-Q-TOF MS) platform. A combined total of 227 drug-related materials (DRM) were detected from all eight test article incubations, and among those, 5% and 4% of DRM were not triggered for MS(2) acquisition with IDA and MMDF-IDA methods, respectively. When the same samples were spiked to an equal volume of blank rat urine (urine sample), the DRM without MS(2) acquisition increased to 29% and 18%, correspondingly. In contrast, 100% of DRM in both matrixes were subjected to MS(2) acquisition with either the SWATH or MS(All) method. However, the quality of the acquired MS(2) spectra decreased in the order of IDA, SWATH, and MS(All) methods. An average of 10, 9, and 6 out of 10 most abundant ions in MS(2) spectra were the real product ions of DRM detected in microsomal samples from IDA, SWATH, and MS(All) methods, respectively. The corresponding numbers declined to 9, 6, and 3 in the urine samples. Overall, IDA-based methods acquired qualitatively better MS(2) spectra but with a lower MS(2) acquisition hit rate than the other two methods. SWATH outperformed the MS(All) method given its better quality of MS(2) spectra with an identical MS(2) acquisition hit rate.
Uploads
Papers by Xiaochun Zhu