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Biomedical Chromatography : BMC Aug 2012Aspirin, the most widely used drug in the world, has been known to mankind for over a century. It is not only the pharmacologically active entity, but is also... (Review)
Review
Aspirin, the most widely used drug in the world, has been known to mankind for over a century. It is not only the pharmacologically active entity, but is also biotransformed into a major metabolite, i.e. salicylic acid, which also exhibits similar pharmacologic/pharmacodynamic properties. Hence it is necessary to quantitate aspirin along with its metabolite(s) in various biological matrices accurately and precisely to correlate with pharmacological/pharmacodynamic activity. This paper provides a comprehensive overview of various bioanalytical methods (HPLC and LC-MS/MS) that have been reported for direct quantitation of aspirin along with its metabolite(s). The review also provides general information on sample collection, sample processing, internal standard selection, conditions for chromatographic separation, succinct validation data and applicable conclusions for reported assays in a structured manner.
Topics: Animals; Aspirin; Chromatography, High Pressure Liquid; Humans; Tandem Mass Spectrometry
PubMed: 22297838
DOI: 10.1002/bmc.2694 -
Drug Metabolism and Disposition: the... Apr 2016Benzbromarone (BBR) is a benzofuran derivative that has been quite useful for the treatment of gout; however, it was withdrawn from European markets in 2003 because of...
Benzbromarone (BBR) is a benzofuran derivative that has been quite useful for the treatment of gout; however, it was withdrawn from European markets in 2003 because of reported serious incidents of drug-induced liver injury. BBR-induced hepatotoxicity has been suggested to be associated with the formation of a quinone intermediate. The present study reported epoxide-derived intermediate(s) of BBR. An N-acetylcysteine (NAC) conjugate derived from epoxide metabolite(s) was detected in both microsomal incubations of BBR and urine samples of mice treated with BBR. The NAC conjugate was identified as 6-NAC BBR. Ketoconazole suppressed the bioactivation of BBR to the epoxide intermediate(s), and the CYP3A subfamily was the primary enzyme responsible for the formation of the epoxide(s). The present study provided new information on metabolic activation of BBR.
Topics: Animals; Benzbromarone; Epoxy Compounds; Humans; Male; Mice; Microsomes, Liver; Uricosuric Agents
PubMed: 26792818
DOI: 10.1124/dmd.115.066803 -
Journal of Bioscience and Bioengineering May 2018Recently, the use of metabolomic analysis of human serum and plasma for biomarker discovery and disease diagnosis in clinical studies has been increasing. The...
Recently, the use of metabolomic analysis of human serum and plasma for biomarker discovery and disease diagnosis in clinical studies has been increasing. The feasibility of using a metabolite biomarker for disease diagnosis is strongly dependent on the metabolite's stability during pre-analytical blood processing procedures, such as serum or plasma sampling and sample storage prior to centrifugation. However, the influence of blood processing procedures on the stability of metabolites has not been fully characterized. In the present study, we compared the levels of metabolites in matched human serum and plasma samples using gas chromatography coupled with mass spectrometry and liquid chromatography coupled with mass spectrometry. In addition, we evaluated the changes in plasma metabolite levels induced by storage at room temperature or at a cold temperature prior to centrifugation. As a result, it was found that 76 metabolites exhibited significant differences between their serum and plasma levels. Furthermore, the pre-centrifugation storage conditions significantly affected the plasma levels of 45 metabolites. These results highlight the importance of blood processing procedures during metabolome analysis, which should be considered during biomarker discovery and the subsequent use of biomarkers for disease diagnosis.
Topics: Biomarkers; Blood Specimen Collection; Chromatography, Liquid; Gas Chromatography-Mass Spectrometry; Healthy Volunteers; Humans; Mass Spectrometry; Metabolome; Metabolomics; Plasma; Serum; Specimen Handling
PubMed: 29258730
DOI: 10.1016/j.jbiosc.2017.11.011 -
Chemical Research in Toxicology Mar 2016Pyrrolizidine alkaloids (PAs) are known hepatotoxins. The execution of the toxicities of the alkaloids requires metabolic activation. Protein modification by reactive...
Pyrrolizidine alkaloids (PAs) are known hepatotoxins. The execution of the toxicities of the alkaloids requires metabolic activation. Protein modification by reactive metabolites of PAs has been suggested to be an important mechanism of the toxic actions of PAs. The objectives of the present study were to define the interactions of dehydromonocrotaline (DHM) with lysine, lysine derivatives, a model peptide, and bovine serum albumin and to explore the lysine modification of hepatic proteins of animals given monocrotaline. DHM was found to react with the ε-amino group of all model compounds tested after incubation with DHM, and the modification reaction preferentially occurred at C7 of the necine base. The lysine residue modification with the same regioselectivity was also observed in hepatic proteins of mice treated with monocrotaline. The observed modification increased with the increase in doses administered to the animals. This work allowed us to better understand the mechanisms of the hepatotoxicity of monocrotaline.
Topics: Animals; Cattle; Injections, Intraperitoneal; Lysine; Male; Mice; Mice, Inbred Strains; Monocrotaline; Peptides; Serum Albumin, Bovine
PubMed: 26812400
DOI: 10.1021/acs.chemrestox.5b00488 -
MBio Oct 2022Fungal secondary metabolites with antibiotic activities can promote fungal adaptation to diverse environments. Besides the global regulator, individual biosynthetic gene...
Fungal secondary metabolites with antibiotic activities can promote fungal adaptation to diverse environments. Besides the global regulator, individual biosynthetic gene clusters (BGCs) usually contain a pathway-specific transcription factor for the tight regulation of fungal secondary metabolism. Here, we report the chemical biology mediated by a supercluster containing three BGCs in the entomopathogenic fungus Metarhizium . These clusters are jointly controlled by an embedded transcription factor that orchestrates the collective production of four classes of chemicals: ustilaginoidin, indigotide, pseurotin, and hydroxyl-ovalicin. The ustilaginoidin BGC is implicated as a late-acquired cluster in Metarhizium to produce both the bis-naphtho-γ-pyrones and the monomeric naphtho-γ-pyrone glycosides (i.e., indigotides). We found that the biosynthesis of indigotides additionally requires the functions of paired methylglucosylation genes located outside the supercluster. The pseurotin/ovalicin BGCs are blended and mesosyntenically conserved to the intertwined pseurotin/fumagillin BGCs of Aspergillus fumigatus. However, the former have lost a few genes, including a polyketide synthase gene responsible for the production of a pentaene chain used for assembly with ovalicin to form fumagillin, as observed in A. fumigatus. The collective production of chemical cocktails by this supercluster was dispensable for fungal virulence against insects and could enable the fungus to combat different bacteria better than the metabolite(s) produced by an individual BGC could. Thus, our results unveil a novel strategy employed by fungi to manage chemical ecology against diverse bacteria. Fungal chemical ecology is largely mediated by the metabolite(s) produced by individual biosynthetic gene clusters (BGCs) with antibiotic activities. We report a supercluster containing three BGCs that are jointly controlled by an embedded master regulator in the insect pathogen Metarhizium . Four classes of chemicals, namely, ustilaginoidin, indigotide, pseurotin, and hydroxyl-ovalicin, are collectively produced by these three BGCs along with the contributions of tailoring enzyme genes located outside the supercluster. The production of these metabolites is not required for the fungal infection of insect hosts, but it benefits the fungus to combat diverse bacteria. The findings reveal and advocate a "the-more-the-better" strategy employed by fungi to manage effective adaptations to diverse environments.
Topics: Polyketide Synthases; Pyrones; Metarhizium; Secondary Metabolism; Multigene Family; Bacteria; Transcription Factors; Anti-Bacterial Agents; Glycosides
PubMed: 36000736
DOI: 10.1128/mbio.01800-22 -
Analytical Chemistry Oct 2014A database searching approach can be used for metabolite identification in metabolomics by matching measured tandem mass spectra (MS/MS) against the predicted fragments...
A database searching approach can be used for metabolite identification in metabolomics by matching measured tandem mass spectra (MS/MS) against the predicted fragments of metabolites in a database. Here, we present the open-source MIDAS algorithm (Metabolite Identification via Database Searching). To evaluate a metabolite-spectrum match (MSM), MIDAS first enumerates possible fragments from a metabolite by systematic bond dissociation, then calculates the plausibility of the fragments based on their fragmentation pathways, and finally scores the MSM to assess how well the experimental MS/MS spectrum from collision-induced dissociation (CID) is explained by the metabolite's predicted CID MS/MS spectrum. MIDAS was designed to search high-resolution tandem mass spectra acquired on time-of-flight or Orbitrap mass spectrometer against a metabolite database in an automated and high-throughput manner. The accuracy of metabolite identification by MIDAS was benchmarked using four sets of standard tandem mass spectra from MassBank. On average, for 77% of original spectra and 84% of composite spectra, MIDAS correctly ranked the true compounds as the first MSMs out of all MetaCyc metabolites as decoys. MIDAS correctly identified 46% more original spectra and 59% more composite spectra at the first MSMs than an existing database-searching algorithm, MetFrag. MIDAS was showcased by searching a published real-world measurement of a metabolome from Synechococcus sp. PCC 7002 against the MetaCyc metabolite database. MIDAS identified many metabolites missed in the previous study. MIDAS identifications should be considered only as candidate metabolites, which need to be confirmed using standard compounds. To facilitate manual validation, MIDAS provides annotated spectra for MSMs and labels observed mass spectral peaks with predicted fragments. The database searching and manual validation can be performed online at http://midas.omicsbio.org.
Topics: Algorithms; Benchmarking; Databases, Factual; Metabolome; Metabolomics; Models, Statistical; Research Design; Synechococcus; Tandem Mass Spectrometry
PubMed: 25157598
DOI: 10.1021/ac5014783 -
Bioanalysis Nov 2019A novel single-stranded deaminated oligonucleotide metabolite resulting from a REVERSIR™ oligonucleotide was discovered and identified in monkey liver after...
A novel single-stranded deaminated oligonucleotide metabolite resulting from a REVERSIR™ oligonucleotide was discovered and identified in monkey liver after subcutaneous administration. REVERSIR-A and its metabolites were extracted from biological matrices by solid phase extraction and analyzed using LC coupled with high-resolution MS under negative ionization mode. A novel 9-mer metabolite of REVERSIR-A, resulting from deamination of the 3' terminal 2'--methyl-adenosine nucleotide to 2'--methyl-inosine, was discovered at significant levels in monkey liver. The metabolite's identity was confirmed by LC-MS/MS. This report describes the first observation of a long-chain deaminated metabolite of a single-stranded REVERSIR oligonucleotide in monkey liver.
Topics: Animals; Deamination; Inosine; Liver; Macaca fascicularis; Mass Spectrometry; Oligonucleotides
PubMed: 31829055
DOI: 10.4155/bio-2019-0118 -
Nature Communications Jun 2023Mycobacterium tuberculosis is one of the global leading causes of death due to a single infectious agent. Pretomanid and delamanid are new antitubercular agents that...
Mycobacterium tuberculosis is one of the global leading causes of death due to a single infectious agent. Pretomanid and delamanid are new antitubercular agents that have progressed through the drug discovery pipeline. These compounds are bicyclic nitroimidazoles that act as pro-drugs, requiring activation by a mycobacterial enzyme; however, the precise mechanisms of action of the active metabolite(s) are unclear. Here, we identify a molecular target of activated pretomanid and delamanid: the DprE2 subunit of decaprenylphosphoribose-2'-epimerase, an enzyme required for the synthesis of cell wall arabinogalactan. We also provide evidence for an NAD-adduct as the active metabolite of pretomanid. Our results highlight DprE2 as a potential antimycobacterial target and provide a foundation for future exploration into the active metabolites and clinical development of pretomanid and delamanid.
Topics: Antitubercular Agents; Molecular Targeted Therapy; Mycobacterium tuberculosis; Alcohol Oxidoreductases; Nitroimidazoles; Cell Wall; Drug Resistance; Prodrugs; Spectrophotometry; NAD; Kinetics
PubMed: 37380634
DOI: 10.1038/s41467-023-39300-z -
Antibodies (Basel, Switzerland) May 2021Antibody-drug conjugates (ADCs) are biopharmaceutical products where a monoclonal antibody is linked to a biologically active drug (a small molecule) forming a... (Review)
Review
Antibody-drug conjugates (ADCs) are biopharmaceutical products where a monoclonal antibody is linked to a biologically active drug (a small molecule) forming a conjugate. Since the approval of first ADC (Gemtuzumab ozogamicin (trade name: Mylotarg)) for the treatment of CD33-positive acute myelogenous leukemia, several ADCs have been developed for the treatment of cancer. The goal of an ADC as a cancer agent is to release the cytotoxic drug to kill the tumor cells without harming the normal or healthy cells. With time, it is being realized that ADCS can also be used to manage or cure other diseases such as inflammatory diseases, atherosclerosis, and bacteremia and some research in this direction is ongoing. The focus of this review is on the clinical pharmacology aspects of ADC development. From the selection of an appropriate antibody to the finished product, the entire process of the development of an ADC is a difficult and challenging task. Clinical pharmacology is one of the most important tools of drug development since this tool helps in finding the optimum dose of a product, thus preserving the safety and efficacy of the product in a patient population. Unlike other small or large molecules where only one moiety and/or metabolite(s) is generally measured for the pharmacokinetic profiling, there are several moieties that need to be measured for characterizing the PK profiles of an ADC. Therefore, knowledge and understanding of clinical pharmacology of ADCs is vital for the selection of a safe and efficacious dose in a patient population.
PubMed: 34063812
DOI: 10.3390/antib10020020 -
Journal of Bioinformatics and... Aug 2022Whilst data on biochemical networks has increased several-fold, our comprehension of the underlying molecular biology is incomplete and inadequate. Simulation studies...
TemporalGSSA: A numerically robust R-wrapper to facilitate computation of a metabolite-specific and simulation time-dependent trajectory from stochastic simulation algorithm (SSA)-generated datasets.
Whilst data on biochemical networks has increased several-fold, our comprehension of the underlying molecular biology is incomplete and inadequate. Simulation studies permit data collation from disparate time points and the imputed trajectories can provide valuable insights into the molecular biology of complex biochemical systems. Although, stochastic simulations are accurate, each run is an independent event and the data that is generated cannot be directly compared even with identical simulation times. This lack of robustness will preclude a biologically meaningful result for the metabolite(s) of concern and is a significant limitation of this approach. "TemporalGSSA" or temporal Gillespie Stochastic Simulation Algorithm is an R-wrapper which will collate and partition SSA-generated datasets with identical simulation times (trials) into finite sets of linear models (technical replicates). Each such model (time step of a single run, absolute number of molecules for a metabolite) computes several coefficients (slope, intercept, etc.). These coefficients are averaged (mean slope, mean intercept) across all trials of a technical replicate and along with an imputed time step (mean, median, random) is incorporated into a linear regression equation. The solution to this equation is the number of molecules of a metabolite which is used to compute the molar concentration of the metabolite per technical replicate. The summarized (mean, standard deviation) data of this vector of technical replicates is the outcome or numerical estimate of the molar concentration of a metabolite and is dependent on the duration of the simulation. If the SSA-generated dataset comprises runs with differing simulation times, "TemporalGSSA" can compute the time-dependent trajectory of a metabolite provided the trials-per technical replicate constraint is complied with. The algorithms deployed by "TemporalGSSA" are rigorous, have a sound theoretical basis and have contributed meaningfully to our comprehension of the mechanism(s) that drive complex biochemical systems. "TemporalGSSA", is robust, freely accessible and easy to use with several readily testable examples.
Topics: Algorithms; Computer Simulation; Linear Models; Models, Biological; Stochastic Processes
PubMed: 35941839
DOI: 10.1142/S0219720022500184