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1.
Anal Chem ; 96(4): 1468-1477, 2024 01 30.
Artículo en Inglés | MEDLINE | ID: mdl-38236168

RESUMEN

Untargeted metabolomics is a growing field, in which recent advances in high-resolution mass spectrometry coupled with liquid chromatography (LC-MS) have facilitated untargeted approaches as a result of improvements in sensitivity, mass accuracy, and resolving power. However, a very large amount of data are generated. Consequently, using computational tools is now mandatory for the in-depth analysis of untargeted metabolomics data. This article describes MetAbolomics ReSearch (MARS), an all-in-one vendor-agnostic graphical user interface-based software applying LC-MS analysis to untargeted metabolomics. All of the analytical steps are described (from instrument data conversion and processing to statistical analysis, annotation/identification, quantification, and preliminary biological interpretation), and tools developed to improve annotation accuracy (e.g., multiple adducts and in-source fragmentation detection, trends across samples, and the MS/MS validator) are highlighted. In addition, MARS allows in-house building of reference databases, to bypass the limits of freely available MS/MS spectra collections. Focusing on the flexibility of the software and its user-friendliness, which are two important features in multipurpose software, MARS could provide new perspectives in untargeted metabolomics data analysis.


Asunto(s)
Cromatografía Líquida con Espectrometría de Masas , Espectrometría de Masas en Tándem , Cromatografía Liquida , Metabolómica/métodos , Programas Informáticos
2.
J Chem Inf Model ; 61(6): 2706-2719, 2021 06 28.
Artículo en Inglés | MEDLINE | ID: mdl-34061520

RESUMEN

Stress testing is one of the most important parts of the drug development process, helping to foresee stability problems and to identify degradation products. One of the processes involving stress testing is represented by forced degradation studies, which can predict the impact of certain conditions of pH, moisture, heat, or other negative effects due to transportation or packaging issues on drug potency and purity, ensuring patient safety. Regulatory agencies have been working on a standardization of laboratory procedures since the past two decades. One of the results of those years of intensive research is the International Conference on Harmonization (ICH) guidelines, which clearly define which forced degradation studies should be performed on new drugs, which become a routine work in pharmaceutical laboratories. Since used techniques based on high-performance liquid chromatography coupled with high-resolution mass spectrometry have been developed years ago and are now mastered by pharmaceutical scientists, automation of data analysis, and thus data processing, is becoming a hot topic nowadays. In this work, we present MassChemSite and WebChembase as a tandem to automatize the routine analysis studies without missing information quality, using as a case study the degradation of lansoprazole under acidic, oxidative, basic, and neutral stress conditions.


Asunto(s)
Espectrometría de Masa por Ionización de Electrospray , Espectrometría de Masas en Tándem , Estabilidad de Medicamentos , Humanos , Hidrólisis , Lansoprazol , Oxidación-Reducción
3.
Bioinformatics ; 35(4): 650-655, 2019 02 15.
Artículo en Inglés | MEDLINE | ID: mdl-30052776

RESUMEN

SUMMARY: More than 150 peptide therapeutics are globally in clinical development. Many enzymatic barriers should be crossed by a successful drug to be prosperous in such a process. Therefore, the new peptide drugs must be designed preventing the potential protease cleavage to make the compound less susceptible to protease reaction. We present a new data analysis tool developed in WebMetabase, an approach that stores the information from liquid chromatography mass spectrometry-based experimental data or from external sources such as the MEROPS database. The tool is a chemically aware system where each peptide substrate is presented as a sequence of structural blocks (SBs) connected by amide bonds and not being limited to the natural amino acids. Each SB is characterized by its pharmacophoric and physicochemical properties including a similarity score that describes likelihood between a SB and each one of the other SBs in the database. This methodology can be used to perform a frequency analysis to discover the most frequent cleavage sites for similar amide bonds, defined based on the similarity of the SB that participate in such a bond within the experimentally derived and/or public database. AVAILABILITY AND IMPLEMENTATION: http://webmetabase.com:8182/WebMetabaseBioinformatics/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Bases de Datos de Proteínas , Péptidos/química , Cromatografía Liquida , Espectrometría de Masas , Especificidad por Sustrato
4.
Rapid Commun Mass Spectrom ; 34(12): e8792, 2020 Jun 30.
Artículo en Inglés | MEDLINE | ID: mdl-32208529

RESUMEN

RATIONALE: Liquid chromatography/mass spectrometry is an essential tool for efficient and reliable quantitative and qualitative analysis and underpins much of contemporary drug metabolism and pharmacokinetics. Data-independent acquisition methods such as MSE have reduced the potential to miss metabolites, but do not formally generate quadrupole-resolved product ion spectra. The addition of ion mobility separation to these approaches, for example, in High-Definition MSE (HDMSE ) has the potential to reduce the time needed to set up an experiment and maximize the chance that all metabolites present can be resolved and characterized. We compared High-Definition Data-Dependent Acquisition (HD-DDA), MSE and HDMSE approaches using automated software processing with Mass-MetaSite and WebMetabase. METHODS: Metabolite identification was performed on incubations of glucagon-like peptide-1 (7-37) (GLP-1) and verapamil hydrochloride. The HD-DDA, MSE and HDMSE experiments were conducted on a Waters ACQUITY UPLC I-Class LC system with a VION IMS quadrupole time-of-flight (QTOF) mass spectrometer operating under UNIFI control. All acquired data were processed using MassMetaSite able to read data from UNIFI 1.9.4. WebMetabase was used to review the detected chromatographic peaks and the spectral data interpretations. RESULTS: A comparison of outcomes obtained for MSE and HDMSE data demonstrated that the same structures were proposed for metabolites of both verapamil and GLP-1. The ratio of structurally matched to mismatched product ions found by MassMetaSite was slightly greater for HDMSE than for MSE , and HD-DDA, thus improving confidence in the structures proposed through the addition of ion mobility based data acquisitions. CONCLUSIONS: HDMSE data acquisition is an effective approach for the elucidation of metabolite structures for both small molecules and peptides, with excellent accuracy and quality, requiring minimal tailoring for the compound under investigation.


Asunto(s)
Iones/análisis , Espectrometría de Masas/métodos , Programas Informáticos , Cromatografía Líquida de Alta Presión/métodos , Iones/química , Péptidos/análisis , Péptidos/química
5.
Rapid Commun Mass Spectrom ; 30(2): 301-10, 2016 Jan 30.
Artículo en Inglés | MEDLINE | ID: mdl-26689160

RESUMEN

RATIONALE: Cytochrome P450 (CYP450) reaction phenotyping (CRP) and kinetic studies are essential in early drug discovery to determine which metabolic enzymes react with new drug entities. A new semi-automated computer-assisted workflow for CRP is introduced in this work. This workflow provides not only information regarding parent disappearance, but also metabolite identification and relative metabolite formation rates for kinetic analysis. METHODS: Time-course experiments based on incubating six probe substrates (dextromethorphan, imipramine, buspirone, midazolam, ethoxyresorufin and diclofenac) with recombinant human enzymes (CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4) and human liver microsomes (HLM) were performed. Liquid chromatography/high-resolution mass spectrometry (LC/HRMS) analysis was conducted with an internal standard to obtain high-resolution full-scan and MS/MS data. Data were analyzed using Mass-MetaSite software. A server application (WebMetabase) was used for data visualization and review. RESULTS: CRP experiments were performed, and the data were analyzed using a software-aided approach. This automated-evaluation approach led to (1) the detection of the CYP450 enzymes responsible for both substrate depletion and metabolite formation, (2) the identification of specific biotransformations, (3) the elucidation of metabolite structures based on MS/MS fragment analysis, and (4) the determination of the initial relative formation rates of major metabolites by CYP450 enzymes. CONCLUSIONS: This largely automated workflow enabled the efficient analysis of HRMS data, allowing rapid evaluation of the involvement of the main CYP450 enzymes in the metabolism of new molecules during drug discovery.


Asunto(s)
Sistema Enzimático del Citocromo P-450/química , Sistema Enzimático del Citocromo P-450/metabolismo , Descubrimiento de Drogas/métodos , Programas Informáticos , Espectrometría de Masas en Tándem/métodos , Sistema Enzimático del Citocromo P-450/genética , Humanos , Cinética , Microsomas Hepáticos/metabolismo , Estructura Molecular , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Flujo de Trabajo
6.
Rapid Commun Mass Spectrom ; 29(21): 2083-9, 2015 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-26443410

RESUMEN

RATIONALE: Structural information on metabolites obtained in relevant biological systems can have considerable impact on the design of new drug candidates. However, with demanding turnaround times, the amount of available structural information may become rate limiting. METHODS: The workflow for metabolite identification used in our laboratory was compared to a workflow using a software tool built for computer-assisted metabolite identification. The present study covered the in vitro metabolism of a diverse set of 65 in-house compounds. The compounds were profiled across three liver-based systems, 17 compounds were tested in human liver microsomes (HLM), 12 in rat hepatocytes (RHEP), and 36 in human hepatocytes (HHEP). RESULTS: For 92% of the metabolites reported, the exact match or Markush representations were in agreement between the two workflows. The major specific biotransformations in hepatocytes which formed the metabolites were aromatic or aliphatic hydroxylations (33%), N-dealkylations (15%) and glucuronidations (12%). CONCLUSIONS: The software was shown to perform well for structural elucidation of metabolites from both phase I and phase II metabolism where the focus was on quickly understanding the rate-limiting metabolic step(s).


Asunto(s)
Preparaciones Farmacéuticas/química , Preparaciones Farmacéuticas/metabolismo , Programas Informáticos , Animales , Descubrimiento de Drogas , Hepatocitos/metabolismo , Humanos , Microsomas Hepáticos/metabolismo , Estructura Molecular , Ratas
7.
Clin Sci (Lond) ; 126(4): 305-13, 2014 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-24015848

RESUMEN

ACE (angiotensin-1-converting enzyme) is a zinc metallopeptidase that plays a prominent role in blood pressure regulation and electrolyte homeostasis. ACE consists of two homologous domains that despite similarities of sequence and topology display differences in substrate processing and inhibitor binding. The design of inhibitors that selectively inhibit the N-domain (N-selective) could be useful in treating conditions of tissue injury and fibrosis due to build-up of N-domain-specific substrate Ac-SDKP (N-acetyl-Ser-Asp-Lys-Pro). Using a receptor-based SHOP (scaffold hopping) approach with N-selective inhibitor RXP407, a shortlist of scaffolds that consisted of modified RXP407 backbones with novel chemotypes was generated. These scaffolds were selected on the basis of enhanced predicted interaction energies with N-domain residues that differed from their C-domain counterparts. One scaffold was synthesized and inhibitory binding tested using a fluorogenic ACE assay. A molecule incorporating a tetrazole moiety in the P2 position (compound 33RE) displayed potent inhibition (K(i)=11.21±0.74 nM) and was 927-fold more selective for the N-domain than the C-domain. A crystal structure of compound 33RE in complex with the N-domain revealed its mode of binding through aromatic stacking with His388 and a direct hydrogen bond with the hydroxy group of the N-domain specific Tyr369. This work further elucidates the molecular basis for N-domain-selective inhibition and assists in the design of novel N-selective ACE inhibitors that could be employed in treatment of fibrosis disorders.


Asunto(s)
Inhibidores de la Enzima Convertidora de Angiotensina/química , Presión Sanguínea/efectos de los fármacos , Diseño de Fármacos , Oligopéptidos/química , Peptidil-Dipeptidasa A/química , Ácidos Fosfínicos/química , Inhibidores de la Enzima Convertidora de Angiotensina/farmacología , Sitios de Unión/fisiología , Conformación Proteica
8.
Rapid Commun Mass Spectrom ; 28(24): 2695-703, 2014 Dec 30.
Artículo en Inglés | MEDLINE | ID: mdl-25380491

RESUMEN

RATIONALE: Analytical methods to assess glutathione (GSH) conjugate formation based on mass spectrometry usually take advantage of the specific fragmentation behavior of the glutathione moiety. However, most methods used for GSH adduct screening monitor only one specific neutral loss or one fragment ion, even though the peptide moiety of GSH adducts shows a number of other specific neutral fragments and fragment ions which can be used for identification. METHODS: Nine reference drugs well known to form GSH adducts were incubated with human liver microsomes. Mass spectrometric analysis was performed with a quadrupole time-of-flight mass spectrometer in untargeted accurate mass MS(E) mode. The data analysis and evaluation was achieved in an automated approach with software to extract and identify GSH conjugates based on the presence of multiple collision-induced neutral losses and fragment ions specific for glutathione conjugates in the high-energy MS spectra. RESULTS: In total 42 GSH adducts were identified. Eight (18%) adducts did not show the neutral loss of 129 but were identified based on the appearance of other GSH-specific neutral losses or fragment ions. In high-energy MS(E) spectra the GSH-specific fragment ions of m/z 308 and 179 as well as the neutral loss of 275 Da were complementary to the commonly used neutral loss of 129 Da. Further, one abundant (yet unpublished) GSH conjugate of troglitazone formed in human liver microsomes was found. CONCLUSIONS: A software-aided approach was developed to reliably retrieve GSH adduct formation data out of untargeted complex full scan QTOFMS(E) data in a fast and efficient way. The present approach to detect and analyze multiple collision-induced neutral losses and fragment ions of glutathione conjugates in untargeted MS(E) data might be applicable to higher throughput to assess reactive metabolite formation in drug discovery.


Asunto(s)
Glutatión/química , Espectrometría de Masas/métodos , Glutatión/metabolismo , Humanos , Iones/química , Microsomas Hepáticos/química , Microsomas Hepáticos/metabolismo , Peso Molecular
9.
J Am Soc Mass Spectrom ; 35(1): 131-139, 2024 Jan 03.
Artículo en Inglés | MEDLINE | ID: mdl-38014625

RESUMEN

Multiple Reaction Monitoring (MRM) is an important MS/MS technique commonly used in drug discovery and development, allowing for the selective and sensitive quantification of compounds in complex matrices. However, compound optimization can be resource intensive and requires experimental determination of product ions for each compound. In this study, we developed a Learning-to-Rank (LTR) model to predict the product ions directly from compound structures, eliminating the requirement for MRM optimization experiments. Experimentally determined MRM conditions for 5757 compounds were used to develop the model. Using the MassChemSite software, theoretical fragments and their mass-to-charge ratios were generated, which were then matched to the experimental product ions to create a data set. Each possible fragment was ranked based on its intensity in the experimental data. Different LTR models were built on a training split. Hyperparameter selection was performed using 5-fold cross validation. The models were evaluated using the Normalized Discounted Cumulative Gain at top k (NDCG@k) and the Coverage at top k (Coverage@k) metrics. Finally, the model was applied to predict MRM conditions for a prospective set of 235 compounds in high-throughput Caco-2 permeability and metabolic stability assays, and quantification results were compared to those obtained with experimentally acquired MRM conditions. The LTR model achieved a NDCG@5 of 0.732 and Coverage@5 of 0.841 on the validation split, and its predictions led to 97% of biologically equivalent results in the Caco-2 permeability and metabolic stability assays.


Asunto(s)
Descubrimiento de Drogas , Espectrometría de Masas en Tándem , Humanos , Espectrometría de Masas en Tándem/métodos , Células CACO-2 , Estudios Prospectivos , Iones/química
10.
Drug Discov Today Technol ; 10(1): e199-205, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-24050248

RESUMEN

One of the key factors in drug discovery is related to the metabolic properties of the lead compound, which may influence the bioavailability of the drug, its therapeutic window, and unwanted side-effects of its metabolites. Therefore, it is of critical importance to enable the fast translation of the experimentally determined metabolic information into design knowledge. The elucidation of the metabolite structure is the most structurally rich and informative end-point in the available range of metabolic assays. A methodology is presented to partially automate the analysis of this experimental information, making the process more efficient. The computer assisted method helps in the chromatographic peak selection and the metabolite structure assignment, enabling automatic data comparison for qualitative applications (kinetic analysis, cross species comparison).


Asunto(s)
Descubrimiento de Drogas , Ensayos Analíticos de Alto Rendimiento , Preparaciones Farmacéuticas/metabolismo , Cromatografía Líquida de Alta Presión , Simulación por Computador , Espectrometría de Masas , Microsomas Hepáticos/metabolismo , Reproducibilidad de los Resultados , Verapamilo/metabolismo
11.
Xenobiotica ; 43(4): 390-8, 2013 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-22931213

RESUMEN

1. There has been a lack of in vivo metabolite profiling update of hydrocodone since the original report on species differences was published in 1978. As such, the mechanism for its analgesic activity in different species has been ambiguous. To address safety concern from regulatory agencies, hydrocodone metabolite profiles in rats and dogs are updated herein aided by a newly developed software, Mass-MetaSite. 2. Samples collected from rats and dogs dosed orally with hydrocodone were analyzed with reversed phase liquid chromatography coupled with LTQ-Orbitrap. The exact mass measurement data collected with data-dependent acquisition methodology were analyzed both traditionally, using Xcalibur Qual Browser and MetWorks, and by Mass-MetaSite. 3. Profiling of hydrocodone metabolites in rat and dog plasma reflected previously reported species differences in circulating metabolites. While hydrocodone mainly underwent O-demethylation and ketone reduction in rats forming hydromorphone and reduced hydromorphone, which were then subsequently cleared via glucuronide conjugation, hydrocodone in dogs was cleared predominantly by N-demethylation and N-oxidation. 4. Given the success ratio of metabolite detection offered by Mass-MetaSite, the software will be able to aid chemists in early identification of drug metabolites from complex biomatrices.


Asunto(s)
Hidrocodona/metabolismo , Metaboloma , Programas Informáticos , Animales , Automatización , Medición de Intercambio de Deuterio , Perros , Hidrocodona/sangre , Hidrocodona/química , Hidrocodona/orina , Masculino , Redes y Vías Metabólicas , Ratas , Ratas Sprague-Dawley , Estándares de Referencia
12.
Rapid Commun Mass Spectrom ; 24(21): 3127-38, 2010 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-20941759

RESUMEN

The identification of metabolites is almost exclusively done with liquid chromatography/tandem mass spectrometry (LC/MSMS) and despite the enormous progress in the development of these techniques and software for handling of data this is a time-consuming task. In this study the use of quadrupole time-of-flight (QTOF)-generated MS(E) and MS/MS data were compared with respect to rationalization of metabolites. In addition Mass-MetaSite, a semi-automated software for metabolite identification, was evaluated. The program combines the information from MS raw data, in the form of collision-induced dissociation spectra, with a prediction of the site of metabolism in order to assign the structure of a metabolite. The aim of the software is to mimic the rationalization of fragment ions performed by a biotransformation scientist in the process of structural elucidation. For this evaluation, metabolite identification in human liver microsomes was accomplished for 19 commercially available compounds and 15 in-house compounds. The results were very encouraging and for 96% of the metabolites the same structures were assigned using MS(E) compared with MSMS acquired data. The possibility of using MS(E) could considerably reduce the analysis time. Moreover, Mass-MetaSite performed well and the correct assigned structure, compared to manual inspection of the data, was picked in the first rank in ∼80% of the cases. In conclusion MS(E) could be successfully used for metabolite identification in order to reduce time of analysis and Mass-MetaSite could alleviate the work of a biotransformation scientist and decrease the workload by assigning the structure for a majority of the metabolites.


Asunto(s)
Cromatografía Liquida/métodos , Programas Informáticos , Espectrometría de Masas en Tándem/métodos , Biotransformación , Simulación por Computador , Humanos , Microsomas Hepáticos/metabolismo , Modelos Químicos , Conformación Molecular , Preparaciones Farmacéuticas/química , Preparaciones Farmacéuticas/metabolismo , Interfaz Usuario-Computador
13.
J Chem Inf Model ; 49(9): 2129-38, 2009 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-19728739

RESUMEN

The information provided by the alignment-independent GRid Independent Descriptors (GRIND) can be condensed by the application of principal component analysis, obtaining a small number of principal properties (GRIND-PP), which is more suitable for describing molecular similarity. The objective of the present study is to optimize diverse parameters involved in the obtention of the GRIND-PP and validate their suitability for applications, requiring a biologically relevant description of the molecular similarity. With this aim, GRIND-PP computed with a collection of diverse settings were used to carry out ligand-based virtual screening (LBVS) on standard conditions. The quality of the results obtained was remarkable and comparable with other LBVS methods, and their detailed statistical analysis allowed to identify the method settings more determinant for the quality of the results and their optimum. Remarkably, some of these optimum settings differ significantly from those used in previously published applications, revealing their unexplored potential. Their applicability in large compound database was also explored by comparing the equivalence of the results obtained using either computed or projected principal properties. In general, the results of the study confirm the suitability of the GRIND-PP for practical applications and provide useful hints about how they should be computed for obtaining optimum results.


Asunto(s)
Evaluación Preclínica de Medicamentos/métodos , Análisis de Componente Principal , Interfaz Usuario-Computador , Bases de Datos de Proteínas , Diseño de Fármacos , Estudios de Factibilidad , Ligandos , Control de Calidad
14.
PLoS One ; 14(1): e0199270, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-30620739

RESUMEN

Peptide drugs have been used in the treatment of multiple pathologies. During peptide discovery, it is crucially important to be able to map the potential sites of cleavages of the proteases. This knowledge is used to later chemically modify the peptide drug to adapt it for the therapeutic use, making peptide stable against individual proteases or in complex medias. In some other cases it needed to make it specifically unstable for some proteases, as peptides could be used as a system to target delivery drugs on specific tissues or cells. The information about proteases, their sites of cleavages and substrates are widely spread across publications and collected in databases such as MEROPS. Therefore, it is possible to develop models to improve the understanding of the potential peptide drug proteolysis. We propose a new workflow to derive protease specificity rules and predict the potential scissile bonds in peptides for individual proteases. WebMetabase stores the information from experimental or external sources in a chemically aware database where each peptide and site of cleavage is represented as a sequence of structural blocks connected by amide bonds and characterized by its physicochemical properties described by Volsurf descriptors. Thus, this methodology could be applied in the case of non-standard amino acid. A frequency analysis can be performed in WebMetabase to discover the most frequent cleavage sites. These results were used to train several models using logistic regression, support vector machine and ensemble tree classifiers to map cleavage sites for several human proteases from four different families (serine, cysteine, aspartic and matrix metalloproteases). Finally, we compared the predictive performance of the developed models with other available public tools PROSPERous and SitePrediction.


Asunto(s)
Aminoácidos/química , Descubrimiento de Drogas , Endopeptidasas/química , Péptidos/química , Análisis de Secuencia de Proteína/métodos , Programas Informáticos , Humanos , Análisis de Secuencia de Proteína/instrumentación , Flujo de Trabajo
15.
J Med Chem ; 51(6): 1755-63, 2008 Mar 27.
Artículo en Inglés | MEDLINE | ID: mdl-18311908

RESUMEN

Type II cytochrome P450 (CYP) ligands cause inhibition by direct coordination to the heme iron atom. This interaction usually leads to high inhibitory potential, which can cause drug-drug interaction. The approach to design compounds with diminished CYP inhibition is different depending on whether the compound binds (type II ligand) or not (type I ligand) to the iron atom of the heme group. In this study, the structural characteristics of nitrogen-containing compounds, which bind to the iron atom in two CYP isoforms (CYP2C9 and CYP3A4), were investigated. The in vitro assays applied were fluorescence inhibition assay, difference spectra measurements, and K s determination. Computational modeling as an alternative method to difference spectra measurements to distinguish between type I and type II ligands was also explored. Since two CYP isoforms were used, information about the isoform specificity of type II ligands was also analyzed. The in silico method developed in this study applied together with the information gained from the experimental measurements may result in better decisions during the drug discovery process.


Asunto(s)
Hidrocarburo de Aril Hidroxilasas/antagonistas & inhibidores , Azoles/farmacología , Inhibidores del Citocromo P-450 CYP3A , Piridinas/farmacología , Azoles/química , Sitios de Unión , Simulación por Computador , Citocromo P-450 CYP2C9 , Citocromo P-450 CYP3A , Diseño de Fármacos , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , Humanos , Ligandos , Modelos Moleculares , Estructura Molecular , Piridinas/química , Estereoisomerismo , Relación Estructura-Actividad
16.
Drug Metab Dispos ; 36(11): 2199-210, 2008 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-18725510

RESUMEN

N-dealkylation is a commonly observed metabolic reaction for drugs containing secondary and tertiary amines. On searching the literature, it is obvious that this reaction is far less common among cytochrome P450 2D6 catalyzed reactions compared with other cytochromes P450. The CYP2D6 pharmacophore and characteristic features in the active site cavity suggest a favored substrate orientation that prevents N-dealkylation from occurring. In this study, the literature was searched for N-dealkylated and non-N-dealkylated CYP2D6 substrates. The hypothesis that was suggested and confirmed demonstrated that N-dealkylation occurs by this enzyme when the preferred site of metabolism is blocked toward other oxidative metabolic pathways. An interesting observation was also that addition of stable groups at preferred sites of metabolism generally improved the metabolic stability but also resulted in retained or increased inhibition of the enzyme. In addition, the effect of pH on N- and O-dealkylation of dextromethorphan was shown to be consistent with the hypothesis that an ionized amino function favored substrate dockings resulting in O-dealkylation.


Asunto(s)
Inhibidores del Citocromo P-450 CYP2D6 , Citocromo P-450 CYP2D6/metabolismo , Dominio Catalítico/genética , Citocromo P-450 CYP2D6/química , Remoción de Radical Alquila/fisiología , Dextrometorfano/análisis , Dextrometorfano/metabolismo , Inhibidores Enzimáticos/análisis , Inhibidores Enzimáticos/metabolismo , Estabilidad de Enzimas/fisiología , Humanos , Proteínas Recombinantes/antagonistas & inhibidores , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Especificidad por Sustrato/genética
18.
J Med Chem ; 50(22): 5382-91, 2007 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-17915853

RESUMEN

The cytochrome P450 (CYP) family is composed of monooxygenases, which mediate the metabolism of xenobiotics and endogenous compounds. The characterization of the interactions between these enzymes and candidate drugs is an important part of the drug discovery process. CYP2C9, one isoform of the CYPs, mediates the oxidation of several important drugs. The aim of this work is to investigate the possibility to study inhibition and substrate interactions with CYP2C9, using docking and the site of metabolism predictions. The model compounds used for the study were the COX-2 inhibitor celecoxib and a series of 13 analogues known to be metabolized by CYP2C9. The results obtained using the two methods gave valuable information about important interactions of inhibitors and substrates with CYP2C9. The two methods could be used to predict the site of metabolism and to determine the productive docking pose for each compound. These predictions were verified by metabolite identification using LC/MS/MS after incubation with recombinant CYP2C9.


Asunto(s)
Hidrocarburo de Aril Hidroxilasas/antagonistas & inhibidores , Hidrocarburo de Aril Hidroxilasas/química , Inhibidores Enzimáticos/química , Modelos Moleculares , Hidrocarburo de Aril Hidroxilasas/metabolismo , Sitios de Unión , Celecoxib , Cromatografía Líquida de Alta Presión , Inhibidores de la Ciclooxigenasa 2/química , Citocromo P-450 CYP2C9 , Humanos , Conformación Proteica , Pirazoles/química , Proteínas Recombinantes/química , Sulfonamidas/química , Espectrometría de Masas en Tándem
19.
J Med Chem ; 50(11): 2708-17, 2007 May 31.
Artículo en Inglés | MEDLINE | ID: mdl-17489578

RESUMEN

A new GRID-based method for scaffold hopping (SHOP) is presented. In a fully automatic manner, scaffolds were identified in a database based on three types of 3D-descriptors. SHOP's ability to recover scaffolds was assessed and validated by searching a database spiked with fragments of known ligands of three different protein targets relevant for drug discovery using a rational approach based on statistical experimental design. Five out of eight and seven out of eight thrombin scaffolds and all seven HIV protease scaffolds were recovered within the top 10 and 31 out of 31 neuraminidase scaffolds were in the 31 top-ranked scaffolds. SHOP also identified new scaffolds with substantially different chemotypes from the queries. Docking analysis indicated that the new scaffolds would have similar binding modes to those of the respective query scaffolds observed in X-ray structures. The databases contained scaffolds from published combinatorial libraries to ensure that identified scaffolds could be feasibly synthesized.


Asunto(s)
Proteasa del VIH/química , Compuestos Heterocíclicos/química , Modelos Moleculares , Neuraminidasa/química , Relación Estructura-Actividad Cuantitativa , Trombina/química , Sitios de Unión , Bases de Datos Factuales , Humanos , Ligandos , Orthomyxoviridae/enzimología , Unión Proteica
20.
J Med Chem ; 50(18): 4444-52, 2007 Sep 06.
Artículo en Inglés | MEDLINE | ID: mdl-17696334

RESUMEN

The cytochrome P450 (CYP) family is composed of a large group of monooxygenases that mediate the metabolism of xenobiotics and endogenous compounds. CYP2C9, one of the major isoforms of the CYP family, is responsible for the phase I metabolism of a variety of drugs. The aim of the present investigation is to use rational design together with MetaSite, a metabolism site prediction program, to synthesize compounds that retain their pharmacological effects but that are metabolically more stable in the presence of CYP2C9. The model compound for the study is the nonsteroidal anti-inflammatory drug celecoxib, a COX-2 selective inhibitor and known CYP2C9 substrate. Thirteen analogs of celecoxib were designed, synthesized, and evaluated with regard to their metabolic properties and pharmacologic effects. The docking solutions and the predictions from MetaSite gave useful information leading to the design of new compounds with improved metabolic properties.


Asunto(s)
Hidrocarburo de Aril Hidroxilasas/química , Inhibidores de la Ciclooxigenasa 2/química , Pirazoles/química , Sulfonamidas/química , Sitios de Unión , Celecoxib , Inhibidores de la Ciclooxigenasa 2/síntesis química , Citocromo P-450 CYP2C9 , Humanos , Modelos Biológicos , Modelos Moleculares , Conformación Molecular , Estructura Molecular , Pirazoles/síntesis química , Proteínas Recombinantes/síntesis química , Proteínas Recombinantes/química , Relación Estructura-Actividad , Sulfonamidas/síntesis química
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