RESUMO
Twenty-one simplified analogues of the natural product domoic acid were designed, synthesized, and then characterized at homomeric kainic acid (KA) receptors (GluK1-3,5). LBG20304 displays a high affinity for homomeric GluK5 receptors (IC50 = 432 nM) with a >40-fold selectivity over homomeric GluK1-3 subtypes and â«100-fold selectivity over native AMPA and N-methyl d-aspartate receptors. Functional studies of LBG20304 on heteromeric GluK2/5 receptors show no agonist or antagonist functional response at 10 µM, while a concentration of 100 µM at neuronal slices (rat) shows low agonist activity. A molecular dynamics simulation of LBG20304, in a homology model of GluK5, suggests specific interactions with the GluK5 receptor and an occluded ligand binding domain, which is translated to agonist or partial agonist activity. LBG20304 is a new compound for the study of the role and function of the KA receptors with the aim of understanding the involvement of these receptors in health and disease.
Assuntos
Ácido Caínico , Simulação de Dinâmica Molecular , Receptores de Ácido Caínico , Receptores de Ácido Caínico/agonistas , Receptores de Ácido Caínico/metabolismo , Receptores de Ácido Caínico/antagonistas & inibidores , Receptores de Ácido Caínico/química , Ácido Caínico/análogos & derivados , Ácido Caínico/farmacologia , Ácido Caínico/metabolismo , Ligantes , Animais , Humanos , Ratos , Relação Estrutura-Atividade , Descoberta de DrogasRESUMO
Amino acids (AAs) have been used as excipients in protein formulations both in solid and liquid state products due to their stabilizing effect. However, the mechanisms by which they can stabilize a protein have not been fully elucidated yet. The purpose of this study was to investigate the effect of AAs with distinct physicochemical properties on the stability of a model protein (lysozyme, LZM) during the spray-drying process and subsequent storage. Molecular descriptor based multivariate data analysis was used to select distinct AAs from the group of 20 natural AAs. Then, LZM and the five selected AAs (1:1 wt ratio) were spray-dried (SD). The solid form, residual moisture content (RMC), hygroscopicity, morphology, secondary/tertiary structure and enzymatic activity of LZM were evaluated before and after storage under 40 °C/75 % RH for 30 days. Arginine (Arg), leucine (Leu), glycine (Gly), tryptophan (Trp), aspartic acid (Asp) were selected because of their distinct properties by using principal component analysis (PCA). The SD LZM powders containing Arg, Trp, or Asp were amorphous, while SD LZM powders containing Leu or Gly were crystalline. Recrystallization of Arg, Trp, Asp and polymorph transition of Gly were observed after the storage under accelerated conditions. The morphologies of the SD particles vary upon the different AAs formulated with LZM, implying different drying kinetics of the five model systems. A tertiary structural change of LZM was observed in the SD powder containing Arg, while a decrease in the enzymatic activity of LZM was observed in the powders containing Arg or Asp after the storage. This can be attributed to the extremely basic and acidic conditions that Arg and Asp create, respectively. This study suggests that when AAs are used as stabilizers instead of traditional disaccharides, not only do classic vitrification theory and water replacement theory play a role, but the microenvironmental pH conditions created by basic or acidic AAs in the starting solution or during the storage of solid matter are also crucial for the stability of SD protein products.
Assuntos
Aminoácidos , Armazenamento de Medicamentos , Excipientes , Muramidase , Secagem por Atomização , Muramidase/química , Aminoácidos/química , Excipientes/química , Pós/química , Estabilidade de Medicamentos , Molhabilidade , Química Farmacêutica/métodosRESUMO
Endocrine-disrupting chemicals (EDCs) may impact the development of prostate cancer (PCa) by altering the steroid metabolism. Although their exact mechanism of action in controlling tumor growth is not known, EDCs may inhibit steroidogenic enzymes such as CYP17A1 or CYP19A1 which are involved in the production of androgens or estrogens. High levels of circulating androgens are linked to PCa in men and Polycystic Ovary Syndrome (PCOS) in women. Essential oils or their metabolites, like lavender oil and tea tree oil, have been reported to act as potential EDCs and contribute towards sex steroid imbalance in cases of prepubertal gynecomastia in boys and premature thelarche in girls due to the exposure to lavender-based fragrances. We screened a range of EO components to determine their effects on CYP17A1 and CYP19A1. Computational docking was performed to predict the binding of essential oils with CYP17A1 and CYP19A1. Functional assays were performed using the radiolabeled substrates or Liquid Chromatography-High-Resolution Mass Spectrometry and cell viability assays were carried out in LNCaP cells. Many of the tested compounds bind close to the active site of CYP17A1, and (+)-Cedrol had the best binding with CYP17A1 and CYP19A1. Eucalyptol, Dihydro-ß-Ionone, and (-)-α-pinene showed 20% to 40% inhibition of dehydroepiandrosterone production; and some compounds also effected CYP19A1. Extensive use of these essential oils in various beauty and hygiene products is common, but only limited knowledge about their potential detrimental side effects exists. Our results suggest that prolonged exposure to some of these essential oils may result in steroid imbalances. On the other hand, due to their effect on lowering androgen output and ability to bind at the active site of steroidogenic cytochrome P450s, these compounds may provide design ideas for novel compounds against hyperandrogenic disorders such as PCa and PCOS.
Assuntos
Óleos Voláteis , Síndrome do Ovário Policístico , Masculino , Humanos , Feminino , Androgênios/metabolismo , Hormônios Esteroides Gonadais , Óleos Voláteis/farmacologia , Esteroides/metabolismo , Síndrome do Ovário Policístico/patologia , Sistema Enzimático do Citocromo P-450RESUMO
This study reports on the synthesis and evaluation of novel compounds replacing the nitrogen-containing heterocyclic ring on the chemical backbone structure of cytochrome P450 17α-hydroxylase/12,20-lyase (CYP17A1) inhibitors with a phenyl bearing a sulfur-based substituent. Initial screening revealed compounds with marked inhibition of CYP17A1 activity. The selectivity of compounds was thereafter determined against cytochrome P450 21-hydroxylase, cytochrome P450 3A4, and cytochrome P450 oxidoreductase. Additionally, the compounds showed weak inhibitory activity against aldo-keto reductase 1C3 (AKR1C3). The compounds' impact on steroid hormone levels was also assessed, with some notable modulatory effects observed. This work paves the way for developing more potent dual inhibitors specifically targeting CYP17A1 and AKR1C3.
Assuntos
Nitrogênio , Enxofre , Metabolismo SecundárioRESUMO
CYP17A1 is an enzyme that plays a major role in steroidogenesis and is critically involved in the biosynthesis of steroid hormones. Therefore, it remains an attractive target in several serious hormone-dependent cancer diseases, such as prostate cancer and breast cancer. The medicinal chemistry community has been committed to the discovery and development of CYP17A1 inhibitors for many years, particularly for the treatment of castration-resistant prostate cancer. The current Perspective reflects upon the discovery and evaluation of non-steroidal CYP17A1 inhibitors from a medicinal chemistry angle. Emphasis is placed on the structural aspects of the target, key learnings from the presented chemotypes, and design guidelines for future inhibitors.
Assuntos
Neoplasias da Próstata , Masculino , Humanos , Esteroides , Esteroide 17-alfa-HidroxilaseRESUMO
Discovery of sustainable and benign-by-design drugs to combat emerging health pandemics calls for new analytical technologies to explore the chemical and pharmacological properties of Nature's unique chemical space. Here, we present a new analytical technology workflow, polypharmacology-labeled molecular networking (PLMN), where merged positive and negative ionization tandem mass spectrometry-based molecular networking is linked with data from polypharmacological high-resolution inhibition profiling for easy and fast identification of individual bioactive constituents in complex extracts. The crude extract of Eremophila rugosa was subjected to PLMN analysis for the identification of antihyperglycemic and antibacterial constituents. Visually easy-interpretable polypharmacology scores and polypharmacology pie charts as well as microfractionation variation scores of each node in the molecular network provided direct information about each constituent's activity in the seven assays included in this proof-of-concept study. A total of 27 new non-canonical nerylneryl diphosphate-derived diterpenoids were identified. Serrulatane ferulate esters were shown to be associated with antihyperglycemic and antibacterial activities, including some showing synergistic activity with oxacillin in clinically relevant (epidemic) methicillin-resistant Staphylococcus aureus strains and some showing saddle-shaped binding to the active site of protein-tyrosine phosphatase 1B. PLMN is scalable in the number and types of assays included and thus holds potential for a paradigm shift toward polypharmacological natural-products-based drug discovery.
Assuntos
Staphylococcus aureus Resistente à Meticilina , Polifarmacologia , Fluxo de Trabalho , Antibacterianos/farmacologia , Hipoglicemiantes/farmacologia , Hipoglicemiantes/química , Extratos Vegetais/farmacologia , Extratos Vegetais/químicaRESUMO
Ionotropic glutamate receptors are ligand-gated ion channels essential for fast excitatory neurotransmission in the brain. In contrast to most other members of the iGluR family, the subfamily of delta receptors, GluD1 and GluD2, does not bind glutamate but glycine/D-serine. GluD1 is widely expressed in the brain and the inner ear, where it is required for high-frequency hearing. Furthermore, it has been associated with schizophrenia, autism and depression. X-ray structures of the ligand-binding domain (LBD) of GluD2 have been published; however, no high-resolution structure is available for the ligand-binding domain of GluD1 (GluD1-LBD). Here, we report the X-ray crystal structure of the GluD1-LBD in its apo form at 2.57 Å resolution. Using isothermal titration calorimetry, we show that D-serine binds to the GluD1-LBD in an exothermic manner with a Kd of 160 µm, which is approximately five-fold greater than at GluD2. Furthermore, we identify Glu822 as a critical determinant of receptor activation in GluD1 A654T. In contrast to studies on the GluD2 lurcher mutant A654T, we did not observe any effect of 1 mm D-serine on the spontaneous currents at mouse GluD1 A654T by electrophysiological recordings of Xenopus laevis oocytes as previously also reported by others. These results point towards differences in the structure and dynamics between GluD1 and GluD2. Molecular dynamics simulations were employed to address this observation, suggesting that the apo structure of GluD1 is less flexible than the apo structure of GluD2 and that Pro725 in GluD1 may affect the interlobe closure of the ligand-binding domain of GluD1.
Assuntos
Simulação de Dinâmica Molecular , Receptores de Glutamato , Camundongos , Animais , Receptores de Glutamato/química , Receptores de Glutamato/metabolismo , Cristalografia por Raios X , Ligantes , Serina/metabolismo , Glutamato Desidrogenase/metabolismoRESUMO
Docetaxel (DTX) was the first chemotherapeutic agent to demonstrate significant efficacy in the treatment of men with metastatic castration-resistant prostate cancer. However, response to DTX is generally short-lived, and relapse eventually occurs due to emergence of drug-resistance. We previously established two DTX-resistant prostate cancer cell lines, LNCaPR and C4-2BR, derived from the androgen-dependent LNCaP cell line, and from the LNCaP lineage-derived androgen-independent C4-2B sub-line, respectively. Using an unbiased drug screen, we identify itraconazole (ITZ), an oral antifungal drug, as a compound that can efficiently re-sensitize drug-resistant LNCaPR and C4-2BR prostate cancer cells to DTX treatment. ITZ can re-sensitize multiple DTX-resistant cell models, not only in prostate cancer derived cells, such as PC-3 and DU145, but also in docetaxel-resistant breast cancer cells. This effect is dependent on expression of ATP-binding cassette (ABC) transporter protein ABCB1, also known as P-glycoprotein (P-gp). Molecular modeling of ITZ bound to ABCB1, indicates that ITZ binds tightly to the inward-facing form of ABCB1 thereby inhibiting the transport of DTX. Our results suggest that ITZ may provide a feasible approach to re-sensitization of DTX resistant cells, which would add to the life-prolonging effects of DTX in men with metastatic castration-resistant prostate cancer.
RESUMO
Twenty new compounds, targeting CYP17A1, were synthesized, based on our previous work on a benzimidazole scaffold, and their biological activity evaluated. Inhibition of CYP17A1 is an important modality in the treatment of prostate cancer, which remains the most abundant cancer type in men. The biological assessment included CYP17A1 hydroxylase and lyase inhibition, CYP3A4 and P450 oxidoreductase (POR) inhibition, as well as antiproliferative activity in PC3 prostate cancer cells. The most potent compounds were selected for further analyses including in silico modeling. This combined effort resulted in a compound (comp 2, IC50 1.2 µM, in CYP17A1) with a potency comparable to abiraterone and selectivity towards the other targets tested. In addition, the data provided an understanding of the structure-activity relationship of this novel non-steroidal compound class.
Assuntos
Inibidores Enzimáticos , Neoplasias da Próstata , Esteroide 17-alfa-Hidroxilase , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Humanos , Masculino , Células PC-3 , Neoplasias da Próstata/tratamento farmacológico , Neoplasias da Próstata/enzimologia , Esteroide 17-alfa-Hidroxilase/antagonistas & inibidores , Relação Estrutura-AtividadeRESUMO
Metabolic control is mediated by the dynamic assemblies and function of multiple redox enzymes. A key element in these assemblies, the P450 oxidoreductase (POR), donates electrons and selectively activates numerous (>50 in humans and >300 in plants) cytochromes P450 (CYPs) controlling metabolism of drugs, steroids and xenobiotics in humans and natural product biosynthesis in plants. The mechanisms underlying POR-mediated CYP metabolism remain poorly understood and to date no ligand binding has been described to regulate the specificity of POR. Here, using a combination of computational modeling and functional assays, we identify ligands that dock on POR and bias its specificity towards CYP redox partners, across mammal and plant kingdom. Single molecule FRET studies reveal ligand binding to alter POR conformational sampling, which results in biased activation of metabolic cascades in whole cell assays. We propose the model of biased metabolism, a mechanism akin to biased signaling of GPCRs, where ligand binding on POR stabilizes different conformational states that are linked to distinct metabolic outcomes. Biased metabolism may allow designing pathway-specific therapeutics or personalized food suppressing undesired, disease-related, metabolic pathways.
Assuntos
Sistema Enzimático do Citocromo P-450/metabolismo , Ligantes , Redes e Vias Metabólicas , Aromatase/metabolismo , Linhagem Celular , Sistema Enzimático do Citocromo P-450/genética , Sistema Enzimático do Citocromo P-450/isolamento & purificação , Ensaios Enzimáticos , Transferência Ressonante de Energia de Fluorescência , Humanos , Lipossomos/metabolismo , Simulação de Acoplamento Molecular , Ligação Proteica , Estrutura Terciária de Proteína , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Imagem Individual de Molécula , Esteroide 17-alfa-Hidroxilase/metabolismo , Esteroide 21-Hidroxilase/metabolismo , Especificidade por SubstratoRESUMO
PTR2/POT/NPF are a family of primarily proton coupled transporters that belong to the major facilitator super family and are found across most kingdoms of life. They are involved in uptake of nutrients, hormones, ions and several orally administered drug molecules. A wealth of structural and functional data is available for this family; the similarity between the protein structural features have been discussed and investigated in detail on several occasions, however there are no reports on the unification of substrate information. In order to fill this gap, we have collected information about substrates across the entire PTR2/POT/NPF family in order to provide key insights into what makes a molecule a substrate and whether there are common features among confirmed substrates. This review will be of particular interest for researchers in the field trying to probe the mechanisms responsible for the different selectivity of these transporters at a molecular resolution, and to design novel substrates.
Assuntos
Proteínas de Membrana Transportadoras , Animais , Transporte Biológico , Humanos , Proteínas de Membrana Transportadoras/química , Proteínas de Membrana Transportadoras/genética , Proteínas de Membrana Transportadoras/metabolismo , Especificidade por SubstratoRESUMO
The aim of this project was to investigate the endocrine disrupting effects of three γ-aminobutyric acid type A receptor (GABAAR) agonists, diazepam (DZ), oxazepam (OX) and alprazolam (AL) using the steroidogenic in vitro H295R cell line assay, a recombinant CYP17A1 assay, qPCR analysis and computational modelling. Similar effects for DZ and OX on the steroidogenesis were observed in the H295R experiment at therapeutically relevant concentrations. Progestagens and corticosteroids were increased up to 10 fold and androgens were decreased indicating CYP17A1 lyase inhibition. For DZ the inhibition on both the hydroxylase and lyase was confirmed by the recombinant CYP17A1 assay, whereas OX did not appear to directly affect the recombinant CYP17A1 enzyme. Androgens were decreased when exposing the H295R cells to AL, indicating a CYP17A1 lyase inhibition. However, this was not confirmed by the recombinant CYP17A1 assay but a down-regulation in gene expression was observed for StAR and CYP17A1. The present study showed that the three investigated benzodiazepines (BZDs) are rather potent endocrine disruptors in vitro, exerting endocrine effects close the therapeutic Cmax. Both direct and indirect effects on steroidogenesis were observed, but molecular modelling indicated no direct interactions between the heme group in the steroidogenic CYP enzymes and the unique diazepin structure. In contrast, physicochemical properties such as high log P, structure and molecular weight similar to that of steroids appeared to influence the endocrine disrupting abilities of the investigated pharmaceuticals in vitro. Docking of the three BZDs in CYP17A1 and CYP21A2 confirmed that shape complementarity and hydrophobic effects seem to determine the binding modes.
Assuntos
Benzodiazepinas/química , Disruptores Endócrinos/química , Esteroide 17-alfa-Hidroxilase/química , Esteroide 21-Hidroxilase/química , Esteroides/biossíntese , Corticosteroides/química , Corticosteroides/farmacologia , Glândulas Suprarrenais/efeitos dos fármacos , Alprazolam/química , Alprazolam/farmacologia , Androgênios/genética , Benzodiazepinas/farmacologia , Diazepam/química , Diazepam/farmacologia , Disruptores Endócrinos/farmacologia , Humanos , Simulação de Acoplamento Molecular , Oxazepam/química , Oxazepam/farmacologia , Receptores Androgênicos/química , Receptores Androgênicos/genética , Receptores de GABA-A/química , Receptores de GABA-A/genética , Esteroide 17-alfa-Hidroxilase/antagonistas & inibidores , Esteroide 17-alfa-Hidroxilase/genética , Esteroide 21-Hidroxilase/antagonistas & inibidores , Esteroide 21-Hidroxilase/genética , Esteroides/químicaRESUMO
The current study presents the design, synthesis, and evaluation of novel cytochrome P450 17A1 (CYP17A1) ligands. CYP17A1 is a key enzyme in the steroidogenic pathway that produces androgens among other steroids, and it is implicated in prostate cancer. The obtained compounds are potent enzyme inhibitors (sub µM) with antiproliferative activity in prostate cancer cell lines. The binding mode of these compounds is also discussed.
Assuntos
Antineoplásicos/farmacologia , Inibidores Enzimáticos/farmacologia , Neoplasias da Próstata/tratamento farmacológico , Esteroide 17-alfa-Hidroxilase/antagonistas & inibidores , Androgênios/metabolismo , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Humanos , Masculino , Células PC-3 , Neoplasias da Próstata/metabolismoRESUMO
Based on recent in vitro data, a relatively large number of the plant nitrate transporter 1/peptide transporter family (NPF) proteins have been suggested to function as gibberellic acid (GA) transporters. Most GA transporting NPF proteins also appear to transport other structurally unrelated phytohormones or metabolites. Several of the GAs used in previous in vitro assays are membrane permeable weak organic acids whose movement across membranes are influenced by the pH-sensitive ion-trap mechanism. Moreover, a large proportion of in vitro GA transport activities have been demonstrated indirectly via long-term yeast-based GA-dependent growth assays that are limited to detecting transport of bioactive GAs. Thus, there is a need for an optimized transport assay for identifying and characterizing GA transport. Here, we develop an improved transport assay in Xenopus laevis oocytes, wherein we directly measure movement of six different GAs across oocyte membranes over short time. We show that membrane permeability of GAs in oocytes can be predicted based on number of oxygen atoms and that several GAs do not diffuse over membranes regardless of changes in pH values. In addition, we show that small changes in internal cellular pH can result in strongly altered distribution of membrane permeable phytohormones. This prompts caution when interpreting heterologous transport activities. We use our transport assay to screen all Arabidopsis thaliana NPF proteins for transport activity towards six GAs (two membrane permeable and four non-permeable). The results presented here, significantly reduce the number of bona fide NPF GA transporters in Arabidopsis and narrow the activity to fewer subclades within the family. Furthermore, to gain first insight into the molecular determinants of substrate specificities toward organic molecules transported in the NPF, we charted all surface exposed amino acid residues in the substrate-binding cavity and correlated them to GA transport. This analysis suggests distinct residues within the substrate-binding cavity that are shared between GA transporting NPF proteins; the potential roles of these residues in determining substrate specificity are discussed.
RESUMO
The bacterial Cytochrome P450 (CYP) BM3 (CYP102A1) is one of the most active CYP isoforms. BM3 mutants can serve as a model for human drug-metabolizing CYPs and/or as biocatalyst for selective formation of drug metabolites. Hence, molecular and computational biologists have in the last two decades shown strong interest in the discovery and design of novel BM3 variants with optimized activity and selectivity for substrate conversion. This led e.g. to the discovery of mutant M11 that is able to metabolize a variety of drugs and drug-like compounds with relatively high activity. In order to further improve our understanding of CYP binding and reactions, we performed a co-crystallization study of mutant M11 and report here the three-dimensional structure M11 in complex with dithiothreitol (DTT) at a resolution of 2.16 Å. The structure shows that DTT can coordinate to the Fe atom in the heme group. UV/Vis spectroscopy and molecular dynamics simulation studies underline this finding and as first structure of the CYP BM3 mutant M11 in complex with a ligand, it offers a basis for structure-based design of novel mutants.
Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Sistema Enzimático do Citocromo P-450/química , Sistema Enzimático do Citocromo P-450/genética , Ditiotreitol/química , NADPH-Ferri-Hemoproteína Redutase/química , NADPH-Ferri-Hemoproteína Redutase/genética , Substituição de Aminoácidos , Proteínas de Bactérias/metabolismo , Cristalografia por Raios X , Sistema Enzimático do Citocromo P-450/metabolismo , Ditiotreitol/metabolismo , Desenho de Fármacos , Heme/química , Humanos , Ligantes , Simulação de Dinâmica Molecular , Mutagênese Sítio-Dirigida , Mutação , NADPH-Ferri-Hemoproteína Redutase/metabolismo , Preparações Farmacêuticas/metabolismo , Conformação Proteica , Domínios Proteicos , Engenharia de Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Especificidade por SubstratoRESUMO
Aldehyde Oxidase (AO) is an enzyme involved in the metabolism of aldehydes and N-containing heterocyclic compounds. Many drug compounds contain heterocyclic moieties, and AO metabolism has lead to failure of several late-stage drug candidates. Therefore, it is important to take AO-mediated metabolism into account early in the drug discovery process, and thus, to have fast and reliable models to predict the site of metabolism (SOM). We have collected a dataset of 78 substrates of human AO with a total of 89 SOMs and 347 non-SOMs and determined atomic descriptors for each compound. The descriptors comprise NMR shielding and ESP charges from density functional theory (DFT), NMR chemical shift from ChemBioDraw, and Gasteiger charges from RDKit. Additionally, atomic accessibility was considered using 2D-SASA and relative span descriptors from SMARTCyp. Finally, stability of the product, the metabolite, was determined with DFT and also used as a descriptor. All descriptors have AUC larger than 0.75. In particular, descriptors related to the chemical shielding and chemical shift (AUCâ¯=â¯0.96) and ESP charges (AUCâ¯=â¯0.96) proved to be good descriptors. We recommend two simple methods to identify the SOM for a given molecule: 1) use ChemBioDraw to calculate the chemical shift or 2) calculate ESP charges or chemical shift using DFT. The first approach is fast but somewhat difficult to automate, while the second is more time-consuming, but can easily be automated. The two methods predict correctly 93% and 91%, respectively, of the 89 experimentally observed SOMs.
RESUMO
Cytochrome P450 102A1 from Bacillus megaterium (BM3) is a fatty acid hydroxylase that has one of the highest turnover rates of any mono-oxygenase. Recent studies have shown how mutants of BM3 can produce metabolites of known drug compounds similar to those observed in humans. Single-point mutations in the binding pocket change the regioselective metabolism of fenamic acids from aromatic hydroxylation to aliphatic hydroxylation. This study is concerned with the individual contribution from accessibility and reactivity for drug metabolism with a future goal to develop fast methods for prediction. For a BM3 M11 mutant as well as the M11 V87F and M11 V87I mutants, we studied the metabolism of the nonsteroidal anti-inflammatory drugs (NSAIDs) mefenamic acid, meclofenamic acid, tolfenamic acid, and diclofenac. Density functional theory (DFT; B3LYP and B3LYP-D3) calculations for all possible reactions were performed using a porphyrin model reacting with the four substrates. Molecular dynamics (MD) simulations were used to determine the potential sites of metabolism that are accessible. Finally, we combine reactivity and accessibility for each potential site to interpret the experimentally determined metabolism. Generally, the 3 and 5 positions (on the ring containing the acidic substituent) and the 2', 3', and 4' positions are most reactive, whereas 4, 5, 3', and 4' are most accessible. Combining reactivity and accessibility show that the 5, 3', and 4' positions are predicted to be most prone to be metabolized, in agreement with experimentally observed data. Reactivity seems to be the dominant factor in the CYP-mediated metabolism of these NSAIDs, which is consistent with previously published methods based solely on reactivity.
Assuntos
Bacillus megaterium/enzimologia , Sistema Enzimático do Citocromo P-450/metabolismo , Teoria da Densidade Funcional , Simulação de Dinâmica Molecular , Mutação , ortoaminobenzoatos/química , ortoaminobenzoatos/metabolismo , Bacillus megaterium/genética , Sítios de Ligação , Sistema Enzimático do Citocromo P-450/genética , Conformação Molecular , Estereoisomerismo , Especificidade por SubstratoRESUMO
MOTIVATION: Cytochromes P450 are the most important class of drug metabolizing enzymes. Prediction of drug metabolism is important in development of new drugs, to understand and reduce adverse drug reactions and to reduce animal testing. RESULTS: SMARTCyp 3.0 is an updated version of our previous web server for prediction of site-of-metabolism for Cytochrome P450-mediated metabolism, now in Python 3 with increased structural coverage and new features. The SMARTCyp program is a first principle-based method using density functional theory determined activation energies for more than 250 molecules to identify the most likely site-of-metabolism. New features include a similarity measure between the query molecule and the model fragment, a new graphical interface and additional parameters expanding the structural coverage of the SMARTCyp program. AVAILABILITY AND IMPLEMENTATION: The SMARTCyp server is freely available for use on the web at smartcyp.sund.ku.dk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Assuntos
Software , Sistema Enzimático do Citocromo P-450 , OxirreduçãoRESUMO
The potential endocrine disrupting effects of the commonly prescribed anti-epileptic drug lamotrigine (LAM) were investigated using the H295R steroidogenic in vitro assay and computational chemistry methods. The H295R cells were exposed to different concentrations of LAM, and a multi-steroid LC-MS/MS method was applied to quantify the amount of secreted steroid hormones. LAM affected several steroid hormones in the steroidogenesis at therapeutic concentrations. All progestagens as well as 11-deoxycorticosterone and corticosterone increased 100-200% with increasing concentrations of LAM suggesting a selective inhibitory effect of LAM on CYP17A1, in particular on the lyase reaction. Recombinant CYP17A1 assay confirmed the competitive inhibition of LAM toward the enzyme with IC50 values of 619 and 764 µM for the lyase and the hydroxylase reaction, respectively. Levels of androstenedione and testosterone decreased at LAM concentrations above the therapeutic concentration range. The ability of LAM to bind to CYP17A1, CYP19A1, and CYP21A2 was investigated using docking and molecular dynamics simulations. This in silico study showed that LAM was able to bind directly to the heme iron in the active site of CYP17A1, but not CYP21A2, thus supporting the results of the in vitro studies. The molecular dynamics simulations also suggested binding of LAM to the heme iron in the CYP19A1 active site. No inhibition of the aromatase enzyme was, however, observed in the H295R assay. This could be due to a sequential effect within the steroidogenesis caused by the inhibition of CYP17A1, which reduced the amounts of androgens available for CYP19A1.
Assuntos
Anticonvulsivantes/farmacologia , Inibidores da Aromatase/farmacologia , Aromatase/metabolismo , Lamotrigina/farmacologia , Anticonvulsivantes/química , Aromatase/química , Inibidores da Aromatase/química , Domínio Catalítico , Linhagem Celular , Disruptores Endócrinos/química , Disruptores Endócrinos/farmacologia , Humanos , Técnicas In Vitro , Lamotrigina/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Esteroides/biossínteseRESUMO
Ionotropic glutamate receptors (iGluRs) are responsible for most of the fast excitatory communication between neurons in our brain. The GluD2 receptor is a puzzling member of the iGluR family: It is involved in synaptic plasticity, plays a role in human diseases, e.g. ataxia, binds glycine and D-serine with low affinity, yet no ligand has been discovered so far that can activate its ion channel. In this study, we show that the hinge region connecting the two subdomains of the GluD2 ligand-binding domain is responsible for the low affinity of D-serine, by analysing GluD2 mutants with electrophysiology, isothermal titration calorimetry and molecular dynamics calculations. The hinge region is highly variable among iGluRs and fine-tunes gating activity, suggesting that in GluD2 this region has evolved to only respond to micromolar concentrations of D-serine.