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1.
Mol Pharmacol ; 99(3): 184-196, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33483427

RESUMEN

The HIV protease inhibitor nelfinavir is currently being analyzed for repurposing as an anticancer drug for many different cancers because it exerts manifold off-target protein interactions, finally resulting in cancer cell death. Xenosensing pregnane X receptor (PXR), which also participates in the control of cancer cell proliferation and apoptosis, was previously shown to be activated by nelfinavir; however, the exact molecular mechanism is still unknown. The present study addresses the effects of nelfinavir and its major and pharmacologically active metabolite nelfinavir hydroxy-tert-butylamide (M8) on PXR to elucidate the underlying molecular mechanism. Molecular docking suggested direct binding to the PXR ligand-binding domain, which was confirmed experimentally by limited proteolytic digestion and competitive ligand-binding assays. Concentration-response analyses using cellular transactivation assays identified nelfinavir and M8 as partial agonists with EC50 values of 0.9 and 7.3 µM and competitive antagonists of rifampin-dependent induction with IC50 values of 7.5 and 25.3 µM, respectively. Antagonism exclusively resulted from binding into the PXR ligand-binding pocket. Impaired coactivator recruitment by nelfinavir as compared with the full agonist rifampin proved to be the underlying mechanism of both effects on PXR. Physiologic relevance of nelfinavir-dependent modulation of PXR activity was investigated in respectively treated primary human hepatocytes, which showed differential induction of PXR target genes and antagonism of rifampin-induced ABCB1 and CYP3A4 gene expression. In conclusion, we elucidate here the molecular mechanism of nelfinavir interaction with PXR. It is hypothesized that modulation of PXR activity may impact the anticancer effects of nelfinavir. SIGNIFICANCE STATEMENT: Nelfinavir, which is being investigated for repurposing as an anticancer medication, is shown here to directly bind to human pregnane X receptor (PXR) and thereby act as a partial agonist and competitive antagonist. Its major metabolite nelfinavir hydroxy-tert-butylamide exerts the same effects, which are based on impaired coactivator recruitment. Nelfinavir anticancer activity may involve modulation of PXR, which itself is discussed as a therapeutic target in cancer therapy and for the reversal of chemoresistance.


Asunto(s)
Hepatocitos/metabolismo , Nelfinavir/análogos & derivados , Nelfinavir/farmacología , Receptor X de Pregnano/metabolismo , Subfamilia B de Transportador de Casetes de Unión a ATP/genética , Sitios de Unión , Citocromo P-450 CYP3A/genética , Relación Dosis-Respuesta a Droga , Regulación de la Expresión Génica/efectos de los fármacos , Células Hep G2 , Hepatocitos/citología , Hepatocitos/efectos de los fármacos , Humanos , Modelos Moleculares , Conformación Molecular , Simulación del Acoplamiento Molecular , Nelfinavir/química , Receptor X de Pregnano/agonistas , Receptor X de Pregnano/antagonistas & inhibidores , Receptor X de Pregnano/química , Cultivo Primario de Células
2.
J Chem Inf Model ; 60(12): 6544-6554, 2020 12 28.
Artículo en Inglés | MEDLINE | ID: mdl-33289563

RESUMEN

Fragment-based drug design is a popular approach in drug discovery, which makes use of computational methods such as molecular docking. To assess fragment placement performance of molecular docking programs, we constructed LEADS-FRAG, a benchmark data set containing 93 high-quality protein-fragment complexes that were selected from the Protein Data Bank using a rational and unbiased process. The data set contains fully prepared protein and fragment structures and is publicly available. Moreover, we used LEADS-FRAG for evaluating the small-molecule docking programs AutoDock, AutoDock Vina, FlexX, and GOLD for their fragment docking performance. GOLD in combination with the scoring function ChemPLP and AutoDock Vina performed best and generated near-native conformations (root mean square deviation <1.5 Å) for more than 50% of the data set considering the top-ranked docking pose. Taking into account all docking poses, the tested programs generated near-native conformations for up to 86% of the fragments in LEADS-FRAG. By rescoring all docking poses with the GOLD scoring functions and the Protein-Ligand Informatics force field, the number of near-native conformations increased up to 40% with respect to the top-rescored poses. Our results show that conventional small-molecule docking programs achieve a satisfactory fragment docking performance when utilizing rescoring.


Asunto(s)
Benchmarking , Programas Informáticos , Ligandos , Simulación del Acoplamiento Molecular , Unión Proteica
3.
Arch Toxicol ; 93(8): 2247-2264, 2019 08.
Artículo en Inglés | MEDLINE | ID: mdl-31312845

RESUMEN

Prediction of drug interactions, based on the induction of drug disposition, calls for the identification of chemicals, which activate xenosensing nuclear receptors. Constitutive androstane receptor (CAR) is one of the major human xenosensors; however, the constitutive activity of its reference variant CAR1 in immortalized cell lines complicates the identification of agonists. The exclusively ligand-dependent isoform CAR3 represents an obvious alternative for screening of CAR agonists. As CAR3 is even more abundant in human liver than CAR1, identification of its agonists is also of pharmacological value in its own right. We here established a cellular high-throughput screening assay for CAR3 to identify ligands of this isoform and to analyse its suitability for identifying CAR ligands in general. Proof-of-concept screening of 2054 drug-like compounds at 10 µM resulted in the identification of novel CAR3 agonists. The CAR3 assay proved to detect the previously described CAR1 ligands in the screened libraries. However, we failed to detect CAR3-selective compounds, as the four novel agonists, which were selected for further investigations, all proved to activate CAR1 in different cellular and in vitro assays. In primary human hepatocytes, the compounds preferentially induced the expression of the prototypical CAR target gene CYP2B6. Failure to identify CAR3-selective compounds was investigated by molecular modelling, which showed that the isoform-specific insertion of five amino acids did not impact on the ligand binding pocket but only on heterodimerization with retinoid X receptor. In conclusion, we demonstrate here the usability of CAR3 for screening compound libraries for the presence of CAR agonists.


Asunto(s)
Hepatocitos/efectos de los fármacos , Ensayos Analíticos de Alto Rendimiento/métodos , Receptores Citoplasmáticos y Nucleares/agonistas , Receptores Citoplasmáticos y Nucleares/química , Núcleo Celular/efectos de los fármacos , Núcleo Celular/metabolismo , Clopidogrel/farmacología , Receptor de Androstano Constitutivo , Citocromo P-450 CYP2B6/genética , Regulación de la Expresión Génica/efectos de los fármacos , Células HEK293 , Hepatocitos/fisiología , Humanos , Modelos Moleculares , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Prueba de Estudio Conceptual , Isoformas de Proteínas , Transporte de Proteínas/efectos de los fármacos , Receptores Citoplasmáticos y Nucleares/metabolismo , Receptores X Retinoide/química , Receptores X Retinoide/metabolismo
4.
Int J Mol Sci ; 20(11)2019 May 31.
Artículo en Inglés | MEDLINE | ID: mdl-31159170

RESUMEN

The serine protease Caseinolytic protease subunit P (ClpP) plays an important role for protein homeostasis in bacteria and contributes to various developmental processes, as well as virulence. Therefore, ClpP is considered as a potential drug target in Gram-positive and Gram-negative bacteria. In this study, we utilized a biochemical assay to screen several small molecule libraries of approved and investigational drugs for Escherichia coli ClpP inhibitors. The approved drugs bortezomib, cefmetazole, cisplatin, as well as the investigational drug cDPCP, and the protease inhibitor 3,4-dichloroisocoumarin (3,4-DIC) emerged as ClpP inhibitors with IC50 values ranging between 0.04 and 31 µM. Compound profiling of the inhibitors revealed cefmetazole and cisplatin not to inhibit the serine protease bovine α-chymotrypsin, and for cefmetazole no cytotoxicity against three human cell lines was detected. Surface plasmon resonance studies demonstrated all novel ClpP inhibitors to bind covalently to ClpP. Investigation of the potential binding mode for cefmetazole using molecular docking suggested a dual covalent binding to Ser97 and Thr168. While only the antibiotic cefmetazole demonstrated an intrinsic antibacterial effect, cDPCP clearly delayed the bacterial growth recovery time upon chemically induced nitric oxide stress in a ClpP-dependent manner.


Asunto(s)
Antibacterianos/química , Antibacterianos/farmacología , Descubrimiento de Drogas , Endopeptidasa Clp/antagonistas & inhibidores , Proteínas de Escherichia coli/antagonistas & inhibidores , Inhibidores de Proteasas/química , Inhibidores de Proteasas/farmacología , Antineoplásicos/química , Antineoplásicos/farmacología , Línea Celular Tumoral , Supervivencia Celular/efectos de los fármacos , Relación Dosis-Respuesta a Droga , Descubrimiento de Drogas/métodos , Humanos , Concentración 50 Inhibidora , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Estructura Molecular , Unión Proteica , Conformación Proteica , Relación Estructura-Actividad
5.
Arch Toxicol ; 92(4): 1435-1451, 2018 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-29356861

RESUMEN

Activation of pregnane X receptor (PXR) results in the induction of first-pass metabolism and drug efflux. Hereby, PXR may cause adverse drug reactions or therapeutic failure of drugs. PXR inhibition is thus an attractive option to minimise adverse effects or to improve therapeutic efficiencies; however, only a limited number of antagonists have been identified so far. We performed a cell-based high-throughput screen to identify PXR antagonists, using a library of approved and investigational drugs. Two approved drugs, pimecrolimus and pazopanib, emerged as novel potent antagonists of PXR activation, with IC50 values of 1.2 and 4.1 µM, respectively. We further characterised these with respect to receptor specificity, assembly of the PXR ligand-binding domain (LBD) and interactions with co-factors. In vitro and in silico assays were carried out to identify the site(s) of interaction with the PXR LBD. Primary human hepatocytes were used to investigate antagonism of the induction of endogenous PXR target genes. Pimecrolimus and pazopanib did not affect the transcriptional activity of other nuclear receptors. Both induced the release of co-repressor from PXR and likewise interfered with agonist-induced recruitment of co-activator. Cumulative evidence from cellular and in vitro assays, as well as molecular docking, suggested additional or exclusive binding outside the PXR ligand-binding pocket for both. The compounds differentially antagonised the induction of PXR-regulated genes by rifampicin in primary human hepatocytes. In conclusion, we here have identified two approved drugs as novel potent PXR inhibitors with differential receptor interaction profiles and gene selectivity in primary human hepatocytes.


Asunto(s)
Hepatocitos/metabolismo , Receptor X de Pregnano/antagonistas & inhibidores , Pirimidinas/farmacología , Sulfonamidas/farmacología , Tacrolimus/análogos & derivados , Línea Celular , Aprobación de Drogas , Células Hep G2 , Hepatocitos/citología , Humanos , Indazoles , Simulación del Acoplamiento Molecular , Unión Proteica , Pirimidinas/administración & dosificación , Sulfonamidas/administración & dosificación , Tacrolimus/administración & dosificación , Tacrolimus/farmacología
6.
Arch Toxicol ; 91(6): 2375-2390, 2017 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-28289823

RESUMEN

Unintentional activation of xenosensing nuclear receptors pregnane X receptor (PXR) and/or constitutive androstane receptor (CAR) by clinical drug use is known to produce severe side effects in patients, which may be overcome by co-administering antagonists. However, especially antagonizing CAR is hampered by the lack of specific inhibitors, which do not activate PXR. Recently, compounds based on a dibenzazepine carbamate scaffold were identified as potent CAR inhibitors. However, their potential to activate PXR was not thoroughly investigated, even if the lead compound was named "CAR inhibitor not PXR activator 1" (CINPA1). Thus, we performed a comprehensive analysis of the interaction of CINPA1 and four analogs with PXR. Cellular assays were used to investigate intra- and intermolecular interactions and transactivation activity of PXR as a function of the compounds. Modulation of PXR target gene expression was analyzed in primary human hepatocytes. Ligand binding to PXR was investigated by molecular docking and limited proteolytic digestion. We show here that CINPA1 induced the assembly of the PXR ligand-binding domain, released co-repressors from and recruited co-activators to the receptor. CINPA1 and its analogs induced the PXR-dependent activation of a CYP3A4 reporter gene and CINPA1 induced the expression of endogenous cytochrome P450 genes in primary hepatocytes, while not consistently inhibiting CAR-mediated induction. Molecular docking revealed favorable binding of CINPA1 and analogs to the PXR ligand-binding pocket, which was confirmed in vitro. Altogether, our data provide consistent evidence that compounds with a dibenzazepine carbamate scaffold, such as CINPA1 and its four analogs, bind to and activate PXR.


Asunto(s)
Benzazepinas/farmacología , Hepatocitos/efectos de los fármacos , Receptores Citoplasmáticos y Nucleares/antagonistas & inhibidores , Receptores de Esteroides/metabolismo , Benzazepinas/química , Receptor de Androstano Constitutivo , Expresión Génica/efectos de los fármacos , Células Hep G2 , Hepatocitos/metabolismo , Humanos , Ligandos , Simulación del Acoplamiento Molecular , Receptor X de Pregnano , Cultivo Primario de Células , Unión Proteica , Receptores de Esteroides/genética
7.
J Chem Inf Model ; 56(1): 188-200, 2016 Jan 25.
Artículo en Inglés | MEDLINE | ID: mdl-26651532

RESUMEN

With increasing interest in peptide-based therapeutics also the application of computational approaches such as peptide docking has gained more and more attention. In order to assess the suitability of docking programs for peptide placement and to support the development of peptide-specific docking tools, an independently constructed benchmark data set is urgently needed. Here we present the LEADS-PEP benchmark data set for assessing peptide docking performance. Using a rational and unbiased workflow, 53 protein-peptide complexes with peptide lengths ranging from 3 to 12 residues were selected. The data set is publicly accessible at www.leads-x.org . In a second step we evaluated several small molecule docking programs for their potential to reproduce peptide conformations as present in LEADS-PEP. While most tested programs were capable to generate native-like binding modes of small peptides, only Surflex-Dock and AutoDock Vina performed reasonably well for peptides consisting of more than five residues. Rescoring of docking poses with scoring functions ChemPLP, ChemScore, and ASP further increased the number of top-ranked near-native conformations. Our results suggest that small molecule docking programs are a good and fast alternative to specialized peptide docking programs.


Asunto(s)
Simulación del Acoplamiento Molecular/métodos , Oligopéptidos/metabolismo , Secuencia de Aminoácidos , Benchmarking , Oligopéptidos/química , Unión Proteica , Conformación Proteica , Proteínas/química , Proteínas/metabolismo
8.
Arch Pharm (Weinheim) ; 349(2): 91-103, 2016 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-26725082

RESUMEN

The inhibition of cellular factors that are involved in viral replication may be an important alternative to the commonly used strategy of targeting viral enzymes. The guanylhydrazone CNI-1493, a potent inhibitor of the deoxyhypusine synthase (DHS), prevents the activation of the cellular factor eIF-5A and thereby suppresses HIV replication and a number of other diseases. Here, we report on the design, synthesis and biological evaluation of a series of CNI-1493 analogues. The sebacoyl linker in CNI-1493 was replaced by different alkyl or aryl dicarboxylic acids. Most of the tested derivatives suppress HIV-1 replication efficiently in a dose-dependent manner without showing toxic side effects. The unexpected antiviral activity of the rigid derivatives point to a second binding mode as previously assumed for CNI-1493. Moreover, the chemical stability of CNI-1493 was analysed, showing a successive hydrolysis of the imino bonds. By molecular dynamics simulations, the behaviour of the parent CNI-1493 in solution and its interactions with DHS were investigated.


Asunto(s)
Fármacos Anti-VIH/química , VIH-1/efectos de los fármacos , Hidrazonas/química , Oxigenasas de Función Mixta/antagonistas & inhibidores , Fármacos Anti-VIH/síntesis química , Fármacos Anti-VIH/farmacología , Línea Celular , Estabilidad de Medicamentos , VIH-1/fisiología , Humanos , Hidrazonas/síntesis química , Hidrazonas/farmacología , Hidrólisis , Oxigenasas de Función Mixta/química , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Relación Estructura-Actividad , Replicación Viral
9.
ACS Infect Dis ; 10(6): 2172-2182, 2024 Jun 14.
Artículo en Inglés | MEDLINE | ID: mdl-38724014

RESUMEN

Lipoic acid (LA) is an essential cofactor in prokaryotic and eukaryotic organisms, required for the function of several multienzyme complexes such as oxoacid dehydrogenases. Prokaryotes either synthesize LA or salvage it from the environment. The salvage pathway in Staphylococcus aureus includes two lipoate-protein ligases, LplA1 and LplA2, as well as the amidotransferase LipL. In this study, we intended to hijack the salvage pathway by LA analogues that are transferred via LplA2 and LipL to the E2 subunits of various dehydrogenases, thereby resulting in nonfunctional enzymes that eventually impair viability of the bacterium. Initially, a virtual screening campaign was carried out to identify potential LA analogues that bind to LplA2. Three selected compounds affected S. aureus USA300 growth in minimal medium at concentrations ranging from 2.5 to 10 µg/mL. Further analysis of the most potent compound (Lpl-004) revealed its transfer to E2 subunits of dehydrogenase complexes and a negative impact on its functionality. Growth impairment caused by Lpl-004 treatment was restored by adding products of the lipoate-dependent enzyme complexes. In addition, Caenorhabditis elegans infected with LpL-004-treated USA300 demonstrated a significantly expanded lifespan compared to worms infected with untreated bacteria. Our results provide evidence that LA analogues exploiting the LA salvage pathway represent an innovative strategy for the development of novel antimicrobial substances.


Asunto(s)
Antibacterianos , Staphylococcus aureus , Ácido Tióctico , Ácido Tióctico/farmacología , Ácido Tióctico/análogos & derivados , Staphylococcus aureus/efectos de los fármacos , Staphylococcus aureus/enzimología , Staphylococcus aureus/genética , Virulencia , Animales , Antibacterianos/farmacología , Antibacterianos/química , Péptido Sintasas/metabolismo , Péptido Sintasas/genética , Caenorhabditis elegans , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/genética , Infecciones Estafilocócicas/microbiología , Infecciones Estafilocócicas/tratamiento farmacológico
10.
Virus Res ; 343: 199356, 2024 05.
Artículo en Inglés | MEDLINE | ID: mdl-38490582

RESUMEN

Coronaviruses contain one of the largest genomes among the RNA viruses, coding for 14-16 non-structural proteins (nsp) that are involved in proteolytic processing, genome replication and transcription, and four structural proteins that build the core of the mature virion. Due to conservation across coronaviruses, nsps form a group of promising drug targets as their inhibition directly affects viral replication and, therefore, progression of infection. A minimal but fully functional replication and transcription complex was shown to be formed by one RNA-dependent RNA polymerase (nsp12), one nsp7, two nsp8 accessory subunits, and two helicase (nsp13) enzymes. Our approach involved, targeting nsp12 and nsp13 to allow multiple starting point to interfere with virus infection progression. Here we report a combined in-vitro repurposing screening approach, identifying new and confirming reported SARS-CoV-2 nsp12 and nsp13 inhibitors.


Asunto(s)
COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/metabolismo , Reposicionamiento de Medicamentos , ARN Polimerasas Dirigidas por ADN , ADN Helicasas/genética , ADN Helicasas/metabolismo , Proteínas no Estructurales Virales/metabolismo
11.
Biomolecules ; 13(6)2023 06 16.
Artículo en Inglés | MEDLINE | ID: mdl-37371580

RESUMEN

Efflux pumps are a relevant factor in antimicrobial resistance. In E. coli, the tripartite efflux pump AcrAB-TolC removes a chemically diverse set of antibiotics from the bacterium. Therefore, small molecules interfering with efflux pump function are considered adjuvants for improving antimicrobial therapies. Several compounds targeting the periplasmic adapter protein AcrA and the efflux pump AcrB have been identified to act synergistically with different antibiotics. Among those, several 4(3-aminocyclobutyl)pyrimidin-2-amines have been shown to bind to both proteins. In this study, we intended to identify analogs of these substances with improved binding affinity to AcrA using virtual screening followed by experimental validation. While we succeeded in identifying several compounds showing a synergistic effect with erythromycin on E. coli, biophysical studies suggested that 4(3-aminocyclobutyl)pyrimidin-2-amines form colloidal aggregates that do not bind specifically to AcrA. Therefore, these substances are not suited for further development. Our study emphasizes the importance of implementing additional control experiments to identify aggregators among bioactive compounds.


Asunto(s)
Proteínas de Escherichia coli , Proteínas de Transporte de Membrana , Proteínas de Transporte de Membrana/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Periplasma/metabolismo , Antibacterianos/farmacología , Antibacterianos/metabolismo , Proteínas Asociadas a Resistencia a Múltiples Medicamentos/metabolismo
12.
Cells ; 11(8)2022 04 07.
Artículo en Inglés | MEDLINE | ID: mdl-35455933

RESUMEN

The pregnane X receptor (PXR) regulates the metabolism of many xenobiotic and endobiotic substances. In consequence, PXR decreases the efficacy of many small-molecule drugs and induces drug-drug interactions. The prediction of PXR activators with theoretical approaches such as machine learning (ML) proves challenging due to the ligand promiscuity of PXR, which is related to its large and flexible binding pocket. In this work we demonstrate, by the example of random forest models and support vector machines, that classifiers generated following classical training procedures often fail to predict PXR activity for compounds that are dissimilar from those in the training set. We present a novel regularization technique that penalizes the gap between a model's training and validation performance. On a challenging test set, this technique led to improvements in Matthew correlation coefficients (MCCs) by up to 0.21. Using these regularized ML models, we selected 31 compounds that are structurally distinct from known PXR ligands for experimental validation. Twelve of them were confirmed as active in the cellular PXR ligand-binding domain assembly assay and more hits were identified during follow-up studies. Comprehensive analysis of key features of PXR biology conducted for three representative hits confirmed their ability to activate the PXR.


Asunto(s)
Receptores de Esteroides , Ligandos , Aprendizaje Automático , Receptor X de Pregnano , Receptores de Esteroides/metabolismo , Xenobióticos
13.
Biotechnol J ; 17(4): e2100266, 2022 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-35075794

RESUMEN

The production of biopharmaceuticals in engineered plant-based systems is a promising technology that has proven its suitability for the production of various recombinant glyco-proteins that are currently undergoing clinical trials. However, compared to mammalian cell lines, the productivity of plant-based systems still requires further improvement. A major obstacle is the proteolytic degradation of recombinant target proteins by endogenous plant proteases mainly from the subtilisin family of serine proteases. In the present study, the authors screened for putative small molecule inhibitors for subtilases that are secreted from tobacco BY-2 suspension cells using an in silico approach. The effectiveness of the substances identified in this screen was subsequently tested in degradation assays using the human broadly-neutralizing anti-HIV monoclonal antibody 2F5 (mAb2F5) and spent BY-2 culture medium as a model system. Among 16 putative inhibitors identified by in silico studies, three naphthalene sulfonic acid derivatives showed inhibitory activity in in vitro degradation assays and are similar to or even more effective than phenylmethylsulfonyl fluoride (PMSF), a classical inhibitor of serine proteases, which served as positive control.


Asunto(s)
Anticuerpos Anti-VIH , VIH-1 , Animales , Anticuerpos Anti-VIH/metabolismo , Proteína gp41 de Envoltorio del VIH/metabolismo , Humanos , Mamíferos , Proteínas Recombinantes/metabolismo , Serina Proteasas/metabolismo , Nicotiana/genética , Nicotiana/metabolismo
14.
Cancers (Basel) ; 14(15)2022 Jul 30.
Artículo en Inglés | MEDLINE | ID: mdl-35954391

RESUMEN

Drug resistance limits the effectiveness of oesophageal adenocarcinoma (OAC) chemotherapies, leading to a poor prognosis for this disease. Elucidation of the underlying resistance mechanisms is key to enabling the identification of more effective treatments. This study, therefore, aims to identify novel therapeutic and/or chemotherapy sensitising drug targets in OAC. Transcriptional data from a cohort of 273 pre-treatment OAC biopsies, from patients who received neoadjuvant chemotherapy followed by surgical resection, were analysed using gene set enrichment analysis (GSEA) to determine differential gene expression between responding and non-responding OAC tumours. From this, 80 genes were selected for high-throughput siRNA screening in OAC cell lines with or without standard chemotherapy treatment. In parallel, cell viability assays were performed using a panel of FDA-approved drugs and combination index (CI) values were calculated to evaluate drug synergy with standard chemotherapy. Mechanisms of synergy were investigated using western blot, propidium iodide flow cytometry, and proliferation assays. Taken together, the screens identified that targeting Src, using either siRNA or the small molecule inhibitor dasatinib, enhanced the efficacy of chemotherapy in OAC cells. Further in vitro functional analysis confirmed Src inhibition to be synergistic with standard OAC chemotherapies, 5-fluorouracil (5-FU), and cisplatin (CDDP). In conclusion, a compound screen together with a functional genomic approach identified Src as a potential chemosensitising target in OAC, which could be assessed in a clinical study for poor prognosis OAC patients.

15.
J Mol Recognit ; 24(5): 875-82, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-21812062

RESUMEN

The constitutive androstane receptor (CAR) possesses, unlike most other nuclear receptors, a pronounced basal activity in vitro whose structural basis is still not fully understood. Using comparative molecular dynamics simulations of CAR X-ray crystal structures, we evaluated the molecular basis for constitutive activity and ligand-dependent receptor activation. Our results suggest that a combination of van der Waals interactions and hydrogen bonds is required to maintain the activation helix in the active conformation also in absence of a ligand. Furthermore, we identified conformational rearrangements within the ligand-binding pocket upon agonist binding and an influence of CAR inducers pregnanedione and CITCO on the helical conformation of the activation helix. Based on the results a model for ligand-dependent CAR activation is suggested.


Asunto(s)
Simulación de Dinámica Molecular , Receptores Citoplasmáticos y Nucleares/química , Receptores Citoplasmáticos y Nucleares/metabolismo , Receptor de Androstano Constitutivo , Cristalografía por Rayos X , Humanos , Unión Proteica
16.
Mol Pharm ; 8(6): 2424-33, 2011 Dec 05.
Artículo en Inglés | MEDLINE | ID: mdl-22044162

RESUMEN

The human constitutive androstane receptor (CAR, NR1I3) is one of the key regulators of xenobiotic and endobiotic metabolism. The unique properties of human CAR, such as the high constitutive activity and the complexity of signaling, as well as the lack of functional and predictive cell-based assays to study the properties of the receptor, have hindered the discovery of selective human CAR ligands. Here we report a novel human CAR inverse agonist, 1-[(2-methylbenzofuran-3-yl)methyl]-3-(thiophen-2-ylmethyl) urea (S07662), which suppresses human CAR activity, recruits the corepressor NCoR in cell-based assays, and attenuates the phenytoin- and 6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime (CITCO)-induced expression of CYP2B6 mRNA in human primary hepatocytes. The properties of S07662 are also compared with those of known human CAR inverse agonists by using an array of different in vitro and in silico assays. The identified compound S07662 can be used as a chemical tool to study the biological functions of human CAR and also as a starting point for the development of new drugs for various conditions involving the receptor.


Asunto(s)
Descubrimiento de Drogas , Compuestos de Metilurea/química , Receptores Citoplasmáticos y Nucleares/agonistas , Tiofenos/química , Animales , Antineoplásicos/química , Línea Celular Tumoral , Receptor de Androstano Constitutivo , Humanos , Isoquinolinas/química , Modelos Moleculares , Simulación de Dinámica Molecular
17.
Sci Total Environ ; 717: 134743, 2020 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-31836225

RESUMEN

Bisphenol A (BPA) is a high production volume chemical with a broad application spectrum. As an endocrine disrupting chemical, mainly by modulation of nuclear receptors (NRs), BPA has an adverse impact on organisms and is identified as a substance of very high concern under the European REACH regulation. Various BPA substitution candidates have been developed in recent years, however, information concerning the endocrine disrupting potential of these substances is still incomplete or missing. In this study, we intended to investigate the endocrine potential of BPA substitution candidates used in environmentally relevant applications such as thermal paper or epoxy resins. Based on an extensive literature and patent search, 33 environmentally relevant BPA substitution candidates were identified. In order to evaluate the endocrine potential of the BPA replacements, a screening cascade consisting of biochemical and cell-based assays was employed to investigate substance binding to the NRs estrogen receptor α and ß, as well as androgen receptor, co-activator recruitment and NR-mediated reporter gene activation. In addition, a computational docking approach for retrospective prediction of receptor binding was carried out. Our results show that some BPA substitution candidates, for which so far no or only very few data were available, possess a substantial endocrine disrupting potential (TDP, BPZ), while several substances (BPS, D-8, DD70, DMP-OH, TBSA, D4, CBDO, ISO, VITC, DPA, and DOPO) did not reveal any NR binding.


Asunto(s)
Compuestos de Bencidrilo/química , Fenoles/química , Disruptores Endocrinos , Receptores Androgénicos , Estudios Retrospectivos
18.
J Biomol Struct Dyn ; 37(17): 4651-4657, 2019 10.
Artículo en Inglés | MEDLINE | ID: mdl-30582418

RESUMEN

The nuclear receptor Nurr1 (NR4A2) has been identified as a potential target for the treatment of Parkinson's disease. In contrast to most other nuclear receptors, the X-ray crystal structure of the Nurr1 ligand-binding domain (LBD) lacks any ligand-binding pocket (LBP). However, NMR spectroscopy measurements have revealed that the known Nurr1 agonist docosahexaenoic acid (DHA) binds to a region within the LBD that corresponds to the classical NR ligand-binding pocket (LBP). In order to investigate the structural dynamics of the Nurr1 LBD and to study potential LBP formation, the conformational space of the receptor was sampled using a molecular dynamics (MD) simulation. Docking of DHA into 50,000 LBD structures extracted from the simulation revealed the existence of a transient LBP that is capable to fully harbor the compound. The location of the identified pocket overlaps with the ligand-binding site suggested by NMR experiments. Structural analysis of the protein-ligand complex showed that only modest structural rearrangements within the Nurr1 LBD are required for LBP formation. These findings may support structure-based drug discovery campaigns for the development of receptor-specific agonists.


Asunto(s)
Simulación de Dinámica Molecular , Miembro 2 del Grupo A de la Subfamilia 4 de Receptores Nucleares/química , Sitios de Unión , Cristalografía por Rayos X , Ácidos Docosahexaenoicos/química , Ligandos , Simulación del Acoplamiento Molecular , Dominios Proteicos , Homología Estructural de Proteína
19.
J Med Chem ; 62(2): 774-797, 2019 01 24.
Artículo en Inglés | MEDLINE | ID: mdl-30571121

RESUMEN

Increased Gram-negative bacteria resistance to antibiotics is becoming a global problem, and new classes of antibiotics with novel mechanisms of action are required. The caseinolytic protease subunit P (ClpP) is a serine protease conserved among bacteria that is considered as an interesting drug target. ClpP function is involved in protein turnover and homeostasis, stress response, and virulence among other processes. The focus of this study was to identify new inhibitors of Escherichia coli ClpP and to understand their mode of action. A focused library of serine protease inhibitors based on diaryl phosphonate warheads was tested for ClpP inhibition, and a chemical exploration around the hit compounds was conducted. Altogether, 14 new potent inhibitors of E. coli ClpP were identified. Compounds 85 and 92 emerged as most interesting compounds from this study due to their potency and, respectively, to its moderate but consistent antibacterial properties as well as the favorable cytotoxicity profile.


Asunto(s)
Endopeptidasa Clp/antagonistas & inhibidores , Proteínas de Escherichia coli/antagonistas & inhibidores , Escherichia coli/enzimología , Organofosfonatos/química , Inhibidores de Serina Proteinasa/química , Antibacterianos/química , Antibacterianos/metabolismo , Antibacterianos/farmacología , Sitios de Unión , Compuestos de Bifenilo/química , Endopeptidasa Clp/metabolismo , Escherichia coli/efectos de los fármacos , Proteínas de Escherichia coli/metabolismo , Concentración 50 Inhibidora , Simulación del Acoplamiento Molecular , Organofosfonatos/metabolismo , Organofosfonatos/farmacología , Estructura Terciaria de Proteína , Inhibidores de Serina Proteinasa/metabolismo , Inhibidores de Serina Proteinasa/farmacología , Relación Estructura-Actividad
20.
Cell Chem Biol ; 26(9): 1295-1305.e6, 2019 09 19.
Artículo en Inglés | MEDLINE | ID: mdl-31353319

RESUMEN

Aberrant activation of caspase-6 (C6) in the absence of other hallmarks of apoptosis has been demonstrated in cells and tissues from patients with Huntington disease (HD) and animal models. C6 activity correlates with disease progression in patients with HD and the cleavage of mutant huntingtin (mHTT) protein is thought to strongly contribute to disease pathogenesis. Here we show that the mHTT1-586 fragment generated by C6 cleavage interacts with the zymogen form of the enzyme, stabilizing a conformation that contains an active site and is prone to full activation. This shift toward enhanced activity can be prevented by a small-molecule inhibitor that blocks the interaction between C6 and mHTT1-586. Molecular docking studies suggest that the inhibitor binds an allosteric site in the C6 zymogen. The interaction of mHTT1-586 with C6 may therefore promote a self-reinforcing, feedforward cycle of C6 zymogen activation and mHTT cleavage driving HD pathogenesis.


Asunto(s)
Caspasa 6/metabolismo , Proteína Huntingtina/genética , Enfermedad de Huntington/metabolismo , Regulación Alostérica/genética , Animales , Apoptosis , Células COS , Caspasa 6/fisiología , Chlorocebus aethiops , Proteína Huntingtina/metabolismo , Enfermedad de Huntington/patología , Simulación del Acoplamiento Molecular/métodos , Proteínas del Tejido Nervioso/metabolismo , Neuronas/metabolismo , Proteínas Nucleares/metabolismo
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