Discovery of a Highly Active Ligand of Human Pregnane X Receptor: A Case Study from Pharmacophore Modeling and Virtual Screening to “In Vivo” Biological Activity

Lemaire, G.; Benod, Cindy; Nahoum, Virginie; Pillon, Arnaud; Boussioux, Anne‐Marie; Guichou, Jean-François; Subra, Guy; Pascussi, Jean‐Marc; Bourguet, William; Chavanieu, Alain; Balaguer, Patrick

doi:10.1124/mol.106.033415

Cited by 52 publications

(37 citation statements)

References 38 publications

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“…It is also interesting to note that the antagonist SPB00574 (Fig. 2E) is similar in structure to C2BA-6 (differing in a chlorine-substituted ring at the hydroxyl and other chlorine substitutions elsewhere), which was previously reported as a PXR agonist (EC 50 , 1.89 M) (Lemaire et al, 2007). In our study, SPB00574 did not seem to show appreciable PXR agonist activity.…”

Section: Novel Pxr Antagonists 667mentioning

confidence: 51%

“…Conversely, there have been very few attempts to address antagonism at PXR, which could be used to diminish agonist interactions that are unavoidable with some treatments, such as with anticancer therapies and macrolide antibiotics such as rifampicin (Mani et al, 2005). There have however been previous efforts to generate antagonists at the LBD using a crystal structure of PXR with T-0901317 (Xue et al, 2007a), but this proved to be quite difficult to achieve (Lemaire et al, 2007). Yet there is a growing list of large-and small-molecule PXR antagonists that includes , 2 nM; mol.…”

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confidence: 99%

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Computational Discovery of Novel Low Micromolar Human Pregnane X Receptor Antagonists

Ekins

Kholodovych

et al. 2008

Mol Pharmacol

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Very few antagonists have been identified for the human pregnane X receptor (PXR). These molecules may be of use for modulating the effects of therapeutic drugs, which are potent agonists for this receptor (e.g., some anticancer compounds and macrolide antibiotics), with subsequent effects on transcriptional regulation of xenobiotic metabolism and transporter genes. A recent novel pharmacophore for PXR antagonists was developed using three azoles and consisted of two hydrogen bond acceptor regions and two hydrophobic features. This pharmacophore also suggested an overall small binding site that was identified on the outer surface of the receptor at the AF-2 site and validated by docking studies. Using computational approaches to search libraries of known drugs or commercially available molecules is preferred over random screening. We have now described several new smaller antagonists of PXR discovered with the antagonist pharmacophore with in vitro activity in the low micromolar range [S-p-tolyl 3Ј,5-dimethyl-3,5Ј-biisoxazole-4Ј-carbothioate (SPB03255) (IC 50 , 6.3 M) and 4-(3-chlorophenyl)-5-(2,4-dichlorobenzylthio)-4H-1,2,4-triazol-3-ol (SPB00574) (IC 50 , 24.8 M)]. We have also used our computational pharmacophore and docking tools to suggest that most of the known PXR antagonists, such as coumestrol and sulforaphane, could also interact on the outer surface of PXR at the AF-2 domain. The involvement of this domain was also suggested by further site-directed mutagenesis work. We have additionally described an FDA approved prodrug, leflunomide (IC 50 , 6.8 M), that seems to be a PXR antagonist in vitro. These observations are important for predicting whether further molecules may interact with PXR as antagonists in vivo with potential therapeutic applications.Our knowledge of ligand-protein interactions for some of the nuclear hormone receptors is in the nascent stages. This has downstream implications for understanding, predicting and modulating the potential xenobiotic and environmental molecule effects on transcription of key genes in human. For example, the pregnane X receptor (PXR; NR1I2; also known as SXR or PAR) regulates multiple genes, including the enzymes CYP3A4 (Bertilsson et al., 1998;Blumberg et al., 1998;Kliewer et al., 1998), CYP2B6 (Goodwin et al., 2001, and CYP2C9 as well as the transporter P-glycoprotein (ABCB1) (Synold et al., 2001) and others. There is a very broad structural diversity in the molecules that bind to human PXR from bile salts (Schuetz and Strom, 2001;Krasowski et al., 2005) to anticancer compounds (Mani et al., 2005;Ekins et al., 2007). Several X-ray crystal structures of the ligand binding domain (LBD) of PXR (Watkins et al., 2001(Watkins et al., , 2002(Watkins et al., , 2003aXue et al., 2007b) have determined that S.E., N.A., V. K., and W.J.W. gratefully acknowledge the support for this work provided by the USEPA-funded Environmental Bioinformatics and Computational Toxicology Center (ebCTC), under STAR Grant number GAD R 832721-010. This work was supported in pa...

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Section: Novel Pxr Antagonists 667mentioning

confidence: 51%

mentioning

confidence: 99%

Computational Discovery of Novel Low Micromolar Human Pregnane X Receptor Antagonists

Ekins

Kholodovych

et al. 2008

Mol Pharmacol

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“…2A). In agreement with our data, PXR ligands such as hyperforin, nifedipine, SR12813, reserpin, o,pЈ-DDT (2,4Ј-DDT), fenvalerate, pesticide oxadiazon, herbicide pretilachlor, steroid 3␣-hydroxy-5␤-pregnane-11,20-dione methanesulfonate, and several other compounds have been shown to be by about 20 to 70% more potent at equimolar concentrations than rifampicin in transient transfection assays with different reporter plasmids of CYP3A4 gene or in transactivation assays with GAL4-PXR LBD (Bertilsson et al, 1998;Moore et al, 2002;Sinz et al, 2006;Lemaire et al, 2007;and others). In our experiments, oxiconazole was by about 60% more potent than rifampicin after 8-h treatment and almost 2-fold more potent after 24-h treatment at the concentration of 20 M in the transient transfection experiment with p3A4-luc, and calculated I max for oxiconazole was higher by 77% than I max for rifampicin ( Fig.…”

Section: Discussionmentioning

confidence: 99%

Azole Antimycotics Differentially Affect Rifampicin-Induced Pregnane X Receptor-Mediated CYP3A4 Gene Expression

Svecova

Vrzal²,

Burýšek³

et al. 2007

Drug Metab Dispos

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We show that oxiconazole is a highly efficacious activator of CYP3A4 transactivation, which could be antagonized by rifampicin in a competitive manner. In addition, we show that activation of the CYP3A4 promoter is a complex process, which is not exclusively determined by azole-PXR interactions, and we suggest that the ability of some azoles to affect recruitment of SRC-1 to PXR modulates their net effects in transactivation of CYP3A4 both in the absence or presence of rifampicin.

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“…Successful induction models combine the crystal structure of nuclear receptor proteins with in silico structural biology (54). For example, the PXR crystal structure and protein indicate that the LBD is hydrophobic with several key polar residues and Compiled from references: (36,81) this information has been used to identify potential ligands (55,56). Evaluation of AhR ligand structures indicates that substrates are planar lipophilic molecules about 6.8×13.7 Å in dimension (57).…”

Section: In Silicomentioning

confidence: 99%

Current Industrial Practices in Assessing CYP450 Enzyme Induction: Preclinical and Clinical

Sinz

Wallace

Sahi³

2008

AAPS J

112

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Abstract. Induction of drug metabolizing enzymes, such as the cytochromes P450 (CYP) is known to cause drug-drug interactions due to increased elimination of co-administered drugs. This increased elimination may lead to significant reduction or complete loss of efficacy of the co-administered drug. Due to the significance of such drug interactions, many pharmaceutical companies employ screening and characterization models which predict CYP enzyme induction to avoid or attenuate the potential for drug interactions with new drug candidates. The most common mechanism of CYP induction is transcriptional gene activation. Activation is mediated by nuclear receptors, such as AhR, CAR, and PXR that function as transcription factors. Early high throughput screening models utilize these nuclear hormone receptors in ligand binding or cell-based transactivation/reporter assays. In addition, immortalized hepatocyte cell lines can be used to assess enzyme induction of specific drug metabolizing enzymes. Cultured primary human hepatocytes, the best established in vitro model for predicting enzyme induction and most accepted by regulatory agencies, is the predominant assay used to evaluate induction of a wide variety of drug metabolizing enzymes. These in vitro models are able to appropriately predict enzyme induction in patients when compared to clinical drug-drug interactions. Finally, transgenic animal models and the cynomolgus monkey have also been shown to recapitulate human enzyme induction and may be appropriate in vivo animal models for predicting human drug interactions.

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Discovery of a Highly Active Ligand of Human Pregnane X Receptor: A Case Study from Pharmacophore Modeling and Virtual Screening to “In Vivo” Biological Activity

Abstract: The human pregnane X receptor (hPXR) is a nuclear receptor that regulates the expression of phase I and II drug-

Cited by 52 publications

References 38 publications

Computational Discovery of Novel Low Micromolar Human Pregnane X Receptor Antagonists

Computational Discovery of Novel Low Micromolar Human Pregnane X Receptor Antagonists

Azole Antimycotics Differentially Affect Rifampicin-Induced Pregnane X Receptor-Mediated CYP3A4 Gene Expression

Current Industrial Practices in Assessing CYP450 Enzyme Induction: Preclinical and Clinical

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