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Schäfer AM, Rysz MA, Schädeli J, Hübscher M, Khosravi H, Fehr M, Seibert I, Potterat O, Smieško M, Meyer Zu Schwabedissen HE. St. John's Wort Formulations Induce Rat CYP3A23-3A1 Independent of Their Hyperforin Content. Mol Pharmacol 2023; 105:14-22. [PMID: 37863663 DOI: 10.1124/molpharm.123.000725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/08/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023] Open
Abstract
The pregnane X receptor (PXR) is a ligand-activated regulator of cytochrome P450 (CYP)3A enzymes. Among the ligands of human PXR is hyperforin, a constituent of St John's wort (SJW) extracts and potent inducer of human CYP3A4. It was the aim of this study to compare the effect of hyperforin and SJW formulations controlled for its content on CYP3A23-3A1 in rats. Hyperiplant was used as it contains a high hyperforin content and Rebalance because it is controlled for a low hyperforin content. In silico analysis revealed a weak hyperforin-rPXR binding affinity, which was further supported in cell-based reporter gene assays showing no hyperforin-mediated reporter activation in presence of rPXR. However, cellular exposure to Hyperiplant and Rebalance transactivated the CYP3A reporter 3.8-fold and 2.8-fold, respectively, and they induced Cyp3a23-3a1 mRNA expression in rat hepatoma cells compared with control 48-fold and 18-fold, respectively. In Wistar rats treated for 10 days with 400 mg/kg of Hyperiplant, we observed 1.8 times the Cyp3a23-3a1 mRNA expression, a 2.6-fold higher CYP3A23-3A1 protein amount, and a 1.6-fold increase in activity compared with controls. For Rebalance we only observed a 1.8-fold hepatic increase of CYP3A23-3A1 protein compared with control animals. Even though there are differing effects on rCyp3a23-3a1/CYP3A23-3A1 in rat liver reflecting the hyperforin content of the SJW extracts, the modulation is most likely not linked to an interaction of hyperforin with rPXR. SIGNIFICANCE STATEMENT: Treatment with St John's wort (SJW) has been reported to affect CYP3A expression and activity in rats. Our comparative study further supports this finding but shows that the pregnane X receptor-ligand hyperforin is not the driving force for changes in rat CYP3A23-3A1 expression and function in vivo and in vitro. Importantly, CYP3A induction mimics findings in humans, but our results suggest that another so far unknown constituent of SJW is responsible for the expression- and function-modifying effects in rat liver.
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Affiliation(s)
- Anima M Schäfer
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Marta A Rysz
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Julia Schädeli
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Michelle Hübscher
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Haleh Khosravi
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Michelle Fehr
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Isabell Seibert
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Olivier Potterat
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Martin Smieško
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Henriette E Meyer Zu Schwabedissen
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
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Kolesnyk S, Prodanchuk M, Zhminko P, Kolianchuk Y, Bubalo N, Odermatt A, Smieško M. A battery of in silico models application for pesticides exerting reproductive health effects: Assessment of performance and prioritization of mechanistic studies. Toxicol In Vitro 2023; 93:105706. [PMID: 37802305 DOI: 10.1016/j.tiv.2023.105706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/12/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023]
Abstract
Given the high attention to endocrine disrupting chemicals (EDC), there is an urgent need for the development of rapid and reliable approaches for the screening of large numbers of chemicals with respect to their endocrine disruption potential. This study aimed at the assessment of the correlation between the predicted results of a battery of in silico tools and the reported observed adverse effects from in vivo reproductive toxicity studies. We used VirtualToxLab (VTL) software and the EndocrineDisruptome (ED) online tool to evaluate the binding affinities to nuclear receptors of 17 pesticides, 7 of which were classified as reprotoxic substances under Regulation (EC) No 1272/2008 on the classification, labelling and packaging of substances and mixtures (CLP). Then, we aligned the results of the in silico modelling with data from ToxCast assays and in vivo reproductive toxicity studies. We combined results from different in silico tools in two different ways to improve the characteristics of their predictive performance. Reproductive toxicity can be caused by various mechanisms; however, in this study, we demonstrated that the use of a battery of in silico tools for assessing the binding to nuclear receptors can be useful for identifying hazardous compounds and for prioritizing further studies.
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Affiliation(s)
- Serhii Kolesnyk
- L.I. Medved's Research Center of Preventive Toxicology, Food and Chemical Safety, Kyiv, Ukraine; Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland; Swiss Centre for Human Applied Toxicology, University of Basel, Missionsstrasse 64, Basel 4055, Switzerland.
| | - Mykola Prodanchuk
- L.I. Medved's Research Center of Preventive Toxicology, Food and Chemical Safety, Kyiv, Ukraine
| | - Petro Zhminko
- L.I. Medved's Research Center of Preventive Toxicology, Food and Chemical Safety, Kyiv, Ukraine
| | - Yana Kolianchuk
- L.I. Medved's Research Center of Preventive Toxicology, Food and Chemical Safety, Kyiv, Ukraine
| | - Nataliia Bubalo
- L.I. Medved's Research Center of Preventive Toxicology, Food and Chemical Safety, Kyiv, Ukraine
| | - Alex Odermatt
- Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland; Swiss Centre for Human Applied Toxicology, University of Basel, Missionsstrasse 64, Basel 4055, Switzerland
| | - Martin Smieško
- Swiss Centre for Human Applied Toxicology, University of Basel, Missionsstrasse 64, Basel 4055, Switzerland; Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland
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Jäger MC, Kędzierski J, Gell V, Wey T, Kollár J, Winter DV, Schuster D, Smieško M, Odermatt A. Virtual screening and biological evaluation to identify pharmaceuticals potentially causing hypertension and hypokalemia by inhibiting steroid 11β-hydroxylase. Toxicol Appl Pharmacol 2023; 475:116638. [PMID: 37499767 DOI: 10.1016/j.taap.2023.116638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
Several drugs were found after their market approval to unexpectedly inhibit adrenal 11β-hydroxylase (CYP11B1)-dependent cortisol synthesis. Known side-effects of CYP11B1 inhibition include hypertension and hypokalemia, due to a feedback activation of adrenal steroidogenesis, leading to supraphysiological concentrations of 11-deoxycortisol and 11-deoxycorticosterone that can activate the mineralocorticoid receptor. This results in potassium excretion and sodium and water retention, ultimately causing hypertension. With the risk known but usually not addressed in preclinical evaluation, this study aimed to identify drugs and drug candidates inhibiting CYP11B1. Two conceptually different virtual screening methods were combined, a pharmacophore based and an induced fit docking approach. Cell-free and cell-based CYP11B1 activity measurements revealed several inhibitors with IC50 values in the nanomolar range. Inhibitors include retinoic acid metabolism blocking agents (RAMBAs), azole antifungals, α2-adrenoceptor ligands, and a farnesyltransferase inhibitor. The active compounds share a nitrogen atom embedded in an aromatic ring system. Structure activity analysis identified the free electron pair of the nitrogen atom as a prerequisite for the drug-enzyme interaction, with its pKa value as an indicator of inhibitory potency. Another important parameter is drug lipophilicity, exemplified by etomidate. Changing its ethyl ester moiety to a more hydrophilic carboxylic acid group dramatically decreased the inhibitory potential, most likely due to less efficient cellular uptake. The presented work successfully combined different in silico and in vitro methods to identify several previously unknown CYP11B1 inhibitors. This workflow facilitates the identification of compounds that inhibit CYP11B1 and therefore pose a risk for inducing hypertension and hypokalemia.
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Affiliation(s)
- Marie-Christin Jäger
- Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland; Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
| | - Jacek Kędzierski
- Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland; Division of Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland.
| | - Victoria Gell
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; Division of Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland.
| | - Tim Wey
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
| | - Jakub Kollár
- Institute of Pharmacy, Department of Pharmaceutical and Medicinal Chemistry, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria.
| | - Denise V Winter
- Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland; Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
| | - Daniela Schuster
- Institute of Pharmacy, Department of Pharmaceutical and Medicinal Chemistry, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria.
| | - Martin Smieško
- Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland; Division of Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland.
| | - Alex Odermatt
- Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland; Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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Kędzierski J, Allard JA, Odermatt A, Smieško M. Assessment of the inhibitory potential of anabolic steroids towards human AKR1D1 by computational methods and in vitro evaluation. Toxicol Lett 2023; 384:1-13. [PMID: 37451653 DOI: 10.1016/j.toxlet.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/21/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Exposure to xenobiotics can adversely affect biochemical reactions, including hepatic bile acid synthesis. Bile acids are essential for dissolving lipophilic compounds in the hydrophilic environment of the gastrointestinal tract. The critical micellar concentration of bile acids depends on the Δ4-reduction stereochemistry, with the 3-oxo-5β-steroid-Δ4-dehydrogenase (AKR1D1) introducing the cis ring A/B conformation. Loss-of-function mutations in AKR1D1 cause hepatic cholestasis, which, if left untreated can progress into steatosis and liver cirrhosis. Furthermore, AKR1D1 is involved in clearing steroids with an A-ring Δ4-double bond. Here, we tested whether anabolic-androgenic steroids (AAS), often taken off-label at high doses, might inhibit AKR1D1, thereby potentially causing hepatotoxicity. A computational molecular model was established and used for virtual screening of the DrugBank database consisting of 2740 molecules, yielding mainly steroidal hits. Fourteen AAS were selected for in vitro evaluation, as such compounds can reach high hepatic concentrations in an abuse situation. Nandrolone, clostebol, methasterone, drostanolone, and methenolone inhibited to various extent the AKR1D1-mediated reduction of testosterone. Molecular modeling suggests that 9 out of 14 investigated AAS are competitive inhibitors. Moreover quantum mechanical calculations show that nadrolone and clostebol are substrates of AKR1D1 with different activation energy barriers for the hydrogen transfer from cofactor to the C5 position affecting their turnover. In this multidisciplinary approach, we established a molecular model of AKR1D1, identified several AAS as inhibitors, and described their binding mode. This approach may be applied to study other classes of inhibitors including non-steroidal compounds.
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Affiliation(s)
- Jacek Kędzierski
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland; Swiss Centre for Human Applied Toxicology, University of Basel, Missionsstrasse 64, Basel 4055, Switzerland
| | - Julien A Allard
- Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland; Swiss Centre for Human Applied Toxicology, University of Basel, Missionsstrasse 64, Basel 4055, Switzerland
| | - Alex Odermatt
- Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland; Swiss Centre for Human Applied Toxicology, University of Basel, Missionsstrasse 64, Basel 4055, Switzerland
| | - Martin Smieško
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland; Swiss Centre for Human Applied Toxicology, University of Basel, Missionsstrasse 64, Basel 4055, Switzerland.
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Wehrli L, Galdadas I, Voirol L, Smieško M, Cambet Y, Jaquet V, Guerrier S, Gervasio FL, Nef S, Rahban R. The action of physiological and synthetic steroids on the calcium channel CatSper in human sperm. Front Cell Dev Biol 2023; 11:1221578. [PMID: 37547474 PMCID: PMC10397409 DOI: 10.3389/fcell.2023.1221578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
The sperm-specific channel CatSper (cation channel of sperm) controls the intracellular Ca2+ concentration ([Ca2+]i) and plays an essential role in sperm function. It is mainly activated by the steroid progesterone (P4) but is also promiscuously activated by a wide range of synthetic and physiological compounds. These compounds include diverse steroids whose action on the channel is so far still controversial. To investigate the effect of these compounds on CatSper and sperm function, we developed a high-throughput screening (HTS) assay to measure changes in [Ca2+]i in human sperm and screened 1,280 approved and off-patent drugs including 90 steroids from the Prestwick chemical library. More than half of the steroids tested (53%) induced an increase in [Ca2+]i and reduced the P4-induced Ca2+ influx in human sperm in a dose-dependent manner. Ten of the most potent steroids (activating and P4-inhibiting) were selected for a detailed analysis of their action on CatSper and their ability to act on sperm acrosome reaction (AR) and penetration in viscous media. We found that these steroids show an inhibitory effect on P4 but not on prostaglandin E1-induced CatSper activation, suggesting that they compete for the same binding site as P4. Pregnenolone, dydrogesterone, epiandrosterone, nandrolone, and dehydroepiandrosterone acetate (DHEA) were found to activate CatSper at physiologically relevant concentrations within the nanomolar range. Like P4, most tested steroids did not significantly affect the AR while stanozolol and estropipate slightly increased sperm penetration into viscous medium. Furthermore, using a hybrid approach integrating pharmacophore analysis and statistical modelling, we were able to screen in silico for steroids that can activate the channel and define the physicochemical and structural properties required for a steroid to exhibit agonist activity against CatSper. Overall, our results indicate that not only physiological but also synthetic steroids can modulate the activity of CatSper with varying potency and if bound to CatSper prior to P4, could impair the timely CatSper activation necessary for proper fertilization to occur.
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Affiliation(s)
- Lydia Wehrli
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- Swiss Centre for Applied Human Toxicology (SCAHT), Basel, Switzerland
| | - Ioannis Galdadas
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Lionel Voirol
- Research Center for Statistics, Geneva School of Economics and Management, University of Geneva, Geneva, Switzerland
| | - Martin Smieško
- Swiss Centre for Applied Human Toxicology (SCAHT), Basel, Switzerland
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Yves Cambet
- Readers, Assay Development and Screening Unit (READS Unit), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Vincent Jaquet
- Readers, Assay Development and Screening Unit (READS Unit), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Stéphane Guerrier
- Research Center for Statistics, Geneva School of Economics and Management, University of Geneva, Geneva, Switzerland
- Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Department of Chemistry, University College London, London, United Kingdom
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- Swiss Centre for Applied Human Toxicology (SCAHT), Basel, Switzerland
| | - Rita Rahban
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- Swiss Centre for Applied Human Toxicology (SCAHT), Basel, Switzerland
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Winker M, Chauveau A, Smieško M, Potterat O, Areesanan A, Zimmermann-Klemd A, Gründemann C. Immunological evaluation of herbal extracts commonly used for treatment of mental diseases during pregnancy. Sci Rep 2023; 13:9630. [PMID: 37316493 DOI: 10.1038/s41598-023-35952-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
Nonpsychotic mental diseases (NMDs) affect approximately 15% of pregnant women in the US. Herbal preparations are perceived a safe alternative to placenta-crossing antidepressants or benzodiazepines in the treatment of nonpsychotic mental diseases. But are these drugs really safe for mother and foetus? This question is of great relevance to physicians and patients. Therefore, this study investigates the influence of St. John's wort, valerian, hops, lavender, and California poppy and their compounds hyperforin and hypericin, protopine, valerenic acid, and valtrate, as well as linalool, on immune modulating effects in vitro. For this purpose a variety of methods was applied to assess the effects on viability and function of human primary lymphocytes. Viability was assessed via spectrometric assessment, flow cytometric detection of cell death markers and comet assay for possible genotoxicity. Functional assessment was conducted via flow cytometric assessment of proliferation, cell cycle and immunophenotyping. For California poppy, lavender, hops, and the compounds protopine and linalool, and valerenic acid, no effect was found on the viability, proliferation, and function of primary human lymphocytes. However, St. John's wort and valerian inhibited the proliferation of primary human lymphocytes. Hyperforin, hypericin, and valtrate inhibited viability, induced apoptosis, and inhibited cell division. Calculated maximum concentration of compounds in the body fluid, as well as calculated concentrations based on pharmacokinetic data from the literature, were low and supported that the observed effects in vitro would probably have no relevance on patients. In-silico analyses comparing the structure of studied substances with the structure of relevant control substances and known immunosuppressants revealed structural similarities of hyperforin and valerenic acid to the glucocorticoids. Valtrate showed structural similarities to the T cells signaling modulating drugs.
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Affiliation(s)
- Moritz Winker
- Translational Complementary Medicine, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Antoine Chauveau
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Martin Smieško
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Olivier Potterat
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Alexander Areesanan
- Translational Complementary Medicine, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Amy Zimmermann-Klemd
- Translational Complementary Medicine, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland.
| | - Carsten Gründemann
- Translational Complementary Medicine, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland.
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Schreier VN, Çörek E, Appenzeller-Herzog C, Brüschweiler BJ, Geueke B, Wilks MF, Schilter B, Muncke J, Simat TJ, Smieško M, Roth N, Odermatt A. Evaluating the food safety and risk assessment evidence-base of polyethylene terephthalate oligomers: A systematic evidence map. Environ Int 2023; 176:107978. [PMID: 37210807 DOI: 10.1016/j.envint.2023.107978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND The presence of polyethylene terephthalate (PET) oligomers in food contact materials (FCMs) is well-documented. Consumers are exposed through their migration into foods and beverages; however, there is no specific guidance for their safety evaluation. OBJECTIVES This systematic evidence map (SEM) aims to identify and organize existing knowledge and associated gaps in hazard and exposure information on 34 PET oligomers to support regulatory decision-making. METHODS The methodology for this SEM was recently registered. A systematic search in bibliographic and gray literature sources was conducted and studies evaluated for inclusion according to the Populations, Exposures, Comparators, Outcomes, and Study type (PECOS) framework. Inclusion criteria were designed to record hazard and exposure information for all 34 PET oligomers and coded into the following evidence streams: human, animal, organism (non-animal), ex vivo, in vitro, in silico, migration, hydrolysis, and absorption, distribution, metabolism, excretion/toxicokinetics/pharmacokinetics (ADME/TK/PK) studies. Relevant information was extracted from eligible studies and synthesized according to the protocol. RESULTS Literature searches yielded 7445 unique records, of which 96 were included. Data comprised migration (560 entries), ADME/TK/PK-related (253 entries), health/bioactivity (98 entries) and very few hydrolysis studies (7 entries). Cyclic oligomers were studied more frequently than linear PET oligomers. In vitro results indicated that hydrolysis of cyclic oligomers generated a mixture of linear oligomers, but not monomers, potentially allowing their absorption in the gastrointestinal tract. Cyclic dimers, linear trimers and the respective smaller oligomers exhibit physico-chemical properties making oral absorption more likely. Information on health/bioactivity effects of oligomers was almost non-existent, except for limited data on mutagenicity. CONCLUSIONS This SEM revealed substantial deficiencies in the available evidence on ADME/TK/PK, hydrolysis, and health/bioactivity effects of PET oligomers, currently preventing appropriate risk assessment. It is essential to develop more systematic and tiered approaches to address the identified research needs and assess the risks of PET oligomers.
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Affiliation(s)
- Verena N Schreier
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland.
| | - Emre Çörek
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland.
| | | | - Beat J Brüschweiler
- Federal Food Safety and Veterinary Office (FSVO), Risk Assessment Division, Bern, Switzerland.
| | - Birgit Geueke
- Food Packaging Forum Foundation, Zurich, Switzerland.
| | - Martin F Wilks
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland.
| | - Benoit Schilter
- Consultant of Food Contact Materials Safety, Lausanne, Switzerland.
| | - Jane Muncke
- Food Packaging Forum Foundation, Zurich, Switzerland.
| | - Thomas J Simat
- Chair of Food Contact Materials, Dresden University of Technology, Dresden, Germany.
| | - Martin Smieško
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland.
| | - Nicolas Roth
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland.
| | - Alex Odermatt
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland.
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Fischer A, Bardakci F, Sellner M, Lill MA, Smieško M. Ligand pathways in estrogen-related receptors. J Biomol Struct Dyn 2023; 41:1639-1648. [PMID: 35068382 DOI: 10.1080/07391102.2022.2027818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The three subtypes of estrogen-related receptors ERRα, ERRβ, and ERRγ are nuclear receptors mediating metabolic processes in various tissues such as the skeletal muscle, fat tissue, bone, and liver. Although the knowledge on their physiological ligands is limited, they have been implicated as drug targets for important indications including diabetes, cardiovascular diseases, and osteoporosis. As in other nuclear receptors, their ligand binding pocket is buried within the core of the receptor and connected to its surrounding by ligand pathways. Here, we investigated these pathways with conventional molecular dynamics as well as metadynamics simulations to reveal their distribution and their capability to facilitate ligand translocation. Dependent on the ERR subtype and the conformational state of the receptor, we could detect different pathways to be favored. Overall, the results suggested pathways IIIa and IIIb to be favored in the agonistic conformation, while antagonists preferred pathways I, II, and V. Along the pathways, the ligands passed different gating mechanisms of the receptor, including groups of protein residues as well as whole secondary structure elements, to leave the binding site. Even though these pathways are suggested to influence ligand specificity of the receptors and their elucidation might advance rational drug design, they have not yet been studied in ERRs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- André Fischer
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Ferhat Bardakci
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Manuel Sellner
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Markus A Lill
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Martin Smieško
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
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9
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Dürr L, Reinhardt JK, Dobrzyński M, Hell T, Smieško M, Pertz O, Hamburger M, Garo E. A Dimerosesquiterpene and Sesquiterpene Lactones from Artemisia argyi Inhibiting Oncogenic PI3K/AKT Signaling in Melanoma Cells. J Nat Prod 2022; 85:2557-2569. [PMID: 36351173 DOI: 10.1021/acs.jnatprod.2c00471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A library of more than 2500 plant extracts was screened for activity on oncogenic signaling in melanoma cells. The ethyl acetate extract from the aerial parts of Artemisia argyi displayed pronounced inhibition of the PI3K/AKT pathway. Active compounds were tracked with the aid of HPLC-based activity profiling, and altogether 21 active compounds were isolated, including one novel dimerosequiterpenoid (1), one new disesquiterpenoid (2), three new guaianolides (3-5), 12 known sesquiterpenoids (6-17), and four known flavonoids (19-22). A new eudesmanolide derivative (13b) was isolated as an artifact formed by methanolysis. Compound 1 is the first adduct comprising a sesquiterpene lactone and a methyl jasmonate moiety. The absolute configurations of compounds 1 and 3-18 were established by comparison of their experimental and calculated ECD spectra. The absolute configuration for 2 was determined by X-ray diffraction analysis. Guaianolide 8 was the most potent sesquiterpene lactone, inhibiting the PI3K/AKT pathway with an IC50 value of 8.9 ± 0.9 μM.
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Affiliation(s)
- Lara Dürr
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Jakob K Reinhardt
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Maciej Dobrzyński
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Tanja Hell
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Martin Smieško
- Division of Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Matthias Hamburger
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Eliane Garo
- Division of Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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10
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Lamers C, Xue X, Smieško M, van Son H, Wagner B, Berger N, Sfyroera G, Gros P, Lambris JD, Ricklin D. Insight into mode-of-action and structural determinants of the compstatin family of clinical complement inhibitors. Nat Commun 2022; 13:5519. [PMID: 36127336 PMCID: PMC9488889 DOI: 10.1038/s41467-022-33003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/17/2022] [Indexed: 12/04/2022] Open
Abstract
With the addition of the compstatin-based complement C3 inhibitor pegcetacoplan, another class of complement targeted therapeutics have recently been approved. Moreover, compstatin derivatives with enhanced pharmacodynamic and pharmacokinetic profiles are in clinical development (e.g., Cp40/AMY-101). Despite this progress, the target binding and inhibitory modes of the compstatin family remain incompletely described. Here, we present the crystal structure of Cp40 complexed with its target C3b at 2.0-Å resolution. Structure-activity-relationship studies rationalize the picomolar affinity and long target residence achieved by lead optimization, and reveal a role for structural water in inhibitor binding. We provide explanations for the narrow species specificity of this drug class and demonstrate distinct target selection modes between clinical compstatin derivatives. Functional studies provide further insight into physiological complement activation and corroborate the mechanism of its compstatin-mediated inhibition. Our study may thereby guide the application of existing and development of next-generation compstatin analogs. Therapeutic modulation of the complement system has gained interest over the past two decades. Here, the authors provide molecular-level insight into the mode-of-action, target selectivity and species specificity of the compstatin family of complement inhibitors, which entered the clinic in 2021.
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Affiliation(s)
- Christina Lamers
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland.,Institute of Drug Discovery, Faculty of Medicine, Leipzig University, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Xiaoguang Xue
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, Utrecht, The Netherlands
| | - Martin Smieško
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Henri van Son
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, Utrecht, The Netherlands
| | - Bea Wagner
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Nadja Berger
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 401 Stellar Chance, 422 Curie Blvd, Philadelphia, 19104, PA, USA
| | - Georgia Sfyroera
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 401 Stellar Chance, 422 Curie Blvd, Philadelphia, 19104, PA, USA
| | - Piet Gros
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, Utrecht, The Netherlands
| | - John D Lambris
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 401 Stellar Chance, 422 Curie Blvd, Philadelphia, 19104, PA, USA.
| | - Daniel Ricklin
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland.
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11
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Kley M, Inderbinen S, Zogg M, Sellner M, Fischer A, Kędzierski J, Boudon S, Jetten A, Smieško M, Odermatt A. P10-02 Parabens and UV-filters activating retinoic acid-related orphan receptor γ(t). Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Schreier VN, Appenzeller-Herzog C, Brüschweiler BJ, Geueke B, Wilks MF, Simat TJ, Schilter B, Smieško M, Muncke J, Odermatt A, Roth N. Evaluating the food safety and risk assessment evidence-base of polyethylene terephthalate oligomers: Protocol for a systematic evidence map. Environ Int 2022; 167:107387. [PMID: 35841728 DOI: 10.1016/j.envint.2022.107387] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/22/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Polyethylene terephthalate (PET) oligomers are ubiquitous in PET used in food contact applications. Consumer exposure by migration of PET oligomers into food and beverages is documented. However, no specific risk assessment framework or guidance for the safety evaluating of PET oligomers exist to date. AIM The aim of this systematic evidence map (SEM) is to identify and organize existing knowledge clusters and associated gaps in hazard and exposure information of PET oligomers. Research needs will be identified as an input for chemical risk assessment, and to support future toxicity testing strategies of PET oligomers and regulatory decision-making. SEARCH STRATEGY AND ELIGIBILITY CRITERIA Multiple bibliographic databases (incl. Embase, Medline, Scopus, and Web of Science Core Collection), chemistry databases (SciFinder-n, Reaxys), and gray literature sources will be searched, and the search results will be supplemented by backward and forward citation tracking on eligible records. The search will be based on a single-concept PET oligomer-focused strategy to ensure sensitive and unbiased coverage of all evidence related to hazard and exposure in a data-poor environment. A scoping exercise conducted during planning identified 34 relevant PET oligomers. Eligible work of any study type must include primary research data on at least one relevant PET oligomer with regard to exposure, health, or toxicological outcomes. STUDY SELECTION For indexed scientific literature, title and abstract screening will be performed by one reviewer. Selected studies will be screened in full-text by two independent reviewers. Gray literature will be screened by two independent reviewers for inclusion and exclusion. STUDY QUALITY ASSESSMENT Risk of bias analysis will not be conducted as part of this SEM. DATA EXTRACTION AND CODING Will be performed by one reviewer and peer-checked by a second reviewer for indexed scientific literature or by two independent reviewers for gray literature. SYNTHESIS AND VISUALIZATION The extracted and coded information will be synthesized in different formats, including narrative synthesis, tables, and heat maps. SYSTEMATIC MAP PROTOCOL REGISTRY AND REGISTRATION NUMBER Zenodo: https://doi.org/10.5281/zenodo.6224302.
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Affiliation(s)
- Verena N Schreier
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland.
| | | | - Beat J Brüschweiler
- Federal Food Safety and Veterinary Office (FSVO), Risk Assessment Division, Bern, Switzerland.
| | - Birgit Geueke
- Food Packaging Forum Foundation, Zurich, Switzerland.
| | - Martin F Wilks
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland.
| | - Thomas J Simat
- Chair of Food Contact Materials, Dresden University of Technology, Dresden, Germany.
| | - Benoit Schilter
- Nestlé Institute of Food Safety and Analytical Sciences, Lausanne, Switzerland.
| | - Martin Smieško
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland.
| | - Jane Muncke
- Food Packaging Forum Foundation, Zurich, Switzerland.
| | - Alex Odermatt
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland.
| | - Nicolas Roth
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland.
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13
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Inderbinen SG, Kley M, Zogg M, Sellner M, Fischer A, Kędzierski J, Boudon S, Jetten AM, Smieško M, Odermatt A. Activation of retinoic acid-related orphan receptor γ(t) by parabens and benzophenone UV-filters. Toxicology 2022; 471:153159. [PMID: 35337918 PMCID: PMC11046913 DOI: 10.1016/j.tox.2022.153159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/09/2022] [Accepted: 03/17/2022] [Indexed: 11/24/2022]
Abstract
Retinoic acid-related orphan receptor γt (RORγt) regulates immune responses and its impaired function contributes to inflammatory and autoimmune diseases and may promote skin cancer. Synthetic inverse RORγt agonists block the production of Th17-associated cytokines including interleukin (IL)-17A and IL-22 and are under investigation for treatment of such pathologies. Unintentional RORγt activation in skin, following exposure to environmental chemicals, may promote inflammatory skin disease. Parabens and UV-filters, frequently used as additives in cosmetics and body care products, are intensively inspected for endocrine disrupting properties. This study assessed whether such compounds can interfere with RORγ activity using a previously established tetracycline-inducible reporter gene assay in CHO cells. These transactivation experiments revealed hexylparaben, benzylparaben and benzophenone-10 as RORγ agonists (EC50 values: 144 ± 97 nM, 3.39 ± 1.74 µM and 1.67 ± 1.04 µM, respectively), and they could restore RORγ activity after suppression by an inverse agonist. Furthermore, they enhanced RORγt-dependent transcription of the pro-inflammatory IL-17A and/or IL-22 genes in the murine T-cell model EL4. Virtual screening of a cosmetics database for structurally similar chemicals and in vitro testing of the most promising hits revealed benzylbenzoate, benzylsalicylate and 4-methylphenylbenzoate as RORγ agonists (low micromolar EC50 values). Moreover, an analysis of mixtures of the newly identified RORγ agonists suggested additive effects. This study presents novel RORγ(t) agonistic structural scaffolds. By activating RORγ(t) the identified parabens and UV-filters may potentially aggravate pathophysiological conditions, especially skin diseases where highest exposure of such chemicals can be expected. Follow-up studies should assess whether such compounds, either alone or as mixtures, can reach relevant concentrations in tissues and target cells to activate RORγ(t) in vivo.
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Affiliation(s)
- Silvia G Inderbinen
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; Swiss Centre for Applied Human Toxicology and Department of Pharmaceutical Sciences, University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland
| | - Manuel Kley
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; Swiss Centre for Applied Human Toxicology and Department of Pharmaceutical Sciences, University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland
| | - Michael Zogg
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Manuel Sellner
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - André Fischer
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Jacek Kędzierski
- Swiss Centre for Applied Human Toxicology and Department of Pharmaceutical Sciences, University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland; Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Stéphanie Boudon
- Swiss Centre for Applied Human Toxicology and Department of Pharmaceutical Sciences, University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland
| | - Anton M Jetten
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111. T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Martin Smieško
- Swiss Centre for Applied Human Toxicology and Department of Pharmaceutical Sciences, University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland; Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Alex Odermatt
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; Swiss Centre for Applied Human Toxicology and Department of Pharmaceutical Sciences, University of Basel, Missionsstrasse 64, 4055 Basel, Switzerland.
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14
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Papaj K, Spychalska P, Kapica P, Fischer A, Nowak J, Bzówka M, Sellner M, Lill MA, Smieško M, Góra A. Evaluation of Xa inhibitors as potential inhibitors of the SARS-CoV-2 Mpro protease. PLoS One 2022; 17:e0262482. [PMID: 35015795 PMCID: PMC8752003 DOI: 10.1371/journal.pone.0262482] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 12/24/2021] [Indexed: 02/07/2023] Open
Abstract
Based on previous large-scale in silico screening several factor Xa inhibitors were proposed to potentially inhibit SARS-CoV-2 Mpro. In addition to their known anticoagulants activity this potential inhibition could have an additional therapeutic effect on patients with COVID-19 disease. In this study we examined the binding of the Apixaban, Betrixaban and Rivaroxaban to the SARS-CoV-2 Mpro with the use of the MicroScale Thermophoresis technique. Our results indicate that the experimentally measured binding affinity is weak and the therapeutic effect due to the SARS-CoV-2 Mpro inhibition is rather negligible.
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Affiliation(s)
- Katarzyna Papaj
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Patrycja Spychalska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Patryk Kapica
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - André Fischer
- Department of Pharmaceutical Sciences, Computational Pharmacy, University of Basel, Basel, Switzerland
| | - Jakub Nowak
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Krakow, Poland
| | - Maria Bzówka
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Manuel Sellner
- Department of Pharmaceutical Sciences, Computational Pharmacy, University of Basel, Basel, Switzerland
| | - Markus A. Lill
- Department of Pharmaceutical Sciences, Computational Pharmacy, University of Basel, Basel, Switzerland
| | - Martin Smieško
- Department of Pharmaceutical Sciences, Computational Pharmacy, University of Basel, Basel, Switzerland
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
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15
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Fischer A, Smieško M. A Conserved Allosteric Site on Drug-Metabolizing CYPs: A Systematic Computational Assessment. Int J Mol Sci 2021; 22:13215. [PMID: 34948012 PMCID: PMC8707821 DOI: 10.3390/ijms222413215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 11/17/2022] Open
Abstract
Cytochrome P450 enzymes (CYPs) are the largest group of enzymes involved in human drug metabolism. Ligand tunnels connect their active site buried at the core of the membrane-anchored protein to the surrounding solvent environment. Recently, evidence of a superficial allosteric site, here denoted as hotspot 1 (H1), involved in the regulation of ligand access in a soluble prokaryotic CYP emerged. Here, we applied multi-scale computational modeling techniques to study the conservation and functionality of this allosteric site in the nine most relevant mammalian CYPs responsible for approximately 70% of drug metabolism. In total, we systematically analyzed over 44 μs of trajectories from conventional MD, cosolvent MD, and metadynamics simulations. Our bioinformatic analysis and simulations with organic probe molecules revealed the site to be well conserved in the CYP2 family with the exception of CYP2E1. In the presence of a ligand bound to the H1 site, we could observe an enlargement of a ligand tunnel in several members of the CYP2 family. Further, we could detect the facilitation of ligand translocation by H1 interactions with statistical significance in CYP2C8 and CYP2D6, even though all other enzymes except for CYP2C19, CYP2E1, and CYP3A4 presented a similar trend. As the detailed comprehension of ligand access and egress phenomena remains one of the most relevant challenges in the field, this work contributes to its elucidation and ultimately helps in estimating the selectivity of metabolic transformations using computational techniques.
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Affiliation(s)
| | - Martin Smieško
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland;
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16
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Papaj K, Spychalska P, Hopko K, Kapica P, Fisher A, Lill MA, Bagrowska W, Nowak J, Szleper K, Smieško M, Kasprzycka A, Góra A. Investigation of Thiocarbamates as Potential Inhibitors of the SARS-CoV-2 Mpro. Pharmaceuticals (Basel) 2021; 14:1153. [PMID: 34832935 PMCID: PMC8621115 DOI: 10.3390/ph14111153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022] Open
Abstract
In the present study we tested, using the microscale thermophoresis technique, a small library of thionocarbamates, thiolocarbamates, sulfide and disulfide as potential lead compounds for SARS-CoV-2 Mpro drug design. The successfully identified binder is a representative of the thionocarbamates group with a high potential for future modifications aiming for higher affinity and solubility. The experimental analysis was extended by computational studies that show insufficient accuracy of the simplest and widely applied approaches and underline the necessity of applying more advanced methods to properly evaluate the affinity of potential SARS-CoV-2 Mpro binders.
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Affiliation(s)
- Katarzyna Papaj
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (K.P.); (P.K.); (W.B.); (K.S.)
| | - Patrycja Spychalska
- Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (P.S.); (K.H.); (A.K.)
| | - Katarzyna Hopko
- Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (P.S.); (K.H.); (A.K.)
| | - Patryk Kapica
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (K.P.); (P.K.); (W.B.); (K.S.)
| | - Andre Fisher
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland; (A.F.); (M.A.L.); (M.S.)
| | - Markus A. Lill
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland; (A.F.); (M.A.L.); (M.S.)
| | - Weronika Bagrowska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (K.P.); (P.K.); (W.B.); (K.S.)
| | - Jakub Nowak
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland;
| | - Katarzyna Szleper
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (K.P.); (P.K.); (W.B.); (K.S.)
| | - Martin Smieško
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland; (A.F.); (M.A.L.); (M.S.)
| | - Anna Kasprzycka
- Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (P.S.); (K.H.); (A.K.)
- Department of Chemistry, Silesian University of Technology, M. Strzody 9, 44-100 Gliwice, Poland
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (K.P.); (P.K.); (W.B.); (K.S.)
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17
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Abstract
Molecular docking is a computational method widely used in drug discovery. Due to the inherent inaccuracies of molecular docking, visual inspection of binding modes is a crucial routine in the decision making process of computational medicinal chemists. Despite its apparent importance for medicinal chemistry projects, guidelines for the visual docking pose assessment have been hardly discussed in the literature. Here, we review the medicinal chemistry literature with the aim of identifying consistent principles for visual inspection, highlighting cases of its successful application, and discussing its limitations. In this context, we conducted a survey reaching experts in both academia and the pharmaceutical industry, which also included a challenge to distinguish native from incorrect poses. We were able to collect 93 expert opinions that offer valuable insights into visually supported decision-making processes. This perspective shall motivate discussions among experienced computational medicinal chemists and guide young scientists new to the field to stratify their compounds.
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Affiliation(s)
- André Fischer
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Martin Smieško
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Manuel Sellner
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Markus A Lill
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
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18
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Fischer A, Sellner M, Mitusińska K, Bzówka M, Lill MA, Góra A, Smieško M. Computational Selectivity Assessment of Protease Inhibitors against SARS-CoV-2. Int J Mol Sci 2021; 22:2065. [PMID: 33669738 PMCID: PMC7922391 DOI: 10.3390/ijms22042065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 12/27/2022] Open
Abstract
The pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a serious global health threat. Since no specific therapeutics are available, researchers around the world screened compounds to inhibit various molecular targets of SARS-CoV-2 including its main protease (Mpro) essential for viral replication. Due to the high urgency of these discovery efforts, off-target binding, which is one of the major reasons for drug-induced toxicity and safety-related drug attrition, was neglected. Here, we used molecular docking, toxicity profiling, and multiple molecular dynamics (MD) protocols to assess the selectivity of 33 reported non-covalent inhibitors of SARS-CoV-2 Mpro against eight proteases and 16 anti-targets. The panel of proteases included SARS-CoV Mpro, cathepsin G, caspase-3, ubiquitin carboxy-terminal hydrolase L1 (UCHL1), thrombin, factor Xa, chymase, and prostasin. Several of the assessed compounds presented considerable off-target binding towards the panel of proteases, as well as the selected anti-targets. Our results further suggest a high risk of off-target binding to chymase and cathepsin G. Thus, in future discovery projects, experimental selectivity assessment should be directed toward these proteases. A systematic selectivity assessment of SARS-CoV-2 Mpro inhibitors, as we report it, was not previously conducted.
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Affiliation(s)
- André Fischer
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; (A.F.); (M.S.)
| | - Manuel Sellner
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; (A.F.); (M.S.)
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, 44-100 Gliwice, Poland; (K.M.); (M.B.)
| | - Maria Bzówka
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, 44-100 Gliwice, Poland; (K.M.); (M.B.)
| | - Markus A. Lill
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; (A.F.); (M.S.)
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, 44-100 Gliwice, Poland; (K.M.); (M.B.)
| | - Martin Smieško
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; (A.F.); (M.S.)
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Fischer A, Häuptli F, Lill MA, Smieško M. Computational Assessment of Combination Therapy of Androgen Receptor-Targeting Compounds. J Chem Inf Model 2021; 61:1001-1009. [PMID: 33523669 DOI: 10.1021/acs.jcim.0c01194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ligand-binding domain of the androgen receptor (AR) is a target for drugs against prostate cancer and offers three distinct binding sites for small molecules. Drugs acting on the orthosteric hormone binding site suffer from resistance mechanisms that can, in the worst case, reverse their therapeutic effect. While many allosteric ligands targeting either the activation function-2 (AF-2) or the binding function-3 (BF-3) have been reported, their potential for simultaneous administration with currently prescribed antiandrogens was disregarded. Here, we report results of 60 μs molecular dynamics simulations to investigate combinations of orthosteric and allosteric AR antagonists. Our results suggest BF-3 inhibitors to be more suitable in combination with classical antiandrogens as opposed to AF-2 inhibitors based on binding free energies and binding modes. As a mechanistic explanation for these observations, we deduced a structural adaptation of helix-12 involved in the formation of the AF-2 site by classical AR antagonists. Additionally, the changes were accompanied by an expansion of the orthosteric binding site. Considering our predictions, the selective combination of AR-targeting compounds may improve the treatment of prostate cancer.
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Affiliation(s)
- André Fischer
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Florian Häuptli
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Markus A Lill
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Martin Smieško
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
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20
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Sellner M, Fischer A, Don CG, Smieško M. Conformational Landscape of Cytochrome P450 Reductase Interactions. Int J Mol Sci 2021; 22:1023. [PMID: 33498551 PMCID: PMC7864194 DOI: 10.3390/ijms22031023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/05/2023] Open
Abstract
Oxidative reactions catalyzed by Cytochrome P450 enzymes (CYPs), which constitute the most relevant group of drug-metabolizing enzymes, are enabled by their redox partner Cytochrome P450 reductase (CPR). Both proteins are anchored to the membrane of the endoplasmic reticulum and the CPR undergoes a conformational change in order to interact with the respective CYP and transfer electrons. Here, we conducted over 22 microseconds of molecular dynamics (MD) simulations in combination with protein-protein docking to investigate the conformational changes necessary for the formation of the CPR-CYP complex. While some structural features of the CPR and the CPR-CYP2D6 complex that we highlighted confirmed previous observations, our simulations revealed additional mechanisms for the conformational transition of the CPR. Unbiased simulations exposed a movement of the whole protein relative to the membrane, potentially to facilitate interactions with its diverse set of redox partners. Further, we present a structural mechanism for the susceptibility of the CPR to different redox states based on the flip of a glycine residue disrupting the local interaction network that maintains inter-domain proximity. Simulations of the CPR-CYP2D6 complex pointed toward an additional interaction surface of the FAD domain and the proximal side of CYP2D6. Altogether, this study provides novel structural insight into the mechanism of CPR-CYP interactions and underlying conformational changes, improving our understanding of this complex machinery Cytochrome P450 reductase; CPR; conformational; dynamicsrelevant for drug metabolism.
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Affiliation(s)
| | | | | | - Martin Smieško
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; (M.S.); (A.F.); (C.G.D.)
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21
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Abstract
Thyroid hormone receptors (TRs) play a critical role in human development, growth, and metabolism. Antagonists of TRs offer an attractive strategy to treat hyperthyroidism without the disadvantage of a delayed onset of drug action. While it is challenging to examine the atomistic behavior of TRs in a laboratory setting, computational methods such as molecular dynamics (MD) simulations have proven their value to elucidate ligand-induced conformational changes in nuclear receptors. Here, we performed MD simulations of TRα and TRβ complexed to their native ligand triiodothyronine (T3) as well as several antagonists. Based on the examination of 27 μs MD trajectories, we showed how binding of these compounds influences various structural features of the receptors including the helicity of helices 3 and 10 as well as the location of helix-12. Helices 3 and 12 are known to mediate coactivator association required for downstream signaling, suggesting these changes to be the molecular basis for TR antagonism. A mechanistic analysis of the trajectories revealed an allosteric pathway between H3 and H12 to be responsible for the conformational adaptations. Even though a mechanistic understanding of conformational adaptations triggered by TR antagonists is important for the development of novel therapeutics, they have not been previously examined in detail as it was done here.
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Affiliation(s)
- André Fischer
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, Basel 4056, Switzerland
| | - Gabriela Frehner
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, Basel 4056, Switzerland
| | - Markus A Lill
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, Basel 4056, Switzerland
| | - Martin Smieško
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, Basel 4056, Switzerland
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22
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Inderbinen SG, Zogg M, Kley M, Smieško M, Odermatt A. Species-specific differences in the inhibition of 11β-hydroxysteroid dehydrogenase 2 by itraconazole and posaconazole. Toxicol Appl Pharmacol 2020; 412:115387. [PMID: 33387577 DOI: 10.1016/j.taap.2020.115387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/11/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022]
Abstract
11β-hydroxysteroid dehydrogenase 2 (11β-HSD2) converts active 11β-hydroxyglucocorticoids to their inactive 11-keto forms, thereby preventing inappropriate mineralocorticoid receptor activation by glucocorticoids. Disruption of 11β-HSD2 activity by genetic defects or inhibitors causes the syndrome of apparent mineralocorticoid excess (AME), characterized by hypokalemia, hypernatremia and hypertension. Recently, the azole antifungals itraconazole and posaconazole were identified to potently inhibit human 11β-HSD2, and several case studies described patients with acquired AME. To begin to understand why this adverse drug effect was missed during preclinical investigations, the inhibitory potential of itraconazole, its main metabolite hydroxyitraconazole (OHI) and posaconazole against 11β-HSD2 from human and three commonly used experimental animals was assessed. Whilst human 11β-HSD2 was potently inhibited by all three compounds (IC50 values in the nanomolar range), the rat enzyme was moderately inhibited (1.5- to 6-fold higher IC50 values compared to human), and mouse and zebrafish 11β-HSD2 were very weakly inhibited (IC50 values above 7 μM). Sequence alignment and application of newly generated homology models for human and mouse 11β-HSD2 revealed significant differences in the C-terminal region and the substrate binding pocket. Exchange of the C-terminus and substitution of residues Leu170,Ile172 in mouse 11β-HSD2 by the corresponding residues His170,Glu172 of the human enzyme resulted in a gain of sensitivity to itraconazole and posaconazole, resembling human 11β-HSD2. The results provide an explanation for the observed species-specific 11β-HSD2 inhibition by the studied azole antifungals. The obtained structure-activity relationship information should facilitate future assessments of 11β-HSD2 inhibitors and aid choosing adequate animal models for efficacy and safety studies.
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Affiliation(s)
- Silvia G Inderbinen
- Swiss Centre for Applied Human Toxicology and Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland
| | - Michael Zogg
- Swiss Centre for Applied Human Toxicology and Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland
| | - Manuel Kley
- Swiss Centre for Applied Human Toxicology and Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland
| | - Martin Smieško
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, Basel 4056, Switzerland
| | - Alex Odermatt
- Swiss Centre for Applied Human Toxicology and Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland.
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23
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Don CG, Smieško M. Deciphering Reaction Determinants of Altered-Activity CYP2D6 Variants by Well-Tempered Metadynamics Simulation and QM/MM Calculations. J Chem Inf Model 2020; 60:6642-6653. [PMID: 33269921 DOI: 10.1021/acs.jcim.0c01091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The xenobiotic metabolizing enzyme CYP2D6 is the P450 cytochrome family member with the highest rate of polymorphism. This causes changes in the enzyme activity and specificity, which can ultimately lead to adverse reactions during drug treatment. To avoid or lower CYP-related toxicity risks, prediction of the most likely positions within a molecule where a metabolic reaction might occur is paramount. In order to obtain accurate predictions, it is crucial to understand all phenomena within the active site of the enzyme that contribute to an efficient substrate recognition and the subsequent catalytic reaction together with their relative weight within the overall thermodynamic context. This study aims to define the weight of the driving forces upon the C-H bond activation within CYP2D6 wild-type and a clinically relevant allelic variant with increased activity (CYP2D6*53) featuring two amino acid mutations in close vicinity of the heme. First, we investigated the steric and electrostatic complementarity of the substrate bufuralol using well-tempered metadynamics simulations with the aim to obtain the free energy profiles for each site of metabolism (SoM) within the different active sites. Second, the stereoelectronic complementarity was determined for each SoM within the two different active-site environments. Relying on the well-tempered metadynamics simulation energy profiles of each SoM, we identified the binding mode that was closest to the preferred transition-state geometry for efficient C-H bond activation. The binding modes were then used as starting structures for the quantum mechanics/molecular mechanics calculations performed to quantify the corresponding activation barriers. Our results show the relevance of the steric component in orienting the SoM in an energetically accessible position toward the heme. However, the corresponding intrinsic reactivity and electronic complementarity within the active site must be accurately evaluated in order to obtain a meaningful reaction prediction, from which the predominant SoM can be determined. The F120I mutation lowered the activation barrier for the major site and one of the minor SoMs. However, it had an impact neither on the CYP2D6 enantioselectivity preference of the oxidation reaction nor on the stereoselectivity from the substrate point of view.
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Affiliation(s)
- Charleen G Don
- Computational Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Martin Smieško
- Computational Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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24
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Reinhardt JK, Zimmermann-Klemd AM, Danton O, Smieško M, Gründemann C, Hamburger M. Compounds from Toddalia asiatica: Immunosuppressant Activity and Absolute Configurations. J Nat Prod 2020; 83:3012-3020. [PMID: 33001647 DOI: 10.1021/acs.jnatprod.0c00564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In a screening of an extract library from plants used in Traditional Chinese Medicine the MeOH extract of Toddalia asiatica inhibited proliferation of human primary T cells with an IC50 of 25.8 μg/mL. Activity in the extract was tracked by HPLC activity profiling, and a total of 15 compounds were characterized. Three compounds, toddalic acid (6) and both enantiomers (7a and 7b) of toddanolic acid (7), were new natural products, and two recently published compounds, (2'R)-toddalolactone 3'-O-β-d-glucopyranoside (10) and (2'S)-toddalolactone 2'-O-β-d-glucopyranoside (11), were described in detail for the first time. The absolute configurations of compounds 8, 9, 10, 12, 13, and 15 were determined by comparison of experimental and calculated ECD spectra. For glucosides 9 and 10, ECD data and chiral-phase HPLC of the aglycones after enzymatic hydrolysis confirmed the results. Nitidine chloride (4) inhibited proliferation of primary human T cells with an IC50 of 0.4 μM.
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Affiliation(s)
- Jakob K Reinhardt
- Pharmaceutical Biology, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Amy M Zimmermann-Klemd
- Center for Complementary Medicine, Institute for Infection Prevention and Hospital Epidemiology, Faculty of Medicine, University of Freiburg, Breisacher Straße 115 B, 79106 Freiburg, Germany
| | - Ombeline Danton
- Pharmaceutical Biology, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Martin Smieško
- Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Carsten Gründemann
- Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Matthias Hamburger
- Pharmaceutical Biology, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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25
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Fischer A, Sellner M, Neranjan S, Smieško M, Lill MA. Potential Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 606 Million Compounds. Int J Mol Sci 2020; 21:E3626. [PMID: 32455534 PMCID: PMC7279339 DOI: 10.3390/ijms21103626] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/15/2020] [Accepted: 05/16/2020] [Indexed: 02/07/2023] Open
Abstract
The rapid outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China followed by its spread around the world poses a serious global concern for public health. To this date, no specific drugs or vaccines are available to treat SARS-CoV-2 despite its close relation to the SARS-CoV virus that caused a similar epidemic in 2003. Thus, there remains an urgent need for the identification and development of specific antiviral therapeutics against SARS-CoV-2. To conquer viral infections, the inhibition of proteases essential for proteolytic processing of viral polyproteins is a conventional therapeutic strategy. In order to find novel inhibitors, we computationally screened a compound library of over 606 million compounds for binding at the recently solved crystal structure of the main protease (Mpro) of SARS-CoV-2. A screening of such a vast chemical space for SARS-CoV-2 Mpro inhibitors has not been reported before. After shape screening, two docking protocols were applied followed by the determination of molecular descriptors relevant for pharmacokinetics to narrow down the number of initial hits. Next, molecular dynamics simulations were conducted to validate the stability of docked binding modes and comprehensively quantify ligand binding energies. After evaluation of potential off-target binding, we report a list of 12 purchasable compounds, with binding affinity to the target protease that is predicted to be more favorable than that of the cocrystallized peptidomimetic compound. In order to quickly advise ongoing therapeutic intervention for patients, we evaluated approved antiviral drugs and other protease inhibitors to provide a list of nine compounds for drug repurposing. Furthermore, we identified the natural compounds (-)-taxifolin and rhamnetin as potential inhibitors of Mpro. Rhamnetin is already commercially available in pharmacies.
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Affiliation(s)
| | | | | | - Martin Smieško
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; (A.F.); (M.S.); (S.N.)
| | - Markus A. Lill
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; (A.F.); (M.S.); (S.N.)
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26
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Don CG, Smieško M. In Silico Pharmacogenetics CYP2D6 Study Focused on the Pharmacovigilance of Herbal Antidepressants. Front Pharmacol 2020; 11:683. [PMID: 32477141 PMCID: PMC7237870 DOI: 10.3389/fphar.2020.00683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/27/2020] [Indexed: 01/27/2023] Open
Abstract
The annual increase in depression worldwide together with an upward trend in the use of alternative medicine as treatment asks for developing reliable safety profiles of herbal based medicine. A considerable risk on adverse reactions exists when herbal remedies are combined with prescription medication. Around 25% of the drugs, including many antidepressants, depend on the activity of CYP2D6 for their metabolism and corresponding efficacy. Therefore, probing CYP2D6 inhibition by the active substances in herbal based medicine within the wild-type enzyme and clinically relevant allelic variants is crucial to avoid toxicity issues. In this in silico study several compounds with herbal origin suggested to have antidepressant activity were analyzed on their CYP2D6 wild-type and CYP2D6*53 inhibition potential using molecular docking. In addition, several pharmacokinetic properties were evaluated to assess their probability to cross the blood brain barrier and subsequently reach sufficient brain bioavailability for the modulation of central nervous system targets as well as characteristics which may hint toward potential safety issues.
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27
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Fischer A, Smieško M. Spontaneous Ligand Access Events to Membrane-Bound Cytochrome P450 2D6 Sampled at Atomic Resolution. Sci Rep 2019; 9:16411. [PMID: 31712722 PMCID: PMC6848145 DOI: 10.1038/s41598-019-52681-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022] Open
Abstract
The membrane-anchored enzyme Cytochrome P450 2D6 (CYP2D6) is involved in the metabolism of around 25% of marketed drugs and its metabolic performance shows a high interindividual variation. While it was suggested that ligands access the buried active site of the enzyme from the membrane, no proof from unbiased simulations has been provided to support this hypothesis. Laboratory experiments fail to capture the access process which is suspected to influence binding kinetics. Here, we applied unbiased molecular dynamics (MD) simulations to investigate the access of ligands to wild-type CYP2D6, as well as the allelic variant CYP2D6*53. In multiple simulations, substrates accessed the active site of the enzyme from the protein-membrane interface to ultimately adopt a conformation that would allow a metabolic reaction. We propose the necessary steps for ligand access and the results suggest that the increased metabolic activity of CYP2D6*53 might be caused by a facilitated ligand uptake.
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Affiliation(s)
- André Fischer
- University of Basel, Department of Pharmaceutical Sciences, Basel, 4056, Switzerland
| | - Martin Smieško
- University of Basel, Department of Pharmaceutical Sciences, Basel, 4056, Switzerland.
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28
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Abstract
Nuclear receptors (NRs) are ligand-inducible transcription factors that play an essential role in a multitude of physiological processes as well as diseases, rendering them attractive drug targets. Crystal structures revealed the binding site of NRs to be buried in the core of the protein, with no obvious route for ligands to access this cavity. The process of ligand binding is known to be an often-neglected contributor to the efficacy of drug candidates and is thought to influence the selectivity and specificity of NRs. While experimental methods generally fail to highlight the dynamic processes of ligand access or egress on the atomistic scale, computational methods have provided fundamental insight into the pathways connecting the buried binding pocket to the surrounding environment. Methods based on molecular dynamics (MD) and Monte Carlo simulations have been applied to identify pathways and quantify their capability to transport ligands. Here, we systematically review findings of more than 20 years of research in the field, including the applied methodology and controversies. Further, we establish a unified nomenclature to describe the pathways with respect to their location relative to protein secondary structure elements and summarize findings relevant to drug design. Lastly, we discuss the effect of NR interaction partners such as coactivators and corepressors, as well as mutations on the pathways.
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Affiliation(s)
- André Fischer
- Molecular Modeling, Pharmacenter of the University of Basel , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
| | - Martin Smieško
- Molecular Modeling, Pharmacenter of the University of Basel , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
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29
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Reinhardt JK, Klemd AM, Danton O, De Mieri M, Smieško M, Huber R, Bürgi T, Gründemann C, Hamburger M. Sesquiterpene Lactones from Artemisia argyi: Absolute Configuration and Immunosuppressant Activity. J Nat Prod 2019; 82:1424-1433. [PMID: 31181920 DOI: 10.1021/acs.jnatprod.8b00791] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A library of extracts from plants used in Chinese Traditional Medicine was screened for inhibition of T lymphocyte proliferation. An ethyl acetate extract from aerial parts of Artemisia argyi showed promising activity and was submitted to HPLC-based activity profiling to track the active compounds. From the most active time window, three guaianolides (1, 2, and 5) and two seco-tanapartholides (3 and 4) were identified and, in a less active time window, five new sesquiterpene lactones (8-11, 17), along with six known sesquiterpene lactones and two known flavonoids. The absolute configurations of compounds 1, 2, 5-10, 13-15, 17, and 18 were established by comparison of experimental with calculated electronic circular dichroism (ECD) spectra. For seco-tanapartholides B (3) and A (4), ECD yielded ambiguous results, and their absolute configurations were determined by comparing experimental and calculated vibrational circular dichroism (VCD) spectra. Compounds 1-5 showed significant, noncytotoxic inhibition of T lymphocyte proliferation, with IC50 values between 1.0 and 3.7 μM.
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Affiliation(s)
- Jakob K Reinhardt
- Pharmaceutical Biology, Pharmacenter , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
| | - Amy M Klemd
- Center for Complementary Medicine, Institute for Infection Prevention and Hospital Epidemiology, Faculty of Medicine , University of Freiburg , Breisacher Straße 115 B , 79106 Freiburg , Germany
| | - Ombeline Danton
- Pharmaceutical Biology, Pharmacenter , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
| | - Maria De Mieri
- Pharmaceutical Biology, Pharmacenter , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
| | - Martin Smieško
- Department of Molecular Modeling , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
| | - Roman Huber
- Center for Complementary Medicine, Institute for Infection Prevention and Hospital Epidemiology, Faculty of Medicine , University of Freiburg , Breisacher Straße 115 B , 79106 Freiburg , Germany
| | - Thomas Bürgi
- Department of Physical Chemistry , University of Geneva , 30 Quai Ernest Ansermet , 1211 Geneva , Switzerland
| | - Carsten Gründemann
- Center for Complementary Medicine, Institute for Infection Prevention and Hospital Epidemiology, Faculty of Medicine , University of Freiburg , Breisacher Straße 115 B , 79106 Freiburg , Germany
| | - Matthias Hamburger
- Pharmaceutical Biology, Pharmacenter , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
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30
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Schönemann W, Cramer J, Mühlethaler T, Fiege B, Silbermann M, Rabbani S, Dätwyler P, Zihlmann P, Jakob RP, Sager CP, Smieško M, Schwardt O, Maier T, Ernst B. Front Cover: Improvement of Aglycone π‐Stacking Yields Nanomolar to Sub‐nanomolar FimH Antagonists (ChemMedChem 7/2019). ChemMedChem 2019. [DOI: 10.1002/cmdc.201900177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wojciech Schönemann
- Department of Pharmaceutical SciencesUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Jonathan Cramer
- Department of Pharmaceutical SciencesUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Tobias Mühlethaler
- Department of Pharmaceutical SciencesUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Brigitte Fiege
- Department of Pharmaceutical SciencesUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Marleen Silbermann
- Department of Pharmaceutical SciencesUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Said Rabbani
- Department of Pharmaceutical SciencesUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Philipp Dätwyler
- Department of Pharmaceutical SciencesUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Pascal Zihlmann
- Department of Pharmaceutical SciencesUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Roman P. Jakob
- Department Biozentrum, Focal Area Structural BiologyUniversity of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Christoph P. Sager
- Department of Pharmaceutical SciencesUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Martin Smieško
- Department of Pharmaceutical SciencesUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Oliver Schwardt
- Department of Pharmaceutical SciencesUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Timm Maier
- Department Biozentrum, Focal Area Structural BiologyUniversity of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Beat Ernst
- Department of Pharmaceutical SciencesUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
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Schönemann W, Cramer J, Mühlethaler T, Fiege B, Silbermann M, Rabbani S, Dätwyler P, Zihlmann P, Jakob RP, Sager CP, Smieško M, Schwardt O, Maier T, Ernst B. Improvement of Aglycone π-Stacking Yields Nanomolar to Sub-nanomolar FimH Antagonists. ChemMedChem 2019; 14:749-757. [PMID: 30710416 DOI: 10.1002/cmdc.201900051] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Indexed: 11/08/2022]
Abstract
Antimicrobial resistance has become a serious concern for the treatment of urinary tract infections. In this context, an anti-adhesive approach targeting FimH, a bacterial lectin enabling the attachment of E. coli to host cells, has attracted considerable interest. FimH can adopt a low/medium-affinity state in the absence and a high-affinity state in the presence of shear forces. Until recently, mostly the high-affinity state has been investigated, despite the fact that a therapeutic antagonist should bind predominantly to the low-affinity state. In this communication, we demonstrate that fluorination of biphenyl α-d-mannosides leads to compounds with perfect π-π stacking interactions with the tyrosine gate of FimH, yielding low nanomolar to sub-nanomolar KD values for the low- and high-affinity states, respectively. The face-to-face alignment of the perfluorinated biphenyl group of FimH ligands and Tyr48 was confirmed by crystal structures as well as 1 H,15 N-HSQC NMR analysis. Finally, fluorination improves pharmacokinetic parameters predictive for oral availability.
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Affiliation(s)
- Wojciech Schönemann
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Jonathan Cramer
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Tobias Mühlethaler
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Brigitte Fiege
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Marleen Silbermann
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Said Rabbani
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Philipp Dätwyler
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Pascal Zihlmann
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Roman P Jakob
- Department Biozentrum, Focal Area Structural Biology, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Christoph P Sager
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Martin Smieško
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Oliver Schwardt
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Timm Maier
- Department Biozentrum, Focal Area Structural Biology, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
| | - Beat Ernst
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
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32
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Wahl J, Smieško M. Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules. J Chem Inf Model 2019; 59:754-765. [DOI: 10.1021/acs.jcim.8b00826] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Joel Wahl
- Molecular Modeling, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Martin Smieško
- Molecular Modeling, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
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33
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Fischer A, Don CG, Smieško M. Molecular Dynamics Simulations Reveal Structural Differences among Allelic Variants of Membrane-Anchored Cytochrome P450 2D6. J Chem Inf Model 2018; 58:1962-1975. [PMID: 30126275 DOI: 10.1021/acs.jcim.8b00080] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cytochrome P450 2D6 (CYP2D6) is an enzyme that is involved in the metabolism of roughly 25% of all marketed drugs and therefore belongs to the most important enzymes in drug metabolism. CYP2D6 features a high degree of genetic polymorphism that can significantly affect the metabolic activity of an individual. In extreme cases, structural changes at the level of single amino acids can either increase its enzymatic activity abolishing the drug therapeutic effect or completely disable the enzyme and elevate drug plasma level potentially leading to adverse effects. In this study, starting from the crystal structure, we built a full-length membrane-anchored all-atom model of the wild-type CYP2D6 as well as five of its variants differing in the enzymatic activity. We validated our models with available experimental data and compared their structural properties with molecular dynamics simulations. The main focus of this study was to identify differences that could mechanistically explain the altered activity of the variants and improve our understanding of their functioning. We observed differences in the opening frequencies and minimal diameters of tunnels that connect the buried active site to the surrounding solvent environment. The variants CYP2D6*4 and CYP2D6*10 associated with missing or decreased activity showed less frequent opening of the tunnels compared to the wild-type. Both CYP2D6*10 and CYP2D6*17 showed a deprivation of an important ligand tunnel suggesting a feasible reason for their altered substrate specificity. Next, the altered fold at the N-terminal anchor region and the decreased active site volume caused by the amino acid mutations of the CYP2D6*4 variant offer an explanation for the absence of its metabolic activity. The mutations in CYP2D6*53 contributed to a significant enlargement of an important ligand tunnel and an extension of the active site cavity. This could explain the altered metabolic profile as well as the enhanced metabolic rates of this particular variant supporting its designation as a possible cause for the ultrarapid metabolizer phenotype. We believe these novel structural insights could advance the fields of personalized medicine and enzyme engineering. Furthermore, they could aid in guiding laboratory as well as computational experiments in the future.
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Affiliation(s)
- André Fischer
- Molecular Modeling, Department of Pharmaceutical Sciences , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
| | - Charleen G Don
- Molecular Modeling, Department of Pharmaceutical Sciences , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
| | - Martin Smieško
- Molecular Modeling, Department of Pharmaceutical Sciences , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
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34
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Dusserre C, Mollergues J, Lo Piparo E, Smieško M, Marin-Kuan M, Schilter B, Fussell K. Using bisphenol A and its analogs to address the feasibility and usefulness of the CALUX-PPARγ assay to identify chemicals with obesogenic potential. Toxicol In Vitro 2018; 53:208-221. [PMID: 30138673 DOI: 10.1016/j.tiv.2018.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/06/2018] [Accepted: 08/18/2018] [Indexed: 12/25/2022]
Abstract
Environmental chemical exposures have been implicated in the obesity epidemic as potential mis-regulators of a variety of metabolic pathways. As agonism of the peroxisome proliferator-activated nuclear hormone receptor γ (PPARγ) is one of the suspected mechanisms involved, a PPARγ screening assay may have relevance for the biodetection of such effects of environmental chemicals. To test this hypothesis, we established the PPARγ2-CALUX® assay in-house and tested it against a number of known and suspected PPARγ modulators. Furthermore, we added a rat liver S9 metabolizing system to the protocol to introduce metabolic competence to the assay. Our results confirmed the responsiveness of the cell line to the known PPARγ agonists and antagonists: rosiglitazone, tributyltin, 15-deoxy-Δ12,14-prostaglandin J2, GW9662 and diclofenac. These data are in agreement with previous studies in various models. Seven bisphenol analogs tested induced little to no agonist activity, but all demonstrated antagonistic properties. These findings were contrary to both our assumptions and literature reports. Addition of the S9-metabolizing system to each of these tests did not alter any of the measured activities. Taken together, it seems probable that there are additional obesogenic effects of these chemicals which would not be detected by this assay.
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Affiliation(s)
- Camille Dusserre
- Université Paris Descartes, Faculté de Pharmacie de Paris, Paris 75006, France
| | - Julie Mollergues
- Nestlé Research, Route du Jorat 57, Lausanne 26 CH-1000, Switzerland
| | - Elena Lo Piparo
- Nestlé Research, Route du Jorat 57, Lausanne 26 CH-1000, Switzerland
| | - Martin Smieško
- Molecular Modeling Group, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | | | - Benoit Schilter
- Nestlé Research, Route du Jorat 57, Lausanne 26 CH-1000, Switzerland
| | - Karma Fussell
- Nestlé Research, Route du Jorat 57, Lausanne 26 CH-1000, Switzerland.
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35
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Wahl J, Smieško M. Endocrine Disruption at the Androgen Receptor: Employing Molecular Dynamics and Docking for Improved Virtual Screening and Toxicity Prediction. Int J Mol Sci 2018; 19:E1784. [PMID: 29914135 PMCID: PMC6032383 DOI: 10.3390/ijms19061784] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 05/28/2018] [Accepted: 06/06/2018] [Indexed: 12/18/2022] Open
Abstract
The androgen receptor (AR) is a key target for the development of drugs targeting hormone-dependent prostate cancer, but has also an important role in endocrine disruption. Reliable prediction of the binding of ligands towards the AR is therefore of great relevance. Molecular docking is a powerful computational method for exploring small-ligand binding to proteins. It can be applied for virtual screening experiments but also for predicting molecular initiating events in toxicology. However, in case of AR, there is no antagonist-bound crystal structure yet available. Our study demonstrates that molecular docking approaches are not able to satisfactorily screen for AR antagonists because of this reason. Therefore, we applied Molecular Dynamics simulations to generate antagonist AR structures and showed that this leads to a vast improvement for the docking of AR antagonists. We benchmarked the ability of these antagonist AR structures discriminate between AR antagonists and decoys using an ensemble docking approach and obtained promising results with good enrichment. However, distinguishing AR antagonists from agonists with high confidence is not possible with the current approach alone.
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Affiliation(s)
- Joel Wahl
- Molecular Modeling, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland.
| | - Martin Smieško
- Molecular Modeling, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland.
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36
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Wahl J, Smieško M. Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations. ChemMedChem 2018; 13:1325-1335. [DOI: 10.1002/cmdc.201800093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/07/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Joel Wahl
- Molecular Modeling, Department of Pharmaceutical Sciences; University of Basel; Klingelbergstrasse 50 4056 Basel Switzerland
| | - Martin Smieško
- Molecular Modeling, Department of Pharmaceutical Sciences; University of Basel; Klingelbergstrasse 50 4056 Basel Switzerland
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37
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Affiliation(s)
- Charleen G. Don
- Department of Pharmaceutical SciencesUniversity of BaselBaselSwitzerland
| | - Martin Smieško
- Department of Pharmaceutical SciencesUniversity of BaselBaselSwitzerland
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38
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Salehi P, Mohebbi M, Bararjanian M, Ebrahimi S, Smieško M. Noscapine Derivatives as New Chiral Catalysts in Asymmetric Synthesis: Highly Enantioselective Addition of Diethylzinc to Aldehydes. SYNTHESIS-STUTTGART 2018. [DOI: 10.1055/s-0037-1609224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Noscapine, a natural alkaloid, has never been used as a parent scaffold in chiral induction. The first examples of noscapinoid compounds as efficient catalysts in asymmetric synthesis are now reported. Three derivatives of noscapine were synthesized from its reaction with different Grignard reagents. Asymmetric addition of diethylzinc to aldehydes was performed in the presence of these catalysts in high yields and good to excellent ees.
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Affiliation(s)
- Peyman Salehi
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University
| | - Maryam Mohebbi
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University
| | - Morteza Bararjanian
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University
| | - Samad Ebrahimi
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University
| | - Martin Smieško
- Division of Molecular Modeling, Department of Pharmaceutical Sciences, University of Basel
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39
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De Mieri M, Smieško M, Ismajili I, Kaiser M, Hamburger M. Acid-Induced Rearrangement of Epoxygermacranolides: Synthesis of Furanoheliangolides and Cadinanes from Nobilin. Molecules 2017; 22:E2252. [PMID: 29258233 PMCID: PMC6149915 DOI: 10.3390/molecules22122252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/13/2017] [Accepted: 12/13/2017] [Indexed: 11/17/2022] Open
Abstract
The acid-induced rearrangement of three epoxyderivatives of nobilin 1, the most abundant sesquiterpene lactone in Anthemisnobilis flowers, was investigated. From the 1,10-epoxyderivative 2, furanoheliangolide 5 was obtained, while the 4,5-epoxy group of 3 did not react. Conversely, when the 3-hydroxy function of nobilin was acetylated (12), the 4,5-epoxy derivative did cyclize into cadinanes (15 and 16) under Lewis acid catalysis. The reactivity of the 4,5- and 1,10-epoxy derivatives of nobilin (2 and 3) was compared with that of parthenolide, and rationalized on the basis of quantum chemical calculations. All isolated reaction products were fully characterized by spectroscopic and computational methods, and their in vitro anti-protozoal activity was evaluated. The paper could provide new insights into the biosynthesis of this class of natural products.
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Affiliation(s)
- Maria De Mieri
- Pharmaceutical Biology, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
| | - Martin Smieško
- Molecular Modeling, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
| | - Isidor Ismajili
- Pharmaceutical Biology, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
| | - Marcel Kaiser
- Department of Medical Parasitology & Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4000 Basel, Switzerland.
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland.
| | - Matthias Hamburger
- Pharmaceutical Biology, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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40
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Sager CP, Eriş D, Smieško M, Hevey R, Ernst B. What contributes to an effective mannose recognition domain? Beilstein J Org Chem 2017; 13:2584-2595. [PMID: 29259668 PMCID: PMC5727865 DOI: 10.3762/bjoc.13.255] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/15/2017] [Indexed: 12/27/2022] Open
Abstract
In general, carbohydrate-lectin interactions are characterized by high specificity but also low affinity. The main reason for the low affinities are desolvation costs, due to the numerous hydroxy groups present on the ligand, together with the typically polar surface of the binding sites. Nonetheless, nature has evolved strategies to overcome this hurdle, most prominently in relation to carbohydrate-lectin interactions of the innate immune system but also in bacterial adhesion, a process key for the bacterium's survival. In an effort to better understand the particular characteristics, which contribute to a successful carbohydrate recognition domain, the mannose-binding sites of six C-type lectins and of three bacterial adhesins were analyzed. One important finding is that the high enthalpic penalties caused by desolvation can only be compensated for by the number and quality of hydrogen bonds formed by each of the polar hydroxy groups engaged in the binding process. In addition, since mammalian mannose-binding sites are in general flat and solvent exposed, the half-lives of carbohydrate-lectin complexes are rather short since water molecules can easily access and displace the ligand from the binding site. In contrast, the bacterial lectin FimH benefits from a deep mannose-binding site, leading to a substantial improvement in the off-rate. Together with both a catch-bond mechanism (i.e., improvement of affinity under shear stress) and multivalency, two methods commonly utilized by pathogens, the affinity of the carbohydrate-FimH interaction can be further improved. Including those just described, the various approaches explored by nature to optimize selectivity and affinity of carbohydrate-lectin interactions offer interesting therapeutic perspectives for the development of carbohydrate-based drugs.
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Affiliation(s)
- Christoph P Sager
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Deniz Eriş
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Martin Smieško
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Rachel Hevey
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Beat Ernst
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
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41
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Aeschbacher T, Zierke M, Smieško M, Collot M, Mallet JM, Ernst B, Allain FHT, Schubert M. A Secondary Structural Element in a Wide Range of Fucosylated Glycoepitopes. Chemistry 2017; 23:11598-11610. [PMID: 28654715 DOI: 10.1002/chem.201701866] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Indexed: 01/12/2023]
Abstract
The increasing understanding of the essential role of carbohydrates in development, and in a wide range of diseases fuels a rapidly growing interest in the basic principles governing carbohydrate-protein interactions. A still heavily debated issue regarding the recognition process is the degree of flexibility or rigidity of oligosaccharides. Combining NMR structure determination based on extensive experimental data with DFT and database searches, we have identified a set of trisaccharide motifs with a similar conformation that is characterized by a non-conventional C-H⋅⋅⋅O hydrogen bond. These motifs are present in numerous classes of oligosaccharides, found in everything from bacteria to mammals, including Lewis blood group antigens but also unusual motifs from amphibians and marine invertebrates. The set of trisaccharide motifs can be summarized with the consensus motifs X-β1,4-[Fucα1,3]-Y and X-β1,3-[Fucα1,4]-Y-a secondary structure we name [3,4]F-branch. The wide spectrum of possible modifications of this scaffold points toward a large variety of glycoepitopes, which nature generated using the same underlying architecture.
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Affiliation(s)
- Thomas Aeschbacher
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland
| | - Mirko Zierke
- Institute of Molecular Pharmacy, University of Basel, Klingelbergstr. 50, 4056, Basel, Switzerland.,Department of Chemistry, University of British Columbia, V6T 1Z1, Vancouver, British Columbia, Canada
| | - Martin Smieško
- Institute of Molecular Pharmacy, University of Basel, Klingelbergstr. 50, 4056, Basel, Switzerland
| | - Mayeul Collot
- Laboratoire des Biomolécules, Département de Chimie, École normale supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 24 rue Lhomond, 75005, Paris, France.,UMR 7213 CNRS, Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, 74 route du Rhin, CS 60024, 67401, Illkirch, France
| | - Jean-Maurice Mallet
- Laboratoire des Biomolécules, Département de Chimie, École normale supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 24 rue Lhomond, 75005, Paris, France
| | - Beat Ernst
- Institute of Molecular Pharmacy, University of Basel, Klingelbergstr. 50, 4056, Basel, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland
| | - Mario Schubert
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland.,Institute of Molecular Biology, University of Salzburg, Billrothstr. 11, 5020, Salzburg, Austria
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42
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Gürsoy O, Smieško M. Searching for bioactive conformations of drug-like ligands with current force fields: how good are we? J Cheminform 2017; 9:29. [PMID: 29086109 PMCID: PMC5432473 DOI: 10.1186/s13321-017-0216-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 05/08/2017] [Indexed: 11/10/2022] Open
Abstract
Drug-like ligands obtained from protein-ligand complexes deposited in the Protein Databank were subjected to conformational searching using various force fields and solvation settings. For each ligand, the resulting conformer pool was examined for the presence of the bioactive (crystal pose-like) conformation. Similarity of conformers toward the crystal-pose was quantified as the best achievable root mean squared deviation (RMSD, heavy atoms only). Analyzing the conformer pools generated by various force fields revealed only small differences in the likelihood of finding a crystal pose-like conformation. However, employing different solvents in the conformational search was found to be very important for achieving RMSDs below 1.0 Å. The best statistical values of likelihood were observed with a recently released force field covering a large portion of dihedral angles occurring in drug-like compounds in combination with the water as solvent. In order to enable computational chemists and modelers to efficiently use available software tools, we have additionally performed several focused analyses on ligands, grouped according to descriptors most relevant for the rational drug design.
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Affiliation(s)
- Oya Gürsoy
- Department of Pharmaceutical Sciences, Molecular Modeling, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Martin Smieško
- Department of Pharmaceutical Sciences, Molecular Modeling, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland.
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43
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Farimani MM, Taleghani A, Aliabadi A, Aliahmadi A, Esmaeili MA, Namazi Sarvestani N, Khavasi HR, Smieško M, Hamburger M, Nejad Ebrahimi S. Labdane Diterpenoids from Salvia leriifolia: Absolute Configuration, Antimicrobial and Cytotoxic Activities. Planta Med 2016; 82:1279-1285. [PMID: 27280932 DOI: 10.1055/s-0042-107798] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Fractionation of an n-hexane extract of the aerial parts of Salvia leriifolia led to the isolation of two new (1, 2) and two known (3, 4) labdane diterpenoids, together with three other known compounds. The structures were established by a combination of 1D and 2D NMR, and HRESIMS. The structures of 1 and 3 were confirmed by single-crystal X-ray analysis. The absolute configuration of 1-4 was established by electronic circular dichroism spectroscopy. Compounds 1-4 were evaluated for their cytotoxic activities against MCF-7 human breast cancer cells. Labdanes 3 and 4 were additionally tested against MDA-MB231 human breast cancer and DU-145 human prostate cancer cell lines. Compound 4 showed IC50 values of 25, 50, and 50 µM against MCF-7, MDA-MB231, and DU-145 cells, respectively. Compounds 1-4 were tested for activity against gram-positive (Staphylococcus aureus) and gram-negative (Escherichia coli) bacteria. Compound 3 showed an MIC of 213 µM against methicillin-resistant S. aureus.
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Affiliation(s)
- Mahdi Moridi Farimani
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G. C., Evin, Tehran, Iran
| | - Akram Taleghani
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G. C., Evin, Tehran, Iran
| | - Abbas Aliabadi
- Khorasan Razavi Agricultural and Natural Resources Research Center, Sabzevar Branch, Sabzevar, Khorasan Razavi, Iran
| | - Atousa Aliahmadi
- Department of Biology, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G. C., Evin, Tehran, Iran
| | - Mohammad Ali Esmaeili
- Department of Biology, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G. C., Evin, Tehran, Iran
| | - Nazanin Namazi Sarvestani
- Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Hamid Reza Khavasi
- Department of Chemistry, Faculty of Chemistry, Shahid Beheshti University, G. C., Evin, Tehran, Iran
| | - Martin Smieško
- Division of Molecular Modeling, University of Basel, Basel, Switzerland
| | - Matthias Hamburger
- Division of Pharmaceutical Biology, University of Basel, Basel, Switzerland
| | - Samad Nejad Ebrahimi
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G. C., Evin, Tehran, Iran
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Jähne EA, Eigenmann DE, Moradi-Afrapoli F, Verjee S, Butterweck V, Hebeisen S, Hettich T, Schlotterbeck G, Smieško M, Hamburger M, Oufir M. Caco-2 Permeability Studies and In Vitro hERG Liability Assessment of Tryptanthrin and Indolinone. Planta Med 2016; 82:1192-1201. [PMID: 27420350 DOI: 10.1055/s-0042-110323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Tryptanthrin and (E,Z)-3-(4-hydroxy-3,5-dimethoxybenzylidene)indolinone (indolinone) were recently isolated from Isatis tinctoria as potent anti-inflammatory and antiallergic alkaloids, and shown to inhibit COX-2, 5-LOX catalyzed leukotriene synthesis, and mast cell degranulation at low µM to nM concentrations. To assess their suitability for oral administration, we screened the compounds in an in vitro intestinal permeability assay using human colonic adenocarcinoma cells. For exact quantification of the compounds, validated UPLC-MS/MS methods were used. Tryptanthrin displayed high permeability (apparent permeability coefficient > 32.0 × 10(-6) cm/s) across the cell monolayer. The efflux ratio below 2 (< 1.12) and unchanged apparent permeability coefficient values in the presence of the P-glycoprotein inhibitor verapamil (50 µM) indicated that tryptanthrin was not involved in P-glycoprotein interactions. For indolinone, a low recovery was found in the human colon adenocarcinoma cell assay. High-resolution mass spectrometry pointed to extensive phase II metabolism of indolinone (sulfation and glucuronidation). Possible cardiotoxic liability of the compounds was assessed in vitro by measurement of an inhibitory effect on human ether-a-go-go-related gene tail currents in stably transfected HEK 293 cells using the patch clamp technique. Low human ether-a-go-go-related gene inhibition was found for tryptanthrin (IC50 > 10 µM) and indolinone (IC50 of 24.96 µM). The analysis of compounds using various in silico methods confirmed favorable pharmacokinetic properties, as well as a slight inhibition of the human ether-a-go-go-related gene potassium channel at micromolar concentrations.
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Affiliation(s)
- Evelyn A Jähne
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Daniela E Eigenmann
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Fahimeh Moradi-Afrapoli
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Sheela Verjee
- Institute for Pharma Technology, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Muttenz, Switzerland
| | - Veronika Butterweck
- Institute for Pharma Technology, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Muttenz, Switzerland
| | - Simon Hebeisen
- B'SYS GmbH, The Ionchannel Company, Witterswil, Switzerland
| | - Timm Hettich
- Institute for Chemistry and Bioanalytics, School of Life Sciences, University of Applied Sciences, Northwestern Switzerland, Muttenz, Switzerland
| | - Götz Schlotterbeck
- Institute for Chemistry and Bioanalytics, School of Life Sciences, University of Applied Sciences, Northwestern Switzerland, Muttenz, Switzerland
| | - Martin Smieško
- Molecular Modeling, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Matthias Hamburger
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Mouhssin Oufir
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
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Jähne EA, Eigenmann DE, Sampath C, Butterweck V, Culot M, Cecchelli R, Gosselet F, Walter FR, Deli MA, Smieško M, Hamburger M, Oufir M. Pharmacokinetics and In Vitro Blood-Brain Barrier Screening of the Plant-Derived Alkaloid Tryptanthrin. Planta Med 2016; 82:1021-1029. [PMID: 27093249 DOI: 10.1055/s-0042-105295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The indolo[2,1-b]quinazoline alkaloid tryptanthrin was previously identified as a potent anti-inflammatory compound with a unique pharmacological profile. It is a potent inhibitor of cyclooxygenase-2, 5-lipooxygenase-catalyzed leukotriene synthesis, and nitric oxide production catalyzed by the inducible nitric oxide synthase. To characterize the pharmacokinetic properties of tryptanthrin, we performed a pilot in vivo study in male Sprague-Dawley rats (2 mg/kg bw i. v.). Moreover, the ability of tryptanthrin to cross the blood-brain barrier was evaluated in three in vitro human and animal blood-brain barrier models. Bioanalytical UPLC-MS/MS methods used were validated according to current international guidelines. A half-life of 40.63 ± 6.66 min and a clearance of 1.00 ± 0.36 L/h/kg were found in the in vivo pharmacokinetic study. In vitro data obtained with the two primary animal blood-brain barrier models showed a good correlation with an immortalized human monoculture blood-brain barrier model (hBMEC cell line), and were indicative of a high blood-brain barrier permeation potential of tryptanthrin. These findings were corroborated by the in silico prediction of blood-brain barrier penetration. P-glycoprotein interaction of tryptanthrin was assessed by calculation of the efflux ratio in bidirectional permeability assays. An efflux ratio below 2 indicated that tryptanthrin is not subjected to active efflux.
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Affiliation(s)
- Evelyn A Jähne
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Daniela E Eigenmann
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Chethan Sampath
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Veronika Butterweck
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Maxime Culot
- Univ. Artois, EA 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Lens Cedex, France
| | - Roméo Cecchelli
- Univ. Artois, EA 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Lens Cedex, France
| | - Fabien Gosselet
- Univ. Artois, EA 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Lens Cedex, France
| | - Fruzsina R Walter
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Mária A Deli
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Martin Smieško
- Molecular Modeling, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Matthias Hamburger
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Mouhssin Oufir
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
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Eigenmann DE, Dürig C, Jähne EA, Smieško M, Culot M, Gosselet F, Cecchelli R, Helms HCC, Brodin B, Wimmer L, Mihovilovic MD, Hamburger M, Oufir M. In vitro blood-brain barrier permeability predictions for GABAA receptor modulating piperine analogs. Eur J Pharm Biopharm 2016; 103:118-126. [PMID: 27018328 DOI: 10.1016/j.ejpb.2016.03.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/14/2016] [Accepted: 03/23/2016] [Indexed: 11/19/2022]
Abstract
The alkaloid piperine from black pepper (Piper nigrum L.) and several synthetic piperine analogs were recently identified as positive allosteric modulators of γ-aminobutyric acid type A (GABAA) receptors. In order to reach their target sites of action, these compounds need to enter the brain by crossing the blood-brain barrier (BBB). We here evaluated piperine and five selected analogs (SCT-66, SCT-64, SCT-29, LAU397, and LAU399) regarding their BBB permeability. Data were obtained in three in vitro BBB models, namely a recently established human model with immortalized hBMEC cells, a human brain-like endothelial cells (BLEC) model, and a primary animal (bovine endothelial/rat astrocytes co-culture) model. For each compound, quantitative UHPLC-MS/MS methods in the range of 5.00-500ng/mL in the corresponding matrix were developed, and permeability coefficients in the three BBB models were determined. In vitro predictions from the two human BBB models were in good agreement, while permeability data from the animal model differed to some extent, possibly due to protein binding of the screened compounds. In all three BBB models, piperine and SCT-64 displayed the highest BBB permeation potential. This was corroborated by data from in silico prediction. For the other piperine analogs (SCT-66, SCT-29, LAU397, and LAU399), BBB permeability was low to moderate in the two human BBB models, and moderate to high in the animal BBB model. Efflux ratios (ER) calculated from bidirectional permeability experiments indicated that the compounds were likely not substrates of active efflux transporters.
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Affiliation(s)
- Daniela Elisabeth Eigenmann
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Carmen Dürig
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Evelyn Andrea Jähne
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Martin Smieško
- Molecular Modeling, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Maxime Culot
- Univ. Artois, EA 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), F-62300 Lens Cedex, France
| | - Fabien Gosselet
- Univ. Artois, EA 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), F-62300 Lens Cedex, France
| | - Romeo Cecchelli
- Univ. Artois, EA 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), F-62300 Lens Cedex, France
| | - Hans Christian Cederberg Helms
- Drug Transporters in ADME, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Birger Brodin
- Drug Transporters in ADME, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Laurin Wimmer
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, A-1060 Vienna, Austria
| | - Marko D Mihovilovic
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, A-1060 Vienna, Austria
| | - Matthias Hamburger
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Mouhssin Oufir
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland.
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Abstract
Docking and quantifying the binding of small molecules to the 3D structure of a macromolecular bioregulator by computational techniques is a typical task in R&D aimed at the design and optimization of medically or otherwise active compounds. Much less known is the fact that these methods can be successfully applied for the purpose of toxicity prediction-for example, detecting a compound's potential binding to so-called "off-targets" already at the preclinical stage. In this chapter, we provide an overview of such a computational approach, discuss its strengths and weaknesses, and include a case study-focused on natural compounds present in traditional medicines.
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Affiliation(s)
- Martin Smieško
- Molecular Modeling, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland.
| | - Angelo Vedani
- Molecular Modeling, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
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Vedani A, Dobler M, Hu Z, Smieško M. OpenVirtualToxLab--a platform for generating and exchanging in silico toxicity data. Toxicol Lett 2014; 232:519-32. [PMID: 25240273 DOI: 10.1016/j.toxlet.2014.09.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/03/2014] [Indexed: 11/30/2022]
Abstract
The VirtualToxLab is an in silico technology for estimating the toxic potential--endocrine and metabolic disruption, some aspects of carcinogenicity and cardiotoxicity--of drugs, chemicals and natural products. The technology is based on an automated protocol that simulates and quantifies the binding of small molecules towards a series of currently 16 proteins, known or suspected to trigger adverse effects: 10 nuclear receptors (androgen, estrogen α, estrogen β, glucocorticoid, liver X, mineralocorticoid, peroxisome proliferator-activated receptor γ, progesterone, thyroid α, thyroid β), four members of the cytochrome P450 enzyme family (1A2, 2C9, 2D6, 3A4), a cytosolic transcription factor (aryl hydrocarbon receptor) and a potassium ion channel (hERG). The toxic potential of a compound--its ability to trigger adverse effects--is derived from its computed binding affinities toward these very proteins: the computationally demanding simulations are executed in client-server model on a Linux cluster of the University of Basel. The graphical-user interface supports all computer platforms, allows building and uploading molecular structures, inspecting and downloading the results and, most important, rationalizing any prediction at the atomic level by interactively analyzing the binding mode of a compound with its target protein(s) in real-time 3D. Access to the VirtualToxLab is available free of charge for universities, governmental agencies, regulatory bodies and non-profit organizations.
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Affiliation(s)
- Angelo Vedani
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; Foundation Biographics Laboratory 3R, Klingelbergstrasse 50, 4056 Basel, Switzerland.
| | - Max Dobler
- Foundation Biographics Laboratory 3R, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Zhenquan Hu
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Martin Smieško
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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Bezençon J, Wittwer MB, Cutting B, Smieško M, Wagner B, Kansy M, Ernst B. pKa determination by ¹H NMR spectroscopy - an old methodology revisited. J Pharm Biomed Anal 2013; 93:147-55. [PMID: 24462329 DOI: 10.1016/j.jpba.2013.12.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 12/12/2013] [Accepted: 12/16/2013] [Indexed: 11/17/2022]
Abstract
pKa values of acids and protonated bases have an essential impact on organic synthesis, medicinal chemistry, and material and food sciences. In drug discovery and development, they are of utmost importance for the prediction of pharmacokinetic and pharmacodynamic properties. To date, various methods for the determination of pKa values are available, including UV-spectroscopic, potentiometric, and capillary electrophoretic techniques. An additional option is provided by nuclear magnetic resonance (NMR) spectroscopy. The underlying principle is the alteration of chemical shifts of NMR-active nuclei (e.g., (13)C and (1)H) depending on the protonation state of adjacent acidic or basic sites. When these chemical shifts are plotted against the pH, the inflection point of the resulting sigmoidal curve defines the pKa value. Although pKa determinations by (1)H NMR spectroscopy are reported for numerous cases, the potential of this approach is not yet fully evaluated. We therefore revisited this method with a diverse set of test compounds covering a broad range of pKa values (pKa 0.9-13.8) and made a comparison with four commonly used approaches. The methodology revealed excellent correlations (R(2)=0.99 and 0.97) with electropotentiometric and UV spectroscopic methods. Moreover, the comparison with in silico results (Epik and Marvin) also showed high correlations (R(2)=0.92 and 0.94), further confirming the reliability and utility of this approach.
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Affiliation(s)
- Jacqueline Bezençon
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Matthias B Wittwer
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Brian Cutting
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Martin Smieško
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Bjoern Wagner
- Pharmaceuticals Division, Non-Clinical Safety, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Manfred Kansy
- Pharmaceuticals Division, Non-Clinical Safety, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Beat Ernst
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland.
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Zierke M, Smieško M, Rabbani S, Aeschbacher T, Cutting B, Allain FHT, Schubert M, Ernst B. Stabilization of branched oligosaccharides: Lewis(x) benefits from a nonconventional C-H···O hydrogen bond. J Am Chem Soc 2013; 135:13464-72. [PMID: 24001318 DOI: 10.1021/ja4054702] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although animal lectins usually show a high degree of specificity for glycan structures, their single-site binding affinities are typically weak, a drawback which is often compensated in biological systems by an oligovalent presentation of carbohydrate epitopes. For the design of monovalent glycomimetics, structural information regarding solution and bound conformation of the carbohydrate lead represents a valuable starting point. In this paper, we focus on the conformation of the trisaccharide Le(x) (Gal[Fucα(1-3)]β(1-4)GlcNAc). Mainly because of the unfavorable tumbling regime, the elucidation of the solution conformation of Le(x) by NMR has only been partially successful so far. Le(x) was therefore attached to a (13)C,(15)N-labeled protein. (13)C,(15)N-filtered NOESY NMR techniques at ultrahigh field allowed increasing the maximal NOE enhancement, resulting in a high number of distance restraints per glycosidic bond and, consequently, a well-defined structure. In addition to the known contributors to the conformational restriction of the Le(x) structure (exoanomeric effect, steric compression induced by the NHAc group adjacent to the linking position of L-fucose, and the hydrophobic interaction of L-fucose with the β-face of D-galactose), a nonconventional C-H···O hydrogen bond between H-C(5) of L-fucose and O(5) of D-galactose was identified. According to quantum mechanical calculations, this C-H···O hydrogen bond is the most prominent factor in stabilization, contributing 40% of the total stabilization energy. We therefore propose that the nonconventional hydrogen bond contributing to a reduction of the conformational flexibility of the Le(x) core represents a novel element of the glycocode. Its relevance to the stabilization of related branched oligosaccharides is currently being studied.
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Affiliation(s)
- Mirko Zierke
- University of Basel , Klingelbergstraße 50, CH-4056 Basel, Basel-City, Switzerland
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