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Fredenhagen A, Schroer K, Schröder H, Hoepfner D, Ligibel M, Porchet Zemp L, Radoch C, Freund E, Meishammer A. Cladosporin Derivatives Obtained by Biotransformation Provide Guidance for the Focused Derivatization of this Antimalarial Lead Compound. Chembiochem 2018; 20:650-654. [PMID: 30347507 DOI: 10.1002/cbic.201800588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Indexed: 12/16/2022]
Abstract
Cladosporin, a natural product known for decades, has recently been discovered to display potent and selective antiplasmodial activity by inhibition of lysyl-tRNA synthetase. It was subjected to a panel of oxidative biotransformations with one fungal and two actinomycetes strains, as well as a triple mutant bacterial CYP102A1, yielding eight, mostly hydroxylated, derivatives. These new compounds covered a wide chemical space and contained two pairs of epimers in the tetrahydropyran ring. Although less potent than the parent compound, all analogues showed activity in a cell-based synthetase assay, thus demonstrating uptake and on-target activity in living cells with varying degrees of selectivity for the enzyme lysyl-tRNA synthetase from Plasmodium falciparum and highlighting sites suitable for synthesis of future cladosporin analogues. Compounds with adjacent hydroxy functions showed different MS/MS fragmentation that can be explained in terms of an, in some cases, regioselective loss of water followed by a retro-Diels-Alder reaction.
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Affiliation(s)
- Andreas Fredenhagen
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry WKL-122.P.37, Postfach, 4002, Basel, Switzerland
| | - Kirsten Schroer
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry WKL-122.P.37, Postfach, 4002, Basel, Switzerland
| | - Harald Schröder
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry WKL-122.P.37, Postfach, 4002, Basel, Switzerland
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Chemical Biology and Therapeutics, Fabrikstrasse 22-3.051, Postfach, 4002, Basel, Switzerland
| | - Mathieu Ligibel
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry WKL-122.P.37, Postfach, 4002, Basel, Switzerland
| | - Liliane Porchet Zemp
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry WKL-122.P.37, Postfach, 4002, Basel, Switzerland
| | - Caroline Radoch
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry WKL-122.P.37, Postfach, 4002, Basel, Switzerland
| | - Ernst Freund
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry WKL-122.P.37, Postfach, 4002, Basel, Switzerland
| | - Aldo Meishammer
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry WKL-122.P.37, Postfach, 4002, Basel, Switzerland
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Winkler M, Geier M, Hanlon SP, Nidetzky B, Glieder A. Human Enzymes for Organic Synthesis. Angew Chem Int Ed Engl 2018; 57:13406-13423. [PMID: 29600541 PMCID: PMC6334177 DOI: 10.1002/anie.201800678] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Indexed: 02/06/2023]
Abstract
Human enzymes have been widely studied in various disciplines. The number of reactions taking place in the human body is vast, and so is the number of potential catalysts for synthesis. Herein, we focus on the application of human enzymes that catalyze chemical reactions in course of the metabolism of drugs and xenobiotics. Some of these reactions have been explored on the preparative scale. The major field of application of human enzymes is currently drug development, where they are applied for the synthesis of drug metabolites.
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Affiliation(s)
- Margit Winkler
- Institute for Molecular BiotechnologyGraz University of TechnologyPetersgasse 148010GrazAustria
- acib GmbHPetersgasse 148010GrazAustria
| | | | | | - Bernd Nidetzky
- acib GmbHPetersgasse 148010GrazAustria
- Institute of Biotechnology and Biochemical EngineeringGraz University of TechnologyPetersgasse 128010GrazAustria
| | - Anton Glieder
- Institute for Molecular BiotechnologyGraz University of TechnologyPetersgasse 148010GrazAustria
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Migglautsch AK, Willim M, Schweda B, Glieder A, Breinbauer R, Winkler M. Aliphatic hydroxylation and epoxidation of capsaicin by cytochrome P450 CYP505X. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.08.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Winkler M, Geier M, Hanlon SP, Nidetzky B, Glieder A. Humane Enzyme für die organische Synthese. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Margit Winkler
- Institut für Molekulare Biotechnologie; Technische Universität Graz; Petersgasse 14 8010 Graz Österreich
- acib GmbH; Petersgasse 14 8010 Graz Österreich
| | | | | | - Bernd Nidetzky
- acib GmbH; Petersgasse 14 8010 Graz Österreich
- Institut für Biotechnologie und Bioprozesstechnik; Technische Universität Graz; Petersgasse 12 8010 Graz Österreich
| | - Anton Glieder
- Institut für Molekulare Biotechnologie; Technische Universität Graz; Petersgasse 14 8010 Graz Österreich
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Wang N, Wang L, Xie XQ. ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research. J Chem Inf Model 2017; 57:2686-2698. [PMID: 29016123 DOI: 10.1021/acs.jcim.7b00277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular docking is widely applied to computer-aided drug design and has become relatively mature in the recent decades. Application of docking in modeling varies from single lead compound optimization to large-scale virtual screening. The performance of molecular docking is highly dependent on the protein structures selected. It is especially challenging for large-scale target prediction research when multiple structures are available for a single target. Therefore, we have established ProSelection, a docking preferred-protein selection algorithm, in order to generate the proper structure subset(s). By the ProSelection algorithm, protein structures of "weak selectors" are filtered out whereas structures of "strong selectors" are kept. Specifically, the structure which has a good statistical performance of distinguishing active ligands from inactive ligands is defined as a strong selector. In this study, 249 protein structures of 14 autophagy-related targets are investigated. Surflex-dock was used as the docking engine to distinguish active and inactive compounds against these protein structures. Both t test and Mann-Whitney U test were used to distinguish the strong from the weak selectors based on the normality of the docking score distribution. The suggested docking score threshold for active ligands (SDA) was generated for each strong selector structure according to the receiver operating characteristic (ROC) curve. The performance of ProSelection was further validated by predicting the potential off-targets of 43 U.S. Federal Drug Administration approved small molecule antineoplastic drugs. Overall, ProSelection will accelerate the computational work in protein structure selection and could be a useful tool for molecular docking, target prediction, and protein-chemical database establishment research.
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Affiliation(s)
- Nanyi Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; NIH National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Lirong Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; NIH National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; NIH National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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Van Veggel M, Westerman E, Hamberg P. Clinical Pharmacokinetics and Pharmacodynamics of Panobinostat. Clin Pharmacokinet 2017; 57:21-29. [DOI: 10.1007/s40262-017-0565-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Goey AK, Sissung TM, Peer CJ, Figg WD. Pharmacogenomics and histone deacetylase inhibitors. Pharmacogenomics 2016; 17:1807-1815. [PMID: 27767376 DOI: 10.2217/pgs-2016-0113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The histone deacetylase inhibitor valproic acid (VPA) has been used for many decades in neurology and psychiatry. The more recent introduction of the histone deacetylase inhibitors (HDIs) belinostat, romidepsin and vorinostat for treatment of hematological malignancies indicates the increasing popularity of these agents. Belinostat, romidepsin and vorinostat are metabolized or transported by polymorphic enzymes or drug transporters. Thus, genotype-directed dosing could improve pharmacotherapy by reducing the risk of toxicities or preventing suboptimal treatment. This review provides an overview of clinical studies on the effects of polymorphisms on the pharmacokinetics, efficacy or toxicities of HDIs including belinostat, romidepsin, vorinostat, panobinostat, VPA and a number of novel compounds currently being tested in Phase I and II trials. Although pharmacogenomic studies for HDIs are scarce, available data indicate that therapy with belinostat (UGT1A1), romidepsin (ABCB1), vorinostat (UGT2B17) or VPA (UGT1A6) could be optimized by upfront genotyping.
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Affiliation(s)
- Andrew Kl Goey
- Clinical Pharmacology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tristan M Sissung
- Clinical Pharmacology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cody J Peer
- Clinical Pharmacology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William D Figg
- Clinical Pharmacology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Ex Vivo Bioactivity and HIV-1 Latency Reversal by Ingenol Dibenzoate and Panobinostat in Resting CD4(+) T Cells from Aviremic Patients. Antimicrob Agents Chemother 2015; 59:5984-91. [PMID: 26169416 DOI: 10.1128/aac.01077-15] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/07/2015] [Indexed: 12/29/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) latent reservoir in resting CD4(+) T cells represents a major barrier to viral eradication. Small compounds capable of latency reversal have not demonstrated uniform responses across in vitro HIV-1 latency cell models. Characterizing compounds that demonstrate latency-reversing activity in resting CD4(+) T cells from aviremic patients ex vivo will help inform pilot clinical trials aimed at HIV-1 eradication. We have optimized a rapid ex vivo assay using resting CD4(+) T cells from aviremic HIV-1(+) patients to evaluate both the bioactivity and latency-reversing potential of candidate latency-reversing agents (LRAs). Using this assay, we characterize the properties of two candidate compounds from promising LRA classes, ingenol 3,20-dibenzoate (a protein kinase C agonist) and panobinostat (a histone deacetylase inhibitor), in cells from HIV-1(+) antiretroviral therapy (ART)-treated aviremic participants, including the effects on cellular activation and cytotoxicity. Ingenol induced viral release at levels similar to those of the positive control (CD3/28 receptor stimulation) in cells from a majority of participants and represents an exciting LRA candidate, as it combines a robust viral reactivation potential with a low toxicity profile. At concentrations that blocked histone deacetylation, panobinostat displayed a wide range of potency among participant samples and consistently induced significant levels of apoptosis. The protein kinase C agonist ingenol 3,20-dibenzoate demonstrated significant promise in a rapid ex vivo assay using resting CD4(+) T cells from treated HIV-1-positive patients to measure latent HIV-1 reactivation.
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A phase I, open-label, multicenter study to evaluate the pharmacokinetics and safety of oral panobinostat in patients with advanced solid tumors and varying degrees of renal function. Cancer Chemother Pharmacol 2014; 75:87-95. [PMID: 25377157 DOI: 10.1007/s00280-014-2612-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
PURPOSE This study assessed the pharmacokinetics and safety of oral panobinostat and its metabolite BJB432 in patients with advanced solid tumors and normal to severely impaired renal function. METHODS Patients with varying degrees of renal impairment, defined by their 24-h baseline urine creatinine clearance (as normal, mild, moderate or severe), received a single oral dose of 30 mg panobinostat. Serial plasma samples were collected pre-dose and up to 96-h post-dose. Serial urine samples were collected for 24-h post-dose. Following the serial PK sampling, patients received 30 mg oral panobinostat thrice weekly for as long as the patient had benefit. Pharmacokinetic parameters were derived using non-compartmental analysis. RESULTS Thirty-seven patients were enrolled, and median age was 64 (range 40-81) years. Eleven patients had normal renal function; 10, 10, and 6 patients had mild, moderate, and severe renal impairment, respectively. Geometric means of AUC(0-∞) in the normal, mild, moderate, and severe groups were 224.5, 144.3, 223.1, and 131.7 ng h/mL, respectively. Geometric mean ratio of BJB432 to parent drug plasma AUC(0-∞) was 0.64 in the normal group and increased to 0.81, 1.13, and 1.20 in the mild, moderate, and severe groups, respectively. The fraction excreted as unchanged panobinostat was small (<2 %), with a large variability. The renal clearance of panobinostat and tolerability was similar across all four groups. CONCLUSION Systemic exposure to panobinostat did not increase with severity of renal impairment, and the drug was tolerated equally; thus, patients with renal impairment do not require starting dose adjustments.
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Indole-3-ethylsulfamoylphenylacrylamides: Potent histone deacetylase inhibitors with anti-inflammatory activity. Eur J Med Chem 2014; 85:468-79. [DOI: 10.1016/j.ejmech.2014.08.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/05/2014] [Accepted: 08/06/2014] [Indexed: 01/04/2023]
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A phase I, open-label, multicenter study to evaluate the pharmacokinetics and safety of oral panobinostat in patients with advanced solid tumors and various degrees of hepatic function. Cancer Chemother Pharmacol 2014; 74:1089-98. [DOI: 10.1007/s00280-014-2594-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/12/2014] [Indexed: 12/22/2022]
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Han H, Xiong AZ, He CY, Liu Q, Yang L, Wang ZT. Combination of UHPLC/Q-TOF-MS, NMR spectroscopy, and ECD calculation for screening and identification of reactive metabolites of gentiopicroside in humans. Anal Bioanal Chem 2014; 406:1781-93. [PMID: 24408300 DOI: 10.1007/s00216-013-7572-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/01/2013] [Accepted: 12/10/2013] [Indexed: 01/09/2023]
Abstract
The metabolic investigation of natural products is a great challenge because of unpredictable metabolic pathways, little knowledge on metabolic effects, and lack of recommended analytical methodology. Herein, a combined strategy based on ultrahigh-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UHPLC/Q-TOF-MS), nuclear magnetic resonance (NMR) spectroscopy, and electronic circular dichroism (ECD) calculation was developed and employed for the human metabolism study of gentiopicroside (GPS), a naturally hepato-protective iridoid glycoside. The whole metabolic study consisted of three major procedures. First, an improved UHPLC/Q-TOF-MS method was used to separate and detect a total of 15 GPS metabolites that were obtained from urine samples (0 to 72 h) of 12 healthy male participants after a single 50-mg oral dose of GPS. Second, a developed "MS-NMR-MS" method was applied to accurately identify molecular structures of the observed metabolites. Finally, given that the associated stereochemistry may be a crucial factor of the metabolic activation, the absolute configuration of the reactive metabolites was revealed through chemical calculations. Based on the combined use, a pair of diastereoisomers (G05 and G06) were experimentally addressed as the bioreactive metabolites of GPS, and the stereochemical determination was completed. Whereas several novel metabolic transformations, occurring via oxidation, N-heterocyclization and glucuronidation after deglycosylation, were also observed. The results indicated that GPS has to undergo in vivo metabolism-based activation to generate reactive molecules capable of processing its hepato-protective activity.
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Affiliation(s)
- Han Han
- The Ministry of Education (MOE) Key Laboratory for Standardization of Chinese Medicines, Institute of Traditional Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201210, China
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