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New Insights into Bitopic Orthosteric/Allosteric Ligands of Cannabinoid Receptor Type 2. Int J Mol Sci 2023; 24:ijms24032135. [PMID: 36768458 PMCID: PMC9917213 DOI: 10.3390/ijms24032135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Very recently, we have developed a new generation of ligands targeting the cannabinoid receptor type 2 (CB2R), namely JR compounds, which combine the pharmacophoric portion of the CB2R positive allosteric modulator (PAM), EC21a, with that of the CB2R selective orthosteric agonist LV62, both synthesized in our laboratories. The functional examination enabled us to identify JR14a, JR22a, and JR64a as the most promising compounds of the series. In the current study, we focused on the assessment of the bitopic (dualsteric) nature of these three compounds. Experiments in cAMP assays highlighted that only JR22a behaves as a CB2R bitopic (dualsteric) ligand. In parallel, computational studies helped us to clarify the binding mode of these three compounds at CB2R, confirming the bitopic (dualsteric) nature of JR22a. Finally, the potential of JR22a to prevent neuroinflammation was investigated on a human microglial cell inflammatory model.
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2
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Wójcik-Pszczoła K, Szafarz M, Pociecha K, Słoczyńska K, Piska K, Koczurkiewicz-Adamczyk P, Kocot N, Chłoń-Rzepa G, Pękala E, Wyska E. In silico and in vitro ADME-Tox analysis and in vivo pharmacokinetic study of representative pan-PDE inhibitors from the group of 7,8-disubstituted derivatives of 1,3-dimethyl-7H-purine-2,6-dione. Toxicol Appl Pharmacol 2022; 457:116318. [PMID: 36414119 DOI: 10.1016/j.taap.2022.116318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/05/2022] [Accepted: 11/12/2022] [Indexed: 11/21/2022]
Abstract
Phosphodiesterase (PDE) inhibitors represent a wide class of chemically different compounds that have been extensively studied in recent years. Their anti-inflammatory and anti-fibrotic effects are particularly desirable in the treatment of chronic respiratory diseases, including asthma and chronic obstructive pulmonary disease (COPD). Due to diversified expression of individual PDEs within cells and/or tissues as well as PDE signaling compartmentalization, pan-PDE inhibitors (compounds capable of simultaneously blocking various PDE subtypes) are of particular interest. Recently, a large group of 7,8-disubstituted derivatives of 1,3-dimethyl-7H-purine-2,6-dione (theophylline) was designed and synthesized. These compounds were characterized as potent pan-PDE inhibitors and their prominent anti-inflammatory and anti-fibrotic activity in vitro has been proved. Herein, we investigated a general in vitro safety profile and pharmacokinetic characteristics of two leading compounds from this group: a representative compound with N'-benzylidenebutanehydrazide moiety (38) and a representative derivative containing N-phenylbutanamide fragment (145). Both tested pan-PDE inhibitors revealed no cytotoxic, mutagenic, and genotoxic activity in vitro, showed moderate metabolic stability in mouse and human liver microsomes, as well as fell into the low or medium permeation category. Additionally, 38 and 145 revealed a lack of interaction with adenosine receptors, including A1, A2A, and A2B. Pharmacokinetic analysis revealed that both tested 7,8-disubstituted derivatives of 1,3-dimethyl-7H-purine-2,6-dione were effectively absorbed from the peritoneal cavity. Simultaneously, they were extensively distributed to mouse lungs and after intraperitoneal (i.p.) administration were detected in bronchoalveolar lavage fluid. These findings provide evidence that investigated compounds represent a new drug candidates with a favorable in vitro safety profile and satisfactory pharmacokinetic properties after a single i.p. administration. As the next step, further pharmacokinetic studies after multiple i.p. and p.o. doses will be conducted to ensure effective 38 and 145 serum and lung concentrations for a longer period of time. In summary, 7,8-disubstituted derivatives of 1,3-dimethyl-7H-purine-2,6-dione represent a promising compounds worth testing in animal models of chronic respiratory diseases, the etiology of which involves various PDE subtypes.
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Affiliation(s)
- Katarzyna Wójcik-Pszczoła
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland.
| | - Małgorzata Szafarz
- Department of Pharmacokinetics and Physical Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland
| | - Krzysztof Pociecha
- Department of Pharmacokinetics and Physical Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland
| | - Karolina Słoczyńska
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland
| | - Kamil Piska
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland
| | - Paulina Koczurkiewicz-Adamczyk
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland
| | - Natalia Kocot
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland
| | - Grażyna Chłoń-Rzepa
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland
| | - Elżbieta Pękala
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland
| | - Elżbieta Wyska
- Department of Pharmacokinetics and Physical Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland.
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3
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Hughes TB, Flynn N, Dang NL, Swamidass SJ. Modeling the Bioactivation and Subsequent Reactivity of Drugs. Chem Res Toxicol 2021; 34:584-600. [PMID: 33496184 DOI: 10.1021/acs.chemrestox.0c00417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrophilically reactive drug metabolites are implicated in many adverse drug reactions. In this mechanism-termed bioactivation-metabolic enzymes convert drugs into reactive metabolites that often conjugate to nucleophilic sites within biological macromolecules like proteins. Toxic metabolite-product adducts induce severe immune responses that can cause sometimes fatal disorders, most commonly in the form of liver injury, blood dyscrasia, or the dermatologic conditions toxic epidermal necrolysis and Stevens-Johnson syndrome. This study models four of the most common metabolic transformations that result in bioactivation: quinone formation, epoxidation, thiophene sulfur-oxidation, and nitroaromatic reduction, by synthesizing models of metabolism and reactivity. First, the metabolism models predict the formation probabilities of all possible metabolites among the pathways studied. Second, the exact structures of these metabolites are enumerated. Third, using these structures, the reactivity model predicts the reactivity of each metabolite. Finally, a feedfoward neural network converts the metabolism and reactivity predictions to a bioactivation prediction for each possible metabolite. These bioactivation predictions represent the joint probability that a metabolite forms and that this metabolite subsequently conjugates to protein or glutathione. Among molecules bioactivated by these pathways, we predicted the correct pathway with an AUC accuracy of 89.98%. Furthermore, the model predicts whether molecules will be bioactivated, distinguishing bioactivated and nonbioactivated molecules with 81.06% AUC. We applied this algorithm to withdrawn drugs. The known bioactivation pathways of alclofenac and benzbromarone were identified by the algorithm, and high probability bioactivation pathways not yet confirmed were identified for safrazine, zimelidine, and astemizole. This bioactivation model-the first of its kind that jointly considers both metabolism and reactivity-enables drug candidates to be quickly evaluated for a toxicity risk that often evades detection during preclinical trials. The XenoSite bioactivation model is available at http://swami.wustl.edu/xenosite/p/bioactivation.
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Affiliation(s)
- Tyler B Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Noah Flynn
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Na Le Dang
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - S Joshua Swamidass
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
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4
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Goracci L, Desantis J, Valeri A, Castellani B, Eleuteri M, Cruciani G. Understanding the Metabolism of Proteolysis Targeting Chimeras (PROTACs): The Next Step toward Pharmaceutical Applications. J Med Chem 2020; 63:11615-11638. [PMID: 33026811 PMCID: PMC8015227 DOI: 10.1021/acs.jmedchem.0c00793] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Indexed: 12/15/2022]
Abstract
Hetero-bifunctional PROteolysis TArgeting Chimeras (PROTACs) represent a new emerging class of small molecules designed to induce polyubiquitylation and proteasomal-dependent degradation of a target protein. Despite the increasing number of publications about the synthesis, biological evaluation, and mechanism of action of PROTACs, the characterization of the pharmacokinetic properties of this class of compounds is still minimal. Here, we report a study on the metabolism of a series of 40 PROTACs in cryopreserved human hepatocytes at multiple time points. Our results indicated that the metabolism of PROTACs could not be predicted from that of their constituent ligands. Their linkers' chemical nature and length resulted in playing a major role in the PROTACs' liability. A subset of compounds was also tested for metabolism by human cytochrome P450 3A4 (CYP3A4) and human aldehyde oxidase (hAOX) for more in-depth data interpretation, and both enzymes resulted in active PROTAC metabolism.
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Affiliation(s)
- Laura Goracci
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Jenny Desantis
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | | | - Beatrice Castellani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Michela Eleuteri
- Montelino
Therapeutics, LLC, 7
Powdermill Lane, Southborough, Massachusetts 01772 Unites States
| | - Gabriele Cruciani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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5
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Viana JO, Scotti MT, Scotti L. Computer-aided Drug Design Investigations for Benzothiazinone Derivatives Against Tuberculosis. Comb Chem High Throughput Screen 2020; 23:66-82. [PMID: 31957611 DOI: 10.2174/1386207323666200117102316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 12/05/2019] [Accepted: 12/11/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Tuberculosis (Mycobacterium tuberculosis) is an infectious bacterial disease with the highest levels of mortality worldwide, presenting numerous cases of resistance. In silico studies, which elaborate chemical and biological models in computational tools and make it possible to interpret molecular characteristics, are among the methods used in the search for new drugs. OBJECTIVE In this perspective, our aim was to use QSAR and molecular modeling to propose possible pharmacophores from benzothiazinone derivatives. METHODS In this study, a set of 69 benzothiazinone derivatives, together with computational tools such as molecular descriptor analysis in chemometrics, metabolic prediction, and molecular coupling to 4 proteins: DprE1, InhA, PS, and DHFR important for the bacillus were investigated. RESULTS The chemometric model computed in the Volsurf+ program presented good predictive values for both amphiphilicity and molecular volume. These are essential for biological activity. Metabolites from the cytochrome isoforms CYP3A4 and 2D6 interactions revealed coupling divergences which, noting that the metabolites did not present changes to the QSAR proposed pharmacophore structures, may be due to the reaction medium and existing differences in the benzothiazinone structures. Similarly, molecular docking with the four TB enzymes presented good interactions for the more active compounds. The fragments found using QSAR (being essential for biological activity) also presented as being essential for ligand-protein site interactions. CONCLUSION From the benzothiazinone derivative series evaluated, compound 11026134 presented the best profile in all study analyses, noting that the trifluoromethyl, nitro group, and piperazine fragment with aliphatic hydrocarbon groups are likely pharmacophores for the benzothiazinones studied.
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Affiliation(s)
- Jéssika O Viana
- Federal University of Paraíba, Health Science Center, 50670-910, Joao Pessoa, PB, Brazil
| | - Marcus T Scotti
- Federal University of Paraíba, Health Science Center, 50670-910, Joao Pessoa, PB, Brazil
| | - Luciana Scotti
- Federal University of Paraíba, Health Science Center, 50670-910, Joao Pessoa, PB, Brazil.,Teaching and Research Management, University Hospital, Federal University of Paraíba, João Pessoa, PB, Brazil
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Broccatelli F, E.C.A Hop C, Wright M. Strategies to optimize drug half-life in lead candidate identification. Expert Opin Drug Discov 2019; 14:221-230. [DOI: 10.1080/17460441.2019.1569625] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Fabio Broccatelli
- Department of Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, CA, USA
| | - Cornelis E.C.A Hop
- Department of Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, CA, USA
| | - Matthew Wright
- Department of Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, CA, USA
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TPT sulfonate, a single, oral dose schistosomicidal prodrug: In vivo efficacy, disposition and metabolic profiling. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2018; 8:571-586. [PMID: 30503203 PMCID: PMC6287543 DOI: 10.1016/j.ijpddr.2018.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 12/16/2022]
Abstract
Treatment of schistosomiasis relies precariously on just one drug, praziquantel (PZQ). In the search for alternatives, 15 S-[2-(alkylamino)alkane] thiosulfuric acids were obtained from a previous research program and profiled in mice for efficacy against both mature (>42-day-old) and juvenile (21-day-old) Schistosoma mansoni using a screening dose of 100 mg/kg PO QDx4. One compound, S-[2-(tert-butylamino)-1-phenylethane] thiosulfuric acid (TPT sulfonate), was the most effective by decreasing female and male worm burdens by ≥ 90% and ≥46% (mature), and ≥89% and ≥79% (juvenile), respectively. In contrast, PZQ decreased mature female and male worm burdens by 95% and 94%, respectively, but was ineffective against juvenile stages. Against 7-day-old lung-stage worms, TPT sulfonate was only effective at twice the dose decreasing female and male burdens by 95 and 80%, respectively. Single oral doses at 400 and/or 600 mg/kg across various developmental time-points (1-, 7-, 15-, 21- and/or 42 day-old) were consistent with the QD x4 data; efficacy was strongest once the parasites had completed lung migration, and female and male burdens were decreased by at least 90% and 80%, respectively. In vitro, TPT sulfonate is inactive against the parasite suggesting a pro-drug mechanism of action. In mice, TPT sulfonate is fully absorbed and subject to rapid, non-CYP-mediated, first-pass metabolism that is initiated by desulfation and yields a series of metabolites. The initially-formed free thiol-containing metabolite, termed TP thiol, was chemically synthesized; it dose-dependently decreased S. mansoni and Schistosoma haematobium motility in vitro. Also, when administered as a single 50 mg/kg IP dose, TP thiol decreased 33-day-old S. mansoni female and male burdens by 35% and 44%, with less severe organomegaly. Overall, TPT sulfonate's efficacy profile is competitive with that of PZQ. Also, the characterization of a parasiticidal metabolite facilitates an understanding and improvement of the chemistry, and identification of the mechanism of action and/or target. TPT sulfonate provides single dose efficacy that is competitive with the current drug, praziquantel. TPT sulfonate must be biotransformed to be active. TPT sulfonate is fully absorbed and subject to rapid, non-CYP-mediated, first-pass metabolism. One of the key metabolites, TP thiol, is anti-schistosomal in vitro and in vivo.
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8
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Vickers C, Backfisch G, Oellien F, Piel I, Lange UEW. Enzymatic Late‐Stage Oxidation of Lead Compounds with Solubilizing Biomimetic Docking/Protecting groups. Chemistry 2018; 24:17936-17947. [DOI: 10.1002/chem.201802331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/12/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Clare Vickers
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Gisela Backfisch
- Development Sciences, DMPK and Bioanalytical ResearchAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Frank Oellien
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Isabel Piel
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Udo E. W. Lange
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
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9
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Li J, Zhang H, Liu G, Tang Y, Tu Y, Li W. Computational Insight Into Vitamin K 1 ω-Hydroxylation by Cytochrome P450 4F2. Front Pharmacol 2018; 9:1065. [PMID: 30319412 PMCID: PMC6167488 DOI: 10.3389/fphar.2018.01065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/03/2018] [Indexed: 12/28/2022] Open
Abstract
Vitamin K1 (VK1) plays an important role in the modulation of bleeding disorders. It has been reported that ω-hydroxylation on the VK1 aliphatic chain is catalyzed by cytochrome P450 4F2 (CYP4F2), an enzyme responsible for the metabolism of eicosanoids. However, the mechanism of VK1 ω-hydroxylation by CYP4F2 has not been disclosed. In this study, we employed a combination of quantum mechanism (QM) calculations, homology modeling, molecular docking, molecular dynamics (MD) simulations, and combined quantum mechanism/molecular mechanism (QM/MM) calculations to investigate the metabolism profile of VK1 ω-hydroxylation. QM calculations based on the truncated VK1 model show that the energy barrier for ω-hydroxylation is about 6-25 kJ/mol higher than those at other potential sites of metabolism. However, results from the MD simulations indicate that hydroxylation at the ω-site is more favorable than at the other potential sites, which is in accordance with the experimental observation. The evaluation of MD simulations was further endorsed by the QM/MM calculation results. Our studies thus suggest that the active site residues of CYP4F2 play a determinant role in the ω-hydroxylation. Our results provide structural insights into the mechanism of VK1 ω-hydroxylation by CYP4F2 at the atomistic level and are helpful not only for characterizing the CYP4F2 functions but also for looking into the ω-hydroxylation mediated by other CYP4 enzymes.
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Affiliation(s)
- Junhao Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China.,Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Hongxiao Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
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10
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Mota C, Coelho C, Leimkühler S, Garattini E, Terao M, Santos-Silva T, Romão MJ. Critical overview on the structure and metabolism of human aldehyde oxidase and its role in pharmacokinetics. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Abstract
Beyond finding inhibitors that show high binding affinity to the respective target, there is the challenge of optimizing their properties with respect to metabolic and toxicological issues, as well as further off-target effects. To reduce the experimental effort of synthesizing and testing actual substances in corresponding assays, virtual screening has become an indispensable toolbox in preclinical development. The scope of application covers the prediction of molecular properties including solubility, metabolic liability and binding to antitargets, such as the hERG channel. Furthermore, prediction of binding sites and drugable targets are emerging aspects of virtual screening. Issues involved with the currently applied computational models including machine learning algorithms are outlined, such as limitations to the accuracy of prediction and overfitting.
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12
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Słoczyńska K, Wójcik-Pszczoła K, Canale V, Żmudzki P, Zajdel P, Pękala E. Biotransformation of 4-fluoro-N-(1-{2-[(propan-2-yl)phenoxy]ethyl}-8-azabicyclo[3.2.1]octan-3-yl)-benzenesulfonamide, a novel potent 5-HT 7 receptor antagonist with antidepressant-like and anxiolytic properties: In vitro and in silico approach. J Biochem Mol Toxicol 2018; 32:e22048. [PMID: 29469967 DOI: 10.1002/jbt.22048] [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: 10/31/2017] [Revised: 01/16/2018] [Accepted: 01/20/2018] [Indexed: 12/15/2022]
Abstract
The aim of the study was to investigate the metabolism of 4-fluoro-N-(1-{2-[(propan-2-yl)phenoxy]ethyl}-8-azabicyclo[3.2.1]octan-3-yl)-benzenesulfonamide (PZ-1150), a novel 5-HT7 receptor antagonist with antidepressant-like and anxiolytic properties, by the following three ways: in vitro with microsomes; in vitro employing Cunninghamella echinulata, and in silico using MetaSite. Biotransformation of PZ-1150 with microsomes resulted in five metabolites, while transformation with C. echinulata afforded two metabolites. In both models, the predominant metabolite occurred due to hydroxylation of benzene ring. In silico data coincide with in vitro experiments, as three MetaSite metabolites matched compounds identified in microsomal samples. In human liver microsomes PZ-1150 exhibited in vitro half-life of 64 min, with microsomal intrinsic clearance of 54.1 μL/min/mg and intrinsic clearance of 48.7 mL/min/kg. Therefore, PZ-1150 is predicted to be a high-clearance agent. The study demonstrated the applicability of using microsomal model coupled with microbial model to elucidate the metabolic pathways of compounds and comparison with in silico metabolite predictions.
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Affiliation(s)
- Karolina Słoczyńska
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, Krakow 30-688, Poland
| | - Katarzyna Wójcik-Pszczoła
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, Krakow 30-688, Poland
| | - Vittorio Canale
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, Krakow 30-688, Poland
| | - Paweł Żmudzki
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, Krakow 30-688, Poland
| | - Paweł Zajdel
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, Krakow 30-688, Poland
| | - Elżbieta Pękala
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, Krakow 30-688, Poland
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13
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Cruciani G, Milani N, Benedetti P, Lepri S, Cesarini L, Baroni M, Spyrakis F, Tortorella S, Mosconi E, Goracci L. From Experiments to a Fast Easy-to-Use Computational Methodology to Predict Human Aldehyde Oxidase Selectivity and Metabolic Reactions. J Med Chem 2017; 61:360-371. [DOI: 10.1021/acs.jmedchem.7b01552] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriele Cruciani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
| | - Nicolò Milani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Paolo Benedetti
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
| | - Susan Lepri
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Lucia Cesarini
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Massimo Baroni
- Molecular Discovery Ltd, Centennial
Park, Borehamwood, Hertfordshire, United Kingdom
| | - Francesca Spyrakis
- Department
of Drug Science and Technology, University of Turin, via P. Giuria
9, 10125 Turin, Italy
| | - Sara Tortorella
- Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
- Molecular Horizon srl, via Montelino
32, 06084 Bettona, Italy
| | - Edoardo Mosconi
- Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
- Computational
Laboratory for Hybrid/Organic Photovoltaics, National Research Council−Institute of Molecular Science and Technologies, Via Elce
di Sotto 8, I-06123 Perugia, Italy
| | - Laura Goracci
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
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14
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Righetti L, Rolli E, Galaverna G, Suman M, Bruni R, Dall’Asta C. Plant organ cultures as masked mycotoxin biofactories: Deciphering the fate of zearalenone in micropropagated durum wheat roots and leaves. PLoS One 2017; 12:e0187247. [PMID: 29145415 PMCID: PMC5690627 DOI: 10.1371/journal.pone.0187247] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 10/17/2017] [Indexed: 12/20/2022] Open
Abstract
"Masked mycotoxins" senso strictu are conjugates of mycotoxins resulting from metabolic pathways activated by the interplay between pathogenic fungi and infected plants. Zearalenone, an estrogenic mycotoxin produced by Fusarium spp, was the first masked mycotoxin ever described in the literature, but its biotransformation has been studied to a lesser extent if compared to other compounds such as deoxynivalenol. We presented herein the first application of organ and tissue culture techniques to study the metabolic fate of zearalenone in durum wheat, using an untargeted HR-LCMS approach. A complete, quick absorption of zearalenone by uninfected plant organs was noticed, and its biotransformation into a large spectrum of phase I and phase II metabolites has been depicted. Therefore, wheat organ tissue cultures can be effectively used as a biocatalytic tool for the production of masked mycotoxins, as well as a replicable model for the investigation of the interplay between mycotoxins and wheat physiology.
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Affiliation(s)
- Laura Righetti
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Enrico Rolli
- Deparment of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Michele Suman
- Barilla G.R. F.lli SpA, Advanced Laboratory Research, Parma, Italy
| | - Renato Bruni
- Department of Food and Drug, University of Parma, Parma, Italy
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15
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De Deurwaerdère P, Binda C, Corne R, Leone C, Valeri A, Valoti M, Ramsay RR, Fall Y, Marco-Contelles J. Comparative Analysis of the Neurochemical Profile and MAO Inhibition Properties of N-(Furan-2-ylmethyl)-N-methylprop-2-yn-1-amine. ACS Chem Neurosci 2017; 8:1026-1035. [PMID: 27977122 DOI: 10.1021/acschemneuro.6b00377] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The regulation of brain monoamine levels is paramount for cognitive functions, and the monoamine oxidase (MAO A and B) enzymes play a central role in these processes. The aim of this study was to evaluate whether the procognitive properties exerted by propargylamine N-(furan-2-ylmethyl)-N-methylprop-2-yn-1-amine (F2MPA) are related to changes in monoamine content via MAO inhibition. In vivo microdialysis and ex vivo amine metabolite measurement demonstrated region-specific alterations in monoamine metabolism that differ from both of the classic MAO A and MAO B inhibitors, clorgyline and l-deprenyl, respectively. Although all the inhibitors (1 and 4 mg/kg) increased cortical serotonin tissue content, only F2MPA increased the levels of cortical noradrenaline. In the striatum, clorgyline (1 mg/kg), but not F2MPA (1 mg/kg), reduced extracellular levels of dopamine metabolites at rest or stimulated by the intrastriatal application of the MAO substrate 3-methoxytyramine. In vitro, F2MPA exhibited a low affinity toward MAO B and MAO A. Nonetheless, it modified the B form of MAO, forming a flavin adduct structurally similar to that with deprenyl. F2MPA was rapidly metabolized in the presence of rat but not human microsomes, producing a hydroxylated derivative. In conclusion, the effect of F2MPA on cognition may arise from monoaminergic changes in the cortex, but the role of MAO in this process is likely to be negligible, consistent with the poor affinity of F2MPA for MAO.
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Affiliation(s)
- Philippe De Deurwaerdère
- Centre National de la Recherche Scientifique, Institut
des Maladies Neurodégénératives, UMR CNRS 5293, 33000 Bordeaux, France
| | - Claudia Binda
- Dipartimento
di Biologia e Biotecnologie, Università di Pavia, 27100 Pavia, Italy
| | - Rémi Corne
- Centre National de la Recherche Scientifique, Institut
des Maladies Neurodégénératives, UMR CNRS 5293, 33000 Bordeaux, France
| | - Cosima Leone
- Dipartimento
di Scienze della Vita, Università di Siena, 53100 Siena, Italy
| | - Aurora Valeri
- Dipartimento
di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Massimo Valoti
- Dipartimento
di Scienze della Vita, Università di Siena, 53100 Siena, Italy
| | - Rona R. Ramsay
- Biomedical
Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, U.K
| | - Yagamare Fall
- Departamento
de Química Orgánica, Universidad de Vigo, 36310 Vigo, Spain
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16
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Goracci L, Tortorella S, Tiberi P, Pellegrino RM, Di Veroli A, Valeri A, Cruciani G. Lipostar, a Comprehensive Platform-Neutral Cheminformatics Tool for Lipidomics. Anal Chem 2017; 89:6257-6264. [DOI: 10.1021/acs.analchem.7b01259] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Laura Goracci
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Sara Tortorella
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Paolo Tiberi
- Molecular Discovery Ltd., Centennial
Park, Borehamwood, Hertfordshire, United Kingdom
| | - Roberto Maria Pellegrino
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Alessandra Di Veroli
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Aurora Valeri
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Gabriele Cruciani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
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17
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Structure-metabolism relationships in human-AOX: Chemical insights from a large database of aza-aromatic and amide compounds. Proc Natl Acad Sci U S A 2017; 114:E3178-E3187. [PMID: 28373537 DOI: 10.1073/pnas.1618881114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aldehyde oxidase (AOX) is a metabolic enzyme catalyzing the oxidation of aldehyde and aza-aromatic compounds and the hydrolysis of amides, moieties frequently shared by the majority of drugs. Despite its key role in human metabolism, to date only fragmentary information about the chemical features responsible for AOX susceptibility are reported and only "very local" structure-metabolism relationships based on a small number of similar compounds have been developed. This study reports a more comprehensive coverage of the chemical space of structures with a high risk of AOX phase I metabolism in humans. More than 270 compounds were studied to identify the site of metabolism and the metabolite(s). Both electronic [supported by density functional theory (DFT) calculations] and exposure effects were considered when rationalizing the structure-metabolism relationship.
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18
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Hughes TB, Swamidass SJ. Deep Learning to Predict the Formation of Quinone Species in Drug Metabolism. Chem Res Toxicol 2017; 30:642-656. [PMID: 28099803 DOI: 10.1021/acs.chemrestox.6b00385] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Many adverse drug reactions are thought to be caused by electrophilically reactive drug metabolites that conjugate to nucleophilic sites within DNA and proteins, causing cancer or toxic immune responses. Quinone species, including quinone-imines, quinone-methides, and imine-methides, are electrophilic Michael acceptors that are often highly reactive and comprise over 40% of all known reactive metabolites. Quinone metabolites are created by cytochromes P450 and peroxidases. For example, cytochromes P450 oxidize acetaminophen to N-acetyl-p-benzoquinone imine, which is electrophilically reactive and covalently binds to nucleophilic sites within proteins. This reactive quinone metabolite elicits a toxic immune response when acetaminophen exceeds a safe dose. Using a deep learning approach, this study reports the first published method for predicting quinone formation: the formation of a quinone species by metabolic oxidation. We model both one- and two-step quinone formation, enabling accurate quinone formation predictions in nonobvious cases. We predict atom pairs that form quinones with an AUC accuracy of 97.6%, and we identify molecules that form quinones with 88.2% AUC. By modeling the formation of quinones, one of the most common types of reactive metabolites, our method provides a rapid screening tool for a key drug toxicity risk. The XenoSite quinone formation model is available at http://swami.wustl.edu/xenosite/p/quinone .
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Affiliation(s)
- Tyler B Hughes
- Department of Pathology and Immunology, Washington University School of Medicine , Campus Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, United States
| | - S Joshua Swamidass
- Department of Pathology and Immunology, Washington University School of Medicine , Campus Box 8118, 660 S. Euclid Avenue, St. Louis, Missouri 63110, United States
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19
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Lepri S, Goracci L, Valeri A, Cruciani G. Metabolism study and biological evaluation of bosentan derivatives. Eur J Med Chem 2016; 121:658-670. [DOI: 10.1016/j.ejmech.2016.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/31/2016] [Accepted: 06/04/2016] [Indexed: 12/11/2022]
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20
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Hughes T, Dang NL, Miller GP, Swamidass SJ. Modeling Reactivity to Biological Macromolecules with a Deep Multitask Network. ACS CENTRAL SCIENCE 2016; 2:529-37. [PMID: 27610414 PMCID: PMC4999971 DOI: 10.1021/acscentsci.6b00162] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Indexed: 05/14/2023]
Abstract
Most small-molecule drug candidates fail before entering the market, frequently because of unexpected toxicity. Often, toxicity is detected only late in drug development, because many types of toxicities, especially idiosyncratic adverse drug reactions (IADRs), are particularly hard to predict and detect. Moreover, drug-induced liver injury (DILI) is the most frequent reason drugs are withdrawn from the market and causes 50% of acute liver failure cases in the United States. A common mechanism often underlies many types of drug toxicities, including both DILI and IADRs. Drugs are bioactivated by drug-metabolizing enzymes into reactive metabolites, which then conjugate to sites in proteins or DNA to form adducts. DNA adducts are often mutagenic and may alter the reading and copying of genes and their regulatory elements, causing gene dysregulation and even triggering cancer. Similarly, protein adducts can disrupt their normal biological functions and induce harmful immune responses. Unfortunately, reactive metabolites are not reliably detected by experiments, and it is also expensive to test drug candidates for potential to form DNA or protein adducts during the early stages of drug development. In contrast, computational methods have the potential to quickly screen for covalent binding potential, thereby flagging problematic molecules and reducing the total number of necessary experiments. Here, we train a deep convolution neural network-the XenoSite reactivity model-using literature data to accurately predict both sites and probability of reactivity for molecules with glutathione, cyanide, protein, and DNA. On the site level, cross-validated predictions had area under the curve (AUC) performances of 89.8% for DNA and 94.4% for protein. Furthermore, the model separated molecules electrophilically reactive with DNA and protein from nonreactive molecules with cross-validated AUC performances of 78.7% and 79.8%, respectively. On both the site- and molecule-level, the model's performances significantly outperformed reactivity indices derived from quantum simulations that are reported in the literature. Moreover, we developed and applied a selectivity score to assess preferential reactions with the macromolecules as opposed to the common screening traps. For the entire data set of 2803 molecules, this approach yielded totals of 257 (9.2%) and 227 (8.1%) molecules predicted to be reactive only with DNA and protein, respectively, and hence those that would be missed by standard reactivity screening experiments. Site of reactivity data is an underutilized resource that can be used to not only predict if molecules are reactive, but also show where they might be modified to reduce toxicity while retaining efficacy. The XenoSite reactivity model is available at http://swami.wustl.edu/xenosite/p/reactivity.
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Affiliation(s)
- Tyler
B. Hughes
- Department
of Pathology and Immunology, Washington
University School of Medicine, Campus
Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Na Le Dang
- Department
of Pathology and Immunology, Washington
University School of Medicine, Campus
Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Grover P. Miller
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - S. Joshua Swamidass
- Department
of Pathology and Immunology, Washington
University School of Medicine, Campus
Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
- E-mail:
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21
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De Vita D, Pandolfi F, Cirilli R, Scipione L, Di Santo R, Friggeri L, Mori M, Fiorucci D, Maccari G, Arul Christopher RS, Zamperini C, Pau V, De Logu A, Tortorella S, Botta M. Discovery of in vitro antitubercular agents through in silico ligand-based approaches. Eur J Med Chem 2016; 121:169-180. [PMID: 27240272 DOI: 10.1016/j.ejmech.2016.05.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 12/13/2022]
Abstract
The development of new anti-tubercular agents represents a constant challenge mostly due to the insurgency of resistance to the currently available drugs. In this study, a set of 60 molecules were selected by screening the Asinex and the ZINC collections and an in house library by means of in silico ligand-based approaches. Biological assays in Mycobacterium tuberculosis H37Ra ATCC 25177 strain highlighted (±)-1-(4-chlorophenyl)-2-(1H-imidazol-1-yl)ethyl-4-(3,4-dichlorophenyl)piperazine-1-carboxylate (5i) and 3-(4-chlorophenyl)-5-(2,4-dimethylpyrimidin-5-yl)-2-methylpyrazolo[1.5-a]pyrimidin-7(4H)-one (42) as the most potent compounds, having a Minimum Inhibitory Concentration (MIC) of 4 and 2 μg/mL respectively. These molecules represent a good starting point for further optimization of effective anti-TB agents.
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Affiliation(s)
- Daniela De Vita
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Fabiana Pandolfi
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Roberto Cirilli
- Dipartimento del Farmaco, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Luigi Scipione
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy; Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Laura Friggeri
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Mattia Mori
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53019 Siena, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Roma, Italy
| | - Diego Fiorucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53019 Siena, Italy
| | - Giorgio Maccari
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53019 Siena, Italy
| | | | - Claudio Zamperini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53019 Siena, Italy
| | - Valentina Pau
- Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, Via Porcell 4, 09124 Cagliari, Italy
| | - Alessandro De Logu
- Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, Via Porcell 4, 09124 Cagliari, Italy
| | - Silvano Tortorella
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy.
| | - Maurizio Botta
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53019 Siena, Italy; Sbarro Institute for Cancer Research & Molecular Medicine, Center for Biotechnology, College of Science & Technology, Temple University, BioLife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, PA 19122, USA.
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22
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Pasqualini S, Paoletti E, Cruciani G, Pellegrino R, Ederli L. Effects of different routes of application on ethylenediurea persistence in tobacco leaves. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 212:559-564. [PMID: 26977961 DOI: 10.1016/j.envpol.2016.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 03/04/2016] [Accepted: 03/04/2016] [Indexed: 06/05/2023]
Abstract
Ethylenediurea (EDU) is a common research tool for investigating ozone impacts on vegetation, although the role of different application routes (foliar spray vs soil drench) on EDU persistence in the leaves is unknown. We quantified EDU concentrations in leaves of the O3-sensitive Bel-W3 cultivar of tobacco treated with EDU as either foliar spray or soil drench. Foliar EDU concentrations were measured by Q-TOF LC/MS. When EDU was applied as foliar spray, 1 h was enough for reaching a measurable concentration within the leaf. EDU concentration increased over the 21-day period when the leaf was not washed after the application (treatment #1), while it decreased when the leaf was washed after the application (treatment #2). These results suggest that: a) dry deposition of EDU onto the leaf surface was gradually absorbed into the unwashed leaf, although the mechanisms of such uptake were unclear; b) concentration of EDU was decreased quickly (-35%) during the first 24 h from application and more slowly during the following three days (-20%) in the washed leaves. Degradation did not involve enzymatic reactions and was not affected by the presence of ROS. When EDU was applied as soil drench, foliar concentrations increased over time, likely due to adsorption onto soil organic matter and gradual re-solubilization by irrigation water. An analysis of EDU concentration in protoplast and intercellular washing fluid showed that EDU did not enter the cells, but was retained in the apoplast only. Possible implications of EDU in the apoplast and recommendations for EDU application are discussed.
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Affiliation(s)
- S Pasqualini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX Giugno 74, I-06121 Perugia, Italy.
| | - E Paoletti
- Institute of Sustainable Plant Protection, National Council of Research, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Firenze, Italy
| | - G Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX Giugno 74, I-06121 Perugia, Italy
| | - R Pellegrino
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX Giugno 74, I-06121 Perugia, Italy
| | - L Ederli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX Giugno 74, I-06121 Perugia, Italy
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23
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Carosati E, Cosimelli B, Ioan P, Severi E, Katneni K, Chiu FCK, Saponara S, Fusi F, Frosini M, Matucci R, Micucci M, Chiarini A, Spinelli D, Budriesi R. Understanding Oxadiazolothiazinone Biological Properties: Negative Inotropic Activity versus Cytochrome P450-Mediated Metabolism. J Med Chem 2016; 59:3340-52. [PMID: 26962886 DOI: 10.1021/acs.jmedchem.6b00030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a series of oxadiazolothiazinones, selective inotropic agents on isolated cardiac tissues, devoid of chronotropy and vasorelaxant activity. Functional and binding data for the precursor of the series (compound 1) let us hypothesize LTCC blocking activity and the existence of a recognition site specific for this scaffold. We synthesized and tested 22 new derivatives: introducing a para-methoxyphenyl at C-8 led to compound 12 (EC50 = 0.022 μM), twice as potent as its para-bromo analogue (1). For 10 analogues, we extended the characterization of the biological properties by including the assessment of metabolic stability in human liver microsomes and cytochrome P450 inhibition potential. We observed that the methoxy group led to active compounds with low metabolic stability and high CYP inhibition, whereas the protective effect of bromine resulted in enhanced metabolic stability and reduced CYP inhibition. Thus, we identified two para-bromo benzothiazino-analogues as candidates for further studies.
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Affiliation(s)
- Emanuele Carosati
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , Via Elce di Sotto 10, 06123 Perugia, Italy.,Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences , 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Barbara Cosimelli
- Dipartimento di Farmacia, Università di Napoli "Federico II" , Via D. Montesano 49, 80131 Napoli, Italy
| | - Pierfranco Ioan
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna , Via Belmeloro 6, 40126 Bologna, Italy
| | - Elda Severi
- Dipartimento di Farmacia, Università di Napoli "Federico II" , Via D. Montesano 49, 80131 Napoli, Italy
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences , 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Francis C K Chiu
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences , 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Simona Saponara
- Dipartimento di Scienze della Vita, Università degli Studi di Siena , Via A. Moro 2, 53100 Siena, Italy
| | - Fabio Fusi
- Dipartimento di Scienze della Vita, Università degli Studi di Siena , Via A. Moro 2, 53100 Siena, Italy
| | - Maria Frosini
- Dipartimento di Scienze della Vita, Università degli Studi di Siena , Via A. Moro 2, 53100 Siena, Italy
| | - Rosanna Matucci
- Dipartimento di Neuroscienze, Area del Farmaco e Salute del Bambino (NEUROFARBA) , Viale Pieraccini 6, 50139 Firenze, Italy
| | - Matteo Micucci
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna , Via Belmeloro 6, 40126 Bologna, Italy
| | - Alberto Chiarini
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna , Via Belmeloro 6, 40126 Bologna, Italy
| | - Domenico Spinelli
- Dipartimento di Chimica 'G. Ciamician', Alma Mater Studiorum-Università di Bologna , Via Selmi 2, 40126 Bologna, Italy
| | - Roberta Budriesi
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna , Via Belmeloro 6, 40126 Bologna, Italy
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24
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Sirakanyan SN, Geronikaki A, Spinelli D, Paronikyan RG, Dzhagatspanyan IA, Nazaryan IM, Akopyan AH, Hovakimyan AA. Pyridofuropyrrolo[1,2-a]pyrimidines and pyridofuropyrimido[1,2-a]azepines: new chemical entities (NCE) with anticonvulsive and psychotropic properties. RSC Adv 2016. [DOI: 10.1039/c6ra06507d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A series of pyridofuropyrrolo[1,2-a]pyrimidines4and of pyridofuropyrimido[1,2-a]azepines5having as precursors a some new condensed furo[2,3-b]pyridines3were synthesized and evaluated for their anticonvulsive and psychotropic properties.
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Affiliation(s)
- Samvel N. Sirakanyan
- Scientific Technological Center of Organic and Pharmaceutical Chemistry of National Academy of Sciences of Republic of Armenia
- Institute of Fine Organic Chemistry of A. L. Mnjoyan
- Yerevan
- Armenia 0014
| | - Athina Geronikaki
- Aristotle University of Thessaloniki
- School of Pharmacy
- Thessaloniki 54124
- Greece
| | - Domenico Spinelli
- Dipartimento di Chimica G. Ciamician
- Alma Mater Studiorum-Università di Bologna
- Bologna 40126
- Italy
| | - Ruzanna G. Paronikyan
- Scientific Technological Center of Organic and Pharmaceutical Chemistry of National Academy of Sciences of Republic of Armenia
- Institute of Fine Organic Chemistry of A. L. Mnjoyan
- Yerevan
- Armenia 0014
| | - Irina A. Dzhagatspanyan
- Scientific Technological Center of Organic and Pharmaceutical Chemistry of National Academy of Sciences of Republic of Armenia
- Institute of Fine Organic Chemistry of A. L. Mnjoyan
- Yerevan
- Armenia 0014
| | - Ivetta M. Nazaryan
- Scientific Technological Center of Organic and Pharmaceutical Chemistry of National Academy of Sciences of Republic of Armenia
- Institute of Fine Organic Chemistry of A. L. Mnjoyan
- Yerevan
- Armenia 0014
| | - Asmik H. Akopyan
- Scientific Technological Center of Organic and Pharmaceutical Chemistry of National Academy of Sciences of Republic of Armenia
- Institute of Fine Organic Chemistry of A. L. Mnjoyan
- Yerevan
- Armenia 0014
| | - Anush A. Hovakimyan
- Scientific Technological Center of Organic and Pharmaceutical Chemistry of National Academy of Sciences of Republic of Armenia
- Institute of Fine Organic Chemistry of A. L. Mnjoyan
- Yerevan
- Armenia 0014
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25
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Sirakanyan SN, Geronikaki A, Spinelli D, Paronikyan RG, Dzhagatspanyan IA, Nazaryan IM, Akopyan AH, Hovakimyan AA. Pyridofuropyrrolo[1,2-a]pyrimidines and pyridofuropyrimido[1,2-a]azepines: new chemical entities (NCE) with anticonvulsive and psychotropic properties. RSC Adv 2016. [DOI: 10.1039/c6ra02581a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A series of pyridofuropyrrolo[1,2-a]pyrimidines4and pyridofuropyrimido[1,2-a]azepines5, with new condensed furo[2,3-b]pyridines3as precursors, were synthesized and evaluated for their anticonvulsive and psychotropic properties.
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Affiliation(s)
- Samvel N. Sirakanyan
- Scientific Technological Center of Organic and Pharmaceutical Chemistry of National Academy of Sciences of Republic of Armenia
- Institute of Fine Organic Chemistry of A. L. Mnjoyan
- Yerevan
- Armenia 0014
| | - Athina Geronikaki
- Aristotle University of Thessaloniki
- School of Pharmacy
- Thessaloniki 54124
- Greece
| | - Domenico Spinelli
- Dipartimento di Chimica G. Ciamician
- Alma Mater Studiorum-Università di Bologna
- Bologna 40126
- Italy
| | - Ruzanna G. Paronikyan
- Scientific Technological Center of Organic and Pharmaceutical Chemistry of National Academy of Sciences of Republic of Armenia
- Institute of Fine Organic Chemistry of A. L. Mnjoyan
- Yerevan
- Armenia 0014
| | - Irina A. Dzhagatspanyan
- Scientific Technological Center of Organic and Pharmaceutical Chemistry of National Academy of Sciences of Republic of Armenia
- Institute of Fine Organic Chemistry of A. L. Mnjoyan
- Yerevan
- Armenia 0014
| | - Ivetta M. Nazaryan
- Scientific Technological Center of Organic and Pharmaceutical Chemistry of National Academy of Sciences of Republic of Armenia
- Institute of Fine Organic Chemistry of A. L. Mnjoyan
- Yerevan
- Armenia 0014
| | - Asmik H. Akopyan
- Scientific Technological Center of Organic and Pharmaceutical Chemistry of National Academy of Sciences of Republic of Armenia
- Institute of Fine Organic Chemistry of A. L. Mnjoyan
- Yerevan
- Armenia 0014
| | - Anush A. Hovakimyan
- Scientific Technological Center of Organic and Pharmaceutical Chemistry of National Academy of Sciences of Republic of Armenia
- Institute of Fine Organic Chemistry of A. L. Mnjoyan
- Yerevan
- Armenia 0014
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26
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Hughes TB, Miller GP, Swamidass SJ. Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network. ACS CENTRAL SCIENCE 2015; 1:168-80. [PMID: 27162970 PMCID: PMC4827534 DOI: 10.1021/acscentsci.5b00131] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Indexed: 05/02/2023]
Abstract
Drug toxicity is frequently caused by electrophilic reactive metabolites that covalently bind to proteins. Epoxides comprise a large class of three-membered cyclic ethers. These molecules are electrophilic and typically highly reactive due to ring tension and polarized carbon-oxygen bonds. Epoxides are metabolites often formed by cytochromes P450 acting on aromatic or double bonds. The specific location on a molecule that undergoes epoxidation is its site of epoxidation (SOE). Identifying a molecule's SOE can aid in interpreting adverse events related to reactive metabolites and direct modification to prevent epoxidation for safer drugs. This study utilized a database of 702 epoxidation reactions to build a model that accurately predicted sites of epoxidation. The foundation for this model was an algorithm originally designed to model sites of cytochromes P450 metabolism (called XenoSite) that was recently applied to model the intrinsic reactivity of diverse molecules with glutathione. This modeling algorithm systematically and quantitatively summarizes the knowledge from hundreds of epoxidation reactions with a deep convolution network. This network makes predictions at both an atom and molecule level. The final epoxidation model constructed with this approach identified SOEs with 94.9% area under the curve (AUC) performance and separated epoxidized and non-epoxidized molecules with 79.3% AUC. Moreover, within epoxidized molecules, the model separated aromatic or double bond SOEs from all other aromatic or double bonds with AUCs of 92.5% and 95.1%, respectively. Finally, the model separated SOEs from sites of sp(2) hydroxylation with 83.2% AUC. Our model is the first of its kind and may be useful for the development of safer drugs. The epoxidation model is available at http://swami.wustl.edu/xenosite.
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Affiliation(s)
- Tyler B. Hughes
- Department
of Pathology and Immunology, Washington
University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Grover P. Miller
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - S. Joshua Swamidass
- Department
of Pathology and Immunology, Washington
University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
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27
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Raunio H, Kuusisto M, Juvonen RO, Pentikäinen OT. Modeling of interactions between xenobiotics and cytochrome P450 (CYP) enzymes. Front Pharmacol 2015; 6:123. [PMID: 26124721 PMCID: PMC4464169 DOI: 10.3389/fphar.2015.00123] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/29/2015] [Indexed: 01/01/2023] Open
Abstract
The adverse effects to humans and environment of only few chemicals are well known. Absorption, distribution, metabolism, and excretion (ADME) are the steps of pharmaco/toxicokinetics that determine the internal dose of chemicals to which the organism is exposed. Of all the xenobiotic-metabolizing enzymes, the cytochrome P450 (CYP) enzymes are the most important due to their abundance and versatility. Reactions catalyzed by CYPs usually turn xenobiotics to harmless and excretable metabolites, but sometimes an innocuous xenobiotic is transformed into a toxic metabolite. Data on ADME and toxicity properties of compounds are increasingly generated using in vitro and modeling (in silico) tools. Both physics-based and empirical modeling approaches are used. Numerous ligand-based and target-based as well as combined modeling methods have been employed to evaluate determinants of CYP ligand binding as well as predicting sites of metabolism and inhibition characteristics of test molecules. In silico prediction of CYP–ligand interactions have made crucial contributions in understanding (1) determinants of CYP ligand binding recognition and affinity; (2) prediction of likely metabolites from substrates; (3) prediction of inhibitors and their inhibition potency. Truly predictive models of toxic outcomes cannot be created without incorporating metabolic characteristics; in silico methods help producing such information and filling gaps in experimentally derived data. Currently modeling methods are not mature enough to replace standard in vitro and in vivo approaches, but they are already used as an important component in risk assessment of drugs and other chemicals.
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Affiliation(s)
- Hannu Raunio
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland Kuopio, Finland
| | - Mira Kuusisto
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland Kuopio, Finland ; Computational Bioscience Laboratory, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä Jyväskylä, Finland
| | - Risto O Juvonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland Kuopio, Finland
| | - Olli T Pentikäinen
- Computational Bioscience Laboratory, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä Jyväskylä, Finland
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28
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Carosati E, Ioan P, Barrano GB, Caccamese S, Cosimelli B, Devlin FJ, Severi E, Spinelli D, Superchi S, Budriesi R. Synthesis and L-type calcium channel blocking activity of new chiral oxadiazolothiazinones. Eur J Med Chem 2015; 92:481-9. [PMID: 25596477 DOI: 10.1016/j.ejmech.2014.12.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 12/19/2014] [Accepted: 12/24/2014] [Indexed: 10/24/2022]
Abstract
Oxadiazolo[3,4-c][1,4]thiazin-3-ones are cardiovascular agents that block L-type calcium channels. Previous data of cardiac and vasorelaxant activity on guinea-pig for several derivatives indicated the two positions ortho to the thiazine's sulphur as crucial for modulating the activity; but these positions are likely susceptible to metabolic biotransformations, as indicated by in silico predictions. We designed new derivatives, and obtained three negative inotropic agents with EC50 in the low nanomolar range, more potent than all the precursors published so far. In particular, benzocondensation at the thiazine ring led to 3a (EC50 = 0.013 μM) and 3b (EC50 = 0.006 μM). Besides negative inotropy, we also observed relaxant activity on nonvascular muscle in the micromolar range. We resolved the new derivatives by chiral chromatography, and determined their absolute configuration by comparing experimental and calculated chiroptical properties (VCD, ECD and ORD): they hold the same absolute configuration-optical rotation relationship, (S)-(+)/(R)-(-). Both cardiac and nonvascular activity are majorly or mostly retained in the R-form for all the compounds, but for the nonvascular activity we observed a strong stereoselectivity for 3a, with the R-form in the nanomolar range (IC50 = 0.020 μM) and 259-fold more potent than the S-one.
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Affiliation(s)
- Emanuele Carosati
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italy.
| | - Pierfranco Ioan
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | | | - Salvatore Caccamese
- Dipartimento di Scienze Chimiche, Università di Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Barbara Cosimelli
- Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy.
| | - Frank J Devlin
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0744, USA
| | - Elda Severi
- Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Domenico Spinelli
- Dipartimento di Chimica "G. Ciamician", Alma Mater Studiorum-Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Stefano Superchi
- Dipartimento di Scienze, Università della Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Roberta Budriesi
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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29
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Wilk-Zasadna I, Bernasconi C, Pelkonen O, Coecke S. Biotransformation in vitro: An essential consideration in the quantitative in vitro-to-in vivo extrapolation (QIVIVE) of toxicity data. Toxicology 2014; 332:8-19. [PMID: 25456264 DOI: 10.1016/j.tox.2014.10.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 06/11/2014] [Accepted: 10/11/2014] [Indexed: 12/14/2022]
Abstract
Early consideration of the multiplicity of factors that govern the biological fate of foreign compounds in living systems is a necessary prerequisite for the quantitative in vitro-in vivo extrapolation (QIVIVE) of toxicity data. Substantial technological advances in in vitro methodologies have facilitated the study of in vitro metabolism and the further use of such data for in vivo prediction. However, extrapolation to in vivo with a comfortable degree of confidence, requires continuous progress in the field to address challenges such as e.g., in vitro evaluation of chemical-chemical interactions, accounting for individual variability but also analytical challenges for ensuring sensitive measurement technologies. This paper discusses the current status of in vitro metabolism studies for QIVIVE extrapolation, serving today's hazard and risk assessment needs. A short overview of the methodologies for in vitro metabolism studies is given. Furthermore, recommendations for priority research and other activities are provided to ensure further widespread uptake of in vitro metabolism methods in 21st century toxicology. The need for more streamlined and explicitly described integrated approaches to reflect the physiology and the related dynamic and kinetic processes of the human body is highlighted i.e., using in vitro data in combination with in silico approaches.
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Affiliation(s)
- Iwona Wilk-Zasadna
- Systems Toxicology Unit/EURL ECVAM, Institute for Health and Consumer Protection, European Commission Joint Research Centre, Ispra, Varese I-21027, Italy
| | - Camilla Bernasconi
- Systems Toxicology Unit/EURL ECVAM, Institute for Health and Consumer Protection, European Commission Joint Research Centre, Ispra, Varese I-21027, Italy
| | - Olavi Pelkonen
- Department of Pharmacology and Toxicology, Institute of Biomedicine, University of Oulu, Oulu, Finland
| | - Sandra Coecke
- Systems Toxicology Unit/EURL ECVAM, Institute for Health and Consumer Protection, European Commission Joint Research Centre, Ispra, Varese I-21027, Italy.
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30
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Rydberg P. Reactivity‐Based Approaches and Machine Learning Methods for Predicting the Sites of Cytochrome P450‐Mediated Metabolism. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/9783527673261.ch11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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31
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Cruciani G, Valeri A, Goracci L, Pellegrino RM, Buonerba F, Baroni M. Flavin monooxygenase metabolism: why medicinal chemists should matter. J Med Chem 2014; 57:6183-96. [PMID: 25003501 DOI: 10.1021/jm5007098] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
FMO enzymes (FMOs) play a key role in the processes of detoxification and/or bioactivation of specific pharmaceuticals and xenobiotics bearing nucleophilic centers. The N-oxide and S-oxide metabolites produced by FMOs are often active metabolites. The FMOs are more active than cytochromes in the brain and work in tandem with CYP3A4 in the liver. FMOs might reduce the risk of phospholipidosis of CAD-like drugs, although some FMOs metabolites seem to be neurotoxic and hepatotoxic. However, in silico methods for FMO metabolism prediction are not yet available. This paper reports, for the first time, a substrate-specificity and catalytic-activity model for FMO3, the most relevant isoform of the FMOs in humans. The application of this model to a series of compounds with unknown FMO metabolism is also reported. The model has also been very useful to design compounds with optimal clearance and in finding erroneous literature data, particularly cases in which substances have been reported to be FMO3 substrates when, in reality, the experimentally validated in silico model correctly predicts that they are not.
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Affiliation(s)
- Gabriele Cruciani
- Laboratory for Chemoinformatics and Molecular Modelling, Department of Chemistry, Biology and Biotechnology, University of Perugia , Via Elce di Sotto 8, 06123 Perugia, Italy
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32
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Zaretzki J, Matlock M, Swamidass SJ. XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks. J Chem Inf Model 2013; 53:3373-83. [DOI: 10.1021/ci400518g] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jed Zaretzki
- Department of Pathology and
Immunology, Washington University School of Medicine, St. Louis, Missouri 63130, United States
| | - Matthew Matlock
- Department of Pathology and
Immunology, Washington University School of Medicine, St. Louis, Missouri 63130, United States
| | - S. Joshua Swamidass
- Department of Pathology and
Immunology, Washington University School of Medicine, St. Louis, Missouri 63130, United States
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33
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Model-based estimates of the effects of efavirenz on bedaquiline pharmacokinetics and suggested dose adjustments for patients coinfected with HIV and tuberculosis. Antimicrob Agents Chemother 2013; 57:2780-7. [PMID: 23571542 DOI: 10.1128/aac.00191-13] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Safe, effective concomitant treatment regimens for tuberculosis (TB) and HIV infection are urgently needed. Bedaquiline (BDQ) is a promising new anti-TB drug, and efavirenz (EFV) is a commonly used antiretroviral. Due to EFV's induction of cytochrome P450 3A4, the metabolic enzyme responsible for BDQ biotransformation, the drugs are expected to interact. Based on data from a phase I, single-dose pharmacokinetic study, a nonlinear mixed-effects model characterizing BDQ pharmacokinetics and interaction with multiple-dose EFV was developed. BDQ pharmacokinetics were best described by a 3-compartment disposition model with absorption through a dynamic transit compartment model. Metabolites M2 and M3 were described by 2-compartment models with clearance of BDQ and M2, respectively, as input. Impact of induction was described as an instantaneous change in clearance 1 week after initialization of EFV treatment and estimated for all compounds. The model predicts average steady-state concentrations of BDQ and M2 to be reduced by 52% (relative standard error [RSE], 3.7%) with chronic coadministration. A range of models with alternative structural assumptions regarding onset of induction effect and fraction metabolized resulted in similar estimates of the typical reduction and did not offer a markedly better fit to data. Simulations to investigate alternative regimens mitigating the estimated interaction effect were performed. The results suggest that simple adjustments of the standard regimen during EFV coadministration can prevent reduced exposure to BDQ without increasing exposures to M2. However, exposure to M3 would increase. Evaluation in clinical trials of adjusted regimens is necessary to ensure appropriate dosing for HIV-infected TB patients on an EFV-based regimen.
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