1
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Guasch L, Maeder N, Cumming JG, Kramer C. From mundane to surprising nonadditivity: drivers and impact on ML models. J Comput Aided Mol Des 2024; 38:26. [PMID: 39052103 DOI: 10.1007/s10822-024-00566-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Nonadditivity (NA) in Structure-Activity and Structure-Property Relationship (SAR) data is a rare but very information rich phenomenon. It can indicate conformational flexibility, structural rearrangements, and errors in assay results and structural assignment. While purely ligand-based conformational causes of NA are rather well understood and mundane, other factors are less so and cause surprising NA that has a huge influence on SAR analysis and ML model performance. We here report a systematic analysis across a wide range of properties (20 on-target biological activities and 4 physicochemical ADME-related properties) to understand the frequency of various different phenomena that may lead to NA. A set of novel descriptors were developed to characterize double transformation cycles and identify trends in NA. Double transformation cycles were classified into "surprising" and "mundane" categories, with the majority being classed as mundane. We also examined commonalities among surprising cycles, finding LogP differences to have the most significant impact on NA. A distinct behavior of NA for on-target sets compared to ADME sets was observed. Finally, we show that machine learning models struggle with highly nonadditive data, indicating that a better understanding of NA is an important future research direction.
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Affiliation(s)
- Laura Guasch
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann- La Roche AG, Basel, 4070, Switzerland.
| | - Niels Maeder
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann- La Roche AG, Basel, 4070, Switzerland
| | - John G Cumming
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann- La Roche AG, Basel, 4070, Switzerland
| | - Christian Kramer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann- La Roche AG, Basel, 4070, Switzerland
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2
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Chicca A, Batora D, Ullmer C, Caruso A, Fingerle J, Hartung T, Degen R, Müller M, Grether U, Pacher P, Gertsch J. A highly potent, orally bioavailable pyrazole-derived cannabinoid CB2 receptor-selective full agonist for in vivo studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591311. [PMID: 38903103 PMCID: PMC11188143 DOI: 10.1101/2024.04.26.591311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The cannabinoid CB2 receptor (CB2R) is a potential therapeutic target for distinct forms of tissue injury and inflammatory diseases. To thoroughly investigate the role of CB2R in pathophysiological conditions and for target validation in vivo, optimal pharmacological tool compounds are essential. Despite the sizable progress in the generation of potent and selective CB2R ligands, pharmacokinetic parameters are often neglected for in vivo studies. Here, we report the generation and characterization of a tetra-substituted pyrazole CB2R full agonist named RNB-61 with high potency (K i 0.13-1.81 nM, depending on species) and a peripherally restricted action due to P-glycoprotein mediated efflux from the brain. 3H and 14C labelled RNB-61 showed apparent K d values < 4 nM towards human CB2R in both cell and tissue experiments. The >6000-fold selectivity over CB1 receptors and negligible off-targets in vitro, combined with high oral bioavailability and suitable systemic pharmacokinetic (PK) properties, prompted the assessment of RNB-61 in a mouse ischemia-reperfusion model of acute kidney injury (AKI) and in a rat model of chronic kidney injury/inflammation and fibrosis (CKI) induced by unilateral ureteral obstruction. RNB-61 exerted dose-dependent nephroprotective and/or antifibrotic effects in the AKI/CKI models. Thus, RNB-61 is an optimal CB2R tool compound for preclinical in vivo studies with superior biophysical and PK properties over generally used CB2R ligands.
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Affiliation(s)
- Andrea Chicca
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern 3012, Switzerland
| | - Daniel Batora
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Christoph Ullmer
- Pharmaceutical Sciences, Roche Innovation Center Basel, Roche Pharma Research and Early Development, Basel 4070, Switzerland
| | - Antonello Caruso
- Pharmaceutical Sciences, Roche Innovation Center Basel, Roche Pharma Research and Early Development, Basel 4070, Switzerland
| | - Jürgen Fingerle
- Pharmaceutical Sciences, Roche Innovation Center Basel, Roche Pharma Research and Early Development, Basel 4070, Switzerland
| | - Thomas Hartung
- Pharmaceutical Sciences, Roche Innovation Center Basel, Roche Pharma Research and Early Development, Basel 4070, Switzerland
| | - Roland Degen
- Pharmaceutical Sciences, Roche Innovation Center Basel, Roche Pharma Research and Early Development, Basel 4070, Switzerland
| | - Matthias Müller
- Pharmaceutical Sciences, Roche Innovation Center Basel, Roche Pharma Research and Early Development, Basel 4070, Switzerland
| | - Uwe Grether
- Pharmaceutical Sciences, Roche Innovation Center Basel, Roche Pharma Research and Early Development, Basel 4070, Switzerland
| | - Pal Pacher
- Laboratory of Cardiovascular Physiology and Tissue Injury (P.P.), National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health (NIH), Bethesda, MD
| | - Jürg Gertsch
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern 3012, Switzerland
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3
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Krummenacher D, He W, Kuhn B, Schnider C, Beurier A, Brom V, Sivasothy T, Marty C, Tosstorff A, Hewings DS, Mesch S, Pinard E, Brändlin M, Hochstrasser R, Westwood P, Rothe J, Kronenberger A, Morandi F, Gutbier S, Schuler A, Heer D, Gloria LE, Joedicke L, Rudolph MG, Müller L, Grüninger F, Baumann K, Kaniyappan S, Manevski N, Bartels B. Discovery of Orally Available and Brain Penetrant AEP Inhibitors. J Med Chem 2023; 66:17026-17043. [PMID: 38090813 DOI: 10.1021/acs.jmedchem.3c01804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Alzheimer's Disease (AD) is the most widespread form of dementia, with one of the pathological hallmarks being the formation of neurofibrillary tangles (NFTs). These tangles consist of phosphorylated Tau fragments. Asparagine endopeptidase (AEP) is a key Tau cleaving enzyme that generates aggregation-prone Tau fragments. Inhibition of AEP to reduce the level of toxic Tau fragment formation could represent a promising therapeutic strategy. Here, we report the first orthosteric, selective, orally bioavailable, and brain penetrant inhibitors with an irreversible binding mode. We outline the development of the series starting from reversible molecules and demonstrate the link between inhibition of AEP and reduction of Tau N368 fragment both in vitro and in vivo.
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Affiliation(s)
- Daniela Krummenacher
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Weiping He
- WuXi AppTec (Wuhan) Co. Ltd., Wuhan East Lake High-Tech Development Zone, 666 GaoXin Road, Wuhan, Hubei 430075, China
| | - Bernd Kuhn
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Christian Schnider
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Angélica Beurier
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Virginie Brom
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Thulase Sivasothy
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Christine Marty
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Andreas Tosstorff
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - David S Hewings
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Stefanie Mesch
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Emmanuel Pinard
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Mathis Brändlin
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Remo Hochstrasser
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Paul Westwood
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Judith Rothe
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Alexandra Kronenberger
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Federica Morandi
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Simon Gutbier
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Angelika Schuler
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Dominik Heer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Ludivine Esteves Gloria
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Lisa Joedicke
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Markus G Rudolph
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Lutz Müller
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Fiona Grüninger
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Karlheinz Baumann
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Senthilvelrajan Kaniyappan
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Nenad Manevski
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Björn Bartels
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
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4
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Manevski N, Umehara K, Parrott N. Drug Design and Success of Prospective Mouse In Vitro-In Vivo Extrapolation (IVIVE) for Predictions of Plasma Clearance (CL p) from Hepatocyte Intrinsic Clearance (CL int). Mol Pharm 2023. [PMID: 37235687 DOI: 10.1021/acs.molpharmaceut.2c01001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Hepatocyte intrinsic clearance (CLint) and methods of in vitro-in vivo extrapolation (IVIVE) are often used to predict plasma clearance (CLp) in drug discovery. While the prediction success of this approach is dependent on the chemotype, specific molecular properties and drug design features that govern these outcomes are poorly understood. To address this challenge, we investigated the success of prospective mouse CLp IVIVE across 2142 chemically diverse compounds. Dilution scaling, which assumes that the free fraction in hepatocyte incubations (fu,inc) is governed by binding to the 10% of serum in the incubation medium, was used as our default CLp IVIVE approach. Results show that predictions of CLp are better for smaller (molecular weight (MW) < 500 Da), less polar (total polar surface area (TPSA) < 100 Å2, hydrogen bond donor (HBD) ≤1, hydrogen bond acceptor (HBA) ≤ 6), lipophilic (log D > 3), and neutral compounds, with low HBD count playing the key role. If compounds are classified according to their chemical space, predictions were good for compounds resembling central nervous system (CNS) drugs [average absolute fold error (AAFE) of 2.05, average fold error (AFE) of 0.90], moderate for classical druglike compounds (according to Lipinski, Veber, and Ghose guidelines; AAFE of 2.55; AFE of 0.68), and poor for nonclassical "beyond the rule of 5" compounds (AAFE of 3.31; AFE of 0.41). From the perspective of measured druglike properties, predictions of CLp were better for compounds with moderate-to-high hepatocyte CLint (>10 μL/min/106 cells), high passive cellular permeability (Papp > 100 nm/s), and moderate observed CLp (5-50 mL/min/kg). Influences of plasma protein binding (fu,p) and P-glycoprotein (Pgp) apical efflux ratio (AP-ER) were less pronounced. If the extended clearance classification system (ECCS) is applied, predictions were good for class 2 (Papp > 50 nm/s; neutral or basic; AAFE of 2.35; AFE of 0.70) and acceptable for class 1A compounds (AAFE of 2.98; AFE of 0.70). Classes 1B, 3 A/B, and 4 showed poor outcomes (AAFE > 3.80; AFE < 0.60). Functional groups trending toward weaker CLp IVIVE were esters, carbamates, sulfonamides, carboxylic acids, ketones, primary and secondary amines, primary alcohols, oxetanes, and compounds liable to aldehyde oxidase metabolism, likely due to multifactorial reasons. Multivariate analysis showed that multiple properties are relevant, combining together to define the overall success of CLp IVIVE. Our results indicate that the current practice of prospective CLp IVIVE is suitable only for CNS-like compounds and well-behaved classical druglike space (e.g., high permeability or ECCS class 2) without challenging functional groups. Unfortunately, based on existing mouse data, prospective CLp IVIVE for complex and nonclassical chemotypes is poor and hardly better than random guessing. This is likely due to complexities such as extrahepatic metabolism and transporter-mediated disposition which are poorly captured by this methodology. With small-molecule drug discovery increasingly evolving toward nonclassical and complex chemotypes, existing CLp IVIVE methodology will require improvement. While empirical correction factors may bridge the gap in the near future, improved and new in vitro assays, data integration models, and machine learning (ML) methods are increasingly needed to address this challenge and reduce the number of nonclinical pharmacokinetic (PK) studies.
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Affiliation(s)
- Nenad Manevski
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Kenichi Umehara
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Neil Parrott
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, 4070 Basel, Switzerland
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5
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Revisiting the distribution/permeability regularities exemplified by cationic drug amitriptyline hydrochloride: Impact of temperature and pH. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Lee KR, Chang JE, Chae YJ. Sensitive and valid assay for reliable evaluation of drug interactions mediated by human organic anion transporter 1 and 3 using 5-carboxyfluorescein. ANAL SCI 2022; 38:1347-1357. [PMID: 35882772 DOI: 10.1007/s44211-022-00166-8] [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: 05/09/2022] [Accepted: 07/13/2022] [Indexed: 11/30/2022]
Abstract
Drug interactions can induce significant clinical impacts, either by increasing adverse effects or by decreasing the therapeutic effect of drugs, and thus, need to be explored thoroughly. Clinically significant drug interactions can be induced by organic anion transporter 1 (OAT1) and OAT3 when concomitant medications competitively interact with the transporters. The purposes of this study were to develop and validate a sensitive and selective analytical method for 5-carboxyfluorescein (5-CF) and optimize the experimental conditions for interaction studies. An analytical method using high-performance liquid chromatography (HPLC) equipped with a fluorescence detector was validated for accuracy, precision, matrix effect, recovery, stability, dilutional integrity, and carry-over effect. In addition, the 5-CF concentration, incubation period, and washing conditions for interaction study were optimized. Using a valid analytical method and optimized conditions, we performed an interaction study for OAT1 and OAT3 using 26 test articles. Some of the test articles showed strong inhibitory potency for the transporters, with IC50 values close to or less than 10 μM. The valid analysis method and optimized systems developed in this study can be utilized to improve the predictability of drug interactions in humans and consequently aid in successful disease treatment by maintaining appropriate systemic exposures.
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Affiliation(s)
- Kyeong-Ryoon Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea.,Department of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Ji-Eun Chang
- College of Pharmacy, Dongduk Women's University, Seoul, 02748, Republic of Korea
| | - Yoon-Jee Chae
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Woosuk University, Wanju, 55338, Republic of Korea.
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7
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Lenz B, Brink A, Mihatsch MJ, Altmann B, Niederhauser U, Steinhuber B, Wyttenbach N, Fischer H. Multiorgan Crystal Deposition of an Amphoteric Drug in Rats Due to Lysosomal Accumulation and Conversion to a Poorly Soluble Hydrochloride Salt. Toxicol Sci 2021; 180:383-394. [PMID: 33454789 PMCID: PMC8041455 DOI: 10.1093/toxsci/kfaa191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Poor solubility of drug candidates mainly affects bioavailability, but poor solubility of drugs and metabolites can also lead to precipitation within tissues, particularly when high doses are tested. RO0728617 is an amphoteric compound bearing basic and acidic moieties that has previously demonstrated good solubility at physiological pH but underwent widespread crystal deposition in multiple tissues in rat toxicity studies. The aim of our investigation was to better characterize these findings and their underlying mechanism(s), and to identify possible screening methods in the drug development process. Main microscopic features observed in rat RO0728617 toxicity studies were extensive infiltrates of crystal-containing macrophages in multiple organs. Matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry revealed that these crystals contained the orally administered parent compound, and locality was confirmed to be intracytoplasmic and partly intralysosomal by electron microscopic examination. Crystal formation was explained by lysosomal accumulation of the compound followed by precipitation of the hydrochloride salt under physiological conditions in the lysosomes, which have a lower pH and higher chloride concentration in comparison to the cytosol. This study demonstrates that risk of drug precipitation can be assessed by comparing the estimated lysosomal drug concentration at a given dose with the solubility of the compound at lysosomal conditions.
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Affiliation(s)
- Barbara Lenz
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Andreas Brink
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Michael J Mihatsch
- Pathology, Institute of Medical Genetics and Pathology, University Hospital of Basel, University of Basel, 4031 Basel, Switzerland
| | - Bernd Altmann
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Urs Niederhauser
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Bernd Steinhuber
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Nicole Wyttenbach
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Holger Fischer
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
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8
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Saretz S, Basset G, Useini L, Laube M, Pietzsch J, Drača D, Maksimović-Ivanić D, Trambauer J, Steiner H, Hey-Hawkins E. Modulation of γ-Secretase Activity by a Carborane-Based Flurbiprofen Analogue. Molecules 2021; 26:2843. [PMID: 34064783 PMCID: PMC8151329 DOI: 10.3390/molecules26102843] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/26/2021] [Accepted: 05/06/2021] [Indexed: 12/25/2022] Open
Abstract
All over the world, societies are facing rapidly aging populations combined with a growing number of patients suffering from Alzheimer's disease (AD). One focus in pharmaceutical research to address this issue is on the reduction of the longer amyloid-β (Aβ) fragments in the brain by modulation of γ-secretase, a membrane-bound protease. R-Flurbiprofen (tarenflurbil) was studied in this regard but failed to show significant improvement in AD patients in a phase 3 clinical trial. This was mainly attributed to its low ability to cross the blood-brain barrier (BBB). Here, we present the synthesis and in vitro evaluation of a racemic meta-carborane analogue of flurbiprofen. By introducing the carborane moiety, the hydrophobicity could be shifted into a more favourable range for the penetration of the blood-brain barrier, evident by a logD7.4 value of 2.0. Furthermore, our analogue retained γ-secretase modulator activity in comparison to racemic flurbiprofen in a cell-based assay. These findings demonstrate the potential of carboranes as phenyl mimetics also in AD research.
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Affiliation(s)
- Stefan Saretz
- Institut für Anorganische Chemie, Universität Leipzig, Johannisallee 29, D-04103 Leipzig, Germany; (S.S.); (L.U.)
- Chemische Biologie, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Gabriele Basset
- Biomedical Center Munich (BMC), Metabolic Biochemistry, Ludwig-Maximilians-University, Feodor-Lynen-Straße 17, D-81377 München, Germany; (G.B.); (J.T.); (H.S.)
| | - Liridona Useini
- Institut für Anorganische Chemie, Universität Leipzig, Johannisallee 29, D-04103 Leipzig, Germany; (S.S.); (L.U.)
| | - Markus Laube
- Department of Radiopharmaceutical and Chemical Biology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Bautzner Landstraße 400, D-01328 Dresden, Germany; (M.L.); (J.P.)
| | - Jens Pietzsch
- Department of Radiopharmaceutical and Chemical Biology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Bautzner Landstraße 400, D-01328 Dresden, Germany; (M.L.); (J.P.)
- Faculty of Chemistry and Food Chemistry, School of Science, Technische Universität Dresden, 01069 Dresden, Germany
| | - Dijana Drača
- Department of Immunology, Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, University of Belgrade, Bul. Despota Stefana 142, 11060 Belgrade, Serbia; (D.D.); (D.M.-I.)
| | - Danijela Maksimović-Ivanić
- Department of Immunology, Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, University of Belgrade, Bul. Despota Stefana 142, 11060 Belgrade, Serbia; (D.D.); (D.M.-I.)
| | - Johannes Trambauer
- Biomedical Center Munich (BMC), Metabolic Biochemistry, Ludwig-Maximilians-University, Feodor-Lynen-Straße 17, D-81377 München, Germany; (G.B.); (J.T.); (H.S.)
| | - Harald Steiner
- Biomedical Center Munich (BMC), Metabolic Biochemistry, Ludwig-Maximilians-University, Feodor-Lynen-Straße 17, D-81377 München, Germany; (G.B.); (J.T.); (H.S.)
- German Center for Neurogenerative Diseases (DZNE) Munich, Feodor-Lynen-Straße 17, D-81377 München, Germany
| | - Evamarie Hey-Hawkins
- Institut für Anorganische Chemie, Universität Leipzig, Johannisallee 29, D-04103 Leipzig, Germany; (S.S.); (L.U.)
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9
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Haider A, Gobbi L, Kretz J, Ullmer C, Brink A, Honer M, Woltering TJ, Muri D, Iding H, Bürkler M, Binder M, Bartelmus C, Knuesel I, Pacher P, Herde AM, Spinelli F, Ahmed H, Atz K, Keller C, Weber M, Schibli R, Mu L, Grether U, Ametamey SM. Identification and Preclinical Development of a 2,5,6-Trisubstituted Fluorinated Pyridine Derivative as a Radioligand for the Positron Emission Tomography Imaging of Cannabinoid Type 2 Receptors. J Med Chem 2020; 63:10287-10306. [PMID: 32787079 DOI: 10.1021/acs.jmedchem.0c00778] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite the broad implications of the cannabinoid type 2 receptor (CB2) in neuroinflammatory processes, a suitable CB2-targeted probe is currently lacking in clinical routine. In this work, we synthesized 15 fluorinated pyridine derivatives and tested their binding affinities toward CB2 and CB1. With a sub-nanomolar affinity (Ki for CB2) of 0.8 nM and a remarkable selectivity factor of >12,000 over CB1, RoSMA-18-d6 exhibited outstanding in vitro performance characteristics and was radiofluorinated with an average radiochemical yield of 10.6 ± 3.8% (n = 16) and molar activities ranging from 52 to 65 GBq/μmol (radiochemical purity > 99%). [18F]RoSMA-18-d6 showed exceptional CB2 attributes as demonstrated by in vitro autoradiography, ex vivo biodistribution, and positron emission tomography (PET). Further, [18F]RoSMA-18-d6 was used to detect CB2 upregulation on postmortem human ALS spinal cord tissues. Overall, these results suggest that [18F]RoSMA-18-d6 is a promising CB2 PET radioligand for clinical translation.
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Affiliation(s)
- Ahmed Haider
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Luca Gobbi
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Julian Kretz
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Christoph Ullmer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Andreas Brink
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Michael Honer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Thomas J Woltering
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Dieter Muri
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Hans Iding
- Pharma Technical Development, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Markus Bürkler
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Martin Binder
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Christian Bartelmus
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Irene Knuesel
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Pal Pacher
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute of Health/NIAAA, 5625 Fishers Lane, Rockville, 20852 Maryland, United States
| | - Adrienne Müller Herde
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Francesco Spinelli
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Hazem Ahmed
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Kenneth Atz
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Claudia Keller
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Markus Weber
- Neuromuscular Diseases Unit/ALS Clinic, Kantonsspital St. Gallen, 9007 St. Gallen, Switzerland
| | - Roger Schibli
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.,Department of Nuclear Medicine, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Linjing Mu
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.,Department of Nuclear Medicine, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Uwe Grether
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Simon M Ametamey
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
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10
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Hu Y, Shi H, Zhou M, Ren Q, Zhu W, Zhang W, Zhang Z, Zhou C, Liu Y, Ding X, Shen HC, Yan SF, Dey F, Wu W, Zhai G, Zhou Z, Xu Z, Ji Y, Lv H, Jiang T, Wang W, Xu Y, Vercruysse M, Yao X, Mao Y, Yu X, Bradley K, Tan X. Discovery of Pyrido[2,3- b]indole Derivatives with Gram-Negative Activity Targeting Both DNA Gyrase and Topoisomerase IV. J Med Chem 2020; 63:9623-9649. [PMID: 32787097 DOI: 10.1021/acs.jmedchem.0c00768] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The rise of multidrug resistant (MDR) Gram-negative (GN) pathogens and the decline of available antibiotics that can effectively treat these severe infections are a major threat to modern medicine. Developing novel antibiotics against MDR GN pathogens is particularly difficult as compounds have to permeate the GN double membrane, which has very different physicochemical properties, and have to circumvent a plethora of resistance mechanisms such as multiple efflux pumps and target modifications. The bacterial type II topoisomerases DNA gyrase (GyrA2B2) and Topoisomerase IV (ParC2E2) are highly conserved targets across all bacterial species and validated in the clinic by the fluoroquinolones. Dual inhibitors targeting the ATPase domains (GyrB/ParE) of type II topoisomerases can overcome target-based fluoroquinolone resistance. However, few ATPase inhibitors are active against GN pathogens. In this study, we demonstrated a successful strategy to convert a 2-carboxamide substituted azaindole chemical scaffold with only Gram-positive (GP) activity into a novel series with also potent activity against a range of MDR GN pathogens. By systematically fine-tuning the many physicochemical properties, we identified lead compounds such as 17r with a balanced profile showing potent GN activity, high aqueous solubility, and desirable PK features. Moreover, we showed the bactericidal efficacy of 17r using a neutropenic mouse thigh infection model.
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Affiliation(s)
| | | | | | - Qingcheng Ren
- WuXi AppTec (Wuhan) Co., Ltd., No. 666 Gaoxin Road, Wuhan East Lake High-tech Development Zone, Hubei 430075, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wen Wang
- MicuRx Pharmaceuticals, Inc. (Shanghai), Floor 3, Building B, 1976 Middle Gaoke Road, Shanghai 201210, China
| | - Yunhua Xu
- MicuRx Pharmaceuticals, Inc. (Shanghai), Floor 3, Building B, 1976 Middle Gaoke Road, Shanghai 201210, China
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11
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Liu Y, Wu J, Zhou M, Chen W, Li D, Wang Z, Hornsperger B, Aebi JD, Märki HP, Kuhn B, Wang L, Kuglstatter A, Benz J, Müller S, Hochstrasser R, Ottaviani G, Xin J, Kirchner S, Mohr S, Verry P, Riboulet W, Shen HC, Mayweg AV, Amrein K, Tan X. Discovery of 3-Pyridyl Isoindolin-1-one Derivatives as Potent, Selective, and Orally Active Aldosterone Synthase (CYP11B2) Inhibitors. J Med Chem 2020; 63:6876-6897. [DOI: 10.1021/acs.jmedchem.0c00233] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Awale M, Riniker S, Kramer C. Matched Molecular Series Analysis for ADME Property Prediction. J Chem Inf Model 2020; 60:2903-2914. [PMID: 32369360 DOI: 10.1021/acs.jcim.0c00269] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Generation and prioritization of new molecules are the most central part of the drug design process. Matched molecular series analysis (MMSA) has recently been proposed as a formal approach that captures both of these key elements of design. In order to better understand the power of MMSA and its specific limitations, we here evaluate its performance as an ADME property prediction tool. We use four large and diverse inhouse data sets, logD, microsomal clearance, CYP2C9, and CYP3A4 inhibition. MMSA follows the concept of parallel structure-activity relationship (SAR), where if two identical substituent series on different scaffolds show similarity in their property profiles, SAR from one series can be transferred to the other series. We test four different similarity metrics to identify pairs of molecular series where information can be transferred. We find that the best prediction performance is achieved by a combination of centered root-mean-square deviation (cRMSD) and a network score approach previously published by Keefer et al. However, cRMSD alone strikes the best balance between accuracy and the number of predictions that can be made. We identify statistical metrics that allow estimating when MMSA predictions will work, similar to the well-known applicability domain concept in machine learning. MMSA achieves a prediction accuracy that is comparable to a standard machine-learning model and matched molecular pair analysis. In contrast to machine learning, however, it is very easy to understand where MMSA predictions are coming from. Finally, to prospectively test the power of MMSA, we retested compounds that were strong outliers in the initial predictions and show how the MMSA model can help to identify erroneous data points.
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Affiliation(s)
- Mahendra Awale
- Computer-Aided Drug Design/Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Christian Kramer
- Computer-Aided Drug Design/Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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13
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Gobbi L, Mercier J, Bang-Andersen B, Nicolas JM, Reilly J, Wagner B, Whitehead D, Briard E, Maguire RP, Borroni E, Auberson YP. A Comparative Study of in vitro Assays for Predicting the Nonspecific Binding of PET Imaging Agents in vivo. ChemMedChem 2019; 15:585-592. [PMID: 31797561 DOI: 10.1002/cmdc.201900608] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/27/2019] [Indexed: 01/23/2023]
Abstract
Nonspecific binding (NSB) is a key parameter in optimizing PET imaging tracers. We compared the ability to predict NSB of three available methods: LIMBA, rat fu,brain , and CHI(IAM). Even though NSB is often associated with lipophilicity, we observed that logD does not correlate with any of these assays, clearly indicating that lipophilicity, while influencing NSB, is insufficient to predict it. A cross-comparison of the methods showed that all three correlate and are useful predictors of NSB. The three assays, however, rank the molecules slightly differently, illustrating the challenge of comparing molecules within a narrow chemical space. We also noted that CHI(IAM) values more effectively predict VNS , a measure of in vivo NSB in the human brain. CHI(IAM) measurements might be a closer model of the actual physicochemical interaction between PET tracer candidates and cell membranes, and seems to be the method of choice for the optimization of in vivo NSB.
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Affiliation(s)
- Luca Gobbi
- Pharma Research and Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd., 4070, Basel, Switzerland
| | - Joël Mercier
- UCB Early Solutions, UCB Biopharma sprl, 1420, Braine-l'Alleud, Belgium
| | - Benny Bang-Andersen
- Molecular Discovery and Innovation, H. Lundbeck A/S, 9 Ottiliavej, 2500, Valby, Denmark
| | | | - John Reilly
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Fabrikstrasse 2, 4056, Basel, Switzerland
| | - Björn Wagner
- Pharma Research and Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd., 4070, Basel, Switzerland
| | - David Whitehead
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Fabrikstrasse 2, 4056, Basel, Switzerland
| | - Emmanuelle Briard
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Fabrikstrasse 2, 4056, Basel, Switzerland
| | - R Paul Maguire
- UCB Early Solutions, UCB Biopharma sprl, 1420, Braine-l'Alleud, Belgium
| | - Edilio Borroni
- Pharma Research and Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd., 4070, Basel, Switzerland
| | - Yves P Auberson
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Fabrikstrasse 2, 4056, Basel, Switzerland
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14
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Jakubiak P, Cantrill C, Urtti A, Alvarez-Sánchez R. Establishment of an In Vitro-In Vivo Correlation for Melanin Binding and the Extension of the Ocular Half-Life of Small-Molecule Drugs. Mol Pharm 2019; 16:4890-4901. [PMID: 31670965 DOI: 10.1021/acs.molpharmaceut.9b00769] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A large variety of drugs bind effectively to melanin, and this binding influences their ocular pharmacokinetic and distribution profiles. We aimed to establish a correlation between in vitro melanin binding and in vivo ocular pharmacokinetics (PK). The extent of melanin binding in vitro was determined for a set of model drugs; binding kinetics and binding isotherms were generated and fitted to a mechanistic model to derive the drug-melanin binding parameters (Bmax, KD, kon, and koff). In addition, in vitro ADME properties such as cellular permeability, P-glycoprotein-mediated efflux, plasma protein binding, and octanol partition coefficients were determined. Moreover, cellular uptake was measured in the nonpigmented ARPE-19 cells and in lightly pigmented human epidermal melanocytes. Finally, in vivo ocular PK studies were performed in albino and pigmented rats using intravenous injections. Substantial drug enrichment accompanied by a very long residence time was observed in pigmented ocular tissues, which could be linked to the melanin binding determined in vitro and to the intracellular drug uptake into the pigmented cells. The resulting ocular PK profile is shown to be a consequence of the interplay of melanin binding with concurrent processes such as systemic clearance, plasma protein binding, cellular permeation, P-glycoprotein efflux, pH partitioning, and tissue binding. Understanding this interplay at a mechanistic level could help in the rational design and development of new small-molecule drug candidates with the desired PK/pharmacodynamic profile to target the back of the eye.
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Affiliation(s)
- Paulina Jakubiak
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland.,School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland
| | - Carina Cantrill
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Arto Urtti
- School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland.,Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Rubén Alvarez-Sánchez
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
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15
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Schnider P, Dolente C, Stalder H, Martin RE, Reinmüller V, Marty R, Wyss Gramberg C, Wagner B, Fischer H, Alker AM, Müller K. Modulation of Pharmacologically Relevant Properties of Piperidine Derivatives by Functional Groups in an Equatorial or Axial β‐Position to the Amino Group. Chembiochem 2019; 21:212-234. [DOI: 10.1002/cbic.201900474] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Patrick Schnider
- F. Hoffmann-La Roche AGPharmaceutical Research and Early DevelopmentRoche Innovation Center Basel Grenzacherstrasse 124 4070 Basel Switzerland
| | - Cosimo Dolente
- F. Hoffmann-La Roche AGPharmaceutical Research and Early DevelopmentRoche Innovation Center Basel Grenzacherstrasse 124 4070 Basel Switzerland
| | - Henri Stalder
- F. Hoffmann-La Roche AGPharmaceutical Research and Early DevelopmentRoche Innovation Center Basel Grenzacherstrasse 124 4070 Basel Switzerland
- Beim Goldenen Löwen 12 4052 Basel Switzerland
| | - Rainer E. Martin
- F. Hoffmann-La Roche AGPharmaceutical Research and Early DevelopmentRoche Innovation Center Basel Grenzacherstrasse 124 4070 Basel Switzerland
| | - Viktoria Reinmüller
- F. Hoffmann-La Roche AGPharmaceutical Research and Early DevelopmentRoche Innovation Center Basel Grenzacherstrasse 124 4070 Basel Switzerland
- Present address: Auxenion Research AG Gewerbestrasse 18 4123 Allschwil Switzerland
| | - Roman Marty
- F. Hoffmann-La Roche AGPharmaceutical Research and Early DevelopmentRoche Innovation Center Basel Grenzacherstrasse 124 4070 Basel Switzerland
- Present address: Auxenion Research AG Gewerbestrasse 18 4123 Allschwil Switzerland
| | - Caroline Wyss Gramberg
- F. Hoffmann-La Roche AGPharmaceutical Research and Early DevelopmentRoche Innovation Center Basel Grenzacherstrasse 124 4070 Basel Switzerland
| | - Björn Wagner
- F. Hoffmann-La Roche AGPharmaceutical Research and Early DevelopmentRoche Innovation Center Basel Grenzacherstrasse 124 4070 Basel Switzerland
| | - Holger Fischer
- F. Hoffmann-La Roche AGPharmaceutical Research and Early DevelopmentRoche Innovation Center Basel Grenzacherstrasse 124 4070 Basel Switzerland
| | - André M. Alker
- F. Hoffmann-La Roche AGPharmaceutical Research and Early DevelopmentRoche Innovation Center Basel Grenzacherstrasse 124 4070 Basel Switzerland
| | - Klaus Müller
- ETH ZürichLaboratorium für Organische Chemie Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
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16
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The impact of lipophilicity on environmental processes, drug delivery and bioavailability of food components. Microchem J 2019. [DOI: 10.1016/j.microc.2019.01.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Giroud M, Dietzel U, Anselm L, Banner D, Kuglstatter A, Benz J, Blanc JB, Gaufreteau D, Liu H, Lin X, Stich A, Kuhn B, Schuler F, Kaiser M, Brun R, Schirmeister T, Kisker C, Diederich F, Haap W. Repurposing a Library of Human Cathepsin L Ligands: Identification of Macrocyclic Lactams as Potent Rhodesain and Trypanosoma brucei Inhibitors. J Med Chem 2018; 61:3350-3369. [DOI: 10.1021/acs.jmedchem.7b01869] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Maude Giroud
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Uwe Dietzel
- Rudolf-Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Lilli Anselm
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - David Banner
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Andreas Kuglstatter
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jörg Benz
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jean-Baptiste Blanc
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Delphine Gaufreteau
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Haixia Liu
- Roche Pharma Research and Early Development, Roche Innovation Center Shanghai, 720 Cailun Road, Pudong, Shanghai 201203, China
| | - Xianfeng Lin
- Roche Pharma Research and Early Development, Roche Innovation Center Shanghai, 720 Cailun Road, Pudong, Shanghai 201203, China
| | - August Stich
- Department of Tropical Medicine, Medical Mission Institute, Salvatorstrasse 7, 97074 Würzburg, Germany
| | - Bernd Kuhn
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Franz Schuler
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Reto Brun
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Caroline Kisker
- Rudolf-Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Wolfgang Haap
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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18
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Giroud M, Kuhn B, Saint-Auret S, Kuratli C, Martin RE, Schuler F, Diederich F, Kaiser M, Brun R, Schirmeister T, Haap W. 2H-1,2,3-Triazole-Based Dipeptidyl Nitriles: Potent, Selective, and Trypanocidal Rhodesain Inhibitors by Structure-Based Design. J Med Chem 2018; 61:3370-3388. [DOI: 10.1021/acs.jmedchem.7b01870] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Maude Giroud
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Bernd Kuhn
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Sarah Saint-Auret
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Christoph Kuratli
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Rainer E. Martin
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Franz Schuler
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Reto Brun
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Wolfgang Haap
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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19
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Ceccarelli M, Wagner B, Alvarez-Sánchez R, Cruciani G, Goracci L. Use of the Distribution Coefficient in Brain Polar Lipids for the Assessment of Drug-Induced Phospholipidosis Risk. Chem Res Toxicol 2017; 30:1145-1156. [DOI: 10.1021/acs.chemrestox.6b00459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- M. Ceccarelli
- Laboratory
for Chemoinformatics and Molecular Modelling, Department of Chemistry,
Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - B. Wagner
- pRED,
Pharma Research and Early Development, Pharmaceutical Research, Innovation
Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - R. Alvarez-Sánchez
- pRED,
Pharma Research and Early Development, Pharmaceutical Research, Innovation
Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - G. Cruciani
- Laboratory
for Chemoinformatics and Molecular Modelling, Department of Chemistry,
Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - L. Goracci
- 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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20
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Hermann KF, Neuhaus CS, Micallef V, Wagner B, Hatibovic M, Aschmann HE, Paech F, Alvarez-Sanchez R, Krämer SD, Belli S. Kinetics of lipid bilayer permeation of a series of ionisable drugs and their correlation with human transporter-independent intestinal permeability. Eur J Pharm Sci 2017; 104:150-161. [PMID: 28366650 DOI: 10.1016/j.ejps.2017.03.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/21/2017] [Accepted: 03/29/2017] [Indexed: 12/28/2022]
Abstract
For low molecular weight drugs, lipid bilayer permeation is considered the major route for in vivo cell barrier passage. We recently introduced a fluorescence assay with liposomes to determine permeation kinetics of ionisable compounds across the lipid bilayer by monitoring drug-induced pH changes inside the liposomes. Here, we determined the permeability coefficients (PFLipP, FLipP for "Fluorescence Liposomal Permeability") across 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers of 35 ionisable drugs at pH6.0 and compared them to available in vivo human jejunal permeability (Peff) data. PFLipP values were furthermore compared with published Caco-2 cell permeability coefficients (PCaco-2), permeability coefficients determined with the parallel artificial membrane permeability assay (PAMPA) and with log D (pH6.0). The log PFLipP, corrected for predicted para-cellular diffusion, and log PCaco-2 correlated best with log Peff, with similar adjusted R2 (0.75 and 0.74, n=12). Our results suggest that transporter-independent intestinal drug absorption is predictable from liposomal permeability.
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Affiliation(s)
- Katharina F Hermann
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Claudia S Neuhaus
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Virgine Micallef
- Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Björn Wagner
- Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Maja Hatibovic
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Hélène E Aschmann
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Franziska Paech
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Rubén Alvarez-Sanchez
- Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Stefanie D Krämer
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland.
| | - Sara Belli
- Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland.
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21
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Kratochwil NA, Meille C, Fowler S, Klammers F, Ekiciler A, Molitor B, Simon S, Walter I, McGinnis C, Walther J, Leonard B, Triyatni M, Javanbakht H, Funk C, Schuler F, Lavé T, Parrott NJ. Metabolic Profiling of Human Long-Term Liver Models and Hepatic Clearance Predictions from In Vitro Data Using Nonlinear Mixed-Effects Modeling. AAPS JOURNAL 2017; 19:534-550. [DOI: 10.1208/s12248-016-0019-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/18/2016] [Indexed: 12/15/2022]
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22
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Assmus F, Ross A, Fischer H, Seelig J, Seelig A. 31P and 1H NMR Studies of the Molecular Organization of Lipids in the Parallel Artificial Membrane Permeability Assay. Mol Pharm 2016; 14:284-295. [PMID: 27977215 DOI: 10.1021/acs.molpharmaceut.6b00889] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The parallel artificial membrane permeability assay (PAMPA) has emerged as a widely used primary in vitro screen for passive permeability of potential drug candidates. However, the molecular structure of the permeation barrier (consisting of a filter-supported dodecane-egg lecithin mixture) has never been characterized. Here, we investigated the long-range order of phospholipids in the PAMPA barrier by means of 31P static solid-state NMR. Diffusion constants of PAMPA membrane components were derived from liquid state NMR and, in addition, drug distribution between the PAMPA lipid phase and buffer (log DPAMPA at pH 7.4) was systematically investigated. Increasing concentration of n-dodecane to the system egg lecithin-water (lamellar phase, Lα) induces formation of inverted hexagonal (Hii) and isotropic phases. At n-dodecane concentrations matching those used in PAMPA (9%, w/v) a purely "isotropic" phase was observed corresponding to lipid aggregates with a diameter in the range 4-7 nm. Drug distribution studies indicate that these reverse micelles facilitate the binding to, and in turn the permeation across, the PAMPA dodecane barrier, in particular for amphiphilic solutes. The proposed model for the molecular architecture and function of the PAMPA barrier provides a fundamental, hitherto missing framework to evaluate the scope but also limitations of PAMPA for the prediction of in vivo membrane permeability.
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Affiliation(s)
- Frauke Assmus
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland.,Division of Biophysical Chemistry, Biozentrum, University of Basel , Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Alfred Ross
- Roche Pharmaceutical Research and Early Development, Therapeutic Modalities, pCMC, Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Holger Fischer
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Joachim Seelig
- Division of Biophysical Chemistry, Biozentrum, University of Basel , Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna Seelig
- Division of Biophysical Chemistry, Biozentrum, University of Basel , Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
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23
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Jakubiak P, Wagner B, Grimm HP, Petrig-Schaffland J, Schuler F, Alvarez-Sánchez R. Development of a Unified Dissolution and Precipitation Model and Its Use for the Prediction of Oral Drug Absorption. Mol Pharm 2016; 13:586-98. [DOI: 10.1021/acs.molpharmaceut.5b00808] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Paulina Jakubiak
- Roche Pharmaceutical Research
and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Björn Wagner
- Roche Pharmaceutical Research
and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Hans Peter Grimm
- Roche Pharmaceutical Research
and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Franz Schuler
- Roche Pharmaceutical Research
and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Rubén Alvarez-Sánchez
- Roche Pharmaceutical Research
and Early Development, Roche Innovation Center Basel, Basel, Switzerland
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24
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Belli S, Assmus F, Wagner B, Honer M, Fischer H, Schuler F, Alvarez-Sánchez R. Estimation of Drug Binding to Brain Tissue: Methodology and in Vivo Application of a Distribution Assay in Brain Polar Lipids. Mol Pharm 2015; 12:4529-41. [DOI: 10.1021/acs.molpharmaceut.5b00717] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sara Belli
- Roche
Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel 4070, Switzerland
| | - Frauke Assmus
- Center
for Applied Pharmacokinetic Research, Manchester Pharmacy School, University of Manchester, Stopford Building, Oxford Road, M13 9PT Manchester, United Kingdom
| | - Bjoern Wagner
- Roche
Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel 4070, Switzerland
| | - Michael Honer
- Roche
Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel 4070, Switzerland
| | - Holger Fischer
- Roche
Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel 4070, Switzerland
| | - Franz Schuler
- Roche
Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel 4070, Switzerland
| | - Rubén Alvarez-Sánchez
- Roche
Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel 4070, Switzerland
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