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Kehrein J, Bunker A, Luxenhofer R. POxload: Machine Learning Estimates Drug Loadings of Polymeric Micelles. Mol Pharm 2024; 21:3356-3374. [PMID: 38805643 PMCID: PMC11394009 DOI: 10.1021/acs.molpharmaceut.4c00086] [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] [Indexed: 05/30/2024]
Abstract
Block copolymers, composed of poly(2-oxazoline)s and poly(2-oxazine)s, can serve as drug delivery systems; they form micelles that carry poorly water-soluble drugs. Many recent studies have investigated the effects of structural changes of the polymer and the hydrophobic cargo on drug loading. In this work, we combine these data to establish an extended formulation database. Different molecular properties and fingerprints are tested for their applicability to serve as formulation-specific mixture descriptors. A variety of classification and regression models are built for different descriptor subsets and thresholds of loading efficiency and loading capacity, with the best models achieving overall good statistics for both cross- and external validation (balanced accuracies of 0.8). Subsequently, important features are dissected for interpretation, and the DrugBank is screened for potential therapeutic use cases where these polymers could be used to develop novel formulations of hydrophobic drugs. The most promising models are provided as an open-source software tool for other researchers to test the applicability of these delivery systems for potential new drug candidates.
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Affiliation(s)
- Josef Kehrein
- Soft Matter Chemistry, Department of Chemistry, Faculty of Science, University of Helsinki, A. I. Virtasen aukio 1, 00014 Helsinki, Finland
- Drug Research Program, Division of Pharmaceutical Biosciences Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00014 Helsinki, Finland
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences Faculty of Pharmacy, University of Helsinki, Viikinkaari 5 E, 00014 Helsinki, Finland
| | - Robert Luxenhofer
- Soft Matter Chemistry, Department of Chemistry, Faculty of Science, University of Helsinki, A. I. Virtasen aukio 1, 00014 Helsinki, Finland
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2
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Sardar S, Bhattacharya A, Amin SA, Jha T, Gayen S. Exploring molecular fingerprints of different drugs having bile interaction: a stepping stone towards better drug delivery. Mol Divers 2024; 28:1471-1483. [PMID: 37369957 DOI: 10.1007/s11030-023-10670-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023]
Abstract
Bile acids are amphiphilic substances produced naturally in humans. In the context of drug delivery and dosage form design, it is critical to understand whether a drug interacts with bile inside the gastrointestinal (GI) tract or not. This study focuses on the identification of structural fingerprints/features important for bile interaction. Molecular modelling methods such as Bayesian classification and recursive partitioning (RP) studies are executed to find important fingerprints/features for the bile interaction. For the Bayesian classification study, the ROC score of 0.837 and 0.950 are found for the training set and the test set compounds, respectively. The fluorine-containing aliphatic/aromatic group, the branched chain of the alkyl group containing hydroxyl moiety and the phenothiazine ring etc. are identified as good fingerprints having a positive contribution towards bile interactions, whereas, the bad fingerprints such as free carboxylate group, purine, and pyrimidine ring etc. have a negative contribution towards bile interactions. The best tree (tree ID: 1) from the RP study classifies the bile interacting or non-interacting compounds with a ROC score of 0.941 for the training and 0.875 for the test set. Additionally, SARpy and QSAR-Co analyses are also been performed to classify compounds as bile interacting/non-interacting. Moreover, forty-six recently FDA-approved drugs have been screened by the developed SARpy and QSAR-Co models to assess their bile interaction properties. Overall, this attempt may facilitate the researchers to identify bile interacting/non-interacting molecules in a faster way and help in the design of formulations and target-specific drug development.
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Affiliation(s)
- Sourav Sardar
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Arijit Bhattacharya
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Sk Abdul Amin
- Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata, West Bengal, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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3
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Hanio S, Möllmert S, Möckel C, Choudhury S, Höpfel AI, Zorn T, Endres S, Schlauersbach J, Scheller L, Keßler C, Scherf-Clavel O, Bellstedt P, Schubert US, Pöppler AC, Heinze KG, Guck J, Meinel L. Bile Is a Selective Elevator for Mucosal Mechanics and Transport. Mol Pharm 2023; 20:6151-6161. [PMID: 37906224 DOI: 10.1021/acs.molpharmaceut.3c00550] [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] [Indexed: 11/02/2023]
Abstract
Mucus mechanically protects the intestinal epithelium and impacts the absorption of drugs, with a largely unknown role for bile. We explored the impacts of bile on mucosal biomechanics and drug transport within mucus. Bile diffused with square-root-of-time kinetics and interplayed with mucus, leading to transient stiffening captured in Brillouin images and a concentration-dependent change from subdiffusive to Brownian-like diffusion kinetics within the mucus demonstrated by differential dynamic microscopy. Bile-interacting drugs, Fluphenazine and Perphenazine, diffused faster through mucus in the presence of bile, while Metoprolol, a drug with no bile interaction, displayed consistent diffusion. Our findings were corroborated by rat studies, where co-dosing of a bile acid sequestrant substantially reduced the bioavailability of Perphenazine but not Metoprolol. We clustered over 50 drugs based on their interactions with bile and mucin. Drugs that interacted with bile also interacted with mucin but not vice versa. This study detailed the dynamics of mucus biomechanics under bile exposure and linked the ability of a drug to interact with bile to its abbility to interact with mucus.
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Affiliation(s)
- Simon Hanio
- Institute for Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Stephanie Möllmert
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und Medizin, Staudtstrasse 2, 91058 Erlangen, Germany
| | - Conrad Möckel
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und Medizin, Staudtstrasse 2, 91058 Erlangen, Germany
| | - Susobhan Choudhury
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Andreas I Höpfel
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Theresa Zorn
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Sebastian Endres
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Jonas Schlauersbach
- Institute for Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Lena Scheller
- Institute for Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Christoph Keßler
- Institute for Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Oliver Scherf-Clavel
- Institute for Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Peter Bellstedt
- Institute of Organic Chemistry, University of Jena, Humboldtstrasse 10, 07743 Jena, Germany
- Institute for Clinical Chemistry, University of Zürich,Rämistrasse 100, 8091 Zurich, Switzerland
| | - Ulrich S Schubert
- Institute of Organic Chemistry, University of Jena, Humboldtstrasse 10, 07743 Jena, Germany
- Jena Center for Soft Matter (JCSM), University of Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Ann-Christin Pöppler
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Katrin G Heinze
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Jochen Guck
- Max Planck Institute for the Science of Light and Max-Planck-Zentrum für Physik und Medizin, Staudtstrasse 2, 91058 Erlangen, Germany
| | - Lorenz Meinel
- Institute for Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Josef-Schneider-Strasse 2, 97080 Wuerzburg, Germany
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Endres S, Ehrmanntraut S, Endres L, Can K, Kraft C, Rasmussen T, Luxenhofer R, Böttcher B, Engels B, Pöppler AC. Structural Investigation on How Guest Loading of Poly(2-oxazoline)-Based Micelles Affects the Interaction with Simulated Intestinal Fluids. ACS Biomater Sci Eng 2023; 9:4821-4830. [PMID: 37441793 DOI: 10.1021/acsbiomaterials.3c00645] [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] [Indexed: 07/15/2023]
Abstract
Drug loading of polymer micelles can have a profound effect on their particle size and morphology as well as their physicochemical properties. In turn, this influences performance in biological environments. For oral delivery of drugs, the intestinal environment is key, and consequently, a thorough structural understanding of what happens at this material-biology interface is required to understand in vivo performance and tailor improved delivery vehicles. In this study, we address this interface in vitro through a detailed structural characterization of the colloidal assemblies of polymeric micelles based on poly(2-oxazolines) with three different guest loadings with the natural product curcumin (17-52 wt %) in fed-state simulated intestinal fluids (FeSSIF). For this, we employ NMR spectroscopy, in particular, 1H NMR, 1H-1H-NOESY, and 1H DOSY experiments complemented by quantum chemical calculations and cryo-TEM measurements. Through this mixture of methods, we identified curcumin-taurocholate interactions as central interaction patterns alongside interactions with the polymer and lipids. Furthermore, curcumin molecules can be exchanged between polymer micelles and bile colloids, an important prerequisite for their uptake. Finally, increased loading of the polymer micelles with curcumin resulted in a larger number of vesicles as taurocholate─through coordination with Cur─is less available to form nanoparticles with the lipids. The loading-dependent behavior found in this study deviates from previous work on a different drug substance highlighting the need for further studies including different drug molecules and polymer types to improve the understanding of events on the molecular level.
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Affiliation(s)
- Sebastian Endres
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Silvia Ehrmanntraut
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lukas Endres
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany
| | - Koray Can
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany
| | - Christian Kraft
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Tim Rasmussen
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
- Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Robert Luxenhofer
- Soft Matter Chemistry, Department of Chemistry and Helsinki Institute of Sustainability Science, Faculty of Science, University of Helsinki, PB55, 00014 Helsinki, Finland
| | - Bettina Böttcher
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
- Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, University of Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany
| | - Ann-Christin Pöppler
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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Parrow A, Larsson P, Augustijns P, Bergström CAS. Molecular Dynamics Simulations of Self-Assembling Colloids in Fed-State Human Intestinal Fluids and Their Solubilization of Lipophilic Drugs. Mol Pharm 2023; 20:451-460. [PMID: 36350845 PMCID: PMC9811461 DOI: 10.1021/acs.molpharmaceut.2c00710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bioavailability of oral drugs often depends on how soluble the active pharmaceutical ingredient is in the fluid present in the small intestine. For efficient drug discovery and development, computational tools are needed for estimating this drug solubility. In this paper, we examined human intestinal fluids collected in the fed state, with coarse-grained molecular dynamics simulations. The experimentally obtained concentrations in aspirated duodenal fluids from five healthy individuals were used in three simulation sets to evaluate the importance of the initial distribution of molecules and the presence of glycerides in the simulation box when simulating the colloidal environment of the human intestinal fluid. We observed self-assembly of colloidal structures of different types: prolate, elongated, and oblate micelles, and vesicles. Glycerides were important for the formation of vesicles, and their absence was shown to induce elongated micelles. We then simulated the impact of digestion and absorption on the different colloidal types. Finally, we looked at the solubilization of three model compounds of increasing lipophilicity (prednisolone, fenofibrate, and probucol) by calculating contact ratios of drug-colloid to drug-water. Our simulation results of colloidal interactions with APIs were in line with experimental solubilization data but showed a dissimilarity to solubility values when comparing fasted-/fed-state ratios between two of the APIs. This work shows that coarse-grained molecular dynamics simulation is a promising tool for investigation of the intestinal fluids, in terms of colloidal attributes and drug solubility.
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Affiliation(s)
- Albin Parrow
- Department
of Pharmacy, Uppsala Biomedical Center,
Uppsala University, P.O. Box 580, SE-751 23 Uppsala, Sweden
| | - Per Larsson
- Department
of Pharmacy, Uppsala Biomedical Center,
Uppsala University, P.O. Box 580, SE-751 23 Uppsala, Sweden,The
Swedish Drug Delivery Center, Department of Pharmacy, Uppsala Biomedical Centre, Uppsala University, P.O. Box 580, SE-751 23 Uppsala, Sweden
| | - Patrick Augustijns
- Department
of Pharmaceutical and Pharmacological Sciences, KU Leuven, O&N II Gasthuisberg, Herestraat 49, Box 921, 3000 Leuven, Belgium
| | - Christel A. S. Bergström
- Department
of Pharmacy, Uppsala Biomedical Center,
Uppsala University, P.O. Box 580, SE-751 23 Uppsala, Sweden,The
Swedish Drug Delivery Center, Department of Pharmacy, Uppsala Biomedical Centre, Uppsala University, P.O. Box 580, SE-751 23 Uppsala, Sweden,. Phone: +46 18 4714118
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