1
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Ebert A, Dahley C. Can membrane permeability of zwitterionic compounds be predicted by the solubility-diffusion model? Eur J Pharm Sci 2024; 199:106819. [PMID: 38815700 DOI: 10.1016/j.ejps.2024.106819] [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: 02/22/2024] [Revised: 04/23/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Zwitterions contain both positively and negatively charged functional groups, resulting in an overall net neutral charge. Nevertheless, the membrane permeability of the zwitterionic form of a compound is assumed to be much lower than the permeability of the uncharged neutral form. Although a significant proportion of pharmaceuticals are zwitterionic, it has not been clear so far whether their permeability is dominated by the permeation of the zwitterionic or the neutral form, since neutral fractions are often quite low as compared to the zwitterionic fraction. This complicates the in silico prediction of the permeability of zwitterionic compounds. In this work, we re-evaluated existing in vitro permeability data from literature measured with Caco-2/MDCK cell assays, using more strict exclusion criteria for effects like diffusion limitation by the aqueous boundary layers, paracellular transport, active transport and retention. Using this re-evaluated data set, we show that extracted intrinsic permeabilities of the neutral fraction are well predicted by the solubility-diffusion model (RMSE = 1.21; n = 18) if the permeability of the zwitterionic species is assumed negligible. Our work thus suggests that only the neutral species is relevant for the membrane permeability of zwitterionic compounds, and that membrane permeability of zwitterionic compounds is indeed predictable by the solubility-diffusion model.
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Affiliation(s)
- Andrea Ebert
- Department of Computational Biology & Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, 04318 Leipzig, Germany.
| | - Carolin Dahley
- Department of Computational Biology & Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, 04318 Leipzig, Germany
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2
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Odehnalová K, Balouch M, Storchmannová K, Petrová E, Konefał M, Zadražil A, Berka K, Brus J, Štěpánek F. Liposomal Copermeation Assay Reveals Unexpected Membrane Interactions of Commonly Prescribed Drugs. Mol Pharm 2024; 21:2673-2683. [PMID: 38682796 DOI: 10.1021/acs.molpharmaceut.3c00766] [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: 05/01/2024]
Abstract
The permeation of small molecules across biological membranes is a crucial process that lies at the heart of life. Permeation is involved not only in the maintenance of homeostasis at the cell level but also in the absorption and biodistribution of pharmacologically active substances throughout the human body. Membranes are formed by phospholipid bilayers that represent an energy barrier for permeating molecules. Crossing this energy barrier is assumed to be a singular event, and permeation has traditionally been described as a first-order kinetic process, proportional only to the concentration gradient of the permeating substance. For a given membrane composition, permeability was believed to be a unique property dependent only on the permeating molecule itself. We provide experimental evidence that this long-held view might not be entirely correct. Liposomes were used in copermeation experiments with a fluorescent probe, where simultaneous permeation of two substances occurred over a single phospholipid bilayer. Using an assay of six commonly prescribed drugs, we have found that the presence of a copermeant can either enhance or suppress the permeation rate of the probe molecule, often more than 2-fold in each direction. This can have significant consequences for the pharmacokinetics and bioavailability of commonly prescribed drugs when used in combination and provide new insight into so-far unexplained drug-drug interactions as well as changing the perspective on how new drug candidates are evaluated and tested.
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Affiliation(s)
- Klára Odehnalová
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Martin Balouch
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic
- Zentiva, k.s., U Kabelovny 130, Prague 10 102 37, Czech Republic
| | - Kateřina Storchmannová
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, Olomouc 771 46, Czech Republic
| | - Eliška Petrová
- Department of Organic Technology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Magdalena Konefał
- Institute of Macromolecular Chemistry of the Czech Academy of Sciences, Prague 6 162 00, Czech Republic
| | - Aleš Zadražil
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Karel Berka
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, Olomouc 771 46, Czech Republic
| | - Jiří Brus
- Institute of Macromolecular Chemistry of the Czech Academy of Sciences, Prague 6 162 00, Czech Republic
| | - František Štěpánek
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic
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3
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Tian R, Posselt M, Miaz LT, Fenner K, McLachlan MS. Influence of Season on Biodegradation Rates in Rivers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7144-7153. [PMID: 38527158 PMCID: PMC11044578 DOI: 10.1021/acs.est.3c10541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024]
Abstract
Biodegradation plays a key role in the fate of chemicals in the environment. The variability of biodegradation in time can cause uncertainty in evaluating the environmental persistence and risk of chemicals. However, the seasonality of biodegradation in rivers has not yet been the subject of environmentally relevant testing and systematic investigation for large numbers of chemicals. In this work, we studied the biodegradation of 96 compounds during four seasons at four locations (up- and downstream of WWTPs located on two Swedish rivers). Significant seasonality (ANOVA, p < 0.05) of the first-order rate constant for primary biodegradation was observed for most compounds. Variations in pH and total bacterial cell count were not the major factors explaining the seasonality of biodegradation. Deviation from the classical Arrhenius-type behavior was observed for most of the studied compounds, which calls into question the application of this relationship to correct biodegradation rate constants for differences in environmental temperature. Similarities in magnitude and seasonality of biodegradation rate constants were observed for some groups of chemicals possessing the same functional groups. Moreover, reduced seasonality of biodegradation was observed downstream of WWTPs, while biodegradation rates of most compounds were not significantly different between up- and downstream.
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Affiliation(s)
- Run Tian
- Department
of Environmental Science (ACES), Stockholm
University, Stockholm 10691, Sweden
| | - Malte Posselt
- Department
of Environmental Science (ACES), Stockholm
University, Stockholm 10691, Sweden
| | - Luc T. Miaz
- Department
of Environmental Science (ACES), Stockholm
University, Stockholm 10691, Sweden
| | - Kathrin Fenner
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
- Department
of Chemistry, University of Zürich, Zürich 8057, Switzerland
| | - Michael S. McLachlan
- Department
of Environmental Science (ACES), Stockholm
University, Stockholm 10691, Sweden
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4
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Huang Z, Ishii M, Watanabe E, Kanamitsu K, Tai K, Kusuhara H, Ohwada T, Otani Y. Effect of N-o-nitrobenzylation on conformation and membrane permeability of linear peptides. Bioorg Chem 2024; 145:107220. [PMID: 38387401 DOI: 10.1016/j.bioorg.2024.107220] [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: 12/25/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
In this study, we explored the potential of the photoremovable o-nitrobenzyl (oNB) group as a tool to manipulate the membrane permeability and regulate the conformation of linear peptides by means of experimental and computational studies. We found that the introduction of one or more oNB groups markedly increased the permeability and altered the conformation, as compared to the corresponding unmodified peptides. We thoroughly investigated the impact of peptide length, number of oNB group, oNB insertion position, and introduction of N- and C-terminal protecting groups on the passive membrane permeability by means of parallel artificial membrane permeability assay (PAMPA). Photoreaction of peptides containing one or two oNB groups proceeded cleanly in moderate to high yields, releasing the unprotected parent linear peptide. The oNB-modified peptides showed a cis/trans conformational equilibrium, while after photolysis, the unprotected linear peptides showed only the trans-amide conformation. Furthermore, a comprehensive comparison of oNB-modified peptides and N-methylated peptides was conducted, encompassing conformational analysis and physicochemical properties. N-Substituted peptides favored a folded-like structure, which may contribute to the improvement in permeability.
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Affiliation(s)
- Zhihan Huang
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mayumi Ishii
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Eri Watanabe
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kayoko Kanamitsu
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kempei Tai
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Kusuhara
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomohiko Ohwada
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuko Otani
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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5
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Ebert A, Dahley C, Goss KU. Pitfalls in evaluating permeability experiments with Caco-2/MDCK cell monolayers. Eur J Pharm Sci 2024; 194:106699. [PMID: 38232636 DOI: 10.1016/j.ejps.2024.106699] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/19/2024]
Abstract
When studying the transport of molecules across biological membranes, intrinsic membrane permeability (P0) is more informative than apparent permeability (Papp), because it eliminates external (setup-specific) factors, provides consistency across experiments and mechanistic insight. It is thus an important building block for modeling the total permeability in any given scenario. However, extracting P0 is often difficult, if not impossible, when the membrane is not the dominant transport resistance. In this work, we set out to analyze Papp values measured with Caco-2/MDCK cell monolayers of 69 literature references. We checked the Papp values for a total of 318 different compounds for the extractability of P0, considering possible limitations by aqueous boundary layers, paracellular transport, recovery issues, active transport, a possible proton flux limitation, and sink conditions. Overall, we were able to extract 77 reliable P0 values, which corresponds to about one quarter of the total compounds analyzed, while about half were limited by the diffusion through the aqueous layers. Compared to an existing data set of P0 values published by Avdeef, our approach resulted in a much higher exclusion of compounds. This is a consequence of stricter compound- and reference-specific exclusion criteria, but also because we considered possible concentration-shift effects due to different pH values in the aqueous layers, an effect only recently described in literature. We thus provide a consistent and reliable set of P0, e.g. as a basis for future modeling.
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Affiliation(s)
- Andrea Ebert
- Department of Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Federal Republic of Germany.
| | - Carolin Dahley
- Department of Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Federal Republic of Germany
| | - Kai-Uwe Goss
- Department of Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Federal Republic of Germany; Institute of Chemistry, University of Halle-Wittenberg, Kurt-Mothes-Straße 2, Halle 06120, Federal Republic of Germany
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6
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Dahley C, Goss KU, Ebert A. Revisiting the pK a-Flux method for determining intrinsic membrane permeability. Eur J Pharm Sci 2023; 191:106592. [PMID: 37751809 DOI: 10.1016/j.ejps.2023.106592] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/11/2023] [Accepted: 09/23/2023] [Indexed: 09/28/2023]
Abstract
Intrinsic membrane permeability is one of several factors that critically determine the intestinal absorption of a chemical. The intrinsic membrane permeability of a chemical is usually extracted from transwell experiments with Caco-2 or MDCK cells, preferably by the pKa-Flux method, which is considered the method of choice when aqueous boundary layer effects need to be excluded. The pKa-Flux method has two variants, the iso-pH method, where apical and basolateral pH are equal, and the gradient-pH method, where apical and basolateral pH are different. The most commonly used method is the gradient-pH method, as it is intended to reflect the pH-conditions in the gastrointestinal tract. However, concentration-shift effects caused by the applied pH-difference between apical and basolateral compartment in the gradient-pH method have not been considered in the evaluation of the experimental data in the past. Consequently, incorrect intrinsic membrane permeabilities have been determined. In this work, we present a revised method for extracting the intrinsic membrane permeability from gradient-pH data that considers concentration-shift effects in the basolateral aqueous boundary layer and filter as well as in the cytosol. Furthermore, we propose the use of the iso-pH method, where only concentration-shift effects in the cytosol need to be considered, as an alternative to the gradient-pH method. We use the five lipophilic bases amantadine, chloroquine, propranolol, venlafaxine and verapamil as examples to compare gradient-pH method and iso-pH method with regard to the extractability of the intrinsic membrane permeability. For lipophilic bases, the iso-pH method proves to be advantageous. All intrinsic membrane permeabilities determined in this work were substantially higher than the intrinsic membrane permeabilities reported in literature.
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Affiliation(s)
- Carolin Dahley
- Department of Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Germany
| | - Kai-Uwe Goss
- Department of Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Germany; Institute of Chemistry, University of Halle-Wittenberg, Kurt-Mothes-Straße 2, Halle 06120, Germany
| | - Andrea Ebert
- Department of Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Germany.
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7
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Mostofian B, Martin HJ, Razavi A, Patel S, Allen B, Sherman W, Izaguirre JA. Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods. J Chem Inf Model 2023; 63:5408-5432. [PMID: 37602861 PMCID: PMC10498452 DOI: 10.1021/acs.jcim.3c00603] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Indexed: 08/22/2023]
Abstract
The therapeutic approach of targeted protein degradation (TPD) is gaining momentum due to its potentially superior effects compared with protein inhibition. Recent advancements in the biotech and pharmaceutical sectors have led to the development of compounds that are currently in human trials, with some showing promising clinical results. However, the use of computational tools in TPD is still limited, as it has distinct characteristics compared with traditional computational drug design methods. TPD involves creating a ternary structure (protein-degrader-ligase) responsible for the biological function, such as ubiquitination and subsequent proteasomal degradation, which depends on the spatial orientation of the protein of interest (POI) relative to E2-loaded ubiquitin. Modeling this structure necessitates a unique blend of tools initially developed for small molecules (e.g., docking) and biologics (e.g., protein-protein interaction modeling). Additionally, degrader molecules, particularly heterobifunctional degraders, are generally larger than conventional small molecule drugs, leading to challenges in determining drug-like properties like solubility and permeability. Furthermore, the catalytic nature of TPD makes occupancy-based modeling insufficient. TPD consists of multiple interconnected yet distinct steps, such as POI binding, E3 ligase binding, ternary structure interactions, ubiquitination, and degradation, along with traditional small molecule properties. A comprehensive set of tools is needed to address the dynamic nature of the induced proximity ternary complex and its implications for ubiquitination. In this Perspective, we discuss the current state of computational tools for TPD. We start by describing the series of steps involved in the degradation process and the experimental methods used to characterize them. Then, we delve into a detailed analysis of the computational tools employed in TPD. We also present an integrative approach that has proven successful for degrader design and its impact on project decisions. Finally, we examine the future prospects of computational methods in TPD and the areas with the greatest potential for impact.
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Affiliation(s)
- Barmak Mostofian
- OpenEye, Cadence Molecular Sciences, Boston, Massachusetts 02114 United States
| | - Holli-Joi Martin
- Laboratory
for Molecular Modeling, Division of Chemical Biology and Medicinal
Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599 United States
| | - Asghar Razavi
- ENKO
Chem, Inc, Mystic, Connecticut 06355 United States
| | - Shivam Patel
- Psivant
Therapeutics, Boston, Massachusetts 02210 United States
| | - Bryce Allen
- Differentiated
Therapeutics, San Diego, California 92056 United States
| | - Woody Sherman
- Psivant
Therapeutics, Boston, Massachusetts 02210 United States
| | - Jesus A Izaguirre
- Differentiated
Therapeutics, San Diego, California 92056 United States
- Atommap
Corporation, New York, New York 10013 United States
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8
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Silva F, Veiga F, Paulo Jorge Rodrigues S, Cardoso C, Cláudia Paiva-Santos A. COSMO Models for the Pharmaceutical Development of Parenteral Drug Formulations. Eur J Pharm Biopharm 2023; 187:156-165. [PMID: 37120066 DOI: 10.1016/j.ejpb.2023.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/31/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023]
Abstract
The aqueous solubility of active pharmaceutical ingredients is one of the most important features to be considered during the development of parenteral formulations in the pharmaceutical industry. Computational modelling has become in the last years an integral part of pharmaceutical development. In this context, ab initio computational models, such as COnductor-like Screening MOdel (COSMO), have been proposed as promising tools for the prediction of results without the effective use of resources. Nevertheless, despite the clear evaluation of computational resources, some authors had not achieved satisfying results and new calculations and algorithms have been proposed over the years to improve the outcomes. In the development and production of aqueous parenteral formulations, the solubility of Active Pharmaceutical Ingredients (APIs) in an aqueous and biocompatible vehicle is a decisive step. This work aims to study the hypothesis that COSMO models could be useful in the development of new parenteral formulations, mainly aqueous ones.
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Affiliation(s)
- Fernando Silva
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal; REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal.
| | - Francisco Veiga
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal; REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal
| | - Sérgio Paulo Jorge Rodrigues
- Coimbra Chemistry Centre, Chemistry Department, Faculty of Sciences and Technology of the University of Coimbra of the University of Coimbra, Coimbra, Portugal
| | - Catarina Cardoso
- Laboratórios Basi, Parque Industrial Manuel Lourenço Ferreira, lote 15, 3450-232 Mortágua, Portugal
| | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal; REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal
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9
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Balouch M, Storchmannová K, Štěpánek F, Berka K. Computational Prodrug Design Methodology for Liposome Formulability Enhancement of Small-Molecule APIs. Mol Pharm 2023; 20:2119-2127. [PMID: 36939094 PMCID: PMC10074381 DOI: 10.1021/acs.molpharmaceut.2c01078] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Encapsulation into liposomes is a formulation strategy that can improve efficacy and reduce side effects of active pharmaceutical ingredients (APIs) that exhibit poor biodistribution or pharmacokinetics when administered alone. However, many APIs are unsuitable for liposomal formulations intended for parenteral administration due to their inherent physicochemical properties─lipid bilayer permeability and water-lipid equilibrium partitioning coefficient. Too high permeability results in premature leakage from liposomes, while too low permeability means the API is not able to pass across biological barriers. There are several options for solving this issue: (i) change of the lipid bilayer composition, (ii) addition of a permeability enhancer, or (iii) modification of the chemical structure of the API to design a prodrug. The latter approach was taken in the present work, and the effect of small changes in the molecular structure of the API on its permeation rate across a lipidic bilayer was systematically explored utilizing computer simulations. An in silico methodology for prodrug design based on the COSMOperm approach has been proposed and applied to four APIs (abiraterone, cytarabine, 5-fluorouracil, and paliperidone). It is shown that the addition of aliphatic hydrocarbon chains via ester or amide bonds can render the molecule more lipophilic and increase its permeability by approximately 1 order of magnitude for each 2 carbon atoms added, while the formation of fructose adducts can provide a more hydrophilic character to the molecule and reduce its lipid partitioning. While partitioning was found to depend only on the size and type of the added group, permeability was found to depend also on the added group location. Overall, it has been shown that both permeability and lipid partitioning coefficient can be systematically shifted into the desired liposome formulability window by appropriate group contributions to the parental drug. This can significantly increase the portfolio of APIs for which liposome or lipid nanoparticle formulations become feasible.
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Affiliation(s)
- Martin Balouch
- Department of Chemical Engineering, University of Chemistry and Technology, Prague, Technická 3, 166 28 Prague 6, Czech Republic
| | - Kateřina Storchmannová
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - František Štěpánek
- Department of Chemical Engineering, University of Chemistry and Technology, Prague, Technická 3, 166 28 Prague 6, Czech Republic
| | - Karel Berka
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
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10
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Harada R, Morita R, Shigeta Y. Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. J Chem Inf Model 2023; 63:259-269. [PMID: 36574612 DOI: 10.1021/acs.jcim.2c01097] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The free-energy profile of a compound is an essential measurement in evaluating the membrane permeation process by means of theoretical methods. Computationally, molecular dynamics (MD) simulation allows the free-energy profile calculation. However, MD simulations frequently fail to sample membrane permeation because they are rare events induced in longer timescales than the accessible timescale of MD, leading to an insufficient conformational search to calculate an incorrect free-energy profile. To achieve a sufficient conformational search, several enhanced sampling methods have been developed and elucidated the membrane permeation process. In addition to these enhanced sampling methods, we proposed a simple yet powerful free-energy calculation of a compound for the membrane permeation process based on originally rare-event sampling methods developed by us. Our methods have a weak dependency on external biases and their optimizations to promote the membrane permeation process. Based on distributed computing, our methods only require the selection of initial structures and their conformational resampling, whereas the enhanced sampling methods may be required to adjust external biases. Furthermore, our methods efficiently search membrane permeation processes with simple scripts without modifying any MD program. As demonstrations, we calculated the free-energy profiles of seven linear compounds for their membrane permeation based on a hybrid conformational search using two rare-event sampling methods, that is, (1) parallel cascade selection MD (PaCS-MD) and (2) outlier flooding method (OFLOOD), combined with a Markov state model (MSM) construction. In the first step, PaCS-MD generated initial membrane permeation paths of a compound. In the second step, OFLOOD expanded the unsearched conformational area around the initial paths, allowing for a broad conformational search. Finally, the trajectories were employed to construct reliable MSMs, enabling correct free-energy profile calculations. Furthermore, we estimated the membrane permeability coefficients of all compounds by constructing the reliable MSMs for their membrane permeation. In conclusion, the calculated coefficients were qualitatively correlated with the experimental measurements (correlation coefficient (R2) = 0.8689), indicating that the hybrid conformational search successfully calculated the free-energy profiles and membrane permeability coefficients of the seven compounds.
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Affiliation(s)
- Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8577, Japan
| | - Rikuri Morita
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki305-8577, Japan
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11
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Hydrophobic Deep Eutectic Solvents Based on Cineole and Organic Acids. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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12
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Gutiérrez A, Rozas S, Hernando P, Alcalde R, Atilhan M, Aparicio S. A theoretical study of CO2 capture by highly hydrophobic type III deep eutectic solvents. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Benito C, Atilhan M, Aparicio S. Liquid Formulations of Local Anesthetics Through Deep Eutectics Based on Monoterpenoids. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Tonnis K, Nitsche JM, Xu L, Haley A, Jaworska J, Kasting GB. Impact of solvent dry down, vehicle pH and slowly reversible keratin binding on skin penetration of cosmetic relevant compounds: I. Liquids. Int J Pharm 2022; 624:122030. [PMID: 35863596 DOI: 10.1016/j.ijpharm.2022.122030] [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: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/14/2022] [Indexed: 11/19/2022]
Abstract
To measure progress and evaluate performance of the newest UB/UC/P&G skin penetration model we simulated an 18-compound subset of finite dose in vitro human skin permeation data taken from a solvent-deposition study of cosmetic-relevant compounds (Hewitt et al., J. Appl. Toxicol. 2019, 1-13). The recent model extension involved slowly reversible binding of solutes to stratum corneum keratins. The selected subset was compounds that are liquid at skin temperature. This set was chosen to distinguish between slow binding and slow dissolution effects that impact solid phase compounds. To adequately simulate the physical experiments there was a need to adjust the evaporation mass transfer coefficient to better represent the diffusion cell system employed in the study. After this adjustment the model successfully predicted both dermal delivery and skin surface distribution of 12 of the 18 compounds. Exceptions involved compounds that were cysteine-reactive, highly water-soluble or highly ionized in the dose solution. Slow binding to keratin, as presently parameterized, was shown to significantly modify the stratum corneum kinetics and diffusion lag times, but not the ultimate disposition, of the more lipophilic compounds in the dataset. Recommendations for further improvement of both modeling methods and experimental design are offered.
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Affiliation(s)
- Kevin Tonnis
- College of Engineering and Applied Science, The University of Cincinnati, Cincinnati, OH 45221, USA
| | - Johannes M Nitsche
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY 14260-4200, USA
| | - Lijing Xu
- The James L. Winkle College of Pharmacy, The University of Cincinnati, Cincinnati, OH 45267-0514, USA
| | - Alison Haley
- College of Engineering and Applied Science, The University of Cincinnati, Cincinnati, OH 45221, USA
| | - Joanna Jaworska
- The Procter & Gamble Company, Data and Modeling Sciences, Brussels Innovation Center, Belgium
| | - Gerald B Kasting
- The James L. Winkle College of Pharmacy, The University of Cincinnati, Cincinnati, OH 45267-0514, USA.
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15
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Barta T, Sandtner W, Wachlmayr J, Hannesschlaeger C, Ebert A, Speletz A, Horner A. Modeling of SGLT1 in Reconstituted Systems Reveals Apparent Ion-Dependencies of Glucose Uptake and Strengthens the Notion of Water-Permeable Apo States. Front Physiol 2022; 13:874472. [PMID: 35784872 PMCID: PMC9242095 DOI: 10.3389/fphys.2022.874472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
The reconstitution of secondary active transporters into liposomes shed light on their molecular transport mechanism. The latter are either symporters, antiporters or exchangers, which use the energy contained in the electrochemical gradient of ions to fuel concentrative uptake of their cognate substrate. In liposomal preparations, these gradients can be set by the experimenter. However, due to passive diffusion of the ions and solutes through the membrane, the gradients are not stable and little is known on the time course by which they dissipate and how the presence of a transporter affects this process. Gradient dissipation can also generate a transmembrane potential (VM). Because it is the effective ion gradient, which together with VM fuels concentrative uptake, knowledge on how these parameters change within the time frame of the conducted experiment is key to understanding experimental outcomes. Here, we addressed this problem by resorting to a modelling approach. To this end, we mathematically modeled the liposome in the assumed presence and absence of the sodium glucose transporter 1 (SGLT1). We show that 1) the model can prevent us from reaching erroneous conclusions on the driving forces of substrate uptake and we 2) demonstrate utility of the model in the assignment of the states of SGLT1, which harbor a water channel.
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Affiliation(s)
- Thomas Barta
- Department of Molecular Biophysics and Membrane Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Walter Sandtner
- Center of Physiology and Pharmacology, Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Medical University of Vienna, Vienna, Austria
| | - Johann Wachlmayr
- Department of Molecular Biophysics and Membrane Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Christof Hannesschlaeger
- Department of Molecular Biophysics and Membrane Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Andrea Ebert
- Department of Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Armin Speletz
- Department of Molecular Biophysics and Membrane Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Andreas Horner
- Department of Molecular Biophysics and Membrane Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
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16
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Rokitskaya TI, Aleksandrova EV, Korshunova GA, Khailova LS, Tashlitsky VN, Luzhkov VB, Antonenko YN. Membrane Permeability of Modified Butyltriphenylphosphonium Cations. J Phys Chem B 2022; 126:412-422. [PMID: 34994564 DOI: 10.1021/acs.jpcb.1c08135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The alkyltriphenylphosphonium (TPP) group is the most widely used vector targeted to mitochondria. Previously, the length of the alkyl linker was varied as well as structural modifications in the TPP phenyl rings to obtain the optimal therapeutic effect of a pharmacophore conjugated with a lipophilic cation. In the present work, we synthesized butyltriphenylphosphonium cations halogenated and methylated in phenyl rings (C4TPP-X) and measured electrical current through a planar lipid bilayer in the presence of C4TPP-X. The permeability of C4TPP-X varied in the range of 6 orders of magnitude and correlates well with the previously measured translocation rate constant for dodecyltriphenylphosphonium analogues. The partition coefficient of the butyltriphenylphosphonium analogues obtained by calculating the difference in the free energy of cation solvation in water and octane using quantum chemical methods correlates well with the permeability values. Using an ion-selective electrode, a lower degree of accumulation of analogues with halogenated phenyl groups was found on isolated mitochondria of rat liver, which is in agreement with their permeability decrease. Our results indicate the translocation of the butyltriphenylphosphonium cations across the hydrophobic membrane core as rate-limiting stage in the permeability process rather than their binding/release to/from the membrane.
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Affiliation(s)
- Tatyana I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | | | - Galina A Korshunova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Ljudmila S Khailova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Vadim N Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Victor B Luzhkov
- Department of Kinetics of Chemical and Biological Processes, Institute of Problems of Chemical Physics, Russian Academy of Sciences, acad. Semenov av. 1, Chernogolovka, Moscow Region 142432, Russia.,Department of Fundamental Physical and Chemical Engineering, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Yuri N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
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17
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Ebert A, Goss KU. Screening of 6000 Compounds for Uncoupling Activity: A Comparison Between a Mechanistic Biophysical Model and the Structural Alert Profiler Mitotox. Toxicol Sci 2021; 185:208-219. [PMID: 34865177 DOI: 10.1093/toxsci/kfab139] [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: 11/13/2022] Open
Abstract
Protonophoric uncoupling of phosphorylation is an important factor when assessing chemicals for their toxicity, and has recently moved into focus in pharmaceutical research with respect to the treatment of diseases such as cancer, diabetes, or obesity. Reliably identifying uncoupling activity is thus a valuable goal. To that end, we screened more than 6000 anionic compounds for in vitro uncoupling activity, using a biophysical model based on ab initio COSMO-RS input parameters with the molecular structure as the only external input. We combined these results with a model for baseline toxicity (narcosis). Our model identified more than 1250 possible uncouplers in the screening dataset, and identified possible new uncoupler classes such as thiophosphoric acids. When tested against 423 known uncouplers and 612 known inactive compounds in the dataset, the model reached a sensitivity of 83% and a specificity of 96%. In a direct comparison, it showed a similar specificity than the structural alert profiler Mitotox (97%), but much higher sensitivity than Mitotox (47%). The biophysical model thus allows for a more accurate screening for uncoupling activity than existing structural alert profilers. We propose to use our model as a complementary tool to screen large datasets for protonophoric uncoupling activity in drug development and toxicity assessment.
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Affiliation(s)
- Andrea Ebert
- Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research-UFZ, D-04318 Leipzig, Germany
| | - Kai-Uwe Goss
- Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research-UFZ, D-04318 Leipzig, Germany.,Institute of Chemistry, Martin Luther University, D-06120 Halle, Germany
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18
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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19
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Yu F, Tonnis K, Xu L, Jaworska J, Kasting GB. Modeling the Percutaneous Absorption of Solvent-deposited Solids Over a Wide Dose Range. J Pharm Sci 2021; 111:769-779. [PMID: 34627876 DOI: 10.1016/j.xphs.2021.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 10/20/2022]
Abstract
The transient absorption of two skin care agents, niacinamide (nicotinamide, NA) and methyl nicotinate (MN), solvent-deposited on ex vivo human skin mounted in Franz diffusion cells has been analyzed according to a new variation on a recently published mechanistic skin permeability model (Yu et al. 2020. J Pharm Sci 110:2149-56). The model follows the absorption and evaporation of two components, solute and solvent, and it includes both a follicular transport component and a dissolution rate limitation for high melting, hydrophilic solids deposited on the skin. Explicit algorithms for improving the simulation of transient diffusion of solvent-deposited solids are introduced. The simulations can account for the ex vivo skin permeation time course of both NA and MN over a dose range exceeding 4.5 orders of magnitude. The model allows one to describe on a mechanistic basis why the percutaneous absorption rate of NA is approximately 60-fold lower than that of its lower melting, more lipophilic analog, MN. It furthermore suggests that MN perturbs stratum corneum barrier lipids and increases their permeability while NA does not, presenting a challenge to molecular modelers engaged in simulating biological lipid barriers.
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Affiliation(s)
- Fang Yu
- College of Engineering and Applied Science, The University of Cincinnati, Cincinnati, Ohio, USA
| | - Kevin Tonnis
- College of Engineering and Applied Science, The University of Cincinnati, Cincinnati, Ohio, USA
| | - Lijing Xu
- The James L. Winkle College of Pharmacy, The University of Cincinnati, Cincinnati, Ohio, USA
| | - Joanna Jaworska
- The Procter & Gamble Company, Data and Modeling Sciences, Brussels Innovation Center, Belgium
| | - Gerald B Kasting
- The James L. Winkle College of Pharmacy, The University of Cincinnati, Cincinnati, Ohio, USA.
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20
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Takahashi T, Matsui T, Hengphasatporn K, Shigeta Y. A Practical Prediction of Log Po/w through Semiempirical Electronic Structure Calculations with Dielectric Continuum Model. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Teruyuki Takahashi
- Department of Physics, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8571, Japan
| | - Toru Matsui
- Department of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8571, Japan
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8571, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Ibaraki 305-8571, Japan
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21
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Hamala V, Červenková Šťastná L, Kurfiřt M, Cuřínová P, Balouch M, Hrstka R, Voňka P, Karban J. The effect of deoxyfluorination and O-acylation on the cytotoxicity of N-acetyl-D-gluco- and D-galactosamine hemiacetals. Org Biomol Chem 2021; 19:4497-4506. [PMID: 33949602 DOI: 10.1039/d1ob00497b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fully acetylated deoxyfluorinated hexosamine analogues and non-fluorinated 3,4,6-tri-O-acylated N-acetyl-hexosamine hemiacetals have previously been shown to display moderate anti-proliferative activity. We prepared a set of deoxyfluorinated GlcNAc and GalNAc hemiacetals that comprised both features: O-acylation at the non-anomeric positions with an acetyl, propionyl and butanoyl group, and deoxyfluorination at selected positions. Determination of the in vitro cytotoxicity towards the MDA-MB-231 breast cancer and HEK-293 cell lines showed that deoxyfluorination enhanced cytotoxicity in most analogues. Increasing the ester alkyl chain length had a variable effect on the cytotoxicity of fluoro analogues, which contrasted with non-fluorinated hemiacetals where butanoyl derivatives had always higher cytotoxicity than acetates. Reaction with 2-phenylethanethiol indicated that the recently described S-glyco-modification is an unlikely cause of cytotoxicity.
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Affiliation(s)
- Vojtěch Hamala
- Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic. and University of Chemistry and Technology Prague, Technická 5, 16628 Praha 6, Czech Republic
| | - Lucie Červenková Šťastná
- Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic.
| | - Martin Kurfiřt
- Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic. and University of Chemistry and Technology Prague, Technická 5, 16628 Praha 6, Czech Republic
| | - Petra Cuřínová
- Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic.
| | - Martin Balouch
- Department of Chemical Engineering, University of Chemistry and Technology, Technická 3, 166 28 Prague 6, Prague, Czech Republic
| | - Roman Hrstka
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, žlutý kopec 7, Brno, 65653, Czech Republic
| | - Petr Voňka
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, žlutý kopec 7, Brno, 65653, Czech Republic
| | - Jindřich Karban
- Institute of Chemical Process Fundamentals of the CAS, v. v. i., Rozvojová 135, 16502 Praha 6, Czech Republic.
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22
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Ashworth IW, Curran TT, Ford JG, Tomasi S. Prediction of N-Nitrosamine Partition Coefficients for Derisking Drug Substance Manufacturing Processes. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.0c00535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ian W. Ashworth
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, U.K
| | - Timothy T. Curran
- Process Chemistry, Vertex Pharmaceuticals, Boston, Massachusetts, United States
| | - J. Gair Ford
- Regulatory CMC, Global Regulatory Excellence, AstraZeneca, Macclesfield, U.K
| | - Simone Tomasi
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, U.K
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23
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Agarwal P, Ishida K, Reid DL, Gupta A. Clearance prediction for Amgen molecules against Extended Clearance Classification System (ECCS) and future directions. Drug Discov Today 2020; 26:10-16. [PMID: 33075472 DOI: 10.1016/j.drudis.2020.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 09/17/2020] [Accepted: 10/12/2020] [Indexed: 10/23/2022]
Abstract
Early prediction of elimination pathways for new chemical entities can have a profound impact on drug discovery programs. The recently proposed Extended Clearance Classification System (ECCS) is a step in the right direction, providing a framework to help identify the major elimination pathway of a drug. A list of 42 Amgen small molecules was evaluated against the ECCS framework to assess its performance in retrospectively predicting their major elimination pathway. Here, we present a critical analysis of the chemical space defined by the ECCS framework with the aim of identifying its applicability and constraints. This evaluation highlights the critical need for periodic review and revision of ECCS, given that target constraints are moving molecules away from the traditional 'drug-like' physicochemical space.
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Affiliation(s)
- Prashant Agarwal
- Drug Product Technologies, Process Development, Amgen, Inc., 360 Binney St, Cambridge, MA 02142 USA
| | - Kazuya Ishida
- Pharmacokinetics and Drug Metabolism, Amgen Research, Amgen Inc., 360 Binney St, Cambridge, MA 02142 USA
| | - Darren L Reid
- Drug Product Technologies, Process Development, Amgen, Inc., 360 Binney St, Cambridge, MA 02142 USA
| | - Anshul Gupta
- Pharmacokinetics and Drug Metabolism, Amgen Research, Amgen Inc., 360 Binney St, Cambridge, MA 02142 USA.
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24
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Ebert A, Goss KU. Predicting Uncoupling Toxicity of Organic Acids Based on Their Molecular Structure Using a Biophysical Model. Chem Res Toxicol 2020; 33:1835-1844. [PMID: 32462864 DOI: 10.1021/acs.chemrestox.0c00063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a purely mechanistic model to predict protonophoric uncoupling activity ECw of organic acids. All required input information can be derived from their chemical structure. This makes it a convenient predictive model to gain valuable information on the toxicity of organic chemicals already at an early stage of development of new commercial chemicals (e.g., in agriculture or pharmaceutical industries). A critical component of the model is the consideration of the possible formation of heterodimers from the neutral and anionic monomer, and its permeation through the membrane. The model was tested against literature data measured in chromatophores, submitochondrial particles, isolated mitochondria, and intact green algae cells with good success. It was also possible to reproduce pH-dependencies in isolated mitochondria and intact cells. Besides the prediction of the ECw, the mechanistic nature of the model allows researchers to draw direct conclusions on the impact of single input factors such as pH- and voltage-gradients across the membrane, the anionic and neutral membrane permeability, and the heterodimerization constant. These insights are of importance in drug design or chemical regulation.
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Affiliation(s)
- Andrea Ebert
- Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig 04318, Germany.,Institute of Biophysics, Johannes Kepler University, Linz 4020, Austria
| | - Kai-Uwe Goss
- Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig 04318, Germany.,Institute of Chemistry, Martin Luther University, Halle 06120, Germany
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25
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Mechanistic skin penetration model by the COSMOperm method: Routes of permeation, vehicle effects and skin variations in the healthy and compromised skin. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.comtox.2019.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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