1
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Pires CL, Moreno MJ. Improving the Accuracy of Permeability Data to Gain Predictive Power: Assessing Sources of Variability in Assays Using Cell Monolayers. MEMBRANES 2024; 14:157. [PMID: 39057665 PMCID: PMC11278619 DOI: 10.3390/membranes14070157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024]
Abstract
The ability to predict the rate of permeation of new compounds across biological membranes is of high importance for their success as drugs, as it determines their efficacy, pharmacokinetics, and safety profile. In vitro permeability assays using Caco-2 monolayers are commonly employed to assess permeability across the intestinal epithelium, with an extensive number of apparent permeability coefficient (Papp) values available in the literature and a significant fraction collected in databases. The compilation of these Papp values for large datasets allows for the application of artificial intelligence tools for establishing quantitative structure-permeability relationships (QSPRs) to predict the permeability of new compounds from their structural properties. One of the main challenges that hinders the development of accurate predictions is the existence of multiple Papp values for the same compound, mostly caused by differences in the experimental protocols employed. This review addresses the magnitude of the variability within and between laboratories to interpret its impact on QSPR modelling, systematically and quantitatively assessing the most common sources of variability. This review emphasizes the importance of compiling consistent Papp data and suggests strategies that may be used to obtain such data, contributing to the establishment of robust QSPRs with enhanced predictive power.
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Affiliation(s)
- Cristiana L. Pires
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- Chemistry Department, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Maria João Moreno
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- Chemistry Department, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
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2
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Paulikat M, Piccini G, Ippoliti E, Rossetti G, Arnesano F, Carloni P. Physical Chemistry of Chloroquine Permeation through the Cell Membrane with Atomistic Detail. J Chem Inf Model 2023; 63:7124-7132. [PMID: 37947485 PMCID: PMC10685453 DOI: 10.1021/acs.jcim.3c01363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
We provide a molecular-level description of the thermodynamics and mechanistic aspects of drug permeation through the cell membrane. As a case study, we considered the antimalaria FDA approved drug chloroquine. Molecular dynamics simulations of the molecule (in its neutral and protonated form) were performed in the presence of different lipid bilayers, with the aim of uncovering key aspects of the permeation process, a fundamental step for the drug's action. Free energy values obtained by well-tempered metadynamics simulations suggest that the neutral form is the only permeating protomer, consistent with experimental data. H-bond interactions of the drug with water molecules and membrane headgroups play a crucial role for permeation. The presence of the transmembrane potential, investigated here for the first time in a drug permeation study, does not qualitatively affect these conclusions.
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Affiliation(s)
- Mirko Paulikat
- Computational
Biomedicine, Institute of Advanced Simulations IAS-5/Institute for
Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany
| | - GiovanniMaria Piccini
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Emiliano Ippoliti
- Computational
Biomedicine, Institute of Advanced Simulations IAS-5/Institute for
Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany
| | - Giulia Rossetti
- Computational
Biomedicine, Institute of Advanced Simulations IAS-5/Institute for
Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany
- Jülich
Supercomputing Centre (JSC), Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany
- Department
of Neurology, RWTH Aachen University, Aachen 52062, Germany
| | - Fabio Arnesano
- Department
of Chemistry, University of Bari “Aldo
Moro”, Bari 70125, Italy
| | - Paolo Carloni
- Computational
Biomedicine, Institute of Advanced Simulations IAS-5/Institute for
Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany
- Department
of Physics, RWTH Aachen University, Aachen 52062, Germany
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3
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Coba-Males MA, Lavecchia MJ, Alcívar-León CD, Santamaría-Aguirre J. Novel Fluoroquinolones with Possible Antibacterial Activity in Gram-Negative Resistant Pathogens: In Silico Drug Discovery. Molecules 2023; 28:6929. [PMID: 37836772 PMCID: PMC10574177 DOI: 10.3390/molecules28196929] [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: 04/10/2023] [Revised: 05/13/2023] [Accepted: 05/19/2023] [Indexed: 10/15/2023] Open
Abstract
Antibiotic resistance is a global threat to public health, and the search for new antibacterial therapies is a current research priority. The aim of this in silico study was to test nine new fluoroquinolones previously designed with potential leishmanicidal activity against Campylobacter jejuni, Escherichia coli, Neisseria gonorrhoeae, Pseudomonas aeruginosa, and Salmonella typhi, all of which are considered by the World Health Organization to resistant pathogens of global concern, through molecular docking and molecular dynamics (MD) simulations using wild-type (WT) and mutant-type (MT) DNA gyrases as biological targets. Our results showed that compound 9FQ had the best binding energy with the active site of E. coli in both molecular docking and molecular dynamics simulations. Compound 9FQ interacted with residues of quinolone resistance-determining region (QRDR) in GyrA and GyrB chains, which are important to enzyme activity and through which it could block DNA replication. In addition to compound 9FQ, compound 1FQ also showed a good affinity for DNA gyrase. Thus, these newly designed molecules could have antibacterial activity against Gram-negative microorganisms. These findings represent a promising starting point for further investigation through in vitro assays, which can validate the hypothesis and potentially facilitate the development of novel antibiotic drugs.
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Affiliation(s)
- Manuel Alejandro Coba-Males
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Salud Pública y Zoonosis (CIZ), Facultad de Ciencias Químicas (FCQ), Universidad Central del Ecuador, Quito 170521, Ecuador
| | - Martin J. Lavecchia
- CEQUINOR (UNLP-CONICET, CCT-La Plata, Associated with CICBA), Universidad Nacional de La Plata, La Plata 1900, Argentina;
| | | | - Javier Santamaría-Aguirre
- Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Salud Pública y Zoonosis (CIZ), Facultad de Ciencias Químicas (FCQ), Universidad Central del Ecuador, Quito 170521, Ecuador
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4
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Song Y, Wang W, Liu X, Chen J, Chen D, Wang X, Li W, Ouyang D. Physiologically Based Pharmacokinetic Modeling for Multiple Oral Administration Labetalol in Pregnant Women. Pharm Res 2023; 40:1765-1775. [PMID: 37142805 DOI: 10.1007/s11095-023-03523-y] [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: 12/27/2022] [Accepted: 04/13/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Labetalol has an irreplaceable role in treating Hypertensive disorders of pregnancy (HDP), a common disease during pregnancy with a prevalence of 5.2-8.2%. However, there were big differences in dosage regimens between various guidelines. PURPOSE A physiologically-based pharmacokinetics (PBPK) model was established and validated to evaluate the existing oral dosage regimens, and to compare the difference in plasma concentration between pregnant and non-pregnant women. METHODS First, non-pregnant woman models with specific plasma clearance or enzymatic metabolism (UGT1A1, UGT2B7, CYP2C19) were established and validated. For CYP2C19, slow, intermediate, and rapid metabolic phenotypes were considered. Then, a pregnant model with proper structure and parameters adjustment was established and validated against the multiple oral administration data. RESULTS The predicted labetalol exposure captured the experimental data well. The following simulations with criteria lowering 15 mmHg blood pressure (corresponding to around 108 ng/ml plasma labetalol) found that the maximum daily dosage in the Chinese guideline may be insufficient for some severe HDP patients. Moreover, similar predicted steady-state trough plasma concentration was found between the maximum daily dosage in the American College of Obstetricians and Gynecologists (ACOG) guideline, 800 mg Q8h and a regimen of 200 mg Q6h. Simulations comparing non-pregnant and pregnant women found that the difference in labetalol exposure highly depended on the CYP2C19 metabolic phenotype. CONCLUSIONS In summary, this work initially established a PBPK model for multiple oral administration of labetalol for pregnant women. This PBPK model may lead to personalized labetalol medication in the future.
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Affiliation(s)
- Yudi Song
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences (ICMS), University of Macau, Macau, China
| | - Wei Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences (ICMS), University of Macau, Macau, China
| | - Xinyang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences (ICMS), University of Macau, Macau, China
| | - Jingsi Chen
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Key Laboratories for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China
| | - Dunjin Chen
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Key Laboratories for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China
| | - Xiaoyi Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Key Laboratories for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China
| | - Wei Li
- Department of Pharmacy, The Third People's Hospital of Shenzhen, Shenzhen, Guangdong, People's Republic of China
| | - Defang Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences (ICMS), University of Macau, Macau, China.
- Department of Public Health and Medicinal Administration, Faculty of Health Sciences (FHS), University of Macau, Macau, China.
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5
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Kesharwani P, Kumari K, Gururani R, Jain S, Sharma S. Approaches to Address PK-PD Challenges of Conventional Liposome Formulation with Special Reference to Cancer, Alzheimer's, Diabetes, and Glaucoma: An Update on Modified Liposomal Drug Delivery System. Curr Drug Metab 2022; 23:678-692. [PMID: 35692131 DOI: 10.2174/1389200223666220609141459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/03/2022] [Accepted: 03/31/2022] [Indexed: 01/05/2023]
Abstract
Liposomes nowadays have become a preferential drug delivery system since they provide facilitating properties to drugs, such as improved therapeutic index of encapsulated drug, target and controlled drug delivery, and less toxicity. However, conventional liposomes have shown some disadvantages, such as less drug loading capacity, poor retention, clearance by kidney or reticuloendothelial system, and less release of hydrophilic drugs. Thus, to overcome these disadvantages recently, scientists have explored new approaches and methods, viz., ligand conjugation, polymer coating, and liposome hybrids, including surface-modified liposomes, biopolymer-incorporated liposomes, guest-in-cyclodextrin-in-liposome, liposome-in-hydrogel, liposome-in-film, liposome-in-nanofiber, etc. These approaches have been shown to improve the physiochemical and pharmacokinetic properties of encapsulated drugs. Lately, pharmacokinetic-pharmacodynamic (PK-PD) computational modeling has emerged as a beneficial tool for analyzing the impact of formulation and system-specific factors on the target disposition and therapeutic efficacy of liposomal drugs. There has been an increasing number of liposome-based therapeutic drugs, both FDA approved and those undergoing clinical trials, having application in cancer, Alzheimer's, diabetes, and glaucoma. To meet the continuous demand of health sectors and to produce the desired product, it is important to perform pharmacokinetic studies. This review focuses on the physical, physicochemical, and chemical factors of drugs that influence the target delivery of drugs. It also explains various physiological barriers, such as systemic clearance and extravasation. A novel approach, liposomal-hybrid complex, an innovative approach as a vesicular drug delivery system to overcome limited membrane permeability and bioavailability, has been discussed in the review. Moreover, this review highlights the pharmacokinetic considerations and challenges of poorly absorbed drugs along with the applications of a liposomal delivery system in improving PKPD in various diseases, such as cancer, Alzheimer's, diabetes, and glaucoma.
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Affiliation(s)
- Payal Kesharwani
- Department of Pharmacy, Banasthali Vidyapith University, Banasthali, P.O. Rajasthan, India
| | - Kajal Kumari
- Department of Pharmacy, Banasthali Vidyapith University, Banasthali, P.O. Rajasthan, India
| | - Ritika Gururani
- Department of Pharmacy, Banasthali Vidyapith University, Banasthali, P.O. Rajasthan, India
| | - Smita Jain
- Department of Pharmacy, Banasthali Vidyapith University, Banasthali, P.O. Rajasthan, India
| | - Swapnil Sharma
- Department of Pharmacy, Banasthali Vidyapith University, Banasthali, P.O. Rajasthan, India
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6
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Cordeiro MM, Salvador A, Moreno MJ. Calculation of Permeability Coefficients from Solute Equilibration Dynamics: An Assessment of Various Methods. MEMBRANES 2022; 12:membranes12030254. [PMID: 35323728 PMCID: PMC8951150 DOI: 10.3390/membranes12030254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023]
Abstract
Predicting the rate at which substances permeate membrane barriers in vivo is crucial for drug development. Permeability coefficients obtained from in vitro studies are valuable for this goal. These are normally determined by following the dynamics of solute equilibration between two membrane-separated compartments. However, the correct calculation of permeability coefficients from such data is not always straightforward. To address these problems, here we develop a kinetic model for solute permeation through lipid membrane barriers that includes the two membrane leaflets as compartments in a four-compartment model. Accounting for solute association with the membrane allows assessing various methods in a wide variety of conditions. The results showed that the often-used expression Papp= β × r/3 is inapplicable to very large or very small vesicles, to moderately or highly lipophilic solutes, or when the development of a significant pH gradient opposes the solute’s flux. We establish useful relationships that overcome these limitations and allow predicting permeability in compartmentalised in vitro or in vivo systems with specific properties. Finally, from the parameters for the interaction of the solute with the membrane barrier, we defined an intrinsic permeability coefficient that facilitates quantitative comparisons between solutes.
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Affiliation(s)
- Margarida M. Cordeiro
- Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal;
- Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Armindo Salvador
- Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal;
- CNC—Centre for Neuroscience Cell Biology, University of Coimbra, UC-Biotech, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal
- Correspondence: (A.S.); (M.J.M.)
| | - Maria João Moreno
- Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal;
- Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- Correspondence: (A.S.); (M.J.M.)
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7
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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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8
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Measuring the oral bioavailability of protein hydrolysates derived from food sources: A critical review of current bioassays. Biomed Pharmacother 2021; 144:112275. [PMID: 34628165 DOI: 10.1016/j.biopha.2021.112275] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Food proteins are a source of hydrolysates with potentially useful biological attributes. Bioactive peptides from food-derived proteins are released from hydrolysates using exogenous industrial processes or endogenous intestinal enzymes. Current in vitro permeability assays have limitations in predicting the oral bioavailability (BA) of bioactive peptides in humans. There are also difficulties in relating the low blood levels of food-derived bioactive peptides detected in preclinical in vivo models to pharmacodynamic read-outs relevant for humans. SCOPE AND APPROACH In this review, we describe in vitro assays of digestion, permeation, and metabolism as indirect predictors of the potential oral BA of hydrolysates and their constituent bioactive peptides. We discuss the relationship between industrial hydrolysis processes and the oral BA of hydrolysates and their peptide by-products. KEY FINDINGS Hydrolysates are challenging for analytical detection methods due to capacity for enzymatic generation of peptides with novel sequences and also new modifications of these peptides during digestion. Mass spectrometry and peptidomics can improve the capacity to detect individual peptides released from complex hydrolysates in biological milieu.
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9
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Bachler S, Ort M, Krämer SD, Dittrich PS. Permeation Studies across Symmetric and Asymmetric Membranes in Microdroplet Arrays. Anal Chem 2021; 93:5137-5144. [PMID: 33721989 PMCID: PMC8014892 DOI: 10.1021/acs.analchem.0c04939] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We investigated the permeation of molecules across lipid membranes on an open microfluidic platform. An array of droplet pairs was created by spotting aqueous droplets, dispersed in a lipid oil solution, onto a plate with cavities surrounded by a hydrophobic substrate. Droplets in two adjacent cavities come in contact and form an artificial lipid bilayer, called a droplet interface bilayer (DIB). The method allows for monitoring permeation of fluorescently tagged compounds from a donor droplet to an acceptor droplet. A mathematical model was applied to describe the kinetics and determine the permeation coefficient. We also demonstrate that permeation kinetics can be followed over a series of droplets, all connected via DIBs. Moreover, by changing the lipid oil composition after spotting donor droplets, we were able to create asymmetric membranes that we used to mimic the asymmetry of the cellular plasma membrane. Finally, we developed a protocol to separate and extract the droplets for label-free analysis of permeating compounds by liquid chromatography-mass spectrometry. Our versatile platform has the potential to become a new tool for the screening of drug membrane permeability in the future.
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Affiliation(s)
- Simon Bachler
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Marion Ort
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Stefanie D Krämer
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zürich 8093, Switzerland
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
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10
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Taddio MF, Mu L, Castro Jaramillo CA, Bollmann T, Schmid DM, Muskalla LP, Gruene T, Chiotellis A, Ametamey SM, Schibli R, Krämer SD. Synthesis and Structure-Affinity Relationship of Small Molecules for Imaging Human CD80 by Positron Emission Tomography. J Med Chem 2019; 62:8090-8100. [PMID: 31430137 DOI: 10.1021/acs.jmedchem.9b00858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The costimulatory molecule CD80 is an early marker for immune activation. It is upregulated on activated antigen-presenting cells. We aimed at developing a tracer for imaging CD80 by positron emission tomography (PET). Novel CD80 ligands were synthesized and tested by SPR for affinity to human CD80 (hCD80) and displacement of endogenous ligands. Several compounds bound with one-digit nanomolar affinity to hCD80 and displaced CTLA-4 and CD28 at nanomolar concentrations. A structure-affinity relationship study revealed relevant moieties for strong affinity to hCD80 and positions for further modifications. Lead compound MT107 (7f) was radiolabeled with carbon-11. In vitro, [11C]MT107 showed specific binding to hCD80-positive tissue and high plasma protein binding. In vivo, [11C]MT107 accumulated in liver, gall bladder, and intestines but only scarcely in hCD80-positive xenografts. The unfavorable in vivo performance may result from high plasma protein binding and extensive biliary excretion.
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Affiliation(s)
- Marco F Taddio
- Center for Radiopharmaceutical Sciences ETH, PSI and USZ, Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Linjing Mu
- Center for Radiopharmaceutical Sciences ETH, PSI and USZ, Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland.,Department of Nuclear Medicine , University Hospital Zurich , CH-8091 Zurich , Switzerland
| | - Claudia A Castro Jaramillo
- Center for Radiopharmaceutical Sciences ETH, PSI and USZ, Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Tanja Bollmann
- Center for Radiopharmaceutical Sciences ETH, PSI and USZ, Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Dominik M Schmid
- Center for Radiopharmaceutical Sciences ETH, PSI and USZ, Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Lukas P Muskalla
- Laboratory for Catalysis and Sustainable Chemistry , Paul Scherrer Institute , CH-5232 Villigen PSI , Switzerland
| | - Tim Gruene
- Laboratory for Catalysis and Sustainable Chemistry , Paul Scherrer Institute , CH-5232 Villigen PSI , Switzerland.,X-ray Structure Analysis Centre, Faculty of Chemistry , University of Vienna , A-1090 Vienna , Austria
| | - Aristeidis Chiotellis
- Center for Radiopharmaceutical Sciences ETH, PSI and USZ, Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Simon M Ametamey
- Center for Radiopharmaceutical Sciences ETH, PSI and USZ, Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Roger Schibli
- Center for Radiopharmaceutical Sciences ETH, PSI and USZ, Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Stefanie D Krämer
- Center for Radiopharmaceutical Sciences ETH, PSI and USZ, Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
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11
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Yue Z, Li C, Voth GA, Swanson JMJ. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules. J Am Chem Soc 2019; 141:13421-13433. [PMID: 31382734 DOI: 10.1021/jacs.9b04387] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Permeability (Pm) across biological membranes is of fundamental importance and a key factor in drug absorption, distribution, and development. Although the majority of drugs will be charged at some point during oral delivery, our understanding of membrane permeation by charged species is limited. The canonical model assumes that only neutral molecules partition into and passively permeate across membranes, but there is mounting evidence that these processes are also facile for certain charged species. However, it is unknown whether such ionizable permeants dynamically neutralize at the membrane surface or permeate in their charged form. To probe protonation-coupled permeation in atomic detail, we herein apply continuous constant-pH molecular dynamics along with free energy sampling to study the permeation of a weak base propranolol (PPL), and evaluate the impact of including dynamic protonation on Pm. The simulations reveal that PPL dynamically neutralizes at the lipid-tail interface, which dramatically influences the permeation free energy landscape and explains why the conventional model overestimates the assigned intrinsic permeability. We demonstrate how fixed-charge-state simulations can account for this effect, and propose a revised model that better describes pH-coupled partitioning and permeation. Our results demonstrate how dynamic changes in protonation state may play a critical role in the permeation of ionizable molecules, including pharmaceuticals and drug-like molecules, thus requiring a revision of the standard picture.
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Affiliation(s)
- Zhi Yue
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Chenghan Li
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Gregory A Voth
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Jessica M J Swanson
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
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12
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Bittner L, Klüver N, Henneberger L, Mühlenbrink M, Zarfl C, Escher BI. Combined Ion-Trapping and Mass Balance Models To Describe the pH-Dependent Uptake and Toxicity of Acidic and Basic Pharmaceuticals in Zebrafish Embryos ( Danio rerio). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:7877-7886. [PMID: 31177773 DOI: 10.1021/acs.est.9b02563] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The aim of the current study was to understand and develop models to predict the pH-dependent toxicity of ionizable pharmaceuticals in embryos of the zebrafish Danio rerio. We found a higher uptake and toxicity with increasing neutral fraction of acids (diclofenac, genistein, naproxen, torasemide, and warfarin) and bases (metoprolol and propranolol). Simple mass balance models accounting for the partitioning to lipids and proteins in the zebrafish embryo were found to be suitable to predict the bioconcentration after 96 h of exposure if pH values did not differ much from the internal pH of 7.55. For other pH values, a kinetic ion-trap model for the zebrafish embryo explained the pH dependence of biouptake and toxicity. The total internal lethal concentrations killing 50% of the zebrafish embryos (ILC50) were calculated from the measured BCF and LC50. The resulting ILC50 were independent of external pH. Critical membrane concentrations were deduced by an internal mass balance model, and apart from diclofenac, whose specific toxicity in fish had already been established, all pharmaceuticals were confirmed to act as baseline toxicants in zebrafish.
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Affiliation(s)
- Lisa Bittner
- Helmholtz Centre for Environmental Research - UFZ , Permoserstrasse 15 , 04318 Leipzig , Germany
| | - Nils Klüver
- Helmholtz Centre for Environmental Research - UFZ , Permoserstrasse 15 , 04318 Leipzig , Germany
| | - Luise Henneberger
- Helmholtz Centre for Environmental Research - UFZ , Permoserstrasse 15 , 04318 Leipzig , Germany
| | - Marie Mühlenbrink
- Helmholtz Centre for Environmental Research - UFZ , Permoserstrasse 15 , 04318 Leipzig , Germany
| | - Christiane Zarfl
- Eberhard Karls University of Tübingen , Center for Applied Geoscience , Hölderlinstrasse 12 , 72074 Tübingen , Germany
| | - Beate I Escher
- Helmholtz Centre for Environmental Research - UFZ , Permoserstrasse 15 , 04318 Leipzig , Germany
- Eberhard Karls University of Tübingen , Center for Applied Geoscience , Hölderlinstrasse 12 , 72074 Tübingen , Germany
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13
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Yamauchi S, Sugano K. Permeation characteristics of tetracyclines in parallel artificial membrane permeation assay. ADMET AND DMPK 2019; 7:151-160. [PMID: 35350658 PMCID: PMC8957236 DOI: 10.5599/admet.657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/06/2019] [Indexed: 11/25/2022] Open
Abstract
The purpose of the present study was to characterize the passive permeation of tetracyclines in the parallel artificial membrane permeation assay (PAMPA). Tetracyclines exist as zwitterion at physiological pH. The PAMPA membrane was prepared by impregnating a phospholipid/decane solution to a filter support. The permeation coefficient (Pe) of tetracycline (TC) was markedly affected by the lipid composition of the PAMPA membrane. No permeation was observed when phospholipid was not added (pure decane membrane, Pe < 0.05 × 10-6 cm/sec). With the addition of 2 % PC, little or no increase in Pe was observed. The addition of 1 % PE increased the Pe value more than tenfold. The addition of 2 % soybean lecithin containing phosphatidylinositol (PI) and phosphatidic acid (PA) increased the Pe value to above 4 × 10-6 cm/sec. The Pe value was further increased to 15 × 10-6 cm/sec by increasing the concentration of soybean lecithin from 2 to 10 %. The Pe value showed pH and temperature dependence, whereas it was not affected by the ionic strength, TC concentration, and ion-pair transport inhibitors. A weak correlation was observed between the Pe values and octanol-buffer distribution coefficients of tetracyclines. These results suggest that inter-molecular interactions between TC and PE, PI and/or PA facilitate the passive diffusion of TC across the PAMPA membrane.
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Affiliation(s)
- Sachika Yamauchi
- Molecular Pharmaceutics Lab., College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1, Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Kiyohiko Sugano
- Molecular Pharmaceutics Lab., College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1, Noji-higashi, Kusatsu, Shiga 525-8577, Japan
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14
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Badaoui M, Kells A, Molteni C, Dickson CJ, Hornak V, Rosta E. Calculating Kinetic Rates and Membrane Permeability from Biased Simulations. J Phys Chem B 2018; 122:11571-11578. [DOI: 10.1021/acs.jpcb.8b07442] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Magd Badaoui
- Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom
| | - Adam Kells
- Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom
| | - Carla Molteni
- Department of Physics, King’s College London, WC2R 2LS London, United Kingdom
| | - Callum J. Dickson
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, Massachusetts 02139, United States
| | - Edina Rosta
- Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom
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15
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Filipe HAL, Javanainen M, Salvador A, Galvão AM, Vattulainen I, Loura LMS, Moreno MJ. Quantitative Assessment of Methods Used To Obtain Rate Constants from Molecular Dynamics Simulations—Translocation of Cholesterol across Lipid Bilayers. J Chem Theory Comput 2018; 14:3840-3848. [DOI: 10.1021/acs.jctc.8b00150] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hugo A. L. Filipe
- Coimbra Chemistry Center, University of Coimbra, P-3004-535 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, P-3004-517 Coimbra, Portugal
| | - Matti Javanainen
- Laboratory of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Armindo Salvador
- Coimbra Chemistry Center, University of Coimbra, P-3004-535 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, P-3004-517 Coimbra, Portugal
| | - Adelino M. Galvão
- CQE—Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1049-001 Lisboa, Portugal
| | - Ilpo Vattulainen
- Laboratory of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
- MEMPHYS—Center
for Biomembrane Physics, FI-00014 Helsinki, Finland
| | - Luís M. S. Loura
- Coimbra Chemistry Center, University of Coimbra, P-3004-535 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, P-3000-548 Coimbra, Portugal
| | - Maria João Moreno
- Coimbra Chemistry Center, University of Coimbra, P-3004-535 Coimbra, Portugal
- Chemistry Department, University of Coimbra, P-3004-535 Coimbra, Portugal
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Samelo J, Mora MJ, Granero GE, Moreno MJ. Partition of Amphiphilic Molecules to Lipid Bilayers by ITC: Low-Affinity Solutes. ACS OMEGA 2017; 2:6863-6869. [PMID: 31457272 PMCID: PMC6645030 DOI: 10.1021/acsomega.7b01145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 09/25/2017] [Indexed: 05/28/2023]
Abstract
A protocol is developed to allow the accurate characterization of partition to lipid bilayers for solutes with low affinity, using isothermal titration calorimetry. The methodology proposed is suitable for studies using complex membranes, such as intact biomembranes or whole cells. In the method developed, the association is characterized at increasing solute concentrations. This allows the characterization of solute partition into unperturbed membranes, as well as effects induced by high solute concentrations. Most druglike molecules are expected to interact with low-to-moderate affinity with relevant cell membranes. This is due to both the need for a relatively high aqueous solubility of the drug and the poor binding properties of the cell membranes. The methodology is applied to characterize the interaction of antibiotic Rifampicin with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and with lipid bilayers representative of bacterial membranes.
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Affiliation(s)
- Jaime Samelo
- Chemistry
Department FCTUC, CQC-Biological Chemistry
Group, Largo D. Dinis,
Rua Larga, 3004-535 Coimbra, Portugal
| | - Maria Julia Mora
- Unidad
de Investigación y Desarrollo en Tecnología Farmacéutica
(UNITEFA), CONICET and Departamento de Ciencias Farmacéuticas,
Facultad de Ciencias Químicas, Universidad
Nacional de Córdoba, Ciudad Universitaria, 5000 Córdoba, Argentina
| | - Gladys Ester Granero
- Unidad
de Investigación y Desarrollo en Tecnología Farmacéutica
(UNITEFA), CONICET and Departamento de Ciencias Farmacéuticas,
Facultad de Ciencias Químicas, Universidad
Nacional de Córdoba, Ciudad Universitaria, 5000 Córdoba, Argentina
| | - Maria João Moreno
- Chemistry
Department FCTUC, CQC-Biological Chemistry
Group, Largo D. Dinis,
Rua Larga, 3004-535 Coimbra, Portugal
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