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Basu S, Mandal S, Maiti PK. Permeability of TB drugs through the mycolic acid monolayer: a tale of two force fields. Phys Chem Chem Phys 2024; 26:21429-21440. [PMID: 39101468 DOI: 10.1039/d4cp02659d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Tuberculosis (TB) treatment becomes challenging due to the unique cell wall structure of Mycobacterium tuberculosis (M. tb). Among various components of the M.tb cell wall, mycolic acid (MA) is of particular interest because it is speculated to exhibit extremely low permeability for most of the drug molecules, thus helping M.tb to survive against medical treatment. However, no quantitative assessment of the thermodynamic barrier encountered by various well-known TB drugs in the mycolic acid monolayer has been performed so far using computational tools. On this premise, our present work aims to probe the permeability of some first and second line TB drugs, namely ethambutol, ethionamide, and isoniazid, through the modelled mycolic acid monolayer, using molecular dynamics (MD) simulation with two sets of force field (FF) parameters, namely GROMOS 54A7-ATB (GROMOS) and CHARMM36 (CHARMM) FFs. Our findings indicate that both FFs provide consistent results in terms of the mode of drug-monolayer interactions but significantly differ in the drug permeability through the monolayer. The mycolic acid monolayer generally exhibited a higher free energy barrier of crossing with CHARMM FF, while with GROMOS FF, better stability of drug molecules on the monolayer surface was observed, which can be attributed to the greater electrostatic potential at the monolayer-water interface, found for the later. Although both the FF parameters predicted the highest resistance against ethambutol (permeability values of 8.40 × 10-34 cm s-1 and 9.61 × 10-31 cm s-1 for the CHARMM FF and the GROMOS FF, respectively), results obtained using GROMOS were found to be consistent with the water solubility of drugs, suggesting it to be a slightly better FF for modelling drug-mycolic acid interactions. Therefore, this study enhances our understanding of TB drug permeability and highlights the potential of the GROMOS FF in simulating drug-mycolic acid interactions.
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Affiliation(s)
- Subhadip Basu
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India.
| | - Sandip Mandal
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India.
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India.
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2
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Labourel FJF, Daubin V, Menu F, Rajon E. Proteome allocation and the evolution of metabolic cross-feeding. Evolution 2024; 78:849-859. [PMID: 38376478 DOI: 10.1093/evolut/qpae008] [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: 12/27/2022] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/21/2024]
Abstract
In a common instance of metabolic cross-feeding (MCF), an organism incompletely metabolizes nutrients and releases metabolites that are used by another to produce energy or building blocks. Why would the former waste edible food, and why does this preferentially occur at specific locations in a metabolic pathway have challenged evolutionary theory for decades. To address these questions, we combine adaptive dynamics with an explicit model of cell metabolism, including enzyme-driven catalysis of metabolic reactions and the cellular constraints acting on the proteome that may incur a cost to expressing all enzymes along a pathway. After pointing out that cells should in principle prioritize upstream reactions when metabolites are restrained inside the cell, we show that the occurrence of permeability-driven MCF is rare and requires that an intermediate metabolite be extremely diffusive. Indeed, only at very high levels of membrane permeability (consistent with those of acetate and glycerol, for instance) and under distinctive sets of parameters should the population diversify and MCF evolve. These results help understand the origins of simple microbial communities, such as those that readily evolve in short-term evolutionary experiments, and may later be extended to investigate how evolution has progressively built up today's extremely diverse ecosystems.
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Affiliation(s)
- Florian J F Labourel
- Univ Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR5558, Villeurbanne, France
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Vincent Daubin
- Univ Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR5558, Villeurbanne, France
| | - Frédéric Menu
- Univ Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR5558, Villeurbanne, France
| | - Etienne Rajon
- Univ Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR5558, Villeurbanne, France
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3
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Li S, Wu B, Luo YL, Han W. Simulations of Functional Motions of Super Large Biomolecules with a Mixed-Resolution Model. J Chem Theory Comput 2024; 20:2228-2245. [PMID: 38374639 PMCID: PMC10938502 DOI: 10.1021/acs.jctc.3c01046] [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: 09/22/2023] [Revised: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
Many large protein machines function through an interplay between large-scale movements and intricate conformational changes. Understanding functional motions of these proteins through simulations becomes challenging for both all-atom and coarse-grained (CG) modeling techniques because neither approach alone can readily capture the full details of these motions. In this study, we develop a multiscale model by employing the popular MARTINI CG model to represent a heterogeneous environment and structurally stable proteins and using the united-atom (UA) model PACE to describe proteins undergoing subtle conformational changes. PACE was previously developed to be compatible with the MARTINI solvent and membrane. Here, we couple the protein descriptions of the two models by directly mixing UA and CG interaction parameters to greatly simplify parameter determination. Through extensive validations with diverse protein systems in solution or membrane, we demonstrate that only additional parameter rescaling is needed to enable the resulting model to recover the stability of native structures of proteins under mixed representation. Moreover, we identify the optimal scaling factors that can be applied to various protein systems, rendering the model potentially transferable. To further demonstrate its applicability for realistic systems, we apply the model to a mechanosensitive ion channel Piezo1 that has peripheral arms for sensing membrane tension and a central pore for ion conductance. The model can reproduce the coupling between Piezo1's large-scale arm movement and subtle pore opening in response to membrane stress while consuming much less computational costs than all-atom models. Therefore, our model shows promise for studying functional motions of large protein machines.
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Affiliation(s)
- Shu Li
- Centre
for Artificial Intelligence Driven Drug Discovery, Faculty of Applied
Sciences, Macao Polytechnic University, Macao 999078, China
- State
Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Bohua Wu
- State
Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yun Lyna Luo
- Department
of Biotechnology and Pharmaceutical Sciences, Western University of Health Sciences, Pomona, California 91766, United States
| | - Wei Han
- State
Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Department
of Chemistry, Faculty of Science, Hong Kong
Baptist University, Hong Kong SAR 999077, China
- Shenzhen
Bay Laboratory, Institute of Chemical Biology, Shenzhen 518132, China
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4
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Kang C, Shoji A, Chipot C, Sun R. Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs. J Chem Inf Model 2024; 64:933-943. [PMID: 38206804 DOI: 10.1021/acs.jcim.3c01629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Over the last two decades, numerous molecular dynamics (MD) simulation-based investigations have attempted to predict the membrane permeability to small-molecule drugs as indicators of their bioavailability, a majority of which utilize the inhomogeneous solubility diffusion (ISD) model. However, MD-based membrane permeability is routinely 3-4 orders of magnitude larger than the values measured with the intestinal perfusion technique. There have been contentious discussions on the sources of the large discrepancies, and the two indisputable, potentially dominant ones are the fixed protonation state of the permeant and the neglect of the unstirred water layer (UWL). Employing six small-molecule drugs of different biopharmaceutical classification system classes, the current MD study relies on the ISD model but introduces the (de)protonation of the permeant by characterizing the permeation free energy of both neutral and charged states. In addition, the role of the UWL as a potential resistance against permeation is explored. The new MD protocol closely mimics the nature of small-molecule permeation and yields estimates that agree well with in vivo intestinal permeability.
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Affiliation(s)
- Christopher Kang
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - Alyson Shoji
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex 54506, France
- Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Rui Sun
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
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5
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Liu H, Wen Z, Liu Z, Yang Y, Wang H, Xia X, Ye J, Liu Y. Unlocking the potential of amorphous calcium carbonate: A star ascending in the realm of biomedical application. Acta Pharm Sin B 2024; 14:602-622. [PMID: 38322345 PMCID: PMC10840486 DOI: 10.1016/j.apsb.2023.08.027] [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: 06/12/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 02/08/2024] Open
Abstract
Calcium-based biomaterials have been intensively studied in the field of drug delivery owing to their excellent biocompatibility and biodegradability. Calcium-based materials can also deliver contrast agents, which can enhance real-time imaging and exert a Ca2+-interfering therapeutic effect. Based on these characteristics, amorphous calcium carbonate (ACC), as a brunch of calcium-based biomaterials, has the potential to become a widely used biomaterial. Highly functional ACC can be either discovered in natural organisms or obtained by chemical synthesis However, the standalone presence of ACC is unstable in vivo. Additives are required to be used as stabilizers or core-shell structures formed by permeable layers or lipids with modified molecules constructed to maintain the stability of ACC until the ACC carrier reaches its destination. ACC has high chemical instability and can produce biocompatible products when exposed to an acidic condition in vivo, such as Ca2+ with an immune-regulating ability and CO2 with an imaging-enhancing ability. Owing to these characteristics, ACC has been studied for self-sacrificing templates of carrier construction, targeted delivery of oncology drugs, immunomodulation, tumor imaging, tissue engineering, and calcium supplementation. Emphasis in this paper has been placed on the origin, structural features, and multiple applications of ACC. Meanwhile, ACC faces many challenges in clinical translation, and long-term basic research is required to overcome these challenges. We hope that this study will contribute to future innovative research on ACC.
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Affiliation(s)
- Han Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhiyang Wen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zihan Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yanfang Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Hongliang Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xuejun Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jun Ye
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yuling Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Delivery Technology and Novel Formulation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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6
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Jorgensen C, Troendle EP, Ulmschneider JP, Searson PC, Ulmschneider MB. A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood-brain barrier endothelium. J Comput Aided Mol Des 2023; 37:537-549. [PMID: 37573260 PMCID: PMC10505096 DOI: 10.1007/s10822-023-00525-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/24/2023] [Indexed: 08/14/2023]
Abstract
The treatment of various disorders of the central nervous system (CNS) is often impeded by the limited brain exposure of drugs, which is regulated by the human blood-brain barrier (BBB). The screening of lead compounds for CNS penetration is challenging due to the biochemical complexity of the BBB, while experimental determination of permeability is not feasible for all types of compounds. Here we present a novel method for rapid preclinical screening of libraries of compounds by utilizing advancements in computing hardware, with its foundation in transition-based counting of the flux. This method has been experimentally validated for in vitro permeabilities and provides atomic-level insights into transport mechanisms. Our approach only requires a single high-temperature simulation to rank a compound relative to a library, with a typical simulation time converging within 24 to 72 h. The method offers unbiased thermodynamic and kinetic information to interpret the passive transport of small-molecule drugs across the BBB.
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Affiliation(s)
- Christian Jorgensen
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark.
| | | | | | - Peter C Searson
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA
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7
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Bernardi A, Bennett WFD, He S, Jones D, Kirshner D, Bennion BJ, Carpenter TS. Advances in Computational Approaches for Estimating Passive Permeability in Drug Discovery. MEMBRANES 2023; 13:851. [PMID: 37999336 PMCID: PMC10673305 DOI: 10.3390/membranes13110851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 11/25/2023]
Abstract
Passive permeation of cellular membranes is a key feature of many therapeutics. The relevance of passive permeability spans all biological systems as they all employ biomembranes for compartmentalization. A variety of computational techniques are currently utilized and under active development to facilitate the characterization of passive permeability. These methods include lipophilicity relations, molecular dynamics simulations, and machine learning, which vary in accuracy, complexity, and computational cost. This review briefly introduces the underlying theories, such as the prominent inhomogeneous solubility diffusion model, and covers a number of recent applications. Various machine-learning applications, which have demonstrated good potential for high-volume, data-driven permeability predictions, are also discussed. Due to the confluence of novel computational methods and next-generation exascale computers, we anticipate an exciting future for computationally driven permeability predictions.
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Affiliation(s)
| | | | | | | | | | | | - Timothy S. Carpenter
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (A.B.); (W.F.D.B.); (S.H.); (D.J.); (D.K.); (B.J.B.)
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8
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Pandey P, MacKerell AD. Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules. J Chem Inf Model 2023; 63:5903-5915. [PMID: 37682640 PMCID: PMC10603762 DOI: 10.1021/acs.jcim.3c00514] [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] [Indexed: 09/10/2023]
Abstract
Membrane permeability of drug molecules plays a significant role in the development of new therapeutic agents. Accordingly, methods to predict the passive permeability of drug candidates during a medicinal chemistry campaign offer the potential to accelerate the drug design process. In this work, we combine the physics-based site identification by ligand competitive saturation (SILCS) method and data-driven artificial intelligence (AI) to create a high-throughput predictive model for the passive permeability of druglike molecules. In this study, we present a comparative analysis of four regression models to predict membrane permeabilities of small druglike molecules; of the tested models, Random Forest was the most predictive yielding an R2 of 0.81 for the independent data set. The input feature vector used to train the developed prediction model includes absolute free energy profiles of ligands through a POPC-cholesterol bilayer based on ligand grid free energy (LGFE) profiles obtained from the SILCS approach. The use of the membrane free energy profiles from SILCS offers information on the physical forces contributing to ligand permeability, while the use of AI yields a more predictive model trained on experimental PAMPA permeability data for a collection of 229 molecules. This combination allows for rapid estimations of ligand permeability at a level of accuracy beyond currently available predictive models while offering insights into the contributions of the functional groups in the ligands to the permeability barrier, thereby offering quantitative information to facilitate rational ligand design.
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Affiliation(s)
- Poonam Pandey
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-633, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-633, Baltimore, Maryland 21201, United States
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9
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Shigematsu T, Koshiyama K. Changes in free energy barrier for water permeation by stretch-induced phase transitions in phospholipid/cholesterol bilayers. J Biomol Struct Dyn 2023:1-8. [PMID: 37656194 DOI: 10.1080/07391102.2023.2250447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Water permeation through phospholipid/cholesterol bilayers is the key to understanding tension-induced rupture of biological cell membranes. We performed molecular dynamics simulations of stretched phospholipid/cholesterol bilayers to investigate changes in the free energy profile of water molecules across the bilayer and the lipid structure responsible for water permeation. We modeled stretching of the bilayer by applying areal strain. In stretched phospholipid/cholesterol bilayers, the hydrophobic tail of the phospholipids became disordered and the free energy barrier to water permeation decreased. Upon exceeding the critical areal strain, a phase transition to an interdigitated gel phase occurred before rupture, and the hydrophobic tail ordering as well as the free energy barrier were restored. In pure phospholipid bilayers, we did not observe such recoveries. These transient recoveries in the phospholipid/cholesterol bilayer suppressed water permeation and membrane rupture, followed by an increase in the critical areal strain at which the bilayer ruptured. This result agrees with experimental results and provides a reasonable molecular mechanism for the toughness of phospholipid/cholesterol bilayers under tension.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Taiki Shigematsu
- Department of Mechanical Science & Bioengineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Kenichiro Koshiyama
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
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10
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Mukhopadhyay S, Dutta R, Dhara A, Das P. Biomonitoring of polycyclic aromatic hydrocarbons (PAHs) by Murraya paniculata (L.) Jack in South Kolkata, West Bengal, India: spatial and temporal variations. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:5761-5781. [PMID: 36823386 DOI: 10.1007/s10653-023-01506-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/10/2023] [Indexed: 06/06/2023]
Abstract
Attempts have been made in the present study for ascertaining the concentrations of atmospheric polycyclic aromatic hydrocarbons (PAHs) using passive biosamplers in preference to conventional air sampling methods. Mechanical stirring, sonication, Soxhlet technique and microwave-assisted Soxhlet extraction (MASE) were employed to extract PAHs from an evergreen plant (Murraya paniculata) leaves (having long life-span) sampled from polluted places of South Kolkata, India, with dense population and heavy traffic. Effects of extraction methods and operational parameters (solvent and time) on the recovery levels of PAHs were also investigated. Purified extracts, acquired through adsorption chromatography, were subjected to GC-MS and HPLC-UV analyses for qualitative and quantitative assessment of PAHs. Spatio-temporal distribution of accumulated PAHs across the sampling sites was monitored over premonsoon, postmonsoon and winter supported by pollutant source characterization. The results displayed that the extraction yields of Soxhlet (272.07 ± 26.15 μg g-1) and MASE (280.17 ± 15.46 μg g-1) were the highest among the four techniques. Conditions of extraction with toluene for 6 h were found to be most favorable for PAHs. In spatio-temporal analysis, total concentrations of PAHs in the foliar samples varied from 200.98 ± 2.72 to 550.79 ± 10.11 μg g-1 dry weight, and the highest values being recorded in the samples of Exide More because of daylong inexorable traffic flow/crowding increasing the burden of ambient PAHs. Widespread changes in meteorology exerted influence on seasonal concentrations of PAHs in plant leaves, and extent of leaf contamination by PAHs was observed extreme in winter followed by postmonsoon and then, premonsoon. Foliar accretion of PAHs differed in the study sites with diverse sources of emission from motor vehicles, fossil fuel and biomass burning along with other human interferences.
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Affiliation(s)
| | - Ratna Dutta
- Department of Chemical Engineering, Jadavpur University, Kolkata, 700032, India.
| | - Aparna Dhara
- Department of Chemical Engineering, Jadavpur University, Kolkata, 700032, India
| | - Papita Das
- Department of Chemical Engineering, Jadavpur University, Kolkata, 700032, India
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11
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Benmameri M, Chantemargue B, Humeau A, Trouillas P, Fabre G. MemCross: Accelerated Weight Histogram method to assess membrane permeability. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184120. [PMID: 36669638 DOI: 10.1016/j.bbamem.2023.184120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
Passive permeation events across biological membranes are determining steps in the pharmacokinetics of xenobiotics. To reach an accurate and rapid prediction of membrane permeation coefficients of drugs is a complex challenge, which can efficiently support drug discovery. Such predictions are indeed highly valuable as they may guide the selection of potential leads with optimum bioavailabilities prior to synthesis. Theoretical models exist to predict these coefficients. Many of them are based on molecular dynamics (MD) simulations, which allow calculation of permeation coefficients through the evaluation of both the potential of mean force (PMF) and the diffusivity profiles. However, these simulations still require intensive computational efforts, and novel methodologies should be developed and benchmarked. Free energy perturbation (FEP) method was recently shown to estimate PMF with a significantly reduced computational cost compared to the adaptive biasing force method. This benchmarking was achieved with small molecules, namely short-chain alcohols. Here, we show that to estimate the PMF of bulkier, drug-like xenobiotics, conformational sampling is a critical issue. To reach a sufficient sampling with FEP calculations requires a relatively long time-scale, which can lower the benefits related to the computational gain. In the present work, the Accelerated Weight Histogram (AWH) method was employed for the first time in all-atom membrane models. The AWH-based protocol, named MemCross, appears affordable to estimate PMF profiles of a series of drug-like xenobiotics, compared to other enhanced sampling methods. The continuous exploration of the crossing pathway by MemCross also allows modeling subdiffusion by computing fractional diffusivity profiles. The method is also versatile as its input parameters are largely insensitive to the molecule properties. It also ensures a detailed description of the molecule orientations along the permeation pathway, picturing all intermolecular interactions at an atomic resolution. Here, MemCross was applied on a series of 12 xenobiotics, including four weak acids, and a coherent structure-activity relationship was established.
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Affiliation(s)
| | | | | | - Patrick Trouillas
- INSERM, UMR 1248, F-87000 Limoges, France; CATRIN RCPTM, 779 00 Olomouc, Holice, Czech Republic
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12
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Zhang Q, Alinaghi A, Williams DB, Roberts MS. A thermodynamic and kinetic analysis of human epidermal penetration of phenolic compounds: II. Maximum flux and solute diffusion through stratum corneum lipids. Int J Pharm 2023; 631:122522. [PMID: 36563793 DOI: 10.1016/j.ijpharm.2022.122522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/17/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Warming the skin is a key means of promoting solute permeation through the skin. Changes in solute permeation associated with variations in skin temperature also assist in understanding the mechanism by which solutes permeate the skin. However, few studies have considered the relative impact of temperature on the main determinants of the maximum flux for a solute across the skin, the solubility of a solute and its diffusivity in the stratum corneum. In this study, we quantified for the first time the thermodynamics associated with the maximum skin fluxes for a series of phenolic compounds of similar size but with varying lipophilicity (defined by the logarithms of their octanol/water partition coefficient, logP). These studies were undertaken using aqueous donor solutions (along with testosterone as a reference solute) across human epidermal membranes in vertical Franz diffusion cells at 4 °C, 24 °C and 37 °C with intermittent receptor sampling and volume replacement over 24 h. Kinetic and thermodynamic analyses included the estimation of the stratum corneum (SC) apparent SC diffusivity from the SC maximum fluxes and SC solubilities and the associated activation energies, enthalpies and entropies for diffusion. The key findings were that the differences in the maximum flux of phenolic compounds varying in lipophilicity mainly arose from differences in SC solubility at the various temperatures and that, at the highest temperature, SC permeability and SC diffusion were affected by SC lipid fluidisation and that variations in SC - water partitioning enthalpies explain some of the previously low activation energies for permeation of the more lipophilic phenols. Higher enthalpies for diffusion were seen for solutes with addition hydrogen bonding capacity and the highest negative entropy was observed with the more compact solutes. Various relationships between the derived thermodynamic parameters were explored and interpreted in a proposed model for solute partitioning into and permeation through the SC intercellular lipid lamellae.
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Affiliation(s)
- Qian Zhang
- Clinical and Health Sciences, University of South Australia, Adelaide SA 5001, Australia; Current address: Acrux DDS Pty Ltd, 103-113 Stanley St, West Melbourne, VIC 3003, Australia
| | - Azadeh Alinaghi
- Clinical and Health Sciences, University of South Australia, Adelaide SA 5001, Australia; Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Adelaide, SA, Australia
| | - Desmond B Williams
- Clinical and Health Sciences, University of South Australia, Adelaide SA 5001, Australia
| | - Michael S Roberts
- Clinical and Health Sciences, University of South Australia, Adelaide SA 5001, Australia; Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital, Adelaide, SA, Australia; Therapeutics Research Centre, Frazer Institute, University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.
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13
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Mitsuta Y, Asada T, Shigeta Y. Calculation of the permeability coefficients of small molecules through lipid bilayers by free-energy reaction network analysis following the explicit treatment of the internal conformation of the solute. Phys Chem Chem Phys 2022; 24:26070-26082. [PMID: 36268802 DOI: 10.1039/d2cp03678a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Biomembrane permeation represents a major barrier to pharmacokinetics. During preclinical drug discovery, the coefficients of the permeation of molecules through lipid bilayers account for a valuable property of such molecules. Therefore, the control of the permeation of molecules through lipid bilayers is an essential factor in drug design, and the estimation of the permeation phenomena is a crucial study in pharmacy. Thus, there are many published studies on the theoretical estimations of permeation coefficients. Here, we propose a molecular dynamics (MD) simulation method for estimating the permeation of small molecules through lipid bilayers based on the free-energy reaction network (FERN) analysis. In this method, the collective variables (CVs) of the free energy calculations explicitly include the conformational changes in the rotational bonds of the solute molecules. The advantages of the present method over the other method are that it is possible to estimate reaction pathways and their reaction rates, i.e., permeation coefficients or passage times, in multidimensional space spanned by CVs though conventional methods such as the umbrella sampling method and target MDs often dealt with a few degrees of freedom. To demonstrate the efficacy of our method, we calculate the coefficients of the permeation of three small aromatic peptides, namely N-acetylphenylalanineamide (Ac-Phe-NH2 or NAFA), N-acetyltyrosineamide (Ac-Tyr-NH2 or NAYA), and N-acetyltryptophanamide (Ac-Trp-NH2 or NATA), through a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer. In these cases we adopted one CV for the permeation direction and four CVs for the internal rotational coordinates. The results reveal that the permeation coefficients of NAFA, NAYA, and NATA are 1.7 × 10-2, 0.51 × 10-4, and 5.7 × 10-4 cm s-1, respectively. Compared with the experimental data, our simulation results followed the same trend, i.e., NAFA > NATA > NAYA. By analyzing the structures of metastable points of the solute molecules, our simulation result reveals that the aforementioned trend is caused by the differences in stability among their rotamers. Furthermore, we evaluate the statistical fluctuation of the rotamers, and the time scale of flipping the side chain reveals that the structures rigidify as the ligand moves deeper into the membrane.
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Affiliation(s)
- Yuki Mitsuta
- Department of Chemistry, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan.
- RIMED, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan
| | - Toshio Asada
- Department of Chemistry, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan.
- RIMED, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
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14
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Foreseeing the future of green Technology. Molecular dynamic investigation on passive membrane penetration by the products of the CO2 and 1,3-butadiene reaction. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Radhakrishnan N, Kaul SC, Wadhwa R, Sundar D. Phosphatidylserine Exposed Lipid Bilayer Models for Understanding Cancer Cell Selectivity of Natural Compounds: A Molecular Dynamics Simulation Study. MEMBRANES 2022; 12:64. [PMID: 35054590 PMCID: PMC8780679 DOI: 10.3390/membranes12010064] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/20/2021] [Accepted: 12/27/2021] [Indexed: 12/17/2022]
Abstract
Development of drugs that are selectively toxic to cancer cells and safe to normal cells is crucial in cancer treatment. Evaluation of membrane permeability is a key metric for successful drug development. In this study, we have used in silico molecular models of lipid bilayers to explore the effect of phosphatidylserine (PS) exposure in cancer cells on membrane permeation of natural compounds Withaferin A (Wi-A), Withanone (Wi-N), Caffeic Acid Phenethyl Ester (CAPE) and Artepillin C (ARC). Molecular dynamics simulations were performed to compute permeability coefficients. The results indicated that the exposure of PS in cancer cell membranes facilitated the permeation of Wi-A, Wi-N and CAPE through a cancer cell membrane when compared to a normal cell membrane. In the case of ARC, PS exposure did not have a notable influence on its permeability coefficient. The presented data demonstrated the potential of PS exposure-based models for studying cancer cell selectivity of drugs.
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Affiliation(s)
- Navaneethan Radhakrishnan
- DAILAB, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India;
| | - Sunil C. Kaul
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan;
| | - Renu Wadhwa
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan;
| | - Durai Sundar
- DAILAB, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India;
- School of Artificial Intelligence, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India
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16
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Paul R, Paul S. Translocation of Endo-Functionalized Molecular Tubes across Different Lipid Bilayers: Atomistic Molecular Dynamics Simulation Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:10376-10387. [PMID: 34415773 DOI: 10.1021/acs.langmuir.1c01594] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Various artificial receptors, such as calixarenes, cyclodextrins, cucurbit[n]urils, and their acyclic compounds, pliiar[n]arenes, deep cavitands, and molecular tweezers, can permeate the lipid membranes and they are used as drug carriers to improve the drug solubility, stability, and bioavailability. Inspired by these, we have employed atomistic molecular dynamics simulation to examine the effects of endo-functionalized molecular tubes or naphthotubes (host-1a and host-1b) on seven different types of model lipid bilayers and the permeation properties of these receptors through these model lipid bilayers. Lipid types include six model lipid bilayers (POPC, POPE, DOPC, POPG, DPPE, POPE/POPG) and one realistic membrane (Yeast). We observe that these receptors are spontaneously translocated toward these model lipid bilayer head regions and do not proceed further into these lipid bilayer tail regions (reside at the interface between lipid head and lipid tail region), except for the DPPE-containing systems. In the DPPE model lipid bilayer-containing systems (1a-dppe and 1b-dppe), receptor molecules are only adsorbed on the bilayer surface and reside at the interface between lipid head and water. This finding is also supported by the biased free-energy profiles of these translocation processes. Passive transport of these receptors may be possible through these model lipid bilayers (due to low barrier height), except for DPPE bilayer-containing systems (that have a very high energy barrier at the center). The results from these simulations provide insight into the biocompatibility of host-1a or host-1b in microscopic detail. Based on this work, more research is needed to fully comprehend the role of these synthesized receptors as a prospective drug carrier.
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Affiliation(s)
- Rabindranath Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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17
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Rózsa ZB, Szőri-Dorogházi E, Viskolcz B, Szőri M. Transmembrane penetration mechanism of cyclic pollutants inspected by molecular dynamics and metadynamics: the case of morpholine, phenol, 1,4-dioxane and oxane. Phys Chem Chem Phys 2021; 23:15338-15351. [PMID: 34254082 DOI: 10.1039/d1cp01521d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of industrially produced chemicals in water is often not monitored, while their passive transport and accumulation can cause serious damage in living cells. Molecular dynamics simulations are an effective way to understand the mechanism of the action of these pollutants. In this paper, the passive membrane transport of 1,4-dioxane, phenol, oxane and morpholine was investigated and analyzed thoroughly from structural and energetic points of view. Free energy profiles for pollutant and water penetration into the bilayer were obtained from well-tempered metadynamics (WT-MD) simulations and a mass density-based approach. It was found that all four investigated compounds can penetrate biological membranes and affect the free energy profile of water penetration. Out of the investigated species, oxane has the thermodynamically most preferred position in the bilayer center, leading to a lower free energy barrier of water molecules by 3 kJ mol-1, resulting in 5 times more water molecules in the bilayer center. The concentration dependence of free energy was tested at two different phenol concentrations using WT-MD, and it was found that the higher phenol concentration lowers the main barrier by 3 kJ mol-1. Density-based free energy calculations were found to reproduce the results of WT-MD within the limits of chemical accuracy.
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Affiliation(s)
- Zsófia Borbála Rózsa
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary.
| | - Emma Szőri-Dorogházi
- Centre for Higher Education and Industrial Cooperation, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary
| | - Béla Viskolcz
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary.
| | - Milán Szőri
- Institute of Chemistry, University of Miskolc, Egyetemváros A/2, H-3515 Miskolc, Hungary.
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18
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Das S, Meinel MK, Wu Z, Müller-Plathe F. The role of the envelope protein in the stability of a coronavirus model membrane against an ethanolic disinfectant. J Chem Phys 2021; 154:245101. [PMID: 34241335 DOI: 10.1063/5.0055331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ethanol is highly effective against various enveloped viruses and can disable the virus by disintegrating the protective envelope surrounding it. The interactions between the coronavirus envelope (E) protein and its membrane environment play key roles in the stability and function of the viral envelope. By using molecular dynamics simulation, we explore the underlying mechanism of ethanol-induced disruption of a model coronavirus membrane and, in detail, interactions of the E-protein and lipids. We model the membrane bilayer as N-palmitoyl-sphingomyelin and 1-palmitoyl-2-oleoylphosphatidylcholine lipids and the coronavirus E-protein. The study reveals that ethanol causes an increase in the lateral area of the bilayer along with thinning of the bilayer membrane and orientational disordering of lipid tails. Ethanol resides at the head-tail region of the membrane and enhances bilayer permeability. We found an envelope-protein-mediated increase in the ordering of lipid tails. Our simulations also provide important insights into the orientation of the envelope protein in a model membrane environment. At ∼25 mol. % of ethanol in the surrounding ethanol-water phase, we observe disintegration of the lipid bilayer and dislocation of the E-protein from the membrane environment.
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Affiliation(s)
- Shubhadip Das
- Technische Universität Darmstadt, Eduard-Zintl-Institute für Anorganische und Physikalische Chemie, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Melissa K Meinel
- Technische Universität Darmstadt, Eduard-Zintl-Institute für Anorganische und Physikalische Chemie, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Zhenghao Wu
- Technische Universität Darmstadt, Eduard-Zintl-Institute für Anorganische und Physikalische Chemie, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Technische Universität Darmstadt, Eduard-Zintl-Institute für Anorganische und Physikalische Chemie, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
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19
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Man VH, Li MS, Derreumaux P, Wang J, Nguyen PH. Molecular Mechanism of Ultrasound-Induced Structural Defects in Liposomes: A Nonequilibrium Molecular Dynamics Simulation Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7945-7954. [PMID: 34161100 DOI: 10.1021/acs.langmuir.1c00555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The use of ultrasound in combination with liposomes is a promising approach to improve drug delivery. To achieve an optimal drug release rate, it is important to understand how ultrasound induces pathways on the liposome surface where drugs can be released from the liposome. To this end, we carry out large-scale ultrasound-induced molecular dynamics simulations for three single lipid component liposomes formed from the commonly used phospholipids: 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dipalmitoylphosphatidylcholine (DPPC), or phosphatidylcholine (POPC). The results show that ultrasound induces the detachment of two leaflets of the DOPC surface, suggesting that the drug release pathway may be through the low lipid packing areas on the stretched surface. In contrast, ultrasound induces pore formation on the surface of DPPC and DOPC, where drugs could escape from the liposomes. While the leaflet detachment and transient pore formation are the mechanisms of DOPC and DPPC, respectively, in both liquid-ordered and liquid-disordered phases, the leaflet detachment mechanism is switched to the transient pore formation mechanism on going from the liquid-ordered phase to the liquid-disordered phase in the POPC liposome. By adding 30% mol cholesterol, the leaflet detachment mechanism is observed in all liposomes. We found that the molecular origin that determines a mechanism is the competition between the intraleaflet and interleaflet interacting energy of lipids. The connection to experimental and theoretical modeling is discussed in some detail.
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Affiliation(s)
- Viet Hoang Man
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Philippe Derreumaux
- CNRS, Université de Paris, UPR9080, Laboratoire de Biochimie Théorique, Paris, France, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Junmei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Phuong H Nguyen
- CNRS, Université de Paris, UPR9080, Laboratoire de Biochimie Théorique, Paris, France, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
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20
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Brantley T, Bogue J, Denny K, Elouafiq S, Madren S, Nakhle B, Khattak S. A novel approach to residence time distribution characterization in a mAb continuous process. Biotechnol Bioeng 2021; 118:3486-3498. [PMID: 33811655 DOI: 10.1002/bit.27775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/03/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022]
Abstract
Residence time distribution modeling of integrated perfusion to capture process can elucidate the impact of product quality excursions and filter fouling on monoclonal antibody production. In this case study, a glycosylation inhibitor and fluorescently labeled antibody are applied to the continuous process to study protein quality modulation, perfusion filter fouling, and unit operation hold times. The unit operations were modeled as continuous-stirred tank reactors and the residence time distribution of a small molecule glycan inhibitor and impact on glycosylation were characterized. A fluorescently labeled antibody was applied as a tracer molecule and confirmed the impact of packed cell volume and filter fouling. This study demonstrates how a biologics continuous process can be modeled and characterized through residence time distribution to ensure a robust, well-understood process.
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Affiliation(s)
- Tim Brantley
- Protein Development, Biogen Inc, Durham, North Carolina, USA
| | - Jon Bogue
- Analytical Development, Biogen Inc, Durham, North Carolina, USA
| | - Kurtis Denny
- Protein Development, Biogen Inc, Durham, North Carolina, USA
| | - Sanaa Elouafiq
- Protein Development, Biogen Inc, Durham, North Carolina, USA
| | - Seth Madren
- Analytical Development, Biogen Inc, Durham, North Carolina, USA
| | - Bassam Nakhle
- Analytical Development, Biogen Inc, Durham, North Carolina, USA
| | - Sarwat Khattak
- Protein Development, Biogen Inc, Durham, North Carolina, USA
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21
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Man VH, Li MS, Derreumaux P, Wang J, Nguyen TT, Nangia S, Nguyen PH. Molecular mechanism of ultrasound interaction with a blood brain barrier model. J Chem Phys 2021; 153:045104. [PMID: 32752695 DOI: 10.1063/5.0010667] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The brain is strictly protected by the blood brain barrier preventing the crossing of therapeutics to treat brain diseases. The high and low intensity focused ultrasound methods have been used to temporarily open the blood brain barrier, facilitating the transport of drugs. The methods are very promising because the opening is transient, localized, and noninvasive. However, the molecular mechanism of the opening is unknown, and this limits the development and application of these methods. With this in mind, we carry out a molecular dynamics simulation study to understand the interaction of ultrasound with the cell membrane and the tight junction. Our minimal blood brain barrier model is composed of two lipid bilayers, mimicking two portions of neighboring cells, connected together by a tight junction formed by a pair of two cis-dimers of the claudin-5 protein. Using an experimental ultrasound frequency of 50 MHz, simulations show that at low intensities, ultrasound does not impact the structure of the cell membranes and tight junction, implying that the direct interaction of ultrasound with the blood brain barrier is not responsible for the experimentally observed opening. At high intensities, the ultrasound pulls the monolayers of individual cell membrane lipid bilayers apart, creating air compartments inside the bilayers. This reduces the free energy barrier for the translocation of drugs across the lipid bilayer and enhances drug permeability. At very high intensities, the two monolayers are largely separated, resulting in cell damage and implying that the blood brain barrier is primarily opened at the experimentally observed damaged areas.
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Affiliation(s)
- Viet Hoang Man
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Philippe Derreumaux
- CNRS, Universite de Paris, UPR9080, Laboratoire de Biochimie Théorique, Paris, France
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Toan T Nguyen
- Key Laboratory for Multiscale Simulation of Complex Systems, VNU University of Science, Vietnam National University, 334 Nguyen Trai Street, Thanh Xuan, Hanoi, Vietnam
| | - S Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, USA
| | - Phuong H Nguyen
- CNRS, Universite de Paris, UPR9080, Laboratoire de Biochimie Théorique, Paris, France
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22
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Matamoros-Recio A, Franco-Gonzalez JF, Forgione RE, Torres-Mozas A, Silipo A, Martín-Santamaría S. Understanding the Antibacterial Resistance: Computational Explorations in Bacterial Membranes. ACS OMEGA 2021; 6:6041-6054. [PMID: 33718695 PMCID: PMC7948216 DOI: 10.1021/acsomega.0c05590] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/09/2021] [Indexed: 05/05/2023]
Affiliation(s)
- Alejandra Matamoros-Recio
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Juan Felipe Franco-Gonzalez
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Rosa Ester Forgione
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant’Angelo, Università di Napoli Federico II, Via Cintia 4, 80126 Napoli, Italy
| | - Angel Torres-Mozas
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant’Angelo, Università di Napoli Federico II, Via Cintia 4, 80126 Napoli, Italy
| | - Sonsoles Martín-Santamaría
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Research Margarita Salas, CIB-CSIC, C/Ramiro de Maeztu, 9, 28040 Madrid, Spain
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23
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Casalini T. Not only in silico drug discovery: Molecular modeling towards in silico drug delivery formulations. J Control Release 2021; 332:390-417. [PMID: 33675875 DOI: 10.1016/j.jconrel.2021.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/18/2022]
Abstract
The use of methods at molecular scale for the discovery of new potential active ligands, as well as previously unknown binding sites for target proteins, is now an established reality. Literature offers many successful stories of active compounds developed starting from insights obtained in silico and approved by Food and Drug Administration (FDA). One of the most famous examples is raltegravir, a HIV integrase inhibitor, which was developed after the discovery of a previously unknown transient binding area thanks to molecular dynamics simulations. Molecular simulations have the potential to also improve the design and engineering of drug delivery devices, which are still largely based on fundamental conservation equations. Although they can highlight the dominant release mechanism and quantitatively link the release rate to design parameters (size, drug loading, et cetera), their spatial resolution does not allow to fully capture how phenomena at molecular scale influence system behavior. In this scenario, the "computational microscope" offered by simulations at atomic scale can shed light on the impact of molecular interactions on crucial parameters such as release rate and the response of the drug delivery device to external stimuli, providing insights that are difficult or impossible to obtain experimentally. Moreover, the new paradigm brought by nanomedicine further underlined the importance of such computational microscope to study the interactions between nanoparticles and biological components with an unprecedented level of detail. Such knowledge is a fundamental pillar to perform device engineering and to achieve efficient and safe formulations. After a brief theoretical background, this review aims at discussing the potential of molecular simulations for the rational design of drug delivery systems.
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Affiliation(s)
- Tommaso Casalini
- Department of Chemistry and Applied Bioscience, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zürich 8093, Switzerland; Polymer Engineering Laboratory, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via la Santa 1, Lugano 6962, Switzerland.
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24
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Andrade S, Ramalho MJ, Loureiro JA, Pereira MC. The biophysical interaction of ferulic acid with liposomes as biological membrane model: The effect of the lipid bilayer composition. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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25
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Chang HY, Tsai HC, Sheng YJ, Tsao HK. Floating and Diving Loops of ABA Triblock Copolymers in Lipid Bilayers and Stability Enhancement for Asymmetric Membranes. Biomacromolecules 2020; 22:494-503. [PMID: 33356177 DOI: 10.1021/acs.biomac.0c01328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hybrid membranes of lipids and AxByAz triblock copolymers can possess better biocompatibility and mechanical stability. In this work, triblock copolymer conformations and stability of asymmetric membranes are explored by dissipative particle dynamics. The triblock copolymers in the membranes exhibit either the bridge or loop conformation. As hydrophobic B-blocks interact attractively with lipid heads, bridge-shaped copolymers are significantly inhibited and loop-shaped copolymers prefer to stay at the interface between hydrophilic and hydrophobic layers. This floating loop has a flattened conformation, consistent with the experimental findings. In contrast, for repulsive interactions between B-blocks and lipid heads, bridge-shaped copolymers are abundant and loop-shaped copolymers tend to plunge into the hydrophobic layer. This diving loop displays a random coil conformation. The asymmetric membrane in which the fractions of loop-shaped copolymers in the upper and lower leaflets are different is thermodynamically unstable. Two approaches are proposed to acquire kinetically stable asymmetric membranes. First, membrane symmetrization is arrested by eliminating bridge-shaped copolymers, which is achieved by B-block/lipid head attraction and B-block/lipid tail repulsion. Second, asymmetric triblock copolymers (x ≠ z) are used to prevent the passage of the long A-block through the hydrophobic layer.
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Affiliation(s)
- Hsin-Yu Chang
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Hsiang-Chi Tsai
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Yu-Jane Sheng
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Heng-Kwong Tsao
- Department of Chemical and Materials Engineering, National Central University, Jhongli 320, Taiwan
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26
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Coimbra JTS, Feghali R, Ribeiro RP, Ramos MJ, Fernandes PA. The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer. RSC Adv 2020; 11:899-908. [PMID: 35423709 PMCID: PMC8693363 DOI: 10.1039/d0ra09995c] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
The number of hydrogen bond donors and acceptors is a fundamental molecular descriptor to predict the oral bioavailability of small drug candidates. In fact, the most widely used oral bioavailability rules (such as the Lipinsky's rule-of-five and the Veber rules) make use of this molecular descriptor. It is generally assumed that hydrogen bond donors and acceptors impact on passive diffusion across cell membranes, a fundamental event during drug absorption and distribution. Although the relationship between the number of these motifs and the probability of having good oral bioavailability has been studied and described for more than 20 years, little attention has been given to their spatial distribution in the molecule. In this paper, we used molecular dynamics to describe the effect of intramolecular hydrogen bonding on the passive diffusion of a small drug (piracetam) through a lipid membrane. The results indicated that the formation of an intramolecular hydrogen bond decreases the barrier for translocation by ca. 4 kcal mol-1 and increases the permeability of the tested molecule, partially compensating the desolvation penalty arising from the penetration of the drug into the biological membrane core. This effect was apparent in simulations where the formation of this interaction was prevented with the help of modified potentials, and in simulations with a similar compound to piracetam that was not able to form this intramolecular hydrogen bond due to a larger distance between the hydrogen bond donor and acceptor groups. These results were also supported by coarse-grained methods, which are becoming an important resource for sampling a larger chemical space of molecules, with reduced computational effort. Furthermore, entropy and enthalpy derived profiles were also obtained as the compounds translocated across the membrane, suggesting that, even though the process of formation of internal hydrogen bonds is entropically unfavorable, the enthalpic gain is such that the formation of these interactions is beneficial for the passive diffusion across cell membranes.
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Affiliation(s)
- João T S Coimbra
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto Rua do Campo Alegre, s/n 4169-007 Porto Portugal
| | - Ralph Feghali
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto Rua do Campo Alegre, s/n 4169-007 Porto Portugal
| | - Rui P Ribeiro
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto Rua do Campo Alegre, s/n 4169-007 Porto Portugal
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto Rua do Campo Alegre, s/n 4169-007 Porto Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto Rua do Campo Alegre, s/n 4169-007 Porto Portugal
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Lee BL, Kuczera K, Lee KH, Childs EW, Jas GS. Unassisted N-acetyl-phenylalanine-amide transport across membrane with varying lipid size and composition: kinetic measurements and atomistic molecular dynamics simulation. J Biomol Struct Dyn 2020; 40:1445-1460. [PMID: 33034537 DOI: 10.1080/07391102.2020.1827037] [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: 10/23/2022]
Abstract
Biological membranes are essential to preserve structural integrity and regulate functional properties through the permeability of nutrients, pharmaceutical drugs, and neurotransmitters of a living cell. The movement of acetylated and amidated phenylalanine (NAFA) across 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane bilayers is investigated to probe physical transport. The rate of transport is measured experimentally applying parallel artificial membrane permeation assay (PAMPA). At the physiological temperature, 310 K, the measured time constants in the neutral pH were ∼6 h in DOPC and ∼3 h in POPC, while in a more acidic condition, at a pH 4.8, the time constants were ∼8 h in both lipids. Computationally, we have expanded our transport study of three aromatic dipeptides across a bilayer composed of DOPC18. In this study, we have examined the effects of lipid composition and bilayer size on the passive transport of NAFA by simulating the dipeptide in three different bilayers, with 50 DOPC lipids, 50 POPC lipids, and 40 POPC molecules. Specifically, atomistic molecular dynamics simulations with umbrella sampling were used to calculate the potential of mean force for the passive permeation of NAFA across the bilayers. Diffusion constants were then calculated by numerically solving the Smoluchowski equation. Permeability coefficients and mean first passage times were then calculated. Structural properties - Ramachandran plots, sidechain torsions, peptide insertion angles, radial distribution functions, and proximal peptide water molecules - were also examined to determine the effect of system size and lipid type. In terms of systems size, we observed a small decrease in the highest barrier of the potential of mean force and fewer sampled sidechain dihedral angle conformations with 40 versus 50 POPC lipids due to weaker membrane deformations within a smaller lipid bilayer. In terms of lipid type, DOPC contains two monounsaturated acyl chains compared to only one such acyl chain in POPC; therefore, DOPC bilayers are less ordered and more easily deformed, as seen by a much broader potential of mean force profile. The NAFA in DOPC lipid also transitioned to an internally hydrogen-bonded backbone conformation at lower membrane depths than in POPC. Similarly, as for other aromatic dipeptides, NAFA tends to insert into the membrane sidechain-first, remains mostly desolvated in the membrane center, and exhibits slow reorientations within the bilayer in both DOPC and POPC. With a joint experimental and computational study we have gained a new insight into the rate of transport and the underlying microscopic mechanism in different lipid bilayer conditions of the simplest hydrophobic aromatic dipeptide.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Brent L Lee
- Department of Chemistry, The University of Kansas, Lawrence, KS, USA
| | - Krzysztof Kuczera
- Department of Chemistry, The University of Kansas, Lawrence, KS, USA.,Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Kyung-Hoon Lee
- Department of Biology, Chowan University, Murfreesboro, NC, USA
| | - Ed W Childs
- Department of Surgery, Morehouse School of Medicine, Atlanta, GA, USA
| | - Gouri S Jas
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
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28
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Brantley TJ, Mitchelson FG, Khattak SF. A class of low-cost alternatives to kifunensine for increasing high mannose N-linked glycosylation for monoclonal antibody production in Chinese hamster ovary cells. Biotechnol Prog 2020; 37:e3076. [PMID: 32888259 DOI: 10.1002/btpr.3076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/21/2020] [Accepted: 09/02/2020] [Indexed: 01/01/2023]
Abstract
N-linked glycosylation of therapeutic monoclonal antibodies is an important product quality attribute for drug safety and efficacy. An increase in the percent of high mannose N-linked glycosylation may be required for drug efficacy or to match the glycosylation profile of the innovator drug during the development of a biosimilar. In this study, the addition of several chemical additives to a cell culture process resulted in high mannose N-glycans on monoclonal antibodies produced by Chinese hamster ovary (CHO) cells without impacting cell culture performance. The additives, which include known mannosidase inhibitors (kifunensine and deoxymannojirimycin) as well as novel inhibitors (tris, bis-tris, and 1-amino-1-methyl-1,3-propanediol), contain one similar molecular structure: 2-amino-1,3-propanediol, commonly referred to as serinol. The shared chemical structure provides insight into the binding and inhibition of mannosidase in CHO cells. One of the novel inhibitors, tris, is safer compared to kifunensine, 35x as cost-effective, and stable at room temperature. In addition, tris and bis-tris provide multiple low-cost alternatives to kifunensine for manipulating glycosylation in monoclonal antibody production in a cell culture process with minimal impact to productivity or cell health.
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Affiliation(s)
- Timothy J Brantley
- Cell Culture Development, Pharmaceutical Operations and Technology, Biogen Inc., Research Triangle Park, North Carolina, USA
| | - Fernie G Mitchelson
- Manufacturing Sciences, Pharmaceutical Operations and Technology, Biogen Inc., Research Triangle Park, North Carolina, USA
| | - Sarwat F Khattak
- Cell Culture Development, Pharmaceutical Operations and Technology, Biogen Inc., Research Triangle Park, North Carolina, USA
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29
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Casalini T, Rosolen A, Henriques CYH, Perale G. Permeation of Biopolymers Across the Cell Membrane: A Computational Comparative Study on Polylactic Acid and Polyhydroxyalkanoate. Front Bioeng Biotechnol 2020; 8:718. [PMID: 32714910 PMCID: PMC7344160 DOI: 10.3389/fbioe.2020.00718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 06/08/2020] [Indexed: 11/23/2022] Open
Abstract
Polymeric nanoparticles, which by virtue of their size (1-1000 nm) are able to penetrate even into cells, are attracting increasing interest in the emerging field of nanomedicine, as devices for, e.g., drugs or vaccines delivery. Because of the involved dimensional scale in the nanoparticle/cell membrane interactions, modeling approaches at molecular level are the natural choice in order to understand the impact of nanoparticle formulation on cellular uptake mechanisms. In this work, the passive permeation across cell membrane of oligomers made of two employed polymers in the biomedical field [poly-D,L-lactic acid (PDLA) and poly(3-hydroxydecanoate) (P3HD)] is investigated at fundamental atomic scale through molecular dynamics simulations. The free energy profile related to membrane crossing is computed adopting umbrella sampling. Passive permeation is also investigated using a coarse-grained model with MARTINI force field, adopting well-tempered metadynamics. Simulation results showed that P3HD permeation is favored with respect to PDLA by virtue of its higher hydrophobicity. The free energy profiles obtained at full atomistic and coarse-grained scale are in good agreement each for P3HD, while only a qualitative agreement was obtained for PDLA. Results suggest that a reparameterization of non-bonded interactions of the adopted MARTINI beads for the oligomer is needed in order to obtain a better agreement with more accurate simulations at atomic scale.
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Affiliation(s)
- Tommaso Casalini
- Polymer Engineering Laboratory, Department of Innovative Technologies, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland, Manno, Switzerland
| | - Amanda Rosolen
- Polymer Engineering Laboratory, Department of Innovative Technologies, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland, Manno, Switzerland
| | - Carolina Yumi Hosoda Henriques
- Polymer Engineering Laboratory, Department of Innovative Technologies, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland, Manno, Switzerland
| | - Giuseppe Perale
- Polymer Engineering Laboratory, Department of Innovative Technologies, Institute for Mechanical Engineering and Materials Technology, University of Applied Sciences and Arts of Southern Switzerland, Manno, Switzerland
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Vienna, Austria
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30
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Martinotti C, Ruiz-Perez L, Deplazes E, Mancera RL. Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes. Chemphyschem 2020; 21:1486-1514. [PMID: 32452115 DOI: 10.1002/cphc.202000219] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/22/2020] [Indexed: 12/12/2022]
Abstract
Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.
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Affiliation(s)
- Carlo Martinotti
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Lanie Ruiz-Perez
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
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31
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Tsai HC, Yang YL, Sheng YJ, Tsao HK. Formation of Asymmetric and Symmetric Hybrid Membranes of Lipids and Triblock Copolymers. Polymers (Basel) 2020; 12:polym12030639. [PMID: 32168935 PMCID: PMC7183320 DOI: 10.3390/polym12030639] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/08/2020] [Accepted: 03/10/2020] [Indexed: 12/28/2022] Open
Abstract
Hybrid membranes formed by co-assembly of AxByAx (hydrophilic-hydrophobic-hydrophilic) triblock copolymers into lipid bilayers are investigated by dissipative particle dynamics. Homogeneous hybrid membranes are developed as lipids and polymers are fully compatible. The polymer conformations can be simply classified into bridge- and loop-structures in the membranes. It is interesting to find that the long-time fraction of loop-conformation (fL) of copolymers in the membrane depends significantly on the hydrophilic block length (x). As x is small, an equilibrium fL* always results irrespective of the initial conformation distribution and its value depends on the hydrophobic block length (y). For large x, fL tends to be time-invariant because polymers are kinetically trapped in their initial structures. Our findings reveal that only symmetric hybrid membranes are formed for small x, while membranes with stable asymmetric leaflets can be constructed with large x. The effects of block lengths on the polymer conformations, such as transverse and lateral spans (d⊥ and d‖) of bridge- and loop-conformations, are discussed as well.
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Affiliation(s)
- Hsiang-Chi Tsai
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Yan-Ling Yang
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Yu-Jane Sheng
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
- Correspondence: (Y.-J.S.); (H.-K.T.)
| | - Heng-Kwong Tsao
- Department of Chemical and Materials Engineering, National Central University, Jhongli 320, Taiwan
- Correspondence: (Y.-J.S.); (H.-K.T.)
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32
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Erimban S, Daschakraborty S. Translocation of a hydroxyl functionalized carbon dot across a lipid bilayer: an all-atom molecular dynamics simulation study. Phys Chem Chem Phys 2020; 22:6335-6350. [DOI: 10.1039/c9cp05999g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Passive permeation of CD across lipid bilayer is almost impossible. Forced permeation results membrane rupture.
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Affiliation(s)
- Shakkira Erimban
- Department of Chemistry
- Indian Institute of Technology Patna
- Bihar 801106
- India
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33
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Tong S, Moyo B, Lee CM, Leong K, Bao G. Engineered materials for in vivo delivery of genome-editing machinery. NATURE REVIEWS. MATERIALS 2019; 4:726-737. [PMID: 34094589 PMCID: PMC8174554 DOI: 10.1038/s41578-019-0145-9] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/03/2019] [Indexed: 05/22/2023]
Abstract
Genome editing technologies, such as CRISPR/Cas9, are promising for treating otherwise incurable genetic diseases. Great progress has been made for ex vivo genome editing; however, major bottlenecks exist in the development of efficient, safe, and targetable in vivo delivery systems, which are needed for the treatment of many diseases. To achieve high efficacy and safety in therapeutic in vivo genome editing, editing activities must be controlled spatially and temporally in the body, which requires novel materials, delivery strategies, and control mechanisms. Thus, there is currently a tremendous opportunity for the biomaterials research community to develop in vivo delivery systems that overcome the problems of low editing efficiency, off-targeting effect, safety, and cell and tissue specificity. In this Review, we summarize delivery approaches and provide perspectives on the challenges and possible solutions, aiming to stimulate further development of engineered materials for in vivo delivery of genome-editing machinery.
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Affiliation(s)
- Sheng Tong
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Buhle Moyo
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Ciaran M. Lee
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Kam Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA
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34
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Vierros S, Sammalkorpi M. Hybrid Atomistic and Coarse-Grained Model for Surfactants in Apolar Solvents. ACS OMEGA 2019; 4:15581-15592. [PMID: 31572859 PMCID: PMC6761742 DOI: 10.1021/acsomega.9b01959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Here, we develop and verify the performance of a hybrid molecular modeling approach that combines coarse-grained apolar solvent and atomistic solute or polar solvent description, for example, for description of reverse micellar systems. The coarse-grained solvent model is directly applicable to organic solvents encompassing alkane, alkene, and fatty acid ester functional groups and connects directly to both standard united-atom GROMOS 53A6 and all-atom CHARMM27 force fields, as well as the atomistic detail water models compatible with these force fields. The different levels of description are coupled via explicit, unscaled electrostatics, and scaled mixing rules for dispersive interactions. The hybrid model is in near-quantitative agreement with fully atomistic simulations when combined with the CHARMM27 model but underestimates modestly surfactant aggregation when using GROMOS 53A6 united-atom description. The use of truncated electrostatics affords up to a 9-fold increase in computational speed without significant loss of accuracy. However, long-range electrostatic calculations and load imbalance at high core counts can significantly degrade the performance. We demonstrate the usability of the hybrid model by assessing the reverse micelle formation of a homologous series of nonionic glycerolipids via large-scale self-assembly simulations. The presented model is demonstrated here for accurate description of surfactant systems in apolar solvents, with and without also polar solvent (water) in the system. The formulation can be expected to describe well also other solute species or interfaces with an apolar solvent in an apolar environment.
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Affiliation(s)
- Sampsa Vierros
- Department
of Chemistry and Materials Science and Department of Biomaterials and
Bioproducts, Aalto University, P. O. Box 16100, 00076 Aalto, Finland
| | - Maria Sammalkorpi
- Department
of Chemistry and Materials Science and Department of Biomaterials and
Bioproducts, Aalto University, P. O. Box 16100, 00076 Aalto, Finland
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35
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Ouchi Y, Unoura K, Nabika H. Role of Oxidized Lipids in Permeation of H 2O 2 Through a Lipid Membrane: Molecular Mechanism of an Inhibitor to Promoter Switch. Sci Rep 2019; 9:12497. [PMID: 31467337 PMCID: PMC6715804 DOI: 10.1038/s41598-019-48954-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/09/2019] [Indexed: 01/10/2023] Open
Abstract
H2O2 permeation through a cell membrane significantly affects living organisms, and permeation is controlled by the physico-chemical nature of lipids and other membrane components. We investigated the molecular relationship between H2O2 permeation and lipid membrane structure using three oxidized lipids. POVPC and PazePC act as intra- and inter-molecular permeation promoters, respectively; however, their underlying mechanisms were different. The former changed the partition equilibrium, while the latter changed the permeation pathway. PoxnoPC inhibited permeation under our experimental conditions via an intra-molecular configuration change. Thus, both intra- and inter-molecular processes were found to control the role of oxidized lipids as inhibitors and promoters towards H2O2 permeation with different mechanisms depending on structure and composition. Here, we identified two independent H2O2 permeation routes: (i) permeation through lipid membrane with increased partition coefficient by intra-molecular configurational change and (ii) diffusion through pores (water channels) formed by inter-molecular configurational change of oxidized lipids. We provide new insight into how biological cells control permeation of molecules through intra- and inter-molecular configurational changes in the lipid membrane. Thus, by employing a rational design for both oxidized lipids and other components, the permeation behaviour of H2O2 and other ions and molecules through a lipid membrane could be controlled.
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Affiliation(s)
- Yuya Ouchi
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, 1-4-12 Kojirakawa, Yamagata, 990-8560, Japan
| | - Kei Unoura
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, 1-4-12 Kojirakawa, Yamagata, 990-8560, Japan
| | - Hideki Nabika
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, 1-4-12 Kojirakawa, Yamagata, 990-8560, Japan.
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36
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Lomize AL, Pogozheva ID. Physics-Based Method for Modeling Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules. J Chem Inf Model 2019; 59:3198-3213. [PMID: 31259555 DOI: 10.1021/acs.jcim.9b00224] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Assessment of permeability is a critical step in the drug development process for selection of drug candidates with favorable ADME properties. We have developed a novel physics-based method for fast computational modeling of passive permeation of diverse classes of molecules across lipid membranes. The method is based on heterogeneous solubility-diffusion theory and operates with all-atom 3D structures of solutes and the anisotropic solvent model of the lipid bilayer characterized by transbilayer profiles of dielectric and hydrogen bonding capacity parameters. The optimal translocation pathway of a solute is determined by moving an ensemble of representative conformations of the molecule through the dioleoyl-phosphatidylcholine (DOPC) bilayer and optimizing their rotational orientations in every point of the transmembrane trajectory. The method calculates (1) the membrane-bound state of the solute molecule; (2) free energy profile of the solute along the permeation pathway; and (3) the permeability coefficient obtained by integration over the transbilayer energy profile and assuming a constant size-dependent diffusivity along the membrane normal. The accuracy of the predictions was evaluated against experimental permeability coefficients measured in pure lipid membranes (for 78 compounds, R2 was 0.88 and rmse was 1.15 log units), PAMPA-DS (for 280 compounds, R2 was 0.75 and rmse was 1.59 log units), BBB (for 182 compounds, R2 was 0.69 and rmse was 0.87 log units), and Caco-2/MDCK assays (for 165 compounds, R2 was 0.52 and rmse was 0.89 log units).
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Affiliation(s)
- Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
| | - Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
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37
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Machado MR, Zeida A, Darré L, Pantano S. From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field. Interface Focus 2019; 9:20180085. [PMID: 31065347 PMCID: PMC6501346 DOI: 10.1098/rsfs.2018.0085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2019] [Indexed: 12/11/2022] Open
Abstract
Modern molecular and cellular biology profits from astonishing resolution structural methods, currently even reaching the whole cell level. This is encompassed by the development of computational methods providing a deep view into the structure and dynamics of molecular processes happening at very different scales in time and space. Linking such scales is of paramount importance when aiming at far-reaching biological questions. Computational methods at the interface between classical and coarse-grained resolutions are gaining momentum with several research groups dedicating important efforts to their development and tuning. An overview of such methods is addressed herein, with special emphasis on the SIRAH force field for coarse-grained and multi-scale simulations. Moreover, we provide proof of concept calculations on the implementation of a multi-scale simulation scheme including quantum calculations on a classical fine-grained/coarse-grained representation of double-stranded DNA. This opens the possibility to include the effect of large conformational fluctuations in chromatin segments on, for instance, the reactivity of particular base pairs within the same simulation framework.
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Affiliation(s)
- Matías R. Machado
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Leonardo Darré
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
- Institut Pasteur de Montevideo, Functional Genomics Unit, Mataojo 2020, CP 11400 Montevideo, Uruguay
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Group of Biomolecular Simulations, Mataojo 2020, CP 11400 Montevideo, Uruguay
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38
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Efremov RG. Dielectric-Dependent Strength of Interlipid Hydrogen Bonding in Biomembranes: Model Case Study. J Chem Inf Model 2019; 59:2765-2775. [PMID: 31135153 DOI: 10.1021/acs.jcim.9b00193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atomistic aspects of the structural organization, dynamics, and functioning of hydrated lipid bilayers-model cell membranes-are primarily governed by the fine balance of intermolecular interactions between all constituents of these systems. Besides the hydrophobic effect, which shapes the overall skeleton of lipid membranes, a very important contribution to their behavior is made by hydrogen bonds (H-bonds) between lipid head groups. The latter determine crucial phenomena in cell membranes, such as dynamic ultrananodomain organization, hydration, and fine-tuning of microscopic physicochemical properties that allow the membrane to adapt quickly when binding/insertion external agents (proteins, etc.). The characteristics of such H-bonds (strength, spatial localization, etc.) dramatically depend on the local polarity properties of the lipid-water environment. In this work, we calculated free energies of H-bonded complexes between typical donor (NH3+, NH, OH) and acceptor (C═O, OH, COO-, COOH) groups of lipids in vacuo and in a set of explicit solvents with dielectric constants (ε) from 1 to 78.3, which mimic membrane environment at different depths. This was done using Monte Carlo simulations and an assessment of the corresponding potential of mean force profiles. The strongest H-bonded complexes were observed in the nonpolar environment, and their strength increased sharply with decreasing ε below 17. When ε changed, the largest free energy gain (>10.8 kcal/mol) was observed for pairs of acceptors C═O and O(H) with donor NH3+. The complexation of the same acceptors with NH donor in this range of ε values was rather less sensitive to the environmental polarity, by ∼1.5 kcal/mol. Dielectric-dependent interactions of polar lipid groups with water were evaluated as well. The results explain the delicate balance that determines the unique pattern of H-bonds for a particular lipid bilayer. Understanding the factors that regulate the propensity for H-bonding in lipid bilayers provides a fundamental basis for the rational design of new membrane nano objects with predefined properties.
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Affiliation(s)
- R G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Sciences , 16/10, Miklukho-Maklaya Str. , Moscow , 117997 Russia.,Higher School of Economics , 20, Myasnitskaya Str. , Moscow , 101000 Russia.,Moscow Institute of Physics and Technology (State University) , 9 Institutskiy per. , Dolgoprudny , Moscow Region , 141700 Russia
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39
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 422] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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40
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Yang YL, Sheng YJ, Tsao HK. Hybridization of lipids to monolayer and bilayer membranes of triblock copolymers. J Colloid Interface Sci 2019; 544:53-60. [DOI: 10.1016/j.jcis.2019.02.071] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/29/2019] [Accepted: 02/21/2019] [Indexed: 01/03/2023]
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41
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Issack BB, Peslherbe GH. Accuracy and precision of simulated free energies: water permeation of hydrated DPPC bilayers as a paradigm. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1572141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Bilkiss B. Issack
- Centre for Research in Molecular Modeling, and Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
- Département des sciences expérimentales, Université de Saint-Boniface, Winnipeg, Canada
| | - Gilles H. Peslherbe
- Centre for Research in Molecular Modeling, and Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
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42
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Tang Z, Zhong F, Cheng J, Nie Z, Han X, Han Y, Yang Y. Concentrations and tissue-specific distributions of organic ultraviolet absorbents in wild fish from a large subtropical lake in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 647:1305-1313. [PMID: 30180338 DOI: 10.1016/j.scitotenv.2018.08.117] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/08/2018] [Accepted: 08/08/2018] [Indexed: 05/14/2023]
Abstract
Organic ultraviolet absorbents (UVAs) have been detected in various materials and biota, but little is known about the distributions of UVAs in the tissues of biota. In this study, tissue-specific UVA accumulation in six fish species from Lake Chaohu, China, was investigated. The sums of 12 UVA concentrations in muscles, gills, and livers were 7.65-120, 10.1-281, and 26.4-359 ng/g dry weight, respectively. Ethylhexyl methoxycinnamate, 4-methylbenzylidene-camphor, and 2-(2'-hydroxy-3',5'-di-tert-butylphenyl)-5-chlorobenzotriazole were the dominant UVAs. Ethylhexyl salicylate and homosalate have been found in the aquatic species firstly. UVAs were taken up to different degrees by different fish species. The UVA muscle bioconcentration factors were lower than predicted by the Estimation Programs Interface Suite model, suggesting that such models may overestimate UVA accumulation in fish. The tissue distribution patterns indicated that UVAs are easily transferred to the muscles after being absorbed through the gills. The liver was found to preferentially accumulate UVAs and have a high UVA accumulation capacity, implying liver damage may be caused by UVAs. This is the first time the partitioning of UVAs between the liver, muscle, and gills of freshwater fish has been studied. The data acquired will improve our understanding of the pharmacokinetics and toxicities of UVAs in aquatic organisms.
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Affiliation(s)
- Zhenwu Tang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
| | - Fuyong Zhong
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jiali Cheng
- Key Laboratory of Trace Element Nutrition of National Health and Family Planning Commission, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Zhiqiang Nie
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Xue Han
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yu Han
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yufei Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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43
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Palaiokostas M, Ding W, Shahane G, Orsi M. Effects of lipid composition on membrane permeation. SOFT MATTER 2018; 14:8496-8508. [PMID: 30346462 DOI: 10.1039/c8sm01262h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Passive permeation through lipid membranes is an essential process in biology. In vivo membranes typically consist of mixtures of lamellar and nonlamellar lipids. Lamellar lipids are characterized by their tendency to form lamellar sheet-like structures, which are predominant in nature. Nonlamellar lipids, when isolated, instead form more geometrically complex nonlamellar phases. While mixed lamellar/nonlamellar lipid membranes tend to adopt the ubiquitous lamellar bilayer structure, the presence of nonlamellar lipids is known to have profound effects on key membrane properties, such as internal distributions of stress and elastic properties, which in turn may alter related biological processes. This work focuses on one such process, i.e., permeation, by utilising atomistic molecular dynamics simulations in order to obtain transfer free energy profiles, diffusion profiles and permeation coefficients for a series of thirteen small molecules and drugs. Each permeant is tested on two bilayer membranes of different lipid composition, i.e., purely lamellar and mixed lamellar/nonlamellar. Our results indicate that the presence of nonlamellar lipids reduces permeation for smaller molecules (molecular weight < 100) but facilitates it for the largest ones (molecular weight > 100). This work represents an advancement towards the development of more realistic in silico permeability assays, which may have a substantial future impact in the area of rational drug design.
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Affiliation(s)
- Michail Palaiokostas
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
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44
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Goossens K, De Winter H. Molecular Dynamics Simulations of Membrane Proteins: An Overview. J Chem Inf Model 2018; 58:2193-2202. [PMID: 30336018 DOI: 10.1021/acs.jcim.8b00639] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Simulations of membrane proteins have been rising in popularity in the past decade. Advancements in technology and force fields made it possible to simulate behavior of membrane proteins. Membrane protein simulations can now be used as supporting evidence for experimental findings, for elucidating protein mechanisms, and validating protein crystal structures. Unrelated to experimental data, these simulations can also serve to investigate larger scale processes like protein sorting, protein-membrane interactions, and more. In this review, the history as well as the state-of-the-art methodologies in membrane protein simulations will be summarized. An emphasis will be put on how to set up the system and on the current models for the different components of the simulation system. An overview of the available tools for membrane protein simulation will be given, and current limitations and prospects will also be discussed.
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Affiliation(s)
- Kenneth Goossens
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium
| | - Hans De Winter
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium
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45
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Vermaas JV, Bentley GJ, Beckham GT, Crowley MF. Membrane Permeability of Terpenoids Explored with Molecular Simulation. J Phys Chem B 2018; 122:10349-10361. [DOI: 10.1021/acs.jpcb.8b08688] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Josh V. Vermaas
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Gayle J. Bentley
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Gregg T. Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Michael F. Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
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46
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Hartkamp R, Moore TC, Iacovella CR, Thompson MA, Bulsara PA, Moore DJ, McCabe C. Composition Dependence of Water Permeation Across Multicomponent Gel-Phase Bilayers. J Phys Chem B 2018; 122:3113-3123. [PMID: 29504755 PMCID: PMC6028149 DOI: 10.1021/acs.jpcb.8b00747] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
The permeability
of multicomponent phospholipid bilayers in the
gel phase is investigated via molecular dynamics simulation. The physical
role of the different molecules is probed by comparing multiple mixed-component
bilayers containing distearylphosphatidylcholine (DSPC) with varying
amounts of either the emollient isostearyl isostearate or long-chain
alcohol (dodecanol, octadecanol, or tetracosanol) molecules. Permeability
is found to depend on both the tail packing density and hydrogen bonding
between lipid headgroups and water. Whereas the addition of emollient
or alcohol molecules to a gel-phase DSPC bilayer can increase the
tail packing density, it also disturbed the hydrogen-bonding network,
which in turn can increase interfacial water dynamics. These phenomena
have opposing effects on bilayer permeability, which is found to depend
on the balance between enhanced tail packing and decreased hydrogen
bonding.
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Affiliation(s)
- Remco Hartkamp
- Process & Energy Department , Delft University of Technology , Leeghwaterstraat 39 , 2628 CB Delft , The Netherlands
| | | | | | - Michael A Thompson
- GlaxoSmithKline Consumer Healthcare , 184 Liberty Corner Road , Suite 200, Warren , New Jersey 07059 , United States
| | - Pallav A Bulsara
- GlaxoSmithKline Consumer Healthcare , 184 Liberty Corner Road , Suite 200, Warren , New Jersey 07059 , United States
| | - David J Moore
- GlaxoSmithKline Consumer Healthcare , 184 Liberty Corner Road , Suite 200, Warren , New Jersey 07059 , United States
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47
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Yang YL, Chen MY, Tsao HK, Sheng YJ. Dynamics of bridge-loop transformation in a membrane with mixed monolayer/bilayer structures. Phys Chem Chem Phys 2018; 20:6582-6590. [PMID: 29450428 DOI: 10.1039/c7cp08107c] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Instead of forming a typical bilayer or monolayer membrane, both the bridge (I-shape) and loop (U-shape) conformations coexist in the planar membranes formed by ABA triblock copolymers in a selective solvent. The non-equilibrium and equilibrium relaxation dynamics of polymer conformations are monitored. The non-equilibrium relaxation time depends on the initial composition and increases with an increase in the immiscibility between A and B blocks. The equilibrium composition of the loop-shape polymer is independent of the initial composition and A-B immiscibility. However, the extent of equilibrium composition fluctuations subsides as the A and B blocks become highly incompatible. The influences of the A-B immiscibility on the geometrical, mechanical, and transport properties of the membrane have also been investigated. As the immiscibility increases, the overall membrane thickness and the B block layer thickness (h) increase because of the increment in the molecular packing density. As a result, both the stretching (KA) and bending (KB) moduli grow significantly with the increasing A-B immiscibility. Consistent with the case of typical membranes, the ratio KB/KAh2 = 2 × 10-3 is a constant. Although the lateral diffusivity of polymers is insensitive to immiscibility, the membrane permeability decreases substantially as the A-B immiscibility is increased.
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Affiliation(s)
- Yan-Ling Yang
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan 106, Republic of China.
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48
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DeMarco KR, Bekker S, Clancy CE, Noskov SY, Vorobyov I. Digging into Lipid Membrane Permeation for Cardiac Ion Channel Blocker d-Sotalol with All-Atom Simulations. Front Pharmacol 2018; 9:26. [PMID: 29449809 PMCID: PMC5799612 DOI: 10.3389/fphar.2018.00026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022] Open
Abstract
Interactions of drug molecules with lipid membranes play crucial role in their accessibility of cellular targets and can be an important predictor of their therapeutic and safety profiles. Very little is known about spatial localization of various drugs in the lipid bilayers, their active form (ionization state) or translocation rates and therefore potency to bind to different sites in membrane proteins. All-atom molecular simulations may help to map drug partitioning kinetics and thermodynamics, thus providing in-depth assessment of drug lipophilicity. As a proof of principle, we evaluated extensively lipid membrane partitioning of d-sotalol, well-known blocker of a cardiac potassium channel Kv11.1 encoded by the hERG gene, with reported substantial proclivity for arrhythmogenesis. We developed the positively charged (cationic) and neutral d-sotalol models, compatible with the biomolecular CHARMM force field, and subjected them to all-atom molecular dynamics (MD) simulations of drug partitioning through hydrated lipid membranes, aiming to elucidate thermodynamics and kinetics of their translocation and thus putative propensities for hydrophobic and aqueous hERG access. We found that only a neutral form of d-sotalol accumulates in the membrane interior and can move across the bilayer within millisecond time scale, and can be relevant to a lipophilic channel access. The computed water-membrane partitioning coefficient for this form is in good agreement with experiment. There is a large energetic barrier for a cationic form of the drug, dominant in water, to cross the membrane, resulting in slow membrane translocation kinetics. However, this form of the drug can be important for an aqueous access pathway through the intracellular gate of hERG. This route will likely occur after a neutral form of a drug crosses the membrane and subsequently re-protonates. Our study serves to demonstrate a first step toward a framework for multi-scale in silico safety pharmacology, and identifies some of the challenges that lie therein.
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Affiliation(s)
- Kevin R DeMarco
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States.,Department of Pharmacology, University of California, Davis, Davis, CA, United States.,Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
| | - Slava Bekker
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States.,Hartnell College, Salinas, CA, United States
| | - Colleen E Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States.,Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Sergei Y Noskov
- Centre for Molecular Simulations, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States.,Department of Pharmacology, University of California, Davis, Davis, CA, United States
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50
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Lee BL, Kuczera K. Simulating the free energy of passive membrane permeation for small molecules. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1407029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Brent L. Lee
- Department of Chemistry, The University of Kansas , Lawrence, KS, USA
| | - Krzysztof Kuczera
- Department of Chemistry, The University of Kansas , Lawrence, KS, USA
- Department of Molecular Biosciences, The University of Kansas , Lawrence, KS, USA
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