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Kaluzhskiy L, Yablokov E, Gnedenko O, Burkatovskii D, Maslov I, Bogorodskiy A, Ershov P, Tsybruk T, Zelepuga E, Rutckova T, Kozlovskaya E, Dmitrenok P, Gilep A, Borshchevskiy V, Strushkevich N, Ivanov A. The effect of membrane composition on the interaction between human CYP51 and its flavonoid inhibitor - luteolin 7,3'-disulfate. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184286. [PMID: 38272204 DOI: 10.1016/j.bbamem.2024.184286] [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: 10/30/2023] [Revised: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
Cytochromes P450 (CYP) are a family of membrane proteins involved in the production of endogenous molecules and the metabolism of xenobiotics. It is well-known that the composition of the membrane can influence the activity and orientation of CYP proteins. However, little is known about how membrane composition affects the ligand binding properties of CYP. In this study, we utilized surface plasmon resonance and fluorescence lifetime analysis to examine the impact of membrane micro-environment composition on the interaction between human microsomal CYP51 (CYP51A1) and its inhibitor, luteolin 7,3'-disulphate (LDS). We observed that membranes containing cholesterol or sphingomyelin exhibited the lowest apparent equilibrium dissociation constant for the CYP51A1-LDS complex. Additionally, the tendency for relation between kinetic parameters of the CYP51A1-LDS complex and membrane viscosity and overall charge was observed. These findings suggest that the specific composition of the membrane, particularly the presence of cholesterol and sphingomyelin, plays a vital role in regulating the interaction between CYP enzymes and their ligands.
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Affiliation(s)
- Leonid Kaluzhskiy
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia.
| | - Evgeniy Yablokov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia.
| | - Oksana Gnedenko
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia.
| | - Dmitrii Burkatovskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia.
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia.
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Pavel Ershov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia
| | - Tatsiana Tsybruk
- Institute of Bioorganic Chemistry NASB, 5 Building 2, V.F. Kuprevich Street, 220141 Minsk, Belarus
| | - Elena Zelepuga
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 159 Prospect 100-letiya Vladivostoka, 690022 Vladivostok, Russia.
| | - Tatyana Rutckova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 159 Prospect 100-letiya Vladivostoka, 690022 Vladivostok, Russia
| | - Emma Kozlovskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 159 Prospect 100-letiya Vladivostoka, 690022 Vladivostok, Russia
| | - Pavel Dmitrenok
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 159 Prospect 100-letiya Vladivostoka, 690022 Vladivostok, Russia.
| | - Andrei Gilep
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; Institute of Bioorganic Chemistry NASB, 5 Building 2, V.F. Kuprevich Street, 220141 Minsk, Belarus.
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - Natallia Strushkevich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia.
| | - Alexis Ivanov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia.
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Ghorbani M, Dehghan G, Allahverdi A. Concentration-dependent mechanism of the binding behavior of ibuprofen to the cell membrane: A molecular dynamic simulation study. J Mol Graph Model 2023; 124:108581. [PMID: 37536233 DOI: 10.1016/j.jmgm.2023.108581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023]
Abstract
Ibuprofen is a commonly used drug for treating headaches, pain, and fever. The lipid bilayer is the primary and most important interface for drugs to interact with biological systems. However, the molecular interactions between ibuprofen and the cell membrane are not well understood. Our findings suggest that the interactions between ibuprofen and the bilayer involve multiple steps and depend on the concentration of the drug. At low concentrations of ibuprofen, it can bind to the surface of the lipid bilayer. The electrostatic and vdW energies of IBU-lipid at 0 ns of the simulation were -22.5 ± 3.2 and -5.9 ± 1.2 kj.mol-1 Fig. 2. In the following, the vdW energy of the IBU-lipid was increased by around -134.6 ± 3.7 kj.mol-1 whereas the electrostatic energy of the IBU-lipid was significantly decreased. This binding is facilitated by electrostatic and vdW interactions between ibuprofen and the head group of lipids. In the second step, ibuprofen is inserted into the lipid bilayer and positioned at the interface between the bilayer and the aqueous phase. In high concentrations of ibuprofen, it moved to the central region of the lipid bilayer. At this concentration, the physical and structural properties of the cell membrane change significantly. Results from the radial distribution function analysis indicate that at low concentrations, ibuprofen molecules are situated close to the head groups of phosphate groups. However, at high concentrations of ibuprofen, these molecules move to the inner side of the lipid bilayer. In addition, our findings indicate that at low concentrations of ibuprofen, these molecules did not significantly alter the physical properties of the cell membrane. In contrast, at high concentrations of ibuprofen, the physical parameters of the hydrocarbon tails, such as thickness, fluidity, and order, changed dramatically. APL parameter for POPC membrane increased slightly to 0.60 and 0.63 nm2 in the presence of low and high concentrations of ibuprofen molecules. The three-step interaction between ibuprofen and the lipid bilayer involves several events, such as the movement of ibuprofen molecules towards the central region of the lipid bilayer and the deformation and alteration of the structural and stability properties of the cell membrane. These effects are observed only at high concentrations of ibuprofen. It appears that the side effects of ibuprofen overdose are related to changes in the properties of the cell membrane and, subsequently, the function of membrane-anchored target proteins.
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Affiliation(s)
| | | | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box: 14115-111, Tehran, Iran.
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Sumangala N, Im SC, Valentín-Goyco J, Auchus RJ. Influence of cholesterol on kinetic parameters for human aromatase (P450 19A1) in phospholipid nanodiscs. J Inorg Biochem 2023; 247:112340. [PMID: 37544101 DOI: 10.1016/j.jinorgbio.2023.112340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 08/08/2023]
Abstract
Cholesterol, a significant constituent of the endoplasmic reticulum membrane, exerts a substantial effect on the membrane's biophysical and mechanical properties. Cholesterol, however, is often neglected in model systems used to study membrane-bound proteins. For example, the influence of cholesterol on the enzymatic functions of type 2 cytochromes P450, which require a phospholipid bilayer and the redox partner P450-oxidoreductase (POR) for activity, are rarely investigated. Human aromatase (P450 19A1) catalyzes three sequential oxygenations of 19‑carbon steroids to estrogens and is widely expressed across various tissues, which are characterized by varying cholesterol compositions. Our study examined the impact of cholesterol on the functionality of the P450 19A1 complex with POR. Nanodiscs containing P450 19A1 with 20% cholesterol/80% phospholipid had similar rates and affinity of androstenedione binding as phospholipid-only P450 19A1 nanodiscs, and rates of product formation were indistinguishable among these conditions. In contrast, the rate of the first electron transfer from POR to P450 19A1 was 3-fold faster in cholesterol-containing nanodiscs than in phospholipid-only nanodiscs. These results suggest that cholesterol influences some aspects of POR interaction with P450 19A1 and might serve as an additional regulatory mechanism in this catalytic system.
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Affiliation(s)
- Nirupama Sumangala
- Division of Metabolism, Endocrinology, & Diabetes, Department of Internal Medicine, Ann Arbor, MI 48109, USA; Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sang-Choul Im
- Division of Metabolism, Endocrinology, & Diabetes, Department of Internal Medicine, Ann Arbor, MI 48109, USA; Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; Veterans Affairs Medical Center, Ann Arbor, MI 48105, United States
| | - Juan Valentín-Goyco
- Division of Metabolism, Endocrinology, & Diabetes, Department of Internal Medicine, Ann Arbor, MI 48109, USA; Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard J Auchus
- Division of Metabolism, Endocrinology, & Diabetes, Department of Internal Medicine, Ann Arbor, MI 48109, USA; Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; Veterans Affairs Medical Center, Ann Arbor, MI 48105, United States.
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Hlavica P. Key regulators in the architecture of substrate access/egress channels in mammalian cytochromes P450 governing flexibility in substrate oxyfunctionalization. J Inorg Biochem 2023; 241:112150. [PMID: 36731371 DOI: 10.1016/j.jinorgbio.2023.112150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/21/2023] [Accepted: 01/22/2023] [Indexed: 01/31/2023]
Abstract
Cytochrome P450s (CYP) represent a superfamily of b-type hemoproteins catalyzing oxifunctionalization of a vast array of endogenous and exogenous compounds. The present review focuses on assessment of the topology of prospective determinants in substrate entry and product release channels of mammalian P450s, steering the conformational dynamics of substrate accessibility and productive ligand orientation toward the iron-oxene core. Based on a generalized, CYP3A4-related construct, the sum of critical elements from diverse target enzymes was found to cluster within the known substrate recognition sites. The majority of prevalent substrate access/egress tunnels revealed to be of fairly balanced functional importance. The hydrophobicity profile of the candidates revealed to be the most salient feature in functional interaction throughout the conduits, while bulkiness of the residues imposes steric restrictions on substrate traveling. Thus, small amino acids such as prolines and glycines serve as hinges, driving conformational flexibility in ligand passage. Similarly, bottlenecks in the tunnel architecture, being narrowest encounter points within the CYP3A4 model, have a vital function in substrate selectivity along with clusters of aromatic amino acids acting as gatekeepers. In addition, peripheral patches in conduits may house determinants modulating allosteric cooperativity between remote and central domains in the P450 structure. Remarkably, the bulk critical residues lining tunnels in the various isozymes reside in helices B'/C and F/G inclusive of their interhelical turns as well as in helix I. This suggests these regions to represent hotspots for targeted genetic engineering to tailor more sophisticated mammalian P450s exploitable in industrial, biotechnological and medicinal areas.
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Affiliation(s)
- Peter Hlavica
- Walther-Straub Institut fuer Pharmakologie und Toxikologie, Goethestrasse 33, D80336 Muenchen, Germany.
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5
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Dos Santos KF, Materón EM, Oliveira ON. Influence of cytochrome P450 3A4 and membrane lipid composition on doxorubicin activity. Colloids Surf B Biointerfaces 2022; 220:112886. [PMID: 36183636 DOI: 10.1016/j.colsurfb.2022.112886] [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: 07/07/2022] [Revised: 08/30/2022] [Accepted: 09/25/2022] [Indexed: 11/28/2022]
Abstract
Drug resistance is known to depend on the interactions with cell membranes and other molecules such as human cytochromes P450 (CYPs) which are anchored on the endoplasmic reticulum (ER) membrane and involved in the metabolism of anticancer drugs. In this study, we determined the influence from cytochrome P450 3A4 (CYP3A4) on the interaction between the drug doxorubicin (DOX) and Langmuir monolayers mimicking cell membranes. The lipid composition was varied by changing the relative concentrations of cholesterol (Chol), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), and L-α-phosphatidylinositol (PI). Three compositions were studied in detail which represented a healthy cell membrane and cancerous cell membranes. DOX induced an expansion in the surface pressure isotherms for all monolayers, with stronger effect for the composition of cancerous cell with a high Chol content, thus confirming the relevance of lipid composition. This effect decreased considerably when CYP3A4 was incorporated with the formation of CYP3A4-DOX complexes, according to results from polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS) measurements. Taken together, these results support the hypothesis of CYP3A4 being involved in drug resistance, which may be exploited to design strategies to enhance chemotherapy efficacy.
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Affiliation(s)
- Kevin F Dos Santos
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Elsa M Materón
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Osvaldo N Oliveira
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil.
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6
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Kano S, Takahashi H. Cholesterol's inhibition effect on entering of chlorzoxazone into phosphatidylethanolamine bilayer: Relevance to cytochrome P450 drug metabolism at endoplasmic reticulum membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183954. [PMID: 35523303 DOI: 10.1016/j.bbamem.2022.183954] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/18/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
Many drugs are metabolized by cytochrome P450 (CYP) in the endoplasmic reticulum (ER) membrane. Recent studies have shown that CYP-substrate drugs reach the CYP active site after entering the lipid hydrophobic part of the ER membrane. To clarify the role of cholesterol (Chol) in the CYP-related drug metabolic process, we investigated the lipid bilayer entry of CYP-substrate drugs using a model membrane system as follows. The model membrane system comprised palmitoyl-oleoyl-phosphatidylethanolamine (POPE) and Chol. Phosphatidylethanolamine is the second major phospholipid component of ER membranes. Chlorzoxazone (CZX) was used as the CYP-substrate drug. Calorimetric measurements showed that the addition of CZX to POPE bilayers decreased the gel-liquid crystal phase transition temperature; X-ray diffraction indicated that CZX distributes into the liquid crystal phase bilayers but not practically the gel phase POPE bilayers. In the presence of Chol, dialysis and X-ray structural analyses showed that Chol inhibited CZX entry into the bilayer with an increase in Chol concentration. The Chol concentration in the ER membrane (5-10 mol%) is much lower than that in the plasma membrane (approximately 30 mol%). This fact may allow CYP-substrate drugs to enter the hydrophobic portion of the ER membrane more easily than other organelle membranes, yielding efficient drug metabolism.
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Affiliation(s)
- Shosei Kano
- Division of Pure and Applied Science, Graduate School of Science and Technology, Gunma University, Maebashi, Gunma 371-8510, Japan
| | - Hiroshi Takahashi
- Division of Pure and Applied Science, Graduate School of Science and Technology, Gunma University, Maebashi, Gunma 371-8510, Japan.
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Oliveira AA, Róg T, da Silva ABF, Amaro RE, Johnson MS, Postila PA. Examining the Effect of Charged Lipids on Mitochondrial Outer Membrane Dynamics Using Atomistic Simulations. Biomolecules 2022; 12:biom12020183. [PMID: 35204684 PMCID: PMC8961577 DOI: 10.3390/biom12020183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/11/2022] Open
Abstract
The outer mitochondrial membrane (OMM) is involved in multiple cellular functions such as apoptosis, inflammation and signaling via its membrane-associated and -embedded proteins. Despite the central role of the OMM in these vital phenomena, the structure and dynamics of the membrane have regularly been investigated in silico using simple two-component models. Accordingly, the aim was to generate the realistic multi-component model of the OMM and inspect its properties using atomistic molecular dynamics (MD) simulations. All major lipid components, phosphatidylinositol (PI), phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS), were included in the probed OMM models. Because increased levels of anionic PS lipids have potential effects on schizophrenia and, more specifically, on monoamine oxidase B enzyme activity, the effect of varying the PS concentration was explored. The MD simulations indicate that the complex membrane lipid composition (MLC) behavior is notably different from the two-component PC-PE model. The MLC changes caused relatively minor effects on the membrane structural properties such as membrane thickness or area per lipid; however, notable effects could be seen with the dynamical parameters at the water-membrane interface. Increase of PS levels appears to slow down lateral diffusion of all lipids and, in general, the presence of anionic lipids reduced hydration and slowed down the PE headgroup rotation. In addition, sodium ions could neutralize the membrane surface, when PI was the main anionic component; however, a similar effect was not seen for high PS levels. Based on these results, it is advisable for future studies on the OMM and its protein or ligand partners, especially when wanting to replicate the correct properties on the water-membrane interface, to use models that are sufficiently complex, containing anionic lipid types, PI in particular.
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Affiliation(s)
- Aline A. Oliveira
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093-0340, USA; (A.A.O.); (R.E.A.)
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos 13560-970, Brazil;
| | - Tomasz Róg
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland;
| | - Albérico B. F. da Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos 13560-970, Brazil;
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093-0340, USA; (A.A.O.); (R.E.A.)
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- InFLAMES Research Flagship Center, Åbo Akademi University, 20520 Turku, Finland
| | - Pekka A. Postila
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093-0340, USA; (A.A.O.); (R.E.A.)
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- InFLAMES Research Flagship Center, Åbo Akademi University, 20520 Turku, Finland
- Institute of Biomedicine, Kiinamyllynkatu 10, Integrative Physiology and Pharmacy, University of Turku, FI-20520 Turku, Finland
- Aurlide Ltd., FI-21420 Lieto, Finland
- InFLAMES Research Flagship Center, University of Turku, FI-20520 Turku, Finland
- Correspondence:
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Raju DR, Kumar A, BK N, Shetty A, PS A, Kumar RP, Lalitha R, Sigamani G. Extensive modelling and quantum chemical study of sterol C-22 desaturase mechanism: A commercially important cytochrome P450 family. Catal Today 2021. [DOI: 10.1016/j.cattod.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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9
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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Effects of cholesterol on chlorzoxazone translocation across POPC bilayer. J Mol Model 2021; 27:146. [PMID: 33934224 DOI: 10.1007/s00894-021-04777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/25/2021] [Indexed: 10/21/2022]
Abstract
Cholesterol plays a crucial role in modulating the physicochemical properties of membranes, thus influencing the membrane transport of drugs. In this paper, the effects caused by cholesterol on the membrane transport of chlorzoxazone (CZX), a centrally acting muscle relaxant drug, were probed through molecular dynamics simulations. POPC was selected as the model lipid, and three different cholesterol concentrations (0%, 20%, and 50% CHOL) were considered. The outcomes reveal that the area per lipid of POPC decreases and the order parameter increases with enhanced concentration of CHOL. CZX prefers to localize at the interface between the headgroup region and the hydrophobic tail region of POPC, and the main energy barrier occurs in the hydrophobic region. The impact of CHOL on the free energy profile is correlated with concentration: low concentration facilitates CZX permeation, while high concentration hinders CZX permeation. Our findings coincide with experimental results, enhancing the mechanism understanding of how drug molecules are transported through membranes in the presence of CHOL. • The effects caused by cholesterol (CHOL) on the membrane transport of chlorzoxazone (CZX) were studied. • Low CHOL concentration facilitates CZX permeation, while high concentration hinders CZX permeation. • Our findings improve the mechanism understanding of CHOL effects on CZX translocation across membrane.
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11
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Wood M, Morales M, Miller E, Braziel S, Giancaspro J, Scollan P, Rosario J, Gayapa A, Krmic M, Lee S. Ibuprofen and the Phosphatidylcholine Bilayer: Membrane Water Permeability in the Presence and Absence of Cholesterol. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:4468-4480. [PMID: 33826350 DOI: 10.1021/acs.langmuir.0c03638] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The interactions between drugs and cell membranes can modulate the structural and physical properties of membranes. The resultant perturbations of the membrane integrity may affect the conformation of the proteins inserted within the membrane, disturbing the membrane-hosted biological functions. In this study, the droplet interface bilayer (DIB), a model cell membrane, is used to examine the effects of ibuprofen, a nonsteroidal anti-inflammatory drug (NSAID), on transbilayer water permeability, which is a fundamental membrane biophysical property. Our results indicate that the presence of neutral ibuprofen (pH 3) increases the water permeability of the lipid membranes composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). When cholesterol is present with the DOPC, however, the water permeability is not influenced by addition of ibuprofen, regardless of the cholesterol content in DOPC. Given the fact that cholesterol is generally considered to impact packing in the hydrocarbon chain regions, our findings suggest that a potential competition between opposing effects of ibuprofen molecules and cholesterol on the hydrocarbon core environment of the phospholipid assembly may influence the overall water transport phenomena. Results from confocal Raman microspectroscopy and interfacial tensiometry show that ibuprofen molecules induce substantial structural and dynamic changes in the DOPC lipid bilayer. These results, demonstrating that the presence of ibuprofen increases the water permeability of pure DOPC but not that of DOPC-cholesterol mixtures, provide insight into the differential effect of a representative NSAID on heterogeneous biological membranes, depending upon the local composition and structure, results which will signal increased understanding of the gastrointestinal damage and toxicity induced by these molecules.
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Affiliation(s)
- Megan Wood
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Michael Morales
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Elizabeth Miller
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Samuel Braziel
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Joseph Giancaspro
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Patrick Scollan
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Juan Rosario
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Alyssa Gayapa
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Michael Krmic
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Sunghee Lee
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
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Mustafa G, Nandekar PP, Bruce NJ, Wade RC. Differing Membrane Interactions of Two Highly Similar Drug-Metabolizing Cytochrome P450 Isoforms: CYP 2C9 and CYP 2C19. Int J Mol Sci 2019; 20:ijms20184328. [PMID: 31487853 PMCID: PMC6770661 DOI: 10.3390/ijms20184328] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/31/2019] [Accepted: 09/01/2019] [Indexed: 12/22/2022] Open
Abstract
The human cytochrome P450 (CYP) 2C9 and 2C19 enzymes are two highly similar isoforms with key roles in drug metabolism. They are anchored to the endoplasmic reticulum membrane by their N-terminal transmembrane helix and interactions of their cytoplasmic globular domain with the membrane. However, their crystal structures were determined after N-terminal truncation and mutating residues in the globular domain that contact the membrane. Therefore, the CYP-membrane interactions are not structurally well-characterized and their dynamics and the influence of membrane interactions on CYP function are not well understood. We describe herein the modeling and simulation of CYP 2C9 and CYP 2C19 in a phospholipid bilayer. The simulations revealed that, despite high sequence conservation, the small sequence and structural differences between the two isoforms altered the interactions and orientations of the CYPs in the membrane bilayer. We identified residues (including K72, P73, and I99 in CYP 2C9 and E72, R73, and H99 in CYP 2C19) at the protein-membrane interface that contribute not only to the differing orientations adopted by the two isoforms in the membrane, but also to their differing substrate specificities by affecting the substrate access tunnels. Our findings provide a mechanistic interpretation of experimentally observed effects of mutagenesis on substrate selectivity.
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Affiliation(s)
- Ghulam Mustafa
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Prajwal P Nandekar
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany.
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany.
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13
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Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
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Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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14
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
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Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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15
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The Catalytic Mechanism of Steroidogenic Cytochromes P450 from All-Atom Simulations: Entwinement with Membrane Environment, Redox Partners, and Post-Transcriptional Regulation. Catalysts 2019. [DOI: 10.3390/catal9010081] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cytochromes P450 (CYP450s) promote the biosynthesis of steroid hormones with major impact on the onset of diseases such as breast and prostate cancers. By merging distinct functions into the same catalytic scaffold, steroidogenic CYP450s enhance complex chemical transformations with extreme efficiency and selectivity. Mammalian CYP450s and their redox partners are membrane-anchored proteins, dynamically associating to form functional machineries. Mounting evidence signifies that environmental factors are strictly intertwined with CYP450s catalysis. Atomic-level simulations have the potential to provide insights into the catalytic mechanism of steroidogenic CYP450s and on its regulation by environmental factors, furnishing information often inaccessible to experimental means. In this review, after an introduction of computational methods commonly employed to tackle these systems, we report the current knowledge on three steroidogenic CYP450s—CYP11A1, CYP17A1, and CYP19A1—endowed with multiple catalytic functions and critically involved in cancer onset. In particular, besides discussing their catalytic mechanisms, we highlight how the membrane environment contributes to (i) regulate ligand channeling through these enzymes, (ii) modulate their interactions with specific protein partners, (iii) mediate post-transcriptional regulation induced by phosphorylation. The results presented set the basis for developing novel therapeutic strategies aimed at fighting diseases originating from steroid metabolism dysfunction.
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16
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Zhou P, Chen Y, Lu Q, Qin H, Ou H, He B, Ye J. Cellular metabolism network of Bacillus thuringiensis related to erythromycin stress and degradation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 160:328-341. [PMID: 29857237 DOI: 10.1016/j.ecoenv.2018.05.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/15/2018] [Accepted: 05/20/2018] [Indexed: 06/08/2023]
Abstract
Erythromycin is one of the most widely used macrolide antibiotics. To present a system-level understanding of erythromycin stress and degradation, proteome, phospholipids and membrane potentials were investigated after the erythromycin degradation. Bacillus thuringiensis could effectively remove 77% and degrade 53% of 1 µM erythromycin within 24 h. The 36 up-regulated and 22 down-regulated proteins were mainly involved in spore germination, chaperone and nucleic acid binding. Up-regulated ribose-phosphate pyrophosphokinase and ribosomal proteins confirmed that the synthesis of protein, DNA and RNA were enhanced after the erythromycin degradation. The reaction network of glycolysis/gluconeogenesis was activated, whereas, the activity of spore germination was decreased. The increased synthesis of phospholipids, especially, palmitoleic acid and oleic acid, altered the membrane permeability for erythromycin transport. Ribose-phosphate pyrophosphokinase and palmitoleic acid could be biomarkers to reflect erythromycin exposure. Lipids, disease, pyruvate metabolism and citrate cycle in human cells could be the target pathways influenced by erythromycin. The findings presented novel insights to the interaction among erythromycin stress, protein interaction and metabolism network, and provided a useful protocol for investigating cellular metabolism responses under pollutant stress.
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Affiliation(s)
- Pulin Zhou
- School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China
| | - Ya Chen
- School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China
| | - Qiying Lu
- College of Biology and Food Engineering, Guangdong University of Education, Guangzhou 510303, Guangdong, China
| | - Huaming Qin
- School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China
| | - Huase Ou
- School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China
| | - Baoyan He
- School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China
| | - Jinshao Ye
- School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China.
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17
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Šrejber M, Navrátilová V, Paloncýová M, Bazgier V, Berka K, Anzenbacher P, Otyepka M. Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners. J Inorg Biochem 2018; 183:117-136. [DOI: 10.1016/j.jinorgbio.2018.03.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/16/2018] [Accepted: 03/01/2018] [Indexed: 01/08/2023]
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18
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Ligand Access Channels in Cytochrome P450 Enzymes: A Review. Int J Mol Sci 2018; 19:ijms19061617. [PMID: 29848998 PMCID: PMC6032366 DOI: 10.3390/ijms19061617] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/27/2018] [Accepted: 05/28/2018] [Indexed: 12/22/2022] Open
Abstract
Quantitative structure-activity relationships may bring invaluable information on structural elements of both enzymes and substrates that, together, govern substrate specificity. Buried active sites in cytochrome P450 enzymes are connected to the solvent by a network of channels exiting at the distal surface of the protein. This review presents different in silico tools that were developed to uncover such channels in P450 crystal structures. It also lists some of the experimental evidence that actually suggest that these predicted channels might indeed play a critical role in modulating P450 functions. Amino acid residues at the entrance of the channels may participate to a first global ligand recognition of ligands by P450 enzymes before they reach the buried active site. Moreover, different P450 enzymes show different networks of predicted channels. The plasticity of P450 structures is also important to take into account when looking at how channels might play their role.
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19
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Navrátilová V, Paloncýová M, Berka K, Otyepka M. Effect of Lipid Charge on Membrane Immersion of Cytochrome P450 3A4. J Phys Chem B 2016; 120:11205-11213. [DOI: 10.1021/acs.jpcb.6b10108] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Veronika Navrátilová
- Regional
Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Markéta Paloncýová
- Regional
Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Karel Berka
- Regional
Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional
Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic
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20
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Shoji A, Ikeya K, Aoyagi M, Takatsuji R, Yanagida A, Shibusawa Y, Sugawara M. Monitoring of cholesterol oxidation in a lipid bilayer membrane using streptolysin O as a sensing and signal transduction element. J Pharm Biomed Anal 2016; 128:455-461. [DOI: 10.1016/j.jpba.2016.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/03/2016] [Accepted: 06/07/2016] [Indexed: 11/26/2022]
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21
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Yamada A, Shimizu N, Hikima T, Takata M, Kobayashi T, Takahashi H. Effect of Cholesterol on the Interaction of Cytochrome P450 Substrate Drug Chlorzoxazone with the Phosphatidylcholine Bilayer. Biochemistry 2016; 55:3888-98. [DOI: 10.1021/acs.biochem.6b00286] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ayumi Yamada
- Biophysics
Laboratory, Division of Pure and Applied Science, Graduate School
of Science and Technology, Gunma University, 4-2 Aramaki, Maebashi, Gunma 371-8510, Japan
| | - Nobutaka Shimizu
- Photon
Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Takaaki Hikima
- RIKEN SPring-8 Center, 1-1-1
Kouto, Sayo, Hyougo 679-5148, Japan
| | - Masaki Takata
- RIKEN SPring-8 Center, 1-1-1
Kouto, Sayo, Hyougo 679-5148, Japan
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1
Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Toshihide Kobayashi
- Lipid
Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroshi Takahashi
- Biophysics
Laboratory, Division of Pure and Applied Science, Graduate School
of Science and Technology, Gunma University, 4-2 Aramaki, Maebashi, Gunma 371-8510, Japan
- RIKEN SPring-8 Center, 1-1-1
Kouto, Sayo, Hyougo 679-5148, Japan
- Lipid
Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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22
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Di Meo F, Fabre G, Berka K, Ossman T, Chantemargue B, Paloncýová M, Marquet P, Otyepka M, Trouillas P. In silico pharmacology: Drug membrane partitioning and crossing. Pharmacol Res 2016; 111:471-486. [PMID: 27378566 DOI: 10.1016/j.phrs.2016.06.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/30/2016] [Accepted: 06/30/2016] [Indexed: 01/09/2023]
Abstract
Over the past decade, molecular dynamics (MD) simulations have become particularly powerful to rationalize drug insertion and partitioning in lipid bilayers. MD simulations efficiently support experimental evidences, with a comprehensive understanding of molecular interactions driving insertion and crossing. Prediction of drug partitioning is discussed with respect to drug families (anesthetics; β-blockers; non-steroidal anti-inflammatory drugs; antioxidants; antiviral drugs; antimicrobial peptides). To accurately evaluate passive permeation coefficients turned out to be a complex theoretical challenge; however the recent methodological developments based on biased MD simulations are particularly promising. Particular attention is paid to membrane composition (e.g., presence of cholesterol), which influences drug partitioning and permeation. Recent studies concerning in silico models of membrane proteins involved in drug transport (influx and efflux) are also reported here. These studies have allowed gaining insight in drug efflux by, e.g., ABC transporters at an atomic resolution, explicitly accounting for the mandatory forces induced by the surrounded lipid bilayer. Large-scale conformational changes were thoroughly analyzed.
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Affiliation(s)
- Florent Di Meo
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Gabin Fabre
- LCSN, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Karel Berka
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Tahani Ossman
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Benjamin Chantemargue
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France; Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Markéta Paloncýová
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Pierre Marquet
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France
| | - Michal Otyepka
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic
| | - Patrick Trouillas
- INSERM UMR 850, Univ. Limoges, Faculty of Pharmacy, 2 rue du Dr Marcland, F-87025, Limoges, France; Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky̿ University, Olomouc, Czech Republic.
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23
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Mustafa G, Nandekar PP, Yu X, Wade RC. On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer. J Chem Phys 2015; 143:243139. [DOI: 10.1063/1.4936909] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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