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Ivánczi M, Balogh B, Kis L, Mándity I. Molecular Dynamics Simulations of Drug-Conjugated Cell-Penetrating Peptides. Pharmaceuticals (Basel) 2023; 16:1251. [PMID: 37765059 PMCID: PMC10535489 DOI: 10.3390/ph16091251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 09/29/2023] Open
Abstract
Cell-penetrating peptides (CPPs) are small peptides capable of translocating through biological membranes carrying various attached cargo into cells and even into the nucleus. They may also participate in transcellular transport. Our in silico study intends to model several peptides and their conjugates. We have selected three CPPs with a linear backbone, including penetratin, a naturally occurring oligopeptide; two of its modified sequence analogues (6,14-Phe-penetratin and dodeca-penetratin); and three natural CPPs with a cyclic backbone: Kalata B1, the Sunflower trypsin inhibitor 1 (SFT1), and Momordica cochinchinensis trypsin inhibitor II (MCoTI-II). We have also built conjugates with the small-molecule drug compounds doxorubicin, zidovudine, and rasagiline for each peptide. Molecular dynamics (MD) simulations were carried out with explicit membrane models. The analysis of the trajectories showed that the interaction of penetratin with the membrane led to spectacular rearrangements in the secondary structure of the peptide, while cyclic peptides remained unchanged due to their high conformational stability. Membrane-peptide and membrane-conjugate interactions have been identified and compared. Taking into account well-known examples from the literature, our simulations demonstrated the utility of computational methods for CPP complexes, and they may contribute to a better understanding of the mechanism of penetration, which could serve as the basis for delivering conjugated drug molecules to their intracellular targets.
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Affiliation(s)
- Márton Ivánczi
- Institute of Organic Chemistry, Semmelweis University, Hőgyes Endre Utca 7., H-1092 Budapest, Hungary (L.K.)
| | - Balázs Balogh
- Institute of Organic Chemistry, Semmelweis University, Hőgyes Endre Utca 7., H-1092 Budapest, Hungary (L.K.)
| | - Loretta Kis
- Institute of Organic Chemistry, Semmelweis University, Hőgyes Endre Utca 7., H-1092 Budapest, Hungary (L.K.)
| | - István Mándity
- Institute of Organic Chemistry, Semmelweis University, Hőgyes Endre Utca 7., H-1092 Budapest, Hungary (L.K.)
- Artificial Transporters Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2., H-1117 Budapest, Hungary
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Ivanova N, Chamati H. The Effect of Cholesterol in SOPC Lipid Bilayers at Low Temperatures. MEMBRANES 2023; 13:275. [PMID: 36984662 PMCID: PMC10058253 DOI: 10.3390/membranes13030275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
We study the behavior of lipid bilayers composed of SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) with different concentrations of cholesterol, ranging from 10 mol% to 50 mol% at 273 K. To this end, we carry out extensive atomistic molecular dynamic simulations with the aid of the Slipid force field aiming at computing basic bilayer parameters, as well as thermodynamic properties and structural characteristics. The obtained results are compared to available relevant experimental data and the outcome of atomistic simulations performed on bilayers composed of analogous phospholipids. Our results show a good quantitative, as well as qualitative, agreement with the main trends associated with the concentration increase in cholesterol. Moreover, it comes out that a change in the behavior of the bilayer is brought about at a concentration of about 30 mol% cholesterol. At this very concentration, some of the bilayer properties are found to exhibit a saturation and a significant long-range ordering of the lipid molecules in the membrane shows up.
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Affiliation(s)
- Nikoleta Ivanova
- Department of Physical Chemistry, University of Chemical Technology and Metallurgy, 8 Kliment Ohridski Blvd., 1756 Sofia, Bulgaria
- Institute of Solid State Physics, Bulgarian Academy of Sciences, 72 Tzarigradsko Chaussee Blvd., 1784 Sofia, Bulgaria
| | - Hassan Chamati
- Institute of Solid State Physics, Bulgarian Academy of Sciences, 72 Tzarigradsko Chaussee Blvd., 1784 Sofia, Bulgaria
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Liang J, Tan P, Hong L, Jin S, Xu Z, Li L. A random batch Ewald method for charged particles in the isothermal-isobaric ensemble. J Chem Phys 2022; 157:144102. [PMID: 36243529 DOI: 10.1063/5.0107140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We develop an accurate, highly efficient, and scalable random batch Ewald (RBE) method to conduct molecular dynamics simulations in the isothermal-isobaric ensemble (the NPT ensemble) for charged particles in a periodic box. After discretizing the Langevin equations of motion derived using suitable Lagrangians, the RBE method builds the mini-batch strategy into the Fourier space in the Ewald summation for the pressure and forces such that the computational cost is reduced to O(N) per time step. We implement the method in the Large-scale Atomic/Molecular Massively Parallel Simulator package and report accurate simulation results for both dynamical quantities and statistics for equilibrium for typical systems including all-atom bulk water and a semi-isotropic membrane system. Numerical simulations on massive supercomputing cluster are also performed to show promising central processing unit efficiency of the RBE.
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Affiliation(s)
- Jiuyang Liang
- School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pan Tan
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Liang Hong
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Shi Jin
- School of Mathematical Sciences, Institute of Natural Sciences and MoE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhenli Xu
- School of Mathematical Sciences, Institute of Natural Sciences and MoE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Li
- School of Mathematical Sciences, Institute of Natural Sciences and MoE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
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Naturally Occurring Genetic Variants in the Oxytocin Receptor Alter Receptor Signaling Profiles. ACS Pharmacol Transl Sci 2021; 4:1543-1555. [PMID: 34661073 PMCID: PMC8506602 DOI: 10.1021/acsptsci.1c00095] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 01/04/2023]
Abstract
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The hormone oxytocin
is commonly administered during childbirth
to initiate and strengthen uterine contractions and prevent postpartum
hemorrhage. However, patients have wide variation in the oxytocin
dose required for a clinical response. To begin to uncover the mechanisms
underlying this variability, we screened the 11 most prevalent missense
genetic variants in the oxytocin receptor (OXTR)
gene. We found that five variants, V45L, P108A, L206V, V281M, and
E339K, significantly altered oxytocin-induced Ca2+ signaling
or β-arrestin recruitment and proceeded to assess the effects
of these variants on OXTR trafficking to the cell membrane, desensitization,
and internalization. The variants P108A and L206V increased OXTR localization
to the cell membrane, whereas V281M and E339K caused OXTR to be retained
inside the cell. We examined how the variants altered the balance
between OXTR activation and desensitization, which is critical for
appropriate oxytocin dosing. The E339K variant impaired OXTR activation,
internalization, and desensitization to roughly equal extents. In
contrast, V281M decreased OXTR activation but had no effect on internalization
and desensitization. V45L and P108A did not alter OXTR activation
but did impair β-arrestin recruitment, internalization, and
desensitization. Molecular dynamics simulations predicted that V45L
and P108A prevent extension of the first intracellular loop of OXTR,
thus inhibiting β-arrestin binding. Overall, our data suggest
mechanisms by which OXTR genetic variants could alter
clinical response to oxytocin.
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Kumar N, Sastry GN. Study of lipid heterogeneity on bilayer membranes using molecular dynamics simulations. J Mol Graph Model 2021; 108:108000. [PMID: 34365255 DOI: 10.1016/j.jmgm.2021.108000] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/17/2021] [Accepted: 07/29/2021] [Indexed: 11/26/2022]
Abstract
Human cell membranes consist of various lipids that are essential for their structure and function. It typically comprises phosphatidylcholine (POPC), phosphatidylethanolamine (POPE), phosphatidylserine (POPS), sphingomyelin (PSM), and cholesterol (CHL). Several experimental and computational techniques have been employed to characterize the composition of human cell membranes, however, CHL enriched membrane is still not clearly understood through these techniques. Molecular dynamics simulation results illustrated the biophysical properties of heterogeneous membranes based on the lipid composition as well as the concentration of lipids, exclusively for CHL and PSM. Herein, we have investigated the structure-function relationships of lipids comparatively to delineate the effect of heterogeneity on the biophysical properties of different membranes. It has been observed that the significant fraction of CHL (i.e., ~33% in ternary, ~25% in quaternary, and ~16% in senary type bilayers) in combination with other lipids introduced compactness, and increased the thickness of the membrane. The analysis of lipid mass density stated that the density of lipid head group, phosphate, and glycerol-ester in presence of CHL with or without PSM is an underlying reason for membrane ordering. Results also revealed that the presence of POPI and POPS are the reasons for an adequate drop in the ordering of lipid chain, particularly on POPE chain. The self-interaction of CHL, PSM, POPE and the interaction of CHL and POPC with POPE seem to determine the structure and function of the heterogeneous membrane. Our findings provide a qualitative understanding of the effect of membrane heterogeneity on the physiological properties of membranes. The structures inspected in this study would help to select the heterogeneous bilayer model to mimic the human cell membranes to analyse or characterize the membrane-associated phenomena.
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Affiliation(s)
- Nandan Kumar
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, Telangana State, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, U. P., India
| | - G Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, Telangana State, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, U. P., India; Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India.
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Ivanova N, Ivanova A. Influence of the dimensionality of the periodic boundary conditions on the transport of a drug-peptide complex across model cell membranes. J Biomol Struct Dyn 2021; 40:5345-5356. [PMID: 33416039 DOI: 10.1080/07391102.2020.1870157] [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: 10/22/2022]
Abstract
Many research efforts are devoted to improving the efficiency of chemotherapy. One of the aspects is to facilitate the transport of drugs across the cell membranes by attaching the therapeutics to a carrier molecule. The current study focuses on computational investigation of such a system with doxorubicin as the model drug, which is covalently bound to a cell-penetrating peptide. The correct description of its membrane translocation at the molecular level requires proper choice of the model membrane and of the simulation parameters. For the purpose, two phospholipid bilayers are built, one containing solely DPPC and another with mixed lipid content mimicking the composition of a human erythrocyte membrane. Atomistic molecular dynamics simulations are carried out in two types of periodic boundary conditions (2D and 3D PBC), in order to assess the effect of the periodicity dimensionality on the intermolecular interactions. The evolution of some basic characteristics of the bilayers and of the drug-peptide complex is tracked: mass density profiles, electrostatic potentials, lateral diffusion coefficients and areas per lipid, lipid-complex radial distribution functions, secondary structure of the peptide and orientation of the drug relative to the membrane. Thus, the influence of the periodic boundary conditions is quantified and it shows that the mixed system in 3D PBC is the most suitable for analysis of the translocation of the transporting moiety across cell membranes.
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Affiliation(s)
- Nikoleta Ivanova
- Department of Physical Chemistry, Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia, Sofia, Bulgaria
| | - Anela Ivanova
- Department of Physical Chemistry, Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia, Sofia, Bulgaria
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Aslanoglu B, Yakavets I, Zorin V, Lassalle HP, Ingrosso F, Monari A, Catak S. Optical properties of photodynamic therapy drugs in different environments: the paradigmatic case of temoporfin. Phys Chem Chem Phys 2020; 22:16956-16964. [PMID: 32672774 DOI: 10.1039/d0cp02055a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Computational tools have been used to study the photophysical and photochemical features of photosensitizers in photodynamic therapy (PDT) - a minimally invasive, less aggressive alternative for cancer treatment. PDT is mainly based on the activation of molecular oxygen through the action of a photoexcited sensitizer (photosensitizer). Temoporfin, widely known as mTHPC, is a second-generation photosensitizer, which produces the cytotoxic singlet oxygen when irradiated with visible light and hence destroys tumor cells. However, the bioavailability of the mostly hydrophobic photosensitizer, and hence its incorporation into cells, is fundamental to achieve the desired effect on malignant tissues via PDT. In this study, we focus on the optical properties of the temoporfin chromophore in different environments -in vacuo, in solution, encapsulated in drug delivery agents, namely cyclodextrin, and interacting with a lipid bilayer.
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Affiliation(s)
- Busenur Aslanoglu
- Bogazici University, Department of Chemistry, Bebek 34342, Istanbul, Turkey.
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Gocheva G, Ivanova N, Iliev S, Petrova J, Madjarova G, Ivanova A. Characteristics of a Folate Receptor-α Anchored into a Multilipid Bilayer Obtained from Atomistic Molecular Dynamics Simulations. J Chem Theory Comput 2019; 16:749-764. [PMID: 31639310 DOI: 10.1021/acs.jctc.9b00872] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Thorough computational description of the properties of membrane-anchored protein receptors, which are important for example in the context of active targeting drug delivery, may be achieved by models representing as close as possible the immediate environment of these macromolecules. An all-atom bilayer, including 35 different lipid types asymmetrically distributed among the two monolayers, is suggested as a model neoplastic cell membrane. One molecule of folate receptor-α (FRα) is anchored into its outer leaflet, and the behavior of the system is explored by atomistic molecular dynamics simulations. The total number of atoms in the model is ∼185 000. Three 1-μs-long simulations are carried out, where physiological conditions (310 K and 1 bar) are maintained with three different pressure scaling schemes. To evaluate the structure and the phase state of the membrane, the density profiles of the system, the average area per lipid, and the deuterium order parameter of the lipid tails are calculated. The bilayer is in liquid ordered state, and the specific arrangement varies between the three trajectories. The changes in the structure of FRα are investigated and are found time- and ensemble-dependent. The volume of the ligand binding pocket fluctuates with time, but this variation remains independent of the more global structural alterations. The latter are mostly "waving" motions of the protein, which periodically approaches and retreats from the membrane. The semi-isotropic pressure scaling perturbs the receptor most significantly, while the isotropic algorithm induces rather slow changes. Maintaining constant nonzero surface tension leads to behavior closest to the experimentally observed one.
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Affiliation(s)
- Gergana Gocheva
- Faculty of Chemistry and Pharmacy, Laboratory of Quantum and Computational Chemistry , Sofia University "St. Kliment Ohridski" , 1 James Bourchier Boulevard , 1164 Sofia , Bulgaria
| | - Nikoleta Ivanova
- Faculty of Chemistry and Pharmacy, Laboratory of Quantum and Computational Chemistry , Sofia University "St. Kliment Ohridski" , 1 James Bourchier Boulevard , 1164 Sofia , Bulgaria
| | - Stoyan Iliev
- Faculty of Chemistry and Pharmacy, Laboratory of Quantum and Computational Chemistry , Sofia University "St. Kliment Ohridski" , 1 James Bourchier Boulevard , 1164 Sofia , Bulgaria
| | - Jasmina Petrova
- Faculty of Chemistry and Pharmacy, Laboratory of Quantum and Computational Chemistry , Sofia University "St. Kliment Ohridski" , 1 James Bourchier Boulevard , 1164 Sofia , Bulgaria
| | - Galia Madjarova
- Faculty of Chemistry and Pharmacy, Laboratory of Quantum and Computational Chemistry , Sofia University "St. Kliment Ohridski" , 1 James Bourchier Boulevard , 1164 Sofia , Bulgaria
| | - Anela Ivanova
- Faculty of Chemistry and Pharmacy, Laboratory of Quantum and Computational Chemistry , Sofia University "St. Kliment Ohridski" , 1 James Bourchier Boulevard , 1164 Sofia , Bulgaria
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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: 46] [Impact Index Per Article: 7.7] [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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Peters BJ, Van Cleave C, Haase AA, Hough JPB, Giffen-Kent KA, Cardiff GM, Sostarecz AG, Crick DC, Crans DC. Structure Dependence of Pyridine and Benzene Derivatives on Interactions with Model Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8939-8951. [PMID: 29958493 PMCID: PMC6106790 DOI: 10.1021/acs.langmuir.8b01661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Pyridine-based small-molecule drugs, vitamins, and cofactors are vital for many cellular processes, but little is known about their interactions with membrane interfaces. These specific membrane interactions of these small molecules or ions can assist in diffusion across membranes or reach a membrane-bound target. This study explores how minor differences in small molecules (isoniazid, benzhydrazide, isonicotinamide, nicotinamide, picolinamide, and benzamide) can affect their interactions with model membranes. Langmuir monolayer studies of dipalmitoylphosphatidylcholine (DPPC) or dipalmitoylphosphatidylethanolamine (DPPE), in the presence of the molecules listed, show that isoniazid and isonicotinamide affect the DPPE monolayer at lower concentrations than the DPPC monolayer, demonstrating a preference for one phospholipid over the other. The Langmuir monolayer studies also suggest that nitrogen content and stereochemistry of the small molecule can affect the phospholipid monolayers differently. To determine the molecular interactions of the simple N-containing aromatic pyridines with a membrane-like interface, 1H one-dimensional NMR and 1H-1H two-dimensional NMR techniques were utilized to obtain information about the position and orientation of the molecules of interest within aerosol-OT (AOT) reverse micelles. These studies show that all six of the molecules reside near the AOT sulfonate headgroups and ester linkages in similar positions, but nicotinamide and picolinamide tilt at the water-AOT interface to varying degrees. Combined, these studies demonstrate that small structural changes of small N-containing molecules can affect their specific interactions with membrane-like interfaces and specificity toward different membrane components.
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Affiliation(s)
| | | | | | | | | | | | - Audra G Sostarecz
- Department of Chemistry , Monmouth College , Monmouth , Illinois 61462 , United States
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