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Molecular simulation of zwitterionic polypeptides on protecting glucagon-like peptide-1 (GLP-1). Int J Biol Macromol 2021; 174:519-526. [PMID: 33539961 DOI: 10.1016/j.ijbiomac.2021.01.207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/23/2021] [Accepted: 01/29/2021] [Indexed: 11/23/2022]
Abstract
Owing to their anti-fouling properties, zwitterionic polypeptides demonstrate great advantage on protecting protein drugs. When conjugated to glucagon-like peptide-1 (GLP-1), a drug for type-II diabetes, zwitterionic polypeptides confer better pharmacokinetics than uncharged counterparts. However, its microscopic mechanism is still unclear due to the complicated conformational space. To address this challenge, this work explored the interaction modes of GLP-1 with the unconnected repeat units, instead of the full-length polypeptides. The three repeat units are two zwitterionic pentapeptides VPKEG and VPREG, and one uncharged control VPGAG. Our molecular simulations revealed that the helical conformation of GLP-1 was stabilized by adding 40 polypeptides. Both VPGAG and VPREG formed dense packing shells around GLP-1, but the driving forces were hydrophobic and electrostatic interactions, respectively. In contrast, the packing shell composed of VPKEG was most loose, while could still stabilize GLP-1. The moderate electrostatic interactions endowed VPKEG an anti-fouling property, thereby avoiding non-specific interaction with other amino acids. The strong electrostatic interactions exerted by arginine promoted atomic contacts between VPREG and other residues, making it as "hydrophobic" as VPGAG. In summary, the combination of hydrophobic and moderate electrostatic interactions in VPKEG brings about a subtle balance between stabilizing GLP-1 and avoiding non-specific interaction.
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2
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Bunker A, Róg T. Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery. Front Mol Biosci 2020; 7:604770. [PMID: 33330633 PMCID: PMC7732618 DOI: 10.3389/fmolb.2020.604770] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.
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Affiliation(s)
- Alex Bunker
- Division of Pharmaceutical Biosciences, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, University of Helsinki, Helsinki, Finland
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3
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Lee H. Molecular Simulations of PEGylated Biomolecules, Liposomes, and Nanoparticles for Drug Delivery Applications. Pharmaceutics 2020; 12:E533. [PMID: 32531886 PMCID: PMC7355693 DOI: 10.3390/pharmaceutics12060533] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
Since the first polyethylene glycol (PEG)ylated protein was approved by the FDA in 1990, PEGylation has been successfully applied to develop drug delivery systems through experiments, but these experimental results are not always easy to interpret at the atomic level because of the limited resolution of experimental techniques. To determine the optimal size, structure, and density of PEG for drug delivery, the structure and dynamics of PEGylated drug carriers need to be understood close to the atomic scale, as can be done using molecular dynamics simulations, assuming that these simulations can be validated by successful comparisons to experiments. Starting with the development of all-atom and coarse-grained PEG models in 1990s, PEGylated drug carriers have been widely simulated. In particular, recent advances in computer performance and simulation methodologies have allowed for molecular simulations of large complexes of PEGylated drug carriers interacting with other molecules such as anticancer drugs, plasma proteins, membranes, and receptors, which makes it possible to interpret experimental observations at a nearly atomistic resolution, as well as help in the rational design of drug delivery systems for applications in nanomedicine. Here, simulation studies on the following PEGylated drug topics will be reviewed: proteins and peptides, liposomes, and nanoparticles such as dendrimers and carbon nanotubes.
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Affiliation(s)
- Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin 16890, Korea
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4
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Taylor PA, Jayaraman A. Molecular Modeling and Simulations of Peptide–Polymer Conjugates. Annu Rev Chem Biomol Eng 2020; 11:257-276. [DOI: 10.1146/annurev-chembioeng-092319-083243] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptide–polymer conjugates are a class of soft materials composed of covalently linked blocks of protein/polypeptides and synthetic/natural polymers. These materials are practically useful in biological applications, such as drug delivery, DNA/gene delivery, and antimicrobial coatings, as well as nonbiological applications, such as electronics, separations, optics, and sensing. Given their broad applicability, there is motivation to understand the molecular and macroscale structure, dynamics, and thermodynamic behavior exhibited by such materials. We focus on the past and ongoing molecular simulation studies aimed at obtaining such fundamental understanding and predicting molecular design rules for the target function. We describe briefly the experimental work in this field that validates or motivates these computational studies. We also describe the various models (e.g., atomistic, coarse-grained, or hybrid) and simulation methods (e.g., stochastic versus deterministic, enhanced sampling) that have been used and the types of questions that have been answered using these computational approaches.
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Affiliation(s)
- Phillip A. Taylor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
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5
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Lebrón JA, Ostos FJ, López-López M, Moyá ML, Kardell O, Sánchez A, Carrasco CJ, García-Calderón M, García-Calderón CB, Rosado IV, López-Cornejo P. Preparation and characterization of metallomicelles of Ru(II). Cytotoxic activity and use as vector. Colloids Surf B Biointerfaces 2018; 175:116-125. [PMID: 30529817 DOI: 10.1016/j.colsurfb.2018.11.081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
Abstract
The use of nanovectors in several medicinal treatments has reached a great importance in the last decade. Some drugs need to be protected to increase their lifetimes in the blood flow, to avoid degradation, to be delivered into target cells or to decrease their side effects. The goal of this work was to design and prepare nanovectors formed by novel surfactants derived from the [Ru(bpy)3]2+ complex. These amphiphilic molecules are assembled to form metallomicelles which can act as pharmaceutical agents and, at the same time, as nanovectors for several drugs. TEM images showed a structural transition from spherical to elongated micelles when the surfactant concentration increased. Fluorescence microscopy confirmed the internalization of these metallomicelles into diverse cell lines and cytotoxicity assays demonstrated specificity for some human cancer cells. The encapsulation of various antibiotics was carried out as well as a thorough study about the DNA condensation by the metallomicelles. To the best of our knowledge, applications of these metallomicelles have not been shown in the literature yet.
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Affiliation(s)
- J A Lebrón
- Departamento de Química Física, Facultad de Química, Universidad de Sevilla, c/ Prof. García González nº 1, Seville, 41012, Spain
| | - F J Ostos
- Departamento de Química Física, Facultad de Química, Universidad de Sevilla, c/ Prof. García González nº 1, Seville, 41012, Spain
| | - M López-López
- Departamento de Ingeniería Química, Química Física y Ciencias de los Materiales. Universidad de Huelva. Campus 'El Carmen', Facultad de Ciencias Experimentales, E-21071, Spain
| | - M L Moyá
- Departamento de Química Física, Facultad de Química, Universidad de Sevilla, c/ Prof. García González nº 1, Seville, 41012, Spain
| | - O Kardell
- Departamento de Química Física, Facultad de Química, Universidad de Sevilla, c/ Prof. García González nº 1, Seville, 41012, Spain
| | - A Sánchez
- Departamento de Química Física, Facultad de Química, Universidad de Sevilla, c/ Prof. García González nº 1, Seville, 41012, Spain
| | - C J Carrasco
- Departamento de Química Inorgánica, Facultad de Química, Universidad de Sevilla. Aptdo. 1203, Sevilla, ES, 41071, Spain
| | - M García-Calderón
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, c/ Prof. García González nº 1, Seville, 41012, Spain
| | - C B García-Calderón
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot s/n, 41013, Seville, Spain
| | - I V Rosado
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot s/n, 41013, Seville, Spain
| | - P López-Cornejo
- Departamento de Química Física, Facultad de Química, Universidad de Sevilla, c/ Prof. García González nº 1, Seville, 41012, Spain.
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6
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Mansfield EDH, Hartlieb M, Catrouillet S, Rho JY, Larnaudie SC, Rogers SE, Sanchis J, Brendel JC, Perrier S. Systematic study of the structural parameters affecting the self-assembly of cyclic peptide-poly(ethylene glycol) conjugates. SOFT MATTER 2018; 14:6320-6326. [PMID: 30019044 DOI: 10.1039/c8sm01133h] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Self-assembling cyclic peptides (CP) consisting of amino acids with alternating d- and l-chirality form nanotubes by hydrogen bonding, hydrophobic interactions, and π-π stacking in solution. These highly dynamic materials are emerging as promising supramolecular systems for a wide range of biomedical applications. Herein, we discuss how varying the polymer conformation (linear vs. brush), as well as the number of polymer arms per peptide unimer affects the self-assembly of PEGylated cyclic peptides in different solvents, using small angle neutron scattering. Using the derived information, strong correlations were drawn between the size of the aggregates, solvent polarity, and its ability to compete for hydrogen bonding interactions between the peptide unimers. Using these data, it could be possible to engineer cyclic peptide nanotubes of a controlled length.
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Affiliation(s)
- Edward D H Mansfield
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
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Ma D, Keten S. Stable micelles based on a mixture of coiled-coils: the role of different oligomeric states. NANOSCALE 2018; 10:7589-7596. [PMID: 29637959 DOI: 10.1039/c7nr09695j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Homomeric micelles with tunable size, shape and stability have been extensively studied for biomedical applications such as drug carriers. However, designing the local valency and self-assembled morphology of nanophase-separated multicomponent micelles with varied ligand binding possibilities remains challenging. Here, we present micelles self-assembled from amphiphilic peptide-PEG-lipid hybrid conjugates, where the peptides can be either a 3-helix or 4-helix coiled-coil. We demonstrate that the micelle size and sphericity can be controlled based on the coiled-coil oligomeric state. Using theory and coarse-grained dissipative particle dynamics (DPD) simulations in an explicit solvent simulation, we studied the distribution of 3-helix and 4-helix conjugates within the mixed micelles and observed self-organization into nanodomains within the mixed micelle. We discovered that the phase separation behavior is dictated by the geometry mismatch in the alkyl chain length from different coiled-coil oligomeric states. Our analyses of the self-assembly tendency and drug delivery potency of mixed micelles with controlled multivalency provide important insights into the assembly and formation of nanophase-separated micelles.
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Affiliation(s)
- Dan Ma
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, USA.
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Ang J, Ma D, Jung BT, Keten S, Xu T. Sub-20 nm Stable Micelles Based on a Mixture of Coiled-Coils: A Platform for Controlled Ligand Presentation. Biomacromolecules 2017; 18:3572-3580. [DOI: 10.1021/acs.biomac.7b00917] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- JooChuan Ang
- Department
of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
| | - Dan Ma
- Department
of Civil and Environmental Engineering and Department of Mechanical
Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Benson T. Jung
- Department
of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
| | - Sinan Keten
- Department
of Civil and Environmental Engineering and Department of Mechanical
Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Ting Xu
- Department
of Materials Science and Engineering, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Material
Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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