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Cao Y, Zhu J, Kou J, Tieleman DP, Liang Q. Unveiling Interactions of Tumor-Targeting Nanoparticles with Lipid Bilayers Using a Titratable Martini Model. J Chem Theory Comput 2024; 20:4045-4053. [PMID: 38648670 DOI: 10.1021/acs.jctc.4c00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
pH-responsive nanoparticles are ideal vehicles for drug delivery and are widely used in cell imaging in targeted therapy of cancer, which usually has a weakly acidic microenvironment. In this work, we constructed a titratable molecular model for nanoparticles grafted with ligands of pH-sensitive carboxylic acids and investigated the interactions between the nanoparticles and the lipid bilayer in varying pH environments. We mainly examined the effect of the grafting density of the pH-sensitive ligands of the nanoparticles on the interactions of the nanoparticles with the lipid bilayer. The results show that the nanoparticles can penetrate the lipid bilayer only when the pH value is lower than a critical value, which can be readily modulated to the specific pH value of the tumor microenvironment by changing the ligand grafting density. This work provides some insights into modulating the interactions between the pH-sensitive nanoparticles and cellular membranes to realize targeted drug delivery to tumors based on their specific pH environment.
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Affiliation(s)
- Yu Cao
- Center for Statistical and Theoretical Condensed Matter Physics & Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Jin Zhu
- Center for Statistical and Theoretical Condensed Matter Physics & Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Jianlong Kou
- Center for Statistical and Theoretical Condensed Matter Physics & Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Science, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics & Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
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2
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Wijesinghe S, Junghans C, Perahia D, Grest GS. Polydots, soft nanoparticles, at membrane interfaces. RSC Adv 2023; 13:19227-19234. [PMID: 37377875 PMCID: PMC10291257 DOI: 10.1039/d3ra02085a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
Soft nanoparticles (NPs) are emerging candidates for nano medicine, particularly for intercellular imaging and targeted drug delivery. Their soft nature, manifested in their dynamics, allows translocation into organisms without damaging their membranes. A crucial step towards incorporating soft dynamic NPs in nano medicine, is to resolve their interrelation with membranes. Here using atomistic molecular dynamics (MD) simulations we probe the interaction of soft NPs formed by conjugated polymers with a model membrane. These NPs, often termed polydots, are confined to their nano dimensions without any chemical tethers, forming dynamic long lived nano structures. Specifically, polydots formed by dialkyl para poly phenylene ethylene (PPE), with a varying number of carboxylate groups tethered to the alkyl chains to tune the interfacial charge of the surface of the NP are investigated at the interface with a model membrane that consists of di-palmitoyl phosphatidylcholine (DPPC). We find that even though polydots are controlled only by physical forces, they retain their NP configuration as they transcend the membrane. Regardless of their size, neutral polydots spontaneously penetrate the membrane whereas carboxylated polydots must be driven in, with a force that depends on the charge at their interface, all without significant disruption to the membrane. These fundamental results provide a means to control the position of the nanoparticles with respect to the membrane interfaces, which is key to their therapeutic use.
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Affiliation(s)
- Sidath Wijesinghe
- Department of Chemistry, Clemson University Clemson South Carolina 29634 USA
| | | | - Dvora Perahia
- Department of Chemistry, Clemson University Clemson South Carolina 29634 USA
| | - Gary S Grest
- Sandia National Laboratories Albuquerque New Mexico 87185 USA
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Macrophage-Targeted Punicalagin Nanoengineering to Alleviate Methotrexate-Induced Neutropenia: A Molecular Docking, DFT, and MD Simulation Analysis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27186034. [PMID: 36144770 PMCID: PMC9505199 DOI: 10.3390/molecules27186034] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/01/2022] [Indexed: 12/05/2022]
Abstract
Punicalagin is the most bioactive pomegranate polyphenol with high antioxidant and free-radical scavenging activity and can potentially cure different ailments related to the cardiovascular system. The current research work was envisioned to predict the targeting efficiency of punicalagin (PG) nanoparticles to the macrophages, more specifically to bone marrow macrophages. For this, we selected mannose-decorated PLGA-punicalagin nanoparticles (Mn-PLGA-PG), and before formulating this nanocarrier in laboratory settings, we predicted the targeting efficiency of this nanocarrier by in silico analysis. The analysis proceeded with macrophage mannose receptors to be acquainted with the binding affinity and punicalagin-based nanocarrier interactions with this receptor. In silico docking studies of macrophage mannose receptors and punicalagin showed binding interactions on its surface. PG interacted with hydrogen bonds to the charged residue ASP668 and GLY666 and polar residue GLN760 of the Mn receptor. Mannose with a docking score of −5.811 Kcal/mol interacted with four hydrogen bonds and the mannose receptor of macrophage, and in PLGA, it showed a −4.334 Kcal/mol docking score. Further, the analysis proceeded with density functional theory analysis (DFT) and HOMO–LUMO analysis, followed by an extensive 100 ns molecular dynamics simulation to analyse the trajectories showing the slightest deviation and fluctuation. While analysing the ligand and protein interaction, a wonderful interaction was found among the atoms of the ligand and protein residues. This computational study confirms that this nanocarrier could be a promising lead molecule to regulate the incidence of drug-induced neutropenia. Furthermore, experimental validation is required before this can be stated with complete confidence or before human use.
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Zhu Y, Sharma A, Spangler EJ, Laradji M. Modes of adhesion of two Janus nanoparticles on the outer or inner side of lipid vesicles. SOFT MATTER 2022; 18:4689-4698. [PMID: 35702934 DOI: 10.1039/d2sm00306f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Using molecular dynamics simulations of a coarse-grained model, in conjunction with the weighted histogram analysis method, the adhesion modes of two spherical Janus nanoparticles (NPs) on the outer or inner side of lipid vesicles are explored. In particular, the effects of the area fraction, J, of the NPs that interact attractively with lipid head groups, the adhesion strength and the size of the NPs on their adhesion modes are investigated. The NPs are found to exhibit two main modes of adhesion when adhered to the outer side of the vesicle. In the first mode, which occurs at relatively low values of J, the NPs are apart from each other. In the second mode, which occurs at higher values of J, the NPs form an in-plane dimer. Janus NPs, which adhere to the inner side of the vesicle, are always found to be apart from each other, regardless of the value of J and their diameter.
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Affiliation(s)
- Yu Zhu
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Abash Sharma
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Eric J Spangler
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Mohamed Laradji
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
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5
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Liu H, Pei Y. Atomistic Molecular Dynamics Simulation Study on the Interaction between Atomically Precise Thiolate-Protected Gold Nanoclusters and Phospholipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1653-1661. [PMID: 35080404 DOI: 10.1021/acs.langmuir.1c02001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The interaction of atomically precise monolayer thiolate (SR) protected gold nanoclusters (Au NCs) with the phospholipid membranes has been studied by the all-atom molecular dynamics (AAMD) simulations. The effect of cluster size, type, and the surface charge density of protection ligand was studied. The simulation results show gold nanoclusters with different size and surface modifications have much different transmembrane behaviors. The Au25(SR)18 cluster was found to possess the best affinity to the phospholipid membranes among six atomically accurate clusters Au25(SR)18, Au36(SR)24, Au44(SR)28, Au68(SR)32, Au144(SR)60, and Au314(SR)96. Using the Au25 NC as a model, this work also found that the aggregation mode of the surface ligands and the surface charge density are the important factors affecting the interaction between the gold nanoclusters and the phospholipid membranes. Moreover, the balance of hydrophilic and hydrophobic ligands on the surface of Au NCs is beneficial to the high permeability.
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Affiliation(s)
- Hengzhi Liu
- Department of Chemistry, Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Xiangtan University, Xiangtan, Hunan Province 411105, China
| | - Yong Pei
- Department of Chemistry, Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Xiangtan University, Xiangtan, Hunan Province 411105, China
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6
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Lin X, Lin X. Designing amphiphilic Janus nanoparticles with tunable lipid raft affinity via molecular dynamics simulation. Biomater Sci 2021; 9:8249-8258. [PMID: 34757373 DOI: 10.1039/d1bm01364e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to the differential interactions among lipids and proteins, the plasma membrane can segregate into a series of functional nanoscale membrane domains ("lipid rafts"), which are essential in multiple biological processes such as signaling transduction, protein trafficking and endocytosis. On the other hand, Janus nanoparticles (NPs) have shown great promise in various biomedical applications due to their asymmetric characteristics and can integrate different surface properties and thus synergetic functions. Hence, in this work, we aim to design an amphiphilic Janus NP to target and regulate lipid rafts via tuning its surface ligand amphiphilicity using coarse-grained molecular dynamics (MD) simulations. Our μs-scale free coarse-grained MD simulations as well as umbrella sampling free energy calculations indicated that the hydrophobicity of the hydrophobic surface ligands not only determined the lateral membrane partitioning thermodynamics of Janus NPs in phase-separated lipid membranes, but also the difficulty in their insertion into different membrane domains of the lipid membrane. These two factors jointly regulated the lipid raft affinity of Janus NPs. Meanwhile, the hydrophilicity of the hydrophilic surface ligands could affect the insertion ability of Janus NPs. Besides, the ultra-small size could ensure the membrane-bound behavior of Janus NPs without disrupting the overall structure and phase separation kinetics of the lipid membrane. These results may provide valuable insights into the design of functional NPs targeting and controllably regulating lipid rafts.
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Affiliation(s)
- Xiaoqian Lin
- Institute of Single Cell Engineering, Key Laboratory of Ministry of Education for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China. .,Shen Yuan Honors College, Beihang University, Beijing 100191, China
| | - Xubo Lin
- Institute of Single Cell Engineering, Key Laboratory of Ministry of Education for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.
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7
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Chen Y, Zhou M, Yang J, Tan Y, Deng W, Xie Q. Tailoring the Photoelectrochemical Activity of Hexametaphosphate-Capped CdS Quantum Dots by Ca 2+-Triggered Surface Charge Regulation: A New Signaling Strategy for Sensitive Immunoassay. Anal Chem 2021; 93:13783-13790. [PMID: 34606246 DOI: 10.1021/acs.analchem.1c02284] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The development of efficient signaling strategies is highly important for photoelectrochemical (PEC) immunoassay. We report here a new and efficient strategy for sensitive PEC immunoassay by tailoring the electrostatic interaction between the photoactive material and the electron donor. The photoelectric conversion of hexametaphosphate (HMP)-capped CdS quantum dots (QDs) in Na2SO3 solution is significantly boosted after Ca2+ incubation. The negative surface charges on CdS@HMP QDs decrease because of the complexation reaction between HMP and Ca2+, and the electrostatic repulsion between CdS@HMP QDs and electron donor (SO32-) becomes weak accordingly, leading to an improved electron-hole separation efficiency. Inspired by the PEC response of CdS@HMP QDs to Ca2+, a novel "signal-on" PEC immunoassay platform is established by employing CaCO3 nanoparticles as labels. By regulating the surface charge of CdS@HMP QDs with in situ-generated Ca2+ from CaCO3 labels, sensitive detection of the carcinoembryonic antigen (CEA) is achieved. The linear detection range is 0.005-50 ng mL-1 and the detection limit is 1 pg mL-1 for CEA detection. Our work not only provides a facile route to tailor the photoelectric conversion but also lays the foundation for sensitive PEC immunoassay by simply regulating the surface charge of photoactive materials.
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Affiliation(s)
- Yanqun Chen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Min Zhou
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Jinhua Yang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Yueming Tan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Wenfang Deng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Qingji Xie
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
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8
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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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9
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Canepa E, Bochicchio D, Gasbarri M, Odino D, Canale C, Ferrando R, Canepa F, Stellacci F, Rossi G, Dante S, Relini A. Cholesterol Hinders the Passive Uptake of Amphiphilic Nanoparticles into Fluid Lipid Membranes. J Phys Chem Lett 2021; 12:8583-8590. [PMID: 34468146 PMCID: PMC8436204 DOI: 10.1021/acs.jpclett.1c02077] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plasma membranes represent pharmacokinetic barriers for the passive transport of site-specific drugs within cells. When engineered nanoparticles (NPs) are considered as transmembrane drug carriers, the plasma membrane composition can affect passive NP internalization in many ways. Among these, cholesterol-regulated membrane fluidity is probably one of the most biologically relevant. Herein, we consider small (2-5 nm in core diameter) amphiphilic gold NPs capable of spontaneously and nondisruptively entering the lipid bilayer of plasma membranes. We study their incorporation into model 1,2-dioleoyl-sn-glycero-3-phosphocholine membranes with increasing cholesterol content. We combine dissipative quartz crystal microbalance experiments, atomic force microscopy, and molecular dynamics simulations to show that membrane cholesterol, at biologically relevant concentrations, hinders the molecular mechanism for passive NP penetration within fluid bilayers, resulting in a dramatic reduction in the amount of NP incorporated.
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Affiliation(s)
- Ester Canepa
- Department
of Chemistry and Industrial Chemistry, University
of Genoa, via Dodecaneso 31, 16146 Genoa, Italy
- Materials
Characterization Facility, Istituto Italiano
di Tecnologia, via Morego 30, 16163 Genoa, Italy
- Department
of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Davide Bochicchio
- Department
of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Matteo Gasbarri
- Institute
of Materials, École Polytechnique
Fédérale de Lausanne, Route Cantonale, 1015 Lausanne, Switzerland
| | - Davide Odino
- Department
of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Claudio Canale
- Department
of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Riccardo Ferrando
- Department
of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Fabio Canepa
- Department
of Chemistry and Industrial Chemistry, University
of Genoa, via Dodecaneso 31, 16146 Genoa, Italy
| | - Francesco Stellacci
- Institute
of Materials, École Polytechnique
Fédérale de Lausanne, Route Cantonale, 1015 Lausanne, Switzerland
| | - Giulia Rossi
- Department
of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Silvia Dante
- Materials
Characterization Facility, Istituto Italiano
di Tecnologia, via Morego 30, 16163 Genoa, Italy
| | - Annalisa Relini
- Department
of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
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10
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Chaudhury A, Varshney GK, Debnath K, Das G, Jana NR, Basu JK. Compressibility of Multicomponent, Charged Model Biomembranes Tunes Permeation of Cationic Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3550-3562. [PMID: 33749276 DOI: 10.1021/acs.langmuir.0c03408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cells respond to external stress by altering their membrane lipid composition to maintain fluidity, integrity and net charge. However, in interactions with charged nanoparticles (NPs), altering membrane charge could adversely affect its ability to transport ions across the cell membrane. Hence, it is important to understand possible pathways by which cells could alter zwitterionic lipid composition to respond to NPs without compromising membrane integrity and charge. Here, we report in situ synchrotron X-ray reflectivity (XR) measurements to monitor the interaction of cationic NPs in the form of quantum dots, with phase-separated supported lipid bilayers of different compositions containing an anionic lipid and zwitterionic lipids having variable degrees of stiffness. We observe that the extent of NP penetration into the respective membranes, as estimated from XR data analysis, is inversely related to membrane compression moduli, which was tuned by altering the stiffness of the zwitterionic lipid component. For a particular membrane composition with a discernible height difference between ordered and disordered phases, we were able to observe subtle correlations between the extent of charge on the NPs and the specificity to bind to the charged and ordered phase, contrary to that observed earlier for phase-separated model biomembranes containing no charged lipids. Our results provide microscopic insight into the role of membrane rigidity and electrostatics in determining membrane permeation. This can lead to great potential benefits in rational designing of NPs for bioimaging and drug delivery applications as well as in assessing and alleviating cytotoxicity of NPs.
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Affiliation(s)
- Anurag Chaudhury
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | | | - Koushik Debnath
- School of Materials Science, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Gangadhar Das
- KEK-High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Nikhil R Jana
- School of Materials Science, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Jaydeep Kumar Basu
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
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11
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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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