1
|
Fullerenes’ Interactions with Plasma Membranes: Insight from the MD Simulations. Biomolecules 2022; 12:biom12050639. [PMID: 35625567 PMCID: PMC9138838 DOI: 10.3390/biom12050639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 12/04/2022] Open
Abstract
Understanding the interactions between carbon nanoparticles (CNPs) and biological membranes is critically important for applications of CNPs in biomedicine and toxicology. Due to the complexity and diversity of the systems, most molecular simulation studies have focused on the interactions of CNPs and single component bilayers. In this work, we performed coarse-grained molecular dynamic (CGMD) simulations to investigate the behaviors of fullerenes in the presence of multiple lipid components in the plasma membranes with varying fullerene concentrations. Our results reveal that fullerenes can spontaneously penetrate the plasma membrane. Interestingly, fullerenes prefer to locate themselves in the region of the highly unsaturated lipids that are enriched in the inner leaflet of the plasma membrane. This causes fullerene aggregation even at low concentrations. When increasing fullerene concentrations, the fullerene clusters grow, and budding may emerge at the inner leaflet of the plasma membrane. Our findings suggest by tuning the lipid composition, fullerenes can be loaded deeply inside the plasma membrane, which can be useful for designing drug carrier liposomes. Moreover, the mechanisms of how fullerenes perturb multicomponent cell membranes and how they directly enter the cell are proposed. These insights can help to determine fullerene toxicity in living cells.
Collapse
|
2
|
Nanocomposite of Fullerenes and Natural Rubbers: MARTINI Force Field Molecular Dynamics Simulations. Polymers (Basel) 2021; 13:polym13224044. [PMID: 34833344 PMCID: PMC8626026 DOI: 10.3390/polym13224044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
The mechanical properties of natural rubber (NR) composites depend on many factors, including the filler loading, filler size, filler dispersion, and filler-rubber interfacial interactions. Thus, NR composites with nano-sized fillers have attracted a great deal of attention for improving properties such as stiffness, chemical resistance, and high wear resistance. Here, a coarse-grained (CG) model based on the MARTINI force field version 2.1 has been developed and deployed for simulations of cis-1,4-polyisoprene (cis-PI). The model shows qualitative and quantitative agreement with the experiments and atomistic simulations. Interestingly, only a 0.5% difference with respect to the experimental result of the glass transition temperature (Tg) of the cis-PI in the melts was observed. In addition, the mechanical and thermodynamical properties of the cis-PI-fullerene(C60) composites were investigated. Coarse-grained molecular dynamics (MD) simulations of cis-PI-C60 composites with varying fullerene concentrations (0-32 parts per hundred of rubber; phr) were performed over 200 microseconds. The structural, mechanical, and thermal properties of the composites were determined. The density, bulk modulus, thermal expansion, heat capacity, and Tg of the NR composites were found to increase with increasing C60 concentration. The presence of C60 resulted in a slight increasing of the end-to-end distance and radius of the gyration of the cis-PI chains. The contribution of C60 and cis-PI interfacial interactions led to an enhancement of the bulk moduli of the composites. This model should be helpful in the investigations and design of effective fillers of NR-C60 composites for improving their properties.
Collapse
|
3
|
Boonnoy P, Jarerattanachat V, Karttunen M, Wong-Ekkabut J. Role of cholesterol flip-flop in oxidized lipid bilayers. Biophys J 2021; 120:4525-4535. [PMID: 34478697 PMCID: PMC8553637 DOI: 10.1016/j.bpj.2021.08.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 08/13/2021] [Accepted: 08/26/2021] [Indexed: 11/21/2022] Open
Abstract
We performed a series of molecular dynamics simulations of cholesterol (Chol) in nonoxidized 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC) bilayer and in binary mixtures of PLPC-oxidized-lipid-bilayers with 0-50% Chol concentration and oxidized lipids with hydroperoxide and aldehyde oxidized functional groups. From the 60 unbiased molecular dynamics simulations (total of 161 μs), we found that Chol inhibited pore formation in the aldehyde-containing oxidized lipid bilayers at concentrations greater than 11%. For both pure PLPC bilayer and bilayers with hydroperoxide lipids, no pores were observed at any Chol concentration. Furthermore, increasing cholesterol concentration led to a change of phase state from the liquid-disordered to the liquid-ordered phase. This condensing effect of Chol was observed in all systems. Data analysis shows that the addition of Chol results in an increase in bilayer thickness. Interestingly, we observed Chol flip-flop only in the aldehyde-containing lipid bilayer but neither in the PLPC nor the hydroperoxide bilayers. Umbrella-sampling simulations were performed to calculate the translocation free energies and the Chol flip-flop rates. The results show that Chol's flip-flop rate depends on the lipid bilayer type, and the highest rate are found in aldehyde bilayers. As the main finding, we shown that Chol stabilizes the oxidized lipid bilayer by confining the distribution of the oxidized functional groups.
Collapse
Affiliation(s)
- Phansiri Boonnoy
- Department of Physics, Kasetsart University, Bangkok, Thailand; Computational Biomodelling Laboratory for Agricultural Science and Technology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Viwan Jarerattanachat
- Computational Biomodelling Laboratory for Agricultural Science and Technology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Thailand Center of Excellence in Physics, Ministry of Higher Education, Science, Research and Innovation, Bangkok, Thailand; NSTDA Supercomputer Center, National Electronics and Computer Technology Center, National Science and Technology Development Agency, Khlong Luang, Pathumthani, Thailand
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada; Department of Physics and Astronomy, The University of Western Ontario, London, Ontario, Canada; The Centre for Advanced Materials Research, The University of Western Ontario, London, Ontario, Canada
| | - Jirasak Wong-Ekkabut
- Department of Physics, Kasetsart University, Bangkok, Thailand; Computational Biomodelling Laboratory for Agricultural Science and Technology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Thailand Center of Excellence in Physics, Ministry of Higher Education, Science, Research and Innovation, Bangkok, Thailand; Specialized Center of Rubber and Polymer Materials for Agriculture and Industry, Faculty of Science, Kasetsart University, Bangkok, Thailand.
| |
Collapse
|
4
|
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.
Collapse
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;
| |
Collapse
|
5
|
Khuntawee W, Amornloetwattana R, Vongsangnak W, Namdee K, Yata T, Karttunen M, Wong-Ekkabut J. In silico and in vitro design of cordycepin encapsulation in liposomes for colon cancer treatment. RSC Adv 2021; 11:8475-8484. [PMID: 35423402 PMCID: PMC8695206 DOI: 10.1039/d1ra00038a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 02/17/2021] [Indexed: 01/04/2023] Open
Abstract
Cordycepin or 3'-deoxyadenosine is an interesting anti-cancer drug candidate that is found in abundance in the fungus Cordyceps militaris. It inhibits cellular growth of many cancers including lung carcinoma, melanoma, bladder cancer, and colon cancer by inducing apoptosis, anti-proliferation, anti-metastasis and by arresting the cell cycle. Cordycepin has, however, poor stability and low solubility in water, resulting in loss of its bioactivity. Liposomes can be used to overcome these obstacles. Our aim is to improve cordycepin's anti-colon cancer activity by liposome encapsulation. Cordycepin-encapsulated liposomes were designed and fabricated based on a combination of theoretical and experimental studies. Molecular dynamics (MD) simulations and free energy calculations suggest that phosphatidylcholine (PC) lipid environment is favorable for cordycepin adsorption. Cordycepin passively permeates into PC lipid bilayers without membrane damage and strongly binds to the lipids' polar groups by flipping its deoxyribose sugar toward the bilayer center. Our fabricated liposomes containing 10 : 1 molar ratio of egg yolk PC : cholesterol showed encapsulation efficiency (%EE) of 99% using microfluidic hydrodynamic focusing (MHF) methods. In our in vitro study using the HT-29 colon cancer cell line, cordycepin was able to inhibit growth by induction of apoptosis. Cell viability was significantly decreased below 50% at 125 μg mL-1 dosage after 48 h treatment with non-encapsulated and encapsulated cordycepin. Importantly, encapsulation provided (1) a 2-fold improvement in the inhibition of cancer cell growth at 125 μg mL-1 dosage and (2) 4-fold increase in release time. These in silico and in vitro studies indicate that cordycepin-encapsulated liposomes could be a potent drug candidate for colon cancer therapy.
Collapse
Affiliation(s)
- Wasinee Khuntawee
- Department of Physics, Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Thailand Center of Excellence in Physics (ThEP Center), Ministry of Higher Education, Science, Research and Innovation Bangkok 10400 Thailand
| | - Rawiporn Amornloetwattana
- Department of Physics, Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Thailand Center of Excellence in Physics (ThEP Center), Ministry of Higher Education, Science, Research and Innovation Bangkok 10400 Thailand
| | - Wanwipa Vongsangnak
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Department of Zoology, Faculty of Science, Kasetsart University Bangkok 10900 Thailand
| | - Katawut Namdee
- National Nanotechnology Centre (NANOTEC), National Science and Technology Development Agency 111 Thailand Science Park, Paholyothin Rd., Klong Luang Pathumthani 12120 Thailand
| | - Teerapong Yata
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University Bangkok 10330 Thailand
- Natural Products and Nanoparticles Research Unit, Chulalongkorn University Bangkok 10330 Thailand
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario 1151 Richmond Street London Ontario N6A 3K7 Canada
- Department of Applied Mathematics, The University of Western Ontario London ON N6A 5B7 Canada
- The Center for Advanced Materials and Biomaterials Research, The University of Western Ontario London ON N6K 3K7 Canada
| | - Jirasak Wong-Ekkabut
- Department of Physics, Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University Bangkok 10900 Thailand
- Thailand Center of Excellence in Physics (ThEP Center), Ministry of Higher Education, Science, Research and Innovation Bangkok 10400 Thailand
| |
Collapse
|
6
|
Gul G, Ileri-Ercan N. Fullerene translocation through peroxidized lipid membranes. RSC Adv 2021; 11:7575-7586. [PMID: 35423238 PMCID: PMC8694942 DOI: 10.1039/d1ra00272d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Recent cytotoxicity research suggests that fullerenes can enter the cell and cross the blood-brain barrier. However, the underlying toxicity mechanism behind the penetration of fullerenes through biological membranes is still not well understood. Here we perform coarse-grained molecular dynamics simulations to investigate the interactions of fullerenes and their polar derivatives (Janus) with model regular and peroxidized bilayers. We show that the translocation of fullerenes and their residence time in bulk water vary depending on the bilayer's peroxidation degree and fullerene polarity. The distribution of fullerenes inside the bilayer is mainly determined by the peroxidation degree and the saturation level of lipid acyl chains. The transport of pristine fullerenes through bilayers occurs at nano timescale while the complete diffusion may not be achieved for Janus fullerenes in micro timescale. As for the toxic response of fullerenes in terms of membrane damage, no mechanical disruption of model bilayers is observed throughout the studied simulation times.
Collapse
Affiliation(s)
- Gulsah Gul
- Department of Chemical Engineering, Bogazici University Istanbul Turkey
| | - Nazar Ileri-Ercan
- Department of Chemical Engineering, Bogazici University Istanbul Turkey
| |
Collapse
|