1
|
Halford GC, McDarby SP, Hertle S, Kiely AF, Luu JT, Wang CJ, Personick ML. Troubleshooting the influence of trace chemical impurities on nanoparticle growth kinetics via electrochemical measurements. NANOSCALE 2024; 16:11038-11051. [PMID: 38691093 DOI: 10.1039/d4nr00070f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Reproducibility issues resulting from particle growth solutions made with cetyltrimethylammonium bromide (CTAB) surfactant from different lots and product lines in a newly developed synthesis of monometallic palladium (Pd) tetrahexahedra (THH) nanoparticles are investigated via a multi-pronged approach. Time-resolved electrochemical measurements of solution potential, variation of chemical parameters in colloidal synthesis, and correlation to electrodeposition syntheses are used together to uncover the effects of the unknown contaminants on the chemical reducing environment during nanoparticle growth. Iodide-a known impurity in commercial CTAB-is identified as one of the required components for equalizing the reducing environment across multiple CTAB sources. However, an additional component-acetone-is critical to establishing the growth kinetics necessary to enable the reproducible synthesis of THH in each of the CTAB formulations. In one CTAB variety, the powdered surfactant contains too much acetone, and drying of the as-received surfactant and re-addition of solvent is necessary for successful Pd THH synthesis. The relevance of solvent impurities to the reducing environment in aqueous nanoparticle synthesis is confirmed via electrochemical measurement approaches and solvent addition experiments. This work highlights the utility of real-time electrochemical potential measurements as a tool for benchmarking of nanoparticle syntheses and troubleshooting of reproducibility issues. The results additionally emphasize the importance of considering organic solvent impurities in powdered commercial reagents as a possible shape-determining factor during shaped nanomaterials synthesis.
Collapse
Affiliation(s)
- Gabriel C Halford
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA.
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
| | - Sean P McDarby
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
| | - Sebastian Hertle
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA.
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
| | - Anne F Kiely
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
| | - Jessica T Luu
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
| | - Claire J Wang
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
| | - Michelle L Personick
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA.
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
| |
Collapse
|
2
|
Cantor RS. Kinetic Model of Adsorption of Aqueous Solutes onto Lipid Bilayers: Modulation of the Activity of Membrane Proteins. J Phys Chem B 2023; 127:1598-1606. [PMID: 36763041 DOI: 10.1021/acs.jpcb.2c08714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
It has been argued that membrane proteins that are activated by agonist binding and whose activity depends on conformational transitions are sensitive to membrane adsorption of agonists as well as other solutes such as anesthetics. Ligand-gated ion channels such as GABAAR have been observed electrophysiologically to exhibit remarkable temporal complexity, with multiple time scales of desensitization and deactivation that depend on concentration over a very broad range. Earlier theoretical work was able to predict much of this complexity for GABAAR using a model that incorporates a simple Langmuir approximation of adsorption and desorption of neurotransmitters and solutes such as anesthetics, along with classical modeling of ligand binding and conformational transitions among the three canonical protein states. Here, a simple kinetic model is developed that improves on the Langmuir approach by incorporating the energetics of adsorbate-adsorbate (and adsorbate-bilayer) interactions. Predicted equilibrium isotherms are compared to experimental results, along with the time-course of adsorption/desorption, over a range of values of energetic parameters. Initial predictions of effects of adsorbate energetics on ion current traces involving long and short pulses of agonists show remarkably large effects on the time scale(s) of desensitization and deactivation.
Collapse
Affiliation(s)
- Robert S Cantor
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| |
Collapse
|
3
|
α-Calcium Sulfate Hemihydrate Bioceramic Prepared via Salt Solution Method to Enhance Bone Regenerative Efficiency. J IND ENG CHEM 2022. [DOI: 10.1016/j.jiec.2022.12.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
4
|
The physicochemical properties and contact angle of sodium dodecyl sulfate in water–acetone with and without sodium nitrate (NaNO3). J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
5
|
Small but Mighty-Exosomes, Novel Intercellular Messengers in Neurodegeneration. BIOLOGY 2022; 11:biology11030413. [PMID: 35336787 PMCID: PMC8945199 DOI: 10.3390/biology11030413] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/27/2022] [Accepted: 03/04/2022] [Indexed: 01/27/2023]
Abstract
Simple Summary Exosomes are biological nanoparticles recently recognized as intercellular messengers. They contain a cargo of lipids, proteins, and RNA. They can transfer their content to not only cells in the vicinity but also to cells at a distance. This unique ability empowers them to modulate the physiology of recipient cells. In brain, exosomes play a role in neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease and amyotrophic lateral sclerosis. Abstract Exosomes of endosomal origin are one class of extracellular vesicles that are important in intercellular communication. Exosomes are released by all cells in our body and their cargo consisting of lipids, proteins and nucleic acids has a footprint reflective of their parental origin. The exosomal cargo has the power to modulate the physiology of recipient cells in the vicinity of the releasing cells or cells at a distance. Harnessing the potential of exosomes relies upon the purity of exosome preparation. Hence, many methods for isolation have been developed and we provide a succinct summary of several methods. In spite of the seclusion imposed by the blood–brain barrier, cells in the CNS are not immune from exosomal intrusive influences. Both neurons and glia release exosomes, often in an activity-dependent manner. A brief description of exosomes released by different cells in the brain and their role in maintaining CNS homeostasis is provided. The hallmark of several neurodegenerative diseases is the accumulation of protein aggregates. Recent studies implicate exosomes’ intercellular communicator role in the spread of misfolded proteins aiding the propagation of pathology. In this review, we discuss the potential contributions made by exosomes in progression of Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis. Understanding contributions made by exosomes in pathogenesis of neurodegeneration opens the field for employing exosomes as therapeutic agents for drug delivery to brain since exosomes do cross the blood–brain barrier.
Collapse
|
6
|
Modelling the transport mechanism of organic molecules into cell membranes: The role of organic solvents. Comput Biol Chem 2022; 98:107663. [DOI: 10.1016/j.compbiolchem.2022.107663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 11/19/2022]
|
7
|
Inci F. Benchmarking a Microfluidic-Based Filtration for Isolating Biological Particles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1897-1909. [PMID: 35041413 DOI: 10.1021/acs.langmuir.1c03119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Isolating particles from complex fluids is a crucial approach in multiple fields including biomedicine. In particular, biological matrices contain a myriad of distinct particles with different sizes and structures. Extracellular vesicles (EVs), for instance, are nanosized particles carrying vital information from donor to recipient cells, and they have garnered significant impact on disease diagnostics, drug delivery, and theranostics applications. Among all the EV types, exosome particles are one of the smallest entities, sizing from 30 to 100 nm. Separating such small substances from a complex media such as tissue culture and serum is still one of the most challenging steps in this field. Membrane filtration is one of the convenient approaches for these operations; yet clogging, low-recovery, and high fouling are still major obstacles. In this study, we design a two-filter-integrated microfluidic device focusing on dead-end and cross-flow processes at the same time, thereby minimizing any interfering factors on the recovery. The design of this platform is also numerically assessed to understand pressure-drop and flow rate effects over the procedure. As a model, we isolate exosome particles from human embryonic kidney cells cultured in different conditions, which also mimic complex fluids such as serum. Moreover, by altering the flow direction, we refresh the membranes for minimizing clogging issues and benchmark the platform performance for multitime use. By comprehensively analyzing the design and operation parameters of this platform, we address the aforementioned existing barriers in the recovery, clogging, and fouling factors, thereby achieving the use of a microfluidic device multiple times for bio-nanoparticle isolation without any notable issues.
Collapse
Affiliation(s)
- Fatih Inci
- UNAM - National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| |
Collapse
|
8
|
Egan-Morriss C, Kimber RL, Powell NA, Lloyd JR. Biotechnological synthesis of Pd-based nanoparticle catalysts. NANOSCALE ADVANCES 2022; 4:654-679. [PMID: 35224444 PMCID: PMC8805459 DOI: 10.1039/d1na00686j] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/22/2021] [Indexed: 06/02/2023]
Abstract
Palladium metal nanoparticles are excellent catalysts used industrially for reactions such as hydrogenation and Heck and Suzuki C-C coupling reactions. However, the global demand for Pd far exceeds global supply, therefore the sustainable use and recycling of Pd is vital. Conventional chemical synthesis routes of Pd metal nanoparticles do not meet sustainability targets due to the use of toxic chemicals, such as organic solvents and capping agents. Microbes are capable of bioreducing soluble high oxidation state metal ions to form metal nanoparticles at ambient temperature and pressure, without the need for toxic chemicals. Microbes can also reduce metal from waste solutions, revalorising these waste streams and allowing the reuse of precious metals. Pd nanoparticles supported on microbial cells (bio-Pd) can catalyse a wide array of reactions, even outperforming commercial heterogeneous Pd catalysts in several studies. However, to be considered a viable commercial option, the intrinsic activity and selectivity of bio-Pd must be enhanced. Many types of microorganisms can produce bio-Pd, although most studies so far have been performed using bacteria, with metal reduction mediated by hydrogenase or formate dehydrogenase enzymes. Dissimilatory metal-reducing bacteria (DMRB) possess additional enzymes adapted for extracellular electron transport that potentially offer greater control over the properties of the nanoparticles produced. A recent and important addition to the field are bio-bimetallic nanoparticles, which significantly enhance the catalytic properties of bio-Pd. In addition, systems biology can integrate bio-Pd into biocatalytic processes, and processing techniques may enhance the catalytic properties further, such as incorporating additional functional nanomaterials. This review aims to highlight aspects of enzymatic metal reduction processes that can be bioengineered to control the size, shape, and cellular location of bio-Pd in order to optimise its catalytic properties.
Collapse
Affiliation(s)
- Christopher Egan-Morriss
- Department of Earth and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science, University of Manchester UK
| | - Richard L Kimber
- Department of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna 1090 Vienna Austria
| | | | - Jonathan R Lloyd
- Department of Earth and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science, University of Manchester UK
| |
Collapse
|
9
|
Chau THT, Nguyen AD, Lee EY. Boosting the acetol production in methanotrophic biocatalyst Methylomonas sp. DH-1 by the coupling activity of heteroexpressed novel protein PmoD with endogenous particulate methane monooxygenase. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:7. [PMID: 35418298 PMCID: PMC8764830 DOI: 10.1186/s13068-022-02105-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/04/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Methylacidiphilum sp. IT6 has been validated its C3 substrate assimilation pathway via acetol as a key intermediate using the PmoCAB3, a homolog of the particulate methane monooxygenase (pMMO). From the transcriptomic data, the contribution of PmoD of strain IT6 in acetone oxidation was questioned. Methylomonas sp. DH-1, a type I methanotroph containing pmo operon without the existence of its pmoD, has been deployed as a biocatalyst for the gas-to-liquid bioconversion of methane and propane to methanol and acetone. Thus, Methylomonas sp. DH-1 is a suitable host for investigation. The PmoD-expressed Methylomonas sp. DH-1 can also be deployed for acetol production, a well-known intermediate for various industrial applications. Microbial production of acetol is a sustainable approach attracted attention so far. RESULTS In this study, bioinformatics analyses elucidated that novel protein PmoD is a C-terminal transmembrane-helix membrane with the proposed function as a transport protein. Furthermore, the whole-cell biocatalyst was constructed in Methylomonas sp. DH-1 by co-expression the PmoD of Methylacidiphilum sp. IT6 with the endogenous pMMO to enable acetone oxidation. Under optimal conditions, the maximum accumulation, and specific productivity of acetol were 18.291 mM (1.35 g/L) and 0.317 mmol/g cell/h, respectively. The results showed the first coupling activity of pMMO with a heterologous protein PmoD, validated the involvement of PmoD in acetone oxidation, and demonstrated an unprecedented production of acetol from acetone in type I methanotrophic biocatalyst. From the data achieved in batch cultivation conditions, an assimilation pathway of acetone via acetol as the key intermediate was also proposed. CONCLUSION Using bioinformatics tools, the protein PmoD has been elucidated as the membrane protein with the proposed function as a transport protein. Furthermore, results from the assays of PmoD-heteroexpressed Methylomonas sp. DH-1 as a whole-cell biocatalyst validated the coupling activity of PmoD with pMMO to convert acetone to acetol, which also unlocks the potential of this recombinant biocatalyst for acetol production. The proposed acetone-assimilated pathway in the recombinant Methylomonas sp. DH-1, once validated, can extend the metabolic flexibility of Methylomonas sp. DH-1.
Collapse
Affiliation(s)
- Tin Hoang Trung Chau
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 17104, Yongin-si, Gyeonggi-do, South Korea
| | - Anh Duc Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 17104, Yongin-si, Gyeonggi-do, South Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 17104, Yongin-si, Gyeonggi-do, South Korea.
| |
Collapse
|
10
|
Ciancetta A, Gill AK, Ding T, Karlov DS, Chalhoub G, McCormick PJ, Tikhonova IG. Probe Confined Dynamic Mapping for G Protein-Coupled Receptor Allosteric Site Prediction. ACS CENTRAL SCIENCE 2021; 7:1847-1862. [PMID: 34841058 PMCID: PMC8614102 DOI: 10.1021/acscentsci.1c00802] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Indexed: 05/06/2023]
Abstract
Targeting G protein-coupled receptors (GPCRs) through allosteric sites offers advantages over orthosteric sites in identifying drugs with increased selectivity and potentially reduced side effects. In this study, we developed a probe confined dynamic mapping protocol that allows the prediction of allosteric sites at both the GPCR extracellular and intracellular sides, as well as at the receptor-lipid interface. The applied harmonic wall potential enhanced sampling of probe molecules in a selected area of a GPCR while preventing membrane distortion in molecular dynamics simulations. The specific probes derived from GPCR allosteric ligand structures performed better in allosteric site mapping compared to commonly used cosolvents. The M2 muscarinic, β2 adrenergic, and P2Y1 purinergic receptors were selected for the protocol's retrospective validation. The protocol was next validated prospectively to locate the binding site of [5-fluoro-4-(hydroxymethyl)-2-methoxyphenyl]-(4-fluoro-1H-indol-1-yl)methanone at the D2 dopamine receptor, and subsequent mutagenesis confirmed the prediction. The protocol provides fast and efficient prediction of key amino acid residues surrounding allosteric sites in membrane proteins and facilitates the structure-based design of allosteric modulators.
Collapse
Affiliation(s)
- Antonella Ciancetta
- School
of Pharmacy, Medical Biology Centre, Queen’s
University Belfast, Belfast, Northern Ireland BT9 7BL, U.K.
| | - Amandeep Kaur Gill
- Centre
for Endocrinology, William Harvey Research Institute, Bart’s
and the London School of Medicine and Dentistry, Queen
Mary, University of London, London, EC1M 6BQ, U.K.
| | - Tianyi Ding
- School
of Pharmacy, Medical Biology Centre, Queen’s
University Belfast, Belfast, Northern Ireland BT9 7BL, U.K.
| | - Dmitry S. Karlov
- School
of Pharmacy, Medical Biology Centre, Queen’s
University Belfast, Belfast, Northern Ireland BT9 7BL, U.K.
| | - George Chalhoub
- Centre
for Endocrinology, William Harvey Research Institute, Bart’s
and the London School of Medicine and Dentistry, Queen
Mary, University of London, London, EC1M 6BQ, U.K.
| | - Peter J. McCormick
- Centre
for Endocrinology, William Harvey Research Institute, Bart’s
and the London School of Medicine and Dentistry, Queen
Mary, University of London, London, EC1M 6BQ, U.K.
| | - Irina G. Tikhonova
- School
of Pharmacy, Medical Biology Centre, Queen’s
University Belfast, Belfast, Northern Ireland BT9 7BL, U.K.
| |
Collapse
|
11
|
Bacterial Resistance against Heavy Metals in Pseudomonas aeruginosa RW9 Involving Hexavalent Chromium Removal. SUSTAINABILITY 2021. [DOI: 10.3390/su13179797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Pseudomonas aeruginosa RW9 is a promising candidate for the bioremediation of chromium hexavalent (Cr(VI)) pollution, as it resists a high concentration of up to 60 mg/L of Cr(VI). Leaving cells exposed to Cr(VI) has large bioreduction potential, implying its capacity to extract the ions from the contaminated medium. In this study, the tolerance for and distribution of Cr(VI) were investigated to identify the cells’ adaptation and removal strategies. Micro-characterization analysis was conducted to assess the effect of Cr(VI) on the cells. The cells’ elongation was observed at higher Cr(VI) concentrations, signifying their adaptation to DNA damage caused by Cr(VI) toxicity. Cr(VI) distribution analysis showed that the strain developed a complex mechanism to adapt to Cr(VI), based on surface-bound (0.46 mg/L), intracellularly accumulated (1.24 mg/L) and extracellular sequestration (6.74 mg/L), which accounted for 85% of the removal efficiency. The extracellular sequestration might be attributable to the production of metabolites, in accordance with the fourier-transform infrared spectroscopy (FTIR) spectra and orcinol analysis that confirmed the presence of a glycolipid biosurfactant, rhamnolipid. Remarkably, the rhamnolipid was slightly induced in the presence of Cr(VI). From the data obtained, it was confirmed that this local strain is well equipped to survive high doses of Cr(VI) and has great potential for application in Cr(VI) bioremediation.
Collapse
|
12
|
Shirejini SZ, Inci F. The Yin and Yang of exosome isolation methods: conventional practice, microfluidics, and commercial kits. Biotechnol Adv 2021; 54:107814. [PMID: 34389465 DOI: 10.1016/j.biotechadv.2021.107814] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/08/2021] [Accepted: 08/08/2021] [Indexed: 12/18/2022]
Abstract
Exosomes are a subset of extracellular vesicles released from various cells, and they can be found in different bodily fluids. Exosomes are used as biomarkers to diagnose many diseases and to monitor therapy efficiency as they represent the status and origin of the cell, which they are released from. Considering that they co-exist in bodily fluids with other types of particles, their isolation still remains challenging since conventional separation methods are time-consuming, user-dependent, and result in low isolation yield. This review summarizes the conventional strategies and microfluidic-based methods for exosome isolation along with their strengths and limitations. Microfluidic devices emerge as a promising approach to overcome the limitations of the conventional methods due to their inherent characteristics, such as the need for minute sample volume and rapid operation, in order to isolate exosomes with a high yield and a high purity in a short amount of time, which make them unprecedented tools for molecular biology and clinical applications. This review elaborates on the existing microfluidic-based exosome isolation methods and denotes their benefits and drawbacks. Herein, we also introduce various commercially available platforms and kits for exosome isolation along with their working principles.
Collapse
Affiliation(s)
- Saeedreza Zeibi Shirejini
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Fatih Inci
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey.
| |
Collapse
|
13
|
Hayashi Y, Nakajima Y, Sugiyama H. Computational screening of cryoprotective agents for regenerative medical products using quantum chemistry and molecular dynamics simulations. Cryobiology 2021; 100:101-109. [PMID: 33766526 DOI: 10.1016/j.cryobiol.2021.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 12/26/2022]
Abstract
Cryoprotective agents (CPAs) are essential for the cryopreservation of cells. Thus far, dimethyl sulfoxide (DMSO) has been widely used as a CPA; however, DMSO is known to be toxic to cells. The damaged cells by the toxicity can present abnormal conditions, and should not be used for regenerative medical products because the cells/products are implanted directly into human bodies. With the aim of searching for an alternative CPA to DMSO, this work presents a computational screening of CPA candidate compounds using quantum chemistry and molecular dynamics (MD) simulations. Forty compounds were evaluated in regard to the solvation free energy and partition coefficient by quantum chemistry simulation and the root mean square deviation (RMSD) of a phospholipid bilayer which composes a cell membrane by MD simulation. The solvation free energy, partition coefficient, and RMSD were defined as indicators of osmoregulatory ability, affinity with a cell membrane, and ability to spread a cell membrane, respectively. The quantum chemistry simulation elucidated that the six compounds of trimethylglycine, formamide, urea, thiourea, diethylene glycol, and dulcitol were better than DMSO in either or both of the physical properties considered. This finding is based on the inherent physical property and is thus case-independent. Further characterization with the MD simulation suggested that formamide, thiourea, and urea should be the first candidates to investigate, although the result was valid only in the simulated condition. This work serves as the first step of multi-faceted computational evaluation of multiple compounds in the search for an effective CPA compound after DMSO.
Collapse
Affiliation(s)
- Yusuke Hayashi
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656, Tokyo, Japan
| | - Yuka Nakajima
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656, Tokyo, Japan
| | - Hirokazu Sugiyama
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656, Tokyo, Japan.
| |
Collapse
|
14
|
Straub CT, Bing RG, Otten JK, Keller LM, Zeldes BM, Adams MWW, Kelly RM. Metabolically engineered Caldicellulosiruptor bescii as a platform for producing acetone and hydrogen from lignocellulose. Biotechnol Bioeng 2020; 117:3799-3808. [PMID: 32770740 DOI: 10.1002/bit.27529] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/12/2020] [Accepted: 08/05/2020] [Indexed: 11/10/2022]
Abstract
The production of volatile industrial chemicals utilizing metabolically engineered extreme thermophiles offers the potential for processes with simultaneous fermentation and product separation. An excellent target chemical for such a process is acetone (Tb = 56°C), ideally produced from lignocellulosic biomass. Caldicellulosiruptor bescii (Topt 78°C), an extremely thermophilic fermentative bacterium naturally capable of deconstructing and fermenting lignocellulose, was metabolically engineered to produce acetone. When the acetone pathway construct was integrated into a parent strain containing the bifunctional alcohol dehydrogenase from Clostridium thermocellum, acetone was produced at 9.1 mM (0.53 g/L), in addition to minimal ethanol 3.3 mM (0.15 g/L), along with net acetate consumption. This demonstrates that C. bescii can be engineered with balanced pathways in which renewable carbohydrate sources are converted to useful metabolites, primarily acetone and H2 , without net production of its native fermentation products, acetate and lactate.
Collapse
Affiliation(s)
- Christopher T Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Ryan G Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Jonathan K Otten
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Lisa M Keller
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| |
Collapse
|
15
|
Can ethanol affect the cell structure? A dynamic molecular and Raman spectroscopy study. Photodiagnosis Photodyn Ther 2020; 30:101675. [PMID: 31991233 DOI: 10.1016/j.pdpdt.2020.101675] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/27/2019] [Accepted: 01/24/2020] [Indexed: 11/24/2022]
Abstract
The role that tobacco consumption plays in the etiology of oral cancer carcinogenesis, and of alcohol consumption acting as a co-factor, have been well established. However, in recent years, the contribution of alcohol consumption alone to oral cancer has been proposed. In fact, a high percentage of patients who develop oral cancer have both habits (tobacco and alcohol consumption), and other small patient groups only consume alcohol or do not have any other identifiable bad habits. In the present study we demonstrate, using a combination of dynamic molecular modelling and Raman spectroscopy, that ethanol has a significant effect on oral cells in vitro, mainly interacting with the lipids of the cell membrane, changing their conformation. Thus, it is possible to conclude that ethanol can affect the cell permeability, and by consequence serve as a possible trigger in oral carcinogenesis.
Collapse
|
16
|
Susceptibility of biomembrane structure towards amphiphiles, ionic liquids, and deep eutectic solvents. ADVANCES IN BIOMEMBRANES AND LIPID SELF-ASSEMBLY 2020. [DOI: 10.1016/bs.abl.2020.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
17
|
The effect of organic solvents on selected microorganisms and model liposome membrane. Mol Biol Rep 2019; 46:3225-3232. [PMID: 30937654 DOI: 10.1007/s11033-019-04782-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/21/2019] [Indexed: 12/19/2022]
Abstract
The effect of methanol, ethanol, acetone, N,N-dimethylformamide (DMF), dimethyl sulfoxide and Nujol on the growth of Escherichia coli DH5α, Bacillus subtilis and Saccharomyces cerevisiae D273 was investigated. All of the tested cultures appeared susceptible to the organic media they were treated with, which evinced in apparent hindering of cell development. The observed diverse solvent tolerance, except from their different biochemical activity, may also be related to the changes in cell membrane fluidity induced by the solvent species. Parallel electron paramagnetic resonance investigations using egg yolk lecithin model liposomes revealed that the fluidity of the phospholipid system in cell membranes may either be considerably decreased (Nujol, DMF, ethanol) or increased (acetone), thus rendering difficult the intracellular nutrient supply. Hence, even the chemically neutral Nujol produced a distinct cell-growth inhibitory effect. These results are fairly consistent with the outcome of the survival tests, particularly for the bacteria strains.
Collapse
|
18
|
Zhang Y, Mao Z, Wang B, Zhang J, Lu N, Hong R, Dong S, Yao C, Liu QH. Enhanced Antitumor Efficacy Achieved Through Combination of nsPEFs and Low-Dosage Paclitaxel. IEEE Trans Biomed Eng 2019; 66:3129-3135. [PMID: 30794505 DOI: 10.1109/tbme.2019.2900720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Looking for a safe and effective cancer therapy for patients is becoming an important and promising research direction. Nanosecond pulsed electric field (nsPEF) has been found to be a potential non-thermal therapeutic technique with few side effects in pre-clinical studies. On the other hand, paclitaxel (PTX), as a common chemotherapeutic agent, shows full anti-tumor activities and is used to treat a wide variety of cancers. However, the delivery of PTX is challenging due to its poor aqueous solubility. Hence, high dosages of PTX have been used to achieve effective treatment, which creates some side effects. In this study, nsPEF was combined with low-level PTX, in order to validate if this combined treatment could bring about enhanced efficacy and allow reduced doses of PTX in clinical application. Cell proliferation, apoptosis, and cell cycle distribution were examined using MTT and flow cytometry assay, respectively. Results showed that combination treatments of nsPEF and PTX exhibited significant synergistic effects in vitro. The underlying mechanism might be that these two agents acted at different targets and coordinately enhanced MDA-MB-231 cell death.
Collapse
|
19
|
Pham-Hoang BN, Romero-Guido C, Phan-Thi H, Waché Y. Strategies to improve carotene entry into cells of Yarrowia lipolytica in a goal of encapsulation. J FOOD ENG 2018. [DOI: 10.1016/j.jfoodeng.2017.12.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
20
|
Kumari P, Kaur S, Sharma S, Kashyap HK. Impact of amphiphilic molecules on the structure and stability of homogeneous sphingomyelin bilayer: Insights from atomistic simulations. J Chem Phys 2018; 148:165102. [DOI: 10.1063/1.5021310] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Pratibha Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Supreet Kaur
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shobha Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| |
Collapse
|
21
|
Location of fluorescent probes (2′-hydroxy derivatives of 2,5-diaryl-1,3-oxazole) in lipid membrane studied by fluorescence spectroscopy and molecular dynamics simulation. Biophys Chem 2018; 235:9-18. [DOI: 10.1016/j.bpc.2018.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 11/20/2022]
|
22
|
Derivatives of 2,5-Diaryl-1,3-Oxazole and 2,5-Diaryl-1,3,4-Oxadiazole as Environment-Sensitive Fluorescent Probes for Studies of Biological Membranes. REVIEWS IN FLUORESCENCE 2017 2018. [DOI: 10.1007/978-3-030-01569-5_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
23
|
White BE, Fenner CJ, Smit MS, Harrison STL. Effect of cell permeability and dehydrogenase expression on octane activation by CYP153A6-based whole cell Escherichia coli catalysts. Microb Cell Fact 2017; 16:156. [PMID: 28931395 PMCID: PMC5607502 DOI: 10.1186/s12934-017-0763-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 09/07/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The regeneration of cofactors and the supply of alkane substrate are key considerations for the biocatalytic activation of hydrocarbons by cytochrome P450s. This study focused on the biotransformation of n-octane to 1-octanol using resting Escherichia coli cells expressing the CYP153A6 operon, which includes the electron transport proteins ferredoxin and ferredoxin reductase. Glycerol dehydrogenase was co-expressed with the CYP153A6 operon to investigate the effects of boosting cofactor regeneration. In order to overcome the alkane supply bottleneck, various chemical and physical approaches to membrane permeabilisation were tested in strains with or without additional dehydrogenase expression. RESULTS Dehydrogenase co-expression in whole cells did not improve product formation and reduced the stability of the system at high cell densities. Chemical permeabilisation resulted in initial hydroxylation rates that were up to two times higher than the whole cell system, but severely impacted biocatalyst stability. Mechanical cell breakage led to improved enzyme stability, but additional dehydrogenase expression was necessary to improve product formation. The best-performing system (in terms of final titres) consisted of mechanically ruptured cells expressing additional dehydrogenase. This system had an initial activity of 1.67 ± 0.12 U/gDCW (32% improvement on whole cells) and attained a product concentration of 34.8 ± 1.6 mM after 24 h (22% improvement on whole cells). Furthermore, the system was able to maintain activity when biotransformation was extended to 72 h, resulting in a final product titre of 60.9 ± 1.1 mM. CONCLUSIONS This study suggests that CYP153A6 in whole cells is limited by coupling efficiencies rather than cofactor supply. However, the most significant limitation in the current system is hydrocarbon transport, with substrate import being the main determinant of hydroxylation rates, and product export playing a key role in system stability.
Collapse
Affiliation(s)
- Bronwyn E White
- Centre for Bioprocess Engineering Research (CeBER), Department of Chemical Engineering, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa.,South African DST-NRF Centre of Excellence in Catalysis, c*change, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Caryn J Fenner
- Centre for Bioprocess Engineering Research (CeBER), Department of Chemical Engineering, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa.,South African DST-NRF Centre of Excellence in Catalysis, c*change, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Martha S Smit
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa.,South African DST-NRF Centre of Excellence in Catalysis, c*change, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Susan T L Harrison
- Centre for Bioprocess Engineering Research (CeBER), Department of Chemical Engineering, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa. .,South African DST-NRF Centre of Excellence in Catalysis, c*change, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa.
| |
Collapse
|
24
|
Size-Exclusion Chromatography-based isolation minimally alters Extracellular Vesicles' characteristics compared to precipitating agents. Sci Rep 2016; 6:33641. [PMID: 27640641 PMCID: PMC5027519 DOI: 10.1038/srep33641] [Citation(s) in RCA: 357] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/01/2016] [Indexed: 12/18/2022] Open
Abstract
Extracellular vesicles (EVs) have become an attractive field among the scientific community. Yet, a major challenge is to define a consensus method for EVs isolation. Ultracentrifugation has been the most widely used methodology but rapid methods, including Size Exclusion Chromatography (SEC) and/or precipitating agents such as Polyethylene glycol (PEG) or PRotein Organic Solvent PRecipitation (PROSPR) have emerged. To evaluate the impact of these different methods on the resulting EV preparations, plasma EVs were isolated using SEC, PEG and PROSPR, and their total protein content, NTA and Cryo-electron microscopy profiles, and EV-markers were compared. Also, their effect on recipient cells was tested. Low protein content and Cryo-EM analysis showed that SEC removed most of the overabundant soluble plasma proteins, which were not removed using PEG and partially by PROSPR. Moreover, only SEC allowed the detection of the EV-markers CD9, CD63 and CD81, LGALS3BP and CD5L, suggesting a putative interference of the precipitating agents in the structure/composition of the EVs. Furthermore, PEG and PROSPR-based EV isolation resulted in reduced cell viability in vitro. These results stress that appropriate EV-isolation method should be considered depending on the forthcoming application of the purified EVs.
Collapse
|
25
|
Posokhov Y. Fluorescent probes sensitive to changes in the cholesterol-to-phospholipids molar ratio in human platelet membranes during atherosclerosis. Methods Appl Fluoresc 2016; 4:034013. [PMID: 28355159 DOI: 10.1088/2050-6120/4/3/034013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Environment-sensitive fluorescent probes were used for the spectroscopic visualization of pathological changes in human platelet membranes during cerebral atherosclerosis. It has been estimated that the ratiometric probes 2-(2'-hydroxyphenyl)-5-phenyl-1,3,4-oxadiazole and 2-phenyl-phenanthr[9,10]oxazole can detect changes in the cholesterol-to-phospholipids molar ratio in human platelet membranes during the disease.
Collapse
Affiliation(s)
- Yevgen Posokhov
- Institute of Chemistry, V.N. Karazin Kharkiv National University, Kharkiv 61022, Ukraine
| |
Collapse
|
26
|
Cao Z, Voth GA. The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites. J Chem Phys 2016; 143:243116. [PMID: 26723601 DOI: 10.1063/1.4933249] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
It is essential to be able to systematically construct coarse-grained (CG) models that can efficiently and accurately reproduce key properties of higher-resolution models such as all-atom. To fulfill this goal, a mapping operator is needed to transform the higher-resolution configuration to a CG configuration. Certain mapping operators, however, may lose information related to the underlying electrostatic properties. In this paper, a new mapping operator based on the centers of charge of CG sites is proposed to address this issue. Four example systems are chosen to demonstrate this concept. Within the multiscale coarse-graining framework, CG models that use this mapping operator are found to better reproduce the structural correlations of atomistic models. The present work also demonstrates the flexibility of the mapping operator and the robustness of the force matching method. For instance, important functional groups can be isolated and emphasized in the CG model.
Collapse
Affiliation(s)
- Zhen Cao
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, USA
| |
Collapse
|
27
|
Izadyar A, Farhadian N, Chenarani N. Molecular dynamics simulation of doxorubicin adsorption on a bundle of functionalized CNT. J Biomol Struct Dyn 2015; 34:1797-805. [PMID: 26375507 DOI: 10.1080/07391102.2015.1092475] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this study, molecular dynamics simulation is used to investigate the adsorption of an anticancer drug, doxorubicin, on bundles of functionalized single-walled carbon nanotubes (SWNTs) in an aqueous solution. Carboxylic group has been selected as the functional group. Molecular dynamics (MD) simulations are performed for both separated systems containing a SWNT bundle and a functionalized carbon nanotube bundle, and results are compared with existing experimental data. MD results show that doxorubicin can be adsorbed on CNTs using different methods such as entrapment within CNT bundle, attachment to the side wall of the CNT, and adsorption on the CNT inner cavity. For functionalized CNT, the adsorption of drugs on the functional groups is essential for predicting the enhancement of drug loading on the functionalized nanotubes. Furthermore, the adsorption behavior of doxorubicin on CNTs is fitted with Langmuir and Freundlich isotherm models. The results show that Langmuir model can predict the adsorption behavior of doxorubicin on CNTs more accurately than Freundlich model does. As predicted by this isotherm model, the adsorption process of doxorubicin on CNTs is relatively difficult, but it can be improved by increasing the functional groups on the CNTs surface.
Collapse
Affiliation(s)
- Akram Izadyar
- a Chemical Engineering Department, Engineering Faculty , Ferdowsi University of Mashhad , Mashhad 9177948974 , Iran
| | - Nafiseh Farhadian
- a Chemical Engineering Department, Engineering Faculty , Ferdowsi University of Mashhad , Mashhad 9177948974 , Iran
| | - Naser Chenarani
- b Chemical Engineering Department , Amirkabir University of Technology (Tehran Polytechnic) , Tehran 1587504413 , Iran
| |
Collapse
|
28
|
Odinokov A, Ostroumov D. Structural Degradation and Swelling of Lipid Bilayer under the Action of Benzene. J Phys Chem B 2015; 119:15006-13. [PMID: 26555804 DOI: 10.1021/acs.jpcb.5b09420] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Benzene and other nonpolar organic solvents can accumulate in the lipid bilayer of cellular membranes. Their effect on the membrane structure and fluidity determines their toxic properties and antibiotic action of the organic solvents on the bacteria. We performed molecular dynamics simulations of the interaction of benzene with the dimyristoylphosphatidylcholine (DMPC) bilayer. An increase in the membrane surface area and fluidity was clearly detected. Changes in the acyl chain ordering, tilt angle, and overall bilayer thickness were, however, much less marked. The dependence of all computed quantities on the benzene content showed two regimes separated by the solubility limit of benzene in water. When the amount of benzene exceeded this point, a layer of almost pure benzene started to grow between the membrane leaflets. This process corresponds to the nucleation of a new phase and provides a molecular mechanism for the mechanical rupture of the bilayer under the action of nonpolar compounds.
Collapse
Affiliation(s)
- Alexey Odinokov
- Photochemistry Center of the Russian Academy of Sciences, 7a Novatorov ul., Moscow, 119421, Russia
| | - Denis Ostroumov
- Photochemistry Center of the Russian Academy of Sciences, 7a Novatorov ul., Moscow, 119421, Russia.,Moscow Institute of Physics and Technology , 9 Institutskiy per., Dolgoprudny, Moscow Region, 141700, Russia
| |
Collapse
|
29
|
Kang M, Loverde SM. Molecular Simulation of the Concentration-Dependent Interaction of Hydrophobic Drugs with Model Cellular Membranes. J Phys Chem B 2014; 118:11965-72. [DOI: 10.1021/jp5047613] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Myungshim Kang
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
| | - Sharon M. Loverde
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York 10314, United States
| |
Collapse
|
30
|
Liu W, Zhang S, Meng F, Tang L. Molecular simulation of ibuprofen passing across POPC membrane. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500333] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Permeability assessment is an important procedure in the drug development process, and drug partitioning in membrane bilayer is related to permeability. To investigate the pH dependence on drug partitioning, the process of different ionization state of ibuprofen passing across POPC bilayer was studied using molecular dynamics simulation. The results show that both atomic charge scheme and ionization state of the drug affect the value and shape of energy profile when passing across the POPC bilayer. The neutral ibuprofen (ibuprofen under acidic condition) has a much lower energy barrier as compared with the anionic ibuprofen (ibuprofen under basic condition). Meantime, hydrogen bond analysis also certifies that it is easy for neutral ibuprofen to pass from bulk water to bilayer center. Our calculation suggests that the ionization state of ibuprofen may be changed between neutral and anionic state when passing across membrane: it may be ionized outside the membrane and neutralized inside the membrane.
Collapse
Affiliation(s)
- Wei Liu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
| | - Shijun Zhang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
| | - Fancui Meng
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
| | - Lida Tang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
| |
Collapse
|