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Rios TB, Rezende SB, Maximiano MR, Cardoso MH, Malmsten M, de la Fuente-Nunez C, Franco OL. Computational Approaches for Antimicrobial Peptide Delivery. Bioconjug Chem 2024; 35:1873-1882. [PMID: 39541149 DOI: 10.1021/acs.bioconjchem.4c00406] [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: 11/16/2024]
Abstract
Peptides constitute alternative molecules for the treatment of infections caused by bacteria, viruses, fungi, and protozoa. However, their therapeutic effectiveness is often limited by enzymatic degradation, chemical and physical instability, and toxicity toward healthy human cells. To improve their pharmacokinetic (PK) and pharmacodynamic (PD) profiles, novel routes of administration are being explored. Among these, nanoparticles have shown promise as potential carriers for peptides, although the design of delivery vehicles remains a slow and painstaking process, heavily reliant on trial and error. Recently, computational approaches have been introduced to accelerate the development of effective drug delivery systems for peptides. Here we present an overview of some of these computational strategies and discuss their potential to optimize drug development and delivery.
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Affiliation(s)
- Thuanny Borba Rios
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 70990-160, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal 71966-700, Brazil
| | - Samilla Beatriz Rezende
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 70990-160, Brazil
| | - Mariana Rocha Maximiano
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 70990-160, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal 71966-700, Brazil
| | - Marlon Henrique Cardoso
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 70990-160, Brazil
| | - Martin Malmsten
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Physical Chemistry 1, University of Lund, S-221 00 Lund, Sweden
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Octávio Luiz Franco
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 70990-160, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal 71966-700, Brazil
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Wu N, Liu Y, Wang S, Xing Z, Tang G. Thermal Rectification in Graphene-Boron Nitride Nanotube Hybrid Structures: An Independent Control Mechanism for Forward and Backward Heat Flux. ACS APPLIED MATERIALS & INTERFACES 2024; 16:42660-42673. [PMID: 39078264 DOI: 10.1021/acsami.4c09390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The weak van der Waals interactions in the out-of-plane direction result in markedly low thermal conductivity in one-dimensional (1D) and two-dimensional (2D) materials, which substantially restricts their applications. Developing three-dimensional (3D) columnar hybrid structures, featuring high thermal conductivity both within and beyond the plane, effectively addresses this challenge. This study investigated a 3D hybrid structure composed of graphene and boron nitride nanotubes (GR-BNNTs) using non-equilibrium molecular dynamics simulations. This approach allowed the examination of the formation mechanisms and key factors influencing thermal rectification (TR) in these materials. Our findings reveal a novel mechanism for independently regulating forward and backward heat fluxes in GR-BNNTs. By manipulating the thermal properties of the BNNTs and the graphene layer, the TR ratio can be controlled flexibly. Additionally, we identify specific strategies for independently adjusting the heat flux, such as altering the intercolumn distance of BNNTs, which impacts the backward flux merely, while applying strain to affect the forward flux merely. This research introduces a novel concept of independent regulation of forward and backward heat fluxes, providing significant insights into phonon thermal transport in 3D hybrid structures.
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Affiliation(s)
- Ning Wu
- Department of Power Engineering, School of Energy and Power Engineering, North China Electric Power University, Baoding 071003, China
| | - Yingguang Liu
- Department of Power Engineering, School of Energy and Power Engineering, North China Electric Power University, Baoding 071003, China
- Hebei Key Laboratory of Low Carbon and High Efficiency Power Generation Technology, North China Electric Power University, Baoding 071003, China
| | - Shuo Wang
- Department of Power Engineering, School of Energy and Power Engineering, North China Electric Power University, Baoding 071003, China
| | - Zhibo Xing
- Department of Power Engineering, School of Energy and Power Engineering, North China Electric Power University, Baoding 071003, China
| | - Guihua Tang
- MOE Key Laboratory of Thermo-Fluid Science and Engineering, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an 710049, China
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Shar A, Shar A, Joung D. Carbon nanotube nanocomposite scaffolds: advances in fabrication and applications for tissue regeneration and cancer therapy. Front Bioeng Biotechnol 2023; 11:1299166. [PMID: 38179128 PMCID: PMC10764633 DOI: 10.3389/fbioe.2023.1299166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/08/2023] [Indexed: 01/06/2024] Open
Abstract
Carbon nanotube (CNT) nanocomposite scaffolds have emerged as highly promising frameworks for tissue engineering research. By leveraging their intrinsic electrical conductivity and valuable mechanical properties, CNTs are commonly dispersed into polymers to create robust, electrically conductive scaffolds that facilitate tissue regeneration and remodeling. This article explores the latest progress and challenges related to CNT dispersion, functionalization, and scaffold printing techniques, including electrospinning and 3D printing. Notably, these CNT scaffolds have demonstrated remarkable positive effects across various cell culture systems, stimulating neuronal growth, promoting cardiomyocyte maturation, and facilitating osteocyte differentiation. These encouraging results have sparked significant interest within the regenerative medicine field, including neural, cardiac, muscle, and bone regenerations. However, addressing the concern of CNT cytotoxicity in these scaffolds remains critical. Consequently, substantial efforts are focused on exploring strategies to minimize cytotoxicity associated with CNT-based scaffolds. Moreover, researchers have also explored the intriguing possibility of utilizing the natural cytotoxic properties of CNTs to selectively target cancer cells, opening up promising avenues for cancer therapy. More research should be conducted on cutting-edge applications of CNT-based scaffolds through phototherapy and electrothermal ablation. Unlike drug delivery systems, these novel methodologies can combine 3D additive manufacturing with the innate physical properties of CNT in response to electromagnetic stimuli to efficiently target localized tumors. Taken together, the unique properties of CNT-based nanocomposite scaffolds position them as promising candidates for revolutionary breakthroughs in both regenerative medicine and cancer treatment. Continued research and innovation in this area hold significant promise for improving healthcare outcomes.
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Affiliation(s)
- Andy Shar
- Department of Physics, Virginia Commonwealth University, Richmond, VA, United States
| | - Angela Shar
- College of Medicine, University of Florida, Gainesville, FL, United States
| | - Daeha Joung
- Department of Physics, Virginia Commonwealth University, Richmond, VA, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
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Khodov IA, Belov KV, Huster D, Scheidt HA. Conformational State of Fenamates at the Membrane Interface: A MAS NOESY Study. MEMBRANES 2023; 13:607. [PMID: 37367811 DOI: 10.3390/membranes13060607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023]
Abstract
The present work analyzes the 1H NOESY MAS NMR spectra of three fenamates (mefenamic, tolfenamic, and flufenamic acids) localized in the lipid-water interface of phosphatidyloleoylphosphatidylcholine (POPC) membranes. The observed cross-peaks in the two-dimensional NMR spectra characterized intramolecular proximities between the hydrogen atoms of the fenamates as well as intermolecular interactions between the fenamates and POPC molecules. The peak amplitude normalization for an improved cross-relaxation (PANIC) approach, the isolated spin-pair approximation (ISPA) model, and the two-position exchange model were used to calculate the interproton distances indicative of specific conformations of the fenamates. The results showed that the proportions of the A+C and B+D conformer groups of mefenamic and tolfenamic acids in the presence of POPC were comparable within the experimental error and amounted to 47.8%/52.2% and 47.7%/52.3%, respectively. In contrast, these proportions for the flufenamic acid conformers differed and amounted to 56.6%/43.4%. This allowed us to conclude that when they bind to the POPC model lipid membrane, fenamate molecules change their conformational equilibria.
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Affiliation(s)
- Ilya A Khodov
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - Konstantin V Belov
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, 04107 Leipzig, Germany
| | - Holger A Scheidt
- Institute for Medical Physics and Biophysics, Leipzig University, 04107 Leipzig, Germany
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Karimzadeh S, Safaei B, Jen TC. Investigation on electrochemical performance of striped, β12 and χ3 Borophene as anode materials for lithium-ion batteries. J Mol Graph Model 2023; 120:108423. [PMID: 36731208 DOI: 10.1016/j.jmgm.2023.108423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/28/2023]
Abstract
By developing next-generation lithium-ion batteries (LIBS), demand for exploring novel anode materials with exclusive electrochemical features and ultra-high capacity is increasing. In the current research, first-principles theory, and density functional theory (DFT) calculations were conducted to extensively investigate and compare the capability of three different borophene nanolayers, including striped, β12, and χ3 borophene, as a novel candidate for anode electrode in LIBs. We first predicted the most preferential Li atom adsorption sites on the three borophene structures. The predicted average formation energies for striped, β12, and χ3 borophene were obtained 3.123, 3.184, and 3.216 eV, respectively. The positive value of formation energy exhibits the sufficient stability of the structures. Moreover, the negative adsorption energy proved that Li atom insertion on all borophene monolayers is thermodynamically favorable. In order to simulate the lithiation process, we gradually increased the concentration of Li atoms. We found that the fully lithiated striped, β12 and χ3 borophenes could provide ultra-high specific capacities of 1700, 1983, and 1859 mAh/g, respectively. Structural analysis proved that the surface area expansion rate of the striped borophene in a fully lithiated state was 1%, which was lower than those of β12 and χ3 borophene with 3.33% and 2.63%, respectively. The analyses of electronic properties confirmed that borophenes were inherently metallic and superior ion conductive agents, even after fully lithiated state. Ion diffusion was studied using Nudged elastic band method and the value of diffusion energy barrier ranged from 0.03 to 0.36 eV which was lower than other promising 2D anode materials. Furthermore, open-circuit voltage results demonstrated that the electronic potential of modeled borophenes was low enough to be in the acceptable range of under 1.2V. All these reports exhibited that borophene nanolayers with excellent specific capacity and superior conductivity were desired candidates for anode materials of next generation LIBs.
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Affiliation(s)
- Sina Karimzadeh
- Department of Mechanical Engineering Science, University of Johannesburg, Gauteng, 2006, South Africa.
| | - Babak Safaei
- Department of Mechanical Engineering Science, University of Johannesburg, Gauteng, 2006, South Africa; Department of Mechanical Engineering, Eastern Mediterranean University, Famagusta, North Cyprus Via Mersin 10, Turkey.
| | - Tien-Chien Jen
- Department of Mechanical Engineering Science, University of Johannesburg, Gauteng, 2006, South Africa.
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Yahyavi M, Badalkhani-Khamseh F, Hadipour NL. Folic acid functionalized carbon nanotubes as pH controlled carriers of fluorouracil: Molecular dynamics simulations. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Jiwanti PK, Wardhana BY, Sutanto LG, Dewi DMM, Putri IZD, Savitri INI. Recent Development of Nano-Carbon Material in Pharmaceutical Application: A Review. Molecules 2022; 27:7578. [PMID: 36364403 PMCID: PMC9654677 DOI: 10.3390/molecules27217578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/21/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Carbon nanomaterials have attracted researchers in pharmaceutical applications due to their outstanding properties and flexible dimensional structures. Carbon nanomaterials (CNMs) have electrical properties, high thermal surface area, and high cellular internalization, making them suitable for drug and gene delivery, antioxidants, bioimaging, biosensing, and tissue engineering applications. There are various types of carbon nanomaterials including graphene, carbon nanotubes, fullerenes, nanodiamond, quantum dots and many more that have interesting applications in the future. The functionalization of the carbon nanomaterial surface could modify its chemical and physical properties, as well as improve drug loading capacity, biocompatibility, suppress immune response and have the ability to direct drug delivery to the targeted site. Carbon nanomaterials could also be fabricated into composites with proteins and drugs to reduce toxicity and increase effectiveness in the pharmaceutical field. Thus, carbon nanomaterials are very effective for applications in pharmaceutical or biomedical systems. This review will demonstrate the extraordinary properties of nanocarbon materials that can be used in pharmaceutical applications.
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Affiliation(s)
- Prastika K. Jiwanti
- Nanotechnology Engineering, Faculty of Advanced Technology and Multidiscipline, Kampus C Universitas Airlangga, Surabaya 60115, Indonesia
| | - Brasstira Y. Wardhana
- Nanotechnology Engineering, Faculty of Advanced Technology and Multidiscipline, Kampus C Universitas Airlangga, Surabaya 60115, Indonesia
| | - Laurencia G. Sutanto
- Nanotechnology Engineering, Faculty of Advanced Technology and Multidiscipline, Kampus C Universitas Airlangga, Surabaya 60115, Indonesia
| | - Diva Meisya Maulina Dewi
- Nanotechnology Engineering, Faculty of Advanced Technology and Multidiscipline, Kampus C Universitas Airlangga, Surabaya 60115, Indonesia
| | | | - Ilmi Nur Indira Savitri
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia
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Guo F, Wang J, Zhou J, Qian K, Qu H, Liu P, Zhai S. All-atom molecular dynamics simulations of the combined effects of different phospholipids and cholesterol content on electroporation. RSC Adv 2022; 12:24491-24500. [PMID: 36128384 PMCID: PMC9425445 DOI: 10.1039/d2ra03895a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/27/2022] [Indexed: 11/21/2022] Open
Abstract
The electroporation mechanism could be related to the composition of the plasma membrane, and the combined effect of different phospholipid molecules and cholesterol content on electroporation has rarely been studied nor conclusions drawn. In this paper, we applied all-atom molecular dynamics (MD) simulations to study the effects of phospholipids and cholesterol content on bilayer membrane electroporation. The palmitoyloleoylphosphatidylcholine (POPC) model, palmitoyloleoylphosphatidylethanolamine (POPE) model, and a 1 : 1 mixed model of POPC and POPE called PEPC, were the three basic models used. An electric field of 0.45 V nm-1 was applied to nine models, which were the three basic models, each with three different cholesterol content values of 0%, 24%, and 40%. The interfacial water molecules moved under the electric field and, once the first water bridge formed, the rest of the water molecules would dramatically flood into the membrane. The simulation showed that a rapid rise in the Z-component of the average dipole moment of the interfacial water molecules (Z-DM) indicated the occurrence of electroporation, and the same increment of Z-DM represented a similar change in the size of the water bridge. With the same cholesterol content, the formation of the first water bridge was the most rapid in the POPC model, regarding the average electroporation time (t ep), and the average t ep of the PEPC model was close to that of the POPE model. We speculate that the differences in membrane thickness and initial number of hydrogen bonds of the interfacial water molecules affect the average t ep for different membrane compositions. Our results reveal the influence of membrane composition on the electroporation mechanism at the molecular level.
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Affiliation(s)
- Fei Guo
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications Chongqing 400065 China
| | - Ji Wang
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications Chongqing 400065 China
| | - Jiong Zhou
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications Chongqing 400065 China
| | - Kun Qian
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications Chongqing 400065 China
| | - Hongchun Qu
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications Chongqing 400065 China
| | - Ping Liu
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications Chongqing 400065 China
| | - Shidong Zhai
- Institute of Ecological Safety, Chongqing University of Posts and Telecommunications Chongqing 400065 China
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Rezaei A, Morsali A, Bozorgmehr MR, Nasrabadi M. Quantum chemical analysis of 5-aminolevulinic acid anticancer drug delivery systems: Carbon nanotube, –COOH functionalized carbon nanotube and iron oxide nanoparticle. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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