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Wang Y, Lu K, Zhou Z, Wang Y, Shen J, Huang D, Xu Y, Wang M. Nanoscale zero-valent iron reverses resistance of Pseudomonas aeruginosa to chloramphenicol. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134698. [PMID: 38788587 DOI: 10.1016/j.jhazmat.2024.134698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Zero-valent iron (ZVI) has been extensively studied for its capacity to remove various contaminants in the environments. However, whether ZVI affects bacterial resistance to antibiotics has not been fully explored. Herein, it was unexpected that, compared with microscale ZVI (mZVI), nanoscale ZVI (nZVI) facilitated the susceptibility of Pseudomonas aeruginosa (P. aeruginosa) to chloramphenicol (CAP), with a decrease in the minimal inhibitory concentration (MIC) of about 60 %, demonstrating a nanosize-specific effect. nZVI enhanced CAP accumulation in P. aeruginosa via inhibitory effect on efflux pumps activated by MexT, thus conferring the susceptibility of P. aeruginosa to CAP. Circular dichroism spectroscopy revealed that the structure of MexT was changed during the evolution. More importantly, molecular dynamic simulations uncovered that, once the structure of MexT changed, it would be more likely to interact with nZVI, resulting in more serious changes in its secondary structure, which was consistent with the increasing susceptibility of P. aeruginosa to CAP. Collectively, this study elucidated the size-specific effect and the underlying mechanism of ZVI on the bacterial evolution of susceptibility toward antibiotics, highlighting the potentials of nZVI-based technologies on the prevention of bacterial resistance to antibiotics, one of the most important issue for globally public health.
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Affiliation(s)
- Yufan Wang
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Kun Lu
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Zhiruo Zhou
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yujie Wang
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Jiawei Shen
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Dan Huang
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yongchang Xu
- Zhejiang Provincial Key Laboratory of Aging and Cancer Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China.
| | - Meizhen Wang
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China.
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Garduño-Juárez R, Tovar-Anaya DO, Perez-Aguilar JM, Lozano-Aguirre Beltran LF, Zubillaga RA, Alvarez-Perez MA, Villarreal-Ramirez E. Molecular Dynamic Simulations for Biopolymers with Biomedical Applications. Polymers (Basel) 2024; 16:1864. [PMID: 39000719 PMCID: PMC11244511 DOI: 10.3390/polym16131864] [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: 02/27/2024] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 07/17/2024] Open
Abstract
Computational modeling (CM) is a versatile scientific methodology used to examine the properties and behavior of complex systems, such as polymeric materials for biomedical bioengineering. CM has emerged as a primary tool for predicting, setting up, and interpreting experimental results. Integrating in silico and in vitro experiments accelerates scientific advancements, yielding quicker results at a reduced cost. While CM is a mature discipline, its use in biomedical engineering for biopolymer materials has only recently gained prominence. In biopolymer biomedical engineering, CM focuses on three key research areas: (A) Computer-aided design (CAD/CAM) utilizes specialized software to design and model biopolymers for various biomedical applications. This technology allows researchers to create precise three-dimensional models of biopolymers, taking into account their chemical, structural, and functional properties. These models can be used to enhance the structure of biopolymers and improve their effectiveness in specific medical applications. (B) Finite element analysis, a computational technique used to analyze and solve problems in engineering and physics. This approach divides the physical domain into small finite elements with simple geometric shapes. This computational technique enables the study and understanding of the mechanical and structural behavior of biopolymers in biomedical environments. (C) Molecular dynamics (MD) simulations involve using advanced computational techniques to study the behavior of biopolymers at the molecular and atomic levels. These simulations are fundamental for better understanding biological processes at the molecular level. Studying the wide-ranging uses of MD simulations in biopolymers involves examining the structural, functional, and evolutionary aspects of biomolecular systems over time. MD simulations solve Newton's equations of motion for all-atom systems, producing spatial trajectories for each atom. This provides valuable insights into properties such as water absorption on biopolymer surfaces and interactions with solid surfaces, which are crucial for assessing biomaterials. This review provides a comprehensive overview of the various applications of MD simulations in biopolymers. Additionally, it highlights the flexibility, robustness, and synergistic relationship between in silico and experimental techniques.
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Affiliation(s)
- Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - David O Tovar-Anaya
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | | | - Rafael A Zubillaga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City 09340, Mexico
| | - Marco Antonio Alvarez-Perez
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
| | - Eduardo Villarreal-Ramirez
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
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3
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Luo Y, Gu Z, Perez-Aguilar JM, Liao W, Huang Y, Luo Y. Moderate binding of villin headpiece protein to C 3N 3 nanosheet reveals the suitable biocompatibility of this nanomaterial. Sci Rep 2023; 13:13783. [PMID: 37612444 PMCID: PMC10447452 DOI: 10.1038/s41598-023-41125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/22/2023] [Indexed: 08/25/2023] Open
Abstract
Since its recent successful synthesis and due to its promising physical and chemical properties, the carbon nitrite nanomaterial, C3N3, has attracted considerable attention in various scientific areas. However, thus far, little effort has been devoted to investigating the structural influence of the direct interaction of this 2D nanomaterial and biomolecules, including proteins and biomembranes so as to understand the physical origin of its bio-effect, particularly from the molecular landscape. Such information is fundamental to correlate to the potential nanotoxicology of the C3N3 nanomaterial. In this work, we explored the potential structural influence of a C3N3 nanosheet on the prototypical globular protein, villin headpiece (HP35) using all-atom molecular dynamics (MD) simulations. We found that HP35 could maintain its native conformations upon adsorption onto the C3N3 nanosheet regardless of the diversity in the binding sites, implying the potential advantage of C3N3 in protecting the biomolecular structure. The adsorption was mediated primarily by vdW interactions. Moreover, once adsorbed on the C3N3 surface, HP35 remains relatively fixed on the nanostructure without a distinct lateral translation, which may aid in keeping the structural integrity of the protein. In addition, the porous topological structure of C3N3 and the special water layer present on the C3N3 holes conjointly contributed to the restricted motion of HP35 via the formation of a high free energy barrier and a steric hindrance to prevent the surface displacement. This work revealed for the first time the potential influence of the 2D C3N3 nanomaterial in the protein structure and provided the corresponding in-depth molecular-level mechanism, which is valuable for future applications of C3N3 in bionanomedicine.
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Affiliation(s)
- Yuqi Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, 518110, Guangdong, China.
| | - Zonglin Gu
- College of Physical Science and Technology, Yangzhou University, Jiangsu, 225009, China
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), 72570, University City, Puebla, Mexico
| | - Weihua Liao
- Department of Radiology, Guangzhou Nansha District Maternal and Child Health Hospital, No. 103, Haibang Road, Nansha District, Guangzhou, 511457, Guangdong, China
| | - Yiwen Huang
- Department of Emergency, Nansha Hospital, Guangzhou First People's Hospital, Guangzhou, Guangdong, China
| | - Yanbo Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, No. 187, Guanlan Road, Longhua District, Shenzhen, 518110, Guangdong, China
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4
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Tan YZ, Thomsen LR, Shrestha N, Camisasca A, Giordani S, Rosengren R. Short-Term Intravenous Administration of Carbon Nano-Onions is Non-Toxic in Female Mice. Int J Nanomedicine 2023; 18:3897-3912. [PMID: 37483316 PMCID: PMC10361275 DOI: 10.2147/ijn.s414438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023] Open
Abstract
Background A nanoscale drug carrier could have a variety of therapeutic and diagnostic uses provided that the carrier is biocompatible in vivo. Carbon nano-onions (CNOs) have shown promising results as a nanocarrier for drug delivery. However, the systemic effect of CNOs in rodents is unknown. Therefore, we investigated the toxicity of CNOs following intravenous administration in female BALB/c mice. Results Single or repeated administration of oxi-CNOs (125, 250 or 500 µg) did not affect mouse behavior or organ weight and there was also no evidence of hepatotoxicity or nephrotoxicity. Histological examination of organ slices revealed a significant dose-dependent accumulation of CNO aggregates in the spleen, liver and lungs (p<0.05, ANOVA), with a trace amount of aggregates appearing in the kidneys. However, CNO aggregates in the liver did not affect CYP450 enzymes, as total hepatic CYP450 as well as CYP3A catalytic activity, as meased by erythromycin N-demethylation, and protein levels showed no significant changes between the treatment groups compared to vehicle control. CNOs also failed to act as competitive inhibitors of CYP3A in vitro in both mouse and human liver microsomes. Furthermore, CNOs did not cause oxidative stress, as indicated by the unchanged malondialdehyde levels and superoxide dismutase activity in liver microsomes and organ homogenates. Conclusion This study provides the first evidence that short-term intravenous administration of oxi-CNOs is non-toxic to female mice and thus could be a promising novel and safe drug carrier.
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Affiliation(s)
- Yi Zhen Tan
- Department of Pharmacology and Toxicology, University of Otago, Dunedin, 9016, New Zealand
| | - Lucy R Thomsen
- Department of Pharmacology and Toxicology, University of Otago, Dunedin, 9016, New Zealand
| | - Nensi Shrestha
- Department of Pharmacology and Toxicology, University of Otago, Dunedin, 9016, New Zealand
| | - Adalberto Camisasca
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, D09 NA55, Ireland
| | - Silvia Giordani
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, D09 NA55, Ireland
| | - Rhonda Rosengren
- Department of Pharmacology and Toxicology, University of Otago, Dunedin, 9016, New Zealand
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5
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Ibrahim MAA, Hamad MHA, Mahmoud AHM, Mekhemer GAH, Sidhom PA, Sayed SRM, Moussa NAM, Rabee AIM, Dabbish E, Shoeib T. Adsorption of Favipiravir on pristine graphene nanosheets as a drug delivery system: a DFT study. RSC Adv 2023; 13:17465-17475. [PMID: 37304808 PMCID: PMC10253565 DOI: 10.1039/d3ra03227b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 05/29/2023] [Indexed: 06/13/2023] Open
Abstract
The efficiency of pristine graphene (GN) in the delivery process of the Favipiravir (FPV) anti-COVID-19 drug was herein revealed within the FPV⋯GN complexes in perpendicular and parallel configurations in terms of the density functional theory (DFT) method. Adsorption energy findings unveiled that the parallel configuration of FPV⋯GN complexes showed higher desirability than the perpendicular one, giving adsorption energy up to -15.95 kcal mol-1. This favorability could be interpreted as a consequence of the contribution of π-π stacking to the overall strength of the adsorption process in the parallel configuration. Frontier molecular orbitals (FMO) findings demonstrated the ability of the GN nanosheet to adsorb the FPV drug by the alteration in the EHOMO, ELUMO, and Egap values before and after the adsorption process. Based on Bader charge results, the FPV drug and GN sheet exhibited electron-donating and -accepting characters, respectively, which was confirmed by the negative sign of the computed charge transfer (Qt) values. The FPV(R)⋯T@GN complex showed the most desirable Qt value of -0.0377e, which was in synoptic with the adsorption energy pattern. Electronic properties of GN were also altered after the adsorption of the FPV drug in both configurations, with more observable changes in the parallel one. Interestingly, the Dirac point of the GN sheet coincided with the Fermi level after the adsorption process, indicating that the adsorption process unaffected the presence of the Dirac point. The occurrence of the adsorption process was also noticed by the existence of new bands and peaks in the band structure and DOS plots, respectively. Short recovery time rendered the GN nanosheet an efficient FPV drug delivery system. The obtained findings provide new insight into the biomedical applications of the GN sheet as a promising drug delivery system.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
- School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4000 South Africa
| | - Manar H A Hamad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Amna H M Mahmoud
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Peter A Sidhom
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University Tanta 31527 Egypt
| | - Shaban R M Sayed
- Department of Botany and Microbiology, College of Science, King Saud University P.O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Nayra A M Moussa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Abdallah I M Rabee
- Leibniz-Institut für Katalyse Albert-Einstein-Str. 29 A 18059 Rostock Germany
| | - Eslam Dabbish
- Department of Chemistry, The American University in Cairo New Cairo 11835 Egypt
| | - Tamer Shoeib
- Department of Chemistry, The American University in Cairo New Cairo 11835 Egypt
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6
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Yan X, Yue T, Winkler DA, Yin Y, Zhu H, Jiang G, Yan B. Converting Nanotoxicity Data to Information Using Artificial Intelligence and Simulation. Chem Rev 2023. [PMID: 37262026 DOI: 10.1021/acs.chemrev.3c00070] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Decades of nanotoxicology research have generated extensive and diverse data sets. However, data is not equal to information. The question is how to extract critical information buried in vast data streams. Here we show that artificial intelligence (AI) and molecular simulation play key roles in transforming nanotoxicity data into critical information, i.e., constructing the quantitative nanostructure (physicochemical properties)-toxicity relationships, and elucidating the toxicity-related molecular mechanisms. For AI and molecular simulation to realize their full impacts in this mission, several obstacles must be overcome. These include the paucity of high-quality nanomaterials (NMs) and standardized nanotoxicity data, the lack of model-friendly databases, the scarcity of specific and universal nanodescriptors, and the inability to simulate NMs at realistic spatial and temporal scales. This review provides a comprehensive and representative, but not exhaustive, summary of the current capability gaps and tools required to fill these formidable gaps. Specifically, we discuss the applications of AI and molecular simulation, which can address the large-scale data challenge for nanotoxicology research. The need for model-friendly nanotoxicity databases, powerful nanodescriptors, new modeling approaches, molecular mechanism analysis, and design of the next-generation NMs are also critically discussed. Finally, we provide a perspective on future trends and challenges.
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Affiliation(s)
- Xiliang Yan
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Tongtao Yue
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Institute of Coastal Environmental Pollution Control, Ocean University of China, Qingdao 266100, China
| | - David A Winkler
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- School of Pharmacy, University of Nottingham, Nottingham NG7 2QL, U.K
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Yongguang Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hao Zhu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Bing Yan
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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7
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Zhang Z, Ren J, Dai W, Zhang H, Wang X, He B, Zhang Q. Fast and Dynamic Mapping of the Protein Corona on Nanoparticle Surfaces by Photocatalytic Proximity Labeling. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206636. [PMID: 36477943 DOI: 10.1002/adma.202206636] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Protein corona broadly affects the delivery of nanomedicines in vivo. Although it has been widely studied by multiple strategies like centrifugal sedimentation, the rapidly forming mechanism and the dynamic structure of the protein corona at the seconds level remains challenging. Here, a photocatalytic proximity labeling technology in nanoparticles (nano-PPL) is developed. By fabricating a "core-shell" nanoparticle co-loaded with chlorin e6 catalyst and biotin-phenol probe, nano-PPL technology is validated for the rapid and precise labeling of corona proteins in situ. Nano-PPL significantly improves the temporal resolution of nano-protein interactions to 5 s duration compared with the classical centrifugation method (>30 s duration). Furthermore, nano-PPL achieves the fast and dynamic mapping of the protein corona on anionic and cationic nanoparticles, respectively. Finally, nano-PPL is deployed to verify the effect of the rapidly formed protein corona on the initial interaction of nanoparticles with cells. These findings highlight a significant methodological advance toward nano-protein interactions in the delivery of nanomedicines in vivo.
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Affiliation(s)
- Zibin Zhang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| | - Junji Ren
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| | - Wenbing Dai
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| | - Hua Zhang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| | - Xueqing Wang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| | - Bing He
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
| | - Qiang Zhang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Rd, Haidian District, Beijing, 100191, P. R. China
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8
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Kariuki R, Penman R, Bryant SJ, Orrell-Trigg R, Meftahi N, Crawford RJ, McConville CF, Bryant G, Voïtchovsky K, Conn CE, Christofferson AJ, Elbourne A. Behavior of Citrate-Capped Ultrasmall Gold Nanoparticles on a Supported Lipid Bilayer Interface at Atomic Resolution. ACS NANO 2022; 16:17179-17196. [PMID: 36121776 DOI: 10.1021/acsnano.2c07751] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nanomaterials have the potential to transform biological and biomedical research, with applications ranging from drug delivery and diagnostics to targeted interference of specific biological processes. Most existing research is aimed at developing nanomaterials for specific tasks such as enhanced biocellular internalization. However, fundamental aspects of the interactions between nanomaterials and biological systems, in particular, membranes, remain poorly understood. In this study, we provide detailed insights into the molecular mechanisms governing the interaction and evolution of one of the most common synthetic nanomaterials in contact with model phospholipid membranes. Using a combination of atomic force microscopy (AFM) and molecular dynamics (MD) simulations, we elucidate the precise mechanisms by which citrate-capped 5 nm gold nanoparticles (AuNPs) interact with supported lipid bilayers (SLBs) of pure fluid (DOPC) and pure gel-phase (DPPC) phospholipids. On fluid-phase DOPC membranes, the AuNPs adsorb and are progressively internalized as the citrate capping of the NPs is displaced by the surrounding lipids. AuNPs also interact with gel-phase DPPC membranes where they partially embed into the outer leaflet, locally disturbing the lipid organization. In both systems, the AuNPs cause holistic perturbations throughout the bilayers. AFM shows that the lateral diffusion of the particles is several orders of magnitude smaller than that of the lipid molecules, which creates some temporary scarring of the membrane surface. Our results reveal how functionalized AuNPs interact with differing biological membranes with mechanisms that could also have implications for cooperative membrane effects with other molecules.
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Affiliation(s)
- Rashad Kariuki
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Rowan Penman
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Saffron J Bryant
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Rebecca Orrell-Trigg
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Nastaran Meftahi
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, VIC 3001, Australia
| | - Russell J Crawford
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Chris F McConville
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
- Deakin University, Geelong, VIC 3220, Australia
| | - Gary Bryant
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Kislon Voïtchovsky
- University of Durham, Physics Department, Durham DH1 3LE, United Kingdom
| | - Charlotte E Conn
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Andrew J Christofferson
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
- ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, VIC 3001, Australia
| | - Aaron Elbourne
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
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9
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Tretiakova D, Kobanenko M, Le-Deygen I, Boldyrev I, Kudryashova E, Onishchenko N, Vodovozova E. Spectroscopy Study of Albumin Interaction with Negatively Charged Liposome Membranes: Mutual Structural Effects of the Protein and the Bilayers. MEMBRANES 2022; 12:1031. [PMID: 36363586 PMCID: PMC9696317 DOI: 10.3390/membranes12111031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Liposomes as drug carriers are usually injected into the systemic circulation where they are instantly exposed to plasma proteins. Liposome-protein interactions can affect both the stability of liposomes and the conformation of the associated protein leading to the altered biodistribution of the carrier. In this work, mutual effects of albumin and liposomal membrane in the course of the protein's adsorption were examined in terms of quantity of bound protein, its structure, liposome membrane permeability, and changes in physicochemical characteristics of the liposomes. Fluorescence spectroscopy methods and Fourier transform infrared spectroscopy (ATR-FTIR), which provides information about specific groups in lipids involved in interaction with the protein, were used to monitor adsorption of albumin with liposomes based on egg phosphatidylcholine with various additives of negatively charged lipidic components, such as phosphatidylinositol, ganglioside GM1, or the acidic lipopeptide. Less than a dozen of the protein molecules were tightly bound to a liposome independently of bilayer composition, yet they had a detectable impact on the bilayer. Albumin conformational changes during adsorption were partially related to bilayer microhydrophobicity. Ganglioside GM1 showed preferable features for evading undesirable structural changes.
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Affiliation(s)
- Daria Tretiakova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Maria Kobanenko
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Irina Le-Deygen
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Ivan Boldyrev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Elena Kudryashova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Natalia Onishchenko
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Elena Vodovozova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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10
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Fang B, Dai X, Li B, Qu Y, Li YQ, Zhao M, Yang Y, Li W. Self-assembly of ultra-small-sized carbon nanoparticles in lipid membrane disrupts its integrity. NANOSCALE ADVANCES 2021; 4:163-172. [PMID: 36132950 PMCID: PMC9417506 DOI: 10.1039/d1na00529d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/12/2021] [Indexed: 06/15/2023]
Abstract
Although nanomaterials are widely studied in biomedical applications, the major concern of nanotoxicity still exists. Therefore, numerous studies have been conducted on the interactions of various biomolecules with various types of nanomaterials, including carbon nanotubes, graphene, fullerene etc. However, the size effect of nanomaterials is poorly documented, especially ultra-small particles. Here, the interactions of the smallest carbon nanoparticle (NP), C28, with the cell membrane were studied using molecular dynamics (MD) simulations. The results show that similar to fullerene C60, the C28 NPs can self-assemble into stable clusters in water. Inside the membrane, the C28 NPs are more prone to aggregate to form clusters than C60 NPs. The reason for C28 aggregation is characterized by the potential of mean force (PMF) and can be explained by the polarized nature of C28 NPs while the acyl chains of lipids are nonpolar. At the C28 cluster regions, the thickness of the membrane is significantly reduced by the C28 aggregation. Accordingly, the membrane loses its structural integrity, and translocation of water molecules through it was observed. Thus, these results predict a stronger cytotoxicity to cells than C60 NPs. The present findings might shed light on the understanding of the cytotoxicity of NPs with different sizes and would be helpful for the potential biomedical applications of carbon NPs, especially as antibacterial agents.
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Affiliation(s)
- Bing Fang
- School of Physics, Shandong University Jinan Shandong 250100 China
| | - Xing Dai
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University Suzhou 215123 China
| | - Baoyu Li
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University Suzhou 215123 China
| | - Yuanyuan Qu
- School of Physics, Shandong University Jinan Shandong 250100 China
| | - Yong-Qiang Li
- School of Physics, Shandong University Jinan Shandong 250100 China
| | - Mingwen Zhao
- School of Physics, Shandong University Jinan Shandong 250100 China
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science, Shandong Normal University Jinan 250014 China
| | - Weifeng Li
- School of Physics, Shandong University Jinan Shandong 250100 China
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11
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Randhawa S, Abidi SMS, Dar AI, Acharya A. The curious cases of nanoparticle induced amyloidosis during protein corona formation and anti-amyloidogenic nanomaterials: Paradox or prejudice? Int J Biol Macromol 2021; 193:1009-1020. [PMID: 34728302 DOI: 10.1016/j.ijbiomac.2021.10.195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/18/2021] [Accepted: 10/26/2021] [Indexed: 12/30/2022]
Abstract
Protein corona (PC) formation remains a major hurdle in the successful delivery of nanomedicines to the target sites. Interacting proteins have been reported to undergo structural changes on the nanoparticle (NP) surface which invariably impacts their biological activities. Such structural changes are the result of opening of more binding sites of proteins to adsorb on the NP surface. The process of conversion of α-helix proteins to their β-sheet enriched counterpart is termed as amyloidosis and in case of PC formation, NPs apparently play the crucial role of being the nucleation centres where this process takes place. Conversely, increasing numbers of artificial nano-chaperones are being used to treat the protein misfolding disorders. Anti-amyloidogenic nanomaterials (NM) have been gaining utmost importance in inhibiting Aβ42 (hallmark peptide for Alzheimer's disease) and Hen egg white lysozyme (HEWL, model protein for systemic amyloidosis) aggregation. Interestingly, in this process, NPs inhibit protein β-sheet enrichment. These two seemingly opposite roles of NPs, propelling confirmatory change onto the smorgasbord of adsorbed native proteins and the ability of NPs in inhibiting amyloidosis creates a paradox, which has not been discussed earlier. Here, we highlight the key points from both the facets of the NP behaviour with respect to their physicochemical properties and the nature of proteins they adsorb onto them to unravel the mystery. BRIEF: Protein corona formation remains a major hurdle in achieving the desired efficacy of nanomedicine. Proteins when interact with nanoparticle (NP) surface, undergo both structural and biological changes. Again, NPs are known to exhibit anti-amyloidogenic behaviour where these play the crucial role of preventing any change in their native structure. Such seemingly different roles of NPs need sincere inquisition.
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Affiliation(s)
- Shiwani Randhawa
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Syed M S Abidi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aqib Iqbal Dar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Amitabha Acharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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12
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A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations. Int J Mol Sci 2021; 22:ijms221910813. [PMID: 34639151 PMCID: PMC8509277 DOI: 10.3390/ijms221910813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 11/17/2022] Open
Abstract
Thermal stability is a limiting factor for effective application of D-psicose 3-epimerase (DPEase) enzyme. Recently, it was reported that the thermal stability of DPEase was improved by immobilizing enzymes on graphene oxide (GO) nanoparticles. However, the detailed mechanism is not known. In this study, we investigated interaction details between GO and DPEase by performing molecular dynamics (MD) simulations. The results indicated that the domain (K248 to D268) of DPEase was an important anchor for immobilizing DPEase on GO surface. Moreover, the strong interactions between DPEase and GO can prevent loop α1′-α1 and β4-α4 of DPEase from the drastic fluctuation. Since these two loops contained active site residues, the geometry of the active pocket of the enzyme remained stable at high temperature after the DPEase was immobilized by GO, which facilitated efficient catalytic activity of the enzyme. Our research provided a detailed mechanism for the interaction between GO and DPEase at the nano–biology interface.
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13
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Zhao Z, Li G, Liu QS, Liu W, Qu G, Hu L, Long Y, Cai Z, Zhao X, Jiang G. Identification and interaction mechanism of protein corona on silver nanoparticles with different sizes and the cellular responses. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125582. [PMID: 34030421 DOI: 10.1016/j.jhazmat.2021.125582] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
With the potential biomedical applications of nanomaterials such as silver nanoparticles (SNPs), nanotoxicity concerns are growing, and the importance of NP and protein interactions is far from being addressed enough. Here, we identified the major binding protein on SNPs in blood as human serum albumin (HSA) using polyacrylamide gel electrophoresis and liquid chromatography-mass spectrometry/mass spectrometry. By comparing with the previous methods, we emphasized surface area concentration as a new dose metric to address the importance of NP curvature. SNPs interacted with cysteine and cystine, disrupting the secondary structure and conformation of HSA, and this tendency became stronger on small SNPs than large ones. The protein corona significantly alleviated the toxicity and decreased SNPs' internalization in a particle size-dependent manner, where more significant inhibition effects occurred on larger particles at the same area concentration. These findings may shed light on nanotoxicity and also the design of safe nanomaterials by a comprehensive preconsideration of the metrological method.
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Affiliation(s)
- Zongshan Zhao
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, PR China
| | - Guoliang Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Qian S Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Wei Liu
- Institute of Chemical Safety, Chinese Academy of Inspection and Quarantine, Beijing 100124, PR China
| | - Guangbo Qu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Ligang Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Yanmin Long
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan 430056, PR China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China.
| | - Xingchen Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China.
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
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14
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Zhao L, Gu Z. Potential Unwinding of Double-Stranded DNA upon Binding to a Carbon Nitride Polyaniline (C 3N) Nanosheet. J Phys Chem B 2021; 125:2258-2265. [PMID: 33625858 DOI: 10.1021/acs.jpcb.0c11288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, carbon nitride polyaniline (C3N) had attracted considerable attention from many scientific fields after its successful synthesis. However, thus far, limited efforts were devoted to reveal its potential effect to biomolecules, which correlated intimately with its further utilization. In this study, by using a molecular dynamics (MD) simulation approach, we investigated in detail the interaction between C3N and a double-stranded DNA (dsDNA) segment to expose the underlying biological effect of C3N to dsDNA and the corresponding molecular basis. MD simulation results demonstrated that dsDNA presented serious damages upon adsorption onto a C3N nanosheet with the terminal base pairs denaturized, unwound, and directly packing on the C3N surface, which implied that C3N was potentially deleterious to biomolecules. This binding/unwinding process was mainly guided by a combination of van der Waals and π-π stacking interactions together with a continuous lateral migration of dsDNA. Moreover, the nanoscale dewetting also played an important role during the adsorption. These findings revealed the potential bio-effect of the C3N nanomaterial and its molecular mechanism, which might benefit the future applications of C3N-based nanostructures.
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Affiliation(s)
- Liang Zhao
- College of Physical Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zonglin Gu
- College of Physical Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
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15
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Meng Y, Liu R, Zhu M, Zhai H, Ren C. Potential toxicity mechanism of MoS 2 nanotube in the interaction between YAP65 WW domain and PRM. Colloids Surf B Biointerfaces 2020; 196:111317. [PMID: 32818927 DOI: 10.1016/j.colsurfb.2020.111317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/04/2020] [Accepted: 08/09/2020] [Indexed: 01/13/2023]
Abstract
With the widespread application of Molybdenum disulfide (MoS2) in biomedicine, its mechanism of action with biomolecules has attracted increasing attention. Herein, molecular dynamics simulations were performed to investigate the effect of MoS2 nanotube on the binding of the signal protein YAP65, an important Yes kinase-associated protein domain (WW domain), to the proline rich motif ligand (PRM). We designed four systems based on the different initial binding modes among WW domain, PRM and MoS2 nanotube, and observed two ways to affect the binding of WW domain to PRM. The first pathway, the active site in WW domain was occupied by MoS2 nanotube, which prevents WW domain from binding to PRM. In the second pathway, WW domain was bound to PRM with residues W17 and F29 instead of the two highly conserved residues (Y28 and W39), forming an unstable combination. These two results might cause WW domain to lose its original function or to pass the mistaken signal. However, MoS2 nanotube did not destroy the structure and binding of WW domain and PRM in the composite. These findings shed light on the interaction between MoS2 nanotube and signal protein system, while providing another valuable insight into the potential nanotoxicity of MoS2 nanotube.
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Affiliation(s)
- Yajie Meng
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, PR China
| | - Ruirui Liu
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, PR China
| | - Min Zhu
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, PR China
| | - Honglin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, PR China.
| | - Cuiling Ren
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, PR China
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16
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Pineux F, Federico S, Klotz KN, Kachler S, Michiels C, Sturlese M, Prato M, Spalluto G, Moro S, Bonifazi D. Targeting G Protein-Coupled Receptors with Magnetic Carbon Nanotubes: The Case of the A 3 Adenosine Receptor. ChemMedChem 2020; 15:1909-1920. [PMID: 32706529 DOI: 10.1002/cmdc.202000466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Indexed: 12/14/2022]
Abstract
The A3 adenosine receptor (AR) is a G protein-coupled receptor (GPCR) overexpressed in the membrane of specific cancer cells. Thus, the development of nanosystems targeting this receptor could be a strategy to both treat and diagnose cancer. Iron-filled carbon nanotubes (CNTs) are an optimal platform for theranostic purposes, and the use of a magnetic field can be exploited for cancer magnetic cell sorting and thermal therapy. In this work, we have conjugated an A3 AR ligand on the surface of iron-filled CNTs with the aim of targeting cells overexpressing A3 ARs. In particular, two conjugates bearing PEG linkers of different length were designed. A docking analysis of A3 AR showed that neither CNT nor linker interferes with ligand binding to the receptor; this was confirmed by in vitro preliminary radioligand competition assays on A3 AR. Encouraged by this result, magnetic cell sorting was applied to a mixture of cells overexpressing or not the A3 AR in which our compound displayed indiscriminate binding to all cells. Despite this, it is the first time that a GPCR ligand has been anchored to a magnetic nanosystem, thus it opens the door to new applications for cancer treatment.
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Affiliation(s)
- Florent Pineux
- Department of Chemistry and Namur Research College (NARC), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Stephanie Federico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via L.Giorgeri 1, 34127, Trieste, Italy
| | - Karl-Norbert Klotz
- Institut für Pharmakologie und Toxikologie, Universität Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany
| | - Sonja Kachler
- Institut für Pharmakologie und Toxikologie, Universität Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany
| | - Carine Michiels
- Namur Research Institute for Life Science (NARILIS), Unité de Recherche en Biologie Cellulaire (URBC), University of Namur, 5000, Namur, Belgium
| | - Mattia Sturlese
- Dipartimento di Scienze del Farmaco Molecular Modeling Section (MMS), Università degli Studi di Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Maurizio Prato
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via L.Giorgeri 1, 34127, Trieste, Italy.,Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, 20014, Donostia-San Sebastián, Spain.,Basque Foundation for Science, Ikerbasque, 48013, Bilbao, Spain
| | - Giampiero Spalluto
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via L.Giorgeri 1, 34127, Trieste, Italy
| | - Stefano Moro
- Dipartimento di Scienze del Farmaco Molecular Modeling Section (MMS), Università degli Studi di Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Davide Bonifazi
- Institut für Organische Chemie, Universität Wien, Währinger Str. 38, 1090, Wien, Austria
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17
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Gu Z, Perez-Aguilar JM, Meng L, Zhou R. Partial Denaturation of Villin Headpiece upon Binding to a Carbon Nitride Polyaniline (C3N) Nanosheet. J Phys Chem B 2020; 124:7557-7563. [DOI: 10.1021/acs.jpcb.0c05850] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Zonglin Gu
- Institute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Lijun Meng
- Institute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, Hangzhou 310027, China
- Department of Chemistry, Columbia University, New York, New York 10027, Unites States
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18
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Di Giosia M, Marforio TD, Cantelli A, Valle F, Zerbetto F, Su Q, Wang H, Calvaresi M. Inhibition of α-chymotrypsin by pristine single-wall carbon nanotubes: Clogging up the active site. J Colloid Interface Sci 2020; 571:174-184. [DOI: 10.1016/j.jcis.2020.03.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 10/24/2022]
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19
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Song W, Jing Z, Meng L, Zhou R. Tungsten Oxide Nanodots Exhibit Mild Interactions with WW and SH3 Modular Protein Domains. ACS OMEGA 2020; 5:11005-11012. [PMID: 32455221 PMCID: PMC7241039 DOI: 10.1021/acsomega.0c00822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
Tungsten oxide nanodot (WO3-x ) is an active photothermal nanomaterial that has recently been discovered as a promising candidate for tumor theranostics and treatments. However, its potential cytotoxicity remains elusive and needs to be evaluated to assess its biosafety risks. Herein, we investigate the interactions between WO3-x and two ubiquitous protein domains involved in protein-protein interactions, namely, WW and SH3 domains, using atomistic molecular dynamics simulations. Our results show that WO3-x interacts only weakly with the key residues at the putative proline-rich motif (PRM) ligand-binding site of both domains. More importantly, our free energy landscape calculations reveal that the binding strength between WO3-x and WW/SH3 is weaker than that of the native PRM ligand with WW/SH3, implying that WO3-x has a limited inhibitory effect over PRM on both the WW and SH3 domains. These findings suggest that the cytotoxic effects of WO3-x on the key modular protein domains could be very mild, which provides new insights for the future potential biomedical applications of this nanomaterial.
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Affiliation(s)
- Wei Song
- Institute of Quantitative
Biology, Zhejiang University, Hangzhou 310027, China
| | - Zhifeng Jing
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Lijun Meng
- Institute of Quantitative
Biology, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Institute of Quantitative
Biology, Zhejiang University, Hangzhou 310027, China
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
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20
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Yan H, Ma J, Zhu F, Quan J, Dhinakaran MK, Li H. Phenethylamine@Pillar[5]arene Biointerface for Highly Enantioselective Adsorption of Protein. Chem Asian J 2020; 15:1025-1029. [DOI: 10.1002/asia.201901821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/16/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Hewei Yan
- Key Laboratory of Pesticide and Chemical Biology (CCNU) Ministry of Education College of ChemistryCentral China Normal University Wuhan 430079 P.R. China
| | - Junkai Ma
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research Department of Chemistry School of PharmacyHubei University of Medicine Shiyan 442000, Hubei Province P. R. China
| | - Fei Zhu
- Key Laboratory of Pesticide and Chemical Biology (CCNU) Ministry of Education College of ChemistryCentral China Normal University Wuhan 430079 P.R. China
| | - Jiaxin Quan
- Key Laboratory of Pesticide and Chemical Biology (CCNU) Ministry of Education College of ChemistryCentral China Normal University Wuhan 430079 P.R. China
| | - Manivannan Kalavathi Dhinakaran
- Key Laboratory of Pesticide and Chemical Biology (CCNU) Ministry of Education College of ChemistryCentral China Normal University Wuhan 430079 P.R. China
| | - Haibing Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU) Ministry of Education College of ChemistryCentral China Normal University Wuhan 430079 P.R. China
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21
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Bhunia AK, Saha S, Kamilya T. Microscopic and spectroscopic study of the corona formation and unfolding of human haemoglobin in presence of ZnO nanoparticles. LUMINESCENCE 2019; 35:144-155. [PMID: 31514262 DOI: 10.1002/bio.3707] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/11/2019] [Accepted: 08/21/2019] [Indexed: 12/23/2022]
Abstract
The interaction of zinc oxide nanoparticles (ZnO NPs) with human haemoglobin (Hb) is studied for the biologically safe application of ZnO NPs in the human body. The Hb corona is formed around the ZnO nanoparticles, directly observed from high-resolution transmission electron microscopy (HRTEM) images. Hb formed 'hard corona' on the surface of ZnO NPs from an exponential association mechanism over a very short duration, as well as unfolding of Hb that occurred over a long lifetime. Dynamic light scattering measurements demonstrated that the ZnO NPs were completely covered by Hb with shell thickness of c. 6 nm that formed a 'hard corona'. Zeta potential measurements represented that the ZnO NPs were fully covered by Hb molecules using an exponential association mechanism. Tryptophans (TRY), as well as heme-porphyrin moieties of Hb, are the major binding sites for ZnO NPs. The nature of the interaction between ZnO NPs and Hb was analysed from the fluorescence quenching of TRYs. Electrostatic interaction, along with the hydrophobic interaction between ZnO NPs and Hb, is responsible for the conformational change in Hb due to increase in the percentage of β-sheets together with a decrease in α-helices.
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Affiliation(s)
- A K Bhunia
- Department of Physics & Technophysics, Vidyasagar University, Paschim Medinipur, India.,Department of Physics, Government General Degree College at Gopiballavpur-II, Jhargram, India
| | - S Saha
- Department of Physics & Technophysics, Vidyasagar University, Paschim Medinipur, India
| | - T Kamilya
- Department of Physics, Narajole Raj College, Paschim Medinip, India
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22
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Liu Y, Li S, Liu X, Sun H, Yue T, Zhang X, Yan B, Cao D. Design of Small Nanoparticles Decorated with Amphiphilic Ligands: Self-Preservation Effect and Translocation into a Plasma Membrane. ACS APPLIED MATERIALS & INTERFACES 2019; 11:23822-23831. [PMID: 31250627 DOI: 10.1021/acsami.9b03638] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Design of nanoparticles (NPs) for biomedical applications requires a thorough understanding of cascades of nano-bio interactions at different interfaces. Here, we take into account the cascading effect of NP functionalization on interactions with target cell membranes by determining coatings of biomolecules in biological media. Cell culture experiments show that NPs with more hydrophobic surfaces are heavily ingested by cells in both the A549 and HEK293 cell lines. However, before reaching the target cell, both the identity and amount of recruited biomolecules can be influenced by the pristine NPs' hydrophobicity. Dissipative particle dynamics (DPD) simulations show that hydrophobic NPs acquire coatings of more biomolecules, which may conceal the properties of the as-engineered NPs and impact the targeting specificity. Based on these results, we propose an amphiphilic ligand coating on NPs. DPD simulations reveal the design principle, following which the amphiphilic ligands first curl in solvent to reduce the surface hydrophobicity, thus suppressing the assemblage of biomolecules. Upon attaching to the membrane, the curled ligands extend and rearrange to gain contacts with lipid tails, thus dragging NPs into the membrane for translocation. Three NP-membrane interaction states are identified that are found to depend on the NP size and membrane surface tension. These results can provide useful guidelines to fabricate ligand-coated NPs for practical use in targeted drug delivery, and motivate further studies of nano-bio-interactions with more consideration of cascading effects.
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Affiliation(s)
- Yuchi Liu
- State Key Laboratory of Organic-Inorganic Composites , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Shixin Li
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Xuejuan Liu
- State Key Laboratory of Organic-Inorganic Composites , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Hainan Sun
- School of Environmental Science and Engineering , Shandong University , Jinan 250100 , China
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Bing Yan
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay , Guangzhou University , Guangzhou 510006 , China
- School of Environmental Science and Engineering , Shandong University , Jinan 250100 , China
| | - Dapeng Cao
- State Key Laboratory of Organic-Inorganic Composites , Beijing University of Chemical Technology , Beijing 100029 , China
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23
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Zhu W, Kong J, Zhang J, Wang J, Li W, Wang W. Consequences of Hydrophobic Nanotube Binding on the Functional Dynamics of Signaling Protein Calmodulin. ACS OMEGA 2019; 4:10494-10501. [PMID: 31460146 PMCID: PMC6648716 DOI: 10.1021/acsomega.9b01217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
The wide applications of nanomaterials in industry and our daily life have raised growing concerns on their toxicity to human body. Increasing evidence links the cytotoxicity of nanoparticles to the disruption of cellular signaling pathways. Here, we report a computational study on the mechanisms of the cytotoxicity of carbon nanotubes (CNTs) by investigating the direct impacts of CNTs on the functional motions of calmodulin (CaM), which is one of the most important signaling proteins in a cell, and its signaling function relies on the Ca2+ binding-coupled conformational switching. Computational simulations with a coarse-grained model showed that binding of CNTs modifies the conformational equilibrium of CaM and induces the closed-to-open conformational transition, leading to the loss of its Ca2+-sensing ability. In addition, the binding of CNTs drastically increases the calcium affinity of CaM, which may disrupt the Ca2+ homeostasis in a cell. These results suggest that the binding of hydrophobic nanotubes not only inhibits the signaling function of CaM as a calcium sensor but also renders CaM to toxic species through sequestering Ca2+ from other competing calcium-binding proteins, suggesting a new physical mechanism of the cytotoxicity of nanoparticles.
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Affiliation(s)
- Wentao Zhu
- National Laboratory of Solid State
Microstructure, and Collaborative Innovation Center of Advanced Microstructures
and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Jianyang Kong
- National Laboratory of Solid State
Microstructure, and Collaborative Innovation Center of Advanced Microstructures
and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Jian Zhang
- National Laboratory of Solid State
Microstructure, and Collaborative Innovation Center of Advanced Microstructures
and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Jun Wang
- National Laboratory of Solid State
Microstructure, and Collaborative Innovation Center of Advanced Microstructures
and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- National Laboratory of Solid State
Microstructure, and Collaborative Innovation Center of Advanced Microstructures
and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State
Microstructure, and Collaborative Innovation Center of Advanced Microstructures
and Department of Physics, Nanjing University, Nanjing 210093, China
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24
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Li J, Chen L, Yan L, Gu Z, Chen Z, Zhang A, Zhao F. A Novel Drug Design Strategy: An Inspiration from Encaging Tumor by Metallofullerenol Gd@C 82(OH) 22. Molecules 2019; 24:molecules24132387. [PMID: 31252662 PMCID: PMC6650816 DOI: 10.3390/molecules24132387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 12/30/2022] Open
Abstract
Cancer remains a major threat to human health worldwide. Cytotoxicity has imposed restrictions on the conventional cytotoxic drug-based chemotherapy. The rapidly-developing nanomedicine has shown great promise in revolutionizing chemotherapy with improved efficiency and reduced toxicity. Gd@C82(OH)22, a novel endohedral metallofullerenol, was first reported by our research group to suppress tumor growth and metastasis efficiently without obvious toxicity. Gd@C82(OH)22 imprisons tumors by facilitating the formation of surrounding fibrous layers which is different from chemotherapeutics that poison tumor cells. In this review, the authors first reported the antineoplastic activity of metallofullerenol Gd@C82(OH)22 followed by further discussions on its new anti-cancer molecular mechanism—tumor encaging. On this basis, the unparalleled advantages of nanomedicine in the future drug design are discussed. The unique interaction modes of Gd@C82(OH)22 with specific targeted biomolecules may shed light on a new avenue for drug design. Depending on the surface characteristics of target biomolecules, nanomedicine, just like a transformable and dynamic key, can self-assemble into suitable shapes to match several locks for the thermodynamic stability, suggesting the target-tailoring ability of nanomedicine.
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Affiliation(s)
- Jinxia Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Linlin Chen
- College of Pharmacy, Shanxi Medical University, Taiyuan 030001, China
| | - Liang Yan
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Zhanjun Gu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Zhaofang Chen
- Jiangsu Key Laboratory of Hazardous Chemicals Safety and Control, College of Safety Science and Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Aiping Zhang
- College of Pharmacy, Shanxi Medical University, Taiyuan 030001, China
| | - Feng Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China.
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25
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Quan X, Liu J, Zhou J. Multiscale modeling and simulations of protein adsorption: progresses and perspectives. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2018.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Chen D, Ganesh S, Wang W, Amiji M. The role of surface chemistry in serum protein corona-mediated cellular delivery and gene silencing with lipid nanoparticles. NANOSCALE 2019; 11:8760-8775. [PMID: 30793730 DOI: 10.1039/c8nr09855g] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Delivery of genetic medicines, such as small interfering RNA (siRNA), by lipid nanoparticles (LNPs) is a promising approach towards the treatment of diseases, such as solid tumors. However, in vitro and in vivo nanoparticle delivery efficiency is influenced by the formation of a protein corona in biological media. In this study, we have formulated four types of EnCore nanoparticles (F1 to F4) with a similar composition, but different polyethylene glycol (PEG) conjugated lipid chain lengths (carbon 14 vs. carbon 18) and molar ratios (6% vs. 3%). These LNPs showed dramatic differences in cellular delivery and transfection in hepatocellular carcinoma (HepG2) cells in the absence and presence of fetal bovine serum (FBS). The presence of proteins inhibited the cellular uptake of C18 (3%) nanoparticles, while it facilitated the cellular uptake of C14 nanoparticles. Among the adsorbed proteins from FBS, apolipoprotein E, but not apolipoprotein A1, affected the cellular uptake of the carbon 14 LNPs. Additionally, surface PEG was one of the determinants for the protein corona amount and composition. Finally, different serum to LNP volume ratios resulted in different protein enrichment patterns. Overall, the results showed a correlation between surface chemistry of LNPs and the protein corona composition suggesting a potential use for targeted delivery.
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Affiliation(s)
- Dongyu Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, MA 02115, USA.
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27
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Wan Y, Guan S, Qian M, Huang H, Han F, Wang S, Zhang H. Structural basis of fullerene derivatives as novel potent inhibitors of protein acetylcholinesterase without catalytic active site interaction: insight into the inhibitory mechanism through molecular modeling studies. J Biomol Struct Dyn 2019; 38:410-425. [DOI: 10.1080/07391102.2019.1576543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yongfeng Wan
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Shanshan Guan
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
- College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun, Jilin, China
| | - Mengdan Qian
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
| | - Houhou Huang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Fei Han
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
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28
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Jin Y, Duan M, Wang X, Kong X, Zhou W, Sun H, Liu H, Li D, Yu H, Li Y, Hou T. Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations. J Chem Inf Model 2019; 59:842-857. [DOI: 10.1021/acs.jcim.8b00796] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ye Jin
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mojie Duan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xuwen Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaotian Kong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wenfang Zhou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huidong Yu
- Rongene Pharma Co., Ltd., Shenzhen, Guangdong 518054, China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Tingjun Hou
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
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29
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Yin X, Li B, Liu S, Gu Z, Zhou B, Yang Z. Effect of the surface curvature on amyloid-β peptide adsorption for graphene. RSC Adv 2019; 9:10094-10099. [PMID: 35520900 PMCID: PMC9062381 DOI: 10.1039/c8ra10015b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/12/2019] [Indexed: 11/21/2022] Open
Abstract
The adsorption of amyloid-β peptide (Aβ) onto graphene nanosheets with curvature at a neutral pH has been studied by using molecular dynamics simulations in combination with umbrella sampling. We found that Aβ adsorbed onto graphene with distinct characteristics, causing the breakage of hydrogen bonds which leads to its conformational change. Interestingly, the adsorption capacity of graphene's surface varies significantly depending on its curvature, namely, the surface with negative curvature has a higher probability to adsorb the Aβ than the one with positive curvature. This phenomenon is further evidenced by the binding energy between the complex of graphene and Aβ derived from the potential of mean force (PMF). The hydrophobic interactions and the direct dispersion interactions between the graphene nanosheet and the Aβ play a dominant role in the adsorption process. These findings indicate that not only is the chemical composition an important factor but also the shape of the nanoparticle is important in determining its interaction with proteins: the contacting surface curvature can lead to different adsorption capability. The adsorbing capacity of graphene's surface varies significantly depending on its curvature, namely, the surface with negative curvature has a higher probability to adsorb the Aβ than the one with positive curvature.![]()
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Affiliation(s)
- Xiuhua Yin
- Institute of Quantitative Biology and Medicine
- State Key Laboratory of Radiation Medicine and Protection
- School of Radiation Medicine and Protection
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions
- Soochow University
| | - Baoyu Li
- Institute of Quantitative Biology and Medicine
- State Key Laboratory of Radiation Medicine and Protection
- School of Radiation Medicine and Protection
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions
- Soochow University
| | - Shengtang Liu
- Institute of Quantitative Biology and Medicine
- State Key Laboratory of Radiation Medicine and Protection
- School of Radiation Medicine and Protection
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions
- Soochow University
| | - Zonglin Gu
- Institute of Quantitative Biology and Medicine
- State Key Laboratory of Radiation Medicine and Protection
- School of Radiation Medicine and Protection
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions
- Soochow University
| | - Bo Zhou
- School of Electronic Engineering
- Chengdu Technological University
- Chengdu 611730
- China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine
- State Key Laboratory of Radiation Medicine and Protection
- School of Radiation Medicine and Protection
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions
- Soochow University
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30
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Devereux SJ, Massaro M, Barker A, Hinds DT, Hifni B, Simpson JC, Quinn SJ. Spectroscopic study of the loading of cationic porphyrins by carbon nanohorns as high capacity carriers of photoactive molecules to cells. J Mater Chem B 2019. [DOI: 10.1039/c9tb00217k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Spherical carbon nanohorns have great potential as drug delivery agents. Here a detailed study of the loading of porphyrin molecules is reported and the influence on their stability described. An optimally loaded sample is shown to cause photoactivated cell death.
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Affiliation(s)
| | - Marina Massaro
- School of Chemistry
- University College Dublin
- Dublin 4
- Ireland
| | - Andrew Barker
- School of Chemistry
- University College Dublin
- Dublin 4
- Ireland
| | - David T. Hinds
- School of Chemistry
- University College Dublin
- Dublin 4
- Ireland
| | - Badriah Hifni
- School of Chemistry
- University College Dublin
- Dublin 4
- Ireland
- School of Biology & Environmental Science, University College Dublin, Belfield
| | - Jeremy C. Simpson
- School of Biology & Environmental Science, University College Dublin, Belfield
- Dublin 4
- Ireland
| | - Susan J. Quinn
- School of Chemistry
- University College Dublin
- Dublin 4
- Ireland
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31
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Saha A, Chakraborti S. Effect of ZnO quantum dots on Escherichia coli global transcription regulator: A molecular investigation. Int J Biol Macromol 2018; 117:1280-1288. [PMID: 29870809 DOI: 10.1016/j.ijbiomac.2018.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 11/17/2022]
Abstract
ZnO quantum dots (QDs) are very well known for their antimicrobial activity against several bacteria, however, we still do not know any protein targets of ZnO QDs. In order to determine possible protein target, interaction of ZnO QDs was studied with CRP (Cyclic AMP Receptor Protein), a global transcription regulator protein. Binding between ZnO QDs and E. coli CRP was mainly studied by isothermal titration calorimetry (ITC), structural changes of protein were monitored by fluorescence and circular dichroism spectroscopy, and in-vitro transcription assay was used to asses CRP activity. Result shows that both electrostatic and hydrophobic interactions are involved in CRP-ZnO binding. Different spectroscopic investigation revealed that ZnO binding to CRP leads to extensive unfolding and destabilization, which ultimately leads to protein aggregation. It was also observed that in presence of ZnO dimerization ability of CRP was sharply reduced. In-vitro transcription assay also shows that CRP activity gets severely compromised on ZnO binding. All our data suggests that ZnO QD binding to CRP and consequent structural and functional changes most probably plays a crucial role in ZnO QD induced antimicrobial action.
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Affiliation(s)
- Abinit Saha
- Department of Biochemistry, Bose Institute, P-1/12, C.I.T. Scheme VIIM, Kolkata 700054, India; Adamas University, Barasat-Barrackpore Road Jagannathpur, Kolkata 700126, India
| | - Soumyananda Chakraborti
- Department of Biochemistry, Bose Institute, P-1/12, C.I.T. Scheme VIIM, Kolkata 700054, India; Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
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32
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Song X, Cao L, Cong S, Song Y, Tan M. Characterization of Endogenous Nanoparticles from Roasted Chicken Breasts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:7522-7530. [PMID: 29932651 DOI: 10.1021/acs.jafc.8b01988] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Emergence of endogenous nanoparticles in thermally processed food has aroused much attention due to their unique properties and potential biological impact. The aim of this study was to investigate the presence of fluorescence nanoparticles in roasted chicken breasts, elemental composition, physicochemical properties, and their molecular interaction with human serum albumin (HSA). Transmission electron microscopy analysis revealed that the foodborne nanoparticles from roasted chicken were nearly spherical with an average particle size of 1.7 ± 0.4 nm. The elemental analysis of X-ray photoelectron spectroscopy showed the composition of nanoparticles as 47.4% C, 25.8% O, and 26.1% N. The fluorescence of HSA was quenched by the nanoparticles following a static mode, and the molecular interaction of nanoparticles with HSA was spontaneous (Δ G0 < 0), where hydrogen bonding and van der Waals forces played an important role during HSA-nanoparticles complex stabilization through thermodynamic analysis by isothermal titration calorimetry. The principal location of the nanoparticles binding site on HSA was primarily in site I as determined by site-specific marker competition. The conformational of HSA was also changed and α-helical structure decreased in the presence of nanoparticles. Our studies revealed that fluorescent nanoparticles were produced after roasting of chicken breast at 230 °C for 30 min for the first time. The obtained nanoparticles can interact with HSA in a spontaneous manner, thus providing valuable insight into foodborne NPs as well as their effects to human albumin protein.
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Affiliation(s)
- Xunyu Song
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Qinggongyuan1 , Ganjingzi District, Dalian 116034 , Liaoning China
- Engineering Research Center of Seafood of Ministry of Education of China , Dalian 116034 , Liaoning China
| | - Lin Cao
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Qinggongyuan1 , Ganjingzi District, Dalian 116034 , Liaoning China
- Engineering Research Center of Seafood of Ministry of Education of China , Dalian 116034 , Liaoning China
| | - Shuang Cong
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Qinggongyuan1 , Ganjingzi District, Dalian 116034 , Liaoning China
- Engineering Research Center of Seafood of Ministry of Education of China , Dalian 116034 , Liaoning China
| | - Yukun Song
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Qinggongyuan1 , Ganjingzi District, Dalian 116034 , Liaoning China
- Engineering Research Center of Seafood of Ministry of Education of China , Dalian 116034 , Liaoning China
| | - Mingqian Tan
- School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Qinggongyuan1 , Ganjingzi District, Dalian 116034 , Liaoning China
- Engineering Research Center of Seafood of Ministry of Education of China , Dalian 116034 , Liaoning China
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33
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Hassanzadeh P, Atyabi F, Dinarvand R. Ignoring the modeling approaches: Towards the shadowy paths in nanomedicine. J Control Release 2018; 280:58-75. [DOI: 10.1016/j.jconrel.2018.04.042] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/22/2018] [Accepted: 04/23/2018] [Indexed: 12/30/2022]
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34
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Kumar S, Yadav I, Aswal VK, Kohlbrecher J. Structure and Interaction of Nanoparticle-Protein Complexes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5679-5695. [PMID: 29672062 DOI: 10.1021/acs.langmuir.8b00110] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The integration of nanoparticles with proteins is of high scientific interest due to the amazing potential displayed by their complexes, combining the nanoscale properties of nanoparticles with the specific architectures and functions of the protein molecules. The nanoparticle-protein complexes, in particular, are useful in the emerging field of nanobiotechnology (nanomedicine, drug delivery, and biosensors) as the nanoparticles having sizes comparable to that of living cells can access and operate within the cell. The understanding of nanoparticle interaction with different protein molecules is a prerequisite for such applications. The interaction of the two components has been shown to result in conformational changes in proteins and to affect the surface properties and colloidal stability of the nanoparticles. In this feature article, our recent studies exploring the driving interactions in nanoparticle-protein systems and resultant structures are presented. The anionic colloidal silica nanoparticles and two globular charged proteins [lysozyme and bovine serum albumin (BSA)] have been investigated as model systems. The adsorption behavior of the two proteins on nanoparticles is found to be completely different, but they both give rise to similar phase transformation from one phase to two phase in respective nanoparticle-protein systems. The presence of protein induces the short-range and long-range attraction between the nanoparticles with lysozyme and BSA, respectively. The observed phase behavior and its dependence on various physiochemical parameters (e.g., nanoparticle size, ionic strength, and solution pH) have been explained in terms of underlying interactions.
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Affiliation(s)
- Sugam Kumar
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085 , India
| | - Indresh Yadav
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085 , India
- Homi Bhabha National Institute , Mumbai 400 094 , India
| | - Vinod Kumar Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085 , India
- Homi Bhabha National Institute , Mumbai 400 094 , India
| | - Joachim Kohlbrecher
- Laboratory for Neutron Scattering and Imaging , Paul Scherrer Institut , CH-5232 PSI Villigen , Switzerland
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35
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Ding HM, Ma YQ. Computational approaches to cell-nanomaterial interactions: keeping balance between therapeutic efficiency and cytotoxicity. NANOSCALE HORIZONS 2018; 3:6-27. [PMID: 32254106 DOI: 10.1039/c7nh00138j] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Owing to their unique properties, nanomaterials have been widely used in biomedicine since they have obvious inherent advantages over traditional ones. However, nanomaterials may also cause dysfunction in proteins, genes and cells, resulting in cytotoxic and genotoxic responses. Recently, more and more attention has been paid to these potential toxicities of nanomaterials, especially to the risks of nanomaterials to human health and safety. Therefore, when using nanomaterials for biomedical applications, it is of great importance to keep the balance between therapeutic efficiency and cytotoxicity (i.e., increase the therapeutic efficiency as well as decrease the potential toxicity). This requires a deeper understanding of the interactions between various types of nanomaterials and biological systems at the nano/bio interface. In this review, from the point of view of theoretical researchers, we will present the current status regarding the physical mechanism of cytotoxicity caused by nanomaterials, mainly based on recent simulation results. In addition, the strategies for minimizing the nanotoxicity naturally and artificially will also be discussed in detail. Furthermore, we should notice that toxicity is not always bad for clinical use since causing the death of specific cells is the main way of treating disease. Enhancing the targeting ability of nanomaterials to diseased cells and minimizing their side effects on normal cells will always be hugely challenging issues in nanomedicine. By combining the latest computational studies with some experimental verifications, we will provide special insights into recent advances regarding these problems, especially for the design of novel environment-responsive nanomaterials.
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Affiliation(s)
- Hong-Ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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36
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Bell DR, Kang SG, Huynh T, Zhou R. Concentration-dependent binding of CdSe quantum dots on the SH3 domain. NANOSCALE 2017; 10:351-358. [PMID: 29215114 DOI: 10.1039/c7nr06148j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Quantum dots (QDs) are being used increasingly in applications for solar panels, consumer electronics, and biomedical imaging. For biomedical applications, QDs are typically coated with a biocompatible molecule for the system of interest. Experiments have indicated a QD dose-dependent and surface coating-dependent toxicity, with a portion of the toxicity being ascribed to interference with biomolecules. In this work, the interaction of trioctylphosphine oxide (TOPO) coated (CdSe)13 QDs with the SRC homology 3 domain (SH3) protein domain are explored using molecular dynamics simulations. The results of this research agree well with experiments that show that at the lowest concentration, the QDs have little affinity for the native proline-rich motif (PRM) binding site of SH3. At higher concentrations, the QDs aggregate and increasingly prefer the PRM binding site, indicating that the normal SH3 function is impeded. This binding dependence is attributed to changes in the local density of the surface coated TOPO molecules upon aggregation. These results present possible interesting QD toxicity patterns and reveal the interdependence between dose and surface coating effects in QD toxicity.
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Affiliation(s)
- David R Bell
- Computational Biology Center, IBM Thomas J Watson Research Center, Yorktown Heights, NY 10598, USA.
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37
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Xu Y, Luo Z, Li S, Li W, Zhang X, Zuo YY, Huang F, Yue T. Perturbation of the pulmonary surfactant monolayer by single-walled carbon nanotubes: a molecular dynamics study. NANOSCALE 2017; 9:10193-10204. [PMID: 28485435 DOI: 10.1039/c7nr00890b] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) are at present synthesized on a large scale with a variety of applications. The increasing likelihood of exposure to SWCNTs, however, puts human health at a high risk. As the front line of the innate host defense system, the pulmonary surfactant monolayer (PSM) at the air-water interface of the lungs interacts with the inhaled SWCNTs, which in turn inevitably perturb the ultrastructure of the PSM and affect its biophysical functions. Here, using molecular dynamics simulations, we demonstrate how the diameter and length of SWCNTs critically regulate their interactions with the PSM. Compared to their diameters, the inhalation toxicity of SWCNTs was found to be largely affected by their lengths. Short SWCNTs with lengths comparable to the monolayer thickness are found to vertically insert into the PSM with no indication of translocation, possibly leading to accumulation of SWCNTs in the PSM with prolonged retention and increased inflammation potentials. The perturbation also comes from the forming water pores across the PSM. Longer SWCNTs are found to horizontally insert into the PSM during inspiration, and they can be wrapped by the PSM during deep expiration via a tube diameter-dependent self-rotation. The potential toxicity of longer SWCNTs comes from severe lipid depletion and the PSM-rigidifying effect. Our findings could help reveal the inhalation toxicity of SWCNTs, and pave the way for the safe use of SWCNTs as vehicles for pulmonary drug delivery.
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Affiliation(s)
- Yan Xu
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Zhen Luo
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Shixin Li
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Weiguo Li
- College of Science, China University of Petroleum (East China), Qingdao 266580, China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yi Y Zuo
- Department of Mechanical Engineering, University of Hawaii at Monoa, Honolulu, Hawaii 96822, USA
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
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Lin S, Mortimer M, Chen R, Kakinen A, Riviere JE, Davis TP, Ding F, Ke PC. NanoEHS beyond Toxicity - Focusing on Biocorona. ENVIRONMENTAL SCIENCE. NANO 2017; 7:1433-1454. [PMID: 29123668 PMCID: PMC5673284 DOI: 10.1039/c6en00579a] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The first phase of environmental health and safety of nanomaterials (nanoEHS) studies has been mainly focused on evidence-based investigations that probe the impact of nanoparticles, nanomaterials and nano-enabled products on biological and ecological systems. The integration of multiple disciplines, including colloidal science, nanomaterial science, chemistry, toxicology/immunology and environmental science, is necessary to understand the implications of nanotechnology for both human health and the environment. While strides have been made in connecting the physicochemical properties of nanomaterials with their hazard potential in tiered models, fundamental understanding of nano-biomolecular interactions and their implications for nanoEHS is largely absent from the literature. Research on nano-biomolecular interactions within the context of natural systems not only provides important clues for deciphering nanotoxicity and nanoparticle-induced pathology, but also presents vast new opportunities for screening beneficial material properties and designing greener products from bottom up. This review highlights new opportunities concerning nano-biomolecular interactions beyond the scope of toxicity.
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Affiliation(s)
- Sijie Lin
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Monika Mortimer
- Bren School of Environmental Science and Management, Earth Research Institute and University of California Center for the Environmental Implications of Nanotechnology (UC CEIN), University of California, Santa Barbara, California 93106, United States
| | - Ran Chen
- Nanotechnology Innovation Center of Kansas State, Kansas State University, Manhattan, Kansas 66506, United States
| | - Aleksandr Kakinen
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Jim E. Riviere
- Nanotechnology Innovation Center of Kansas State, Kansas State University, Manhattan, Kansas 66506, United States
| | - Thomas P. Davis
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, United Kingdom
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Pu Chun Ke
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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39
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The effects of single-walled carbon nanotubes (SWCNTs) on the structure and function of human serum albumin (HSA): Molecular docking and molecular dynamics simulation studies. Struct Chem 2017. [DOI: 10.1007/s11224-017-0963-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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40
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Jana P, Samanta K, Bäcker S, Zellermann E, Knauer S, Schmuck C. Efficient Gene Transfection through Inhibition of β-Sheet (Amyloid Fiber) Formation of a Short Amphiphilic Peptide by Gold Nanoparticles. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Poulami Jana
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Krishnananda Samanta
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Sandra Bäcker
- Institute for Biology; University of Duisburg-Essen; 45117 Essen Germany
| | - Elio Zellermann
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Shirley Knauer
- Institute for Biology; University of Duisburg-Essen; 45117 Essen Germany
| | - Carsten Schmuck
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
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41
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Jana P, Samanta K, Bäcker S, Zellermann E, Knauer S, Schmuck C. Efficient Gene Transfection through Inhibition of β-Sheet (Amyloid Fiber) Formation of a Short Amphiphilic Peptide by Gold Nanoparticles. Angew Chem Int Ed Engl 2017; 56:8083-8088. [DOI: 10.1002/anie.201700713] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Poulami Jana
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Krishnananda Samanta
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Sandra Bäcker
- Institute for Biology; University of Duisburg-Essen; 45117 Essen Germany
| | - Elio Zellermann
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
| | - Shirley Knauer
- Institute for Biology; University of Duisburg-Essen; 45117 Essen Germany
| | - Carsten Schmuck
- Institute for Organic Chemistry; University of Duisburg-Essen; 45117 Essen Germany
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42
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Soltani N, Gholami MR. Increase in the β-Sheet Character of an Amyloidogenic Peptide upon Adsorption onto Gold and Silver Surfaces. Chemphyschem 2017; 18:526-536. [DOI: 10.1002/cphc.201601000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/23/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Nima Soltani
- Department of Chemistry; Sharif University of Technology; Tehran 11365-11155 Iran), Fax: (+98) 216 600 5718
| | - Mohammad Reza Gholami
- Department of Chemistry; Sharif University of Technology; Tehran 11365-11155 Iran), Fax: (+98) 216 600 5718
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Abstract
The ability of nanoparticles to alter protein structure and dynamics plays an important role in their medical and biological applications. We investigate allosteric effects of gold nanoparticles on human serum albumin protein using molecular simulations. The extent to which bound nanoparticles influence the structure and dynamics of residues distant from the binding site is analyzed. The root mean square deviation, root mean square fluctuation and variation in the secondary structure of individual residues on a human serum albumin protein are calculated for four protein-gold nanoparticle binding complexes. The complexes are identified in a brute-force search process using an implicit-solvent coarse-grained model for proteins and nanoparticles. They are then converted to atomic resolution and their structural and dynamic properties are investigated using explicit-solvent atomistic molecular dynamics simulations. The results show that even though the albumin protein remains in a folded structure, the presence of a gold nanoparticle can cause more than 50% of the residues to decrease their flexibility significantly, and approximately 10% of the residues to change their secondary structure. These affected residues are distributed on the whole protein, even on regions that are distant from the nanoparticle. We analyze the changes in structure and flexibility of amino acid residues on a variety of binding sites on albumin and confirm that nanoparticles could allosterically affect the ability of albumin to bind fatty acids, thyroxin and metals. Our simulations suggest that allosteric effects must be considered when designing and deploying nanoparticles in medical and biological applications that depend on protein-nanoparticle interactions.
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Affiliation(s)
- Qing Shao
- Department of Chemical and Biomolecular Engineering, North Carolina State University Raleigh, NC, 27695, USA.
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44
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Chen R, Riviere JE. Biological Surface Adsorption Index of Nanomaterials: Modelling Surface Interactions of Nanomaterials with Biomolecules. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 947:207-253. [PMID: 28168670 DOI: 10.1007/978-3-319-47754-1_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Quantitative analysis of the interactions between nanomaterials and their surrounding environment is crucial for safety evaluation in the application of nanotechnology as well as its development and standardization. In this chapter, we demonstrate the importance of the adsorption of surrounding molecules onto the surface of nanomaterials by forming biocorona and thus impact the bio-identity and fate of those materials. We illustrate the key factors including various physical forces in determining the interaction happening at bio-nano interfaces. We further discuss the mathematical endeavors in explaining and predicting the adsorption phenomena, and propose a new statistics-based surface adsorption model, the Biological Surface Adsorption Index (BSAI), to quantitatively analyze the interaction profile of surface adsorption of a large group of small organic molecules onto nanomaterials with varying surface physicochemical properties, first employing five descriptors representing the surface energy profile of the nanomaterials, then further incorporating traditional semi-empirical adsorption models to address concentration effects of solutes. These Advancements in surface adsorption modelling showed a promising development in the application of quantitative predictive models in biological applications, nanomedicine, and environmental safety assessment of nanomaterials.
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Affiliation(s)
- Ran Chen
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Kansas State University, Manhattan, KS, 66506, USA
| | - Jim E Riviere
- Institute of Computational Comparative Medicine, Department of Anatomy and Physiology, Kansas State University, Manhattan, KS, 66506, USA
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45
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Zhao D, Zhou J. Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes. Phys Chem Chem Phys 2017; 19:986-995. [DOI: 10.1039/c6cp04962a] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes.
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Affiliation(s)
- Daohui Zhao
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
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Arakha M, Borah SM, Saleem M, Jha AN, Jha S. Interfacial assembly at silver nanoparticle enhances the antibacterial efficacy of nisin. Free Radic Biol Med 2016; 101:434-445. [PMID: 27845185 DOI: 10.1016/j.freeradbiomed.2016.11.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 11/17/2022]
Abstract
Nisin is a well-recognised antimicrobial peptide (AMP) used in food industry. However, efficacy of the peptide has been compromised due to development of resistance in different bacterial strains. Here, efficacy of the peptide upon assembly at a silver nanoparticle (AgNP) interface has been characterized. To this end, experimental and simulation studies are done to characterize the interfacial assembly of nisin and underlie antibacterial mechanism. Being an AMP, efficacy of an intact nisin is explored against Gram-positive and Gram-negative bacteria, and compared with antibacterial propensity of the interfacially assembled nisin. Antibacterial propensity, upon the assembly, increases against both kinds of bacteria. Interestingly, the growth inhibition studies of the interfacially assembled nisin indicate that the originally nisin resistant Gram-negative bacteria become sensitive to the nanomolar nisin concentrations. Furthermore, reactive oxygen species (ROS) measurements together with confocal microscopy imaging indicate that the increase in interfacial and intracellular ROS production upon the treatment is underling mechanism of enhanced antibacterial propensity of the assembled nisin. Thus, the study observed that the interfacial assembly of nisin at AgNP interface enhances the efficacy of nisin against different spectrum of bacteria, where the intact nisin is largely ineffective for the studied concentrations.
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Affiliation(s)
- Manoranjan Arakha
- Department of Life Science, National Institute of Technology Rourkela, Odisha 769008, India
| | - Sapna M Borah
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam 784028, India
| | - Mohammed Saleem
- Department of Life Science, National Institute of Technology Rourkela, Odisha 769008, India
| | - Anupam N Jha
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam 784028, India
| | - Suman Jha
- Department of Life Science, National Institute of Technology Rourkela, Odisha 769008, India.
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47
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Zaheer Z, Aazam ES, Kosa SA. Effects of cationic and anionic micelles on the morphology of biogenic silver nanoparticles, and their catalytic activity for congo red. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.04.089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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48
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Abd Ellah NH, Abouelmagd SA. Surface functionalization of polymeric nanoparticles for tumor drug delivery: approaches and challenges. Expert Opin Drug Deliv 2016; 14:201-214. [DOI: 10.1080/17425247.2016.1213238] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Noura H. Abd Ellah
- Department of Pharmaceutics, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Sara A. Abouelmagd
- Department of Pharmaceutics, Faculty of Pharmacy, Assiut University, Assiut, Egypt
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49
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Bhunia AK, Kamilya T, Saha S. Temperature Dependent and Kinetic Study of the Adsorption of Bovine Serum Albumin to ZnO Nanoparticle Surfaces. ChemistrySelect 2016. [DOI: 10.1002/slct.201600446] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Amit K. Bhunia
- Department of Physics & Technophysics; Vidyasagar University; Paschim Medinipur -721102 India
- Department of Physics; Government General Degree College at Gopiballabpur-II, Beliaberh; Paschim Medinipur- 721517 India
| | - Tapanendu Kamilya
- Department of Physics; Narajole Raj College; Paschim Medinipur- 721211 India
| | - Satyajit Saha
- Department of Physics & Technophysics; Vidyasagar University; Paschim Medinipur -721102 India
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50
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Robust Denaturation of Villin Headpiece by MoS2 Nanosheet: Potential Molecular Origin of the Nanotoxicity. Sci Rep 2016; 6:28252. [PMID: 27312409 PMCID: PMC4911589 DOI: 10.1038/srep28252] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/02/2016] [Indexed: 12/13/2022] Open
Abstract
MoS2 nanosheet, a new two-dimensional transition metal dichalcogenides nanomaterial, has attracted significant attentions lately due to many potential promising biomedical applications. Meanwhile, there is also a growing concern on its biocompatibility, with little known on its interactions with various biomolecules such as proteins. In this study, we use all-atom molecular dynamics simulations to investigate the interaction of a MoS2 nanosheet with Villin Headpiece (HP35), a model protein widely used in protein folding studies. We find that MoS2 exhibits robust denaturing capability to HP35, with its secondary structures severely destroyed within hundreds of nanosecond simulations. Both aromatic and basic residues are critical for the protein anchoring onto MoS2 surface, which then triggers the successive protein unfolding process. The main driving force behind the adsorption process is the dispersion interaction between protein and MoS2 monolayer. Moreover, water molecules at the interface between some key hydrophobic residues (e.g. Trp-64) and MoS2 surface also help to accelerate the process driven by nanoscale drying, which provides a strong hydrophobic force. These findings might have shed new light on the potential nanotoxicity of MoS2 to proteins with atomic details, which should be helpful in guiding future biomedical applications of MoS2 with its nanotoxicity mitigated.
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