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Ayyari N, Vaezi Z, Ashin ZF, Karimi E, Mohsenzadeh Haji F, Nikkhah M, Naderi-Manesh H. Porphysome Engineered With Specific Protein Binding Sites as a Multimodal Theranostic Nanocarrier for Targeted Protein Delivery. Chem Biodivers 2024:e202400348. [PMID: 38616166 DOI: 10.1002/cbdv.202400348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
The immobilization of proteins on the surface of carriers is challenging due to the loss of protein structure and function in this process. Here, we report the development of the protein immobilization on the surface of the metallated-porphyrin complex in the porphysome nanocarrier. The conjugated Ni-porphyrin to fatty acid (as a tail) has been synthesized and independently placed at the depth of the bilayer center of Dipalmitoylphosphatidylcholine (DPPC) in which the Ni-porphyrin was at the polar region of the membrane and is thus superficial. This porphysome (DPPC: Ni-porphyrin, 4 : 1 mole ratio) was formed by supramolecular self-assembly with a diameter of 173±7 nm and zeta potential -8.5±3.4 mv, which exhibited no significant toxicity at the experimental concentrations and acceptable cellular uptake on MCF-7 cells. The physicochemical properties and specific protein binding sites of the firefly luciferase as a model protein into the porphysome (1 : 2 mole ratio) show the conjugation efficiency about 80 % and the conformation of protein was completely maintained. Furthermore, bioluminescence assay and SDS-PAGE confirmed the preservation of protein function. The stabilized platform of porphyrin-lipid structure can potentially improve the efficacy of protein functionality for a particular display, shifting porphysomes from a simple carrier to a therapeutic agent.
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Affiliation(s)
- Niloofar Ayyari
- Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, PO Box, 14115-154, Tehran, Iran
| | - Zahra Vaezi
- Department of Bioactive compounds, Faculty of Interdisciplinary Science and Technologies, Tarbiat Modares University, Postal codes, 14115-154, Tehran, Iran
| | - Zeinab Fotouhi Ashin
- Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, PO Box, 14115-154, Tehran, Iran
| | - Elham Karimi
- Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, PO Box, 14115-154, Tehran, Iran
| | - Fatemeh Mohsenzadeh Haji
- Department of Organic chemistry, Faculty of Chemistry, Tarbiat Modares University, Postal codes, 14115-154, Tehran, Iran
| | - Maryam Nikkhah
- Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, PO Box, 14115-154, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, PO Box, 14115-154, Tehran, Iran
- Department of Bioactive compounds, Faculty of Interdisciplinary Science and Technologies, Tarbiat Modares University, Postal codes, 14115-154, Tehran, Iran
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Abedini-Nassab R, Taheri F, Emamgholizadeh A, Naderi-Manesh H. Single-Cell RNA Sequencing in Organ and Cell Transplantation. Biosensors (Basel) 2024; 14:189. [PMID: 38667182 PMCID: PMC11048310 DOI: 10.3390/bios14040189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024]
Abstract
Single-cell RNA sequencing is a high-throughput novel method that provides transcriptional profiling of individual cells within biological samples. This method typically uses microfluidics systems to uncover the complex intercellular communication networks and biological pathways buried within highly heterogeneous cell populations in tissues. One important application of this technology sits in the fields of organ and stem cell transplantation, where complications such as graft rejection and other post-transplantation life-threatening issues may occur. In this review, we first focus on research in which single-cell RNA sequencing is used to study the transcriptional profile of transplanted tissues. This technology enables the analysis of the donor and recipient cells and identifies cell types and states associated with transplant complications and pathologies. We also review the use of single-cell RNA sequencing in stem cell implantation. This method enables studying the heterogeneity of normal and pathological stem cells and the heterogeneity in cell populations. With their remarkably rapid pace, the single-cell RNA sequencing methodologies will potentially result in breakthroughs in clinical transplantation in the coming years.
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Affiliation(s)
- Roozbeh Abedini-Nassab
- Faculty of Mechanical Engineering, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran
| | - Fatemeh Taheri
- Biomedical Engineering Department, University of Neyshabur, Neyshabur P.O. Box 9319774446, Iran
| | - Ali Emamgholizadeh
- Faculty of Mechanical Engineering, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology, Faculty of Bioscience, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran;
- Department of Biophysics, Faculty of Bioscience, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran
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Vaezi Z, Baradaran Ghavami S, Farmani M, Mahdavian R, Asadzadeh Aghdaei H, Naderi-Manesh H. Oral Formulation of 5-Aminosalicylic Acid-Hemoglobin Bio-Adhesive Nanoparticles Enhance Therapeutic Efficiency in Ulcerative Colitis Mice: A Preclinical Evaluation. J Pharm Sci 2024:S0022-3549(24)00127-8. [PMID: 38582281 DOI: 10.1016/j.xphs.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/31/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
The oral formulation design for colon-specific drug delivery brings some therapeutic benefits in the ulcerative colitis treatment. We recently reported the specific delivery of hemoglobin nanoparticles-conjugating 5-aminosalicylic acid (5-ASA-HbNPs) to the inflamed site. In the current study, the therapeutic effect of the 5-ASA-HbNPs formulation was confirmed in vivo. This evaluation of 5-ASA-HbNPs not only shows longer colonic retention time due to adhesive properties, also provides full support for it as compared with free 5-ASA. It was considered as a suitable bio-adhesive nanoparticle with mucoadhesive property to pass through the mucus layer and accumulate into the mucosa. In UC model mice, a two-fold decrease in the disease activity indexes and colon weight/length ratios was significantly observed in the group treated with 5-ASA-HbNPs. This group received one percent of the standard dosage of 5-ASA (50 μg/kg), while, a similar result was observed for a significant amount of free 5-ASA (5 mg/kg). Furthermore, microscopic images of histological sections of the extracted colons demonstrated that the 5-ASA-HbNPs and 5-ASA groups displayed instances of inflammatory damage within the colon. However, in comparison to the colitis group, the extent of this damage was relatively moderate, suggesting 5-ASA-HbNPs improved therapeutic efficacy with the lower dosage form.
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Affiliation(s)
- Zahra Vaezi
- Department of Bioactive compounds, Faculty of Interdisciplinary Sciences and Technologies, Tarbiat Modares University, Postal codes: 14115-154, Tehran, Iran.
| | - Shaghayegh Baradaran Ghavami
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, P.O.BOX: 1985717411, Tehran, Iran
| | - Maryam Farmani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, P.O.BOX: 1985717411, Tehran, Iran
| | - Reza Mahdavian
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Postal codes: 14115-154, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, P.O.BOX: 1985717411, Tehran, Iran.
| | - Hossein Naderi-Manesh
- Department of Bioactive compounds, Faculty of Interdisciplinary Sciences and Technologies, Tarbiat Modares University, Postal codes: 14115-154, Tehran, Iran; Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Postal codes: 14115-154, Tehran, Iran.
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Afsharian MH, Mahdavian R, Jafari S, Allahverdi A, Soleymani H, Naderi-Manesh H. Investigation of synergic effects of nanogroove topography and polyaniline-chitosan nanocomposites on PC12 cell differentiation and axonogenesis. iScience 2024; 27:108828. [PMID: 38303727 PMCID: PMC10831943 DOI: 10.1016/j.isci.2024.108828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/09/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024] Open
Abstract
Axonal damage is the main characteristic of neurodegenerative diseases. This research was focused on remodeling cell morphology and developing a semi-tissue nanoenvironment via mechanobiological stimuli. The combination of nanogroove topography and polyaniline-chitosan enabled the manipulation of the cells by changing the morphology of PC12 cells to spindle shape and inducing the early stage of signal transduction, which is vital for differentiation. The nanosubstarte embedded with nanogooves induced PC12 cells to elongate their morphology and increase their size by 51% as compared with controls. In addition, the use of an electroconductive nanocomposite alongside nanogrooves resulted in the differentiation of PC12 cells into neurons with an average length of 193 ± 7 μm for each axon and an average number of seven axons for each neurite. Our results represent a combined tool to initiate a promising future for cell reprogramming by inducing cell differentiation and specific cellular morphology in many cases, including neurodegenerative diseases.
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Affiliation(s)
- Mohammad Hossein Afsharian
- Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box: 14115-111, Tehran, Iran
| | - Reza Mahdavian
- Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box: 14115-111, Tehran, Iran
| | - Samira Jafari
- Pharmaceutical Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box: 14115-111, Tehran, Iran
| | - Hossein Soleymani
- Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box: 14115-111, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box: 14115-111, Tehran, Iran
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Mahafel N, Vaezi Z, Barzegar M, Hekmat A, Naderi-Manesh H. Synergistic antibacterial effect of the pistachio green hull extract-loaded porphysome decorated with 4-nitroimidazole against bacteria. J Liposome Res 2024:1-14. [PMID: 38252419 DOI: 10.1080/08982104.2024.2304755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
'Active targeting' refers to modifying a nanocarrier's surface with targeting ligands. This study introduced an efficient approach for immobilizing imidazole-based drugs onto the metallated-porphyrin complex within the porphysome nanocarrier. To enhance cellular and bacterial uptake, a Ni-porphyrin with a fatty acid tail was synthesized and placed in the bilayer center of DPPC, facilitating receptor-mediated endocytosis. The Ni-porphyrin in the head group of the Ni-porphyrin-tail was placed superficially in the polar region of the membrane. Spherical unilamellar vesicle formation (DPPC: Ni-porphyrin-tail 4:1 mole ratio), as metallo-porphysome, was achieved through supramolecular self-assembly in an aqueous buffer. These vesicles exhibited a diameter of 279 ± 7 nm and a zeta potential of -15.3 ± 2.5 mV, showcasing their unique cytocompatibility. Nitroimidazole was decorated on the surface of metallo-porphysomes and pistachio green hull extract (PGHE) was loaded into the carrier for synergistic activity against (E. coli) and (S. aureus) bacteria strains. The physicochemical properties of Nitroimidazole-porphysome-PGHE, including size, zeta potential, morphology, loading efficiency, and release profile under various pH and temperature conditions in simulated gastrointestinal fluids were characterized. This combination therapy prevented bacterial cell attachment and biofilm formation in Caco-2 cells, as colon epithelial cells. The remarkable benefit of this system is that it does not affect cell viability even at 0.5 mg/ml. This study demonstrates the potential of a new co-delivery system using biocompatible metallo-porphysomes to decrease bacterial infections.
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Affiliation(s)
- Nastaran Mahafel
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Zahra Vaezi
- Department of Bioactive Compounds, Faculty of Interdisciplinary Science and Technologies, Tarbiat Modares University, Tehran, Iran
| | - Mohsen Barzegar
- Department of Bioactive Compounds, Faculty of Interdisciplinary Science and Technologies, Tarbiat Modares University, Tehran, Iran
- Department of Food Science and Technology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Azadeh Hekmat
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Bioactive Compounds, Faculty of Interdisciplinary Science and Technologies, Tarbiat Modares University, Tehran, Iran
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
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Tajik E, Vaezi Z, Tabarsa M, Hekmat A, Naderi-Manesh H. Grafting of sinapic acid onto glucosamine nanoparticle as a potential therapeutic drug with enhanced anti-inflammatory activities in osteoarthritis treatment. Int J Biol Macromol 2023; 253:127454. [PMID: 37844822 DOI: 10.1016/j.ijbiomac.2023.127454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/25/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
Glucosamine (Glu) is a cartilage and joint fluid matrix precursor that modulates osteoarthritic joint changes. To improve the enzymatic stability, glucosamine was developed into nanoglucosamine by the ionic gelation method through sodium tripolyphosphate (TPP) as cross-linking agent. The optimized mass ratio of Glu:TPP was (3:1) with the particle size 163 ± 25 nm and surface charge -5 mV. Then Sinapic acid (SA) as a natural phenolic acid with strong antioxidant and antimicrobial activities has been grafted onto glucosamine nanoparticles (GluNPs) with grafting efficiency (73 ± 6 %). The covalent insertion of SA was confirmed by UV-Vis, FTIR, 1HNMR, XRD, and FESEM analyses and the other physicochemical properties were also characterized. SA-g-GluNPs showed spherical shape with a mean diameter of 255 ± 20 nm and zeta potential +16 mV. The in vitro release profile of SA-g-GluNPs exhibited the sustained and pH-dependent drug release property. SA-g-GluNPs had a more pronounced effect on reducing the elevated levels of LPS-induced oxidative stress and pro-inflammatory cytokines than free SA in the human chondrocyte C28/I2 cell line. Furthermore, the antibacterial properties against E. coli and S. aureus were also improved by SA-g-GluNPs. This study demonstrated the potential of phenolic acid grafted GluNPs in therapeutic drug applications for chondroprotection and food industries.
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Affiliation(s)
- Ehteram Tajik
- Department of Biophysics, Science and Research branch, Islamic Azad University, Tehran, Iran
| | - Zahra Vaezi
- Department of Bioactive Compounds, Faculty of Interdisciplinary Science and Technologies, Tarbiat Modares University, Tehran, Iran
| | - Mehdi Tabarsa
- Department of Bioactive Compounds, Faculty of Interdisciplinary Science and Technologies, Tarbiat Modares University, Tehran, Iran; Department of Seafood Processing, Faculty of Marine Sciences, Tarbiat Modares University, Noor, Iran
| | - Azadeh Hekmat
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | - Hossein Naderi-Manesh
- Department of Bioactive Compounds, Faculty of Interdisciplinary Science and Technologies, Tarbiat Modares University, Tehran, Iran; Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Postal codes: 14115-154 Tehran, Iran.
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Zare AA, Naderi-Manesh H, Naghib SM, Shamsipur M, Molaabasi F. Label-free electrochemical cancer cell detection leveraging hemoglobin-encapsulated silver nanoclusters and Cu-MOF nanohybrids on a graphene-assisted dual-modal probe. Sci Rep 2023; 13:21980. [PMID: 38082024 PMCID: PMC10713537 DOI: 10.1038/s41598-023-49418-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
Breast cancer detection at an early stage significantly increases the chances of successful treatment and survival. This study presents an electrochemical biosensor for detecting breast cancer cells, utilizing silver nanoclusters encapsulated by hemoglobin and Cu (II)-porphyrin-metal organic framework (BioMOF) in a graphene-incorporated nanohybrid probe. This Hb-AgNCs@MOF-G probe demonstrates high electrochemical activity, superior dispersity, porosity, and a large surface area for effective functionalization. Using a green ultrasonic-assisted stirring method, we fabricate ultra-small 5 nm particles that readily immobilize on a glassy carbon electrode, generating a detection signal when interacting with ferricyanide/ferrocyanide redox probes. The resulting immunosensor detects as few as 2 cells/mL using Electrochemical Impedance Spectroscopy (EIS) "signal on" and 16 cells/mL via Square Wave Voltammetry (SWV) "signal off", within a broad range of cell concentrations (102-5 × 104 cells/mL). Our designed sensor shows improved selectivity (5- to 16-fold) and robust detection in human blood with a recovery efficiency between 94.8-106% (EIS method) and 95.4-111% (SWV method). This sensor could streamline early cancer diagnosis and monitor patient treatment without requiring labelling or signal amplification. As a pioneering endeavor, we've utilized integrated porous MOFs with Hb-encapsulated silver nanoclusters in cancer detection, where these components collectively enhance the overall functionality.
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Affiliation(s)
- Ali-Akbar Zare
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Seyed Morteza Naghib
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran, Iran
| | | | - Fatemeh Molaabasi
- Biomaterials and Tissue Engineering Research Group, Department of Interdisciplinary Technologies, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
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Irani K, Siampour H, Allahverdi A, Moshaii A, Naderi-Manesh H. Lung Cancer Cell-Derived Exosome Detection Using Electrochemical Approach towards Early Cancer Screening. Int J Mol Sci 2023; 24:17225. [PMID: 38139054 PMCID: PMC10743818 DOI: 10.3390/ijms242417225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 12/24/2023] Open
Abstract
Lung cancer is one of the deadliest cancers worldwide due to the inability of existing methods for early diagnosis. Tumor-derived exosomes are nano-scale vesicles released from tumor cells to the extracellular environment, and their investigation can be very useful in both biomarkers for early cancer screening and treatment assessment. This research detected the exosomes via an ultrasensitive electrochemical biosensor containing gold nano-islands (Au-NIs) structures. This way, a high surface-area-to-volume ratio of nanostructures was embellished on the FTO electrodes to increase the chance of immobilizing the CD-151 antibody. In this way, a layer of gold was first deposited on the electrode by physical vapor deposition (PVD), followed by thermal annealing to construct primary gold seeds on the surface of the electrode. Then, gold seeds were grown by electrochemical deposition through gold salt. The cell-derived exosomes were successfully immobilized on the FTO electrode through the CD-151 antibody, and cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) methods were used in this research. In the CV method, the change in the current passing through the working electrode is measured so that the connection of exosomes causes the current to decrease. In the EIS method, surface resistance changes were investigated so that the binding of exosomes increased the surface resistance. Various concentrations of exosomes in both cell culture and blood serum samples were measured to test the sensitivity of the biosensor, which makes our biosensor capable of detecting 20 exosomes per milliliter.
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Affiliation(s)
- Koosha Irani
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran P.O. Box 14115-154, Iran; (K.I.); (H.N.-M.)
| | - Hossein Siampour
- Biosensor Research Center (BRC), Isfahan University of Medical Sciences, Isfahan P.O. Box 81746-73461, Iran;
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran P.O. Box 14115-154, Iran; (K.I.); (H.N.-M.)
| | - Ahmad Moshaii
- Department of Physics, Tarbiat Modares University, Tehran P.O. Box 14115-175, Iran;
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran P.O. Box 14115-154, Iran; (K.I.); (H.N.-M.)
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Dehghanbanadaki N, Mehralitabar H, Sotoudeh R, Naderi-Manesh H. The role of Wnt palmitoleylated loop conserved disulfide bonds in Wnt-frizzled complex structural dynamics: Insights from molecular dynamics simulations. Comput Biol Med 2023; 167:107703. [PMID: 37979393 DOI: 10.1016/j.compbiomed.2023.107703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Wnts are lipid-modified proteins rich in cysteine, regulating developmental processes, and are involved in various pathological conditions. Wnts structure resembles a hand, with a palmitoleylated thumb and an index finger-like domain interacting with frizzled (FZ) receptors. Previous research shows the palmitoleyl group and the disulfides importance in Wnt folding, secretion, and function, but the structural basis is not fully understood. Here, we utilized classical molecular dynamics simulation (800-ns in total) to investigate how the thumb palmitoleyl and its close conserved disulfides (183-190, 181-195) regulated Wnt-FZ interaction and structural dynamics. Using Steered molecular dynamics experiment followed by a relaxing procedure, we also explored if these disulfides are important in Wnt-FZ complex formation. According to our results, the palmitoleyl group contributes significantly to stabilize Wnt-FZ interaction, and the disulfides modulate this contribution. We also demonstrated that disulfide 183-190 regulates the Wnt thumb fluctuation, hydrogen bond network, and secondary structure. The DCCM analysis depicted disulfide 183-190 roles in regulating native-like collective movement in the palmitoleylated loop, which changed after this disulfide removal. The pulling-relaxing experiment showed that both the disulfides, and especially, the disulfide 183-190, are highly important for long-range salt-bridge interaction establishment between Wnt Lys182 and FZ Glu64, led palmitoleyl group appropriate positioning to FZ, suggested this disulfide essential role in Wnt-FZ complex formation. Together, our findings provide new insights to how thumb-positioned disulfides contribute to Wnt-FZ complex formation, structural dynamics, and stability, introducing disulfide 183-190 as a consequential element to target in drug design and development against Wnt signalling.
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Affiliation(s)
- N Dehghanbanadaki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, PO Box: 14115-154, Tehran, Iran
| | - H Mehralitabar
- Department of Basic Sciences, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, PO Box. 48181 68984, Sari, Iran
| | - R Sotoudeh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, PO Box: 14115-154, Tehran, Iran
| | - H Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, PO Box: 14115-154, Tehran, Iran.
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Ghorbani M, Ghorbani F, Kahrizi S, Naderi-Manesh H, Kahrizi D. The application of nano-hydrogels and hydrogels in wound dressings. Cell Mol Biol (Noisy-le-grand) 2023; 69:125-131. [PMID: 38015531 DOI: 10.14715/cmb/2023.69.11.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 11/29/2023]
Abstract
Wounds and the healing process are one of the main concerns of medical science today. A wound is any loss of integrity, or rupture of the layers of skin (epidermis, dermis, and hypodermis) or subcutaneous tissue caused by physical factors (surgical incision, trauma, pressure, and gunshot wounds) or chemical factors (acid burns). It is observed that soft tissue, muscle, or bone is involved in occurrences of wounds. Lesions and fractures of the skin surface necessitate medical attention, wherein dressings expedite the healing process by establishing a physical barrier between the wound and the external environment, thereby preventing further injury or infection. Hydrogel dressings create a moist environment that facilitates common healing steps, such as granulation hyperplasia, epidermal repair, and removal of excess dead tissue. The limited adhesion of the hydrogel and the hydrated wound bed allows for easy removal of the dressing without secondary damage, thereby significantly reducing the discomfort and risk of infection during dressing changes. These modern, wet dressings foster a moist healing environment by absorbing excess inflammatory secretions and allowing proper passage of steam and air, which expedites the healing process. In this analysis, the utilization of hydrogels as wound dressings is briefly presented.
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Affiliation(s)
- Masoumeh Ghorbani
- Nanobiotechnology Department, Faculty of Innovative Science and Technology, Razi University, Kermanshah, Iran.
| | - Fatemeh Ghorbani
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Sepehr Kahrizi
- School of Medicine, Islamic Azad University, Qeshm Branch, Qeshm, Iran.
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran.
| | - Danial Kahrizi
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
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Mohammadi R, Asghari M, Colombo M, Vaezi Z, Richards DA, Stavrakis S, Naderi-Manesh H, DeMello A. Hybrid Microfluidic Device for High Throughput Isolation of Cells Using Aptamer Functionalized Diatom Frustules. Chimia (Aarau) 2022; 76:661-668. [PMID: 38071633 DOI: 10.2533/chimia.2022.661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/13/2022] [Indexed: 12/18/2023] Open
Abstract
Circulating tumor cells (CTCs), secreted from primary and metastatic malignancies, hold a wealth of essential diagnostic and prognostic data for multiple cancers. Significantly, the information contained within these cells may hold the key to understanding cancer metastasis, both individually and fundamentally. Accordingly, developing ways to identify, isolate and interrogate CTCs plays an essential role in modern cancer research. Unfortunately, CTCs are typically present in the blood in vanishingly low titers and mixed with other blood components, making their isolation and analysis extremely challenging. Herein, we report the design, fabrication and optimization of a microfluidic device capable of automatically isolating CTCs from whole blood. This is achieved in two steps, via the passive viscoelastic separation of CTCs and white blood cells (WBCs) from red blood cells (RBCs), and subsequent active magnetophoretic separation of CTCs from WBCs. We detail the specific geometries required to balance the elastic and inertial forces required for successful passive separation of RBCs, and the use of computational fluid dynamics (CFD) to optimize active magnetophoretic separation. We subsequently describe the use of magnetic biosilica frustules, extracted from Chaetoceros sp. diatoms, to fluorescently tag CTCs and facilitate magnetic isolation. Finally, we use our microfluidic platform to separate HepG2-derived CTCs from whole blood, demonstrating exceptional CTC recovery (94.6%) and purity (89.7%).
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Affiliation(s)
- Rashin Mohammadi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog Weg 1, CH-8093 Zurich, Switzerland
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran
| | - Mohammad Asghari
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog Weg 1, CH-8093 Zurich, Switzerland
| | - Monika Colombo
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog Weg 1, CH-8093 Zurich, Switzerland
| | - Zahra Vaezi
- Department of Bioactive Compounds, Faculty of Interdisciplinary Science and Technology, Tarbiat Modares University, Tehran, 14115-154, Iran
| | - Daniel A Richards
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog Weg 1, CH-8093 Zurich, Switzerland
| | - Stavros Stavrakis
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog Weg 1, CH-8093 Zurich, Switzerland
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran
| | - Andrew DeMello
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog Weg 1, CH-8093 Zurich, Switzerland.
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12
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Kelkawi AHA, Hashemzadeh H, Pashandi Z, Tiraihi T, Naderi-Manesh H. Differentiation of PC12 cell line into neuron by Valproic acid encapsulated in the stabilized core-shell liposome-chitosan Nano carriers. Int J Biol Macromol 2022; 210:252-260. [PMID: 35537586 DOI: 10.1016/j.ijbiomac.2022.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/17/2022] [Accepted: 05/04/2022] [Indexed: 12/29/2022]
Abstract
Valproic acid (VPA) usage in high dose is teratogen with low bioavailability. Hence to improve its efficacy and reduce its side effect it was encapsulated by the Nano liposomes and stabilized by the chitosan at different concentrations. The cellular uptake, biocompatibility, loading and encapsulation efficiency of the six-different formulations (1:1, 2:1, and 4:1 of chitosan-phospholipids: VPA), PC12 differentiation to neuron cells assays (gene-expression level by qRT-PCR) were conducted for the efficacy assessment of the Nano carriers. The encapsulation efficiency (EE) results revealed that the encapsulation of the VPA corresponds to the phospholipids dose, where 2:1 formulations showed higher encapsulating rate (64.5% for non-coated and 80% for coated by chitosan). The time monitored released of VPA also showed that the chitosan could enhance its controlled release too. The cellular uptake exhibited similar uptake behavior for both the coated and the non-coated Nano carriers and cytoplasmic distribution. We witnessed no toxicity effects, at different concentrations, for both formulations. Moreover, the results indicated that the gene expression level of SOX2, NeuroD1, and Neurofilament 200 increased from 1 to 5 folds for different genes. The qRT-PCR data were confirmed by the immunofluorescence antibodies staining, where Neurofilament 68 and SOX2 cell markers were modulated during differentiation of PC12 cells. Finally, our findings suggest promising potential for the Lip-VPA-Chit Nano carrier in inducing the differentiation of PC12 into neuron for treating neurodegenerative disorders.
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Affiliation(s)
- Ali Hamad Abd Kelkawi
- Nanobiotechnology Department, Faculty of Bioscience, Tarbiat Modares University, Tehran, Iran; Biology Department, College of Science, University of Kerbala, Karbala, Iraq
| | - Hadi Hashemzadeh
- Nanobiotechnology Department, Faculty of Bioscience, Tarbiat Modares University, Tehran, Iran
| | - Zaiddodine Pashandi
- Biophysics Department, Faculty of Bioscience, Tarbiat Modares University, Tehran, Iran
| | - Taki Tiraihi
- Department of Anatomy, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hossein Naderi-Manesh
- Nanobiotechnology Department, Faculty of Bioscience, Tarbiat Modares University, Tehran, Iran; Biophysics Department, Faculty of Bioscience, Tarbiat Modares University, Tehran, Iran.
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13
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Parchekani J, Allahverdi A, Taghdir M, Naderi-Manesh H. Design and simulation of the liposomal model by using a coarse-grained molecular dynamics approach towards drug delivery goals. Sci Rep 2022; 12:2371. [PMID: 35149771 PMCID: PMC8837752 DOI: 10.1038/s41598-022-06380-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/27/2022] [Indexed: 12/19/2022] Open
Abstract
The simulated liposome models provide events in molecular biological science and cellular biology. These models may help to understand the cell membrane mechanisms, biological cell interactions, and drug delivery systems. In addition, the liposomes model may resolve specific issues such as membrane transports, ion channels, drug penetration in the membrane, vesicle formation, membrane fusion, and membrane protein function mechanism. One of the approaches to investigate the lipid membranes and the mechanism of their formation is by molecular dynamics (MD) simulations. In this study, we used the coarse-grained MD simulation approach and designed a liposome model system. To simulate the liposome model, we used phospholipids that are present in the structure of natural cell membranes (1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)). Simulation conditions such as temperature, ions, water, lipid concentration were performed based on experimental conditions. Our results showed a liposome model (ellipse vesicle structure) during the 2100 ns was formed. Moreover, the analysis confirmed that the stretched and ellipse structure is the best structure that could be formed. The eukaryotic and even the bacterial cells have elliptical and flexible structures. Usually, an elliptical structure is more stable than other assembled structures. The results indicated the assembly of the lipids is directed through short-range interactions (electrostatic interactions and, van der Waals interactions). Total energy (Van der Waals and electrostatic interaction energy) confirmed the designed elliptical liposome structure has suitable stability at the end of the simulation process. Our findings confirmed that phospholipids DOPC and DOPE have a good tendency to form bilayer membranes (liposomal structure) based on their geometric shapes and chemical-physical properties. Finally, we expected the simulated liposomal structure as a simple model to be useful in understanding the function and structure of biological cell membranes. Furthermore, it is useful to design optimal, suitable, and biocompatible liposomes as potential drug carriers.
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Affiliation(s)
- Jalil Parchekani
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran.
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran. .,Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran.
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14
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Vaezi Z, Asadzadeh Aghdaei H, Sedghi M, Mahdavian R, Molakarimi M, Hashemi N, Naderi-Manesh H. Hemoglobin bio-adhesive nanoparticles as a colon-specific delivery system for sustained release of 5-aminosalicylic acid in the effective treatment of inflammatory bowel disease. Int J Pharm 2022; 616:121531. [PMID: 35121044 DOI: 10.1016/j.ijpharm.2022.121531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 10/19/2022]
Abstract
A colonic drug delivery system was developed to specifically deliver 5-aminosalicylic acid (5-ASA) to the inflamed site by conjugating with hemoglobin nanoparticles (HbNPs). The 5-ASA-HbNPs (eight 5-ASA molecules per Hb molecule) with the size of 220 nm and zeta potential of -14.6 mV is a tailored nanoparticle able to pass through the mucus layer. The 5-ASA-HbNPs do not undergo chemical and enzymatic hydrolysis in the simulated gastrointestinal fluids over 6 h. Significantly higher cellular uptakes and prolonged release was seen for the 5-ASA-HbNPs in Caco-2 cells, compared to free 5-ASA over 72 h. In addition, 5-ASA-HbNPs revealed similar therapeutic effectiveness with free 5-ASA against tumor necrosis factor and showed less inhibitory concentration (IC50) for myeloperoxidase enzyme activity. In vivo imaging of mouse demonstrated the localization of drug in the descending colon after oral administration and about 15% of the administered dose was recovered as 5-ASA from urine in 6 h. The use of these nanoparticles with the mucus adhesion properties and permeability to intestinal epithelial cells can be a good candidate with potential application in the colonic drug delivery field.
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Affiliation(s)
- Zahra Vaezi
- Department of Bioactive Compounds, Faculty of Interdisciplinary Science and Technologies, Tarbiat Modares University, 14115-154 Tehran, Iran; Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, P.O.BOX: 1985717411, Tehran, Iran.
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, P.O.BOX: 1985717411, Tehran, Iran.
| | - Mosslim Sedghi
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154 Tehran, Iran
| | - Reza Mahdavian
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154 Tehran, Iran
| | - Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, 14115-154 Tehran, Iran
| | - Naimeh Hashemi
- Ludwig Boltzmann Institute for Traumatology, Research Centre in coopoeration with AUVA, DonaueschingenstraBe 13, 1200 Vienna, Austria
| | - Hossein Naderi-Manesh
- Department of Bioactive Compounds, Faculty of Interdisciplinary Science and Technologies, Tarbiat Modares University, 14115-154 Tehran, Iran; Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154 Tehran, Iran.
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15
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Hashemzadeh H, Kelkawi AHA, Allahverdi A, Rothbauer M, Ertl P, Naderi-Manesh H. Fingerprinting Metabolic Activity and Tissue Integrity of 3D Lung Cancer Spheroids under Gold Nanowire Treatment. Cells 2022; 11:cells11030478. [PMID: 35159286 PMCID: PMC8834455 DOI: 10.3390/cells11030478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Inadequacy of most animal models for drug efficacy assessments has led to the development of improved in vitro models capable of mimicking in vivo exposure scenarios. Among others, 3D multicellular spheroid technology is considered to be one of the promising alternatives in the pharmaceutical drug discovery process. In addition to its physiological relevance, this method fulfills high-throughput and low-cost requirements for preclinical cell-based assays. Despite the increasing applications of spheroid technology in pharmaceutical screening, its application, in nanotoxicity testing is still in its infancy due to the limited penetration and uptake rates into 3D-cell assemblies. To gain a better understanding of gold nanowires (AuNWs) interactions with 3D spheroids, a comparative study of 2D monolayer cultures and 3D multicellular spheroids was conducted using two lung cancer cell lines (A549 and PC9). Cell apoptosis (live/dead assay), metabolic activity, and spheroid integrity were evaluated following exposure to AuNWs at different dose-time manners. Results revealed a distinct different cellular response between 2D and 3D cell cultures during AuNWs treatment including metabolic rates, cell viability, dose–response curves and, uptake rates. Our data also highlighted further need for more physiologically relevant tissue models to investigate in depth nanomaterial–biology interactions. It is important to note that higher concentrations of AuNWs with lower exposure times and lower concentrations of AuNWs with higher exposure times of 3 days resulted in the loss of spheroid integrity by disrupting cell–cell contacts. These findings could help to increase the understanding of AuNWs-induced toxicity on tissue levels and also contribute to the establishment of new analytical approaches for toxicological and drug screening studies.
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Affiliation(s)
- Hadi Hashemzadeh
- Nanobiotechnology Department, Faculty of Biosciences, Tarbiat Modares University, Tehran 14115-111, Iran; (H.H.); (A.H.A.K.)
| | - Ali Hamad Abd Kelkawi
- Nanobiotechnology Department, Faculty of Biosciences, Tarbiat Modares University, Tehran 14115-111, Iran; (H.H.); (A.H.A.K.)
| | - Abdollah Allahverdi
- Biophysics Department, Faculty of Biosciences, Tarbiat Modares University, Tehran 14115-111, Iran;
| | - Mario Rothbauer
- Faculty of Technical Chemistry, Vienna University of Technology (TUW), Getreidemarkt 9/163-164, 1060 Vienna, Austria;
- Orthopedic Microsystems Group, Karl Chiari Lab for Orthopedic Biology, Department of Orthopedics and Trauma Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Peter Ertl
- Faculty of Technical Chemistry, Vienna University of Technology (TUW), Getreidemarkt 9/163-164, 1060 Vienna, Austria;
- Correspondence: (P.E.); (H.N.-M.)
| | - Hossein Naderi-Manesh
- Nanobiotechnology Department, Faculty of Biosciences, Tarbiat Modares University, Tehran 14115-111, Iran; (H.H.); (A.H.A.K.)
- Biophysics Department, Faculty of Biosciences, Tarbiat Modares University, Tehran 14115-111, Iran;
- Correspondence: (P.E.); (H.N.-M.)
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16
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Mohammadi R, Naderi-Manesh H, Farzin L, Vaezi Z, Ayarri N, Samandari L, Shamsipur M. Fluorescence sensing and imaging with carbon-based quantum dots for early diagnosis of cancer: A review. J Pharm Biomed Anal 2022; 212:114628. [DOI: 10.1016/j.jpba.2022.114628] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/10/2022] [Accepted: 01/25/2022] [Indexed: 12/13/2022]
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17
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Parchekani J, Hashemzadeh H, Allahverdi A, Siampour H, Abbasian S, Moshaii A, Naderi-Manesh H. Zepto molar miRNA-21 detection in gold Nano-islands platform toward early cancer screening. Sensing and Bio-Sensing Research 2021. [DOI: 10.1016/j.sbsr.2021.100449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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18
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Sadeghi Mohammadi S, Vaezi Z, Naderi-Manesh H. Improvement of anti-biofilm activities via co-delivery of curcumin and gentamicin in lipid-polymer hybrid nanoparticle. J Biomater Sci Polym Ed 2021; 33:174-196. [PMID: 34605363 DOI: 10.1080/09205063.2021.1982159] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Pseudomonas aeruginosa is the most common pathogen that causes chronic lung infections and recurrence of the disease in cystic fibrosis patients by hiding inside cells and biofilm matrix. Herein, we developed gentamicin and curcumin-loaded lipid-polymer hybrid nanoparticle- (termed CG-HNPs) to evaluate in vitro activities against biofilm-embedded P. aeruginosa and compared with lipid nanoparticles containing the same drugs (CG-Lip). The nanoparticles were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), dynamic light scattering (DLS), fluorescence spectroscopy, and ultraviolet-visible (UV-vis) spectroscopy, which demonstrated that HNPs with a diameter of approximately 340 nm were uniform. The optimal CG-HNPs formulation illustrated high encapsulation (∼70%) and controlled release characteristics (gradually released in 72 h). The antibacterial activities of generated nanoparticles are maintained against planktonic and biofilm bacteria and it is effective in damage established biofilms. Besides, HNPs were biocompatible and nontoxic to J774 and HFF cell lines and uptake by the macrophages (J774), which facilitated the killing of intracellular bacteria in macrophages. These results introduced CG-HNPs as a promising antibacterial agent for the treatment of chronic infections and intracellular bacteria due to excellent antibacterial activity.
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Affiliation(s)
- Sanam Sadeghi Mohammadi
- Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Zahra Vaezi
- Department of Bioactive compounds, Faculty of Interdisciplinary Science and Technologies, Tarbiat Modares University, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.,Department of Bioactive compounds, Faculty of Interdisciplinary Science and Technologies, Tarbiat Modares University, Tehran, Iran
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19
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Ghorbani M, Soleymani H, Hashemzadeh H, Mortezazadeh S, Sedghi M, Shojaeilangari S, Allahverdi A, Naderi-Manesh H. Microfluidic investigation of the effect of graphene oxide on mechanical properties of cell and actin cytoskeleton networks: experimental and theoretical approaches. Sci Rep 2021; 11:16216. [PMID: 34376720 PMCID: PMC8355332 DOI: 10.1038/s41598-021-95624-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/28/2021] [Indexed: 11/09/2022] Open
Abstract
Biomechanical and morphological analysis of the cells is a novel approach for monitoring the environmental features, drugs, and toxic compounds’ effects on cells. Graphene oxide (GO) has a broad range of medical applications such as tissue engineering and drug delivery. However, the effects of GO nanosheets on biological systems have not been completely understood. In this study, we focused on the biophysical characteristics of cells and their changes resulting from the effect of GO nanosheets. The biophysical properties of the cell population were characterized as follows: cell stiffness was calculated by atomic force microscopy, cell motility and invasive properties were characterized in the microfluidic chip in which the cells are able to visualize cell migration at a single-cell level. Intracellular actin was stained to establish a quantitative picture of the intracellular cytoskeleton. In addition, to understand the molecular interaction of GO nanosheets and actin filaments, coarse-grained (CG) molecular dynamics (MD) simulations were carried out. Our results showed that GO nanosheets can reduce cell stiffness in MCF7 cells and MDA-MB-231 cell lines and highly inhibited cell migration (39.2%) in MCF-7 and (38.6%) in MDA-MB-231 cell lines through the GO nanosheets-mediated disruption of the intracellular cytoskeleton. In the presence of GO nanosheets, the cell migration of both cell lines, as well as the cell stiffness, significantly decreased. Moreover, after GO nanosheets treatment, the cell actin network dramatically changed. The experimental and theoretical approaches established a quantitative picture of changes in these networks. Our results showed the reduction of the order parameter in actin filaments was 23% in the MCF7 cell line and 20.4% in the MDA-MB-231 cell line. The theoretical studies also showed that the GO nanosheet–actin filaments have stable interaction during MD simulation. Moreover, the 2D free energy plot indicated the GO nanosheet can induce conformational changes in actin filaments. Our findings showed that the GO nanosheets can increase the distance of actin-actin subunits from 3.22 to 3.5 nm and in addition disrupt native contacts between two subunits which lead to separate actin subunits from each other in actin filaments. In this study, the biomechanical characteristics were used to explain the effect of GO nanosheets on cells which presents a novel view of how GO nanosheets can affect the biological properties of cells without cell death. These findings have the potential to be applied in different biomedical applications.
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Affiliation(s)
- Mohammad Ghorbani
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154, Tehran, Iran
| | - Hossein Soleymani
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154, Tehran, Iran
| | - Hadi Hashemzadeh
- Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, 14115-154, Tehran, Iran
| | - Saeed Mortezazadeh
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154, Tehran, Iran
| | - Mosslim Sedghi
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154, Tehran, Iran
| | - Seyedehsamaneh Shojaeilangari
- Biomedical Engineering Group, Department of Electrical Engineering and Information Technology, Iranian Research Organization for Science and Technology (IROST), P.O. Box 33535111, Tehran, Iran
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154, Tehran, Iran. .,Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, 14115-154, Tehran, Iran.
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20
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Dehghanbanadaki N, Taghdir M, Naderi-Manesh H. Investigation of Atrial Natriuretic Peptide as A Competitive Inhibitory Candidate Against Wnt/β-Catenin Signalling: A Molecular Dynamics Approach. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-020-10085-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Tavaddod S, Shojaedin-Givi B, Mahmoudi-Rad M, Naderi-Manesh H. Morphometry and Modeling of Label-Free Human Melanocytes and Melanoma Cells. Cell Biochem Biophys 2021; 79:253-260. [PMID: 33443651 DOI: 10.1007/s12013-020-00963-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2020] [Indexed: 11/29/2022]
Abstract
A combination of light microscopy and image processing was applied to investigate morphology of label-free primary-melanocytes and melanoma cells. A novel methodological approach based on morphology of nuclear body was used to find those single cells, which were at the same phase of cell cycle. The area and perimeter of melanocytes and melanoma cells were quantified. We found that there was a significant difference between area and perimeter of adendritic-shaped melanocytes with melanoma cells and the reason(s) of this finding was speculated. Finally, a theoretical model based on losing dendrites was proposed, which was in agreement with our experimental data.
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Affiliation(s)
- Sharareh Tavaddod
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK. .,Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Behnaz Shojaedin-Givi
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahnaz Mahmoudi-Rad
- Skin Research Center, Shahid Beheshti University of Medical Sciences and Health Services, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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22
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Peyvand P, Vaezi Z, Sedghi M, Dalir N, Ma’mani L, Naderi-Manesh H. Imidazolium-based ionic liquid functionalized mesoporous silica nanoparticles as a promising nano-carrier: response surface strategy to investigate and optimize loading and release process for Lapatinib delivery. Pharm Dev Technol 2020; 25:1150-1161. [DOI: 10.1080/10837450.2020.1803909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Parvaneh Peyvand
- Department of Biophysics/Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Zahra Vaezi
- Department of Biophysics/Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Mosslim Sedghi
- Department of Biophysics/Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Nima Dalir
- Department of Physical Chemistry, Faculty of Basic Science, Tarbiat Modares University, Tehran, Iran
| | - Leila Ma’mani
- Department of Nanotechnology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics/Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
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23
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Esfandyari J, Shojaedin-Givi B, Hashemzadeh H, Mozafari-Nia M, Vaezi Z, Naderi-Manesh H. Capture and detection of rare cancer cells in blood by intrinsic fluorescence of a novel functionalized diatom. Photodiagnosis Photodyn Ther 2020; 30:101753. [DOI: 10.1016/j.pdpdt.2020.101753] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/18/2020] [Accepted: 03/23/2020] [Indexed: 12/29/2022]
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24
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Siampour H, Abbasian S, Moshaii A, Omidfar K, Sedghi M, Naderi-Manesh H. Seed-mediated Electrochemically Developed Au Nanostructures with Boosted Sensing Properties: An Implication for Non-enzymatic Glucose Detection. Sci Rep 2020; 10:7232. [PMID: 32350345 PMCID: PMC7190711 DOI: 10.1038/s41598-020-64082-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/25/2020] [Indexed: 11/21/2022] Open
Abstract
A new approach has been developed to improve sensing performances of electrochemically grown Au nanostructures (AuNSs) based on the pre-seeding of the electrode. The pre-seeding modification is simply carried out by vacuum thermal deposition of 5 nm thin film of Au on the substrate followed by thermal annealing at 500 °C. The electrochemical growth of AuNSs on the pre-seeded substrates leads to impressive electrochemical responses of the electrode owing to the seeding modification. The dependence of the morphology and the electrochemical properties of the AuNSs on various deposition potentials and times have been investigated. For the positive potentials, the pre-seeding leads to the growth of porous and hole-possess networks of AuNSs on the surface. For the negative potentials, AuNSs with carved stone ball shapes are produced. The superior electrode was achieved from AuNSs developed at 0.1 V for 900 s with pre-seeding modification. The sensing properties of the superior electrode toward glucose detection show a high sensitivity of 184.9 µA mM−1 cm−2, with a remarkable detection limit of 0.32 µM and a wide range of linearity. The excellent selectivity and reproducibility of the sensors propose the current approach as a large-scale production route for non-enzymatic glucose detection.
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Affiliation(s)
- Hossein Siampour
- Department of Physics, Tarbiat Modares University, P.O Box, 14115-175, Tehran, Iran
| | - Sara Abbasian
- School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box, 19395-5531, Tehran, Iran
| | - Ahmad Moshaii
- Department of Physics, Tarbiat Modares University, P.O Box, 14115-175, Tehran, Iran.
| | - Kobra Omidfar
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Science, Tehran, Iran
| | - Mosslim Sedghi
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran
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Rezaei N, Mehrnejad F, Vaezi Z, Sedghi M, Asghari SM, Naderi-Manesh H. Corrigendum to “Encapsulation of an endostatin peptide in liposomes: Stability, release, and cytotoxicity study” [Colloids Surf. B Biointerfaces 185 (October) (2019) 110552]. Colloids Surf B Biointerfaces 2020; 186:110694. [DOI: 10.1016/j.colsurfb.2019.110694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hashemzadeh H, Allahverdi A, Ghorbani M, Soleymani H, Kocsis Á, Fischer MB, Ertl P, Naderi-Manesh H. Gold Nanowires/Fibrin Nanostructure as Microfluidics Platforms for Enhancing Stem Cell Differentiation: Bio-AFM Study. Micromachines (Basel) 2019; 11:mi11010050. [PMID: 31906040 PMCID: PMC7019962 DOI: 10.3390/mi11010050] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/26/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023]
Abstract
Organ-on-a-chip technology has gained great interest in recent years given its ability to control the spatio-temporal microenvironments of cells and tissues precisely. While physical parameters of the respective niche such as microchannel network sizes, geometric features, flow rates, and shear forces, as well as oxygen tension and concentration gradients, have been optimized for stem cell cultures, little has been done to improve cell-matrix interactions in microphysiological systems. Specifically, detailed research on the effect of matrix elasticity and extracellular matrix (ECM) nanotopography on stem cell differentiation are still in its infancy, an aspect that is known to alter a stem cell’s fate. Although a wide range of hydrogels such as gelatin, collagen, fibrin, and others are available for stem cell chip cultivations, only a limited number of elasticities are generally employed. Matrix elasticity and the corresponding nanotopography are key factors that guide stem cell differentiation. Given this, we investigated the addition of gold nanowires into hydrogels to create a tunable biointerface that could be readily integrated into any organ-on-a-chip and cell chip system. In the presented work, we investigated the matrix elasticity (Young’s modulus, stiffness, adhesive force, and roughness) and nanotopography of gold nanowire loaded onto fibrin hydrogels using the bio-AFM (atomic force microscopy) method. Additionally, we investigated the capacity of human amniotic mesenchymal stem cells (hAMSCs) to differentiate into osteo- and chondrogenic lineages. Our results demonstrated that nanogold structured-hydrogels promoted differentiation of hAMSCs as shown by a significant increase in Collagen I and II production. Additionally, there was enhanced calcium mineralization activity and proteoglycans formation after a cultivation period of two weeks within microfluidic devices.
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Affiliation(s)
- Hadi Hashemzadeh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran;
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran; (A.A.); (M.G.); (H.S.)
| | - Mohammad Ghorbani
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran; (A.A.); (M.G.); (H.S.)
| | - Hossein Soleymani
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran; (A.A.); (M.G.); (H.S.)
| | - Ágnes Kocsis
- Department of Health Science and Biomedicine, Danube University Krems, 3500 Vienna, Austria; (Á.K.); (M.B.F.)
| | - Michael Bernhard Fischer
- Department of Health Science and Biomedicine, Danube University Krems, 3500 Vienna, Austria; (Á.K.); (M.B.F.)
| | - Peter Ertl
- Faculty of Technical Chemistry, Institute of Applied Synthetic Chemistry and Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
- Correspondence: (P.E.); (H.N.-M.); Tel.: +43(1)-58801-163605 (H.N.M.)
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran;
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran; (A.A.); (M.G.); (H.S.)
- Correspondence: (P.E.); (H.N.-M.); Tel.: +43(1)-58801-163605 (H.N.M.)
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Rezaei N, Mehrnejad F, Vaezi Z, Sedghi M, Asghari SM, Naderi-Manesh H. Encapsulation of an endostatin peptide in liposomes: Stability, release, and cytotoxicity study. Colloids Surf B Biointerfaces 2019; 185:110552. [PMID: 31648117 DOI: 10.1016/j.colsurfb.2019.110552] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/21/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022]
Abstract
The endostatin protein is a potent inhibitor of angiogenesis and tumor growth. The anti-angiogenic and antitumor properties of full-length endostatin can be mimicked by its N-terminal segment, including residues 1-27. Therefore, our previous studies have shown that a mutant N-terminal peptide which the Zn-binding loop was replaced by a disulfide loop (referred to as the ES-SS peptide) has preserved antiangiogenic and antitumor properties compared to the native peptide. To increase stability and plasma half-life of the ES-SS peptide, the nano-sized liposomal formulations of the peptide with different ratio of phosphocholine (PC) were synthesized. The liposomal peptide formulations possessed an average size of around 100 nm with (-4 to -36 mv) in zeta potential. The encapsulation efficiency of the ES-SS peptide was in the range of 24-54% with different lipid: peptide molar ratios. In vitro release of the peptide from liposomes indicated a complete peptide release after 7 days. Cytotoxicity assay was evaluated using the human umbilical vein endothelial cells (HUVECs) for various concentrations of the liposomal peptide. The results depicted the gradual release of the peptide through liposomes. By comparing with the free peptide, the liposomal peptide formulations have indicated higher cell viability with IC50 value about 0.1 μM. The peptide-liposome interactions, as well as the peptide effect on the liposome structure, were also investigated through coarse-grained molecular dynamics (CG-MD) simulation. The results revealed that the peptides were assembled in the hydrophilic core of the liposome. The peptide behavior in liposome can stabilize the liposome structure and be a response to the observed low peptide release rate. The investigation is promising for designing a liposome-based anti-angiogenesis peptide delivery system.
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Affiliation(s)
- Nastaran Rezaei
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, 14395-1561 Tehran, Iran.
| | - Zahra Vaezi
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154 Tehran, Iran
| | - Mosslim Sedghi
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154 Tehran, Iran
| | - S Mohsen Asghari
- Department of Biology, Faculty of Sciences, University of Guilan, 41335-19141 Rasht, Iran
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Science, Tarbiat Modares University, 14115-154 Tehran, Iran.
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Sheykhi E, Sajad B, Tavaddod S, Naderi-Manesh H, Roostaiei N. Tuning fluorophore excitation in a total-internal-reflection-fluorescence microscopy. Appl Opt 2019; 58:8055-8060. [PMID: 31674360 DOI: 10.1364/ao.58.008055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
In a total-internal-reflection-fluorescence-microscopy method, there is anisotropy in the polarized evanescent wave. Since the evanescent wave is used as an excitation field, the mentioned anisotropy is a disadvantage in using the total-internal-reflection-fluorescence-microscopy technique. Therefore, by theoretical and analytical approaches, and based on the Fresnel coefficients, the effect of three dielectrics media on the anisotropy of the evanescent wave is investigated. Following that, a proper combination of the cover glass, oil immersion, and prism for both living and non-living samples is suggested that not only enhances the intensity of the evanescent wave, but also and importantly, decreases the essential anisotropy of the evanescent wave.
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Mehrdad-Vahdati B, Pourhashem S, Sedghi M, Vaezi Z, Shojaedin-Givi B, Rashidi A, Naderi-Manesh H. A novel aspect of functionalized graphene quantum dots in cytotoxicity studies. Toxicol In Vitro 2019; 61:104649. [PMID: 31518670 DOI: 10.1016/j.tiv.2019.104649] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/02/2019] [Accepted: 09/09/2019] [Indexed: 12/14/2022]
Abstract
Graphene quantum dots (GQDs) represent a new generation of graphene-based nanomaterials with enormous potential for use and development of a variety of biomedical applications. However, up to now little studies have investigated the impact of GQDs on human health in case of exposure. GQDs were synthesized from citric acid as carbon precursor by hydrothermal treatment at 160 °C for 4 h. The synthesized GQDs showed strong blue emission under UV-Irradiation with fluorescence quantum yield of 9.8%. The obtained GQDs were further carbonized, activated and functionalized by nitric acid vapor method. Nitrogen adsorption/desorption isotherms were used to analyze the surface area and porous structures of GQDs. The results revealed that compared to GQDs, the specific surface area of functionalized graphene quantum dots (fGQDs) has been increased from 0.0667 to 2.5747 m2/g and pore structures have been enhanced significantly. The potential cytotoxic effect of GQDs, fGQDs and GO suspensions was evaluated on HFF cell line using MTT assays and flow cytometry method after 24 h incubation. We have for the first time demonstrated that by carbonization, activation and functionalization of GQDs they still showed cytocompatible properties. We observed excellent biocompatibility of GQDs and fGQDs at low concentrations. Moreover, the results suggested that modification of GQDs yields product suspensions with high surface area, enhanced pore volume and loading capacities. Thus, fGQDs represent an attractive candidate for further use in drug delivery systems and bio-imaging application.
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Affiliation(s)
- Bahare Mehrdad-Vahdati
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154 Tehran, Iran
| | - Sepideh Pourhashem
- Nanotechnology Research Center, Research Institute of Petroleum Industry (RIPI), P.O. Box: 14665-1998, Tehran, Iran
| | - Mosslim Sedghi
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154 Tehran, Iran
| | - Zahra Vaezi
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154 Tehran, Iran
| | - Behnaz Shojaedin-Givi
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154 Tehran, Iran
| | - Alimorad Rashidi
- Nanotechnology Research Center, Research Institute of Petroleum Industry (RIPI), P.O. Box: 14665-1998, Tehran, Iran.
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154 Tehran, Iran.
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Ghorbani M, Soleymani H, Allahverdi A, Shojaeilangari S, Naderi-Manesh H. Effects of natural compounds on conformational properties and hairpin formation of amyloid-β 42 monomer: docking and molecular dynamics simulation study. J Biomol Struct Dyn 2019; 38:3371-3383. [PMID: 31496378 DOI: 10.1080/07391102.2019.1664934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The β42 amyloid peptides (Aβ) are identified as a candidate target for Alzheimer's drugs. Phenolic compounds can bind to the Aβ and inhibit amyloid formation. However, the inhibitory mechanism of phenolic compounds remains unclear. In this study, the molecular dynamic simulation and docking program were used to characterize the molecular details of inhibitory mechanism of the phenolic compounds. Our Results show that the phenolic compounds can bind to hydrophobic region in Aβ42 monomer and alter hydrophobic interactions network at Aβ42 which play a key role in β-sheet formation. The cluster analysis and interactions network analysis were used to probe conformational changes in Aβ42. In most populated clusters of Aβ42-phenolic compounds complexes, the sheet structures were not observed or reduced. It seems that the binding of phenolic compounds can induce larger conformational diversity for amyloid peptide and changes conformational properties of amyloid peptide. The phenolic compounds can deform β-Hairpin structure of Aβ by destabilizing salt bridges E22-K28 and D23-K28 which can alter the conformation of Aβ42 in aqueous solution. These findings are in accordance with experimental results, to some extent give a molecular level interpretation for the inhibitory mechanism of phenolic compounds .In addition, this study may add important new details to the inhibitory mechanism of Alzheimer's drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Ghorbani
- Faculty of Biological Sciences, Biophysics Department, Tarbiat Modares University, Tehran, Iran
| | - Hossein Soleymani
- Faculty of Biological Sciences, Biophysics Department, Tarbiat Modares University, Tehran, Iran
| | - Abdollah Allahverdi
- Faculty of Biological Sciences, Biophysics Department, Tarbiat Modares University, Tehran, Iran
| | | | - Hossein Naderi-Manesh
- Faculty of Biological Sciences, Biophysics Department, Tarbiat Modares University, Tehran, Iran.,School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
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Soleymani H, Ghorbani M, Allahverdi A, Shojaeilangari S, Naderi-Manesh H. Activation of human insulin by vitamin E: A molecular dynamics simulation study. J Mol Graph Model 2019; 91:194-203. [PMID: 31265936 DOI: 10.1016/j.jmgm.2019.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 11/17/2022]
Abstract
Lack of perfect insulin signaling can lead to the insulin resistance, which is the hallmark of diabetes mellitus. Activation of insulin and its binding to the receptor for signaling process initiates via B-chain C-terminal hinge conformational change through an open structure to "wide-open" conformation. Observational studies and basic scientific evidence suggest that vitamin D and E directly and/or indirectly prevent diabetes through improving glucose secretion and tolerance, activating calcium dependent endopeptidases and thus improving insulin exocytosis, antioxidant effect and reducing insulin resistance. On the contrary, clinical trials have yielded inconsistent results about the efficacy of vitamin D supplementations for the control of glucose hemostasis. In this work, best binding modes of vitamin D3 and E on insulin obtained from AutoDock Vina were selected for Molecular Dynamic, MD, study. The binding energy obtained from Molecular Mechanics- Poisson Boltzman Surface Area, MM-PBSA method, revealed that Vitamins D3 and E have good affinity to bind to the insulin and vitamin E has higher binding energy (-46 kj/mol) by engaging more residues in binding site. Distance and angle calculation results illustrated that vitamin E changes the B-chain conformation and it causes the formation of wide-open/active form of insulin. Vitamin E increases the ValB12-TyrB26 distance to ∼15 Å and changes the hinge angle to ∼65°. Consequently, essential hydrophobic residues for binding to insulin receptor exposed to surface in the presence of vitamin E. However, our data illustrated that vitamin D3 cannot change B-chain conformation. Thus our MD simulations propose a model for insulin activation through vitamin E interaction for therapeutic approaches.
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Affiliation(s)
- Hossein Soleymani
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran.
| | - Mohammad Ghorbani
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran.
| | - Abdollah Allahverdi
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran.
| | | | - Hossein Naderi-Manesh
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran; School of Biological Science, Institute for Research in Fundamental Sciences (IPM), 19395-5746, Tehran, Iran.
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Sadeghi Mohammadi S, Vaezi Z, Shojaedin-Givi B, Naderi-Manesh H. Chemiluminescent liposomes as a theranostic carrier for detection of tumor cells under oxidative stress. Anal Chim Acta 2019; 1059:113-123. [DOI: 10.1016/j.aca.2019.01.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 01/20/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
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Mortezazadeh S, Jamali Y, Naderi-Manesh H, Lyubartsev AP. Implicit solvent systematic coarse-graining of dioleoylphosphatidylethanolamine lipids: From the inverted hexagonal to the bilayer structure. PLoS One 2019; 14:e0214673. [PMID: 30951539 PMCID: PMC6450619 DOI: 10.1371/journal.pone.0214673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/18/2019] [Indexed: 11/21/2022] Open
Abstract
Lamellar and hexagonal lipid structures are of particular importance in the biological processes such as membrane fusion and budding. Atomistic simulations of formation of these phases and transitions between them are computationally prohibitive, hence development of coarse-grained models is an important part of the methodological development in this area. Here we apply systematic bottom-up coarse-graining to model different phase structures formed by 1,2-dioleoylphosphatidylethanolamine (DOPE) lipid molecules. We started from atomistic simulations of DOPE lipids in water carried out at two different water/lipid molar ratio corresponding to the lamellar Lα and inverted hexagonal HII structures at low and high lipid concentrations respectively. The atomistic trajectories were mapped to coarse-grained trajectories, in which each lipid was represented by 14 coarse-grained sites. Then the inverse Monte Carlo method was used to compute the effective coarse-grained potentials which for the coarse-grain model reproduce the same structural properties as the atomistic simulations. The potentials derived from the low concentration atomistic simulation were only able to form a bilayer structure, while both Lα and HII lipid phases were formed in simulations with potentials obtained at high concentration. The typical atomistic configurations of lipids at high concentration combine fragments of both lamellar and non-lamellar structures, that is reflected in the extracted coarse-grained potentials which become transferable and can form a wide range of structures including the inverted hexagonal, bilayer, tubule, vesicle and micellar structures.
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Affiliation(s)
- Saeed Mortezazadeh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Yousef Jamali
- Department of Mathematics, Tarbiat Modares University, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
- * E-mail: (HN); (APL)
| | - Alexander P. Lyubartsev
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- * E-mail: (HN); (APL)
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Molakarimi M, Gorman MA, Mohseni A, Pashandi Z, Taghdir M, Naderi-Manesh H, Sajedi RH, Parker MW. Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations. J Biol Chem 2019; 294:20-27. [PMID: 30420427 PMCID: PMC6322872 DOI: 10.1074/jbc.ra118.006053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/05/2018] [Indexed: 11/06/2022] Open
Abstract
Bioluminescence of a variety of marine organisms, mostly cnidarians and ctenophores, is carried out by Ca2+-dependent photoproteins. The mechanism of light emission operates via the same reaction in both animal families. Despite numerous studies on the ctenophore photoprotein family, the detailed catalytic mechanism and arrangement of amino acid residues surrounding the chromophore in this family are a mystery. Here, we report the crystal structure of Cd2+-loaded apo-mnemiopsin1, a member of the ctenophore family, at 2.15 Å resolution and used quantum mechanics/molecular mechanics (QM/MM) to investigate its reaction mechanism. The simulations suggested that an Asp-156-Arg-39-Tyr-202 triad creates a hydrogen-bonded network to facilitate the transfer of a proton from the 2-hydroperoxy group of the chromophore coelenterazine to bulk solvent. We identified a water molecule in the coelenteramide-binding cavity that forms a hydrogen bond with the amide nitrogen atom of coelenteramide, which, in turn, is hydrogen-bonded via another water molecule to Tyr-131. This observation supports the hypothesis that the function of the coelenteramide-bound water molecule is to catalyze the 2-hydroperoxycoelenterazine decarboxylation reaction by protonation of a dioxetanone anion, thereby triggering the bioluminescence reaction in the ctenophore photoprotein family.
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Affiliation(s)
- Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Michael A Gorman
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia; Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Ammar Mohseni
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Zaiddodine Pashandi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran.
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia; Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.
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Hosseini S, Naderi-Manesh H, Vali H, Baghaban Eslaminejad M, Azam Sayahpour F, Sheibani S, Faghihi S. Contribution of osteocalcin-mimetic peptide enhances osteogenic activity and extracellular matrix mineralization of human osteoblast-like cells. Colloids Surf B Biointerfaces 2019; 173:662-671. [DOI: 10.1016/j.colsurfb.2018.10.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 09/22/2018] [Accepted: 10/14/2018] [Indexed: 12/20/2022]
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Mehralitabar H, Taghdir M, Naderi-Manesh H. A combination of bioactive and nonbioactive alkyl-peptides form a more stable nanofiber structure for differentiating neural stem cells: a molecular dynamics simulation survey. J Biomol Struct Dyn 2018; 37:3434-3444. [PMID: 30238829 DOI: 10.1080/07391102.2018.1516571] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Self-assembling alkyl-peptides are important molecules due to their ability to construct nano-level structures such as nanofibers to be utilized as tissue engineering scaffolds. The bioactive epitope of FAQRVPP which acts as neural stem cells (NSCs) outgrowth inducing factor is used in nanofiber structures. Based on previous experimental studies the density and distribution pattern of the epitopes on the surface of the nanofibers plays an important role in the differentiation function efficiency. We decided to survey and compare the stability of two pre-constructed fiber structures in the forms of all-functionalized nanofiber (containing only bioactive alkyl-peptides) and distributed functionalized nanofiber (a combination of nonbioactive and bioactive alkyl-peptides with ratio 2:1). Our findings reveal that the all-functionalized fiber shows an unstable structure and is split into intermediate micelle-like structures to reduce compactness and steric hindrance of functional epitopes whereas the distributed functionalized fiber shows an integrated stable nanofiber with a more amount of beta sheets that are well-organized and oriented around the hydrophobic core. The hydrogen bonds and energy profiles of the structures indicate the role of hydrophobic interactions during the alkyl-chain core formation and the important role of electrostatic interactions and hydrogen bond network in the stability of the final structures. Finally, it seems that the possibility of the presence of intermediate structure is increased in the all-functionalized nanofiber environment, and it can reduce functional efficiency of the scaffolds. These findings can help to design more efficient nanofiber structures with different goals in scaffolds for tissue engineering. Abbreviations MD Molecular Dynamics NSCs Neural Stem Cells PME Particle mesh Ewald RDF Radial Distribution Function RG Radius of gyration RASA Relative Accessible Surface Area RMSD Root Mean Square Deviations SASA Solvent Accessible Surface Area. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Havva Mehralitabar
- a Department of Biological Science , Tarbiat Modares University , Tehran , Iran
| | - Majid Taghdir
- a Department of Biological Science , Tarbiat Modares University , Tehran , Iran
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Albukhaty S, Naderi-Manesh H, Tiraihi T, Sakhi Jabir M. Poly-l-lysine-coated superparamagnetic nanoparticles: a novel method for the transfection of pro-BDNF into neural stem cells. Artif Cells Nanomed Biotechnol 2018; 46:S125-S132. [PMID: 30033772 DOI: 10.1080/21691401.2018.1489272] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Poly-l-lysine-coated superparamagnetic iron oxide nanoparticles (SPIONs-PLL) were prepared and used as a novel-carrier for the transfer of brain-derived neurotrophic factor (BDNF) into neural stem cells (NSCs) under the beneficial influence of an external magnetic field. Pro-BDNF, a gene from human brain cDNA libraries, was obtained by polymerase chain reaction and constructed in a mammalian expression vector (PSecTag2/HygroB). The nanoparticles (NPs) were examined using Fourier transform infrared spectroscopy, zeta potential, and Transmission electron microscopy. From the results, the levels of BDNF among the transfected and untransfected cells were 30.326 ± 5.9 and 5.85 ± 3.11 pg/mL, respectively, as detected by an ELISA method. Moreover, the enhanced green fluorescent protein vector was used to evaluate the gene expression efficiency for SPIONs-PLL as a non-viral carrier in NSCs. This was performed under the influence of a magnetic field and the transfection reagents (such as Lipofectamine 2000), which served as a positive control. The histological analysis revealed that the concentration of intracellular NPs was significantly higher than intercellular NPs. These results suggest that SPIONs-PLL can serve as a novel alternative for the transfection of BDNF-NSCs and could be used in gene therapy.
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Affiliation(s)
- Salim Albukhaty
- a Department of Basic Science, College of Nursing , University of Misan , Maysan , Iraq
| | - Hossein Naderi-Manesh
- b Department of Nanobiotechnology, Faculty of Biological Sciences , Tarbiat Modares University , Tehran , Iran
| | - Taki Tiraihi
- c Department of Anatomical Science , Tarbiat Modares University , Tehran , Iran
| | - Majid Sakhi Jabir
- d Division of Biotechnology , University of technology , Baghdad , Iraq ; Department of Biotechnology , University of technology , Baghdad , Iraq
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Sohi AN, Naderi-Manesh H, Soleimani M, Mirzaei S, Delbari M, Dodel M. Influence of Chitosan Molecular Weight and Poly(ethylene oxide): Chitosan Proportion on Fabrication of Chitosan Based Electrospun Nanofibers. Polym Sci Ser A 2018. [DOI: 10.1134/s0965545x18040077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Manjili HK, Ma'mani L, Naderi-Manesh H. Monodisperse Rattle-Structured Gold Nanorod-Mesoporous Silica Nanoparticles Core-Shell as Sulforaphane Carrier and its Sustained-Release Property. Drug Res (Stuttg) 2018; 68:504-513. [PMID: 29660748 DOI: 10.1055/a-0573-8966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Sulforaphane (SF) was loaded into the multi-functioned rattle-structured gold nanorod mesoporous silica nanoparticles core-shell to improve its stability and efficacy through its efficient delivery to tumors. The rattle-structured gold nanorod mesoporous silica nanoparticles (rattle-structured AuNR@mSiO2 core-shell NPs) were obtained by covering the surface of Au NPs with Ag and mSiO2 shell and subsequently selective Ag shell etching strategy. Then the surface of rattle-structured AuNR@mSiO2 NPs was decorated with thiolated polyethylene glycol-FITC and thiolated polyethylene glycol-folic acid to the designed form. The obtained FITC/FA@ [rattle-structured AuNR@mSiO2] NPs was characterized by different techniques including energy dispersive X-ray spectroscopy (EDX), scanning and transmission electron microscopy (SEM & TEM), UV-visible spectrophotometer and dynamic light scattering (DLS). The FITC/FA@ [rattle-structured AuNR@mSiO2] NPs has an average diameter around ~33 nm, which increases to ~38 nm after the loading of sulforaphane. The amount of the loaded drug was ~ 2.8×10-4 mol of SF per gram of FITC/FA@ [rattle-structured AuNR@mSiO2] NPs. The rattle-structured AuNR@mSiO2 and FITC/FA@ [rattle-structured AuNR@mSiO2] NPs showed little inherent cytotoxicity, whereas the SF loaded FITC/FA@ [rattle-structured AuNR@mSiO2] NPs was highly cytotoxic in the case of MCF-7 cell line. Finally, Fluorescence microscopy and flow cytometry were used to demonstrate that the nanoparticles could be accumulated in specific regions and SF loaded FITC/FA@ [Fe3O4@Au] NPs efficiently induce apoptosis in MCF-7 cell line Graphical Abstract.
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Affiliation(s)
- Hamidreza Kheiri Manjili
- Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Leila Ma'mani
- Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Hashemi N, Vaezi Z, Sedghi M, Naderi-Manesh H. Hemoglobin-incorporated iron quantum clusters as a novel fluorometric and colorimetric probe for sensing and cellular imaging of Zn(II) and cysteine. Mikrochim Acta 2017; 185:60. [DOI: 10.1007/s00604-017-2600-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/01/2017] [Indexed: 12/14/2022]
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Molakarimi M, Mohseni A, Taghdir M, Pashandi Z, Gorman MA, Parker MW, Naderi-Manesh H, Sajedi RH. QM/MM simulations provide insight into the mechanism of bioluminescence triggering in ctenophore photoproteins. PLoS One 2017; 12:e0182317. [PMID: 28777808 PMCID: PMC5544205 DOI: 10.1371/journal.pone.0182317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/16/2017] [Indexed: 11/28/2022] Open
Abstract
Photoproteins are responsible for light emission in a variety of marine ctenophores and coelenterates. The mechanism of light emission in both families occurs via the same reaction. However, the arrangement of amino acid residues surrounding the chromophore, and the catalytic mechanism of light emission is unknown for the ctenophore photoproteins. In this study, we used quantum mechanics/molecular mechanics (QM/MM) and site-directed mutagenesis studies to investigate the details of the catalytic mechanism in berovin, a member of the ctenophore family. In the absence of a crystal structure of the berovin-substrate complex, molecular docking was used to determine the binding mode of the protonated (2-hydroperoxy) and deprotonated (2-peroxy anion) forms of the substrate to berovin. A total of 13 mutants predicted to surround the binding site were targeted by site-directed mutagenesis which revealed their relative importance in substrate binding and catalysis. Molecular dynamics simulations and MM-PBSA (Molecular Mechanics Poisson-Boltzmann/surface area) calculations showed that electrostatic and polar solvation energy are +115.65 and -100.42 kcal/mol in the deprotonated form, respectively. QM/MM calculations and pKa analysis revealed the deprotonated form of substrate is unstable due to the generation of a dioxetane intermediate caused by nucleophilic attack of the substrate peroxy anion at its C3 position. This work also revealed that a hydrogen bonding network formed by a D158- R41-Y204 triad could be responsible for shuttling the proton from the 2- hydroperoxy group of the substrate to bulk solvent.
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Affiliation(s)
- Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ammar Mohseni
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zaiddodine Pashandi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Michael A. Gorman
- Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Michael W. Parker
- Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- * E-mail: (RHS); (MNM)
| | - Reza H. Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- * E-mail: (RHS); (MNM)
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Mobasseri R, Karimi M, Tian L, Naderi-Manesh H, Ramakrishna S. Hydrophobic lapatinib encapsulated dextran-chitosan nanoparticles using a toxic solvent free method: fabrication, release property & in vitro anti-cancer activity. Materials Science and Engineering: C 2017; 74:413-421. [DOI: 10.1016/j.msec.2016.12.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 11/20/2016] [Accepted: 12/06/2016] [Indexed: 10/25/2022]
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Shams E, Yeganeh H, Naderi-Manesh H, Gharibi R, Mohammad Hassan Z. Polyurethane/siloxane membranes containing graphene oxide nanoplatelets as antimicrobial wound dressings: in vitro and in vivo evaluations. J Mater Sci Mater Med 2017; 28:75. [PMID: 28386852 DOI: 10.1007/s10856-017-5881-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/08/2017] [Indexed: 05/20/2023]
Abstract
Preserving wounds from bacterial and fungal infections and retaining optimum moist environment over damaged tissue are major challenges in wound care management. Application of wound dressings with antimicrobial activity and appropriate wound exudates handling ability is of particular significance for promoting wound healing. To this end, preparation and evaluation of novel wound dres1sings made from polyurethane/siloxane network containing graphene oxide (GO) nanoplatelets are described. The particular sol-gel hydrolysis/condensation procedure applied for the preparation of dressings leads to an appropriate distribution of GO nanoplatelets in the dressing membranes. The crosslinked siloxane domains and the presence of GO nanoplatelets within polymeric chains offered necessary mechanical strength for dressings. Meanwhile, a combination of hydrophilic and hydrophobic moieties in dressing backbone enabled suitable wound exudate management. Therefore, both of physical protection from external forces and preservation of moist environment over wound were attained by using the designed dressings. Widespread antimicrobial activity against gram-positive, gram-negative and fungal strains was recorded for the dressing with the optimum amount of GO, meanwhile, very good cytocompatibility against fibroblast cells was noted for these dressings. In vivo assay of the GO containing dressing on rat animal model reveals that the dressing can promote wound healing by complete re-epithelization, enhanced vascularization and collagen deposition on healed tissue.
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Affiliation(s)
- Elias Shams
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, PO Box 14115-154, Tehran, Iran
| | - Hamid Yeganeh
- Iran Polymer and petrochemical Institute, PO Box 14965/115, Tehran, Iran.
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology/Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, PO Box 14115-154, Tehran, Iran.
| | - Reza Gharibi
- Faculty of Chemistry, Kharazmi University, Tehran, Iran
| | - Zuhair Mohammad Hassan
- Department of Immunology, School of Medical Science, Tarbiat Modares University, PO Box 14115-331, Tehran, Iran
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Tarokh Z, Naderi-Manesh H, Nazari M. Towards prostate cancer gene therapy: Development of a chlorotoxin-targeted nanovector for toxic (melittin) gene delivery. Eur J Pharm Sci 2017; 99:209-218. [DOI: 10.1016/j.ejps.2016.12.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 11/10/2016] [Accepted: 12/20/2016] [Indexed: 11/29/2022]
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Azimzadeh M, Nasirizadeh N, Rahaie M, Naderi-Manesh H. Early detection of Alzheimer's disease using a biosensor based on electrochemically-reduced graphene oxide and gold nanowires for the quantification of serum microRNA-137. RSC Adv 2017. [DOI: 10.1039/c7ra09767k] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Serum miR-137 is quantified for the early detection of Alzheimer's disease using a electrochemically reduced graphene oxide and gold nanowire modified electrode.
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Affiliation(s)
- Mostafa Azimzadeh
- Stem Cell Biology Research Center
- Yazd Reproductive Sciences Institute
- Shahid Sadoughi University of Medical Sciences
- Yazd
- Iran
| | - Navid Nasirizadeh
- Department of Textile and Polymer Engineering
- Yazd Branch
- Islamic Azad University
- Yazd
- Iran
| | - Mahdi Rahaie
- Department of Life Science Engineering
- Faculty of New Sciences and Technologies
- University of Tehran
- Tehran
- Iran
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology/Biophysics
- Faculty of Biological Sciences
- Tarbiat Modares University
- Tehran
- Iran
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Pajoohesh M, Naderi-Manesh H, Soleimani M. MicroRNA-145-based differentiation of human mesenchymal stem cells to smooth muscle cells. Biotechnol Lett 2016; 38:1975-1981. [PMID: 27439694 DOI: 10.1007/s10529-016-2177-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/14/2016] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To investigate the role of microRNA-145, that regulates gene expression of genes related to differentiation, proliferation and the phenotype of smooth muscle cells (SMCs), in the differentiation of human bone marrow mesenchymal stem cells (hBM-MSCs) to SMCs. RESULTS Real-time PCR analysis indicated significant upregulation of SMC markers, including SM-α-actin, calponin, caldesmon and SMMHC, in SMCs compared to hBM-MSCs. Conversely, Krüppel-like factor 4, the direct target of microRNA-145 and the suppressor of smooth muscle differentiation, was suppressed in hBM-MSC-derived SMCs. Western blot analysis and immunocytochemistry also confirmed that the introduction of microRNA-145 into hBM-MSCs induced mature contractile SMCs. The functionality of hBM-MSC-derived SMCs was assessed by proliferation assay using PDGF-BB and contractility assay using carbachol. The results showed that the produced SMCs contracted in response to carbachol stimulation. CONCLUSION Overexpression of microRNA-145 in undifferentiated hBM-MSCs results in functionally mature contractile SMCs that can be used in drug discovery and cell therapy in SMC disorders such as vascular disease.
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Affiliation(s)
- Maryam Pajoohesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Molecular Biology and Genetic Engineering, Stem Cell Technology Research Center, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Masoud Soleimani
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Pashandi Z, Molakarimi M, Sajedi RH, Taghdir M, Naderi-Manesh H. Light induced structural changes of the photoprotein mnemiopsin: Characterization and contribution in photoinactivation. J Photochem Photobiol B 2016; 165:133-140. [PMID: 27780117 DOI: 10.1016/j.jphotobiol.2016.10.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/14/2016] [Indexed: 10/20/2022]
Abstract
Mnemiopsin, an EF-hand Ca2+ binding photoprotein isolated from luminous ctenophore Mnemiopsis leidyi, emits blue light from its chromophore, coelenterazine, which is non-covalently bond in its central hydrophobic core. Previous studies have revealed unique biochemical properties for ctenophore photoproteins such as inactivation by light, but only few have focused on photoinactivation process. To understand the nature of photoinactivation process we have investigated the impact of light alone and in the presence of Ca2+ ion on the structure of this photoprotein. We used UV-Vis, circular dichroism (CD) and fluorescence spectroscopy following Ca2+ binding assay to analyze the light effects on mnemiopsin conformation in comparison with aequorin at both apo and holo form. Our results showed light induced structural changes which resulted into photoinactivation. These changes include significant modification on secondary structure of mnemiopsin in comparison with aequorin. Our data also revealed that light could influence structure of apo protein regardless of presence of coelenterazine. The comparative studies of Ca2+ ion binding affinity following light exposure, also showed that light induced structural changes could presumably affect coelenterazine binding or its conformation in binding site in such a way that causes photoinactivation. In conclusion, we have proposed that structural rearrangement of helix 5 and C-terminal motif could be responsible for light induced structural changes.
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Affiliation(s)
- Zaiddodine Pashandi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Niknam N, Khakzad H, Arab SS, Naderi-Manesh H. PDB2Graph: A toolbox for identifying critical amino acids map in proteins based on graph theory. Comput Biol Med 2016; 72:151-9. [PMID: 27043857 DOI: 10.1016/j.compbiomed.2016.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 02/15/2016] [Accepted: 03/17/2016] [Indexed: 12/31/2022]
Abstract
The integrative and cooperative nature of protein structure involves the assessment of topological and global features of constituent parts. Network concept takes complete advantage of both of these properties in the analysis concomitantly. High compatibility to structural concepts or physicochemical properties in addition to exploiting a remarkable simplification in the system has made network an ideal tool to explore biological systems. There are numerous examples in which different protein structural and functional characteristics have been clarified by the network approach. Here, we present an interactive and user-friendly Matlab-based toolbox, PDB2Graph, devoted to protein structure network construction, visualization, and analysis. Moreover, PDB2Graph is an appropriate tool for identifying critical nodes involved in protein structural robustness and function based on centrality indices. It maps critical amino acids in protein networks and can greatly aid structural biologists in selecting proper amino acid candidates for manipulating protein structures in a more reasonable and rational manner. To introduce the capability and efficiency of PDB2Graph in detail, the structural modification of Calmodulin through allosteric binding of Ca(2+) is considered. In addition, a mutational analysis for three well-identified model proteins including Phage T4 lysozyme, Barnase and Ribonuclease HI, was performed to inspect the influence of mutating important central residues on protein activity.
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Affiliation(s)
- Niloofar Niknam
- Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Hamed Khakzad
- Department of Computer Engineering, Iran University of Science and Technology, Tehran, Iran.
| | - Seyed Shahriar Arab
- Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Hossein Naderi-Manesh
- Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Kheiri Manjili H, Ma’mani L, Tavaddod S, Mashhadikhan M, Shafiee A, Naderi-Manesh H. D, L-Sulforaphane Loaded Fe3O4@ Gold Core Shell Nanoparticles: A Potential Sulforaphane Delivery System. PLoS One 2016; 11:e0151344. [PMID: 26982588 PMCID: PMC4794166 DOI: 10.1371/journal.pone.0151344] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 02/08/2016] [Indexed: 11/19/2022] Open
Abstract
A novel design of gold-coated iron oxide nanoparticles was fabricated as a potential delivery system to improve the efficiency and stability of d, l-sulforaphane as an anticancer drug. To this purpose, the surface of gold-coated iron oxide nanoparticles was modified for sulforaphane delivery via furnishing its surface with thiolated polyethylene glycol-folic acid and thiolated polyethylene glycol-FITC. The synthesized nanoparticles were characterized by different techniques such as FTIR, energy dispersive X-ray spectroscopy, UV-visible spectroscopy, scanning and transmission electron microscopy. The average diameters of the synthesized nanoparticles before and after sulforaphane loading were obtained ∼ 33 nm and ∼ 38 nm, respectively, when ∼ 2.8 mmol/g of sulforaphane was loaded. The result of cell viability assay which was confirmed by apoptosis assay on the human breast cancer cells (MCF-7 line) as a model of in vitro-cancerous cells, proved that the bare nanoparticles showed little inherent cytotoxicity, whereas the sulforaphane-loaded nanoparticles were cytotoxic. The expression rate of the anti-apoptotic genes (bcl-2 and bcl-xL), and the pro-apoptotic genes (bax and bak) were quantified, and it was found that the expression rate of bcl-2 and bcl-xL genes significantly were decreased when MCF-7 cells were incubated by sulforaphane-loaded nanoparticles. The sulforaphane-loaded into the designed gold-coated iron oxide nanoparticles, acceptably induced apoptosis in MCF-7 cells.
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Affiliation(s)
- Hamidreza Kheiri Manjili
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Leila Ma’mani
- Department of Nanotechnology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Sharareh Tavaddod
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Maedeh Mashhadikhan
- Department of Biology, Faculty of Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Abbas Shafiee
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran 14176, Iran
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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50
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Heidari HR, Bandehpour M, Vahidi H, Barar J, Kazemi B, Naderi-Manesh H. Cloning and Expression of TNF Related Apoptosis Inducing Ligand in Nicotiana tabacum. Iran J Pharm Res 2015; 14:189-201. [PMID: 25561925 PMCID: PMC4277632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Molecular farming has been considered as a secure and economical approach for production of biopharmaceuticals. Human TNF Related Apoptosis Inducing Ligand (TRAIL) as a promising biopharmaceutical candidate has been produced in different expression hosts. However, little attention has been paid to molecular farming of the TRAIL in spite of numerous advantages of plant expression systems. Therefore, in this study the cytoplasmic production of the TRAIL was tackled in Nicotiana tabacum using Agrobacterium tumefaciens LBA 4404. Initially, the desired coding sequence was obtained using PCR technique on the constructed human cDNA library. Afterward, the necessary requirements for expression of the TRAIL in plant cell system were provided through sub-cloning into 35S-CaMV (Cauliflower Mosaic Virus) helper and final 0179-pGreen expression vectors. Then, the final TRAIL-pGreen expression vector was cloned into A. tumefaciens LBA 4404. Subsequently, the N. tabacum cells were transformed through co-culture method and expression of the TRAIL was confirmed by western blot analysis. Finally, the recombinant TRAIL was extracted through chromatographic technique and biological activity was evaluated through MTT assay (Methylthiazol Tetrazolium Assay). The result of western blot analysis indicated that only monomer and oxidized dimer forms of the TRAIL can be extracted from the N. tabacum cells. Moreover, the lack of trimeric assembly of the extracted TRAIL diminished its biological activity in sensitive A549 cell line. In conclusion, although N. tabacum cells can successfully produce the TRAIL, proper assembly and functionality of the TRAIL were unfavorable.
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Affiliation(s)
- Hamid Reza Heidari
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mojgan Bandehpour
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Biotechnology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hossein Vahidi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Jaleh Barar
- Research Centre for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran.,Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, USA.
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Biotechnology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Co-corresponding authors: E-mail: , E-mail:
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,Co-corresponding authors: E-mail: , E-mail:
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