184 results on '"Naderi-Manesh H"'
Search Results
2. The next generation personalized models to screen hidden layers of breast cancer tumorigenicity
- Author
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Afzali, F., Akbari, P., Naderi-Manesh, H., and Gardaneh, M.
- Published
- 2019
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3. A simple 2-step purification process of α-amylase from Bacillus subtilis: Optimization by response surface methodology
- Author
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Ataallahi, E., primary, Naderi-Manesh, H., additional, Roostaazad, R., additional, and Yeganeh, S., additional
- Published
- 2021
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4. Thermal denaturation of yeast alcohol dehydrogenase and protection of secondary and tertiary structural changes by sugars: CD and fluorescence studies
- Author
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Miroliaei, Mehran, Ranjbar, B., Naderi-Manesh, H., and Nemat-Gorgani, Mohsen
- Published
- 2007
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5. Effective factors in thermostability of thermophilic proteins
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Sadeghi, M., Naderi-Manesh, H., Zarrabi, M., and Ranjbar, B.
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- 2006
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6. Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations
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Molakarimi, M, Gorman, MA, Mohseni, A, Pashandi, Z, Taghdir, M, Naderi-Manesh, H, Sajedi, RH, Parker, MW, Molakarimi, M, Gorman, MA, Mohseni, A, Pashandi, Z, Taghdir, M, Naderi-Manesh, H, Sajedi, RH, and Parker, MW
- 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.
- Published
- 2019
7. QM/MM simulations provide insight into the mechanism of bioluminescence triggering in ctenophore photoproteins
- Author
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Khodarahmi, R, Molakarimi, M, Mohseni, A, Taghdir, M, Pashandi, Z, Gorman, MA, Parker, MW, Naderi-Manesh, H, Sajedi, RH, Khodarahmi, R, Molakarimi, M, Mohseni, A, Taghdir, M, Pashandi, Z, Gorman, MA, Parker, MW, Naderi-Manesh, H, and Sajedi, RH
- 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.
- Published
- 2017
8. Genetic variation within and among rainbow trout, onchorhynchus mykiss, hatchery populations from Iran assessed by PCR-RFLP analysis of mitochondrial DNA segments
- Author
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Sajedi, R.H., Aminzadeh, S., Naderi-Manesh, H., Sadeghizadeh, M., Abdolhay, H., and Naderi-Manesh M.
- Subjects
Genetic variation -- Research ,Genetic variation -- Forecasts and trends ,Rainbow trout -- Genetic aspects ,Primers (Molecular genetics) -- Research ,Mitochondrial DNA -- Research ,Market trend/market analysis ,Business ,Food/cooking/nutrition - Abstract
Genetic differences of rainbow trout, onchorhynchus mykiss and hatchery populations are studied. Polymerase chain reaction-restriction fragment length polymorphism is used to study their mitochondrial deoxyribonucleic acid segments.
- Published
- 2003
9. Conformational instability of human prion protein upon residue modification: a molecular dynamics simulation study
- Author
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Kourosh Bamdad, Naderi-Manesh, H., and Baumgaertner, A.
- Subjects
molecular dynamics simulation ,electrostatic interaction ,human prion protein ,amino acid substitution - Abstract
Technical strategies like amino acid substitution and residue modification have been widely used to characterize the importance of key amino acids and the role that each residue plays in the structural and functional properties of protein molecules. However, there is no systematic approach to assess the impact of the substituted/modified amino acids on the conformational dynamics of proteins. In this investigation to clarify the effects of residue modifications on the structural dynamics of human prion protein (PrP), a comparative molecular dynamics simulation study on the native and the amino acid-substituted analog at position 208 of PrP has been performed. It is believed that Arginine to Histidine mutation at position 208 is responsible for the structural transition of the native form of human prion protein to the pathogenic isoform causing Creutzfeldt-Jakob disease (CJD). So, three 10 ns molecular dynamics simulations on three model constructs have been performed. Simulation results indicated considerable differences of conformational fluctuations for Alanine substituted construct (PrPALA) and the analog form (PrPSB) comprising the neutralized state of the Arginine residue at position 208 of the human prion protein. According to our data, substitution of the Arginine residue by the uncharged state of this residue induces some reversible structural alterations in the intrinsically flexible loop area including residues 167–171 of PrP. Thus, deprotonation of Arg208 is a weak perturbation to the structural fluctuations of the protein backbone and the resulting construct behaves almost identical as its native form. Otherwise, Alanine substitution at position 208 imposed an irreversible impact on the secondary and tertiary structure of the protein, which leads to conformational instabilities in the remote hot region comprising residues 190–195 of the C–terminal part of helix 2. Based on the results, it could be deduced that the observed conformational transitions upon Arg208 to His point mutation, which is the main reason for CJD, may be mainly related to the structural instabilities due to the induced-conformational changes that caused alterations in local/spatial arrangements of the force distributions in the backbone of the human prion protein., EXCLI Journal ; Vol. 13, 2014
- Published
- 2014
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10. Molecular Dynamics and Circular Dichroism Studies on Aurein 1.2 and Retro Analog
- Author
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Safyeh Soufian, Naderi-Manesh, H., Alizadeh, A., and Sarbolouki, M. N.
- Subjects
retro ,circular dichroism ,molecular dynamic ,Antimicrobial peptides - Abstract
Aurein 1.2 is a 13-residue amphipathic peptide with antibacterial and anticancer activity. Aurein1.2 and its retro analog were synthesized to study the activity of the peptides in relation to their structure. The antibacterial test result showed the retro-analog is inactive. The secondary structural analysis by CD spectra indicated that both of the peptides at TFE/Water adopt alpha-helical conformation. MD simulation was performed on aurein 1.2 and retro-analog in water and TFE in order to analyse the factors that are involved in the activity difference between retro and the native peptide. The simulation results are discussed and validated in the light of experimental data from the CD experiment. Both of the peptides showed a relatively similar pattern for their hydrophobicity, hydrophilicity, solvent accessible surfaces, and solvent accessible hydrophobic surfaces. However, they showed different in directions of dipole moment of peptides. Also, Our results further indicate that the reversion of the amino acid sequence affects flexibility .The data also showed that factors causing structural rigidity may decrease the activity. Consequently, our finding suggests that in the case of sequence-reversed peptide strategy, one has to pay attention to the role of amino acid sequence order in making flexibility and role of dipole moment direction in peptide activity. KeywordsAntimicrobial peptides, retro, molecular dynamic, circular dichroism., {"references":["Leban, J. J., Kull, F. C., Jr., Landavazo, A., Stockstill, B., and\nMcDermed, J. D. Development of Potent Gastrin-Releasing Peptide\nAntagonists Having a D-Pro- (CH2NH)-Phe-NH2 C Terminus. Proc.\nNatl. Acad. Sci 90: 1922-1926. 1993.","Chorev, M. The partial retro-inverso modification: A road traveled\ntogether. Biopolymers 80 (2-3): 67-84 .2005.","Peer R. E. Mittl, C. D., David Sargent, Niankun Liu, Stephan Klauser,\nRichard M. Thomas. The retro-GCN4 leucine zipper sequence forms a\nstable three-dimensional structure. PNAS 97: 2562-2566. 2000","Stephan Lorenzen, C. G., Robert Preissner and Cornelius Frömmel.\nInverse sequence similarity of proteins does not imply structural\nsimilarity. FEBS Letters 545: 105-109. 2003.","Fischer, P. The design,synthesis and application of stereochemical and\ndirectional peptide isomers: A critical review. Current Protein & Peptide\nScience 4 (5): 339-356. 2003","Guptasarma. FEBS Lett, Reversal of peptide backbone direction may\nresult in the mirroring of protein structure , 310: 205-210. 1992.","Zhao M, K. m. H., Mokotoff M. Briand retro-inverso peptide\ncorresponding to the GH loop of foot-and-mouth disease virus elicits\nhigh levels of long-lasting protective neutralizing antibodies. Proc Natl\nAcad Sci U S 94(23): 12545-12550. 1997","Meziere C, V. M., Dumortier H, Lo-Man R, Leclerc C, Guillet JG,\nBriand JP, Muller S. In vivo T helper cell response to retro-inverso\npeptidomimetics. J Immunol 159(7): 3230-3237. 1997.","Carmona AK, J. L. Inhibition of angiotensin converting enzyme and\npotentiation of bradykinin by retro-inverso analogues of short peptides\nand sequences related to angiotensin I and bradykininl. Biochem\nPharmaco 51(8): 1051-1060. 1996.\n[10] Bonelli F, P. A., Verdini AS. . Solid phase synthesis of retro-inverso\npeptide analogues. Synthesis and biological activity of the partially\nmodified retro-inverso analogue of the bradykinin potentiating peptide BPP9a (gLys6, (RS)-mPhe7, Ala8] .Int J Pept Protein Res 24(6): 553-\n556. 1984.\n[11] Rozek, T., J. H. Bowie, J. C. Wallace, M. J. Tyler. The antibiotic and\nanticancer active aurein peptides from the Australian Bell Frogs Litoria\naurea and Litoria raniformis. Part 2. Sequence determination using\nelectrospray mass spectrometry. Rapid Commun. Mass Spectrom 14:\n2002-2011. 2000.\n[12] Rozek T., K. L. W., J. H. Bowie, I. N. Olver, J. A. Carver, J. C. Wallace,\nand M. J. Tyler. The antibiotic and anticancer active aurein peptides\nfrom the Australian Bell Frogs Litoria aurea and Litoria raniformis the\nsolution structure of aurein 1.2. Eur. J. Biochem 267: 5330-5341. 2000.\n[13] Dennison, S. R. W., Michelle; Harris, Frederick; Phoenix, David\nAnticancer ╬▒-Helical Peptides and Structure / Function Relationships\nUnderpinning Their Interactions with Tumour Cell Membranes. Current\nProtein and Peptide Science 7: 487-499. 2006.\n[14] Sarah R. Dennison a, F. H. b., David A. Phoenix. The interactions of\naurein 1.2 with cancer cell membranes. Biophysical Chemistry 127: 78-\n83. 2007.\n[15] Fields, G. B., Z. Tian, and G. Barany. Synthetic peptide: a user-s guide.\n77-183. 1992\n[16] Furka, A., F. Sebestyen, M. Asgedom, and G. Dibo. General method for\nrapid synthesis of multicomponent peptide mixtures. Int. J. Peptide\nProtein Res 37: 487-493. 1991\n[17] Goodman, M. Synthesis of Peptides and Peptidomimetics,\nThieme/Houben-Weyl Series.2005.\n[18] ChemPep Protocol,http://www.chempep.com/ChemPep-Boc-Solid-\nPhase-Peptide-Synthesis.htm, 2006\n[19] A.J. Smith, B. J. S. AAA, Postcolumn amino acid analysis. Methods in\nMolecular Biology: Protein Sequencing Protocols 64,: 139-146. 1997.\n[20] Vydac, G. The Handbook of analysis and purification of peptide and\nproteins by reversed -phase HPLC.2002.\n[21] Igor A. Kaltashov, S. J. E (Ed.) Conformation and Dynamics of\nBiomolecules.2005.\n[22] Hancock, b. in first Gordon conference on antimicrobial peptides.\n[23] Hancock, R. Peptide antibiotics. Lancet 349: 418 - 422. 1997.\n[24] Woody, R. Circular dichroism and conformation of unordered\npolypeptides. Adv biophys Chem 2: 37-79. 1992.\n[25] W.J. Waddell. A simple ultraviolet spectrophotometric method for the\ndetermination of protein. J. Lab. Clin. Med 48: 311-314. 1956.\n[26] HyperChem® Release 7 for Windows, Hypercube. 2002.\n[27] Berendsen H. J. C., P., J. P. M., van Gunsteren, W. F., Di Nola, A. &\nHaak, J. R. Molecular Dynamics with Coupling to an External Bath. J.\nChem. Phys 81: 3684-3690. 1984.\n[28] van Gunsteren W. F., D., X. & Mark, A. E. GROMOS forcefield. In\nEncyclopedia of Computational Chemistry. Encycl. Comput. Chem 2:\n1211-1216. 1998.\n[29] van Gunsteren WF, B. S., Eising AA, H├╝nenberger PH,Kr├╝ger P, Mark\nAE, Scott WRP and Tironi IG. Biomolecular simulation: the\nGROMOS96 manual and user guide. 1996\n[30] Hess, B., Bekker, H., Berendsen, H.J.C., and Fraaije, J.G.E.M. LINCS:\nA linear constraint solver for molecular simulations. J. Comp. Chem. 18:\n1463-1472. 1997.\n[31] Deserno, M. a. H., C. 1998. . How to mesh up Ewald sums:A theoretical\nand numerical comparison of various particle mesh routines. J. Chem.\nPhys 109: 7678-7693. 1998.\n[32] Gromacs User Manual.2006.\n[33] Kabsch, W. and C. Sander. Dictionary of protein secondary structure:\npattern-recognition of hydrogen-bonded and geometrical features.\nBiopolymers 22: 2577-2637. 1983.\n[34] Taylor, W. R. Identification of protein sequence homology by consensus\ntemplate alignment. J. Mol. Bio 188: 233-258. 1986.\n[35] Johannes Buchner, T. K. Protein Folding Handbook, Vol. 1. 2005.\n[36] S Gnanakaran, H. N., John Portman. Peptide folding simulations.\nCurrent Opnion in structural Biology 13: 168-174. 2003.\n[37] Doig, A. J. a. B., R.L. N- and C-capping preferences for all 20 amino\nacids in -helical peptides. Protein Sci. 4: 1325-1336. 1995.\n[38] Ernesto E. Ambroggio, F. S., John H. Bowie, Gerardo D. Fidelio, Luis\nA. Bagatolli. Direct visualization of membrane leakage induced by the\nantibiotic peptides: Maculatin, Citropin and Aurein. Biophys J. 89:\n1874-1881. 2005.\n[39] H.A.Carlson. Protein flexibility is an important component of structurebased\ndrug discovery. Curr. Pharm. Des 8: 1571-1578. 2002.\n[40] R. Antoine, I. C., D. Rayane, M. Broyer, Ph. Dugourd, G. Breaux, F.C.\nHagemeister, D. Pippen, R.R. Hudgins and M.F. Jarrold,. Electric dipole\nmoments and conformations of isolated peptides. Eur. Phy. J. 20: 583.\n2002.\n[41] Simonson. Dielectric relaxation in proteins: macroscopic and\nmicroscopic models. Int J Quantum Chem 73: 45-57. 1999.\n[42] Persson, S., Killian, A., and Lindblom, G. Molecular ordering, and 2HNMR,\nBiophys. J. 75: 1365-1371. 1998."]}
- Published
- 2009
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11. Crystal structure of a green-emitter native of Lampyris turkestanicus luciferase
- Author
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Sharafian, Z., primary, Hosseinkhani, S., additional, and Naderi-manesh, H., additional
- Published
- 2013
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12. Crystal structure of a red-emitter mutant of Lampyris turkestanicus luciferase
- Author
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Kheirabadi, M., primary, Gohlke, U., additional, Hossein Khani, S., additional, Heinemann, U., additional, and Naderi-Manesh, H., additional
- Published
- 2012
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13. The Crystal Structure of Methylglyoxal Synthase from Thermus sp. GH5 Bound to Phosphate Ion.
- Author
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Shahsavar, A., primary, Erfani Moghaddam, M., additional, Antonyuk, S.V., additional, Khajeh, K., additional, and Naderi-Manesh, H., additional
- Published
- 2011
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14. The Crystal Structure of Methylglyoxal Synthase from Thermus sp. GH5 Bound to Malonate.
- Author
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Shahsavar, A., primary, Erfani Moghaddam, M., additional, Antonyuk, S.V., additional, Khajeh, K., additional, and Naderi-Manesh, H., additional
- Published
- 2011
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15. Remarkable improvements of a neutral protease activity and stability share the same structural origins
- Author
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Asghari, S. M., primary, Pazhang, M., additional, Ehtesham, S., additional, Karbalaei-Heidari, H. R., additional, Taghdir, M., additional, Sadeghizadeh, M., additional, Naderi-Manesh, H., additional, and Khajeh, K., additional
- Published
- 2010
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16. Engineering of a Bacillus α-amylase whose stability is independent of calcium
- Author
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Ghollasi, M., primary, Khajeh, K., additional, and Naderi-Manesh, H., additional
- Published
- 2009
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17. High resolution crystal structure of Bacillus amyloliquefaciens alpha-amylase
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Alikhajeh, J., primary, Khajeh, K., additional, Ranjbar, B., additional, Naderi-Manesh, H., additional, Lin, Y.H., additional, Liu, M.Y., additional, and Chen, C.J., additional
- Published
- 2008
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18. Crystal structure of native alpha-amylase from Bacillus sp. KR-8104
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Alikhajeh, J., primary, Khajeh, K., additional, Ranjbar, B., additional, Naderi-Manesh, M., additional, Naderi-Manesh, H., additional, and Chen, C.J., additional
- Published
- 2008
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19. The investigation of interactions of κ‐Hefutoxin1 with the voltage‐gated potassium channels: A computational simulation
- Author
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Zarrabi, M., primary and Naderi‐Manesh, H., additional
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- 2007
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20. Computational simulations of interactions of the κ-hefutoxin1 with the voltage-gated potassium ion channels
- Author
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Zarrabi, M, primary and Naderi-Manesh, H, additional
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- 2007
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21. Impacts of Persian Gulf blackfin stonefish crude venom on the haematological factors and serum enzymes levels of laboratory rat.
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Vazirizadeh, A., Naderi-Manesh, H., Bargahi, A., Nabipour, I., and Mohebbi, G. H.
- Abstract
Background: One of the venomous fishes of Persian Gulf is a type of stonefish called blackfin stonefish (Pseudosynanceia melanostigma) that is very poorly-known. This fish lives on the muddy bottoms of marine shallow waters and have venomous spines on its stone like body. The envenomation usually is happened by unwanted contact of human body to its body and the proteinic venom is injected into the skin. Upon the venom entrance to the body various symptoms and signs will occur that their intensity depends on the venom amount. The aim of study is the understanding of some pharmacological impacts of blackfin stonefish for future studies. Material and Methods: A total of 18 male laboratory rats were divided into three groups of control, second and third and envenomed by sub lethal doses (1/3 LD50 and ½ LD50) intravenously and the serum enzymes namely Creatine Phosphokinase, Lactate Dehydrogenase, Glutamate-Oxaloacetate Transaminase, Gamma-Glutamyl Transpeptidase, Alkaline Phosphatase and Amylase, serum electrolytes namely Sodium. Potassium and Calcium and also complete blood cells of control and experimental rats were measured. Results: The serum enzymes levels, potassium and calcium levels and withe blood cells count in envenomed rats by blackfin stonefish crude venom in compare with control rats had significant increase while the haemoglobin level, red blood cells count and also serum sodium level had significant decrease (p<0.001). Conclusion: The increase in hepatomascular enzyme levels, and the decrease in haemoglobin level can be a probable marker of the presence of rhabdomyolysis, haemolysis and also hepatotoxicity activities in the blackfin stonefish venom and that needs to the histopathologic studies in these systems. [ABSTRACT FROM AUTHOR]
- Published
- 2014
22. The investigation of interactions of κ-Hefutoxin1 with the voltage-gated potassium channels: A computational simulation.
- Author
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Zarrabi, M. and Naderi-Manesh, H.
- Abstract
κ-Hefutoxin1 is a K
+ channel-blocking toxin from the scorpion Heterometrus fluvipes. It is a 22-residue protein that adapts a novel fold of two parallel helices linked by two disulfide bridges without β-sheets. Recognition of interactions of κ-Hefutoxin1 with the voltage-gated potassium channels, Kv1.1, Kv1.2, and Kv1.3, was studied by 3D-Dock software package. All structures of κ-Hefutoxin1 were considered during the simulations, which indicated that even small changes in the structure of κ-Hefutoxin1 considerably affected both the recognition and the binding between κ-Hefutoxin1 and the Kv1 channels. κ-Hefutoxin1 is located around the extracellular part of the Kv1 channels, making contacts with its helices. Lys 19, Tyr 5, Arg 6, Trp 9, or Arg 10 in the toxin and residues Asp 402, His 404, Thr 407,Gly 401, and Asp 386 in each subunit of the Kv potassium channel are the key residues for the toxin-channel recognition. Moreover, the simulation result demonstrates that the hydrophobic interactions are important in interaction of negatively charged toxins with potassium channels. The results of our docking/molecular dynamics simulations indicate that our 3D model structure of the κ-Hefutoxin1-complex is both reasonable and acceptable and could be helpful for smarter drug design and the blocking agents of Kv1 channels. Proteins 2008. © 2007 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]- Published
- 2008
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23. The Role of Charge Distribution on the Antimalarial Activity of Artemisinin Analogues
- Author
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Rafiee, M. A., Hadipour, N. L., and Naderi-manesh, H.
- Abstract
In this work the calculated nuclear quadrupole coupling constants (NQCC; χ) of 17O in artemisinin and some of its derivatives and the effects of charge density due to the nature of ligands on NQCC of 17O were investigated. All calculations were performed at the HF/3-21G level using the Gaussian 98 program. The results show that the O−O linkage has a characteristic role in the antimalarial activity of artemisinin. In addition, various substitutions on C4 change the charge density on these oxygens and consequently change the pharmaceutical effect of artemisinin. Our results suggest that due to a larger charge density on O1, the heme iron approaches the endoperoxide moiety at the O1 position with preference to the O2 position.
- Published
- 2005
24. Chemical modification of lysine residues in Bacillus a-amylases: effect on activity and stability
- Author
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Khajeh, K., Naderi-Manesh, H., Ranjbar, B., Moosavi-Movahedi, A. a., and Nemat-Gorgani, M.
- Published
- 2001
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25. Homology-based molecular modelling of PLP-dependent histidine decarboxylase from Morganella morganii
- Author
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Tahanejad, F. S., Naderi-Manesh, H., Habibinejad, B., and Mahmoudian, M.
- Published
- 2000
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26. Quantum mechanical study of the intermediates formed following the reaction of the histidine decarboxylase's substrate and inhibitors with coenzyme
- Author
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Tahanejad, F. S. and Naderi-Manesh, H.
- Published
- 2000
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27. Cloning and Expression of TNF Related Apoptosis Inducing Ligand in Nicotiana tabacum
- Author
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Heidari, H. R., Mojgan Bandehpour, Vahidi, H., Barar, J., Kazemi, B., and Naderi-Manesh, H.
- Subjects
Recombinant protein ,Nicotiana tabacum ,Agrobacterium tumefaciens ,fungi ,Molecular Farming ,food and beverages ,Original Article ,TRAIL - 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.
28. Novel water-soluble polyurethane nanomicelles for cancer chemotherapy: physicochemical characterization and cellular activities
- Author
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Khosroushahi Ahmad, Naderi-Manesh Hossein, Yeganeh Hamid, Barar Jaleh, and Omidi Yadollah
- Subjects
Bioactive biocompatible polymer ,Cancer chemotherapy ,Nanomicelle ,Nanoparticle ,Polyurethane ,Paclitaxel ,Biotechnology ,TP248.13-248.65 ,Medical technology ,R855-855.5 - Abstract
Abstract Background Efficient delivery of anticancer chemotherapies such as paclitaxel (PTX) can improve treatment strategy in a variety of tumors such as breast and ovarian cancers. Accordingly, researches on polymeric nanomicelles continue to find suitable delivery systems. However, due to biocompatibility concerns, a few micellar nanoformulations have exquisitely been translated into clinical uses. Here, we report the synthesis of novel water-soluble nanomicelles using bioactive polyurethane (PU) polymer and efficient delivery of PTX in the human breast cancer MCF-7 cells. Results The amphiphilic polyurethane was prepared through formation of urethane bounds between hydroxyl groups in poly (tetramethylene ether) glycol (PTMEG) and dimethylol propionic acid with isocyanate groups in toluene diisocyanate (TDI). The free isocyanate groups were blocked with phenol, while the free carboxyl groups of dimethylol propionic acid were reacted with triethylamine to attain ionic centers in the polymer backbone. These hydrophobic PTMEG blocks displayed self-assembly forming polymeric nanomicelles in water. The PTX loaded PU nanomicelles showed suitable physical stability, negative zeta potential charge (-43) and high loading efficiency (80%) with low level of critical micelle concentration (CMC). In vitro drug release profile showed a faster rate of drug liberation at pH 5.4 as compared to that of pH 7.4, implying involvement of a pH-sensitive mechanism for drug release from the nanomicelles. The kinetic of release exquisitely obeyed the Higuchi model, confirming involvement of diffusion and somewhat erosion at pH 5.4. These nanomicelles significantly inhibited the growth and proliferation of the human breast cancer MCF-7 cells, leading them to apoptosis. The real time RT-PCR analysis confirmed the activation of apoptosis as result of liberation of cytochrome c in the cells treated with the PTX loaded PU nanomicelles. The comet assay analysis showed somewhat DNA fragmentation in the treated cells. Conclusions Based upon these findings, we propose that the bioactive waterborne polyurethane nanomicelles can be used as an effective nanocarrier for delivery of anticancer chemotherapies such as paclitaxel.
- Published
- 2012
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29. Computational simulations of interactions of the κ-hefutoxin 1 with the voltage-gated potassium ion channels.
- Author
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Zarrabi, M. and Naderi-Manesh, H.
- Subjects
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ION channels - Abstract
An abstract of the article "Computational simulations of interactions of the κ-hefutoxin 1 with the voltage-gated potassium ion channels," by M. Zarrabi and H. Naderi-Manesh is presented.
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- 2007
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30. Single-layer graphene oxide nanosheets induce proliferation and Osteogenesis of single-cell hBMSCs encapsulated in Alginate Microgels.
- Author
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Soleymani H, Moghaddam MM, Naderi-Manesh H, and Taheri RA
- Subjects
- Humans, Microgels chemistry, Hydrogels chemistry, Nanostructures chemistry, Cells, Cultured, Osteocalcin metabolism, Osteocalcin genetics, Cell Differentiation drug effects, Core Binding Factor Alpha 1 Subunit metabolism, Core Binding Factor Alpha 1 Subunit genetics, Tissue Engineering methods, Graphite chemistry, Graphite pharmacology, Alginates chemistry, Alginates pharmacology, Cell Proliferation drug effects, Osteogenesis drug effects, Mesenchymal Stem Cells drug effects, Mesenchymal Stem Cells cytology, Mesenchymal Stem Cells metabolism
- Abstract
Microfluidics cell encapsulation offers a way to mimic a 3D microenvironment that supports cell growth and proliferation, while also protecting cells from environmental stress. This technique has found extensive applications in tissue engineering and cell therapies. Several studies have demonstrated the advantages of graphene oxide (GO) as an osteogenic inducer; however, the significance of GO on stem cell fate in the single-cell state is still unclear. Here, a microfluidics-based approach is developed for continuous encapsulation of mesenchymal stem cells (MSCs) at the single-cell level using alginate microgels. So, single-layer graphene oxide (slGO) nanosheet is used to be encapsulated inside the alginate droplets. The results of AFM and SEM show that slGO can increase the roughness and reduce the stiffness of alginate hydrogels. The Young's modulus of the alginate and alginate-slGO was obtained as 1414 kPa and 985.9 kPa, respectively. Live/dead assay and fluorescence microscopy images illustrate that slGO can maintain the viability and proliferation of microencapsulated hBMSCs. The obtained results show that slGO increases the mineralization of the encapsulated hBMSCs, so that microgels containing hBMSCs gradually became opaque during 21 days of culture. RT-qPCR results indicate that the expression of OCN, Runx2, and ALP in the alginate-slGO microgels is significantly higher than in the alginate microgels. The expression of OCN and Runx2 in the alginate-slGO microgels is 4.27 and 5.87-fold higher than in the alginate microgels, respectively. It can be concluded that low doses of slGO nanosheets have the potential to be utilized in the development of tissue engineering and bone regeneration. This finding offers a new method for creating injectable tissue transplants that are minimally invasive., (© 2024. The Author(s).)
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- 2024
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31. Nanosystems for targeted drug Delivery: Innovations and challenges in overcoming the Blood-Brain barrier for neurodegenerative disease and cancer therapy.
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Rafati N, Zarepour A, Bigham A, Khosravi A, Naderi-Manesh H, Iravani S, and Zarrabi A
- Abstract
The evolution of sophisticated nanosystems has revolutionized biomedicine, notably in treating neurodegenerative diseases and cancer. These systems show potential in delivering medication precisely to affected tissues, improving treatment effectiveness while minimizing side effects. Nevertheless, a major hurdle in targeted drug delivery is breaching the blood-brain barrier (BBB), a selective shield separating the bloodstream from the brain and spinal cord. The tight junctions between endothelial cells in brain capillaries create a formidable physical barrier, alongside efflux transporters that expel harmful molecules. This presents a notable challenge for brain drug delivery. Nanosystems present distinct advantages in overcoming BBB challenges, offering enhanced drug efficacy, reduced side effects, improved stability, and controlled release. Despite their promise, challenges persist, such as the BBB's regional variability hindering uniform drug distribution. Efflux transporters can also limit therapeutic agent efficacy, while nanosystem toxicity necessitates rigorous safety evaluations. Understanding the long-term impact of nanomaterials on the brain remains crucial. Additionally, addressing nanosystem scalability, cost-effectiveness, and safety profiles is vital for widespread clinical implementation. This review delves into the advancements and obstacles of advanced nanosystems in targeted drug delivery for neurodegenerative diseases and cancer therapy, with a focus on overcoming the BBB., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)
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- 2024
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32. Design, Synthesis, Docking Studies, and Biological Activity of Novel Analogs of Cyclophosphamide as Potential Anticancer Agents.
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Gholivand K, Rostami SA, Sabaghian M, Sadeghi-Mohammadi S, Babaei A, Malekshah RE, and Naderi-Manesh H
- Abstract
Introduction: This study aimed to present the synthesis and characterization of four novel analogs of cyclophosphamide (2, 3, 4, 7) and their related precursors (1, 5, 6) and assess their anticancer activity against breast cancerous (MCF-7) and normal (HUVEC) cells., Method: Notably, 2-(bis(2-chloroethyl)amino)-1,3,2-diazaphospholidine 2-oxide ((2)) and 2-(bis(2-hydroxyethyl)amino)-1,3,2-diazaphospholidine 2-oxide ((7)) exhibited concentration- dependent cytotoxicity against the MCF-7 cell line, with IC50 values of 8.98 and 28.74 μM, respectively., Result: Annexin V/PI staining and ROS assays demonstrated reduced cell viability and mitochondrial dysfunction. in silico studies involving DFT-D optimization and Molegro virtual docking against B-DNA dodecamer and STAT3 receptors revealed enhanced interactions for certain compounds compared to cyclophosphamide., Conclusion: Importantly, the in silico and in vitro results corroborated each other, supporting the potential anticancer efficacy of these novel analogs., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)
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- 2024
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33. Synergistic effect of curcumin and tamoxifen loaded in pH-responsive gemini surfactant nanoparticles on breast cancer cells.
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Ashin ZF, Sadeghi-Mohammadi S, Vaezi Z, Najafi F, AdibAmini S, Sadeghizadeh M, and Naderi-Manesh H
- Subjects
- Humans, Hydrogen-Ion Concentration, Female, Drug Synergism, MCF-7 Cells, Cell Line, Tumor, Antineoplastic Agents pharmacology, Antineoplastic Agents chemistry, Drug Carriers chemistry, Curcumin pharmacology, Curcumin chemistry, Tamoxifen pharmacology, Tamoxifen chemistry, Nanoparticles chemistry, Breast Neoplasms drug therapy, Surface-Active Agents chemistry, Surface-Active Agents pharmacology
- Abstract
Background: Drug combination therapy is preferred over monotherapy in clinical research to improve therapeutic effects. Developing a new nanodelivery system for cancer drugs can reduce side effects and provide several advantages, including matched pharmacokinetics and potential synergistic activity. This study aimed to examine and determine the efficiency of the gemini surfactants (GSs) as a pH-sensitive polymeric carrier and cell-penetrating agent in cancer cells to achieve dual drug delivery and synergistic effects of curcumin (Cur) combined with tamoxifen citrate (TMX) in the treatment of MCF-7 and MDA-MB-231 human BC cell lines., Methods: The synthesized NPs were self-assembled using a modified nanoprecipitation method. The functional groups and crystalline form of the nanoformulation were examined by Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), differential scanning calorimetry (DSC), and dynamic light scattering (DLS) used to assess zeta potential and particle size, and the morphological analysis determined by transmission electron microscopy (TEM). The anticancer effect was evaluated through an in vitro cytotoxicity MTT assay, flow cytometry analysis, and apoptosis analysis performed for mechanism investigation., Results: The tailored NPs were developed with a size of 252.3 ± 24.6 nm and zeta potential of 18.2 ± 4.4 mV capable of crossing the membrane of cancer cells. The drug loading and release efficacy assessment showed that the loading of TMX and Cur were 93.84% ± 1.95% and 90.18% ± 0.56%, respectively. In addition, the drug release was more controlled and slower than the free state. Polymeric nanocarriers improved controlled drug release 72.19 ± 2.72% of Tmx and 55.50 ± 2.86% of Cur were released from the Tmx-Cur-Gs NPs after 72 h at pH = 5.5. This confirms the positive effect of polymeric nanocarriers on the controlled drug release mechanism. moreover, the toxicity test showed that combination-drug delivery was much more greater than single-drug delivery in MCF-7 and MDA-MB-231 cell lines. Cellular imaging showed excellent internalization of TMX-Cur-GS NPs in both MCF-7 and MDA-MB-231 cells and synergistic anticancer effects, with combination indices of 0.561 and 0.353, respectively., Conclusion: The combined drug delivery system had a greater toxic effect on cell lines than single-drug delivery. The synergistic effect of TMX and Cur with decreasing inhibitory concentrations could be a more promising system for BC-targeted therapy using GS NPs., (© 2024. The Author(s).)
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- 2024
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34. Synergistic antibacterial effect of the pistachio green hull extract-loaded porphysome decorated with 4-nitroimidazole against bacteria.
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Mahafel N, Vaezi Z, Barzegar M, Hekmat A, and Naderi-Manesh H
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- Humans, Porphyrins chemistry, Porphyrins pharmacology, Imidazoles chemistry, Imidazoles pharmacology, Particle Size, Drug Carriers chemistry, Drug Synergism, Caco-2 Cells, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemistry, Escherichia coli drug effects, Staphylococcus aureus drug effects, Microbial Sensitivity Tests, Plant Extracts chemistry, Plant Extracts pharmacology, Pistacia chemistry
- 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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- 2024
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35. Oral Formulation of 5-Aminosalicylic Acid-Hemoglobin Bio-Adhesive Nanoparticles Enhance Therapeutic Efficiency in Ulcerative Colitis Mice: A Preclinical Evaluation.
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Vaezi Z, Baradaran Ghavami S, Farmani M, Mahdavian R, Asadzadeh Aghdaei H, and Naderi-Manesh H
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- Animals, Mice, Administration, Oral, Male, Anti-Inflammatory Agents, Non-Steroidal administration & dosage, Anti-Inflammatory Agents, Non-Steroidal pharmacokinetics, Anti-Inflammatory Agents, Non-Steroidal pharmacology, Disease Models, Animal, Drug Delivery Systems methods, Drug Carriers chemistry, Colitis, Ulcerative drug therapy, Colitis, Ulcerative metabolism, Mesalamine administration & dosage, Mesalamine chemistry, Mesalamine pharmacology, Hemoglobins administration & dosage, Nanoparticles chemistry, Colon drug effects, Colon metabolism, Colon pathology
- 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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 American Pharmacists Association. Published by Elsevier Inc. All rights reserved.)
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- 2024
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36. Microfluidics single-cell encapsulation reveals that poly-l-lysine-mediated stem cell adhesion to alginate microgels is crucial for cell-cell crosstalk and its self-renewal.
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Soleymani H, Ghorbani M, Sedghi M, Allahverdi A, and Naderi-Manesh H
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- Humans, Microfluidics methods, Cell Communication drug effects, Cell Survival drug effects, Hydrogels chemistry, Hydrogels pharmacology, Cell Encapsulation methods, Single-Cell Analysis, Cell Self Renewal drug effects, Cell Differentiation drug effects, Alginates chemistry, Alginates pharmacology, Polylysine chemistry, Polylysine pharmacology, Cell Adhesion drug effects, Mesenchymal Stem Cells cytology, Mesenchymal Stem Cells drug effects, Mesenchymal Stem Cells metabolism, Cell Proliferation drug effects, Microgels chemistry
- Abstract
Microfluidic cell encapsulation has provided a platform for studying the behavior of individual cells and has become a turning point in single-cell analysis during the last decade. The engineered microenvironment, along with protecting the immune response, has led to increasingly presenting the results of practical and pre-clinical studies with the goals of disease treatment, tissue engineering, intelligent control of stem cell differentiation, and regenerative medicine. However, the significance of cell-substrate interaction versus cell-cell communications in the microgel is still unclear. In this study, monodisperse alginate microgels were generated using a flow-focusing microfluidic device to determine how the cell microenvironment can control human bone marrow-derived mesenchymal stem cells (hBMSCs) viability, proliferation, and biomechanical features in single-cell droplets versus multi-cell droplets. Collected results show insufficient cell proliferation (234 % and 329 %) in both single- and multi-cell alginate microgels. Alginate hydrogels supplemented with poly-l-lysine (PLL) showed a better proliferation rate (514 % and 780 %) in a comparison of free alginate hydrogels. Cell stiffness data illustrate that hBMSCs cultured in alginate hydrogels have higher membrane flexibility and migration potency (Young's modulus equal to 1.06 kPa), whereas PLL introduces more binding sites for cell attachment and causes lower flexibility and migration potency (Young's modulus equal to 1.83 kPa). Considering that cell adhesion is the most important parameter in tissue engineering, in which cells do not run away from a 3D substrate, PLL enhances cell stiffness and guarantees cell attachments. In conclusion, cell attachment to PLL-mediated alginate hydrogels is crucial for cell viability and proliferation. It suggests that cell-cell signaling is good enough for stem cell viability, but cell-PLL attachment alongside cell-cell signaling is crucial for stem cell proliferation and self-renewal., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)
- Published
- 2024
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37. Porphysome Engineered With Specific Protein Binding Sites as a Multimodal Theranostic Nanocarrier for Targeted Protein Delivery.
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Ayyari N, Vaezi Z, Ashin ZF, Karimi E, Mohsenzadeh Haji F, Nikkhah M, and Naderi-Manesh H
- Subjects
- Humans, Binding Sites drug effects, MCF-7 Cells, Drug Carriers chemistry, Theranostic Nanomedicine, Nanoparticles chemistry, Cell Survival drug effects, 1,2-Dipalmitoylphosphatidylcholine chemistry, Drug Delivery Systems, Particle Size, Porphyrins chemistry, Porphyrins pharmacology
- 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., (© 2024 Wiley-VHCA AG, Zurich, Switzerland.)
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- 2024
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38. Single-Cell RNA Sequencing in Organ and Cell Transplantation.
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Abedini-Nassab R, Taheri F, Emamgholizadeh A, and Naderi-Manesh H
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- Animals, Humans, Single-Cell Analysis, Cell Transplantation, Organ Transplantation, Sequence Analysis, RNA
- 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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- 2024
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39. Investigation of synergic effects of nanogroove topography and polyaniline-chitosan nanocomposites on PC12 cell differentiation and axonogenesis.
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Afsharian MH, Mahdavian R, Jafari S, Allahverdi A, Soleymani H, and Naderi-Manesh H
- 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., Competing Interests: The authors declare there is no conflict of interest., (© 2024 The Author(s).)
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- 2024
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40. Grafting of sinapic acid onto glucosamine nanoparticle as a potential therapeutic drug with enhanced anti-inflammatory activities in osteoarthritis treatment.
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Tajik E, Vaezi Z, Tabarsa M, Hekmat A, and Naderi-Manesh H
- Subjects
- Humans, Glucosamine, Escherichia coli, Staphylococcus aureus, Anti-Inflammatory Agents pharmacology, Chitosan chemistry, Osteoarthritis drug therapy, Nanoparticles chemistry
- 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,
1 HNMR, 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., Competing Interests: Declaration of competing interest The authors declare that they have no conflict of interest., (Copyright © 2023 Elsevier B.V. All rights reserved.)- Published
- 2023
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41. Label-free electrochemical cancer cell detection leveraging hemoglobin-encapsulated silver nanoclusters and Cu-MOF nanohybrids on a graphene-assisted dual-modal probe.
- Author
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Zare AA, Naderi-Manesh H, Naghib SM, Shamsipur M, and Molaabasi F
- Subjects
- Humans, Female, Silver chemistry, Electrochemical Techniques methods, Immunoassay, Hemoglobins, Limit of Detection, Graphite chemistry, Biosensing Techniques methods, Breast Neoplasms diagnosis, Metal Nanoparticles chemistry
- 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 (10
2 -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., (© 2023. The Author(s).)- Published
- 2023
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42. Lung Cancer Cell-Derived Exosome Detection Using Electrochemical Approach towards Early Cancer Screening.
- Author
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Irani K, Siampour H, Allahverdi A, Moshaii A, and Naderi-Manesh H
- Subjects
- Humans, Early Detection of Cancer, Electrodes, Gold chemistry, Electrochemical Techniques, Alpha-Ketoglutarate-Dependent Dioxygenase FTO, Lung Neoplasms diagnosis, Exosomes chemistry, Biosensing Techniques methods
- 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.
- Published
- 2023
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43. The application of nano-hydrogels and hydrogels in wound dressings.
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Ghorbani M, Ghorbani F, Kahrizi S, Naderi-Manesh H, and Kahrizi D
- Subjects
- Humans, Bandages, Skin, Hydrogels, Wounds, Gunshot, Fractures, Bone
- 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.
- Published
- 2023
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44. Quantifying F-actin patches in single melanoma cells using total-internal reflection fluorescence microscopy.
- Author
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Sheykhi E, Shojaedin-Givi B, Sajad B, Naderi-Manesh H, and Tavaddod S
- Subjects
- Humans, Microscopy, Fluorescence methods, Actin Cytoskeleton metabolism, Image Processing, Computer-Assisted methods, Fluorescent Dyes, Actins metabolism, Melanoma
- Abstract
Total-internal reflection fluorescence (TIRF) microscope is a unique technique for selective excitation of only those fluorophore molecules in a cellular environment, which are located at the sub-diffraction axial distance of a cell's contact-area. Despite this prominent feature of the TIRF microscope, making quantitative use of this technique has been a challenge, since the excitation intensity strongly depends on the axial position of a fluorophore molecule. Here, we present an easy-implemented data analysis method to quantitatively characterize the fluorescent signal, without considering the intensity-value. We use F-actin patches in single-melanoma cells as an example and define two quantities of elongation and surface density for F-actin patches at the contact-area of a melanoma cell. The elongation parameter can evaluate the dispersion of F-actin patches at the contact-area of a cell and is useful to classify the attaching, spreading, and expanding stages of a cell. Following that, we present the profile of the surface density of F-actin patches as a quantity to probe the spatio-temporal distribution of the F-actin patches at the contact-area of a cell. The data analysis methods that are proposed here will also be applicable in the image analysis of the other advanced optical microscopic methods., (© 2022. The Author(s).)
- Published
- 2022
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45. Hybrid Microfluidic Device for High Throughput Isolation of Cells Using Aptamer Functionalized Diatom Frustules.
- Author
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Mohammadi R, Asghari M, Colombo M, Vaezi Z, Richards DA, Stavrakis S, Naderi-Manesh H, and DeMello A
- Subjects
- Humans, Cell Separation, Cell Line, Tumor, Lab-On-A-Chip Devices, Diatoms, Neoplastic Cells, Circulating pathology
- 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%)., (Copyright 2022 Rashin Mohammadi, Mohammad Asghari, Monika Colombo, Zahra Vaezi , Daniel Richards, Stavros Stavrakis, Hossein Naderi-Manesh, Andrew deMello. License: This work is licensed under a Creative Commons Attribution 4.0 International License.)
- Published
- 2022
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46. Differentiation of PC12 cell line into neuron by Valproic acid encapsulated in the stabilized core-shell liposome-chitosan Nano carriers.
- Author
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Kelkawi AHA, Hashemzadeh H, Pashandi Z, Tiraihi T, and Naderi-Manesh H
- Subjects
- Animals, Drug Carriers, Liposomes, Neurons, PC12 Cells, Phospholipids, Rats, Valproic Acid pharmacology, Chitosan
- 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., (Copyright © 2022. Published by Elsevier B.V.)
- Published
- 2022
- Full Text
- View/download PDF
47. Fluorescence sensing and imaging with carbon-based quantum dots for early diagnosis of cancer: A review.
- Author
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Mohammadi R, Naderi-Manesh H, Farzin L, Vaezi Z, Ayarri N, Samandari L, and Shamsipur M
- Subjects
- Carbon, Early Detection of Cancer, Fluorescent Dyes, Humans, Reproducibility of Results, Biosensing Techniques methods, Neoplasms diagnostic imaging, Quantum Dots
- Abstract
This review discusses recent advances and the reported strategies over the last ten years on the use of carbon-based quantum dots (QDs), including carbon dots (CDs), graphene quantum dots (GQDs), and polymer dots (PDs) in the design of fluorescence imaging and biosensing system for early diagnosis of cancers. Besides, this study comprehensively reports the latest developments in these years in the fluorescence imaging (FI) area with special attention to carbon-based QDs that take advantage of the excellent properties offered by these zero-dimensional (0D) nanomaterials as fluorescent tags. The most remarkable advantages of these carbon nanomaterials in the development of fluorescence sensing and imaging strategies compared to the conventional dyes arise from sharp emission spectra, long photostability, low-cost synthesis, reliability, reproducibility, high fluorescent intensity, and high surface functional groups such as carboxyl and amide, which impart better solubility in many solvents and aqueous media and facilitate their easy functionalization with biological species. The final section discusses the main challenges to be met to take full advantage of these properties in fluorescence bio-sensing and imaging as well as the possible future trends in this field based on the great advances that have occurred in recent years., (Copyright © 2022 Elsevier B.V. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
48. 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.
- Author
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Vaezi Z, Asadzadeh Aghdaei H, Sedghi M, Mahdavian R, Molakarimi M, Hashemi N, and Naderi-Manesh H
- Subjects
- Adhesives pharmacology, Animals, Anti-Inflammatory Agents, Non-Steroidal chemistry, Caco-2 Cells, Colon, Delayed-Action Preparations pharmacology, Hemoglobins, Humans, Mesalamine, Mice, Colitis, Ulcerative drug therapy, Inflammatory Bowel Diseases drug therapy, Nanoparticles
- 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., (Copyright © 2022 Elsevier B.V. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
49. Design and simulation of the liposomal model by using a coarse-grained molecular dynamics approach towards drug delivery goals.
- Author
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Parchekani J, Allahverdi A, Taghdir M, and Naderi-Manesh H
- Subjects
- Drug Delivery Systems methods, Lipid Bilayers chemistry, Molecular Dynamics Simulation, Pharmaceutical Preparations chemistry, Phospholipids chemistry, Static Electricity, Drug Carriers chemistry, Drug Delivery Systems instrumentation, Liposomes chemistry
- 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., (© 2022. The Author(s).)
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- 2022
- Full Text
- View/download PDF
50. Improvement of anti-biofilm activities via co-delivery of curcumin and gentamicin in lipid-polymer hybrid nanoparticle.
- Author
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Sadeghi Mohammadi S, Vaezi Z, and Naderi-Manesh H
- Subjects
- Anti-Bacterial Agents pharmacology, Biofilms, Gentamicins pharmacology, Humans, Lipids, Liposomes, Microbial Sensitivity Tests, Persistent Infection, Polymers, Pseudomonas aeruginosa, Curcumin pharmacology, Nanoparticles
- 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.
- Published
- 2022
- Full Text
- View/download PDF
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