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Total 140 records

    Molecular dynamics simulation and MM-PBSA calculations of sickle cell hemoglobin in dimer form with Val, Trp, or Phe at the lateral contact

    , Article Journal of Physical Organic Chemistry ; Volume 23, Issue 9 , March , 2010 , Pages 866-877 ; 08943230 (ISSN) Abroshan, H ; Akbarzadeh, H ; Parsafar, G. A ; Sharif University of Technology
    Abstract
    As the delay time and hence nuclei formation play a crucial role in the pathophysiology of sickle cell disease, MD simulation and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) calculations have been performed on three systems of hemoglobin; namely dimer of hemoglobin with valine (Hb S), tryptophan (Hbβ6W), and phenylalanine (Hbβ6F) at β6 position. The structural changes due to these aromatic substitutions are investigated. It is shown that β subunits have significant impact on the differences between a dimer and other crystal structures. Transition from a dimer to polymer for Hb S system affects the donor molecule more than that of the acceptor. In the case of donor and... 

    NMR spectroscopy-based metabolomic study of serum in sulfur mustard exposed patients with lung disease

    , Article Biomarkers ; Volume 22, Issue 5 , 2017 , Pages 413-419 ; 1354750X (ISSN) Nobakht, B.F., M. Gh ; Arefi Oskouie, A ; Rezaei Tavirani, M ; Aliannejad, R ; Taheri, S ; Fathi, F ; Naseri, M. T ; Sharif University of Technology
    Taylor and Francis Ltd  2017
    Abstract
    Sulfur mustard (SM) is a vesication chemical warfare agent for which there is currently no antidote. Despite years of research, there is no common consensus about the pathophysiological basis of chronic pulmonary disease caused by this chemical warfare agent. In this study, we combined chemometric techniques with nuclear magnetic resonance (NMR) spectroscopy to explore the metabolic profile of sera from SM-exposed patients. A total of 29 serum samples obtained from 17 SM-injured patients, and 12 healthy controls were analyzed by Random Forest. Increased concentrations of seven amino acids, glycerol, dimethylamine, ketone bodies, lactate, acetate, citrulline and creatine together with the... 

    Metabolomics analysis of the saliva in patients with chronic hepatitis b using nuclear magnetic resonance: A pilot study

    , Article Iranian Journal of Basic Medical Sciences ; Volume 22, Issue 9 , 2019 , Pages 1044-1049 ; 20083866 (ISSN) Gilany, K ; Mohamadkhani, A ; Chashmniam, S ; Shahnazari, P ; Amini, M ; Arjmand, B ; Malekzadeh, R ; Nobakht Motlagh Ghoochani, B. F ; Sharif University of Technology
    Mashhad University of Medical Sciences  2019
    Abstract
    Objective(s): Hepatitis B virus infection causes chronic disease such as cirrhosis and hepatocellular carcinoma. The metabolomics investigations have been demonstrated to be related to pathophysiologic mechanisms in many disorders such as hepatitis B infection. The aim of this study was to investigate the saliva metabolic profile of patients with chronic hepatitis B infection and to identify underlying mechanisms as well as potential biomarkers associated with the disease. Materials and Methods: Saliva from 16 healthy subjects and 20 patients with chronic hepatitis B virus were analyzed by nuclear magnetic resonance (NMR). Then, multivariate statistical analysis was performed to identify... 

    The metabolomics signature associated with responsiveness to steroid therapy in focal segmental glomerulosclerosis: A pilot study

    , Article Revista de Investigacion Clinica ; Volume 71, Issue 2 , 2019 , Pages 106-115 ; 00348376 (ISSN) Chashmniam, S ; Kalantari, S ; Nafar, M ; Boroumandnia, N ; Sharif University of Technology
    Instituto Nacional de la Nutricion Salvador Zubiran  2019
    Abstract
    Background: Focal segmental glomerulosclerosis (FSGS) is considered one of the most severe glomerular diseases and around 80% of cases are resistant to steroid treatment. Since a large proportion of steroid-resistant (SR) FSGS patients progress to end-stage renal disease, other therapeutic strategies may benefit this population. However, identification of non-invasive biomarkers to predict this high-risk population is needed. Objective: We aimed to identify the biomarker candidates to distinguish SR from steroid-sensitive (SS) patients using metabolomics approach and to identify the possible molecular mechanism of resistance. Methods: Urine was collected from biopsy-proven FSGS patients... 

    Design of peptide-based inhibitor agent against amyloid-β aggregation: Molecular docking, synthesis and in vitro evaluation

    , Article Bioorganic Chemistry ; Volume 102 , September , 2020 Jokar, S ; Erfani, M ; Bavi, O ; Khazaei, S ; Sharifzadeh, M ; Hajiramezanali, M ; Beiki, D ; Shamloo, A ; Sharif University of Technology
    Academic Press Inc  2020
    Abstract
    Formation of the amyloid beta (Aβ) peptide aggregations represents an indispensable role in appearing and progression of Alzheimer disease. β-sheet breaker peptides can be designed and modified with different amino acids in order to improve biological properties and binding affinity to the amyloid beta peptide. In the present study, three peptide sequences were designed based on the hopeful results of LIAIMA peptide and molecular docking studies were carried out onto the monomer and fibril structure of amyloid beta peptide using AutoDock Vina software. According to the obtained interactions and binding energy from docking, the best-designed peptide (D-GABA-FPLIAIMA) was chosen and... 

    New proline, alanine, serine repeat sequence for pharmacokinetic enhancement of anti-vegf single-domain antibody

    , Article Journal of Pharmacology and Experimental Therapeutics ; Volume 375, Issue 1 , July , 2020 , Pages 69-75 Khodabakhsh, F ; Salimian, M ; Mehdizadeh, A ; Khosravy, M. S ; Vafabakhsh, A ; Karami, E ; Cohan, R. A ; Sharif University of Technology
    American Society for Pharmacology and Experimental Therapy  2020
    Abstract
    Therapeutic fragmented antibodies show a poor pharmacokinetic profile that leads to frequent high-dose administration. In the current study, for the first time, a novel proline, alanine, serine (PAS) repeat sequence called PAS#208 was designed to extend the plasma half-life of a nanosized anti-vascular endothelial growth factor-A single-domain antibody. Polyacrylamide gel electrophoresis, circular dichroism, dynamic light scattering, and electrophoretic light scattering were used to assess the physicochemical properties of the newly designed PAS sequence. The effect of PAS#208 on the biologic activity of a single-domain antibody was studied using an in vitro proliferation assay. The... 

    PASylation enhances the stability, potency, and plasma half-life of interferon α-2a: A molecular dynamics simulation

    , Article Biotechnology Journal ; Volume 15, Issue 8 , 2020 Shamloo, A ; Rostami, P ; Mahmoudi, A ; Sharif University of Technology
    Wiley-VCH Verlag  2020
    Abstract
    In this study, the effectiveness of PASylation in enhancing the potency and plasma half-life of pharmaceutical proteins has been accredited as an alternative technique to the conventional methods such as PEGylation. Proline, alanine, and serine (PAS) chain has shown some advantages including biodegradability improvement and plasma half-life enhancement while lacking immunogenicity or toxicity. Although some experimental studies have been performed to find the mechanism behind PASylation, the detailed mechanism of PAS effects on the pharmaceutical proteins has remained obscure, especially at the molecular level. In this study, the interaction of interferon α-2a (IFN) and PAS chain is... 

    Fabrication of a sensitive colorimetric nanosensor for determination of cysteine in human serum and urine samples based on magnetic-sulfur, nitrogen graphene quantum dots as a selective platform and Au nanoparticles

    , Article Talanta ; Volume 226 , 2021 ; 00399140 (ISSN) Afsharipour, R ; Dadfarnia, S ; Haji Shabani, A. M ; Kazemi, E ; Pedrini, A ; Verucchi, R ; Sharif University of Technology
    Elsevier B.V  2021
    Abstract
    A novel colorimetric nanosensor is reported for the selective and sensitive determination of cysteine using magnetic-sulfur, nitrogen graphene quantum dots (Fe3O4/S, N-GQDs), and gold nanoparticles (Au NPs). Thus, S, N-GQDs was firstly immobilized on Fe3O4 nanoparticles through its magnetization in the presence of Fe3+ in the alkali solution. The prepared Fe3O4/S, N-GQDs were dispersed in cysteine solution resulting in its quick adsorption on the surface of the Fe3O4/S, N-GQDs through hydrogen bonding interaction. Then, Au NPs solution was added to this mixture that after a short time, the color of Au NPs changed from red to blue, the intensity of surface plasmon resonance peak of Au NPs at... 

    Fabrication of a sensitive colorimetric nanosensor for determination of cysteine in human serum and urine samples based on magnetic-sulfur, nitrogen graphene quantum dots as a selective platform and Au nanoparticles

    , Article Talanta ; Volume 226 , 2021 ; 00399140 (ISSN) Afsharipour, R ; Dadfarnia, S ; Haji Shabani, A. M ; Kazemi, E ; Pedrini, A ; Verucchi, R ; Sharif University of Technology
    Elsevier B.V  2021
    Abstract
    A novel colorimetric nanosensor is reported for the selective and sensitive determination of cysteine using magnetic-sulfur, nitrogen graphene quantum dots (Fe3O4/S, N-GQDs), and gold nanoparticles (Au NPs). Thus, S, N-GQDs was firstly immobilized on Fe3O4 nanoparticles through its magnetization in the presence of Fe3+ in the alkali solution. The prepared Fe3O4/S, N-GQDs were dispersed in cysteine solution resulting in its quick adsorption on the surface of the Fe3O4/S, N-GQDs through hydrogen bonding interaction. Then, Au NPs solution was added to this mixture that after a short time, the color of Au NPs changed from red to blue, the intensity of surface plasmon resonance peak of Au NPs at... 

    Structural stability and sustained release of protein from a multilayer nanofiber/nanoparticle composite

    , Article International Journal of Biological Macromolecules ; Volume 75 , April , 2015 , Pages 248-257 ; 01418130 (ISSN) Vakilian, S ; Mashayekhan, S ; Shabani, I ; Khorashadizadeh, M ; Fallah, A ; Soleimani, M ; Sharif University of Technology
    Elsevier  2015
    Abstract
    The cellular microenvironment can be engineered through the utilization of various nano-patterns and matrix-loaded bioactive molecules. In this study, a multilayer system of electrospun scaffold containing chitosan nanoparticles was introduced to overcome the common problems of instability and burst release of proteins from nanofibrous scaffolds. Bovine serum albumin (BSA)-loaded chitosan nanoparticles was fabricated based on ionic gelation interaction between chitosan and sodium tripolyphosphate. Suspension electrospinning was employed to fabricate poly-e{open}-caprolacton (PCL) containing protein-loaded chitosan nanoparticles with a core-shell structure. To obtain the desired scaffold... 

    A colorimetric sensor array for detection and discrimination of biothiols based on aggregation of gold nanoparticles

    , Article Analytica Chimica Acta ; Volume 882 , July , 2015 , Pages 58-67 ; 00032670 (ISSN) Ghasemi, F ; Hormozi-Nezhad, M.R ; Mahmoudi, M ; Sharif University of Technology
    Elsevier  2015
    Abstract
    Developments of sensitive, rapid, and cheap systems for identification of a wide range of biomolecules have been recognized as a critical need in the biology field. Here, we introduce a simple colorimetric sensor array for detection of biological thiols, based on aggregation of three types of surface engineered gold nanoparticles (AuNPs). The low-molecular-weight biological thiols show high affinity to the surface of AuNPs; this causes replacement of AuNPs' shells with thiol containing target molecules leading to the aggregation of the AuNPs through intermolecular electrostatic interaction or hydrogen-bonding. As a result of the predetermined aggregation, color and UV-vis spectra of AuNPs... 

    Synthesis and properties of novel fluorinated polyamides based on noncoplanar sulfoxide containing aromatic bis(ether amine)

    , Article Polymer Journal ; Volume 41, Issue 3 , 2009 , Pages 174-180 ; 00323896 (ISSN) Shockravi, A ; Abouzari Lotf, E ; Javadi, A ; Taheri, S ; Sharif University of Technology
    2009
    Abstract
    A novel sulfoxide containing bis(ether amine) monomer, 2,2'-sulfoxide- bis[4-methyl(2-trifluoromethyl)4-aminophenoxy) phenyl ether] (M2), was synthesized from the halogen displacement of 2-chloro-5-nitrobenzotrifluoride with dibenzosulfoxide (DH) in the presence of potassium carbonate, followed by catalytic reduction of bis(ether nitro) intermediate with Zinc/Ammonium chloride. A series of organic-soluble poly(ether amide)s (PA1-7) bearing sulfoxide and electronwithdrawing trifiuoromethyl group were synthesized from bis(ether amine) with various aromatic diacids (1-7) via a direct polycondensation with triphenyl phosphite and pyridine. The resulting polymers had inherent viscosities ranging... 

    Graphene oxide-l-arginine nanogel: A pH-sensitive fluorouracil nanocarrier

    , Article Biotechnology and Applied Biochemistry ; Volume 66, Issue 5 , 2019 , Pages 772-780 ; 08854513 (ISSN) Malekimusavi, H ; Ghaemi, A ; Masoudi, G ; Chogan, F ; Rashedi, H ; Yazdian, F ; Omidi, M ; Javadi, S ; Haghiralsadat, B. F ; Teimouri, M ; Faal Hamedani, N ; Sharif University of Technology
    Wiley-Blackwell Publishing Ltd  2019
    Abstract
    Nowadays, putting forward an accurate cancer therapy method with minimal side effects is an important topic of research. Nanostructures, for their ability in controlled and targeted drug release on specific cells, are critical materials in this field. In this study, a pH-sensitive graphene oxide-l-arginine nanogel was synthesized to carry and release 5-fluorouracil. Optimized conditions using statistical analysis, based on the maximum relative viscosity of nanogel, were evaluated: 5.489 for the concentration of l-arginine and 2.404 for pH. The prepared nanogels were characterized using scanning electron microscope and transmission electron microscope images and Fourier-transform infrared... 

    Copper(ii) ions supported on functionalized graphene oxide: an organometallic nanocatalyst for oxidative amination of azolesviaC-H/C-N bond activation

    , Article New Journal of Chemistry ; Volume 45, Issue 6 , 2021 , Pages 3242-3251 ; 11440546 (ISSN) Behzadi, M ; Mahmoodi Hashemi, M ; Roknizadeh, M ; Nasiri, S ; Ramazani Saadatabadi, A ; Sharif University of Technology
    Royal Society of Chemistry  2021
    Abstract
    Graphene oxide (GO) was chemically modified withpara-aminobenzoic acid (PABA) to immobilize copper(ii) ions on its surface and used as a nanocatalyst for the oxidative C(sp2)-H bond amination reaction. A practical method to prepare Cu2+supported onpara-aminobenzoic acid grafted on GO was reported. The prepared Cu2+@GO/PABA was characterized by FT-IR, XRD, SEM, AFM, TEM, UV-Vis, and ICP techniques. The results showed that the morphology, distribution, and loading of copper ions could be well-adjusted by grafting of PABA on GO. Moreover, just 2 mol% of Cu2+@GO-PABA could catalyze the C-H activation reaction of benzoxazole and benzothiazole with secondary amines in >94% yields. Also, the... 

    Development of a novel nano-sized anti-VEGFA nanobody with enhanced physicochemical and pharmacokinetic properties

    , Article Artificial Cells, Nanomedicine and Biotechnology ; Volume 46, Issue 7 , 2018 , Pages 1402-1414 ; 21691401 (ISSN) Khodabakhsh, F ; Norouzian, D ; Vaziri, B ; Ahangari Cohan, R ; Sardari, S ; Mahboudi, F ; Behdani, M ; Mansouri, K ; Mehdizadeh, A ; Sharif University of Technology
    Abstract
    Since physiological and pathological processes occur at nano-environments, nanotechnology has considered as an efficient tool for designing of next generation specific biomolecules with enhanced pharmacodynamic and pharmacodynamic properties. In the current investigation, by control of the size and hydrodynamic volume at the nanoscale, for the first time, physicochemical and pharmacokinetic properties of an anti-VEGFA nanobody was remarkably improved by attachment of a Proline-Alanine-Serine (PAS) rich sequence. The results elucidated unexpected impressive effects of PAS sequence on physicochemical properties especially on size, hydrodynamics radius, and even solubility of nanobody. CD... 

    Multifunctional core-shell nanoplatforms (gold@graphene oxide) with mediated NIR thermal therapy to promote miRNA delivery

    , Article Nanomedicine: Nanotechnology, Biology, and Medicine ; Volume 14, Issue 6 , 2018 , Pages 1891-1903 ; 15499634 (ISSN) Assali, A ; Akhavan, O ; Adeli, M ; Razzazan, S ; Dinarvand, R ; Zanganeh, S ; Soleimani, M ; Dinarvand, M ; Atyabi, F ; Sharif University of Technology
    Elsevier Inc  2018
    Abstract
    Recent insights into the nanomedicine have revealed that nanoplatforms enhance the efficacy of carrier in therapeutic applications. Here, multifunctional nanoplatforms were utilized in miRNA-101 delivery and NIR thermal therapy to induce apoptosis in breast cancer cells. Au nanorods (NRs) or nanospheres (NSs) covered with graphene oxide (GO) were prepared and functionalized with polyethylene glycol as a stabilizer and poly-L-arginine (P-L-Arg) as a targeting agent. In nanoplatforms, coupling Au@GO prepared stable structures with higher NIR reactivity. P-L-Arg substantially enhanced the cellular uptake and gene retardation of stuffs coated by them. However, rod-shape nanoplatforms indicated... 

    The metabolome profiling of obese and non-obese individuals: Metabolically healthy obese and unhealthy non-obese paradox

    , Article Iranian Journal of Basic Medical Sciences ; Volume 23, Issue 2 , 2020 , Pages 186-194 Chashmniam, S ; Madani, N. H ; Ghoochani, B. F. N. M ; Safari Alighiarloo, N ; Khamseh, M. E ; Sharif University of Technology
    Mashhad University of Medical Sciences  2020
    Abstract
    Objective(s): The molecular basis of “metabolically healthy obese” and “metabolically unhealthy non-obese” phenotypes is not fully understood. Our objective was to identify metabolite patterns differing in obese (metabolically healthy vs unhealthy (MHO vs MUHO)) and non-obese (metabolically healthy vs unhealthy (MHNO vs MUHNO)) individuals. Materials and Methods: This case-control study was performed on 86 subjects stratified into four groups using anthropometric and clinical measurements: MHO (21), MUHO (21), MHNO (22), and MUHNO (22). Serum metabolites were profiled using nuclear magnetic resonance (NMR). Multivariate analysis was applied to uncover discriminant metabolites, and enrichment... 

    Biomimetic proteoglycan nanoparticles for growth factor immobilization and delivery

    , Article Biomaterials Science ; Volume 8, Issue 4 , 2020 , Pages 1127-1136 Zandi, N ; Mostafavi, E ; Shokrgozar, M. A ; Tamjid, E ; Webster, T. J ; Annabi, N ; Simchi, A ; Sharif University of Technology
    Royal Society of Chemistry  2020
    Abstract
    The delivery of growth factors is often challenging due to their short half-life, low stability, and rapid deactivation. In native tissues, the sulfated residual of glycosaminoglycan (GAG) polymer chains of proteoglycans immobilizes growth factors through the proteoglycans'/proteins' complexation with nanoscale organization. These biological assemblies can influence growth factor-cell surface receptor interactions, cell differentiation, cell-cell signaling, and mechanical properties of the tissues. Here, we introduce a facile procedure to prepare novel biomimetic proteoglycan nanocarriers, based on naturally derived polymers, for the immobilization and controlled release of growth factors.... 

    An in vitro study of bare and poly(ethylene glycol)-co-fumarate-coated superparamagnetic iron oxide nanoparticles: A new toxicity identification procedure

    , Article Nanotechnology ; Volume 20, Issue 22 , 2009 ; 09574484 (ISSN) Mahmoudi, M ; Simchi, A ; Imani, M ; Milani, A. S ; Stroeve, P ; Sharif University of Technology
    2009
    Abstract
    As the use of superparamagnetic iron oxide nanoparticles (SPION) in biomedical applications increases (e.g. for targeting drug delivery and imaging), patients are likely to be exposed to products containing SPION. Despite their high biomedical importance, toxicity data for SPION are limited to date. The aim of this study is to investigate the cytotoxicity of SPION and its ability to change cell medium components. Bare and poly(ethylene glycol)-co-fumarate (PEGF)-coated SPION with narrow size distributions were synthesized. The particles were prepared by co-precipitation using ferric and ferrous salts with a molar Fe3+/Fe2+ ratio of 2. Dulbecco's modified Eagle's medium (DMEM) and primary... 

    Silica nanoparticle surface chemistry: An important trait affecting cellular biocompatibility in two and three dimensional culture systems

    , Article Colloids and Surfaces B: Biointerfaces ; Volume 182 , 2019 ; 09277765 (ISSN) Hasany, M ; Taebnia, N ; Yaghmaei, S ; Shahbazi, M. A ; Mehrali, M ; Dolatshahi Pirouz, A ; Arpanaei, A ; Sharif University of Technology
    Elsevier B.V  2019
    Abstract
    Great advantages bestowed by mesoporous silica nanoparticles (MSNs) including high surface area, tailorable pore diameter and surface chemistry, and large pore volume render them as efficient tools in biomedical applications. Herein, MSNs with different surface chemistries were synthesized and investigated in terms of biocompatibility and their impact on the morphology of bone marrow-derived mesenchymal stem cells both in 2D and 3D culture systems. Bare MSNs (BMSNs) were synthesized by template removing method using tetraethylorthosilicate (TEOS) as a precursor. The as-prepared BMSNs were then used to prepare amine-functionalized (AMSNs), carboxyl-functionalized (CMSNs) and polymeric...