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    Synthesis and Study of the Interaction of Aza-Crwon Macrocyclic Ligands with Carboxylate Side Arms with Cd Salts

    , M.Sc. Thesis Sharif University of Technology Mohammadzadeh, Amir Hossein (Author) ; Ghanbari, Bahram (Supervisor)
    In the present study, the coordination chemistry of an amino acid azacrown macrocycle ligand bearing one carboxylic acid arm (MA1) was investigated by employing NMR spectroscopy, crystallography and computational chemistry. MA1 was synthetized by the reaction of chloroacetic acid with the parent azacrown macrocycle and its purity was confirmed with 13C and 1H NMR for the first time. A new MA1 homologue, MA3 was also successfully prepared and characterized with NMR, mass spectrometry, and elemental analysis. NMR studies showed that MA1 binds to cadmium via the carboxylate arm in solution. Crystallographic studies showed that MA1 formed a one-dimensional polymer with cadmium, wherein the... 

    Finding protein active sites using approximate sub-graph isomorphism

    , Article 2011 1st Middle East Conference on Biomedical Engineering, MECBME 2011, Sharjah, 21 February 2011 through 24 February 2011 ; 2011 , Pages 432-435 ; 9781424470006 (ISBN) Dezfouli, M. E. A ; Arab, S. S ; Fatemizadeh, E ; Hosseynimanesh, N ; Sharif University of Technology
    Prediction of the amino acids that have a catalytic effect on the enzymes is a major stage in appointing the activity of the enzymes and classification. The biological activity of a protein usually depends on the existence of a small number of amino acids. Recently, many algorithms have been proposed in the literature for finding these amino acids which are complex and time consuming. In this paper, we will introduce a new method for predicting the active sites that will use the spatial coordinates and the type of amino acids that contain the active sites. In order to increase the speed we use an approximate graph isomorphism algorithm. Furthermore, this algorithm allows us to find several... 

    Oxido-peroxido W(VI)-histidine–MgAl-layered double hydroxide composite as an efficient catalyst in sulfide oxidation

    , Article Applied Organometallic Chemistry ; Volume 32, Issue 6 , 2018 ; 02682605 (ISSN) Nikkhoo, M ; Amini, M ; Morteza, S ; Farnia, F ; Bayrami, A ; Bagherzadeh, M ; Gautam, S ; Chae, K. H ; Sharif University of Technology
    John Wiley and Sons Ltd  2018
    Oxido-peroxido W(VI)-histidine–MgAl-layered double hydroxide composite was prepared by using MgAl-layered double hydroxide as a host and oxido-peroxido W(VI)-histidine complex as a guest. The composite was characterized by XRD, IR, EDX,SEM and TEM techniques. This composite is tested for catalytic selective sulfoxidation reactions using hydrogen peroxide as oxidant showing good to moderate conversion along with high selectivity. Copyright © 2018 John Wiley & Sons, Ltd  

    A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins

    , Article BMC Bioinformatics ; Volume 9 , 2008 ; 14712105 (ISSN) Sheari, A ; Kargar, M ; Katanforoush, A ; Arab, S ; Sadeghi, M ; Pezeshk, H ; Eslahchi, C ; Marashi, S. A ; Sharif University of Technology
    Background: It has been previously shown that palindromic sequences are frequently observed in proteins. However, our knowledge about their evolutionary origin and their possible importance is incomplete. Results: In this work, we tried to revisit this relatively neglected phenomenon. Several questions are addressed in this work. (1) It is known that there is a large chance of finding a palindrome in low complexity sequences (i.e. sequences with extreme amino acid usage bias). What is the role of sequence complexity in the evolution of palindromic sequences in proteins? (2) Do palindromes coincide with conserved protein sequences? If yes, what are the functions of these conserved segments?... 

    LiClO4-accelerated three-component Mannich-type reaction of diethyl malonate with imines: An efficient synthesis of β-amino esters under solvent-free conditions

    , Article Synthetic Communications ; Volume 38, Issue 22 , 2008 , Pages 4036-4044 ; 00397911 (ISSN) Aryanasab, F ; Saidi, M. R ; Sharif University of Technology
    LiClO4 is used as catalyst for direct Mannich-type reaction of aryl aldehydes, aryl amines, and diethyl malonic ester under solvent-free conditions. This three-component reaction afforded the corresponding β-amino esters in good yields with simple and environmentally benign procedure. Copyright © Taylor & Francis Group, LLC  

    Synthesis of high surface area nanocrystalline anatase-TiO2 powders derived from particulate sol-gel route by tailoring processing parameters

    , Article Journal of Sol-Gel Science and Technology ; Volume 40, Issue 1 , 2006 , Pages 15-23 ; 09280707 (ISSN) Mohammadi, M. R ; Cordero Cabrera, M. C ; Ghorbani, M ; Fray, D.J ; Sharif University of Technology
    Stabilised titania sols were prepared using an additive free particulate sol-gel route, via electrostatic stabilisation mechanism, with various processing parameters. Peptisation temperature, 50°C and 70°C, and TiO2 concentration, 0.1, 0.2 and 0.4 molar, were chosen as processing parameters during sol preparation. Results from TiO2 particle size and zeta potential of sols revealed that the smallest titania hydrodynamic diameter (13 nm) and the highest zeta potential (47.7 mV) were obtained for the sol produced at the lower peptisation temperature of 50°C and lower TiO 2 concentration of 0.1 M. On the other hand, between the sols prepared at 70°C, smaller titania particles (20 nm) and higher... 

    Study and optimization of Amino Acid Extraction by emulsion Liquid Membrane

    , Article CHISA 2006 - 17th International Congress of Chemical and Process Engineering, Prague, 27 August 2006 through 31 August 2006 ; 2006 ; 8086059456 (ISBN); 9788086059457 (ISBN) Mohagheghe, E ; Vosoughi, M ; Alemzadeh, I ; Hexion Specialty Chemicals; Mitsubishi Chemical Corporation; CS Cabot; Zentiva; BorsodChem MCHZ ; Sharif University of Technology
    A batch extraction of an essential amino acid, Phenylalanine, from an aqueous solution of different concentrations by an Emulsion Liquid Membrane (ELM) was developed using D2EHPA as a cationic carrier, Span 80 as the surfactant, paraffin and kerosene as the diluents, and HCl as the internal electrolyte. All effective parameters such as pH of initial aqueous external phase, electrolyte concentration in aqueous internal phase, carrier and surfactant concentration in emulsion, volume ratio of the organic to aqueous internal phase (Roi), volume ratio of the W/O emulsion to aqueous external phase (Rew) and time were examined and optimized using Taguchi method which was the first time of... 

    Amino acids and their complex formation properties with divalent metal ions, a comparative investigation of structure and stability in binary systems

    , Article Current Pharmaceutical Analysis ; Volume 10, Issue 2 , 2014 , Pages 122-134 ; ISSN: 15734129 Sajadi, S. A. A ; Sharif University of Technology
    A comparative investigation has been developed for the stability constants of several amino acid complexes with divalent metal ions, which have been determined by potentiometric pH titration. Depending on the metal ion-binding properties, vital differences in the building complexes were observed. The present study indicates that in some M(L) complexes, metal ions are arranged in carboxyl groups, but in other M(L)complexes, some metal ions are able to build chelate over amine groups. The results mentioned-above demonstrate that for some M(L) complexes, the stability constants are also largely determined by the affinity of metal ions for amine group. This leads to a kind of selectivity of... 

    Metabonomics exposes metabolic biomarkers of Crohn's disease by 1HNMR

    , Article Gastroenterology and Hepatology from Bed to Bench ; Volume 6, Issue SUPPL , 2013 , Pages S19-S22 ; 2008-4234 (EISSN) Fathi, F ; Ektefa, F ; Hagh-Azali, M ; Aghdaie, H. A ; Sharif University of Technology
    Metabonomics and other "omic" fields are essential science in analytical chemistry. Modern analytical instruments such as proton nuclear magnetic resonance (1H-NMR) can provide the great quantity of analytical information. In order to assign unknown samples, chemometric methods recognition build classification model based on experimental data. Firstly, some current strategies regarding disease diagnosis are exhibited in metabonomic studies. Some diseases such as crohn's disease can be difficult to diagnose since its signs and symptoms may be similar to other medical problems or often mimic other symptoms. Applications of NMR and supervised pattern recognition in the field of metabonomics are... 

    Designed amino acid feed in improvement of production and quality targets of a therapeutic monoclonal antibody

    , Article PLoS ONE ; Volume 10, Issue 10 , October , 2015 ; 19326203 (ISSN) Torkashvand, F ; Vaziri, B ; Maleknia, S ; Heydari, A ; Vossoughi, M ; Davami, F ; Mahboudi, F ; Sharif University of Technology
    Public Library of Science  2015
    Cell culture feeds optimization is a critical step in process development of pharmaceutical recombinant protein production. Amino acids are the basic supplements of mammalian cell culture feeds with known effect on their growth promotion and productivity. In this study, we reported the implementation of the Plackett-Burman (PB) multifactorial design to screen the effects of amino acids on the growth promotion and productivity of a Chinese hamster ovary DG-44 (CHO-DG44) cell line producing bevacizumab. After this screening, the amino acid combinations were optimized by the response surface methodology (RSM) to determine the most effective concentration in feeds. Through this strategy, the... 

    Study and optimization of amino acid extraction by emulsion liquid membrane

    , Article Separation Science and Technology ; Volume 43, Issue 11-12 , 2008 , Pages 3075-3096 ; 01496395 (ISSN) Mohagheghi, E ; Alemzadeh, I ; Vossoughi, M ; Sharif University of Technology
    A batch extraction of an essential amino acid, phenylalanine, from an aqueous solution of different concentrations by an Emulsion Liquid Membrane (ELM) was developed using D2EHPA as a cationic carrier, Span 80 as the surfactant, paraffin, and kerosene as the diluents, and HCl as the internal electrolyte. All effective parameters such as the initial pH of the aqueous external phase, the electrolyte concentration in the aqueous internal phase, carrier, and surfactant concentration in the emulsion, the volume ratio of the organic to aqueous internal phase (Roi), the volume ratio of the W/O emulsion to the aqueous external phase (Rew) and time were examined and optimized using the Taguchi... 

    Boron nitride nanotube as an antimicrobial peptide carrier: A theoretical insight

    , Article International Journal of Nanomedicine ; Volume 16 , 2021 , Pages 1837-1847 ; 11769114 (ISSN) Zarghami Dehaghani, M. Z ; Bagheri, B ; Yousefi, F ; Nasiriasayesh, A ; Mashhadzadeh, A. H ; Zarrintaj, P ; Rabiee, N ; Bagherzadeh, M ; Fierro, V ; Celzard, A ; Saeb, M. R ; Mostafavi, E ; Sharif University of Technology
    Dove Medical Press Ltd  2021
    Introduction: Nanotube-based drug delivery systems have received considerable attention because of their large internal volume to encapsulate the drug and the ability to penetrate tissues, cells, and bacteria. In this regard, understanding the interaction between the drug and the nanotube to evaluate the encapsulation behavior of the drug in the nanotube is of crucial importance. Methods: In this work, the encapsulation process of the cationic antimicrobial peptide named cRW3 in the biocompatible boron nitride nanotube (BNNT) was investigated under the Canonical ensemble (NVT) by molecular dynamics (MD) simulation. Results: The peptide was absorbed into the BNNT by van der Waals (vdW)... 

    Conservation of statistical results under the reduction of pair-contact interactions to solvation interactions

    , Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 72, Issue 6 , 2005 ; 15393755 (ISSN) Radja, N.H ; Farzami, R. R ; Ejtehadi, M. R ; Sharif University of Technology
    We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting in a clear vector manipulation of energy. The reduced (additive) potential performs considerably successful in predicting the statistical properties of arbitrary structures. The evaluated designabilities of the structures by both models are highly correlated. Suggesting geometrically nondegenerate vectors (structures) as proteinlike structures, the additive model is a powerful tool for protein design. Moreover, a crossing point in the log-linear diagram of... 

    Artificial neural network modeling of peptide mobility and peptide mapping in capillary zone electrophoresis

    , Article Journal of Chromatography A ; Volume 1096, Issue 1-2 , 2005 , Pages 58-68 ; 00219673 (ISSN) Jalali Heravi, M ; Shen, Y ; Hassanisadi, M ; Khaledi, M. G ; Sharif University of Technology
    Recently, we have developed an artificial neural network model, which was able to predict accurately the electrophoretic mobilities of relatively small peptides. To examine the robustness of this methodology, a 3-3-1 back-propagation artificial neural network (BP-ANN) model was developed using the same inputs as the previous model, which were the Offord's charge over mass term (Q/M2/3), corrected steric substituent constant (E s,c) and molar refractivity (MR). The data set consisted of 102 peptides with a larger range of size than that of our earlier report - up to 42 amino acid residues as compared to 13 amino acids in the initial study - that also included highly charged and hydrophobic... 

    On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices

    , Article Journal of Theoretical Biology ; Volume 235, Issue 3 , 2005 , Pages 318-325 ; 00225193 (ISSN) Goodarzi, H ; Shateri Najafabadi, H ; Hassani, K ; Ahmadi Nejad, H ; Torabi, N ; Sharif University of Technology
    Statistical and biochemical studies have revealed non-random patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslation errors and point mutations, since it is known that when an amino acid is converted to another due to error, the biochemical properties of the resulted amino acid are usually very similar to those of the original one. In this study, using altered forms of the fitness functions used in the prior studies, we have optimized the parameters involved in the calculation of the error minimizing property of the genetic code so that the genetic code outscores the random codes as much as possible. This work also... 

    Investigating the effects of amino acid-based surface modification of carbon nanoparticles on the kinetics of insulin amyloid formation

    , Article Colloids and Surfaces B: Biointerfaces ; Volume 176 , 2019 , Pages 471-479 ; 09277765 (ISSN) Kalhor, H. R ; Yahyazadeh, A ; Sharif University of Technology
    Elsevier B.V  2019
    Surface functionality of nanoparticles has been pivotal in defining interactions of nanoparticles and biomolecules. To explore various functionalities on the surface of nanoparticle through a facile procedure, various carbon-based nanoparticles, modified with a specific natural amino acid, were synthesized; the amino acids were chosen in order that almost all classes of amino acids were included. After characterizations of the nanoparticles using several spectroscopic methods, the effects of surface modification of nanoparticles were examined against amyloid formation, exploiting insulin as a model amyloidogenic polypeptide. Although most amino acids afforded carbon nanoparticles, only... 

    Synthesis of Amino Acids Schiff Base Complexes of Gadolinium and Study of Their Interaction with BSA

    , M.Sc. Thesis Sharif University of Technology Abedi, Najmeh (Author) ; Mohammadi Boghaei, Davar (Supervisor)
    Salicylaldehyde-amino acid Schiff base complexes are used as non-enzymatic models for the metal-pyridoxal (Vitamin B6) amino acid Schiff base systems which are key intermediates in many metabolic reactions of amino acids catalyzed by enzymes which require pyridoxal as a cofactor (transamination, decarboxylation, α and β elimination, racemization, etc.). In addition, complexes of amino acid Schiff bases are considered to constitute new kinds of potential anticancer, antitumor, antiradical and antibacterial reagents. On the other hand nuclear magnetic resonance imaging (MRI), has become a powerful tool for clinical diagnostics thanks to the development of a new class of pharmaceuticals... 

    Computational Design of Novel Medicines as Inhibitors in Case of Cancer and Autoimmune Disease Treatment Based on Amino Acid and Sugar

    , M.Sc. Thesis Sharif University of Technology Feghhi, Razieh (Author) ; Fattahi, Alireza (Supervisor)
    SHP2 has been reported as a critical non-receptor phosphatase enzyme that plays crucial roles in numerous disorders like cancer. The previous studies on this enzyme showed that inhibiting the action of the enzyme comes as a way of controlling enzyme activity. SHP099 was discovered as an Allosteric inhibitor of the enzyme with the most inhibitory effect among all of the studied compounds. In this study we aimed to design novel dipeptide-and sugar-based inhibitors for the allosteric binding site of this enzyme with in-silico studies including docking, molecular dynamic simulation, and free binding energy analysis. Our novel designed drugs possess enough binding properties, low toxicity, and... 

    Design a New Sugar- amino Acid-based Drug Structure as an Alternative to Methotrexate, with the Aim of Treating Leukemia and some Autoimmune Diseases

    , M.Sc. Thesis Sharif University of Technology Shapouri, Amin Mohammad (Author) ; Fattahi, Alireza (Supervisor)
    This project aims to design a drug to fight leukemia and some autoimmune diseases having few side effects. These drugs are composed of natural sugar and amino acid structures. Among the various treatments available, drug structures as inhibitors of enzymes involved in cancer-related cellular processes is an important treatment. Methotrexate is one of the most widely used anticancer drugs in the last half-century and treats leukemia and many autoimmune diseases such as psoriasis. It is a derivative of folic acid (vitamin B9) and one of the drugs with specific properties. It is an anti-folate whose anti-metabolic effects can help kill cancer cells. One of the problems with using this drug to... 

    Design of Methods for Synthesis and Immobilization of Nitrogen Ligands Such as Pyridine onto the Mesoporous Silica Nanoparticles and Design of Pharmaceutical Structures Based on Amino Acids and Carbohydrates to Inhibit Polymerase Η for the Treatment of Leukemia and their Applications In Resins and Ionic Liquids

    , Ph.D. Dissertation Sharif University of Technology Kalhor, Sepideh (Author) ; Matloubi Moghaddam, Firouz (Supervisor) ; Fattahi, Alireza (Supervisor)
    1- Mesoporous silica materials have been found to possess pore sizes ranging from 2 -10 nm alongside 2D-hexagonal and 3D-cubic structural features. The specific properties of nanoparticles of the mesoporous silica family, such as the collected size, porosity, morphology, and high chemical stability, make them among the best drug delivery systems and catalysts. Designing the catalysts with advanced structures that effectively locate the transition metals and create active centres onto the surfaces of mesoporous silica materials has attracted extraordinary attention. According to many studies, mesoporous silica materials without organic functional groups cannot be used as catalysts in chemical...