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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) ; Yahyazadeh, A ; Sharif University of Technology
Elsevier B.V
2019
Abstract
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 ; Mohammadi Boghaei, Davar (Supervisor)
Abstract
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 ; Fattahi, Alireza (Supervisor)
Abstract
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 ; Fattahi, Alireza (Supervisor)
Abstract
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 ; Matloubi Moghaddam, Firouz (Supervisor) ; Fattahi, Alireza (Supervisor)
Abstract
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...
Application of Cellulose Nanofibers Coated Quartz Crystal Microbalance (QCM)Biosensor for Amino Acid Detection in Aqueous Media
, Ph.D. Dissertation Sharif University of Technology ; Iraji Zad, Azam (Supervisor) ; Vossoughi, Manouchehr (Supervisor)
Abstract
Developing a simple, cost effective and accurate detection method for L-lysine (Lys), L-leucine (Leu) and glycine (Gly) as the important analytes in clinical diagnostics, biological processes and food industries is of great interest. Therefore, in the first part of this research, cellulose nanofibrils (CNFs) were coated on a quartz crystal microbalance (QCM) surface by spin coating to achieve a QCM biodetector for Gly. Thus, the two-layer CNFs coating was selected as sensing film and was applied for following experiments. In the next step, the coated QCMs were carefully characterized before and after interaction with Gly using water contact angle (WCA), Fourier transform infrared...
Design and Computational Evaluation of Sugar-Amino Acid Conjugates as CK2α Inhibitor
, M.Sc. Thesis Sharif University of Technology ; Fattahi, Alireza (Supervisor)
Abstract
The aim of this study is to devise innovative compounds that impede the function of CK2α enzyme by incorporating amino acids and sugars into their molecular structure. CK2α, a catalytic subunit of CK2 enzyme, operates autonomously and is the only continuously active kinase that does not require an upstream regulator. Emerging evidence highlights CK2α's crucial role in various cancers and infectious diseases, including Covid-19, indicating that suppressing its function could provide a promising approach to improve patient outcomes. To accomplish this objective, the drug design process must take into account both pharmacokinetic and pharmacodynamic properties. Pharmacokinetics, encompassing...
Design of Drug Structures in Order to Inhibit Met, A Member of the Tyrosine Phosphatase Protein Family to Replace Existing Drugs
, M.Sc. Thesis Sharif University of Technology ; Fattahi, Alireza (Supervisor)
Abstract
This project aims to design a novel structure that can inhibit the activitvation of the c-Met enzyme using amino acids and sugars building blocks. The c-Met enzyme is a receptor tyrosine kinase that plays a significant role in several biological activities such as cell proliferation, survival, and invasion. Abnormal activity of the enzyme is linked to the progression of various types of cancer, including breast, lung, liver, and stomach cancer. The proposed sugar amino acid conjugate structures is expected to increase stability amino acids and dipeptides in the physiological environment, improve membrane permeability via active transport mechanism, and reduce toxicity and side effects by...
Dependency of codon usage on protein sequence patterns: A statistical study
, Article Theoretical Biology and Medical Modelling ; Vol. 11, issue. 1 , 2014 ; ISSN: 17424682 ; Goliaei, B ; Alishahi, K ; Sadeghi, M ; Sharif University of Technology
Abstract
Background: Codon degeneracy and codon usage by organisms is an interesting and challenging problem. Researchers demonstrated the relation between codon usage and various functions or properties of genes and proteins, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Researchers usually represent segments of proteins responsible for specific functions or structures in a family of proteins as sequence patterns or motifs. We asked the question if organisms use the same codons in pattern segments as compared to the rest of the sequence. Methods. We used the likelihood ratio test, Pearson's chi-squared test, and mutual information...
The Differential Diagnosis of Crohn's Disease and Celiac Disease Using Nuclear Magnetic Resonance Spectroscopy
, Article Applied Magnetic Resonance ; Volume 45, Issue 5 , May , 2014 , Pages 451-459 ; Kasmaee, L. M ; Sohrabzadeh, K ; Nejad, M. R ; Tafazzoli, M ; Oskouie, A. A ; Sharif University of Technology
Abstract
Crohn's disease and celiac disease belong to a group of autoimmune conditions that affect the digestive system, specifically the small intestine. They both attack the digestive tract and share many symptoms. Thus, the discovery of proper methods would be a major step toward differentiating celiac disease from Crohn's disease. The aim of this study was to search for the metabolic biomarkers to differentiate between these two diseases. Proton nuclear magnetic resonance spectroscopy (1H NMR) was employed as the metabolic profiling method to look for serum metabolites that differentiate between celiac disease and Crohn's disease. Classification of celiac disease and Crohn's disease was done...
Electrostatically defying cation-cation clusters: Can likes attract in a low-polarity environment?
, Article Journal of Physical Chemistry A ; Volume 117, Issue 38 , 2013 , Pages 9252-9258 ; 10895639 (ISSN) ; Ramezani, M ; Fattahi, A ; Kass, S. R ; Sharif University of Technology
2013
Abstract
Like-charge ion pairing is commonly observed in protein structures and plays a significant role in biochemical processes. Density functional calculations combined with the conductor-like polarizable continuum model were employed to study the formation possibilities of doubly charged noncovalently linked complexes of a series of model compounds and amino acids in the gas phase and in solution. Hydrogen bond interactions were found to offset the Coulombic repulsion such that cation-cation clusters are minima on the potential energy surfaces and neither counterions nor solvent molecules are needed to hold them together. In the gas phase the dissociation energies are exothermic, and the...
Immobilization of α -chymotrypsin on the surface of magnetic/gold core/shell nanoparticles
, Article Journal of Nanotechnology ; Volume 2013 , 2013 ; 16879503 (ISSN) ; Vossoughi, M ; Sharif University of Technology
Hindawi Publishing Corporation
2013
Abstract
Over the last decade, nanoparticles used as protein carriers have opened new avenues for a variety of biomedical applications. The main concern for these applications is changes in biological activity of immobilized proteins due to conformational changes on the surface of the carrier. To evaluate this concern, the preparation and biocatalyst activity of α-chymotrypsin-Fe 3O4 @ Au core/shell nanoparticles were investigated. First, Fe3O4 @ Au core/shell nanoparticles were synthesized by coprecipitation method and citrate reduction of HAuCl 4. TEM imaging revealed a core size of 13 ± 3 nm and a shell thickness of 4 ± 1 nm for synthesized nanoparticles. X-ray diffraction (XRD) was used to study...
A simple approach to the synthesis of 3-substituted rhodanines and thiazolidine-2,4-diones
, Article Scientia Iranica ; Volume 20, Issue 6 , 2013 , Pages 1833-1838 ; 10263098 (ISSN) ; Shokri, A ; Saidi, M. R ; Sharif University of Technology
Sharif University of Technology
2013
Abstract
A novel synthesis of 3-substituted rhodanine and thiazolidine-2,4-dione derivatives, starting from aliphatic primary amines, carbon disulfide, and methyl 2-bromoacetate, is described. The reaction proceeds successfully both in water and under solvent-free conditions, but 2-thioxothiazolidin-4-one (rhodanine) derivatives were obtained under solvent free-conditions, and thiazolidine-2,4-dions were formed when water was used as the solvent
Production of l-asparaginase from Escherichia coli ATCC 11303: Optimization by response surface methodology
, Article Food and Bioproducts Processing ; Volume 89, Issue 4 , Oct , 2011 , Pages 315-321 ; 09603085 (ISSN) ; Alemzadeh, I ; Maghsodi, V ; Sharif University of Technology
2011
Abstract
This paper discusses the studies carried out for the optimal production of enzyme l-asparaginase (l-asparagine amidohydrolase, EC 3.5.1.1) from Escherichia coli (ATCC 11303). It was found that inoculum age of 18 h and inoculum size of 10% were the most favorable operating conditions for enzyme production. Lactose, yeast extract and KH 2PO 4 were found to be the best carbon, nitrogen and ion sources, respectively. Statistical method was used to survey how various medium conditions affect the enzyme production. By response surface methodology, the values of lactose, tryptone, yeast extract, KH 2PO 4 and l-asparagine concentration were investigated to obtain the maximum enzyme activity. The...
Failure tolerance of motif structure in biological networks
, Article PLoS ONE ; Volume 6, Issue 5 , May , 2011 ; 19326203 (ISSN) ; Jalili, M ; Sharif University of Technology
2011
Abstract
Complex networks serve as generic models for many biological systems that have been shown to share a number of common structural properties such as power-law degree distribution and small-worldness. Real-world networks are composed of building blocks called motifs that are indeed specific subgraphs of (usually) small number of nodes. Network motifs are important in the functionality of complex networks, and the role of some motifs such as feed-forward loop in many biological networks has been heavily studied. On the other hand, many biological networks have shown some degrees of robustness in terms of their efficiency and connectedness against failures in their components. In this paper we...
Colorimetric detection of glutathione based on transverse overgrowth of high aspect ratio gold nanorods investigated by MCR-ALS
, Article RSC Advances ; Volume 5, Issue 101 , 2015 , Pages 82906-82915 ; 20462069 (ISSN) ; Shadabipour, P ; Hormozi-Nezhad, M. R ; Sharif University of Technology
Royal Society of Chemistry
2015
Abstract
In this paper, we present a simple platform for colorimetric detection of glutathione using gold nanorods (AR ∼ 6.5 ± 0.2) as a plasmonic sensor. The functional mechanism of the sensor is based on shifts of longitudinal plasmon resonance during selective transverse overgrowth induced by preferential binding of glutathione at the nanorod tips. Under the optimum conditions, a calibration curve showed two linear regimes at the range of 50 nM to 20 μM of glutathione with a detection limit as low as 40 nM. The nanosensor maintains relatively high selectivity for determination of glutathione in the presence of several other amino acids. However, cysteine at similar concentration levels strongly...
Dual improvement of DNA-directed antibody immobilization utilizing magnetic fishing and a polyamine coated surface
, Article RSC Advances ; Volume 6, Issue 112 , 2016 , Pages 111210-111216 ; 20462069 (ISSN) ; Soleimani, M ; Shamloo, A ; Mahmoudifard, M ; Vossoughi, M ; Sharif University of Technology
Royal Society of Chemistry
2016
Abstract
The present study is aimed at the development of a novel approach based on the magnetic improvement of DNA-directed antibody immobilization to prepare a highly efficient sensing platform. Magnetic nanoparticle substrates with high surface area capture the dual DNA-conjugated antibodies in a solution. This allows overcoming the typical mass transport limitation of the surface-based antibody immobilization. Antibody-magnetic nanoparticle conjugation is based on a robust hybridization between a DNA tether (attached to the antibody) and its complementary sequence (immobilized on the nanoparticle). Conventional antibody immobilization for the detection of proteins is often insignificant for the...
A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory
, Article Journal of Computational Chemistry ; Volume 37, Issue 14 , 2016 , Pages 1296-1305 ; 01928651 (ISSN) ; Ebrahimi, H. P ; Fathi, F ; Bahrami Panah, N ; Jalali Heravi, M ; Tafazzoli, M ; Sharif University of Technology
John Wiley and Sons Inc
2016
Abstract
The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of 13Cα chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of 13Cβ, and 1Hα chemical shifts nor on the variation of absolute deviation of 13Cα chemical shifts relative to ψ dihedral angle. The 13Cα absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of...
Experimental investigation and thermodynamic modeling of amino acids partitioning in a water/ionic liquid system
, Article Journal of Molecular Liquids ; Volume 260 , 15 June , 2018 , Pages 386-390 ; 01677322 (ISSN) ; Ghotbi, C ; Habibi Zare, M ; Shirazian, S ; Sharif University of Technology
Elsevier B.V
2018
Abstract
Amino acids partitioning including phenylalanine, glutamic acid, and tryptophan in aqueous and ionic liquid phases at temperature of 298.15 K and atmospheric pressure were measured. 1-Butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide used in this work can produce two phases with water immediately. The effect of aqueous solution pH on amino acids partitioning was studied and revealed that amino acid partitioning coefficient was decreased with increasing pH. This phenomenon pertains to the electrostatic interaction between cations of amino acid and the anions of ionic liquid which is decreased when pH increases. Considering the effect of pH, liquid-liquid equilibrium data of amino...
Synthesis of “L-cysteine–graphene oxide” hybrid by new methods and elucidation of its uptake properties for Hg(II) ion
, Article Separation Science and Technology (Philadelphia) ; Volume 53, Issue 6 , 2018 , Pages 843-855 ; 01496395 (ISSN) ; Outokesh, M ; Akbari, A ; Kosari, M ; Tayyebi, A ; Sharif University of Technology
Taylor and Francis Inc
2018
Abstract
This study introduces two new, simple, and scalable methods for synthesis of “cysteine–graphene oxide” hybrid, namely nucleophilic and covalent methods. Produced adsorbents could uptake 500 and 600 mg Hg2+/g, respectively, which are larger than capacities of most of the commercial adsorbents. By means of different instrumental techniques, chemical structures of the obtained graphene products were disclosed, and two pertinent mechanisms for their formations were suggested. Time for attaining uptake equilibrium for nucleophilic/covalent samples was 30 min/150 min, and kinetics was controlled by liquid film resistance/chemical reaction mechanisms, respectively. High selectivity and good...