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    Synthesis of Selected Pyridazine-based Organic Compounds and Investigation of Their Inhibitory Effects Against Amyloid Formation

    , M.Sc. Thesis Sharif University of Technology Ghasemi, Elham (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    At the molecular level, proteins control almost all the biochemical reactions in the cells. In order for proteins to function, they must be able to fold into their unique 3D structure. Deformation of protein structure due to some environmental phenomena such as pH, high temperature, and stress may cause unfolding of proteins and finally result in formation of protein fibrils called "amyloid". Amyloid has been found in a number of human diseases such as Alzheimer, type II diabetes, and Parkinson. Recently pyridazine has been under spotlight due to its unique chemical properties such as high dipole moment and higher solubility in biological solvents. In this study, we aim at using a... 

    Investigation of Novel Bioorthogonal Chemical Reactions on Proteins and Amyloid Formation

    , M.Sc. Thesis Sharif University of Technology Rezaei, Mohsen (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    Bioorthogonal chemistry defines any reaction, inside or outside the living systems, without interfering with native chemical processes and 3dimensional structure of proteins. In these types of reactions water is the sole solvent; a neutral pH is required; the temperature must be up to 40 oC. The kinetics of reactions must be on the hour scale and the nontoxic reagents with low concentration must be used. One of the simplest methods of visualizing protein molecule is covalent attachment of fluorescein to protein. In this work several fluorescent compounds were synthesized. These novel compounds include acylchloride fluorescein, N-hydroxysuccinimide fluorescein, thiophenol fluorescein, and... 

    Design and Construction of Novel Intein Mediated Biosensor in Order to Detect Amyloid Fibrils

    , M.Sc. Thesis Sharif University of Technology Miri, Mohammad (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    The most important factor in protein's function and its 3D structure is folding. Misfolding or native folding perturbation in some peptides and proteins force them get into amyloid fibril aggregation. It has been observed that these aggregations are the cause of some debilitative diseases especially ones that are related to aging like Alzheimer disease, Hantington's disease, typeII diabets etc. Recently it has been shown that specific regions in human catalase protein interact with some amyloid fibrils, such as Aß, IAPP, PrP etc. Inteins are self-splicing protein enzymes, which excise themselves from the mature protein and join the two flanking adjacent sequences by a new peptide bond in a... 

    Design and Synthesis of Novel Coumarin Derivatives as Quorum Sensing Inhibitors & Performing Click Chemistry Involving Lysozyme Protein and a Novel Synthetic Fluorecent Compound

    , M.Sc. Thesis Sharif University of Technology Mansoori, Sirwan (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    Quorum Sensing is a cell-to-cell communication pr°Cess depending on cell concentration. Communication among bacterial cells °Ccurs through small molecular signals called autoinducers. The consequences of quorum sensing include the activation of pathogenic properties and activation of the gene for biofilm formation. Biofilms are aggregations of bacteria that adhere to surfaces through extracellular polymeric substances. Bacteria in the biofilm phase are much more resistant to antimicrobial agents than their free-swimming counterparts (i.e. the bacteria in planktonic form). In this study, first a series of coumarin derivatives were synthesized; but due to low solubility of the synthesized... 

    Directed Evolution of the Asparaginase Enzyme to Alter Substrate Specificity

    , M.Sc. Thesis Sharif University of Technology Yousefi, Danial (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    Asparagainase is a therapeutic enzyme which has been a subject of research for decades. The enzyme catalyzes the hydrolysis of the amide group in asparagine and similar amides. Altering the substrate specificity and stabilization of this enzyme can increase its therapeutic properties. Moreover, asparaginases may be evolved to catalyze the hydrolysis of other similar compounds. These can be achieved through directed evolution and computational methods.In this study, the gene encoding L-asparaginase II enzyme from E. coli was amplified by polymerase chain reaction (PCR) and was cloned into an expression vector. The recombinant protein was expressed by an appropriate host secreting the... 

    Cloning and Production of the Flavin Reductase Enzyme in Order to Perform Organic Reaction and Synthesis of Cation Exchange Column for Protein Purification

    , M.Sc. Thesis Sharif University of Technology Hayati, Fatemeh (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    The reductase enzymes perform an important function in the cell. These enzymes are usually coupled with other enzymes and participate in reactions such as halogenation, reduction of alkene, and carboxylic acids. These reactions are carried out by reproducing cofactors such as FADH2 and NAD+; however, there is no evidence that this enzyme alone can perform an organic reaction. In this work, we aim to examine whether recombinant flavin reductase can carry out organic reactions. In order to amplify the flavin reductase enzyme gene from the E. coli genome by PCR (Polymerase Chain Reaction) method, two synthetic primers were designed; The forward primer of the gene contained a cleavage site for... 

    Creating Random Mutations on The Human Transglutaminase 2 Gene and Lysozyme Gene to Increase The Solubility of the Enzymes in order to Perform Promiscuous Organic Reactions Using The Recombinant Enzymes

    , M.Sc. Thesis Sharif University of Technology Moghaddasi, Ahmad (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    Transglutaminase 2 enzyme is expressed in various parts of the human body and is present in almost all tissue cells. The function of this enzyme is multiple and it catalyzes different reactions depending on where it is located in the cell. The most important activities of this enzyme are: isopeptide bond formation between the side chains of two proteins (transamidation reaction), diamidation reaction (hydrolysis of amide bond), esterification, kinase activity. The hen egg white lysozyme protein is another natural antimicrobial protein that has been extensively studied. The muramidase activity of egg white lysozyme against highly gram-positive bacteria is well known, and this property has... 

    Controlling Amyloid Formation Using Novel Carbon Based Nanoparticles

    , M.Sc. Thesis Sharif University of Technology Yahyazadeh, Amin (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    Proteins carry out most important roles in the organisms and they have a number of functions including structural, catalytically, regulatory and transportal, However for protein to have functional role they must be able to possess tridimensional structure. Several proteins due to various genetic and physico-chemical conditions have shown to alter their tridimensional structure leading to insoluble fibrilar structure. One of the properties of these insoluble fibrils is conformational change, converting to β-sheet rich structures; the entire process of converting soluble to proteins insoluble fibrils known as amyloid formation. The proteins amyloidosis have been seen as causative role in a... 

    The Use of Flavin Reductase Enzyme as Biocatalyst in Promiscuous Catalyzing Organic Reactions and Investigating Amyloid Inhibition in Proteins Using Aromatic Compounds

    , M.Sc. Thesis Sharif University of Technology Masihzadeh, Zahra (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    Enzymes are proteins that carry out chemical reactions in the form of chemo, stereo, and regioselective under mild conditions. One of the characteristics of enzymes is that they perform a specific chemical reaction on a selective substrate and under specific environmental conditions. However, in recent years, a number of enzymes have been identified to display promiscous behavior. This promiscousity includes catalytic activity, variety of substrates, and environmental conditions. Promiscous activities of enzymes can be a good starting point for creating new and more favorable engineered pathways for the production of chemical and medicinal drugs. One of the aims of this project is to exploit... 

    Expression and Purification of Amyloid Beta Recombinant Peptide and the Effecs of Ultrasmall Peptides Enriched in Branch Chain Amino Acids as Inhibitors in Amyloid Formation

    , M.Sc. Thesis Sharif University of Technology Rezaei Adariani, Soheila (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    Nowdays, it has been shown that protein misfolding is involved in more than forty diseases including Alzheimer’s and Parkinson’s. Alzheimer’s disease is one of the most common neurodegenerative diseases that disrupts brain function. The main cause of this illness is due to formation of extracellular amyloid plaque from a 42-amino acid-peptide called amyloid beta. Amyloidosis is caused by missfolding of peptides and proteins mainly because of physical and chemical changes in biomolecule or their environment.
    Therefore, in this dissertation, using synthetic and recombinant abeta peptide, kinetic of amyloidosis was examined. Ultrasmall peptides (three-amino acid), containing branched chain... 

    Synthesis and Structural Activity Relationship (SAR) of Novel Pyridazine-based Inhibitors for Inhibition of Amyloid Fibril Formation, and Biosynthesis and Optimization of L-AsparaginaseII Enzyme for Hydrolysis of Non-Native Substrate

    , M.Sc. Thesis Sharif University of Technology Nazari Khodadadi, Alireza (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    After proteins, one of the important biological macromolecules, are synthesized by ribosomes,they automatically reach their own special 3-D structure. This native structur or better known as folded state is what determines the function of a protein. In some situations, the proteins become misfolded leading to its lack of biological function through aggregation or fibril formation known as "amyloid". The amyloid fibrils have been shown to be a causative factor in nerve decay such as Alzheimer's. Therefore, inhibition of amyloid formation using different approaches such as synthetic organic and natural compounds has, recently, been under spotlight. A pyridazine basedcompound (RS-0406) has... 

    Using Vitamin B1 as a Catalyst in Performing Multi-Component Reactions and Synthesis of Affinity Column ChromatograpHy for Purification of Recombinant Proteins

    , M.Sc. Thesis Sharif University of Technology Lohi Khosroshahi, Ameneh (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    Due to the importance of using pure proteins in the industry and basic research in order to study them in the structural contexts and interactions of proteins in recent years, purification methods have been extensively developed. The purification steps usually depend on the size of the protein, its physical and chemical properties, the binding affinity and the biological activity of the protein in question, In the purification process, the protein portion is separated from the non-protein portion. The biggest challenge is when we want to separate different proteins. Different chromatographic methods are used, depending on the properties of the impure proteins. One of these chromatographic... 

    Molecular Engineering of Recombinant Human Transglutaminase 2 with Correct Folding ( Soluble ) for Studying Promiscuous Organic Reactions

    , M.Sc. Thesis Sharif University of Technology Gholami, Amir Hossein (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    Transglutaminases of family enzymes are implicated in different functions in cell including cellular division and cell adhesion. Several members of this family catalyze formation of isopeptide bond that involved in wound restoration and angiogenesis. Transglutaminase 2 that have been studied in this project, are found in almost every human cell tissue. This enzyme has multiple functions depending on its cell location. In cytoplasm TG2 act as GTPase and is involve in post translational modifications. This enzyme by using calcium form a isopeptide bond between two proteins, isopeptide bond is function in brain cortex and cells creates amyloid structures that including brain diseases, Parkinson... 

    Investigate Kinetic Parameters of L-Asparaginase Ii as Well as its Performance in Organic Reactions and Modifying the Enzyme Through Directed Evolution for Carrying Out Promiscuous Reactions

    , M.Sc. Thesis Sharif University of Technology Noori Hosseinabadi, Zahra (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    L-asparaginase II is an amidohydrolase which hydrolyzes L-asparagine to furnish L-aspartic acid and ammonia. The enzyme has played an important role for 40 years in treating cancer in persons with juvenile leukemias or lymphomas. Furthermore, the enzyme has become important in food industries and biosensors technology.In this study, the expression of recombinant L-asparaginase II in E. Coli was optimized and the purification of this enzyme from growth culture was carried out with nickel-charged affinity resin. Afterwards, the activity, and kinetic parameters of purified recombinant L-asparaginase II including Km, kcat, Vmax, and enzyme efficiency were measured.In the next step, random... 

    Design and Development of Electrochemical DNA Nanobiosensors for Identification and Determination of Important Biomarkers

    , Ph.D. Dissertation Sharif University of Technology Salimian, Razieh (Author) ; Shahrokhian, Saeed (Supervisor) ; Kalhor, Hamid Reza (Co-Supervisor)
    Abstract
    The main purpose of this Ph.D. Thesis is to develop DNA-based biosensors using Label-free approaches applying simple, inexpensive and fast electrochemical techniques to measure the biological markers of cancer.In the first part, a simple protocol for detection of specific-sequence DNA is introduced. In this method carbon nanotube is used as a hybridization indicator. This label-free system provides the advantage of eliminating additional labeling procedure. As the signal enhances in the presence of MWCNT and decreases in the presence of target, the fabricated sensor is known as a signal-off device. The oxidation signal of Fe(CN)63-/4- is followed as an analytical signal to detect target... 

    Investigation of Textile Dyeing Wastewater Treatment by Vermifiltration and Troubleshooting and Modification of the Chemical/Biological Treatment Plant of the Ekbatan Textile Factory

    , M.Sc. Thesis Sharif University of Technology Purehie, Omid (Author) ; Hashemian, Jamaloddin (Supervisor) ; kalhor, Hamid Reza (Supervisor)
    Abstract
    Water is the essence of life. On average, a human being consumes about 2 liters of water every day and it accounts for about 70% of the weight of human body and this alone reflects the importance of water for continuation of life. The production process in textile and dyeing factories as increasingly growing industrial units consume large amounts of water and consequently produce large volumes of wastewater. Such industries face environmental regulations on one hand and are unable to compete with foreign products on the other since the imported counterparts are low-priced. Therefore, finding a cost-effective and efficient solution for treatment of waste water and troubleshooting and... 

    Identification and Characterization Natural Products from Borage Leaves Extract Acting as Anti-amyloid Inhibitors

    , M.Sc. Thesis Sharif University of Technology Ashrafian, Hossein (Author) ; Kalhor, Hamid Reza (Supervisor) ; Sajadi, Ali Akbar (Co-Advisor)
    Abstract
    Natural products obtained from plant extract are well known as a valuable source for research and assessments which eventuates to the discovery of some compounds possessing biological and pharmacological properties. Our aims have been to investigate and identify some natural products having the ability to effect on protein misfolding. In neurodegenerative disorders, like Alzheimer’s and Parkinson’s, a protein or a peptide undergoes conformational changes, and consequently the protein transform to fibrils coined amyloid. To determine the effective anti-amyloid compounds in natural products, Borage leaves was chosen. The plant extract was extracted using soxhlet and applied to hen white egg... 

    Enhancing Compound and Gene Image-based Profiling for Drug Discovery and Validation based on Structural/Computational Methods

    , M.Sc. Thesis Sharif University of Technology Talaei, Tahereh (Author) ; Rohban, Mohammad Hossein (Supervisor) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    The image-based profile is a technology by which image morphology information is transformed into a multidimensional profile from a set of image-derived features. These profiles can be used to extract biologically meaningful biological information. For example, in the drug discovery process, the mechanism of action of a drug or disease can be identified by examining the morphological properties of the drug in the patient’s cell or tissue and used to design new drugs or use existing drugs for various diseases. High-throughput imaging technology allows the imaging of a large number of different experiments. Extracting valuable features and a good representation of features is the main... 

    Prediction of Protein Ligand Binding Affinity Using Deep Networks

    , M.Sc. Thesis Sharif University of Technology Gholamzadeh Lanjavi, Atena (Author) ; Kalhor, Hamid Reza (Supervisor) ; Motahhari, Abolfazl (Co-Supervisor)
    Abstract
    Protein-ligand binding affinity is extremely important for finding new candidates in drug discovery and computational biochemistry. One of the physical characteristics for protein ligand interactions has been dissociation constant (KD) which can be obtain experimentally. However, there have been tremendous efforts to predict KD using modeling and computational approaches for protein-ligand interactions. In this project, we have exploited Convolutional Neural Network (CNN) model based on KDeep design, PDBBind version 2016 refined set training data, and examining it with KDeep core set test data. In order to modify KDeep,instead of 24 rotations (0, 90, 180 and 270 degrees in selection of two... 

    Synthesis & Characterization of Au-HKUST-1 Nanocomposite and Evaluation of Plasmonic Properties of Gold Nanoparticles in this Nanocomposite

    , M.Sc. Thesis Sharif University of Technology Moazzeni, Hamid Reza (Author) ; Madaah Hosseini, Hamid Reza (Supervisor)
    Abstract
    In the past few years, many research works on the controllable integration of metal nanoparticles and metal-organic frameworks were done, since the obtained composite material shows a synergism effect in catalysis and photocatalysis, drug delivery applications, gas, and energy storage, as well as sensing. For the first time, in this study, we employed template-assisted growth to synthesize Au-HKUST-1 Nanocomposite. XRD analysis entirely confirms that employing this strategy in synthesizing Au-HKUST-1 was wholly successful, and the plasmonic properties of this nanostructure were studied via UV-visible spectroscopy. In the course of synthesis, gold nanoparticles with 70nm diameter were...