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Total 21 records

    Atomic scale interactions between RNA and DNA aptamers with the TNF- α protein

    , Article BioMed Research International ; Volume 2021 , 2021 ; 23146133 (ISSN) Asadzadeh, H ; Moosavi, A ; Alexandrakis, G ; Mofrad, M. R. K ; Sharif University of Technology
    Hindawi Limited  2021
    Abstract
    Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for... 

    A review on computer-aided chemogenomics and drug repositioning for rational COVID-19 drug discovery

    , Article Chemical Biology and Drug Design ; Volume 100, Issue 5 , 2022 , Pages 699-721 ; 17470277 (ISSN) Maghsoudi, S ; Taghavi Shahraki, B ; Rameh, F ; Nazarabi, M ; Fatahi, Y ; Akhavan, O ; Rabiee, M ; Mostafavi, E ; Lima, E. C ; Saeb, M. R ; Rabiee, N ; Sharif University of Technology
    John Wiley and Sons Inc  2022
    Abstract
    Application of materials capable of energy harvesting to increase the efficiency and environmental adaptability is sometimes reflected in the ability of discovery of some traces in an environment―either experimentally or computationally―to enlarge practical application window. The emergence of computational methods, particularly computer-aided drug discovery (CADD), provides ample opportunities for the rapid discovery and development of unprecedented drugs. The expensive and time-consuming process of traditional drug discovery is no longer feasible, for nowadays the identification of potential drug candidates is much easier for therapeutic targets through elaborate in silico approaches,... 

    In Silico Designing and Docking Evaluation of the Small Lectins to Inhibit Falciparum Attachment to the Midgut Epithelium of Anopheles Mosquito

    , M.Sc. Thesis Sharif University of Technology Jafarabadi, Amir Hossein (Author) ; Alemzadeh, Iran (Supervisor) ; Raaz, Abbasali (Supervisor)
    Abstract
    The parasite entering into the blood of a malaria infected individual eventually causes the formation of gametocytes inside the blood cells. With the insect bite, the male and female gametes will enter the insect's stomach and form the zygote. After developing in the stomach, the zygote first turns into an ookinete and then into an oocyst, and by passing through the stomach wall and tearing the sporozoites, it enters the salivary glands of the insect, and if another person is bitten by that insect, the parasite enters the body of that person. and this cycle continues between the insect and the human body. Stopping this cycle requires blocking one part of this cycle. Studies show that... 

    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... 

    In Vitro Study of Drug Release from the Metal-organic Frameworks (MOFs) for Melanoma Cancer Drug Delivery

    , Ph.D. Dissertation Sharif University of Technology Barjasteh, Mahdi (Author) ; Vossoughi, Manouchehr (Supervisor) ; Bagherzadeh, Mojtaba (Supervisor) ; Pooshang Bagheri, Kamran (Co-Supervisor)
    Abstract
    Metal-organic frameworks (MOFs) are a new class of biocompatible nanomaterials with high specific surface area, which provide the possibility of loading various therapeutic agents. Considering the few studies on the use of MOFs in melanoma cancer treatment, the main goal of this research is to investigate the loading and controlling the release of dacarbazine (DTIC) and also the interaction of DTIC and MOF structure in aqueous environments. Based on this, this study was done in three main parts. In the first part, several types of well-known and often used structures in the drug delivery field, including ZIF-8 (based on zinc), MIL-101-NH2(Fe), and MIL-100(Fe) (both based on iron), were... 

    Identification of an aspidospermine derivative from borage extract as an anti-amyloid compound: A possible link between protein aggregation and antimalarial drugs

    , Article Phytochemistry ; Volume 140 , 2017 , Pages 134-140 ; 00319422 (ISSN) Kalhor, H. R ; Ashrafian, H ; Sharif University of Technology
    Elsevier Ltd  2017
    Abstract
    A number of human diseases, including Alzheimer's and Parkinson's have been linked to amyloid formation. To search for an anti-amyloidogenic product, alkaloid enriched extract from borage leaves was examined for anti-amyloidogenic activity using Hen Egg White Lysozyme (HEWL) as a model protein. After isolation of the plant extract using rHPLC, only one fraction indicated a significant bioactivity. TEM analysis confirmed a remarkable reduction of amyloid fibrils in the presence of the bioactive fraction. To identify the effective substance in the fraction, mass spectrometry, FTIR, and NMR were performed. Our analyses determined that the bioactive compound as... 

    Design of Novel Drugs Based on Tyrosine and Phenylalanine Amino Acids to Inhibit Cyclin-Dependent Kinases 2 (CDK2) Proteins Modeled on Flavopiridol Drug

    , M.Sc. Thesis Sharif University of Technology Aghili, Farshad (Author) ; Fattahi, Alireza (Supervisor)
    Abstract
    Cyclin-dependent kinases 2 (CDK2) are one of the important proteins in cell cycle regulation and progression. In many human cancer cells, the activity of CDK2 kinases and their related subunits are deregulated, leading to tumor formation. Therefore, inhibition of this enzyme as an attractive therapeutic target can cause cancer cell death in glioblastoma and diffuse large B-cell lymphoma. Using new pharmaceutical structures based on sugar and amino acids is a new approach due to its greater efficacy and fewer side effects than old drugs. In this research, according to the structure of Flavopiridol as one of the CDK2 inhibitors, the active site of CDK2, and the structure of ATP molecule, 50... 

    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... 

    Synthesis and characterization of 1-amidino-O-alkylureas metal complexes as α- glucosidase Inhibitors: Structure-activity relationship, molecular docking, and kinetic studies

    , Article Journal of Molecular Structure ; Volume 1250 , 2022 ; 00222860 (ISSN) Moghaddam, F. M ; Daneshfar, M ; Daneshfar, Z ; Iraji, A ; Samandari Najafabad, A ; Faramarzi, M. A ; Mahdavi, M ; Sharif University of Technology
    Elsevier B.V  2022
    Abstract
    In the present study, metal complexes of 1-amidino-O-alkylureas were designed, synthesized and characterized by elemental analyses, FT-IR spectra, XRD, Mass analyses and scanning electron microscopy (SEM). All synthesized complexes were screen as α-Glucosidase inhibitors. According to the in vitro results, the Cu (II) complexes showed superior potency compared to other tested metal complexes. Particularly, [Cu(L-Me)2](Cl)2 (1b) showed the strongest inhibition against α-Glucosidase with an IC50 value of 2.75 ± 0.3 µM which was comparable to that of acarbose (IC50 = 750 µM). These findings are supported by the ligands and enzyme interactions through molecular docking. © 2021 Elsevier B.V  

    Protein G selects two binding sites for carbon nanotube with dissimilar behavior; a molecular dynamics study

    , Article Journal of Molecular Graphics and Modelling ; Volume 87 , 2019 , Pages 257-267 ; 10933263 (ISSN) Ebrahim Habibi, M. B ; Ghobeh, M ; Aghakhani Mahyari, F ; Rafii Tabar, H ; Sasanpour, P ; Sharif University of Technology
    Elsevier Inc  2019
    Abstract
    Background: Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure. Methods: Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized. Results: Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the... 

    Discovery of a tetracyclic indole alkaloid that postpones fibrillation of hen egg white lysozyme protein

    , Article International Journal of Biological Macromolecules ; Volume 183 , 2021 , Pages 1939-1947 ; 01418130 (ISSN) Ashrafian, H ; Zadeh, E.H ; Tajbakhsh, M ; Majid, N ; Srivastava, G.N ; Khan, R.H ; Sharif University of Technology
    Elsevier B.V  2021
    Abstract
    Protein aggregation, such as amyloid fibril formation, is molecular hallmark of many neurodegenerative disorders including Alzheimer's, Parkinson's, and Prion disease. Indole alkaloids are well-known as the compounds having the ability to inhibit protein fibrillation. In this study, we experimentally and computationally have investigated the anti-amyloid property of a derivative of a synthesized tetracyclic indole alkaloid (TCIA), possessing capable functional groups. The fibrillation reaction of Hen White Egg Lysozyme (HEWL) was performed in absence and presence of the indole alkaloid. For quantitative analysis, we used Thioflovin T binding assay which showed ~50% reduction in fibril... 

    Binding assessment of two arachidonic-based synthetic derivatives of adrenalin with β-lactoglobulin: Molecular modeling and chemometrics approach

    , Article Biophysical Chemistry ; Volume 207 , 2015 , Pages 97-106 ; 03014622 (ISSN) Gholami, S ; Bordbar, A. K ; Akvan, N ; Parastar, H ; Fani, N ; Gretskaya, N. M ; Bezuglov, V. V ; Haertlé, T ; Sharif University of Technology
    Elsevier  2015
    Abstract
    A computational approach to predict the main binding modes of two adrenalin derivatives, arachidonoyl adrenalin (AA-AD) and arachidonoyl noradrenalin (AA-NOR) with the β-lactoglubuline (BLG) as a nano-milk protein carrier is presented and assessed by comparison to the UV-Vis absorption spectroscopic data using chemometric analysis. Analysis of the spectral data matrices by using the multivariate curve resolution-alternating least squares (MCR-ALS) algorithm led to the pure concentration calculation and spectral profiles resolution of the chemical constituents and the apparent equilibrium constants computation. The negative values of entropy and enthalpy changes for both compound indicated... 

    Atorvastatin treatment softens human red blood cells: an optical tweezers study

    , Article Biomedical Optics Express ; Volume 9, Issue 3 , 2018 ; 21567085 (ISSN) Sheikh Hasani, V ; Babaei, M ; Azadbakht, A ; Pazoki Toroudi, H ; Mashaghi, A ; Moosavi Movahedi, A. A ; Seyed Reihani, .N ; Sharif University of Technology
    OSA - The Optical Society  2018
    Abstract
    Optical tweezers are proven indispensable single-cell micro-manipulation and mechanical phenotyping tools. In this study, we have used optical tweezers for measuring the viscoelastic properties of human red blood cells (RBCs). Comparison of the viscoelastic features of the healthy fresh and atorvastatin treated cells revealed that the drug softens the cells. Using a simple modeling approach, we proposed a molecular model that explains the drug-induced softening of the RBC membrane. Our results suggest that direct interactions between the drug and cytoskeletal components underlie the drug-induced softening of the cells. © 2018 Optical Society of America  

    Identification of a novel multifunctional ligand for simultaneous inhibition of amyloid-beta (aβ42) and chelation of zinc metal ion

    , Article ACS Chemical Neuroscience ; Volume 10, Issue 11 , 2019 , Pages 4619-4632 ; 19487193 (ISSN) Asadbegi, M ; Shamloo, A ; Sharif University of Technology
    American Chemical Society  2019
    Abstract
    Zinc binding to β-amyloid structure could promote amyloid-β aggregation, as well as reactive oxygen species (ROS) production, as suggested in many experimental and theoretical studies. Therefore, the introduction of multifunctional drugs capable of chelating zinc metal ion and inhibiting Aβ aggregation is a promising strategy in the development of AD treatment. The present study has evaluated the efficacy of a new bifunctional peptide drug using molecular docking and molecular dynamics (MD) simulations. This drug comprises two different domains, an inhibitor domain, obtained from the C-terminal hydrophobic region of Aβ, and a Zn2+ chelating domain, derived from rapeseed meal, merge with a... 

    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... 

    Amyloid fibril reduction through covalently modified lysine in HEWL and insulin

    , Article Archives of Biochemistry and Biophysics ; Volume 727 , 2022 ; 00039861 (ISSN) Rezaei, M ; Kalhor, H. R ; Sharif University of Technology
    Academic Press Inc  2022
    Abstract
    Proteins possess a variety of nucleophiles, which can carry out different reactions in the functioning cells. Proteins endogenously and synthetically can be modified through their nucleophilic sites. The roles of these chemical modifications have not been completely revealed. These modifications can alter the protein folding process. Protein folding directly affects the function of proteins. If an error in protein folding occurs, it may cause protein malfunction leading to several neurodegenerative disorders such as Alzheimer's and Parkinson's. In this study, Hen Egg White Lysozyme (HEWL) and bovine insulin, as model proteins for studying the amyloid formation, were covalently attached with... 

    Some natural hypomethylating agents in food, water and environment are against distribution and risks of COVID-19 pandemic: Results of a big-data research

    , Article Avicenna Journal of Phytomedicine ; Volume 12, Issue 3 , 2022 , Pages 309-324 ; 22287930 (ISSN) Besharati, M. R ; Izadi, M ; Talebpour, A ; Sharif University of Technology
    Mashhad University of Medical Sciences  2022
    Abstract
    Objective: This study analyzes the effects of lifestyle, nutrition, and diets on the status and risks of apparent (symptomatic) COVID-19 infection in Iranian families. Materials and Methods: A relatively extensive questionnaire survey was conducted on more than 20,000 Iranian families (residing in more than 1000 different urban and rural areas in the Islamic Republic of Iran) to collect the big data of COVID-19 and develop a lifestyle dataset. The collected big data included the records of lifestyle effects (e.g. nutrition, water consumption resources, physical exercise, smoking, age, gender, health and disease factors, etc.) on the status of COVID-19 infection in families (i.e. residents of... 

    Personalised deposition maps for micro- and nanoparticles targeting an atherosclerotic plaque: attributions to the receptor-mediated adsorption on the inflamed endothelial cells

    , Article Biomechanics and Modeling in Mechanobiology ; Volume 18, Issue 3 , 2019 , Pages 813-828 ; 16177959 (ISSN) Shamloo, A ; Forouzandehmehr, M ; Sharif University of Technology
    Springer Verlag  2019
    Abstract
    Endothelial inflammation as a prominent precursor to atherosclerosis elicits a distinct pathological surface expression of particular vascular proteins. To exhibit a site-specific behaviour, micro- and nanoparticles, as carriers of therapeutics or imaging agents, can distinguish and use these proteins as targeted docking sites. Here, a computational patient-specific model capturing the exclusive luminal qualities has been developed to study the transport and adsorption of particles decorated with proper antibodies over an atherosclerotic plaque located in the LAD artery of the patient. Particles, in nano- and micron sizes, have been decorated with Sialyl Lewisx (sLex), P-selectin aptamer... 

    Green chemistry and coronavirus

    , Article Sustainable Chemistry and Pharmacy ; Volume 21 , 2021 ; 23525541 (ISSN) Ahmadi, S ; Rabiee, N ; Fatahi, Y ; Hooshmand, S. E ; Bagherzadeh, M ; Rabiee, M ; Jajarmi, V ; Dinarvand, R ; Habibzadeh, S ; Saeb, M. R ; Varma, R. S ; Shokouhimehr, M ; Hamblin, M. R ; Sharif University of Technology
    Elsevier B.V  2021
    Abstract
    The novel coronavirus pandemic has rapidly spread around the world since December 2019. Various techniques have been applied in identification of SARS-CoV-2 or COVID-19 infection including computed tomography imaging, whole genome sequencing, and molecular methods such as reverse transcription polymerase chain reaction (RT-PCR). This review article discusses the diagnostic methods currently being deployed for the SARS-CoV-2 identification including optical biosensors and point-of-care diagnostics that are on the horizon. These innovative technologies may provide a more accurate, sensitive and rapid diagnosis of SARS-CoV-2 to manage the present novel coronavirus outbreak, and could be... 

    Green chemistry and coronavirus

    , Article Sustainable Chemistry and Pharmacy ; Volume 21 , 2021 ; 23525541 (ISSN) Ahmadi, S ; Rabiee, N ; Fatahi, Y ; Hooshmand, S. E ; Bagherzadeh, M ; Rabiee, M ; Jajarmi, V ; Dinarvand, R ; Habibzadeh, S ; Saeb, M. R ; Varma, R.S ; Shokouhimehr, M ; Hamblin, M. R ; Sharif University of Technology
    Elsevier B.V  2021
    Abstract
    The novel coronavirus pandemic has rapidly spread around the world since December 2019. Various techniques have been applied in identification of SARS-CoV-2 or COVID-19 infection including computed tomography imaging, whole genome sequencing, and molecular methods such as reverse transcription polymerase chain reaction (RT-PCR). This review article discusses the diagnostic methods currently being deployed for the SARS-CoV-2 identification including optical biosensors and point-of-care diagnostics that are on the horizon. These innovative technologies may provide a more accurate, sensitive and rapid diagnosis of SARS-CoV-2 to manage the present novel coronavirus outbreak, and could be...