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Atomic scale interactions between RNA and DNA aptamers with the TNF- α protein
, Article BioMed Research International ; Volume 2021 , 2021 ; 23146133 (ISSN) ; 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...
Enhancing Compound and Gene Image-based Profiling for Drug Discovery and Validation based on Structural/Computational Methods
, M.Sc. Thesis Sharif University of Technology ; 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 ; 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) ; 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 ; 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 ; 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...
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) ; 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) ; 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) ; 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) ; 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) ; 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 ; 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...
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) ; 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) ; 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) ; 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...