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    Glycan-mediated functional assembly of IL-1RI: structural insights into completion of the current description for immune response

    , Article Journal of Biomolecular Structure and Dynamics ; Volume 40, Issue 6 , 2022 , Pages 2575-2585 ; 07391102 (ISSN) Azimzadeh Irani, M ; Ejtehadi, M. R ; Sharif University of Technology
    Taylor and Francis Ltd  2022
    Abstract
    Interleukin 1 Receptor type I (IL-1RI) is a multi-domain transmembrane receptor that triggers the inflammatory response. Understanding its detailed mechanism of action is crucial for treating immune disorders. IL-1RI is activated upon formation of its functional assembly that occurs by binding of the IL-1 cytokine and the accessory protein (Il-1RAcP) to it. X-ray crystallography, small-Angle X-ray Scattering and molecular dynamics simulation studies showed that IL-1RI adopts two types of ‘compact’ and ‘extended’ conformational states in its dynamical pattern. Furthermore, glycosylation has shown to play a critical role in its activation process. Here, classical and accelerated atomistic... 

    Margination and adhesion of micro- and nanoparticles in the coronary circulation: A step towards optimised drug carrier design

    , Article Biomechanics and Modeling in Mechanobiology ; Volume 17, Issue 1 , 2018 , Pages 205-221 ; 16177959 (ISSN) Forouzandehmehr, M ; Shamloo, A ; Sharif University of Technology
    Springer Verlag  2018
    Abstract
    Obstruction of left anterior descending artery (LAD) due to the thrombosis or atherosclerotic plaques is the leading cause of death worldwide. Targeted delivery of drugs through micro- and nanoparticles is a very promising approach for developing new strategies in clot-busting or treating restenosis. In this work, we modelled the blood flow characteristics in a patient-specific reconstructed LAD artery by the fluid–solid interaction method and based on physiological boundary conditions. Next, we provided a Lagrangian description of micro- and nanoparticles dynamics in the blood flow considering their Brownian motion and the particle–particle interactions. Our results state that the number of... 

    Targeted drug delivery of magnetic microbubble for abdominal aortic aneurysm: an in silico study

    , Article Biomechanics and Modeling in Mechanobiology ; Volume 21, Issue 2 , 2022 , Pages 735-753 ; 16177959 (ISSN) Shamloo, A ; Ebrahimi, S ; Ghorbani, G ; Alishiri, M ; Sharif University of Technology
    Springer Science and Business Media Deutschland GmbH  2022
    Abstract
    Targeted drug delivery (TDD) to abdominal aortic aneurysm (AAA) using a controlled and efficient approach has recently been a significant challenge. In this study, by using magnetic microbubbles (MMBs) under a magnetic field, we investigated the MMBs performance in TDD to AAA based on the amount of surface density of MMBs (SDMM) adhered to the AAA lumen. The results showed that among the types of MMBs studied in the presence of the magnetic field, micromarkers are the best type of microbubble with a −50 % increase in SDMM adhered to the critical area of AAA. The results show that applying a magnetic field causes the amount of SDMM adhered to the whole area of AAA to increase −1.54 times... 

    Stereoelectronic effects: A simple yet powerful tool to manipulate anion affinity

    , Article Organic and Biomolecular Chemistry ; Volume 13, Issue 7 , Dec , 2015 , Pages 2170-2176 ; 14770520 (ISSN) Samet, M ; Fattahi, A ; Kass, S.R ; Sharif University of Technology
    Royal Society of Chemistry  2015
    Abstract
    Different strategies are employed in designing strong and selective anion receptors but stereoelectronic effects have been largely ignored. In this work, the stereo configuration of a non-interacting ether is found to have a large impact of more than two orders of magnitude on the binding of a rigid diol with tetrabutylammonium chloride in acetonitrile-d3. A favorable carbon-oxygen dipole and an intramolecular C-H⋯OH hydrogen bond in an equatorially substituted ether is found to be energetically more important than a stabilizing hydrogen bond in the corresponding axially oriented alcohol. IR spectroscopy is also used to probe the structures of the bound complexes and several binding motifs... 

    Mining the potential of label-free biosensors for in vitro antipsychotic drug screening

    , Article Biosensors ; Volume 8, Issue 1 , 2018 ; 20796374 (ISSN) Kilic, T ; Soler, M ; Fahimi Kashani, N ; Altug, H ; Carrara, S ; Sharif University of Technology
    MDPI AG  2018
    Abstract
    The pharmaceutical industry is facing enormous challenges due to high drug attribution rates. For the past decades, novel methods have been developed for safety and efficacy testing, as well as for improving early development stages. In vitro screening methods for drug-receptor binding are considered to be good alternatives for decreasing costs in the identification of drug candidates. However, these methods require lengthy and troublesome labeling steps. Biosensors hold great promise due to the fact that label-free detection schemes can be designed in an easy and low-cost manner. In this paper, for the first time in the literature, we aimed to compare the potential of label-free optical and... 

    On the capacity of level and type modulations in Molecular communication with ligand receptors

    , Article IEEE International Symposium on Information Theory - Proceedings, 14 June 2015 through 19 June 2015 ; Volume 2015-June , 2015 , Pages 1951-1955 ; 21578095 (ISSN) ; 9781467377041 (ISBN) Aminian, G ; Mirmohseni, M ; Nasiri Kenari, M ; Fekri, F ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2015
    Abstract
    In this paper, we consider the bacterial point-to-point communication problem with one transmitter and one receiver by considering the ligand receptor binding process. The most commonly investigated signalling model, referred to as the Level Scenario (LS), uses one type of a molecule with different concentration levels for signaling. An alternative approach is to employ multiple types of molecules with a single concentration level, referred to as the Type Scenario (TS). We investigate the trade-offs between the two scenarios for the ligand receptor from the capacity point of view. For this purpose, we evaluate the capacity using numerical algorithms. Moreover, we derive an upper bound on the... 

    Physical layer network coding in molecular two-way relay networks

    , Article IWCIT 2016 - Iran Workshop on Communication and Information Theory, 3 May 2016 through 4 May 2016 ; 2016 ; 9781509019229 (ISBN) Farahnak Ghazani, M ; Aminian, G ; Mirmohseni, M ; Gohari, A ; Nasiri Kenari, M ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2016
    Abstract
    In traditional wireless networks, physical layer network coding (PNC) exploits the inverse additivity property of broadcast signals in the medium, an idea which is not directly applicable to molecular networks. In this paper, to make the natural XOR operation possible at the physical layer, we exploit the reaction of different molecule types and we propose a PNC scheme in diffusion-based molecular relay networks. For comparison, we consider the straightforward network coding (SNC) scheme in molecular networks. Assuming the ligand-receptor binding process at the receivers, we investigate the error performance of both schemes. It is observed that in addition to the simplicity of the proposed... 

    Modeling of an ultrasound system in targeted drug delivery to abdominal aortic aneurysm: a patient-specificin silico study based on ligand-receptor binding

    , Article IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control ; Volume 69, Issue 3 , 2022 , Pages 967-974 ; 08853010 (ISSN) Shamloo, A ; Boroumand, A ; Ebrahimi, S ; Kalantarnia, F ; Maleki, S ; Moradi, H ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2022
    Abstract
    Targeted drug delivery methods have shown a significant impact on enhancing drug delivery efficiency and reducing drug side effects. While various stimuli have been used to promote the drug delivery process, applying ultrasound (US) waves to control drug particles through the human body, noninvasively, has drawn the scientist's attention. However, microcarriers delivery reaches the aneurysmal artery by US waves that exert volumetric forces on blood, and drug carriers, which can therefore affect blood flow patterns and movement pathways of drug carriers, have not yet been studied. In this study, we developed a 3-D patient-specific model of abdominal aortic aneurysm (AAA) to evaluate the... 

    Drug delivery performance of nanocarriers based on adhesion and interaction for abdominal aortic aneurysm treatment

    , Article International Journal of Pharmaceutics ; Volume 594 , 2021 ; 03785173 (ISSN) Ebrahimi, S ; Vatani, P ; Amani, A ; Shamloo, A ; Sharif University of Technology
    Elsevier B.V  2021
    Abstract
    Targeted drug delivery using nanocarriers (NCs) is one of the novel techniques that has recently been used to improve drug delivery to the Abdominal aortic aneurysm (AAA) disease. The purpose of this study is to evaluate the surface density of NCs (SDNC) adhered via ligand-receptor binding to the inner wall of AAA. For this purpose, fluid–structure interaction (FSI) analysis was first performed for the patient-specific and ideal AAA models. Then, by injecting NCs into the aortic artery, the values of SDNC adhered to and interacted with AAA wall were obtained. Two types of NCs, liposomes, and solid particles in four different diameters, were used to investigate the effect of the diameter and... 

    Effect of cysteine oxidation in SARS-CoV-2 receptor-binding domain on its interaction with two cell receptors: Insights from atomistic simulations

    , Article Journal of Chemical Information and Modeling ; Volume 62, Issue 1 , 2022 , Pages 129-141 ; 15499596 (ISSN) Ghasemitarei, M ; Privat Maldonado, A ; Yusupov, M ; Rahnama, S ; Bogaerts, A ; Ejtehadi, M. R ; Sharif University of Technology
    American Chemical Society  2022
    Abstract
    Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly... 

    Chemometrics-assisted effect-directed analysis of crude and refined oil using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry

    , Article Environmental Science and Technology ; Vol. 48, issue. 5 , 2014 , pp. 3074-3083 ; ISSN: 0013936X Radovic, J. R ; Thomas, K. V ; Parastar, H ; Diez, S ; Tauler, R ; Bayona, J. M ; Sharif University of Technology
    Abstract
    An effect-directed analysis (EDA) of fresh and artificially weathered (evaporated, photooxidized) samples of North Sea crude oil and residual heavy fuel oil is presented. Aliphatic, aromatic, and polar oil fractions were tested for the presence of aryl hydrocarbon receptor (AhR) agonist and androgen receptor (AR) antagonist, demonstrating for the first time the AR antagonist effects in the aromatic and, to a lesser extent, polar fractions. An extension of the typical EDA strategy to include an N-way partial least-squares (N-PLS) model capable of relating the comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) data set to the bioassay data...