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Article: In silico

Aghaee, Elham / Ghodrati, Marzieh / Ghasemi, Jahan B

Informatics in medicine unlocked

2021 Volume 23, Page(s) 100516

Abstract: The spread of SARS-CoV-2 has affected human health globally. Hence, it is necessary to rapidly find the drug-candidates that can be used to treat the infection. Since the main protease ( ... ...

Abstract	The spread of SARS-CoV-2 has affected human health globally. Hence, it is necessary to rapidly find the drug-candidates that can be used to treat the infection. Since the main protease (M
Language	English
Publishing date	2021-01-12
Publishing country	England
Document type	Journal Article
ISSN	2352-9148
ISSN	2352-9148
DOI	10.1016/j.imu.2021.100516
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Impostor Phenomenon and L2 willingness to communicate: Testing communication anxiety and perceived L2 competence as mediators.

Brauer, Kay / Barabadi, Elyas / Aghaee, Elham / Alrabai, Fakieh / Elahi Shirvan, Majid / Sendatzki, Rebekka / Vierow, Linnea Marie

Frontiers in psychology

2023 Volume 13, Page(s) 1060091

Abstract: The Impostor Phenomenon (IP) describes experiences of perceived intellectual fraudulence despite the existence of objectively good performances, and it is a robust predictor of experiences and outcomes in higher education. We examined the role of the IP ... ...

Abstract	The Impostor Phenomenon (IP) describes experiences of perceived intellectual fraudulence despite the existence of objectively good performances, and it is a robust predictor of experiences and outcomes in higher education. We examined the role of the IP in the domain of second language (L2) acquisition by testing its relations with a robust predictor of L2 use, willingness to communicate (WTC). We collected self-reports of 400 adult Iranian L2 learners and tested the associations between the IP and WTC. As expected, we found a negative association between IP and WTC (
Language	English
Publishing date	2023-01-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2563826-9
ISSN	1664-1078
ISSN	1664-1078
DOI	10.3389/fpsyg.2022.1060091
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Article: MiR-548c-3p through suppressing

Khalili, Elham / Afgar, Ali / Rajabpour, Azam / Aghaee-Bakhtiari, Seyed Hamid / Jamialahmadi, Khadijeh / Teimoori-Toolabi, Ladan

Heliyon

2023 Volume 9, Issue 11, Page(s) e21775

Abstract: Background: Colorectal cancer, is one of most prevalent the cancer in the world. 5-Fluorouracil is a standard chemotherapeutic drug while the acquisition of resistance to 5-Fluorouracil is one of the problems during treatment. In this study, we aimed to ...

Abstract	Background: Colorectal cancer, is one of most prevalent the cancer in the world. 5-Fluorouracil is a standard chemotherapeutic drug while the acquisition of resistance to 5-Fluorouracil is one of the problems during treatment. In this study, we aimed to find the miRNAs that modulate the expression of Methods: 5-Fluorouracil-resistant HCT116 and SW480 cell lines were generated by consecutive treatment of cells with 5-Fluorouracil. This resistance induction was validated by MTT assays. The expression of the Results: We hypothesized that miR-548c-3p is targeting Conclusion: It can be concluded downregulation of miR548c-3p is in line with
Language	English
Publishing date	2023-11-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e21775
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Article ; Online: In silico exploration of novel protease inhibitors against coronavirus 2019 (COVID-19)

Elham Aghaee / Marzieh Ghodrati / Jahan B. Ghasemi

Informatics in Medicine Unlocked, Vol 23, Iss , Pp 100516- (2021)

2021

Abstract	The spread of SARS-CoV-2 has affected human health globally. Hence, it is necessary to rapidly find the drug-candidates that can be used to treat the infection. Since the main protease (Mpro) is the key protein in the virus's life cycle, Mpro is served as one of the critical targets of antiviral treatment. We employed virtual screening tools to search for new inhibitors to accelerate the drug discovery process. The hit compounds were subsequently docked into the active site of SARS-CoV-2 main protease and ranked by their binding energy. Furthermore, in-silico ADME studies were performed to probe for adoption with the standard ranges. Finally, molecular dynamics simulations were applied to study the protein-drug complex's fluctuation over time in an aqueous medium. This study indicates that the interaction energy of the top ten retrieved compounds with COVID-19 main protease is much higher than the interaction energy of some currently in use protease drugs such as ML188, nelfinavir, lopinavir, ritonavir, and α-ketoamide. Among the discovered compounds, Pubchem44326934 showed druglike properties and was further analyzed by MD and MM/PBSA approaches. Besides, the constant binding free energy over MD trajectories suggests a probable drug possessing antiviral properties. MD simulations demonstrate that GLU166 and GLN189 are the most important residues of Mpro, which interact with inhibitors.
Keywords	Virtual screening ; COVID-19 ; Main protease ; Molecular docking ; Molecular dynamics simulation ; ADME studies ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	540
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Association between Clinical Characteristics and Laboratory Findings with Outcome of Hospitalized COVID-19 Patients: A Report from Northeast Iran.

Sobhani, Sahar / Aryan, Reihaneh / Kalantari, Elham / Soltani, Salman / Malek, Nafise / Pirzadeh, Parisa / Yarahmadi, Amir / Aghaee, Atena

Interdisciplinary perspectives on infectious diseases

2021 Volume 2021, Page(s) 5552138

Abstract: Coronavirus disease 2019 (COVID-19) was first discovered in December 2019 in China and has rapidly spread worldwide. Clinical characteristics, laboratory findings, and their association with the outcome of patients with COVID-19 can be decisive in ... ...

Abstract	Coronavirus disease 2019 (COVID-19) was first discovered in December 2019 in China and has rapidly spread worldwide. Clinical characteristics, laboratory findings, and their association with the outcome of patients with COVID-19 can be decisive in management and early diagnosis. Data were obtained retrospectively from medical records of 397 hospitalized COVID-19 patients between February and May 2020 in Imam Reza Hospital, northeast Iran. Clinical and laboratory features were evaluated among survivors and nonsurvivors. The correlation between variables and duration of hospitalization and admission to the intensive care unit (ICU) was determined. Male sex, age, hospitalization duration, and admission to ICU were significantly related to mortality rate. Headache was a more common feature in patients who survived (
Language	English
Publishing date	2021-02-05
Publishing country	Egypt
Document type	Journal Article
ZDB-ID	2478373-0
ISSN	1687-7098 ; 1687-708X
ISSN (online)	1687-7098
ISSN	1687-708X
DOI	10.1155/2021/5552138
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Article: Effect of incorporation of zinc oxide nanoparticles on mechanical properties of conventional glass ionomer cements.

Panahandeh, Narges / Torabzadeh, Hassan / Aghaee, Mohammadamin / Hasani, Elham / Safa, Saeed

Journal of conservative dentistry : JCD

2018 Volume 21, Issue 2, Page(s) 130–135

Abstract: Aim: The aim of this study is to investigate the physical properties of conventional and resin-modified glass ionomer cements (GICs) compared to GICs supplemented with zinc oxide (ZnO) nanofiller particles at 5% (w/w).: Methods: In this : Results: ...

Abstract	Aim: The aim of this study is to investigate the physical properties of conventional and resin-modified glass ionomer cements (GICs) compared to GICs supplemented with zinc oxide (ZnO) nanofiller particles at 5% (w/w). Methods: In this Results: Flexural strength of glass ionomer containing nanoparticles was not significantly different from the control group ( Conclusions: Incorporation of nanospherical and nanoflower ZnO to glass ionomer decreased their surface hardness, without any changes on their flexural strength. Incorporation of nanorod ZnO particles caused no effect on the mechanical properties.
Language	English
Publishing date	2018-04-19
Publishing country	India
Document type	Journal Article
ZDB-ID	2064481-4
ISSN	0972-0707
ISSN	0972-0707
DOI	10.4103/JCD.JCD_170_17
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Article: Antibacterial cuminaldehyde/hydroxypropyl-β-cyclodextrin inclusion complex electrospun fibers mat: Fabrication and characterization

Sharif, Niloufar / Golmakani, Mohammad-Taghi / Hajjari, Mohammad Mahdi / Aghaee, Elham / Ghasemi, Jahan Bakhsh

Food packaging and shelf life. 2021 Sept., v. 29

2021

Abstract: Electrospinning process has been applied to fabricate hydroxypropyl-β-cyclodextrin fibers mat incorporating of cuminaldehyde. The inclusion complex formation between cuminaldehyde and hydroxypropyl-β-cyclodextrin was proved by computational molecular ... ...

Abstract	Electrospinning process has been applied to fabricate hydroxypropyl-β-cyclodextrin fibers mat incorporating of cuminaldehyde. The inclusion complex formation between cuminaldehyde and hydroxypropyl-β-cyclodextrin was proved by computational molecular docking. The proton nuclear magnetic resonance results revealed that cuminaldehyde was present in final inclusion complex at 0.92:1 molecular ratio. Moreover, the presence of cuminaldehyde in the electrospun fibers in the inclusion state along with the host hydroxypropyl-β-cyclodextrin molecules was proved by Fourier-transform infrared spectroscopy. The results of scanning electron microscopy and confocal Raman spectroscopy revealed the formation of uniform ﬁber morphology with average fibers diameter of 381 ± 178 nm. The thermal stability of cuminaldehyde was improved after electrospinning process. Finally, the promising antibacterial activity of fibers against Escherichia coli and Staphylococcus aureus confirmed the suitability of electrospinning process for the developing cuminaldehyde-loaded fibers with potential application in food area such as active packaging structures.
Keywords	Escherichia coli ; Fourier transform infrared spectroscopy ; Raman imaging ; Staphylococcus aureus ; antibacterial properties ; nuclear magnetic resonance spectroscopy ; shelf life ; thermal stability
Language	English
Dates of publication	2021-09
Publishing place	Elsevier Ltd
Document type	Article
ISSN	2214-2894
DOI	10.1016/j.fpsl.2021.100738
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Article ; Online: The role of microRNA-induced apoptosis in diverse radioresistant cancers.

Darvish, Leili / Bahreyni Toossi, Mohammad Taghi / Azimian, Hosein / Shakeri, Mahsa / Dolat, Elham / Ahmadizad Firouzjaei, Ali / Rezaie, Samaneh / Amraee, Azadeh / Aghaee-Bakhtiari, Seyed Hamid

Cellular signalling

2022 Volume 104, Page(s) 110580

Abstract: Resistance to cancer radiotherapy is one of the biggest concerns for success in treating and preventing recurrent disease. Malignant tumors may develop when they block genetic mutations associated with apoptosis or abnormal expression of apoptosis; Tumor ...

Abstract	Resistance to cancer radiotherapy is one of the biggest concerns for success in treating and preventing recurrent disease. Malignant tumors may develop when they block genetic mutations associated with apoptosis or abnormal expression of apoptosis; Tumor treatment may induce the expression of apoptosis-related genes to promote tumor cell apoptosis. MicroRNAs have been shown to contribute to forecasting prognosis, distinguishing between cancer subtypes, and affecting treatment outcomes in cancer. Constraining these miRNAs may be an attractive treatment strategy to help overcome radiation resistance. The delivery of these future treatments is still challenging due to the excess downstream targets that each miRNA can control. Understanding the role of miRNAs brings us one step closer to attaining patient treatment and improving patient outcomes. This review summarized the current information on the role of microRNA-induced apoptosis in determining the radiosensitivity of various cancers.
MeSH term(s)	Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Neoplasms/genetics ; Neoplasms/radiotherapy ; Apoptosis/genetics ; Radiation Tolerance ; Gene Expression Regulation, Neoplastic
Chemical Substances	MicroRNAs
Language	English
Publishing date	2022-12-26
Publishing country	England
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1002702-6
ISSN	1873-3913 ; 0898-6568
ISSN (online)	1873-3913
ISSN	0898-6568
DOI	10.1016/j.cellsig.2022.110580
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Zs.A 2579: Show issues

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Article ; Online: 10-(4-Phenylpiperazine-1-carbonyl)acridin-9(10H)-ones and related compounds: Synthesis, antiproliferative activity and inhibition of tubulin polymerization.

Waltemate, Jana / Ivanov, Igor / Ghasemi, Jahan B / Aghaee, Elham / Daniliuc, Constantin Gabriel / Müller, Klaus / Prinz, Helge

Bioorganic & medicinal chemistry letters

2020 Volume 32, Page(s) 127687

Abstract: As part of our continuing search for potent inhibitors of tubulin polymerization, two novel series of 42 10-(4-phenylpiperazine-1-carbonyl)acridin-9(10H)-ones and N-benzoylated acridones were synthesized on the basis of a retrosynthetic approach. All ... ...

Abstract	As part of our continuing search for potent inhibitors of tubulin polymerization, two novel series of 42 10-(4-phenylpiperazine-1-carbonyl)acridin-9(10H)-ones and N-benzoylated acridones were synthesized on the basis of a retrosynthetic approach. All newly synthesized compounds were tested for antiproliferative activity and interaction with tubulin. Several analogs potently inhibited tumor cell growth. Among the compounds tested, 10-(4-(3-methoxyphenyl)piperazine-1-carbonyl)acridin-9(10H)-one (17c) exhibited excellent growth inhibitory effects on 93 tumor cell lines, with an average GI
MeSH term(s)	Acridines/chemistry ; Acridines/metabolism ; Acridines/pharmacology ; Antineoplastic Agents/chemical synthesis ; Antineoplastic Agents/metabolism ; Antineoplastic Agents/pharmacology ; Binding Sites ; Cell Proliferation/drug effects ; G2 Phase Cell Cycle Checkpoints/drug effects ; Humans ; K562 Cells ; M Phase Cell Cycle Checkpoints/drug effects ; Molecular Conformation ; Molecular Docking Simulation ; Piperazines/chemistry ; Structure-Activity Relationship ; Tubulin/chemistry ; Tubulin/metabolism ; Tubulin Modulators/chemical synthesis ; Tubulin Modulators/metabolism ; Tubulin Modulators/pharmacology
Chemical Substances	Acridines ; Antineoplastic Agents ; Piperazines ; Tubulin ; Tubulin Modulators
Language	English
Publishing date	2020-11-17
Publishing country	England
Document type	Journal Article
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2020.127687
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Article ; Online: Experimental, computational and chemometrics studies of BSA-vitamin B6 interaction by UV-Vis, FT-IR, fluorescence spectroscopy, molecular dynamics simulation and hard-soft modeling methods.

Manouchehri, Firouzeh / Izadmanesh, Yahya / Aghaee, Elham / Ghasemi, Jahan B

Bioorganic chemistry

2016 Volume 68, Page(s) 124–136

Abstract: The interaction of pyridoxine (Vitamin B6) with bovine serum albumin (BSA) is investigated under pseudo-physiological conditions by UV-Vis, fluorescence and FTIR spectroscopy. The intrinsic fluorescence of BSA was quenched by VB6, which was rationalized ... ...

Abstract	The interaction of pyridoxine (Vitamin B6) with bovine serum albumin (BSA) is investigated under pseudo-physiological conditions by UV-Vis, fluorescence and FTIR spectroscopy. The intrinsic fluorescence of BSA was quenched by VB6, which was rationalized in terms of the static quenching mechanism. According to fluorescence quenching calculations, the bimolecular quenching constant (kq), dynamic quenching (KSV) and static quenching (KLB) at 310K were obtained. The efficiency of energy transfer and the distance between the donor (BSA) and the acceptor (VB6) were calculated by Foster's non-radiative energy transfer theory and were equal to 41.1% and 2.11nm. The collected UV-Vis and fluorescence spectra were combined into a row-and column-wise augmented matrix and resolved by multivariate curve resolution-alternating least squares (MCR-ALS). MCR-ALS helped to estimate the stoichiometry of interactions, concentration profiles and pure spectra for three species (BSA, VB6 and VB6-BSA complex) existed in the interaction procedure. Based on the MCR-ALS results, using mass balance equations, a model was developed and binding constant of complex was calculated using non-linear least squares curve fitting. FT-IR spectra showed that the conformation of proteins was altered in presence of VB6. Finally, the combined docking and molecular dynamics (MD) simulations were used to estimate the binding affinity of VB6 to BSA. Five-nanosecond MD simulations were performed on bovine serum albumin (BSA) to study the conformational features of its ligand binding site. From MD results, eleven BSA snapshots were extracted, at every 0.5ns, to explore the binding affinity (GOLD score) of VB6 using a docking procedure. MD simulations indicated that there is a considerable flexibility in the structure of protein that affected ligand recognition. Structural analyses and docking simulations indicated that VB6 binds to site I and GOLD score values depend on the conformations of both BSA and ligand. Molecular modeling results showed that VB6-BSA complex formed not only on the basis of electrostatic forces, but also on the basis of π-π staking and hydrogen bond. There was an excellent agreement between the experimental and computational results. The results presented in this paper, will offer a reference for detailed and systematic studies on the biological effects and action mechanism of small molecules with proteins.
MeSH term(s)	Animals ; Cattle ; Molecular Docking Simulation ; Serum Albumin, Bovine/chemistry ; Spectrometry, Fluorescence ; Spectrophotometry, Ultraviolet ; Spectroscopy, Fourier Transform Infrared ; Vitamin B 6/chemistry
Chemical Substances	Serum Albumin, Bovine (27432CM55Q) ; Vitamin B 6 (8059-24-3)
Language	English
Publishing date	2016-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	120080-x
ISSN	1090-2120 ; 0045-2068
ISSN (online)	1090-2120
ISSN	0045-2068
DOI	10.1016/j.bioorg.2016.07.014
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