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  1. Article ; Online: Selection of Efficient Inhibitors for Caspas-9 according to Structure-Based Pharmacophore Screening Strategy and Molecular Dynamics Simulations

    Samira Ansari / Ali Naghi Kamali / Kowsar Bagherzadeh / Masoud Amanlou / Sajjad Aghabalazadeh

    Trends in Peptide and Protein Sciences, Vol 2, Iss 1, Pp 35-

    2020  Volume 43

    Abstract: Caspases are enzymes which are the main pathways for apoptosis. Any irregulation in their functions causes increase or decrease in cell death, which result in autoimmune disease or cancer, respectively. In this study, structure-based pharmacophore drug ... ...

    Abstract Caspases are enzymes which are the main pathways for apoptosis. Any irregulation in their functions causes increase or decrease in cell death, which result in autoimmune disease or cancer, respectively. In this study, structure-based pharmacophore drug discovery method as a virtual screening was used to discover selective inhibitors for caspase-9. This enzyme is an initiator caspase that is the main pathway in Alzheimer’s disease. A pharmacophore model was developed by investigating essential interactions among the reported potent inhibitors employing a docking analysis methodology. Applying pharmacophore virtual screening, nine compounds from both National Cancer Institute (NCI), and ZINC databases were filtered as potent inhibitors of caspase-9. The efficiency of the discovered compounds was further investigated by docking studies. HIGHLIGHTS •Caspase-9 is an important enzyme for apoptosis and its activity is pivotal in cell death. •A computational design of small molecular inhibitors for caspase-9 performed by structure-based pharmacophore model. •9 compounds from both National Cancer Institute (NCI) and ZINC databases were discovered as potent inhibitors.
    Keywords alzheimer’s disease ; virtual screening ; pharmacophore ; docking ; caspase-9 ; inhibitor ; Medicine ; R ; Biology (General) ; QH301-705.5
    Subject code 540
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Shahid Beheshti University of Medical Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: The protection quest is a primary key to sharing the neutralizing antibody response to cover against all emerging VOCs based on BIV1-CovIran studies

    Maryam Shafaati / Kowsar Bagherzadeh / Majid Lotfinia / Hesam Karimi / Ali Teimoori / Mehdi Razazian / Sepideh Meidaninikjeh / Hamed Hosseini / Hamid Reza Jamshidi / Hasan Jalili / Asghar Abdoli

    Heliyon, Vol 9, Iss 3, Pp e14108- (2023)

    2023  

    Abstract: Over time, the antigenic evolution of emerging variants of SARS-CoV-2 has demanded the development of potential protective vaccines. Administration of additional doses of current vaccines based on the WT spike protein may boost immunity, but their ... ...

    Abstract Over time, the antigenic evolution of emerging variants of SARS-CoV-2 has demanded the development of potential protective vaccines. Administration of additional doses of current vaccines based on the WT spike protein may boost immunity, but their effectiveness has dwindled for patients with more recent variants. Here, we studied the neutralization activity of post-WT strain-based vaccination and a structural simulation in-silico based on the interactions of the RBD-hACE2 as the key to initiating infection among the VOCs of SARS-CoV-2. Our data display shows that WT sera showed a markedly greater reduction in Delta and Omicron, suggesting that the Wuhan-based vaccines may be more susceptible to breakthrough and new VOCs. According to the MD simulation, mutations of Omicron result in a significant change in the variant charge distribution throughout the binding interface that consequently alters the critical interface electrostatic potential in comparison to other variants. This observation provides new insights into immunization policy and next-generation vaccine development.
    Keywords SARS-CoV-2 ; Variants of concern ; Neutralizing antibody ; Molecular dynamic simulations ; Vaccine ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Human IL-2Rɑ subunit binding modulation of IL-2 through a decline in electrostatic interactions

    Arezoo Beig Parikhani / Kowsar Bagherzadeh / Rada Dehghan / Alireza Biglari / Mohammad Ali Shokrgozar / Farhad Riazi Rad / Sirous Zeinali / Yeganeh Talebkhan / Soheila Ajdary / Reza Ahangari Cohan / Mahdi Behdani

    PLoS ONE, Vol 17, Iss 2, p e

    A computational and experimental approach.

    2022  Volume 0264353

    Abstract: Although high-dose IL-2 has clear antitumor effects, severe side effects like severe toxicity and activation of Tregs by binding of IL-2 to high-affinity IL-2R, hypotension, and vascular leak syndrome limit its applications as a therapeutic antitumor ... ...

    Abstract Although high-dose IL-2 has clear antitumor effects, severe side effects like severe toxicity and activation of Tregs by binding of IL-2 to high-affinity IL-2R, hypotension, and vascular leak syndrome limit its applications as a therapeutic antitumor agent. Here in this study, a rational computational approach was employed to develop and design novel triple-mutant IL-2 variants with the aim of improving IL-2-based immunotherapy. The affinity of the mutants towards IL-2Rα was further computed with the aid of molecular dynamic simulations and umbrella sampling techniques and the obtained results were compared to those of wild-type IL-2. In vitro experiments by flow cytometry showed that the anti-CD25 mAb was able to bind to PBMC cells even after mutant 2 preincubation, however, the binding strength of the mutant to α-subunit was less than of wtIL-2. Additionally, reduction of IL-2Rα subunit affinity did not significantly disturb IL-2/IL2Rβγc subunits interactions.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Destruction mechanisms of ozone over SARS-CoV-2

    Angila Ataei-Pirkooh / Ali Alavi / Mehran Kianirad / Kowsar Bagherzadeh / Alireza Ghasempour / Omid Pourdakan / Reza Adl / Seyed Jalal Kiani / Mehdi Mirzaei / Bita Mehravi

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 10

    Abstract: Abstract In this pandemic SARS-CoV-2 crisis, any attempt to contain and eliminate the virus will also stop its spread and consequently decrease the risk of severe illness and death. While ozone treatment has been suggested as an effective disinfection ... ...

    Abstract Abstract In this pandemic SARS-CoV-2 crisis, any attempt to contain and eliminate the virus will also stop its spread and consequently decrease the risk of severe illness and death. While ozone treatment has been suggested as an effective disinfection process, no precise mechanism of action has been previously reported. This study aimed to further investigate the effect of ozone treatment on SARS-CoV-2. Therefore, virus collected from nasopharyngeal and oropharyngeal swab and sputum samples from symptomatic patients was exposed to ozone for different exposure times. The virus morphology and structure were monitored and analyzed through Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), Atomic Absorption Spectroscopy (AAS), and ATR-FTIR. The obtained results showed that ozone treatment not only unsettles the virus morphology but also alters the virus proteins’ structure and conformation through amino acid disturbance and Zn ion release from the virus non-structural proteins. These results could provide a clearer pathway for virus elimination and therapeutics preparation.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Large Scale Screening of Commonly Used Iranian Traditional Medicinal Plants against Urease Activity

    Farzaneh Nabati / Faraz Mojab / Mehran Habibi-Rezaei / Kowsar Bagherzadeh / Massoud Amanlou / Behnam Yousefi

    DARU : Journal of Pharmaceutical Sciences, Vol 20, Iss October, Pp 1-

    2012  Volume 18

    Abstract: Background and purpose of the study:H. pylori infection is an important etiologic impetus usually leading to gastric disease andurease enzyme is the most crucial role is to protect the bacteria in the acidic environment of the stomach. Then urease ... ...

    Abstract Background and purpose of the study:H. pylori infection is an important etiologic impetus usually leading to gastric disease andurease enzyme is the most crucial role is to protect the bacteria in the acidic environment of the stomach. Then urease inhibitors would increase sensitivity of the bacteria in acidic medium.Methods:137 Iranian traditional medicinal plants were examined against Jack bean urease activity by Berthelot reaction. Each herb was extracted using 50% aqueous methanol. The more effectiveextracts were further tested and their IC50 values were determined.Results:37 plants out of the 137 crude extracts revealed strong urease inhibitory activity (more than 70% inhibition against urease activity at 10 mg/ml concentration). Nine of the whole studiedplants crude extracts were found as the most effective with IC50 values less than 500 μg/ml including; Rheum ribes, Sambucus ebulus, Pistachia lentiscus, Myrtus communis, Areca catechu, Citrus aurantifolia, Myristica fragrans, Cinnamomum zeylanicum and Nicotianatabacum.Conclusions:The most potent urease inhibitory was observed for Sambucus ebulus and Rheum ribes extracts with IC50 values of 57 and 92 μg/ml, respectively.
    Keywords Urease Inhibitor ; Iranian Traditional Medicinal Plants ; Sambucus Ebulus ; Rheum Ribes ; Screening of Natural Products ; Therapeutics. Pharmacology ; RM1-950 ; Medicine ; R ; DOAJ:Therapeutics ; DOAJ:Medicine (General) ; DOAJ:Health Sciences ; Pharmacy and materia medica ; RS1-441 ; DOAJ:Pharmacy and materia medica
    Subject code 540
    Language English
    Publishing date 2012-10-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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