Akdoğan, Ebru Demet

Profile Picture
Name Variants
Akdoğan, E.
Akdoğan, EBRU DEMET
E. D. Akdoğan
A., Ebru Demet
Ebru Demet Akdoğan
Akten E.
Akdoğan,E.D.
AKDOĞAN, EBRU DEMET
Akdogan,Ebru Demet
Akdogan,E.D.
Akdogan, Ebru Demet
Ebru Demet AKDOĞAN
E. Akdoğan
EBRU DEMET AKDOĞAN
Ebru Demet, Akdogan
Akdoğan, Ebru Demet
Akdoğan, E. D.
A.,Ebru Demet
AKDOĞAN, Ebru Demet
Demet Akdoğan, Ebru
Akten, Ebru Demet
Akdoğan, Ebru Demet
Akdoğan, Ebru Demet
Akdoğan, Demet Akten
Job Title
Prof. Dr.
Email Address
demet.akten@khas.edu.tr
Main Affiliation
Molecular Biology and Genetics
Status
Website
ORCID ID
0000-0002-0358-3171
Scopus Author ID
6507297154
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
AAG-7752-2019 
Scholarly Output

38

Articles

22

Citation Count

41

Supervised Theses

7

Filters

2012 - 20172
Reset filters

Settings

Author: Aviyente, Viktorya

Scholarly Output Search Results

Now showing 1 - 2 of 2
  • Thumbnail Image
    Article
    Citation - WoS: 1
    Citation - Scopus: 1
    Assessing Protein-Ligand Binding Modes With Computational Tools: the Case of Pde4b
    (Springer, 2017) Çifii, Gülşah; Akdoğan, Ebru Demet; Aviyente, Viktorya; Akten, Ebru Demet; Monard, Gerald
    In a first step in the discovery of novel potent inhibitor structures for the PDE4B family with limited side effects we present a protocol to rank newly designed molecules through the estimation of their IC values. Our protocol is based on reproducing the linear relationship between the logarithm of experimental IC values [(IC)] and their calculated binding free energies (). From 13 known PDE4B inhibitors we show here that (1) binding free energies obtained after a docking process by AutoDock are not accurate enough to reproduce this linear relationship
  • Thumbnail Image
    Article
    Citation - WoS: 5
    Citation - Scopus: 7
    Molecular Docking Study Based on Pharmacophore Modeling for Novel Phosphodiesteraseiv Inhibitors
    (Wiley-VCH Verlag GmbH, 2012) Cifci, Gulsah; Akdoğan, Ebru Demet; Aviyente, Viktorya; Akten, Ebru Demet
    In this study pharmacophore modelling was carried out for novel PhosphodiesteraseIV (PDEIV) inhibitors. A pharmacophore-based virtual screening which resulted in 1959 hit compounds was performed with six chemical databases. The pharmacophore screening was proven to be successful in discriminating active and inactive inhibitors using a set of compounds with known activity obtained from ChEMBL database. Furthermore the Lipinskis rule of five was applied for physicochemical filtering of the hit molecules and this yielded 1840 compounds. Three docking software tools AutoDock 4.0 AutoDock Vina and Gold v5.1 were used for the docking process. All 1840 compounds and the known selective inhibitor rolipram were docked into the active site of the target protein. A total of 234 compounds with all three scoring values higher than those of rolipram were determined with the three docking tools. The interaction maps of 14 potent inhibitors complexed with PDEIV B and D isoforms have been analyzed and seven key residues (Asn 395 Gln 443 Tyr 233 Ile 410 Phe 446 Asp 392 Thr 407) were found to interact with more than 80?% of the potent inhibitors. For each one of the 234 hit compounds using the bound conformation with the highest AutoDock score the interacting residues were determined. 117 out of 234 compounds are found to interact with at least five of the seven key residues and these were selected for further evaluation. The conformation with the highest AutoDock score for each 117 compounds were rescored using the DSX scoring function. This yielded a total of 101 compounds with better score values than the natural ligand rolipram. For ADME/TOX calculations the FAF-Drugs2 server was used and 32 out of 101 compounds were found to be non-toxic.