Araştırma Çıktıları

Permanent URI for this communityhttps://hdl.handle.net/11443/931

Browse

Subject: search.filters.subject.Homology modelling

Search Results

Now showing 1 - 2 of 2
  • No Thumbnail Available
    Item
    Cryo-EM density map fitting driven in-silico structure of human soluble guanylate cyclase (hsGC) reveals functional aspects of inter-domain cross talk upon NO binding
    (ELSEVIER SCIENCE INC, 2019-01-01) Khalid, Rana Rehan; Maryam, Arooma; Fadouloglou, Vasiliki E.; Siddiqi, Abdul Rauf; Zhang, Yang
    The human soluble Guanylate Cyclase (hsGC) is a heterodimeric heme-containing enzyme which regulates many important physiological processes. In eukaryotes, hsGC is the only known receptor for nitric oxide (NO) signaling. Improper NO signaling results in various disease conditions such as neuro-degeneration, hypertension, stroke and erectile dysfunction. To understand the mechanisms of these diseases, structure determination of the hsGC dimer complex is crucial. However, so far all the attempts for the experimental structure determination of the protein were unsuccessful. The current study explores the possibility to model the quaternary structure of hsGC using a hybrid approach that combines state-of-the-art protein structure prediction tools with cryo-EM experimental data. The resultant 3D model shows close consistency with structural and functional insights extracted from biochemistry experiment data. Overall, the atomic-level complex structure determination of hsGC helps to unveil the inter-domain communication upon NO binding, which should be of important usefulness for elucidating the biological function of this important enzyme and for developing new treatments against the hsGC associated human diseases. (C) 2019 Elsevier Inc. All rights reserved.
  • No Thumbnail Available
    Item
    An integrated approach towards the development of novel antifungal agents containing thiadiazole: synthesis and a combined similarity search, homology modelling, molecular dynamics and molecular docking study
    (SPRINGEROPEN, 2018-01-01) Er, Mustafa; Abounakhla, Abdulati Miftah; Tahtaci, Hakan; Bawah, Ali Hasin; Cinaroglu, Suleyman Selim; Onaran, Abdurrahman; Ece, Abdulilah
    BackgroundThis study aims to synthesise and characterise novel compounds containing 2-amino-1,3,4-thiadiazole and their acyl derivatives and to investigate antifungal activities. Similarity search, molecular dynamics and molecular docking were also studied to find out a potential target and enlighten the inhibition mechanism.ResultsAs a first step, 2-amino-1,3,4-thiadiazole derivatives (compounds 3 and 4) were synthesised with high yields (81 and 84\%). The target compounds (6a-n and 7a-n) were then synthesised with moderate to high yields (56-87\%) by reacting 3 and 4 with various acyl chloride derivatives (5a-n). The synthesized compounds were characterized using the IR, H-1-NMR, C-13-NMR, Mass, X-ray (compound 7n) and elemental analysis techniques. Later, the in vitro antifungal activities of the synthesised compounds were determined. The inhibition zones exhibited by the compounds against the tested fungi, their minimum fungicidal activities, minimum inhibitory concentration and the lethal dose values (LD50) were determined. The compounds exhibited moderate to high levels of activity against all tested pathogens. Finally, in silico modelling was used to enlighten inhibition mechanism using ligand and structure-based methods. As an initial step, similarity search was carried out and the resulting proteins that belong to Homo sapiens were used as reference in sequence similarity search to find the corresponding amino acid sequences in target organisms. Homology modelling was used to construct the protein structure. The stabilised protein structure obtained from molecular dynamics simulation was used in molecular docking.ConclusionThe overall results presented here might be a good starting point for the identification of novel and more active compounds as antifungal agents.