Browsing by Author "Rafienia, M."
Now showing 1 - 2 of 2
Results Per Page
Sort Options
Item Open Access In silico activity of AS1411 aptamer against nucleolin of cancer cells(Iranian Pediatric Hematology and Oncology Society, 2020) Farahbakhsh, Z.; Zamani, M. R.; Rafienia, M.; Gülseren, Oğuz; Mirzaei, M.Background: It has been expected that AS1411 aptamer could work against the cancer cells. Although the general information is available, there is still lack of details for the purpose. Therefore, activity of AS1411 aptamer against the nucleolin (NCL) target of cancer cells has been investigated in current work at the molecular scale. In addition, the same features have been also investigated for examining the activity of AT11, one of AS1411 derivatives. Methods: This work has been done employing in silico Molecular Docking simulations. Ten starting 3D configurations have been considered for each aptamer to be docked against the NCL target. Conformational search processes of ligands against the target indicated that the starting configuration of ligand could play an important role in determining the final complex formation in both of quantitative and qualitative aspects. Results: A04 and B01 are those starting configurations of AS1411 and AT11 making the strongest complexes with the NCL target among other ligands. The analyses indicated that the complexes of AT11 are slightly stronger than those of AS1411, in which the NCL target structure is more involved in the chelated complexes with the AT11 in comparison with the AS1411. Conclusion: AS1411 and AT11 are specified for targeting the NCL of cancer cells for the diagnosis and therapeutic purposes. They have reasonable binding affinity and could work as possible inhibitors of NCL.Item Open Access Nanocarbon-assisted biosensor for diagnosis of exhaled biomarkers of lung cancer: DFT approach(Sami Publishing Company, 2021-03) Mirzaei, M.; Gülseren, Oğuz; Rafienia, M.; Zare, A.Density functional theory (DFT) calculations were performed to investigate a nanocarbon-assisted biosensor for diagnosis of exhaled biomarkers of lung cancer. To this aim, an oxidized model of C20 fullerene (OC) was chosen as the surface for adsorbing each of five remarkable volatile organic compounds (VOC) biomarkers including hydrogen cyanide, methanol, methyl cyanide, isoprene, and 1-propanol designated by B1-B5. Geometries of the models were first optimized to achieve the minimum energy structures to be involved in further optimization of B@OC bi-molecular complexes. The relaxation of B counterparts at the surface of OC provided insightful information for capability of the investigated system for possible diagnosis of such biomarkers. In this case, B1 was placed at the highest rank of adsorption to make the strongest B1@OC complex among others whereas the weakest complex was seen for B4@OC complex. The achievement was very much important for differential detection of each of VOC biomarkers by the investigated OC nanocarbon. Moreover, the recorded infrared spectra indicated that the complexes could be very well recognized in complex forms and also among other complexes. As a final remark, such proposed nanocarbon-assisted biosensor could work for diagnosis of remarkable VOC biomarkers of lung cancer.