New Protocol for Scanning Minor and Major Grooves Along DNA to Find Best Interaction Mode With Drug Molecules

Gülkaya, Aybüke
Major and minor groove binder drugs could function as possible treatment agents in genetic disorders or cancer. DNA is recognized by different proteins during replication, translation, and transcription. Basically, by binding to the grooves of DNA, small drug molecules can change the helical structure of DNA, interfere with protein binding and prevent replication, translation or transcription. To alter and inhibit DNA - protein interactions, especially sequence specific ligands should be designed. Accordingly, we investigated the interactions of different anticancer drugs binding to specific DNA sequences via minor or major grooves by a novel, automatizated protocol as a combination of docking and molecular mechanics refinement. With this methodology, we obtained best interaction modes of the drug molecules with given DNA sequences and most preferred sequences.


Comparison of trace metal concentrations in malign and benign human prostate
Yaman, Mehmet; Atici, Demet; Bakirdere, Sezgin; Akdeniz, Ismail (American Chemical Society (ACS), 2005-01-27)
Imbalance in the composition of trace metals, recognized to be essential to normal human homeostasis, besides the accumulation of potentially toxic or nonessential trace metals, may cause disease. Thus, there is a need for their analysis in cancerous and noncancerous human tissues to examine the relationship between cancer and these elements. Trace metal concentrations including Cd, Ni, Zn, Cu, Fe, Mg, and Ca in both malign and benign prostate samples were determined by atomic absorption spectrophotometry. ...
New Steroidal 4-Aminoquinolines Antagonize Botulinum Neurotoxin Serotype A in Mouse Embryonic Stem Cell Derived Motor Neurons in Postintoxication Model.
Konstantinović, J; Kiriş, Erkan; Kota, KP; Kugelman-Tonos, J; Videnović, M; Cazares, LH; Terzić, Jovanović; Verbić, TŽ; Andjelković, B; Duplantier, AJ; Bavari, S; Šolaja, BA (American Chemical Society (ACS), 2018-02-22)
The synthesis and inhibitory potencies against botulinum neurotoxin serotype A light chain (BoNT/A LC) using in vitro HPLC based enzymatic assay for various steroidal, benzothiophene, thiophene, and adamantane 4-aminoquinoline derivatives are described. In addition, the compounds were evaluated for the activity against BoNT/A holotoxin in mouse embryonic stem cell derived motor neurons. Steroidal derivative 16 showed remarkable protection (up to 89% of uncleaved SNAP-25) even when administered 30 min postin...
Structural and functional characterization of simvastatin-induced myotoxicity in different skeletal muscles
Ozek, Nihal Simsek; Bal, I. Burak; SARA, MEHMET YILDIRIM; Onur, Rustu; Severcan, Feride (Elsevier BV, 2014-01-01)
Background: Statins are the most commonly used drugs for the treatment of hypercholesterolemia. Their most frequent side effect is myotoxicity. To date, it remains unclear whether statins preferentially induce myotoxicity in fast- or in slow-twitch muscles. Therefore, we investigated these effects on fast- (extensor digitorum longus; EDL), slow- (soleus; SOL), and mixed-twitch muscles (diaphragm; DIA) in rats by comparing their contractile and molecular structural properties.
Multifaceted Transport Characteristics of Nanomedicine: Needs for Characterization in Dynamic Environment
Özçelikkale, Altuğ; Han, Bumsoo (American Chemical Society (ACS), 2013-06-01)
Nanomedicine for cancer, where nanoparticles (NPs) are used to deliver drugs, imaging agents, and heat to tumors, shows great potential of improved therapeutic outcomes. In spite of promising early stage results, its clinical efficacy is still significantly limited due to complex transport barriers in vivo. These transport barriers are associated with tumor microenvironment, which is highly complex and heterogeneous and varies spatiotemporally. Thus, in order to improve the in vivo efficacy of nanomedicine,...
Improving the sub-cortical gm segmentation using evolutionary hierarchical region merging
Çiftçioğlu, Mustafa Ulaş; Gökçay, Didem; Department of Medical Informatics (2011)
Segmentation of sub-cortical Gray Matter (GM) structures in magnetic resonance brain images is crucial in clinic and research for many purposes such as early diagnosis of neurological diseases, guidance of surgical operations and longitudinal volumetric studies. Unfortunately, the algorithms that segment the brain into 3 tissues usually suffer from poor performance in the sub-cortical region. In order to increase the detection of sub-cortical GM structures, an evolutionary hierarchical region merging approa...
Citation Formats
A. Gülkaya, “New Protocol for Scanning Minor and Major Grooves Along DNA to Find Best Interaction Mode With Drug Molecules,” M.S. - Master of Science, Middle East Technical University, 2022.