A5025292130- Protein Structure and Dynamics
- Cellular transport and secretion
- Click Chemistry and Applications
- Computational Drug Discovery Methods
- Quinazolinone synthesis and applications
- Enzyme Structure and Function
- Genetics and Neurodevelopmental Disorders
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- Chronic Myeloid Leukemia Treatments
- Endoplasmic Reticulum Stress and Disease
- Monoclonal and Polyclonal Antibodies Research
- RNA regulation and disease
- Pharmacological Effects of Natural Compounds
- Synthesis and Characterization of Heterocyclic Compounds
- Receptor Mechanisms and Signaling
- Phenothiazines and Benzothiazines Synthesis and Activities
- Neuroscience and Neural Engineering
- Protein Kinase Regulation and GTPase Signaling
- Cardiac electrophysiology and arrhythmias
- Acute Lymphoblastic Leukemia research
- Cancer therapeutics and mechanisms
- Drug Transport and Resistance Mechanisms
- Fungal and yeast genetics research
- Families in Therapy and Culture
Istanbul Bilgi University
2021-2024
Saarland University
2012-2017
Koç University
2011
Hydrophilic protein-protein interfaces constitute a major part of all and are thus great importance. However, the quantitative characterization their association is still an ongoing challenge driving force behind remains poorly characterized. Here, we have addressed hydrophilic proteins role water by means extensive molecular dynamics simulations in explicit using three well studied protein complexes; Barnase-Barstar, cytochrome c-cytochrome c peroxidase, N-terminal domain enzyme...
The Sec61 channel mediates protein translocation across the endoplasmic reticulum (ER) membrane during secretory biogenesis, and likely also export of misfolded proteins for ER-associated degradation (ERAD). mechanisms opening different modes are not understood so far, but position large ER-lumenal loop 7 Sec61p suggests a decisive role. We show here that Y345H mutation in L7 which causes diabetes mouse displays no ER import defects yeast, delay export. A complete deletion resulted viable,...
Histone modifications have great importance in epigenetic regulation. JMJD2A is a histone demethylase which selective for di- and trimethyl forms of residues Lys9 Lys36 3 tail (H3K9 H3K36). We present molecular dynamics simulations mono-, trimethylated tails complex with catalytic domain to gain insight into how discriminates between the methylation states H3K9. The methyl groups are located at specific distances orientations respect Fe(II) methylammonium binding pocket. For trimethyllysine...
In the crowded environment of cells, proteins frequently encounter other in many possible orientations. Most these encounters are short-lived because physicochemical properties two binding patches do not match. However, even for protein pairs that bind tightly, it is an easy task to find correct site on partner and align with it. So far well understood source interaction specificity favors a small set specific "native" interactions over multitude alternative We used molecular dynamics...
Abstract A series of novel 1,2,3,4‐tetrazines were designed and synthesized. 1 H‐NMR spectroscopy, 13 C NMR HRMS used to determine the structures this compounds. Computational approaches suggested that DHFR is a putative target for newly synthesized 11 Extensive molecular dynamics simulations followed by docking employed evaluate as potential protein. The anticancer activities compounds evaluated against five different types leukemia cell lines (Jurkat, Nalm‐6, Reh, K562, Molt‐4) one...
Precision oncology promises individually tailored drugs and clinical care for patients with cancer: That is, "the right drug, the patient, at dose, time." Although stratification of risk treatment resistance toxicity is key to precision oncology, there are multiple ways in which such can be achieved, example, genetic, functional pathway based, among others. Moving toward sorely needed case acute lymphoblastic leukemia (ALL) wherein adult display survival rates ranging from 30% 70%. The...
Abstract A series of novel maleimide derivatives were synthesized, with various heterocyclic compounds serving as side chains in the synthesis process. The structural characteristics these elucidated through application 1 H‐NMR spectroscopy, 13 C‐NMR (APT) and high‐resolution mass spectrometry (HRMS). anti‐cancer potential was subsequently assessed vitro, utilizing two distinct breast cancer cell lines, namely MDA‐MB‐231 MCF‐7, via MTT assay. Among 12 newly synthesized compounds, 4 a , b c d...
It is estimated that approximately one in every 100 children diagnosed with autism spectrum disorder (ASD) around the globe. Currently, there are no curative pharmacological treatments for ASD. Discoveries on key molecular mechanisms of ASD essential precision medicine strategies. Considering atypical brain connectivity patterns have been observed individuals ASD, this study examined connectivity-associated genes and their putatively distinct expression samples from using an iterative...
The structural analysis of protein-protein interactions and the prediction their functional properties are important areas in modern bioinformatics. First, we review concepts for classifying interactions, analyzing geometry composition binding interfaces. Next, computational methods discussed that allow predicting hot-spot residues kinetics rmodynamics binding. Then, focus on mode action small molecule effectors may either act as competitive antagonists protein binders or allosteric...
Abstract Different derivatives of imatinib, the first targeted BCR-ABL fusion tyrosine kinase inhibitor, were synthesized by a 3-step reaction method. Firstly, benzamide derivative was obtained then aryl piperazine groups or morpholine linked S N 2 reaction. Lastly, palladium catalyzed C-N coupling conducted with hetaryl amine groups. The structures new compounds characterized spectroscopic methods. For quantitative evaluation biological activity compounds, MTT assays performed, where four...
Different derivatives of imatinib were synthesized by a 3-step reaction method. The structures the new compounds characterized spectroscopic methods. For quantitative evaluation biological activity compounds, MTT assays performed, where four BCR-ABL negative leukemic cell lines (Jurkat, Reh, Nalm-6 and Molt-4), one positive line (K562), non-leukemic (Hek293T) incubated with various concentrations derivatives. Although was specifically designed for protein, our results showed that it also...