Dr. Gözde Yalçın Özkat
Molecular Simulations and Design
Curriculum Vitae
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1. Personal profile
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Surname |
Yalçın Özkat |
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First name |
Gözde |
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Date of birth |
31.10.1988 |
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Address |
Recep Tayyip Erdogan University, Faculty of Engineering, Bioengineering Department, Rize 53100, Turkey |
2. Researcher profile
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Researcher ID |
B-8759-2017 |
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Scopus Author ID |
57188733064 |
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ORCID ID |
0000-0002-9689-2239 |
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Google Scholar |
https://scholar.google.com.tr/citations?user=2SSTD-IAAAAJ&hl=tr |
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ResearchGate |
https://www.researchgate.net/profile/Goezde_Yalcin2 |
3. Education
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PhD education |
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Dates: from-to |
2013-2018 |
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Institution |
Ankara University Biotechnology Institute |
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Country of Institution |
TURKEY |
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Project title |
Development of New Leader Compounds Intended to Treatment of Alzheimer's Disease |
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PI/supervisor |
Prof. Dr. Ilkay Yildiz |
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Research description (100 words) |
This thesis aims to develop new leader drug molecules for Alzheimer’s Diseases (AD). β secretase1 (BACE1) and Glycogen Synthase Kinase 3β (GSK3β) are effective receptors in important mechanisms for AD and they are basic targets for drug design studies. I worked on a multi-target drug that could inhibit BACE1 and GSK3β. For this purpose, I used computational methods, such as homology modeling, structure, and ligand-based drug design, molecular docking, and molecular dynamics simulations. Pharmacophore Hypotheses were generated by “Common Feature Pharmacophore Generation” and “3D QSAR Pharmacophore Generation” methods by Discovery Studio Client (DSC) Molecular Modeling Program. Molecular docking studies were performed by CDOCKER module of DSC and AutoDock Vina programs. Also, AMBER Molecular Dynamics Program was used for molecular dynamics simulations of ligand-receptor interactions. |
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MSc Education |
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Dates: from-to |
2011-2013 |
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Institution |
Ankara University Biotechnology Institute |
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Country of Institution |
TURKEY |
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Project title |
In Vitro Shoot Regeneration in Different Cotton Cultivars. |
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PI/supervisor |
Prof. Dr. Sebahattin ÖZCAN |
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DOI |
DOI:10.13140/RG.2.2.20812.41602 |
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Dates: from-to |
2007-2011 |
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Institution |
Ege University, Faculty of Engineering, Bioengineering |
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Country of Institution |
TURKEY |
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Project title |
Researches on the solving of the browning on the mastic tree explants on in vitro |
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PI/supervisor |
Prof. Dr. Aynur GÜREL |
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DOI |
DOI:10.13140/RG.2.2.30878.74568 |
4. Work Experience
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Dates: from-to |
Sept 2013-Dec 2018 |
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Institution |
Ankara University, Department of Biotechnology, Turkey |
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Position |
Research Assistant |
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Dates: from-to |
Jan 2019-Oct 2019 |
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Institution |
Recep Tayyip Erdogan University, Bioengineering Department, Turkey |
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Position |
Research Assistant |
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Dates: from-to |
Oct 2019-Present |
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Institution |
Recep Tayyip Erdogan University, Bioengineering Department, Turkey |
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Position |
Assistant Professor |
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Dates: from-to |
July 2021- March 2022 |
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Institution |
Max-Planck-Institute for Dynamics of Complex Technical Systems, Germany |
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Position |
Post- Doctoral Researcher |
5. Other research or relevant work experience
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Dates: from-to |
July 2021 – Present |
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Details (100 words) |
Max-Planck-Institute for Dynamics of Complex Technical Systems, Germany Quantum Mechanical Approaches to Drug Discovery Studies For Alzheimer’s Diseases The GFN2-xTB semi-empirical tight bond model quantum chemistry method was implemented on 1000 atoms in the binding pocket of GSK3β enzyme and ligand. |
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Dates: from-to |
Jan 2018 – Dec 2019 |
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Details (100 words) |
Recep Tayyip Erdogan University, Bioengineering Department, Turkey Molecular Docking Studies with Human COX1 Enzyme Inhibitors (Benzothiazolinone acetamide analogs). CDOCKER module of DSC program was used for molecular docking studies. |
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Article |
Spectroscopic, quantum mechanical studies, ligand protein interactions and photovoltaic efficiency modeling of some bioactive benzothiazolinone acetamide analogs (https://link.springer.com/article/10.1007/s11696-019-01047-7) |
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Dates: from-to |
Oct 2018 – Jan 2020 |
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Details (100 words) |
Recep Tayyip Erdogan University, Bioengineering Department, Turkey Molecular Docking Studies with DNA-gyrase AND FtsA Enzyme Inhibitors (Benzamides). AutoDock Vina program was used for molecular docking studies. |
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Article |
Synthesis and molecular docking studies of some novel antimicrobial benzamides (https://doi.org/10.1016/j.bioorg.2019.103368) |
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Dates: from-to |
Oct 2016 – Dec 2018 |
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Details (100 words) |
Ankara University, Department of Biotechnology, Turkey Molecular Docking Studies with Decaprenylphoshoryl-D-ribose oxidase Enzyme Inhibitors (Chalcone and Benzimidazole Derivatives). CDOCKER module of DSC and AutoDock Vina programs were used for molecular docking studies. Molecular dynamic simulations were implemented by AMBER. |
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Article |
Molecular docking studies on fluoro-substituted chalcones as potential DprE1 enzyme inhibitors” was pressed in Journal of Molecular Structure. |
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Dates: from-to |
Jan 2016 – July 2017 |
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Details (100 words) |
Ankara University, Department of Biotechnology, Turkey Molecular Docking Studies between benzoxazole derivatives and GyrB complex |
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Article |
Modification of benzoxazole derivative by bromine-spectroscopic, antibacterial and reactivity study using experimental and theoretical procedures |
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Dates: from-to |
Jan 2016 – Mar 2016 |
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Details (100 words) |
Ankara University, Department of Biotechnology, Turkey Molecular docking studies with the cyclin D1-cyclin-dependent kinases (CDK4, CDK5, CDK6) AutoDock Vina program was used for understanding of the binding profile of new drug molecules. Chimera and DSC were used for virtual screening. |
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Dates: from-to |
Sep 2015 – May 2016 |
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Details (100 words) |
Ankara University, Department of Biotechnology, Turkey Molecular docking study of 5-Nitro-2-phenoxymethyl benzimidazole AutoDock Vina program was used for molecular docking studies. Chimera and DSC were used for virtual screening. |
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Article |
Vibrational spectroscopic analysis, molecular dynamics simulations and molecular docking study of 5-Nitro-2-phenoxymethyl benzimidazole |
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Dates: from-to |
Sep 2015 – Dec 2018 |
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Details (100 words) |
Ankara University, Department of Biotechnology, Turkey Homology Modelling of Topo izomeraz II-α. Discovery Studio Client was used for the insertion of lack aminoacid residues. Molecular Dynamics Simulation was implemented for the formation of α helix and β sheet structure of these residues. Validation of tertiary structure was done by QMEAN Server in Swiss-Model. |
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Article |
Preparing for publication |
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Dates: from-to |
Nov 2014 – May 2016 |
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Details (100 words) |
Ankara University, Department of Biotechnology, Turkey Molecular Dynamics Simulations between LyP-1 and p32 MM-PBSA and ALA-SCAN analysis were used by AMBER Molecular Dynamics Simulation Package. For these purpose 100 ns simulation with explicit solvent was conducted by AMBER. Chosen residues which effects binding properties were subjected to ALA-SCAN analysis to understand the interaction mechanism of LyP-1 and p32. |
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Article |
Molecular Dynamics, Thermodynamic and Mutational Binding Studies for Tumor Specific LyP-1 in Complex with p32 (https://www.tandfonline.com/doi/full/10.1080/07391102.2017.1313779) |
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Dates: from-to |
Nov 2014 – Jun 2015 |
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Details (100 words) |
Mevlana University, Faculty of Medicine, Turkey A Mechanistic Approach: Conformational Changes of the G Protein-Coupled Dopaminergic D2 Receptors by the Binding of Agonists, Antagonists and Inverse agonists Dopaminergic D2 Receptor was embedded to membrane (POPC, POPE, CHL) with CHARMM membrane builder. Membrane-receptor-ligand complex system, which includes nearly 150000 atoms, was simulated with implicit solvents for 70 ns with AMBER Molecular Dynamics Simulation Package. |
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Article |
Preparing for publication |
6. Awards or Fellowships
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Date |
July 2018 |
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Description |
18TH FEBS YOUNG SCIENTIST FORUM (YSF) GRANT Given by: THE FEDERATION OF EUROPIAN BIOCHEMICAL SOCIETIES This financial support for participation in YSF and ensuing Congress to those selected to take part in YSF, via YSF grants. Grant will cover registration, accommodation and travel costs to Prague. |
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Date |
March 2017 |
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Description |
5th DRUG CHEMISTRY CONGRESS POSTER AWARD Given by: ATATURK UNIVERSITY/TURKEY “Some New Benzoxazoles as Topoisomerase II Inhibitors” |
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Dates: from-to |
Nov 2014 – May 2015 |
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Description |
SCHOLARSHIP HOLDER Given by: THE SCIENTIFIC AND TECHNOLOGICAL RESEARCH COUNCIL OF TURKEY Design, synthesis and anticancer effects on cancer stem cells of novel 1-(2- methylthio-10H-phenothiazine-10-yl-propyl)pyrimidine-2,4(1H,3H)-dione 2- (2-methylthio-10H-phenothiazine-10-yl-propyl)pyrimidine-2,4(1H,3H)-dione phenothiazine compounds |
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Date |
December- 2013 |
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Description |
PATENT SUPPORT Given by: THE SCIENTIFIC AND TECHNOLOGICAL RESEARCH COUNCIL OF TURKEY Patent Name: Effective compound in anticancer therapy Patented by: Turkish Patent and Trademark Office Explanation: New lead drug molecules as dopaminergic 2 receptor inhibitors. |
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Date |
2012-present |
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Description |
TEACHING STAFF TRAINING PROGRAM Given by: HIGHER EDUCATION COUNCIL OF TURKEY My MSc and PhD educations were supported by this program with full scholarship. |
7. Publications
Journal Publications
1. Esin Karatas, Egemen Foto, Tugba Ertan-Bolelli, Gozde Yalcin-Ozkat, Serap Yilmaz, Sanaz Ataei, Fatma Zilifdar, Ilkay Yildiz: Discovery of 5-(or 6)-benzoxazoles and oxazolo[4,5-b]pyridines as novel candidate antitumor agents targeting hTopo IIa. Bioorganic Chemistry, Volume 112, 104913, ISSN 0045-2068, (2021). https://doi.org/10.1016/j.bioorg.2021.104913.
2. Serdar Burmaoglu, Arzu Gobek, Busra Ozturk Aydin, Emine Yurtoglu, Busra Nur Aydin, Gozde Yalcin Ozkat, Ceylan Hepokur, Nihal Simsek Ozek, Ferhunde Aysin, Ramazan Altundas, Oztekin Algul: Design, synthesis and biological evaluation of novel bischalcone derivatives as potential anticancer agents. Bioorganic Chemistry, Volume 111, 104882, ISSN 0045-2068, (2021). https://doi.org/10.1016/j.bioorg.2021.104882.
3. Cemre Acar, Gozde Yalçın, Tuğba Ertan-Bolelli, Fatma Kaynak Onurdağ, Suzan Ökten, Funda Şener, İlkay Yıldız: Synthesis and molecular docking studies of some novel antimicrobial benzamides. Bioorganic Chemistry, Volume 94, 103368, (2020). https://doi.org/10.1016/j.bioorg.2019.103368.
4. Mary, Y.S., Yalcin, G., Mary, Y.S. et al. Spectroscopic, quantum mechanical studies, ligand protein interactions and photovoltaic efficiency modeling of some bioactive benzothiazolinone acetamide analogs. Chem. Pap. 74, 1957–1964 (2020). https://doi.org/10.1007/s11696-019-01047-7
5. GOZDE YALCIN, Serdar Burmaoglu, Ilkay Yildiz, Oztekin Algul: Molecular docking studies on fluoro-substituted chalcones as potential DprE1 enzyme inhibitors. Journal of Molecular Structure 07/2018;, DOI:10.1016/j.molstruc.2018.02.087
6. Turkan Toka Ozer, Alper Karagoz, GOZDE YALCIN, Cenk A. Andac: Determination of Antibiotic Resistance and Pulsed-Field Gel Electrophoresis Profiles for the Extended-Spectrum β-Lactamase Producing Escherichia coli. Jundishapur Journal of Microbiology 02/2018; In Press(In Press)., DOI:10.5812/jjm.57878
7. V.V. Aswathy, Sabiha Alper-Hayta, GÖZDE YALCIN, Y. Sheena Mary, C. Yohannan Panicker, P.J. Jojo, Fatma Kaynak-Onurdag, Stevan Armaković, Sanja J. Armaković, Ilkay Yildiz, C. Van Alsenoy: Modification of benzoxazole derivative by bromine-spectroscopic, antibacterial and reactivity study using experimental and theoretical procedures. DOI:10.1016/j.molstruc.2017.04.010
8. Selin Seda Timur, GÖZDE YALÇIN, Özge Çevik, Cenk Andaç, R. Neslihan Gürsoy: Molecular dynamics, thermodynamic, and mutational binding studies for tumor-specific LyP-1 in complex with p32. Journal of biomolecular Structure & Dynamics 04/2017; 36(5):1-11., DOI:10.1080/07391102.2017.1313779
9. Vidya V. Menon, Egemen Foto, Y. Sheena Mary, Esin Karatas, C. Yohannan Panicker, GÖZDE YALCIN, Stevan Armaković, Sanja J. Armaković, C. Van Alsenoy, Ilkay Yildiz: Vibrational spectroscopic analysis, molecular dynamics simulations and molecular docking study of 5-nitro-2-phenoxymethyl benzimidazole. Journal of Molecular Structure 02/2017; 1129:86-97., DOI:10.1016/j.molstruc.2016.09.059
10. Alper Karagöz, Mahmut Sunnetcioglu, Mehmet Resat Ceylan, Yasemin Bayram, GOZDE YALCIN, Nadir Kocak, Burak Suvak, Cenk A Andac: Characterisation of drug resistance of nosocomial ESBL-producing E. Coli isolates obtained from a Turkish university hospital between 2009 and 2012 by pulsed field gel electrophoresis and antibiotic resistance tests. Le infezioni in medicina: rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive 03/2016; 24(1):24-31.
11. Muhammad Aasim, Khalid Mahmood Khawar, GOZDE YALCIN, Allah Bakhsh: Current Trends In Fenugreek Bıotechnology And Approaches Towards Its Improvement. American Journal of Social Issues and Humanities, 128–136.
Conference Publications
Posters
1. Yalcin, G., Yildiz, I. (2018). Pharmacophore Generation Studies for the Discovery of Potential Glycogen Synthase Kinase 3β Enzyme Inhibitors. In The 43rd FEBS Congress. Prague.
2. Yalçin Gözde, Yildiz Ilkay (2017). Protoberberine Alkoloids As A Drug Candidate For Alzheimer’s Diseases. 2nd International Gazi Pharma Symposium Series (GPSS-2017)
3. Yalçin Gözde, Yildiz Ilkay (2017). Molecular modelling studies on Glycogen Synthase Kinase 3 Inhibitors for Alzheimer’s Diseases. 2nd International Gazi Pharma Symposium Series (GPSS- 2017)
4. Yalçin Gözde, Yildiz Ilkay (2017). Pharmacophore Generation Studies for the Discovery of Potential BACE1 Enzyme Inhibitors. 3rd International Turkic World Conferenceon Chemical Sciences Technologies
5. Karataş Esin, Foto Egemen, Yalçin Gözde, Zülifdar Fatma,Ertan Bolelli Tuğba,Yildiz Lkay (2017). New Nitro-Benzoxazoles as Antitumor Agents Targeting hTopo II. 17th Hellenic Symposium on Medicinal Chemistry: Designing targeted and safer drugs
6. Gözde Yalçin, İlkay Yıldız: P-03.03.2-004 Molecular binding profile of protoberberine alkoloids on amyloid precursor proteincleaving enzyme 1 (BACE1) as a drug candidate for Alzheimer’s diseases. 41st FEBS Congress, Molecular and Systems Biology for a Better Life; FEBS Journal. 2016. p. 1–6.
7. Yalçın G, Göbek A, Anıl DA, Burmaoğlu S, Algül Ö, Yıldız İ. PP-51 Molecular Docking Studies on Some Chalcone Derivatives as Possible Decaprenylphoshoryl-D-ribose oxidase (DprE1) Enzyme Inhibitors. 4th BAU Drug Des. Abstr. B. 2016. p. 155–6.
8. Gözde Yalçin, Cenk A. Andaç: LB-016 Inverse-agonistic mechanisms of thioridazine on Gi protein-coupled D2L dopamine receptors. 40th FEBS Congress, The Biochemical Basis of Life, Berlin, Germany; FEBS Journal. 2015. p. 1–2.
9. Yalçın G, Ataei S, Yıldız İ. PP – 84 Pharmacophore Generation Studies For The Discovery Of Potential Acetylcholinesterase. 3 th Int. BAU-DRUG Des. Symp. Nov. Methods Emerg. Targets Drug ABSTRACT B. 2015. p. 213–4.
10. Yalçın G, Andac CA. PP 51.Determination Of Binding Properties Of Butaclamol In Complex With A Membrane-Bound Human Gi-Coupled D2L Dopamine Receptor. 8th Eurasian Meet. Heterocycl. Chem. 2014. p. 239.
11. Yalçın G, Andac CA. P – 58 Investigation of Agonistic and Inverse-agonistic Effects on D2 Subtype Dopamine Receptors. 2 nd Int. BAU-DRUG Des. Symp. Nov. Methods Emerg. Targets Drug ABSTRACT B. 2014. p. 132.
Oral Presentations
1. YALCIN, G., ERSAN, R. H., ALGUL, O., & YILDIZ, I. (2018). DprE1-Benzimidazole Derivatives Interactions using Molecular Modelling. In Ramazan ALTUNDAŞ (Ed.), 6th Drug Chemistry Congress. Antalya. Retrieved from http://ilackongresi.org/
2. YALCIN, G., & YILDIZ, I. (2018). Computational Studies for Drug Design on Beta-secretase 1 Inhibition. In R. ALTUNDAŞ (Ed.), 6th Drug Chemistry Congress. Antalya. Retrieved from http://ilackongresi.org/
3. Yalcin, G., & Yildiz, I. (2018). Molecular Binding Profile of Protoberberine Alkaloids on Glycogen Synthase Kinase 3β as a Drug Candidate for Alzheimer’s Diseases. In M. Karatas (Ed.), International Molecular Biology and Biotechnology Congress. Konya. Retrieved from http://www.molbiotech.gen.tr/
4. Yalcin, G., & Yildiz, I. (2017). Molecular Docking Studies on Some Benzimidazole Derivatives as Possible Decaprenylphoshoryl-D-ribose oxidase Enzyme Inhibitors. In Ramazan ALTUNDAŞ (Ed.), 5th Drug Design Congress. Antalya.
5. Yalcin G, Andac CA. OP-3 Effect of spiperone binding on a membrane-bound human Gi-coupled D2L dopamine receptor. The 3rd International Conference of Organic Chemistry. 2014. p. 44.
6. Yalçın G, Andac CA. OP – 3 Homology Modelling and Explicit Solvent Molecular Dynamics of Stimulated Human Gi-coupled D2 Dopamine Receptor in a Membrane System. 2 nd Int. BAU- DRUG Des. Symp. Nov. Methods Emerg. Targets Drug ABSTRACT B. 2014. p. 44.
7. Yalçın G, Andac CA. ALA-SCAN mutational analysis on the agonist binding state of human Gi-coupled D2L dopamine receptor complex. Workshop and Summer School on Protein Structure, Function, and Dynamics, Antalya,TURKEY, 2014.
8. Citations
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Total Citations |
h index |
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WOS |
60 |
5 |
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SCOPUS |
70 |
6 |
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Scholar Google |
96 |
6 |
9. Skills & Activities
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Skills |
Molecular Dynamics, Docking Studies, Molecular Docking, Homology Modeling, Synthetic Biology, Bioinformatics and Computational Biology, Computer Aided Drug Design |
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Scientific Memberships |
Turkish Biochemical Society |
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Languages |
English (Fluent), Turkish (Native) |
10. References
Dr. Ilkay Yildiz (PhD supervisor)
Professor
Ankara University, Faculty of Pharmacy
Phone: +905335705033
E-mail: Ilkay.Yildiz@pharmacy.ankara.edu.tr, iyildiz@pharmacy.ankara.edu.tr
Dr. Hilal Ozdag (Vice Director of Biotechnology Institute)
Professor
Ankara University, Biotechnology Institute
Phone: +905333717401 Web: www.ozdaglab.com
E-mail: hilalozdag@gmail.com