Teaching Experience

Teaching Experience

TEACHING EXPERIENCE / LEADERSHIP ACTIVITIES IN THE RESEARCH DOMAIN


Participation in Training Activities

Supervised PhD projects at the University of Calgary, Dept. of Bio Sci. “The construction of the open, closed and open-inactivated states of 3D homology models of hERG ion channels” and “Molecular Mechanisms of high-affinity blockers at the different states of hERG ion channels”.

Supervised PhD projects at the BAU School of Medicine.

Supervised 6 students on short-term research projects (1. Mr. Trevor Randal, Research Project: “The Pharmacophore Models of hERG Potassium Ion Channels” May 2010 - September 2010; and May 2011- September 2011, University of Calgary, Dept. of Bio Sci.; 2. Mr. Orhan Yasar, Research Project: “Parameterization of Structural and Dynamics Properties of Li+ and Ca2+ ions” July 2010 – September 2010; University of Calgary, Dept. of Bio Sci.; 3. Mr. Konstantinos Thanapoulos, B.Sc., Research Project: “In Silico Rational Drug Design Techniques in GPCRs” September 2008 – April 2009, National Hellenic Research Foundation, Athens; 4. Mr. Yiannis Xenos, B.Sc., Research Project: “In Silico Rational Drug Design Studies in anti-HIV Drugs” September 2008 – April 2009, National Hellenic Research Foundation, Athens; 5. Matthew Patterson, Research Project: “Ligand-based potassium channel activators design” May 2011-present, University of Calgary, Dept. of Bio Sci. 6. Ms. Elisha Chapman, Research Project: Homology modeling and drug-target interactions for human neuronal glutamate transporters January 2011 - May 2011, University of Calgary, Dept. of Bio. Sci.).


Training Education/Formation

I attended and completed successfully “Instructional Skills Workshop” at the Teaching and Learning Centre of the University of Calgary (24 hours, March 2010).


Teaching Activities:

@BAU School of Medicine: I gave several lectures ("Biophysics", "Bioinformatics", "Mol. Pharmacology", "Molecular Simulations in Drug Design") in School of Medicine; "Special Topics in Bioinformatics" for Molecular Biology and Genetics students and "Chemistry of Life" and "Clinical Engineering" for Biomedical Engineering students.

@University of Calgary: I gave lectures in “Molecular Biophysics” -a graduate students level course- as guest lecturer. In these lectures, thermodynamics of the folding process in proteins, toy protein model, partition function, structural basis of action potential are covered.

@NHRF: I gave several departmental lectures and seminars on computer-aided drug design techniques. In addition, I assisted several undergraduate and graduate students in their projects both in theory and applications.

@Bilkent University: I taught “Laboratory of General Chemistry-I and II” courses as TA at the Bilkent University, Ankara (September 2002-September 2004). Students were 1st year undergraduates from three departments (Chemistry, Physics and Molecular Biology and Genetics).

Participation as External Reviewer

I am reviewing about 40 papers per year for the articles submitted to the journals at the field of Medicinal Chemistry, Molecular Modeling, Quantum Chemistry, Structural Biology, Computational Chemistry and Biophysics. (i.e., J. Chem. Inf. Model.; Biophys. J.; Eur. Biophys. J.; Curr. Med. Chem.; J. Enzy. Inh. Med. Chem, Bioorg. Med. Chem, Bioorg Med Chem Lett.; Inorg. Chem.; J. Mol. Model.; J. Comput. Aid. Mol. Des., etc.)


Membership
Biophysical Society (BPS)
American Association for Cancer Research (AACR)
American Society of Gene & Cell Therapy (ASGCT)
American Chemical Society (ACS)
Canadian Society for Chemistry
EU Marie Curie Assoc.

Editor
All Life
https://www.tandfonline.com/toc/tfls21/current

Editorial Board
Journal of Enzyme Inhibition and Medicinal Chemistry (2011- current)
E Journal of Chemistry (2012- current)
Biochem Pharmacol. (2012- current)
Turkish Journal of Chemistry (2013- current)
Frontiers in Medicinal and Pharmaceutical Chemistry  (2014 -current)
BMC Pharmacology and Toxicology (2014- current)
Current Enzyme Inhibition (2015 -current)
Turkish Journal of Biology (2017 -current)



Supervised PhD theses:

  • Beril Çolak Günay (2024). Investigation of the mechanisms of hERG1 blocker toxins as anti-cancer agent with molecular modeling techniques — Thesis No: 876534 

  • İsmail Erol (2023). Investigation of dimerization in angiotensin receptors by computational methods — Thesis No: 806943 

  • Hind Al-Janabi (2022). Drug repurposing effort for the novel acetylcholinesterase and butyrylcholinesterase targets: A combined in silico and in vitro study — Thesis No: 717729 

  • Busecan Aksoydan (2021). Integrated molecular modeling approaches for the novel therapeutics by using cytosolic and membrane-bound target proteins as model systems — Thesis No: 692481 

  • Gülşah Aydın (2020). Identification of p53-MDM2 potential inhibitors with virtual screening and multidimensional molecular modeling methods — Thesis No: 636315 

  • Yusuf Serhat İş (2019). Design of monoamine oxidase enzyme (MAO) inhibitors play important role in the treatment of neurodegenerative diseases using computer aided methods — Thesis No: 608516 

  • Gülru Kayık (2017). In silico design of hERG non-blocker compounds with retained pharmacological activity using multi-scale molecular modeling applications — Thesis No: 485207

  • Ramin Ekhteiari Salmas (2015). Multi-scale modeling and investigation of activation mechanisms of G protein-coupled receptors — Thesis No: 363831 


Supervised MSc theses:

  • Ezgi Sambur (2023). Virtual screening of large-scale small molecule libraries against Bruton tyrosine kinase effective in chronic lymphocytic leukaemia — Thesis No: 814375 

  • Ehsan Sayyah (2023). Novel resistance-free RET tyrosine kinase inhibitor discovery through dynamic structure-based pharmacophore and QSAR modeling and virtual screening of ultra-large ligand libraries — Thesis No: 816163 

  • Safa Haddad (2023). Developing novel hERG blocker models using heteroatom type and numbers from extensive ligand libraries — Thesis No: 816749 

  • Haneen Ammuri (2022). Identification of novel PARP1 inhibitors based on structural similarities of FDA approved drugs — Thesis No: 793527 

  • İlayda Tolu (2022). In silico screening of the approved drugs, peptidomimetics and designing of new peptides against Axl-Gas6 target — Thesis No: 751106 

  • Ntsoaki Baithédi Motapanyane (2022). Applications of molecular modelling approaches for the identification of novel SARS-CoV-2 RdRp inhibitors — Thesis No: 758552 

  • Md Kamrul Hasan (2021). Molecular mechanism of AT1R/PARP1 inhibitors interactions using combined molecular modeling approaches and physics-driven virtual identification of novel therapeutics against retinal inflammation — Thesis No: 710115 

  • Lalehan Oktay (2020). Integrated ligand- and target-driven-based virtual screening studies for the identification of novel therapeutics against breast cancer — Thesis No: 648941 

  • Arhun Ali Balkan (2020). Investigation of anti-quorum sensing and anti-biofilm activities on Pseudomonas aeruginosa of Peltigera species by lichen and endolichenic fungus specimens in vitro and in silico methods — Thesis No: 634588 

  • Ayla Yıldız (2020). Determination of the effects of Chrysophanol on Pseudomonas aeruginosa quorum sensing mechanism and biofilm formation via in vitro and in silico methods — Thesis No: 634586 

  • Asena Himmetoğlu (2020). Machine learning algorithms and combined multi-scale molecular modeling simulations against NADPH oxidase (NOX) enzymes for designing of small molecule therapeutics — Thesis No: 650515 

  • Vuslat Öykü Sayın (2019). Structure-based drug design studies for the discovery of novel carbonic anhydrase IX-selective inhibitors — Thesis No: 595464 

  • Gurbet Tutumlu (2019). Identification of novel hit molecules against B-Cell Leukemia/Lymphoma-2 (Bcl-2) — Thesis No: 535273 

  • Işık Kantarıcıoğlu (2017). Discovery of novel AT1 inhibitors using computational methods — Thesis No: 491210