Academics
The Program of Information Technology

Name/ Surname: Kemal Yelekçi

Date of Birth :
02.01.1953

Title :
Professor Dr.

Contact Details


Office: +90 0212-533 65 32 / 1332
E-mail: yelekci@khas.edu.tr

Education

 

Degree

Major

University

Year

B.S.

Chemistry

Middle East Technical University

1979

M.S.

Chemistry

Çukurova University

1981

Ph. D.

Chemistry

Ohio University

1987

Post.Doc

Chemistry

Northwestern University

1988

 

Career Objectives and Interest

 

Research and development involving studies of enzymatic reaction, receptor ligand interaction and transporter protein mechanisms. Calculation of free energy profile, elucidation of the flexibility and dynamical behavior of the protein-substrate complex are some of the major goals. To these aims our research group exploits computational techniques such as classical molecular dynamics (MD) simulations, quantum mechanics (QM) and docking methods to investigate the structure, kinetics and thermodynamics of biological molecules, especially enzyme-ligand complexes. Applications of drug design tools to case studies are of special interest.


Selected Scientific Skills


• Considerable experience of in silico modelling
• Hightroughput screening of drug candiates
• Extensive experience in synthesis of biologically active compouns
• Structure determination of organic compounds by spectroscopic (UV, IR, FT-NMR, 2D-NMR, MS etc.)
• Chromatographic separation methods (LC, GC, HPLC, GS-MS, etc.)

 

Technical Skills

 

• Unix (Linux, MacOS) operating systems, cluster experience
• Experience in using Computer-aided drug design (CADD) packges:
Accelrys’ Discovery Studio 2.5 ( 16 different moduls)
NAMD (Nanoscale Molecular Dynamics)
VMD (Visual Molacular Dynamics)
AutoDock 4.2 (Automated Docking Tools)
ADT (Autodock Tools)
• Gaussian 09 and Gauss View 5
• Widows operating system and office applications
• Creating a three-dimensional in silico model of dopamine bound to the dopamine transporter with application to Parkinson`s Disease.


Ongoing Projects:

 

1. EU Project
Title: Characterisation of mitochondrial proteins in brain
Project Acronym: COMPIB
Start date: 2006-05-01 

End date:2010-04-30
Project Funding: 1199583 EURO 

Programme Acronym: FP6-MOBILITY 



Subprogramme Area:Marie Curie Host Fellowships - Transfer of Knowledge (TOK) Development Scheme.

 

2. TUBITAK Project
Title: Research and Developmet of Drugs Preventing RNA Splicing Errors in Inherited Diseases. Sponsor: The Scientific and Technological Research Council of Turkey, TÜBİTAK, (about 700 000 EURO for 3 yeras)

 

3. TUBITAK Project
Design of Monoamine Oxidase Enzyme (A and B) Inhibitors using molecular modeling and synthesis of these inhibitors: Determination of their kinetic constants computationally and experimentally. The Scientific and Technological Research Council of Turkey, TÜBİTAK, (about 125 000 EURO for 2 yeras)

 

Academic Positions Held:


Assist. Prof. Dr. Department of Chemistry, Ege University, Izmir, 1988-1989.


Assos. Prof. Dr. Department of Chemistry, Marmara University, Istanbul, 1990-1995.

 

Prof. Dr. Department of Chemistry, Marmara University, Istanbul, 1996- 2001.

 

Prof. Dr. Faculty of Arts and Sciences, Kadir Has University, Istanbul, 2001-Present.


Theses Advised:


M.Sc Theses

Memet Vezir KAHRAMAN ; 1995
"a-(2-Aminomethyl)-N-Phenyl-Nitrone Synthesis"

 

Dilber DAMAR ; 2001
"Ethyl 2- Nitro-3-Hydroxy-3-(3,4 Dimethoxy phenyl) Propanoate Synthesis"

 

Gül ALTINBAŞ ; 2001
"Freidel Crafts Acylation Reaction of Benzene and Toluene with Different Substrates"

 

Ozlem KARAHAN; 2005 (Co-advisor)
“Investigation of Mechanisnm of Monoamine Oxidase Enzyme oxidation via Computational Methods”

 

Fahriye UYAR; 2005 (Co-advisor)
“Modeling of Thermal Pyrolysis of 2- Acetoxy-2,6,6-Trimethylbicycle [3.1.0]hexane using QM methods”

 

Ph. D. Theses:

 

Memet Vezir KAHRAMAN ; 2001
"Synthesis of Biologically Active Monoamine Oxidase Enzyme Inhibitors"

 

Sevim KARATAŞ ; 2001

"Ethyl Halogenated-3,4-Disubstitutedcinamates"

 

Recent Publications:

 

1. M. Toprakçı , K. Yelekçi
“Docking studies on Monoamine Oxidase-B inhibitors: estimation of inhibition
constants (Ki) of a series of experimentally tested compounds”,
Bioorganic & Medicinal Chemistry Letters, 15 (2005) 4438-4446

 

2. Safiye Sağ Erdem, Ö zlem Karahan, İbrahim Yıldız and Kemal Yelekçi .
“A computational study on the amine-oxidation mechanism of monoamine oxidase:
Insight into the polar nucleophilic mechanism”,
Organic & Biomolecular Chemistry, 2006, 4, 646-658.

 

3. Kemal Yelekçi, S. Erdem, Ö. Karahan, F. Uyar
“Synthesis and Thermal Reactions of -Acetoxy-2,6,6-Trimethylbicyclo[3.1.0] hexane:
Elucidation of the Mechanism of the Reaction with Coputational Approach”,
Journal of Molecular Structure: THEOCHEM, 814 (2007) 61-73.

 

4. Kemal Yelekçi, Özlem Karahan, Mustafa Toprakçı
“Docking of novel reversible monoamine oxidase-B inhibitors: efficient prediction of
ligand binding sites and estimation of inhibitors thermodynamic properties (G and Ki)”
Journal of Neural Transmission, (2007) 114: 725-732.

 

5. Nesrin Gökhan-Kelekçi, Semra Koyunoğlu, Samiye Yabanoğlu, Kemal Yelekçi, Özen
Özgen, Gulberk Uçar, Kevser Erol, Engin Kendi, Akgul Yeşilada,
"New Pyrazoline Bearing 4(3H)-quinazolinone Inhibitors of Monoamine Oxidase:
Synthesis, biological evaluation, and structural determinants of MAO-A and MAO-B
selectivity"
Bioorganic & MedicinalChemistry. (2009), 17(2), 675-689.

 

6. Didem Dayangaç-Erden, Gamze Bora, Peruze Ayhan, Çetin Kocaefe,
Sevim Dalkara, Kemal Yelekçi, Ayhan S. Demir, Hayat Erdem-Yurter,
“Histone Deacetylase Inhibition Activity and Molecular Docking of (E )-Resveratrol: Its
Therapeutic Potential in Spinal Muscular Atrophy”,
Chemical Biology & Drug Design, (2009), 37(3), 355-364.

7. Gamze Bora-Tatar, Didem Dayangaç-Erden, Ayhan S. Demir, Sevim Dalkar, Kemal Yelekçi, Hayat Erdem-Yurter,
“Molecular modifications on carboxylic acid derivatives as potent histone deacetylase
inhibitors: Activity and docking studies”,
Bioorganic & Medicinal Chemistry, (2009), 17(18), 6761-6772.

 

8. Nesrin Gökhan-Kelekçi, Ö. Özgün Şimşek, Ayşe Ercan, Kemal Yelekçi, Z. Sibel Şahin,
Şamil Işık, Gülberk Uçar, A. Altan Bilgin.
“Synthesis and molecular modeling of some novel hexahydroindazole derivatives as
“potent monoamine oxidase inhibitors”,
Bioorganic & Medicinal Chemistry (2009), 17(4), 5219-5228.

 

Recent Conferences Attended:

 

1. Kemal Yelekçi, Özlem Karahan, Mustafa Toprakçı
“ Docking of novel reversible monoamine oxidase-B inhibitors: efficient prediction of
ligand binding sites” “12th International Amine Oxidase Workshop “
University of Erasmus, 30th July – 03th August 2006, Rotterdam, Nederland

 

2. Kemal Yelekçi, Mustafa Toprakçı
“Docking of novel reversible monoamine oxidase-B inhibitors: efficient prediction
of ligand binding sites and estimation of inhibitors thermodynamic properties”
232nd ACS National Meeting, San Francisco, CA, USA, September 10-14, 2006

 

3. Kemal Yelekci,
“Thermal rearrangement of 2-acetoxy-2,6,6 trimethylbicyclo[3.1.0]hexane:
Theoretical elucidation of the mechanism”
234th ACS National Meeting, Boston, MA, (USA), August 19-23, 2007.

 

4. G.Bora, D.Dayangaç-Erden, P.Ayhan, K.Yelekçi, S.Dalkara, A.S.Demir,
H.Erdem-Yurter.
“Determination of inhibition activity of histone deactylase enzyme by flourimetric
method”
Turkish Biological Society, 6-9 September, Antalya, TURKIYE.

 

5. Kemal Yelekci, Gamze Bora, Didem Dayangac-Erden, Peruze Ayhan, Sevim
Dalkara, Ayhan S. Demir, and Hayat Erdem-Yurter.
“Experimental and molecular docking simulation studies of Histone deacetylases
(HDACs) enzyme inhibitors”
234th ACS National Meeting, Boston, MA, (USA), August 19-23, 2007.

 

6. Didem Dayangaç-Erden, Peruze Ayhan, Gamze Bora, Kemal Yelekçi, Sevim Dalkara,
Ayhan S. Demir, Hayat Erdem-Yurter.
“Deacetylase Inhibition Activity of Resveratrol and Its Analogues”
234th ACS National Meeting, Boston, MA, (USA), August 19-23, 2007.


7. Kemal Yelekçi, Nesrin Gökhan-Kelekci, Samiye Yabanoğlu, Gülberk Uçar
“Design and Biological Evaluation of New Pyrazoline Bearing 4(3H)-Quinazolinone Inhibitors of Monoamine Oxidase A and B: Binding Mode Studies Performed Through Docking Procedures.
13th International Amine Oxidase and Related Diseases Workshop ,Century
Huatian Hotel, Beijing, China, October 11 – 15, 2008

8. Seyhan Türkkan, Safiye Sağ Erdem, Kemal Yelekçi, Nesrin Gökhan Kelekçi, Umut Salgın Gökşen, Molecular Docking Of New Pyrazoline Derivatives To The Active Site Of Monoamine Oxidase, Fifth International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, 04-08 July 2009 Istanbul - TURKEY.


9. Seyhan Türkkan, Safiye Sağ Erdem, Kemal Yelekçi, Nesrin Gökhan Kelekçi, Umut Salgın Gökşen, Molecular Docking Of New Pyrazoline Derivatives To The Active Site Of Monoamine Oxidase, Fifth International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, 04-08 July 2009 Istanbul - TURKEY.

 

10. Kemal Yelekçi
“Methods and solutions for lead discovery and optimization, structure and fragment-based design, transmembrane protein analysis, and enzyme modeling”, Workshop
European DS Pharmacophore Meeting, 1-3 July 2009, Romainville, Paris, FRANCE.

 

Administrative Duties:


Chairman of Chemistry Department 11.03.1988- 15.11.2000


Dean, The Faculty of Arts and Sciences 15.09.1998- 16.07.2006


Vice Rector (responsible for academic affair and resarch) (17.07.2001- 18.12.2003)


Member of University Board (2007- )

 

Membership of Professional Organizations:

 

Turkish Chemical Sciety


Alumnia of Middle East Technical University of Istanbul Chapter

 

American Chemical Sciety

 

Grants and Awards

 

- NATO Grant (Collaborative Research with Prof. Richard B. Silverman at Northwestrn
University, 1995-1997)
- NIH (National Institues of Health) Post-doctorate grant (with Prof. Richard B. Silverman
at Northwestrn University, 1986-1988).
- FULBRIGHT Scholarship (For Ph. D. Work at Ohio University).
- DAAD Scholarship (To learn German at Goethe Institute in Germany).
- High Honor Student (at Senior class).
- Honor Student (at Junior class).
- Distinguish Teaching and Research awards from Kadir Has University (5 times at different terms).

- 2008 Novartis Award of TURKEY for Drug Design and Drug Development Study.

 

Teaching experience


Undergraduate

 

1. General Chemistry
2. Organic Chemistry
3. Introduction to Spectroscopy
4. Nuclear Magnetic Resonance Spectroscopy
5. Instrumental Analysis
6. Introduction to Stereochemistry

Graduate

1. Advanced Nuclear Magnetic Resonance Spectroscopy
2. Advanced Organic Chemistry
3. Advanced Stereochemistry
4. Modern Synthetic Reaction
5. Essential Cell Biology
6. The Organic Chemistry of Drug Design and Drug Action
7. Computer Aided Drug Design

 

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