Computational Structural Biology and Drug Discovery Laboratory

As the “Computational Structural Biology and Drug Discovery” group, we conduct research on human, parasite, bacterial and viral proteins and cells.

One of the priority areas of our group is computational structural biology and ligand/structure-based drug design. For this purpose, we perform protein structure modeling, high-throughput virtual screening, molecular docking and molecular dynamics simulations to select chemicals that can act on drug target proteins. At the same time, cloning of drug target protein genes, recombinant protein production (E. coli expression system), high quantity and high purity purification by affinity chromatography and biochemical-biophysical analysis are carried out. In addition, the design of anti-cancer and anti-microbial peptides, cell membrane-peptide/ligand interactions, protein-peptide and protein-DNA/RNA aptamer interactions are also included in these drug studies.

Another area of our work involves structural bioinformatics studies to understand the evolution and structural biology of polyextremophilic proteins.

 

Team:

Associate Professor Özal MUTLU (Department Head)

https://scholar.google.com.tr/citations?user=wkjEJMkAAAAJ&hl=tr&oi=ao

https://avesis.marmara.edu.tr/ozal.mutlu

Esra ALBAYRAK (PhD Candidate): Anticancer peptide discovery, computational structural biology, structural biology of realistic cancer cell membranes

Can AYGÜN (PhD Candidate): Antimicrobial drug discovery, computational structural biology

 

Previous theses

Sude BÜYÜKKURT (YL, 2022-25): Study of the effects of temporin (1RNa and 1RNb) and its derivatives on bacterial cell membranes with computational structural biology approach.

1. Merve BOSTANCIOĞLU (PhD, 2018-25): Molecular Characterisation of Babesia bigemina lactate dehydrogenase enzyme and investigation of the enzyme by computational structural biology approach.

Mustafa Necati Haşimoğlu (MSc, 2021-24): Identification of novel inhibitors targeting 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase in Neisseria gonorrhoeae with computational chemistry methods (Co-advisor, Ad: Prof. Dilek Turgut-Balık)

Sura Sanem KÖSE (MSc, 2021-23): Analysis of Cryobacterium aureum FabH enzyme via computational structural biology approach.

Seda Nematipour (MSc, 2020-23): In silico characterization of the Klebsiella pneumoniae tetrahydrodipicolinate N-succinyl transferase enzyme and identification of potential inhibitors (Co-advisor, Ad: Prof. Safiye ERDEM).

Can Aygün (MSc, 2018-20): Recombinant production, biochemical, biophysical and In silico analysis of the Toxoplasma gondii FabG (3-Oxoacyl-[Acyl-Carrier-Protein] Reductase) enzyme for drug development studies.

 

Undergraduate projects

Rabia Başer, Mehdi Eslami (2025-26): Determination of the interaction of E. coli LoLA protein with antimicrobial peptides by computer-aided drug discovery approach (Support: TÜBİTAK 2209A).

Gamze Rusçuklu, Göksu Çalı (2025-26): Structural modeling of P. aeruginosa LoLA protein and in silico investigation of its inhibition potential by antimicrobial peptides (Support: TÜBİTAK 2209A).

Hümeyra Şehnaz Sezen, Tuğba Kurçenli (2023-24): In silico investigation of the interaction of Acinetobacter baumannii Thiamine Monophosphate Kinase (AbTMPK) enzyme with lasioglossin I, II and III peptides and derivatives (Support: TÜBİTAK 2209A).

Sude Büyükkurt (2020-21): Investigating thermal adaptation of bacterial FabI enzyme using a computational structural biology approach (Support: TÜBİTAK 2209A).

Gizem Kuğu, Merve Gürboğa (2018-19): Identification of Histone deacetylase 1 (HDAC1) inhibitors for veterinary drug discovery using a computer-aided and structure-based drug design approach (Support: TÜBİTAK 2209A).

Associates:

Prof. Dilek TURGUT-BALIK (Yildiz Technical University-Department of Bioengineering)

Prof. Nagihan GÜLSOY (Marmara University-Department of Biology)

Prof. Safiye ERDEM (Marmara University-Chemistry Department)

Prof. Ayşe OGAN (Marmara University-Chemistry Department)

Prof. Özkan GÜLSOY (Marmara University-Department of Metallurgical and Materials Engineering)

Prof. Ajda Ç. GÜRKAN (Marmara University-Department of Biology)

Prof. Hiqmet KAMBERAJ (International Balkan University-Department of Computer Engineering / North Macedonia)

Prof. Özkan DANIŞ (Marmara University-Chemistry Department)

Prof. Soner ÇUBUK (Marmara University- Chemistry Department)

Prof. Serap DERMAN (YTU-Department of Bioengineering)

Assoc. Prof. Emrah SARIYER (Artvin Çoruh University)

Asst. Prof. Sinem KOÇER (Yeni Yüzyil University-Faculty of Pharmacy)