Computational Structural Biology and Drug Discovery Laboratory

“Computational Structural Biology and Drug Discovery" group conducts research on proteins and cells of humans, parasites, bacteria and viruses.

One of our group’s predominantly studied areas of research is; computational structural biology and structure-based drug design. In line with this objective; gene cloning, recombinant protein production (in E. coli. expression systems), robust and clean purification by affinity chromatograpy and certain biochemical and biophysical analyses of target proteins take place in our laboratory. Structural modelling, high-througput virtual screening, molecular docking and molecular dynamics simulations of druggable proteins also take place with the aim of revealing compounds that are potent inhibitor candidates. Additionally, the design of anti-cancer and anti-microbial peptides, computational analysis of the protein-peptide and protein DNA/RNA aptamer interactions are also among the drug studies performed.

Another valuable research purpose for the team consists of our work aimed at a greater general understanding of the structural biology and molecular evolution of poly-extremophilic 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

1. Merve BOSTANCIOĞLU (PhD Candidate): Antiprotozoal drug discovery, computational structural biology

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

Sude BÜYÜKKURT (MSc Student.): Antimicrobial peptide discovery, computational structural biology, structural biology of bacterial membranes

 

Previous theses

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

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

Prof. Özkan DANIŞ (Marmara University-Chemistry Department)

Assoc. Prof. Soner ÇUBUK (Marmara University- Chemistry Department)

Assoc. Prof. Serap DERMAN (YTU-Department of Bioengineering)

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

Assoc. Prof. Emrah SARIYER (Artvin Çoruh University)