Ezgi SAMBUR-Computational Drug Design

Ezgi SAMBUR-Computational Drug Design

About Me ;

Hello, I'm Ezgi. I'm 24 years old. Currently, I am continuing my Master's degree 'In Tissue Eng. and Regenerative Medicine' program at Bahçeşehir University (full scholarship). At the same time, as an Vice-Specialist in Prof. Dr. Serdar DURDAĞI's team, I take part in the 'Software Based Pharmaceutical Design' project. (durdagilab.com). 
I was born and raised in a region called Thrace in Turkey. My family is Turks who immigrated to Turkey from Greece, Bulgaria, and Macedonia. They call us Balkan Turks. I completed my high school education at Edirne-Keşan Science High School (96.8 honors degree)
I completed my bachelor degree in Molecular Biology and Genetics at Muğla Sıtkı Koçman University (3.02/4.00). I completed my summer internships at the Faculty of Medicine and Engineering by participating in various research in the field of Neuroscience and Cancer at Wetlab.
I completed my undergraduate thesis in Neuroscience with the study 'MiRNA Signature of Prion-induced Neurodegeneration'.
Center of Supercomputer VSC-4
Computational Drug Design, MD Simulations, Genetic Engineering, Molecular Simulations , GPUs, CPUs and more in here !

What are my research projects about ?

While doing my master's degree, I took part in the 'Software Based Covid Drug Development – Discovery of Paxlovid Analogs as SARS-CoV-2 Main-Protease Inhibitors' at Durdagilab (durdagilab.com). The results of this project are about to end. I use Schrödinger/Maestro in my work. Cov-Dock (Covalent Docking) is the area I particularly focus on in my work. Specifically, i am interested in Protein-Ligand Interactions. I am applying Covalent Docking strategies to obtain Protein-Ligand complexes, where ligands are attached to specific residues at the Binding Pocket of the Protein via Covalent bonds. After ranking ligands based on their interaction energies with the target protein, I am planning to proceed end-state free energy calculatins using MM/GBSA method.
Simultaneously, I am currently continuing my search for more than 2 million molecules  from 5 different libraries for a protein associated with Bruton Tyrosine Kinases and Leukemia.

Now, What am I doing with the SoHPC program?

I have lost many of my family members because of Cancer. When people are seriously ill, they can take medicine to relieve their pain. I would love to be able to make discoveries in the field of medicine so that people can continue their lives painlessly. Of course, I want this to be done with the least harm to nature. I think the solution to every problem is hidden in nature. That’s why I want to move forward by being inspired by nature.

With the training I will receive with SoHPC

First of all, I was very happy to be selected for the Vienna Technical University-VSC Research Center as I work in the field of Software Based Drug Development. In this direction, I will learn to use Linux commands and AMBER.

My Project Number is 2222 ; Derived Affinity Enhancement of Antiviral Drugs

SoHPC Project aims to carry out HPC based computational screening for novel variants of the TAT-I24 peptide with improved binding affinity to ds-DNA.

HPC-based computational screening for novel variants of the TAT-I24 peptide with improved binding affinity to ds-DNA. A particular class of well-tolerated drugs is formed by small peptides because their building blocks are simply the 20 naturally occurring amino acids – the most fundamental constituents of any living cell. To transform such peptidic compounds into effective medical drugs, high-affinity binding to the target must be accomplished (and is usually the outcome of a tedious and long-lasting optimization process).

Consequently, the next simple step to further enhance drug efficacy was to change any of the 22 amino acids and examine the effect for improved or impaired binding strength.
Regarding the methods, the MM-PBSA technique can be applied. This computational approach allows semi-quantitative estimates of binding free energies (∆G) using standard tools in contemporary biophysical/biochemical research.

Computational Biology , Drug Design and Drug Repurposing,AMBER, Linux Commands, GPU Architectures, HPC, summer of HPC 2022

Computational Drug Design, AMBER, HPC

life is beautiful as you discover..

Ezgi .. 

I am doing my master's degree in Tissue Engineering and Regenerative Medicine at Bahçeşehir University / Faculty of Medicine. I also work in the Computational Biology and Molecular Simulation Laboratory (Durdagi Research Group (durdagilab.com)). Project 1: Software Based Drug Development Project: 'Discovery of Paxlovid Analogs as SARS-CoV-2 Main Protease Inhibitors'. Project 2: Structure of human Bruton's Tyrosine Kinase-associated protein virtual screening and reconstruction of target drug molecules, (Covdock-MD-MMGBSA at Schrödinger) Project 3: HPC-Derived Affinity Enhancement of Antiviral Drugs

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