New Protocol for Scanning Minor and Major Grooves Along DNA to Find Best Interaction Mode With Drug Molecules

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Aybuke_Gülkaya_Msc.pdf

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2022-1-18

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Gülkaya, Aybüke

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Major and minor groove binder drugs could function as possible treatment agents in genetic disorders or cancer. DNA is recognized by different proteins during replication, translation, and transcription. Basically, by binding to the grooves of DNA, small drug molecules can change the helical structure of DNA, interfere with protein binding and prevent replication, translation or transcription. To alter and inhibit DNA - protein interactions, especially sequence specific ligands should be designed. Accordingly, we investigated the interactions of different anticancer drugs binding to specific DNA sequences via minor or major grooves by a novel, automatizated protocol as a combination of docking and molecular mechanics refinement. With this methodology, we obtained best interaction modes of the drug molecules with given DNA sequences and most preferred sequences.

Subject Keywords

Molecular Docking, Molecular Mechanics, Binding Free Energy, Molecular Modelling, Drug Discovery

URI

https://hdl.handle.net/11511/95952

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Graduate School of Natural and Applied Sciences, Thesis

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Citation Formats

A. Gülkaya, “New Protocol for Scanning Minor and Major Grooves Along DNA to Find Best Interaction Mode With Drug Molecules,” M.S. - Master of Science, Middle East Technical University, 2022.