New protocol for scanning minor and major grooves along DNA to find best interaction mode with drug molecules

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Tezin Türü: Yüksek Lisans

Tezin Yürütüldüğü Kurum: Orta Doğu Teknik Üniversitesi, Fen Bilimleri Enstitüsü, KİMYA ANABİLİM DALI, Türkiye

Tezin Onay Tarihi: 2022

Tezin Dili: İngilizce

Öğrenci: AYBÜKE GÜLKAYA

Danışman: ANTOINE MARION

Açık Arşiv Koleksiyonu: AVESİS Açık Erişim Koleksiyonu

Özet:

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.