Molecular Structure And Docking Analysis Of The Integrin Inhibitor Cyclo (Arg-Gly-Asp-D-Phe-Val) Peptide

Year 2021, Volume: 6 Issue: 2, 1 - 6, 31.12.2021

Sefa Çelik , A. Demet Demirag , Hira Civelek Ayşen Özel , Sevim Akyüz

Abstract

All possible conformations of Cyclo (Arg-Gly-Asp-D-Phe-Val) (C26H38N8O7) with antitumor activity were determined and the most stable conformer elucidated by MMFF method using the Spartan06 program. The differences in energy between the conformers were determined, and the low energy conformers, which are required for determination of the biological activity, were characterized. Since as an anticancer candidate, the investigated molecule is expected to be an integrin inhibitor, a molecular docking study was conducted with αvβ3 integrin to determine the mechanism of interaction. As a result of docking simulations, the binding affinity ( ΔG = -10.5 kcal/mol) and the interactions between the investigated peptide and target integrin were determined.

Keywords

Antitumor activity, Spartan06 program, Integrin inhibitor, Docking simulation

Supporting Institution

IOCENS Gümüşhane University International Online Conference on ENGINEERING and NATURAL SCIENCES

İntegrin İnhibitör Cyclo (Arg-Gly-Asp-D-Phe-Val) Peptidinin Moleküler Yapısı ve Kenetlenme Analizi

Abstract

Antitümör aktiviteye sahip Cyclo (Arg-Gly-Asp-D-Phe-Val) (C26H38N8O7) peptidinin tüm olası konformasyonları Spartan06 programı ve MMFF yöntemi ile hesaplanmış ve en kararlı konformer belirlenmiştir. Konformerler arasındaki enerji farklılıkları belirlenmiş, biyolojik aktivitenin belirlenmesi için gerekli olan düşük enerjili konformerler karakterize edilmiştir. Bir antikanser adayı olarak incelenen molekülün integrin inhibitörü olması beklendiğinden, etkileşim mekanizmasını belirlemek için αvβ3 integrini ile moleküler kenetlenme çalışması yapılmıştır. Kenetlenme simülasyonları sonucunda bağlanma afinitesi ( ΔG = -10.5 kcal/mol) ve incelenen peptit ile hedef integrin arasındaki etkileşimler belirlenmiştir.

Keywords

Antitümör aktivitesi, Spartan06 programı, integrin inhibitörü, Docking simülasyonu

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