Clarification Of The Structure Of 1,4-Bis(2-Chloro-4-Nitrophenyl)Piperazine Molecule And Its Molecular Docking Analysis With DNA

Year 2022, Volume: 5 Issue: 1, 19 - 25, 30.06.2022

A. Demet Demirag , Sefa Çelik , Berkant İlgin , Ayşen Özel , Sevim Akyüz

https://doi.org/10.55117/bufbd.1006221

Abstract

Piperazine-derived molecules have important anticancer activities. In this study, conformational analysis was performed using the Spartan06 program to elucidate the structure of 1,4-Bis(2-chloro-4-nitrophenyl)piperazine (C16H14Cl2N4O4). Among the conformations determined as a result of the conformation analysis, the molecular structure with the lowest energy was determined. DNA is an important target for anticancer molecules. For this reason, the interaction of 1,4-Bis(2-chloro-4-nitrophenyl)piperazine with DNA (PDB ID: 1BNA) was investigated through docking simulations. The obtained lowest energy conformer of the title molecule was taken as the starting geometry of the ligand for docking simulations with target DNA. As a result, the binding affinity and the binding mode of the title molecule with DNA were evaluated. 1,4-Bis(2-chloro-4-nitrophenyl)piperazine has -7.5 and -7.4 kcal/mol binding affinities to DNA, in two different sites. Depending on the molecular docking studies, the 1,4-Bis(2-chloro-4-nitrophenyl)piperazine was predicted to possess strong anti-tumor effects.

Keywords

Piperazine, Anticancer, DNA, Molecular Docking, Conformational analysis

Supporting Institution

IOCENS Gümüşhane University International Online Conference on ENGINEERING and NATURAL SCIENCES

1,4-Bis(2-Kloro-4-Nitrofenil)Piperazin Molekülünün Yapısının Aydınlatılması ve DNA ile Moleküler Kenetlenme Analizi

Abstract

Piperazin türevi moleküller önemli antikanser aktivitelere sahiptir. Bu çalışmada 1,4-Bis(2-kloro-4-nitrofenil)piperazinin (C16H14Cl2N4O4) yapısını aydınlatmak için Spartan06 programı kullanılarak konformasyon analizi yapılmıştır. Konformasyon analizi sonucunda belirlenen konformasyonlar arasından en düşük enerjiye sahip moleküler yapı belirlenmiştir. DNA antikanser moleküller için önemli bir hedeftir. Bu nedenle 1,4-Bis(2-kloro-4-nitrofenil)piperazinin DNA (PDB ID: 1BNA) ile etkileşimi kenetlenme simülasyonları ile incelenmiştir. Molekülün elde edilen en düşük enerjili konformeri, hedef DNA ile kenetlenme simülasyonları için ligandın başlangıç geometrisi olarak alınmıştır. Sonuç olarak, DNA ile molekülün bağlanma afinitesi ve bağlanma modu değerlendirilmiştir. 1,4-Bis(2-kloro-4-nitrofenil)piperazin, DNA ile iki farklı bölgede -7.5 ve -7.4 kcal/mol bağlanma afinitelerine sahiptir. Moleküler kenetlenme çalışmalarına göre 1,4-Bis(2-kloro-4-nitrofenil)piperazinin güçlü anti-tümör etkilere sahip olduğu tahmin edilmektedir.

Keywords

Piperazin, Antikanser, DNA, Konformasyon Analizi, Moleküler Kenetlenme

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