3-Dimensional Molecular Structure of Cyclo (Trp-Trp) Dipeptide with Antimicrobial and Anticancer Activity

Year 2021, Volume: 26 Issue: 2, 80 - 87, 31.08.2021

Sefa Çelik Sevim Akyüz Ayşen Özel

https://doi.org/10.53433/yyufbed.908710

Cited By: 1

Abstract

The lowest energy molecular geometry of the Cyclo(Trp-Trp) dipeptide (C₂₂H₂₀N₄O₂), which has important biological activities such as antimicrobial and anticancer, was determined by Density Functional Theory calculations made following theoretical conformation analysis calculation. First, the most probable molecular geometries of the dipeptide were determined with the contribution of Ramachandran maps and sidechain dihedral angles (χ), and the dihedral angles belonging to the eight conformations with the lowest energy were tabulated in comparison with before and after conformation analysis. The total energy of these conformation and van der Waals, electrostatic, hydrogen and torsion energy values contributing to this total energy were calculated. Among these eight conformations, the lowest energy conformer was introduced as the starting data to the Gaussian03 program and optimized at DFT/B3LYP/6-31++G(d,p) level of theory. In addition, the changes in dihedral angles were determined by comparing the lowest energy conformer found as a result of theoretical conformation analysis and optimized molecular geometry.

Keywords

Cyclo(Trp-Trp), Tryptophan, Conformational analysis, Molecular modeling

Project Number

ÖNAP-2423

Antimikrobiyal ve Antikanser Aktiviteye Sahip Cyclo(Trp-Trp) Dipeptidinin 3-Boyutlu Moleküler Yapısı

Abstract

Antimikrobiyal ve antikanser gibi önemli biyolojik aktivitelere sahip olan Cyclo(Trp-Trp) dipeptidinin (C₂₂H₂₀N₄O₂) en düşük enerjili moleküler geometrisi, teorik konformasyon analizi hesabını takiben yapılan Yoğunluk Fonksiyoneli Teorisi hesaplamalarıyla belirlenmiştir. İlk olarak Ramachandran haritaları ve yan zincir dihedral açıları (χ) katkısıyla yapılan konformasyon analizi ile dipeptide ait en olası moleküler geometriler belirlenmiş, bunlar içerisinden en düşük enerjili sekiz konformasyona ait dihedral açılar konformasyon analizi öncesi ve sonrası olmak üzere karşılaştırmalı olarak verilmiştir. Bu konformasyonlara ait toplam enerji ve toplam enerjiye katkı veren van der Waals, elektrostatik, hidrojen ve torsiyon enerjileri hesaplanmıştır. Bu sekiz konformasyon içerisinden en düşük enerjili konformer, Gaussian03 programına başlangıç verisi olarak tanıtılmış ve DFT/B3LYP/6-31++G(d,p) teori seviyesinde optimize edilmiştir. Ayrıca teorik konformasyon analizi sonucunda bulunan en düşük enerjili konformer ile optimize moleküler geometri karşılaştırmalı olarak verilerek dihedral açılardaki değişimler belirlenmiştir.

Keywords

Cyclo(Trp-Trp), Konformasyon Analizi, Moleküler Modelleme, Triptofan

Supporting Institution

İstanbul Üniversitesi Bilimsel Araştırma Projeleri Yürütücü Sekreterliği

Project Number

ÖNAP-2423

Thanks

Bu çalışma, İstanbul Üniversitesi Bilimsel Araştırma Projeleri Yürütücü Sekreterliğinin ÖNAP-2423 numaralı projesi ile desteklenmiştir.

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