Computational Investigation of 5.5'',7''-trihydroxy-3,7-dimethoxy-4'-4'''-O-biflavone from Flavonoids Using DFT Calculations and Molecular Docking

Year 2022, Volume: 12 Issue: 2, 283 - 298, 30.12.2022

Mehmet BAĞLAN Ümit YILDIKO Kenan GÖREN

https://doi.org/10.37094/adyujsci.1121018

Abstract

The structural characterization of the 5.5",7"-trihydroxy-3,7-dimethoxy-4'-4'''-O-biflavone (TDOB) molecule was done in this study. For the structural characterization of this molecule, based on the molecule's stable phase geometry, entire calculations were done using the CAM-B3LYP and PBEPBE approaches with SDD and LanL2DZ basis sets respectively. In our study, many calculations, such as HOMO-LUMO energy gaps, inter-orbital, and inter-orbital bond interactions, and electrostatic surface mapping processes of the TDOB molecule, have also been made. In the continuation of our study, the specific binding site and mechanism of the ligand on the protein were investigated using molecular docking. In the molecular docking study, affinity scores for TDOB- aldose reductase (PDB: 4ICC) and (PDB: 4IGS) were found to be -8.559 kcal/mol and -5.461 kcal/mol, respectively. The 4ICC receptor binding score was found to be greater. In the continuation of the molecular docking study, the inhibitory properties of TDOB were investigated against the aldose reductase enzymes (PDB: 4ICC) and (PDB: 4IGS), both of which showed effective inhibition, and it was seen that the TDOB molecule effectively inhibited the enzymes (PDB: 4ICC) and aldose reductase (PDB: 4IGS).

Keywords

Flavonoids, TDOB, HOMO-LUMO, Molecular docking

5,5'',7''-trihidroksi-3,7-dimetoksi-4'-4'''-O-biflavon Bileşiğinde DFT ve Moleküler Doking Çalışması

Abstract

Bu çalışmada, 5,5'',7''-trihidroksi-3,7-dimetoksi-4'-4'''-O-biflavon (TDOB) molekülünün yapısal karakterizasyonu yapıldı. Bu molekülün yapısal karakterizasyonu için, molekülün kararlı faz geometrisine dayalı olarak, tüm hesaplamalar sırasıyla CAM-B3LYP ve PBEPBE metotlarını SDD ve LanL2DZ temel seti kullanılarak yapıldı. Çalışmamızda TDOB molekülünün HOMO-LUMO enerji boşlukları, yörüngeler arası ve yörüngeler arası bağ etkileşimleri, elektrostatik yüzey haritalama işlemleri gibi birçok hesaplamalarda yapılmıştır. Çalışmamızın devamında moleküler doking kullanılarak ligandın protein üzerindeki spesifik bağlanma yeri ve mekanizması araştırıldı. Doking çalışmasında, TDOB- aldoz reduktaz (PDB: 4ICC) ve TDOB- aldoz reduktaz (PDB: 4IGS) ile afinite skorları sırasıyla -8.559 kcal/mol ve -5.461 kcal/mol olarak bulundu. TDOB- aldoz reduktaz (PDB: 4ICC) reseptör bağlanma skoru daha büyük olduğu tespit edildi. Moleküler doking çalışmasının devamında TDOB'nin inhibitör özellikleri, her ikisi de etkili inhibisyon gösteren (PDB: 4ICC) ve (PDB: 4IGS) enzimlerine karşı araştırıldı ve TDOB molekülünün, (PDB: 4ICC) ve (PDB: 4IGS) aldoz reduktaz enzimlerini etkili bir şekilde inhibe ettiği görüldü.

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