Antioxidant Activity of Pectolinarigenin: DFT Studies, Hirshfeld Surface Analysis, Molecular Docking Investigation and ADME/T Prediction

Year 2025, Volume: 25 Issue: 5, 1018 - 1031, 01.10.2025

Tugba Göcen

https://doi.org/10.35414/akufemubid.1641818

Abstract

Pectolinarigenin (5,7-dihydroxy-6,4'-dimethoxyflavone) has been investigated as a potential antioxidant drug candidate by determining its molecular structure parameters, electronic properties, and chemical reactivity descriptors using density functional theory (DFT). The molecular structure was optimized at the B3LYP/6-311G(d,p) level and compared with the X-ray crystal structure reported in the literature. Furthermore, intermolecular interactions in the crystal structure were visualized through three-dimensional Hirshfeld surface analysis and two-dimensional fingerprint plots. The molecular electrostatic potential (MEP) map, frontier molecular orbitals (FMOs), and Mulliken atomic charges were calculated to identify chemically active regions. Additionally, a molecular docking study was conducted to assess the binding affinity of Pectolinarigenin to NADPH oxidase (PDB ID: 2CDU), an enzyme involved in the activation of the body's antioxidant defense system. The results revealed that Pectolinarigenin exhibits strong interactions with the active site of the target protein and possesses a high binding affinity with a binding energy of -8.5 kcal/mol. Moreover, pharmacokinetic property analysis and drug-likeness evaluations indicate that Pectolinarigenin is a promising candidate for development as an antioxidant drug.

Keywords

Flavonoid , DFT , Antioxsidant , Hirshfeld surface analysis , Molecular docking , ADMET

Project Number

2019-43399189-01

Pektolinarigenin'in Antioksidan Aktivitesi: DFT Çalışmaları, Hirshfeld Yüzey Analizi, Moleküler Kenetleme Araştırması ve ADME/T Tahmini

Abstract

Pektolinarigenin’in (5,7-dihidroksi-6,4'-dimetoksiflavon) potansiyel bir antioksidan ilaç adayı olarak değerlendirilmesi amacıyla moleküler yapı parametreleri, elektronik ve kimyasal reaktivite tanımlayıcıları belirlemek için yoğunluk fonksiyoneli teorisi (DFT) kullanılanılarak hesaplanmıştır. B3LYP/6-311G(d,p) baz seti ile optimize edilen moleküler yapı, literatürde rapor edilen X-ışını kristal yapısı ile karşılaştırılmıştır. Ayrıca, kristal yapısındaki moleküller arası etkileşimler, üç boyutlu Hirshfeld yüzeyi ve iki boyutlu parmak izi çizimleri ile görselleştirilmiştir. Molekülün elektrostatik potansiyel haritası (MEP), sınır moleküler orbitalleri (FMOs) ve Mulliken atomik yükleri hesaplanarak kimyasal olarak aktif bölgeler belirlenmiştir. Ek olarak, Pektolinarigenin’in vücudun antioksidan savunma sisteminin aktivasyonunda rol oynayan NADPH oksidaz enzimi (PDB ID: 2CDU) ile afinitesini değerlendirmek amacıyla moleküler kenetleme çalışması yapılmıştır. Bu analizler, Pektolinarigenin’in hedef proteinin aktif bölgesiyle güçlü bir etkileşim gösterdiğini ve -8.5 kcal/mol bağlanma enerjisiyle yüksek bir bağlanma afinitesine sahip olduğunu ortaya koymuştur. Ayrıca, farmakokinetik özellikler ve ilaç benzerliği analizleri, Pektolinarigenin’in antioksidan ilaç olarak geliştirilmesi için uygun bir aday olduğunu göstermektedir.

Keywords

Flavonoid , DFT , Antioksidan , Hirshfeld yüzey analizi , Moleküler kenetleme , ADMET

Supporting Institution

Zonguldak Bülent Ecevit Üniversitesi

Project Number

2019-43399189-01

Thanks

Bu çalışma Zonguldak Bülent Ecevit Üniversitesi Bilimsel Araştırma Projeleri Koordinatörlüğü tarafından desteklenmiştir.

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