Moleküler Docking Yöntemi ile Vitis vinifera L. İçeriğindeki Fitokimyasal Bileşiklerin İnsan Hemoglobin Proteini ile Etkileşiminin İncelenmesi

Yıl 2025, Cilt: 1 Sayı: 1, 9 - 21, 30.01.2025

Şeyda Kaya

Öz

Amaç: Hemoglobin, dokulara oksijen taşıyan kırmızı kan hücrelerinde bulunan proteindir, özellikle anemi
(kansızlık) teşhisinde dikkate alınan önemli bir belirteçtir. Vitis vinifera, içerdiği birçok fitokimyasal bileşikler
sayesinde, anemiye iyi geldiği belirtilen bir bitkidir. Bu çalışmada V. vinifera içeriğinde bulunan etken maddeler
ile hemoglobin proteini arasındaki etkileşimin moleküler docking yöntemi ile araştırılması amaçlanmıştır.
Yöntem: Bitki içeriğinde bulunan etken maddelerin hemoglobin proteinine bağlanma afinitelerini hesaplamak için
Maestro Schödinger paket programı kullanıldı. Ligandların moleküler yapısını bulmak için Pubchem veri tabanı
kullanıldı. Hemoglobine (PDB ID: 2D60) ait protein yapısı RCSB Protein Veri Bankasından elde edildi.
Bulgular: Bu çalışmada V. vinifera içeriğinde bulunan 16 etken madde ile hemoglobin proteini arasında etkileşim
olduğu belirlendi. Hemoglobin proteini ile en iyi bağlanma afinitesine sahip fitokimyasal bileşenler vitisin A
(-9.144 kcal/mol), proanthocyanidin (-7.791 kcal/mol) ve anthocyanin a2 (-7.356 kcal/mol) olarak belirlendi.
Sonuç: Bu çalışma ile insan hemoglobin proteini ile V. vinifera içeriğinde bulunan fitokimyasal bileşiklerin
moleküler docking bağlanma skoru ile, gerçekleştirdiği etkileşimler gösterilmiştir. Vitisin A, proanthocyanidin ve
anthocyanin a2’nin bağlanma enerjilerinin düşük olması bu bileşiklerin hemoglobin proteininin birer bağlayıcısı
olma potansiyelini göstermektedir.

Anahtar Kelimeler

Vitis vinifera, Fitokimyasal, Etnobotanik, Hemoglobin, Moleküler kenetleme.

Investigation of the Interaction of Phytochemical Compounds in Vitis vinifera L. with Human Hemoglobin Protein by Molecular Docking Method

Öz

Purpose: Hemoglobin is a protein found in red blood cells that carries oxygen to tissues and is an important
marker, especially in the diagnosis of anemia. Vitis vinifera is a plant that is reported to be beneficial for anemia
due to its rich content of phytochemical compounds. This study aimed to investigate the interactions between the
active compounds in Vitis vinifera and hemoglobin protein using the molecular docking method.
Methods: The Maestro Schrödinger software package was utilized to calculate the binding affinity of the plant's
active compounds to the hemoglobin protein. The molecular structures of the ligands were retrieved from the
PubChem database, while the hemoglobin protein structure (PDB ID: 2D60) was obtained from the RCSB Protein
Data Bank.
Results: In this study, the interactions between 16 active compounds of V. vinifera and hemoglobin protein were
analyzed. The phytochemical components with the highest binding affinities to hemoglobin protein were identified
as vitisin A (-9.144 kcal/mol), proanthocyanidin (-7.791 kcal/mol), and anthocyanin a2 (-7.356 kcal/mol).
Conclusion: This study demonstrated the interactions between human hemoglobin protein and phytochemical
compounds in Vitis vinifera using molecular docking binding scores. The low binding energies of Vitisin A,
proanthocyanidin, and anthocyanin a2 indicate the potential of these compounds to act as binders for the
hemoglobin protein.

Anahtar Kelimeler

Vitis vinifera, Phytochemical, Ethnobotany, Hemoglobin, Molecular docking.

Kaynakça

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