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.

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

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.

Kaynakça

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