Investigation of Active Compounds in Propolis Structure Against Sars Cov-2 Main Protease by Molecular Docking Method: In Silico Study

Erkan Öner; İlter Demirhan; Serap Yalın; Ergul Belge Kurutas

doi:10.18016/ksutarimdoga.vi.1093707

EN TR

Investigation of Active Compounds in Propolis Structure Against Sars Cov-2 Main Protease by Molecular Docking Method: In Silico Study

Abstract

It was aimed to investigate the active ingredients limonin, quercetin and kaempferol in propolis against SARS-CoV-2 main protease(MPro) using in silico methods. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) screening of ligands assists US to state their absorption properties, toxicity, and drug-likeness. Ligand molecules obtained from PubChem in smiles format were loaded on SWISSADME and PROTOX-II webservers for ADMET screening. The three compounds in propolis were obtained from the PubChem database. Compounds were located at the active site of the SARS-CoV-2 MPro receptor with PDB ID:6LU7. Molecular docking work was done with Autodock program. Molecular docking results were found as -8.7 kcal/mol in limonin, -7.5 kcal/mol in quercetin and -7.7 kcal/mol in kaempferol. In silico ADMET estimation showed they have a potential for antiviral therapy. In conclusion, we thought that propolis active components limonin, quercetin and kaempferol have the potential to be a SARS CoV-2 MPro inhibitor.

Keywords

Sars Cov-2 Ana Proteaz'da Propolis Yapısındaki Aktif Bileşiklerin Moleküler Yerleştirme Yöntemiyle Araştırılması: In Silico Çalışması

Öz

Propolisin aktif bileşikleri olan limonin, quercetin ve kaempferol'ü SARS-CoV-2 ana proteaza (MPro) karşı in silico yöntemlerle araştırması amaçlandı. Ligandların absorpsiyon, dağılım, metabolizma, atılım ve toksisite (ADMET) taraması, absorpsiyon özelliklerini, toksisitesini ve ilaca benzerliğini belirtmesine yardımcı olur. PubChem'den smiless formatında elde edilen ligand molekülleri, ADMET taraması için SWISSADME ve PROTOX-II web sunucularına yüklendi. Propolisteki üç bileşik, PubChem veritabanından elde edildi. Bileşikler, PDB ID:6LU7 ile SARS-CoV-2 MPro reseptörünün aktif bölgesine yerleştirildi. Autodock programı ile moleküler yerleştirme çalışması yapıldı. Moleküler yerleştirme sonuçları limoninde -8,7 kcal/mol, quercetin'de -7,5 kcal/mol ve kaempferol'de -7,7 kcal/mol olarak bulundu. In silico ADMET tahmini, antiviral tedavi potansiyeline sahip olduklarını gösterdi. Sonuç olarak, propolis aktif bileşenleri limonin, quercetin ve kaempferol'ün SARS CoV-2 MPro inhibitörü olma potansiyeline sahip olabileceği düşünülmektedir.

Anahtar Kelimeler

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Details

Primary Language

English

Subjects

Structural Biology

Journal Section

Research Article

Authors

Erkan Öner ^*
0000-0002-6332-6484
Türkiye

İlter Demirhan
0000-0003-0054-7893
Türkiye

Serap Yalın
0000-0002-1286-2172
Türkiye

Ergul Belge Kurutas
0000-0002-6653-4801
Türkiye

Early Pub Date

October 13, 2023

Publication Date

February 28, 2024

Submission Date

March 26, 2022

Acceptance Date

August 22, 2022

Published in Issue

Year 2024 Volume: 27 Number: 1

DOI

https://doi.org/10.18016/ksutarimdoga.vi.1093707

IZ

https://izlik.org/JA33RU63CH

Cite

RIS / Bibtex

APA

Öner, E., Demirhan, İ., Yalın, S., & Belge Kurutas, E. (2024). Investigation of Active Compounds in Propolis Structure Against Sars Cov-2 Main Protease by Molecular Docking Method: In Silico Study. Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi, 27(1), 46-55. https://doi.org/10.18016/ksutarimdoga.vi.1093707

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