Antiviral peptidlerin SARS COV-2 ana proteaz yapısına bağlanma etkinliklerinin protein-yanaştırma yöntemi ile incelenmesi: In silico bir çalışma

Year 2022, Volume: 3 Issue: 3, 121 - 127, 30.12.2022

İlter Demirhan , Erkan Öner , Ergul Belge Kurutas

https://doi.org/10.51753/flsrt.1092767

Abstract

Virüsler günümüzde hastalıklarının önemli etkenleri arasında yer almaktadır. Viral hastalıklar için tasarlanan tedavilerin yetersizliği yeni tedavi yöntemlerinin tasarlanması ihtiyacını doğurmaktadır. 2019 yılında ortaya çıkan COVID-19 (SARS COV-2) de yeni antiviral ajanların ihtiyacı olduğu görülmüştür. Yapılan çalışmalar sonucu sunulan raporlarda viral direncin artığı görülmektedir. Bu çalışmanın amacı, antiviral/antimikrobiyal etkinliğe sahip peptidlerin SARS COV-2 ana proteaz yapısında protein-peptid yanaştırma yöntemiyle araştırılmasıdır. Antiviral aktiviteye sahip antimikrobiyal peptidlerin sayısı hala düşük olsada, hali hazırda farmasötik olarak temin edilebilen antiviral ilaçlar olma yolunda muazzam bir potansiyel göstermektedir. Antiviral etkinliğe sahip alloferon 1, e ctry2801, temporin 1ta, dermaseptin s4, clavanin b, magainin b2 ve magainin b1 peptidlerinin SARS COV-2 ana proteaz (PDB ID:6LU7) yapısında protein çalışması CABSDOCK ile yapılmıştır. Magainin b2 ve peptid ctyr2801 peptidleri bağlanmalarının yüksek düzeyde olduğu, alloferon 1 ve magainin b1 in orta düzeyde bağlanma afinitesinin olduğu, termorin 1ta, dermaseptin s4 ve clavanin b’nin düzey düzeyde bağlanma afinitesine sahip olduğu gözlemlenmiştir. Sonuçlarımıza göre; peptid ctyr2801 ve magainin b2’nin, SARS COV-2 ana proteaz yapısında in vivo çalışmalara ve diğer çalışmalara öncülük edeceği düşünülmektedir.

Keywords

Antiviral peptid, CABSDOCK, protein peptid yanaştırma, SARS COV-2 Mpro

Investigation of antiviral peptides in SARS COV-2 major protease structure by protein-e docking method: An in silico study

Abstract

Viruses are among the important factors of diseases today. The inadequacy of the treatments designed for viral diseases necessitates the design of new treatment methods. It has been seen that there is a need for new antiviral agents in COVID-19. In the reports presented as a result of the studies, it was seen that the viral resistance has increased. The aim of this study is to investigate peptides with antiviral/antimicrobial activity in the main protease (Mpro) structure of SARS COV-2 by protein-peptide docking method. Although the number of antimicrobial peptides with antiviral activity is still low, they still show enormous potential as pharmaceutically available antiviral drugs. Protein analysis of alloferon 1, ctry2801, temporin 1ta, dermaceptin-s4, clavanin b, magainin b2 and magainin b1 peptides with antiviral activity in the SARS COV-2 Mpro (PDB ID: 6LU7) structure was performed
with CABSDOCK. It has been observed that the binding affinity of magainin b2 and peptide ctyr2801 is high, alloferon 1 and magainin b1 have a moderate binding affinity, and thermorin-1ta, dermaseptin s4 and clavanin b have a high level of binding affinity. According to our results; Peptide ctyr2801 and magainin b2 are thought to lead to in vivo studies and other studies on the SARS COV-2 Mpro structure.

Keywords

Antiviral peptide, CABSDOCK, protein peptide docking, SARS COV-2 Mpro

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