In silico Investigation of the Interactions of Thymol and Carvacrol on the Spike Protein of Omicron Variant and MPro Enzyme of Coronavirus

Year 2024, Volume: 14 Issue: 3, 997 - 1005, 15.09.2024

Füreya Elif Öztürkkan , Giray Buğra Akbaba , Pinar Aksu Kılıçle

https://doi.org/10.31466/kfbd.1338012

Abstract

Many drug studies have been conducted against the coronavirus disease, which has affected the whole world since December 2019, and some studies have been carried out on natural treatment methods. Many ideas for curing coronavirus disease of T. vulgaris known as thyme plant have been presented, although there are gaps in the literature on the subject. In this work, the anti-severe acute respiratory syndrome coronavirus 2 potential of the major compounds of the T. vulgaris plant’s essential oil was investigated in silico. The major components of the T. vulgaris plant's essential oil are thymol and carvacrol. Using molecular docking experiments, we evaluated the effects of thymol and carvacrol in thyme essential oil on Omicron variant spike protein and main protease enzyme (Mpro) of severe acute respiratory syndrome coronavirus 2. We also used online databases to investigate the adsorption, distribution, metabolism, absorption, and toxic (ADMET) aspects of these two compounds. It was determined that thymol and carvacrol have strong binding affinity to the spike protein of the Omicron variant and the main protease enzyme. The compounds interact with target proteins through electrostatic, hydrogen bonds, and hydrophobic interactions. More promising findings are obtained when the contacts of carvacrol with target proteins are assessed in terms of the structure-activity relationship.

Keywords

T. vulgaris, Thymol, Carvacrol, Severe acute respiratory syndrome coronavirus 2, Molecular Docking, ADMET

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Thanks

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Timol ve Karvakrolün Koronavirüsün Ana Proteaz Enzimi ve Omicron Varyantının Spike Proteini ve Üzerindeki Etkileşimlerinin In Silico Araştırılması

Abstract

Aralık 2019'dan beri dünyayı etkisi almış olan koronavirüs hastalığına karşı birçok ilaç çalışması yapılmış ve doğal tedavi yöntemleri üzerine bazı çalışmalar yapılmıştır. Kekik olarak bilinen T. vulgaris’in koronavirüs hastalığı tedavisi ile ilgili birçok öneride bulunulmuş ancak bu konu ile ilgili literatürde boşluklar bulunmaktadır. Bu çalışmada, T. vulgaris'in ana bileşenlerinin anti-şiddetli akut solunum sendromu koronavirüs 2 potansiyeli in silico olarak araştırılmıştır. Timol ve karvakrol, T. vulgaris bitkisinin uçucu yağının ana bileşenleridir. Kekik esansiyel yağının ana bileşenlerinin SARS CoV-2 ana proteaz ve Omicron varyantı Spike proteini üzerindeki etkilerini moleküler yerleştirme çalışmaları kullanılarak incelenmiştir. Ayrıca bu iki bileşiğin adsorpsiyon, dağılım, metabolizma, absorpsiyon ve toksik (ADMET) özelliklerini çevrimiçi veritabanlarının yardımıyla incelenmiştir. Timol ve karvakrol, şiddetli akut solunum sendromu koronavirüs 2'nin Omicron varyantının spike proteinine, ana proteaz enzimine kıyasla güçlü bir bağlanma afinitesine sahiptir. Bileşikler, hedef proteinler ile elektrostatik, hidrojen bağı ve hidrofobik etkileşimlerle bağlanmaktadır. Karvakrol bileşiğinin hedef proteinlerle olan etkileşimleri yapı-aktivite ilişkisi açısından değerlendirildiğinde daha umut verici bulgular göstermektedir.

Keywords

T. vulgaris, Timol, Karvakrol, Şiddetli akut solunum sendromu koronavirüs 2, Moleküler Docking, ADMET

Project Number

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