Ellen, Ruth (2021) Identifikasi anti-SARS-CoV-2 Metabolit Sekunder Phyllantus niruri, Curcuma xanthorrhiza dan Orthosiphon aristatus Melalui Pendekatan Penambatan Molekul dan Simulasi Dinamika Molekul. Masters thesis, Institut Teknologi Sepuluh Nopember.
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Abstract
SARS-CoV-2 merupakan virus yang menyebabkan pandemi global pada tahun 2019 dengan gejala klinis ringan menyerupai flu hingga gejala berat yang dapat menyebabkan kematian. Penelitian untuk menemukan obat SARS-CoV-2 telah dilakukan baik melalui studi literatur maupun uji in silico senyawa metabolit sekunder terhadap target SARS-CoV-2. Beberapa penelitian telah melaporkan mengenai sifat antivirus tanaman Phyllantus niruri, Curcuma xanthorrhiza dan Orthosiphon aristatus, namun pengujian kandungan senyawa metabolit sekunder terhadap anti-SARS-CoV-2 belum dilaporkan. Oleh karena itu, penelitian ini bertujuan untuk mengungkap kemampuan anti-SARS-CoV-2 senyawa metabolit sekunder P. niruri, C. xanthorrhiza dan O. aristatus menggunakan penambatan molekul dengan target obat spike (S) glikoprotein dan 3-chymotrypsin-like protease (3CLpro). Penelitian lebih lanjut dilakukan untuk analisis kemiripan obat terhadap senyawa yang berpotensi sebagai anti-SARS-CoV-2 serta sifat Absorpsi, Distribusi, Metabolisme, Ekskresi dan Toksisitas (ADMET). Hasil penelitian menunjukkan senyawa rutin (-7,3 kcal/mol), asam elagat (-7,2 kcal/mol) dan asam ursolat (-6,8 kcal/mol) memiliki skor penambatan terhadap S-glikoprotein lebih baik dibandingkan nelfinavir (-6.7 kcal/mol) dan remdesivir (-6,6 kcal/mol). Selain itu, rutin (-8,8 kcal/mol) memiliki skor penambatan terhadap 3CLpro lebih baik dari obat nelfinavir (-8,2 kcal/mol) dan remdesivir (-7,8 kcal/mol). Rutin mampu untuk mengikat domain reseptor ikatan S-glikoprotein dan 3CLpro. Simulasi dinamika molekul menunjukkan kompleks rutin-3CLpro stabil. Oleh karena itu, rutin merupakan inhibitor 3CLpro yang baik dan berpotensi mejadi obat SARS-CoV-2.
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SARS-CoV-2 is a coronavirus that causes a global pandemic in 2019 with
mild flu-like clinical symptoms to severe symptoms that can cause death. Research
to find the SARS-CoV-2 drug has been carried out through literature studies and in
silico studies of secondary metabolites against the SARS-CoV-2 target. Previous
studies have reported the antiviral properties of the plants Phyllantus niruri,
Curcuma xanthorrhiza and Orthosiphon aristatus. However, secondary metabolites
from these plants have not been tested for anti-SARS-CoV-2. Therefore, the aim of
this study is to reveal the anti-SARS-CoV-2 activity of P. niruri, C. xanthorrhiza
and O. aristatus secondary metabolites using molecular docking and molecular
dynamic simulation with spike (S) glycoprotein and 3 -chymotrypsin-like protease
as drug target. (3CLpro). Further, the potential anti-SARS-CoV-2 compounds were
analyzed for drug similarity and Absorption, Distribution, Metabolism, Excretion
and Toxicity (ADMET) properties. The results exhibited that rutin (-7.3 kcal/mol),
ellagic acid (-7.2 kcal/mol) and ursolic acid (-6.8 kcal/mol) has better docking score
for S-glycoprotein than nelfinavir ( -6.7 kcal/mol) and remdesivir (-6.6 kcal/mol).
In addition, rutin (-8.8 kcal/mol) has a better docking score for 3CLpro than
nelfinavir (-8.2 kcal/mol) and remdesivir (-7.8 kcal/mol). Rutin is able to bind to
the S-glycoprotein binding receptor domain and 3CLpro. Molecular dynamics
simulations showed a stable 3CLpro-rutin complex. Therefore, rutin is a good 3CLpro
inhibitor and has the potential to be a SARS-CoV-2 drug.
| Item Type: | Thesis (Masters) |
|---|---|
| Uncontrolled Keywords: | SARS-CoV-2, penambatan molekul, simulasi dinamika molekul, ADMET, Phyllantus niruri, Curcuma xanthorrhiza, Orthosiphon aristatus SARS-CoV-2, molecular docking, molecular dynamic simulation, ADMET, Phyllantus niruri, Curcuma xanthorrhiza, Orthosiphon aristatus |
| Subjects: | Q Science > QD Chemistry > QD251.2 Chemistry, Organic. Biochemistry |
| Divisions: | Faculty of Science and Data Analytics (SCIENTICS) > Chemistry > 47101-(S2) Master Thesis |
| Depositing User: | Ruth Ellen |
| Date Deposited: | 03 Sep 2021 13:55 |
| Last Modified: | 03 Sep 2021 13:55 |
| URI: | http://repository.its.ac.id/id/eprint/91617 |
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