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3. Molecular docking simulation of copper oxide and zinc oxide nanoparticles toward target enzyme SARS-CoV-2 Rdrp.

Author

Kurnianto, Syarafina Ramadhanisa, Simarmata, Ara Gamaliel Boanerges, Fatriansyah, Jaka Fajar, Anis, Muhammad, Rizqillah, Raihan Kenji, and Yasin, Muhammad Ariq

Subjects
ZINC oxide, MOLECULAR docking, SARS-CoV-2, COPPER oxide, LIFE cycles (Biology), NANOPARTICLES
Abstract

The COVID-19 pandemic caused by the SARS-CoV-2 virus has infected over 2 million people in Indonesia and has killed over 60 thousand. The urgency of the situation drove researchers to prevent the spread of SARS-CoV-2. One method to disinfect surfaces contaminated by SARS-CoV-2 is by attacking RdRp, an enzyme crucial to the virus's life cycle. This in silico research has simulated molecular docking of copper oxide (CuO) and zinc oxide (ZnO) nanoparticles to determine the best nanoparticles for inhibiting the SARS-CoV-2 RdRp enzyme. The results of molecular docking were compared. The CuO nanoparticles obtained a docking score of −5.9 kcal/mol, whereas the ZnO nanoparticles obtained a docking score of −5.5 kcal/mole. Both nanoparticles show potential as antiviral agents against the SARS-CoV-2 RdRp enzyme. However, CuO nanoparticles have a better potential than ZnO nanoparticles. This study may serve as a reference to identify an antiviral agent suitable for disinfecting surfaces from SARS-CoV-2 contamination. [ABSTRACT FROM AUTHOR]

Published
2024
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5. In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease

Author

Rizqillah Raihan Kenji, Fatriansyah Jaka Fajar, Fadilah, Sulhadi, Wahyuni Siti, Sudirman Muhammad Arif, Nafisah Helya Chafshoh, and Lestari Sukma Dewi

Subjects
in silico molecular docking, molecular dynamics, sars-cov-2, andrographis paniculata, remdesivir, Microbiology, QR1-502, Physiology, QP1-981, Zoology, QL1-991
Abstract

In this work, Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS CoV-2 main protease were examined through in silico molecular docking and molecular dynamics simulation, with Remdesivir as control ligand. Docking score and MMGBSA were examined as well as molecular dynamics parameters: RMSD, RMSF and Protein ligand contact fraction. Our study found that Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone have comparable inhibition activity to SARS CoV-2 main protease in comparison to Remdesivir. 5-hydroxy7,8,2’,3’-tetramethoxyflavone has the lowest docking score, which was further validated by protein ligand contact fraction examination, although MMGBSA score is lowest for Remdesivir.

Published
2021
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