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All Journal HAYATI Journal of Biosciences VALENSI International Journal of Renewable Energy Development JURNAL KIMIA SAINS DAN APLIKASI Jurnal Sains Materi Indonesia Science and Technology Indonesia Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) Chimica et Natura Acta Indonesian Journal of Chemistry Jurnal Jamu Indonesia Kappa Journal Molekul: Jurnal Ilmiah Kimia International Journal of Renewable Energy Development Borneo Journal of Pharmacy Indonesian Journal of Jamu
Setyanto Tri Wahyudi
Department Of Physics, Faculty Of Mathematical And Natural Sciences, IPB University, IPB Dramaga Campus, Bogor 16680, Indonesia
Agriculture, Biological Sciences & Forestry Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Control & Systems Engineering Earth & Planetary Sciences Electrical & Electronics Engineering Energy Engineering Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Physics Other

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Journal : VALENSI

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Molecular Dynamics Simulation of Bioactive Compounds Against Six Protein Target of Sars-Cov-2 As Covid-19 Antivirus Candidates Fikry Awaluddin; Irmanida Batubara; Setyanto Tri Wahyudi
Jurnal Kimia Valensi Jurnal Kimia VALENSI Volume 7, No. 2, November 2021
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v7i2.21634

Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the virus that causes Coronavirus 2019 (COVID-19). To date, there has been no proven effective drug for the treatment or prevention of COVID-19. A study on developing inhibitors for this virus was performed using molecular dynamics simulation. 3CL-Pro, PL-Pro, Helicase, N, E, and M protein were used as protein targets. This study aimed to determine the stability of the selected protein-ligand complex through molecular dynamics simulation by Amber20 to propose bioactive compounds from natural products that have potential as a drug for COVID-19. Based on our previous study, the best value of free binding energy and protein-ligand interactions of the candidate compounds are obtained for each target protein through molecular docking. Corilagin (-14.42 kcal/mol), Scutellarein 7-rutinoside (-13.2 kcal/mol), Genistein 7-O-glucuronide (-10.52 kcal/mol), Biflavonoid-flavone base + 3O (-11.88 and -9.61 kcal/mol), and Enoxolone (-6.96 kcal/mol) has the best free energy value at each protein target. In molecular dynamics simulation, the 3CL-Pro-Corilagin complex was the most stable compared to other complexes, so that it was the most recommended compound. Further research is needed to test the selected ligand activity, which has the lowest free energy value of the six target proteins.
Component Discrimination and Anti-skin-aging Potency of Emprit and Red Ginger Essential Oil: Chemometric, Molecular Docking and Molecular Dynamics Study Badrunanto, Badrunanto; Asoka, Shadila Fira; Wahyuni, Wulan Tri; Farid, Muhammad; Wahyudi, Setyanto Tri; Batubara, Irmanida
Jurnal Kimia Valensi Jurnal Kimia VALENSI Volume 9, No. 2, November 2023
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v9i2.32765

Abstract

Emprit and red ginger essential oils (EOs) are natural sources of antioxidants that have the potential to be used in cosmetics, one of which is as an anti-skin-aging. The aim of this study was to determine the component differences and anti-skin-aging potential of the two EOs. The components were determined by GC-MS, while discrimination was done by chemometric. The potential of the components as the anti-skin-aging were evaluated by molecular docking and molecular dynamics (MD) simulations. A total 66 components were identified in both EOs, where eucalyptol (17.92%) and camphene (15.12%) were the main component in emprit and red ginger, respectively. Chemometric analysis revealed two discriminant clusters highlighting their dissimilarity with germacrene D and α-zingiberene are the key markers for differentiation. The docking and MD simulations were demonstrated the four main components of emprit EO, namely α-curcumene, α-zingiberene, β-bisabolene and β-sesquiphellandrene, have the best docking scores and interact with the enzymes with a relatively stable interaction. AdmetSAR evaluation of the four components has shown good bioavailability and declared safe. This study succeeded in revealing two ginger EOs differences based on their components and demonstrated the emprit ginger EO was more promising as a natural anti-skin-aging agent for further research.
Co-Authors Abdulloh Rifai Agus Kartono Ahmad Aminuddin Ahmad, Faozan Ajeng Widya Roslia Akhiruddin Maddu Alfi Afifah Andry Nur-Hidayat Arba, Muhammad Arba, Muhammad Ardian Arif Arry Yanuar Asoka, Shadila Fira Auliya Ilmiawati Ayu Rahmania Lestari Badrunanto, Badrunanto Bagaskoro Tuwalaid Charlena Chun Wu Dwi Iryani, Ryscha Dyah Iswantini Dylan James Brunt Farhan Azhwin Maulana Fikry Awaluddin Fikry Awaluddin Gilbert Fleischer Hamdani Zain Harry Noviardi Ida Usman Ifwarisan Defri Ilham Kurniawan Ilham Kurniawan Irmanida Batubara Johan D. Sirait Joni Prasetyo, Joni Kania Nur Sawitri LAKSMI AMBARSARI Muhammad Farid Muscifa, Zahra Silmi Nancy Dewi Yuliana Nurmawan, Cucu Putri Palupi, Nurheni Sri Rini Kurniasih, Rini Sianipar, Rut Novalia Rahmawati Sri Mulijani Sulaeman, Ahmad Sofyan Tatik Khusniati Tony Sumaryada Wulan Tri Wahyuni Yuantoro, Yandra Zahra Silmi Muscifa