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All Journal Jurnal Teknologi Perikanan dan Kelautan Jurnal Pangan dan Gizi Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences JURNAL KIMIA SAINS DAN APLIKASI Interaksi Online Microbiology Indonesia Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Pro-Life Jurnal Profesi Medika: Jurnal Kedokteran dan Kesehatan Jurnal Kimia Terapan Indonesia Indonesian Journal of Chemistry MITRA: Jurnal Pemberdayaan Masyarakat Warta Ikatan Sarjana Komunikasi Indonesia Journal of Tropical Biodiversity Jurnal Informasi Pengabdian Masyarakat Journal of Communication Studies and Society Jurnal Pengabdian Kepada Masyarakat
Vivitri Dewi Prasasty
Faculty Of Biotechnology, Atma Jaya Catholic University Of Indonesia
Religion Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Decision Sciences, Operations Research & Management Economics, Econometrics & Finance Education Engineering Environmental Science Health Professions Immunology & microbiology Languange, Linguistic, Communication & Media Library & Information Science Materials Science & Nanotechnology Medicine & Pharmacology Public Health Social Sciences

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Journal : Journal of Tropical Biodiversity

 1 
Therapeutic Potential of Quercetin Derivatives: In Silico Investigation of HIV-1 Protease Inhibition Aziz, Husna Abdul; Camin, Yeremiah Rubin; Prasasty, Vivitri Dewi
Journal of Tropical Biodiversity Vol 4 No 2 (2024): April 2024
Publisher : Universitas Nasional Jakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.59689/bio.v4i2.215

Abstract

Human Immunodeficiency Virus (HIV) type 1 is the predominant strain known for its impact on the immune system and its propensity for mutation. According to the World Health Organization (WHO), the global infection count reached 37.9 million in 2018, with alarming rates of mortality and morbidity. Ongoing drug discovery endeavors encompass various facets, including investigations into HIV protease—a key enzyme in the cleavage process of gag and gag-pol polyprotein chains essential for the genesis of new virions. While numerous studies suggest the inhibitory potential of quercetin against HIV-1, comprehensive exploration regarding its interaction with the HIV-1 protease receptor remains limited. This study aimed to elucidate the therapeutic potential of quercetin derivative compounds as viable candidates for HIV protease inhibition. Employing in silico analysis, molecular docking of 36 quercetin derivative compounds with the HIV-1 protease receptor (code 3SO9) using the Pyrx-Autodock Vina-Open Babel platform was conducted. Prior to docking, ligand preparation was meticulously performed using Autodock Tools 1.5.6, with geometry optimization utilizing Avogadro software. The interaction was assessed through Gibbs free energy (∆G) scoring, where a more negative ∆G value indicated a stronger binding propensity between the ligand and receptor. The docking results revealed that 22 quercetin derivative compounds exhibited Gibbs energy (∆G) values lower than the original ligand, darunavir. However, 5 compounds deviated from Lipinski's rule, while 17 compounds adhered to Lipinski's criteria. Consequently, these 17 quercetin derivative compounds exhibit promising potential as candidate drugs for HIV-1 protease inhibition.
Potential of Flavonoid Compounds from Rhodomyrtus tomentosa as Anticholesterol: An In Silico Study Lumbantoruan, Lamtiur; Sinaga, Ernawati; Simanjuntak, Kristina; Nurbaya, Siti; Prasasty, Vivitri Dewi
Journal of Tropical Biodiversity Vol 4 No 3 (2024): August 2024
Publisher : Universitas Nasional Jakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.59689/bio.v4i3.232

Abstract

Indonesia's biodiversity ranks second largest in the world. This vast potential, if managed well, can be utilized as raw materials for medicines. Currently, 96% of drug raw materials in Indonesia are still imported, making medicines expensive. Therefore, efforts are needed to achieve self-sufficiency in drug raw materials, including researching Indonesian plants with potential as hypercholesterolemia drugs to be used as native raw materials. This study aims to determine the potential of flavonoid compounds in Rhodomyrtus tomentosa fruit as an alternative hypercholesterolemia drug. Six flavonoids were identified: myricetin, quercetin, quercetin 7,4'-diglucoside, dihydromyricetin, kaempferol, and vitexin in R. tomentosa (Karamunting) fruit. The method used was an in silico study. In silico studies are used to screen compounds based on their mechanism of action against target proteins. In this study, myricetin, quercetin, dihydromyricetin, kaempferol, quercetin 7,4'-diglucoside, and vitexin were subjected to molecular docking using Autodock Vina software to determine the affinity and interaction of these six compounds with the HMG-CoA reductase enzyme, which acts as an intermediary in the mevalonate pathway for cholesterol metabolism. Simvastatin, a drug used for hypercholesterolemia treatment, was used as a comparison. The molecular docking results showed that the binding energy values for myricetin, quercetin, dihydromyricetin, kaempferol, quercetin 7,4'-diglucoside, and vitexin were -10.0, -9.4, -9.6, -9.2, -11.4, and -9.9 kcal/mol, respectively. These six flavonoid derivatives from Karamunting fruit have better inhibition scores compared to simvastatin, indicating that these flavonoid derivatives can inhibit cholesterol biosynthesis better than simvastatin and have potential as anticholesterol drugs.
Anti-Aging Potential of Moringa oleifera Bioactive Compounds: A Molecular Docking Approach Targeting Sirtuin Proteins Marthin, Jeffrey; Noverita, Noverita; Prasasty, Vivitri Dewi
Journal of Tropical Biodiversity Vol 5 No 2 (2025): April 2025
Publisher : Universitas Nasional Jakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.59689/bio.v5i2.268

Abstract

Moringa oleifera has long been valued in traditional skincare, but its molecular interactions with key aging regulators remain poorly understood. This study elucidates the anti-aging potential of Moringa oleifera bioactive compounds through their modulation of sirtuin proteins (SIRT2, SIRT5, SIRT6), which govern genomic stability and oxidative stress responses. Using computational approaches, we performed molecular docking simulations (AutoDock Vina) on 20 bioactive compounds against sirtuin crystal structures from the Protein Data Bank. Comparative analysis with commercial anti-aging agents (niacinamide, AHA, ceramide) identified three Moringa compounds with superior binding affinities: rutin (-10.7 kcal/mol), quercetin (-8.9 kcal/mol), and chlorogenic acid (-7.9 kcal/mol), all outperforming niacinamide (-6.1 kcal/mol). SwissADME profiling confirmed their drug-like properties, including high oral bioavailability, blood-brain barrier penetration, and minimal toxicity risks. Mechanistically, these compounds demonstrated dual antioxidant and anti-inflammatory capacities, suggesting synergistic protection against oxidative damage and inflammation-driven aging. Our results position Moringa oleifera as a rich source of multitarget anti-aging candidates, combining computational validation with biological relevance to advance natural product-based interventions against cellular senescence.
Co-Authors A.A. Ketut Agung Cahyawan W ADI YULANDI Albert Deniel Sitorus Alfonsus Samuel Satya Pradipta Anam, M. Khairul Anastasia Tatik Hartanti Atiatul Manna Aziz, Husna Abdul Berliana, Ester Bryant Adelar Bungaran David Simanjuntak Camin, Yeremiah Rubin David Tandjung Desak Putu Oki Lestari Dinar Kadarsih DR Sunarto Dwi Hudiyanti Enade Perdana Istyastono Enade Perdana Istyastono Ernawati Sinaga Fatmawaty Fatmawaty Febriani, Amadhea Zahra Firyal Nailah Khansa Gian Primahana Gracia Halim Hapsari Dwiningtyas Hildayani, Suci Jason Wiranata Sanjaya Jeremy Oktavian Kartika Sari Khairul Anam Linar Zalinar Udin Linar Zalinar Udin, Linar Zalinar Lumbantoruan, Lamtiur M Bayu Widagdo Mario Gunadi Marthin, Jeffrey Meda Canti Mira Adita Widianti Muhammad Hanafi Muhammad Hanafi Muhammad Iqbal Aulia Noverita Novitasari Novitasari Nur’aida, Tasya Parsaoran Siahaan Pradhana, Yudha Primahana, Gian Putra, Ariandi Qonitah, Tsabitah Athifah Ragamustari, Safendrri K Ramadhan, Muhammad Alfahrezi Baihaqi Rianita Pramitasari Roihandro, Mohammad Daffa Rory Anthony Hutagalung Rosmalena Rosmalena Rosmalena Rosmalena Rosmalena, Rosmalena Septi Panca Sakti Simanjuntak, Bungaran David Simanjuntak, Kristina Siti Nurbaya Soewono, Arka Dwinanda Suci Hildayani Tati Barus Vinella Winata Vinvin Vinvin Wicaksono, Wisnu Adi Widianti, Mira Adita Widyah Widyah Widyah, Widyah Wisnu Adi Wicaksono Yudhi Nugraha Zulfa, Astri