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All Journal Indonesian Journal of Conservation JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA Jurnal Kimia Riset Jurnal Fitofarmaka Indonesia Jurnal Penjaskesrek CARADDE: Jurnal Pengabdian Kepada Masyarakat Jurnal Ilmu Kefarmasian Indonesia Jurnal Jamu Indonesia Pharmacoscript Jurnal Farmamedika (Pharmamedica Journal) SULUH: Jurnal Abdimas Indonesia Natural Research Pharmaceutical Journal (INRPJ) Lumbung Farmasi : Jurnal Ilmu Kefarmasian PROFICIO: Jurnal Pengabdian Masyarakat Pharmaceutical And Biomedical Sciences Journal (PBSJ) Capacitarea : Jurnal Pengabdian Kepada Masyarakat Abdi Implementasi Pancasila: Jurnal Pengabdian kepada Masyarakat Ranah Research : Journal of Multidisciplinary Research and Development Jurnal Ilmiah Multidisiplin Indonesia Jurnal Ilmiah Farmasi Simplisia Aktual : Jurnal Pengabdian Kepada Masyarakat Jurnal Kesehatan Bakti Tunas Husada Aisyah Journal Of Physical Education Journal of Natural Product for Degenerative Diseases Indonesian Journal of Jamu
Andri Prasetiyo
Universitas Pancasila
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Journal : JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA

 1 
Analysis of Molecular Docking and Dynamics Simulation of Mahogany (Swietenia macrophylla King) Compounds Against the PLpro Enzyme SARS-COV-2 Lalu Sanik Wahyu Fadil Amrulloh; Nuraini Harmastuti; Andri Prasetiyo; Rina Herowati
JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA Vol. 10 No. 3 (2023): JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jfiki.v10i32023.347-359

Abstract

Background: Using natural ingredients as antivirals can be considered a treatment for SARS-CoV-2. One of the potential plants, mahogany (Swietenia macrophylla King), is widely used in various countries as an antiviral treatment. Paparin-like protease (PLpro) is an essential cysteine "‹"‹protease that regulates viral replication and interferes with the regulation of immune sensing. Objective: This study aims to predict which compounds in the mahogany plant have good affinity, patterns, and stability interaction against the target protein of SARS-CoV-2. Methods: The drug-likeness parameter using SwissADME was used to screen compounds that will be docked against PLpro using the Autodock program. The parameters observed in molecular docking analysis are the value of bond energy and interaction model to amino acid residues. The compounds in mahogany plants that have the best interactions were then analyzed using molecular dynamics simulation methods to determine the stability of their bonds based on the values of Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF). Results: Twenty-two compounds met the drug-likeness requirements. Molecular docking analysis showed that the compounds predicted to have the best binding affinity and have an interaction pattern similar to natural ligands towards the molecular target of PLpro are 7-deacetoxy-7-oxogedunin and 3β-hydroxy-stigmast-5-en-7-one. The molecular dynamics simulation results revealed that based on the RMSD and RMSF values, the compound 3β-hydroxy-stigmast-5-en-7-one showed higher stability than 7-deacetoxy-7-oxogedunin. Conclusion: 3β-hydroxy-stigmast-5-en-7-one and 7-deacetoxy-7-oxogedunin were predicted to have good interaction with PLPro; however, 3β-hydroxy-stigmast-5-en-7-one showed the higher interaction stability.
Co-Authors Ade Yeni Aprilia Aey Fadilah, Yasin Agustia, Rini Ahmad Nuruhidin Alwie, Rakhmat Ramdhani Armanjaya, Satria Audrey, Cresentia Bambang Pontjo Priosoeryanto Bastian, Arif Alexander Bella Rofi Bungsudi Desi Nadya Aulena Dhani, Muhammad Elvi Sahri Maulinda Esti Mumpuni Esti Mumpuni Esti Mumpuni, Esti Evi Susanti Fadlu Rachman Fitry Angger Pangestu Gayatri Indah Pramesti Gumay, Jovana Renaldy Haikal Shaquille Hutagaol, Lungguk Indriani, Aqilah Idelia Julian Rahmat Lalu Sanik Wahyu Fadil Amrulloh Lidya Luziana Lilik Sulastri Lilik Sulastri LUNGGUK HUTAGAOL Lungguk Hutagaol Marlien Bokko Martati, Titiek Mawijaya, Agus Megawati Megawati Muhamad Yamin Muhamad Yamin Muhammad Yamin Muhammad Zulfadhli, Muhammad Mulatsari, Esti Nabila Prihantini Khairunnisa Natthawani, Amitta Nawasiah, Nana Novi Yantih Noviyantih, Noviyantih Nuraini Harmastuti Nurmala Ahmar Nuruhidin, Ahmad Panca Bayu Chandra, Pra Pratama, Rendy Yudha Putri Windari Saputra Rachman, Fadlu Rachmi Ridho Rahmat, Ayi Ramadhan, Islami Al-Kaffah Ramadhani, Karina Natasya Ramani, Sofyan Raymond R. Tjandrawinata Rhahmadini, Yahdi Thia Risna Rosmiyati Saeful Amin Saeful Amin Salsabila Adlina Saputra, Putri Windari Sarah Annisaa Nurwan Sari Dewi, Rika Sari, Felinda Sekar Harsti Rahmadhani Shirly Kumala Simanjuntak, Josua Donrio Simanjuntak, Vino Soaduon Siswandono, Siswandono Syaifurrohman, Amir Syamsudin Abdillah Syifa Aulia Taqwa, Iqbal Ananda Titiek Martati Ulfa Isni Kurnia Utami, Santi Yanuarti Winana Kartika Dewi Wiwi Winarti Yogaswara, Amira Thufailla Zahra, Nurulita Az Zainur Rahman Hakim Ziko Fajar Ramadhan, Ziko Fajar