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All Journal JURNAL KIMIA SAINS DAN APLIKASI AKADEMIKA JURNAL PENGABDIAN KEPADA MASYARAKAT Jurnal Pemberdayaan Masyarakat Madani (JPMM) Jurnal Pendidikan Kimia (JPKim) Indonesian Journal of Chemistry Chemistry Indonesian Journal of Chemical Research Dalton : Jurnal Pendidikan Kimia dan Ilmu Kimia Jambura Journal of Health Sciences and Research Jambura Journal of Food Technology Jambura FIsh Processing Journal Jambura Journal of Educational Chemistry Jambura Journal of Chemistry Abdimas Umtas : Jurnal Pengabdian kepada Masyarakat Mattawang: Jurnal Pengabdian Masyarakat Lumbung Inovasi: Jurnal Pengabdian Kepada Masyarakat Indonesian Journal of Pharmaceutical Education Damhil: Jurnal Pengabdian kepada Masyarakat
Yuszda K Salimi
Universitas Negeri Gorontalo
Religion Agriculture, Biological Sciences & Forestry Arts Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Economics, Econometrics & Finance Education Engineering Environmental Science Health Professions Industrial & Manufacturing Engineering Languange, Linguistic, Communication & Media Materials Science & Nanotechnology Medicine & Pharmacology Nursing Public Health Social Sciences Other

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Journal : JURNAL KIMIA SAINS DAN APLIKASI

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Screening of Secondary Metabolite Compounds of Gorontalo Traditional Medicinal Plants Using the In Silico Method as a Candidate for SARS-CoV-2 Antiviral Yuszda K. Salimi; La Ode Aman; Zaenul Wathoni; Netty Ino Ischak; Akram La Kilo; La Alio
Jurnal Kimia Sains dan Aplikasi Vol 25, No 10 (2022): Volume 25 Issue 10 Year 2022
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jksa.25.10.382-393

Abstract

COVID-19 is a disease that caused a prolonged pandemic in many countries caused by the SARS-CoV-2 virus. This study aims to identify the antiviral potential of secondary metabolites in Gorontalo traditional medicinal plants, which are believed to have the ability to inhibit the main protease protein of this virus. The methods used in this research were molecular docking and molecular dynamic. The main protease proteins for SARS-CoV-2 used based on the homology modeling results were 3V3M and 7TE0. The results of the active compounds in the paxlovid drug were also compared to obtain accurate data comparisons. The validation of the docking method on the 3V3M protein using the natural ligand 0EN revealed an RMSD of 0.75 Å. The RMSD value for validating the 7TE0 protein and natural ligand 4WI was 1.65 Å. The best molecular docking results were obtained using physalin F with a binding affinity of −10.3 kcal/mol for the 3V3M protein and physalin J with a binding affinity of −8.9 kcal/mol for the 7TE0 protein. The outcomes of the molecular dynamic method on the best complexes were determined by examining the value of changes in system energy, changes in system temperature, changes in system pressure, RMSD, RMSF, and bond-free energy (ΔG) of the complex. The standard 0EN ligand had a ΔG of −26.53 kcal/mol, while the standard 4WI ligand had a ΔG of −47.16 kcal/mol. The ΔG of the 3V3M-physalin F and 3V3M-physalin J complexes were respectively −28.22 kcal/mol and −26.62 kcal/mol. The ΔG of the 7TE0-Vitexin 2”-O-gallate and 7TE0-physalin J complexes were found to be −28.08 kcal/mol and −26.62 kcal/mol, respectively. The ΔG produced in paxlovid with complexes 3V3M and 7TE0 was −19.38 kcal/mol and −25.44 kcal/mol, respectively. Physalin F, physalin J, and Vitexin 2”-O-gallate have great potential to become SARS-CoV-2 inhibitor agents. However, in terms of structural stability and binding-active residues, these three compounds do not outperform the active substance in paxlovid.
Co-Authors Abdul Rasyid Abidin, Khoirul Agus Malik Ibrahim Ahmad, Halid S. Akram La Kilo Alimuddin Alimuddin Alwi S. Hasan Anna Y. Pomalingo Arafat, Muhammad Yasser Ari Widiantoro Ari Widiyantoro Arifasno Napu Arviani Arviani Astin Lukum Astin Lukum Boima Ramses Situmeang Bumulo, Nuraini Citron S Payu Deasy N Botutihe Deasy Natalia Botutihe Delvi Suleman Djalil, Jhodi Pratama Domu, Siti Afdianti Erni Mohamad Hapsawati Taan Haris Munandar Hartati Inaku Hendri Iyabu Herinda Mardin Ibrahim, Yusni Irwan irwan Ishak Isa Jafar La Kilo Jhodi Pratama Djalil Julhim S Tangio Julinton Sianturi Jumarni Kamarudin Karim, Fadila La Alio La Ode Aman Laliyo, Lukman A.R Lanto Ningrayati Amali Larosa, Esta Lisna Ahmad Lukman A. R. Laliyo M. Yogi Riyantama Isjoni Mangara Sihaloho Mardjan Paputungan Masrid Pikoli Melizubaida Mahmud Moh Adam Mustapa Moh Izwarto Piyohu Moh. Karmin Baruadi Mohamad Adam Mustapa Mohammad Zubair Hippy Murniati . Muti, Nurfadila Najmah Najmah Najmah, Najmah Netty I Ischak Netty Ino Ischak Nita Suleman Noka, Isara Abda Novianti, Rani Nurhayati Bialangi Nurkhaliq, Nurkhaliq Opir Rumape Opir Rumape Parulian, Boima Ramses Podungge, Muhamad Ramdhan Pomuato, Sasmita R Tulie, Wina Zulviana Rahmatia Rahmiyati Kasim Said, Sriyanti S Saiman Saiman Siti Aisa Liputo Siti Rahmatia Machieu Solang, Sriwanda Van Sri Ayu Ashari Suleman Duengo Sunarty Suly Eraku Suryanto Suryanto Syarbin, Ruslun A. R. Tahir, Wawan Umar Sako, Umar Weny J.A Musa Weny Musa Widy Susanti Abdulkadir Wisna Taniyo Wiwin Rewini Kunusa Yayurulia Hadju Yoyanda Bait Yuliyanti Kadir Yusni Ibrahim Yusuf, Novalita Zaenul Wathoni