Docking and Molecular Dynamic Simulations Study to Search Curcumin Analogue Compounds as Potential Inhibitor Against SARS-CoV-2: A Computational Approach

*Neni Frimayanti orcid scopus  -  Sekolah Tinggi Ilmu Farmasi Riau, Indonesia
Adel Zamri orcid scopus  -  Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Riau, Indonesia
Yum Eryanti orcid scopus  -  Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Riau, Indonesia
Noval Herfindo  -  Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Riau, Indonesia
Veza Azteria  -  Study Program of Public Health, Faculty of Health Science, Esa Unggul University, Indonesia
Received: 17 Nov 2020; Revised: 24 Mar 2021; Accepted: 29 Mar 2021; Published: 31 Mar 2021.
Open Access Copyright 2021 Jurnal Kimia Sains dan Aplikasi
License URL: http://creativecommons.org/licenses/by-sa/4.0

Citation Format:
Cover Image
Abstract
Coronavirus is a pandemic in the world. It requires researchers and scientists to work hard to find a vaccine or drug to inhibit the development of the coronavirus. Many drugs have been used, such as remdesivir, lopinavir, and chloroquine. However, how effective is the use of these drugs for inhibiting the coronavirus’s growth? There is no research has been done. Curcumin is now known as one of the compounds that have some biological activities, and it is also can potentially be used as a CoV-2 inhibitor. The computational study, i.e., molecular docking and molecular dynamic, can help researchers to predict which compounds have the potential as an inhibitor against the CoV-2 coronavirus. In this study, lopinavir was used as a positive control. Lopinavir and 45 curcumin analog compounds were docked against the main protease protein with 6LU7 PDB ID. Based on the docking results, it was discovered that compound 1, compound 2, and compound 4 have the same binding orientation as lopinavir. Molecular dynamic simulation with the lowest binding free energy conformation was used to check these compounds’ stability. Only compound 4 was maintained to observe hydrogen bonding with Lys5 and Lys137 with a distance of 2.9 Å. The distance of hydrogen bonds and binding free energy over simulation time is essential to elucidate the potential compound’s affinity. For then, compound 4 can be used as a potential inhibitor against the CoV-2 coronavirus.
Keywords: coronavirus; docking; molecular dynamic; curcumin; lopinavir
Funding: Sekolah Tinggi Ilmu Farmasi Riau

Article Metrics:

Article Info
Section: Research Articles
Language: EN
In Vol 24, No 3 (2021): Volume 24 Issue 3 Year 2021
Statistics: 185 106
Related articles
Study of Kinetics and Adsorption Isotherm of Methylene Blue Dye using Tannin Gel from Ceriops tagal Antioxidant potential and identification of active compounds on Kabau seed (Archidendron bubalinum) flesh and husk extract Characterization and Application of Chitosan as a Natural Coagulant in Reducing Remazol Red Dyestuff Concentration and COD Value of Batik Liquid Waste Utilization of Jengkol Peel (Pithecellobium jiringa (Jack) Prain) as Lead (II) Ions Bio-sorbent with Column Method Cytotoxic, Antiproliferation, and Necrosis Effects of the n-Hexane Fraction Extract of Gendola Leaf (Basella rubra Linn.) Study of Adsorption-Desorption on Batik Industrial Dyes (Naphthol Blue Black) on Magnetite Modified Humic Acid (HA-Fe3O4)
  1. Wei Ji, Wei Wang, Xiaofang Zhao, Junjie Zai, Xingguang Li, Cross-species transmission of the newly identified coronavirus 2019-nCoV, Journal of Medical Virology, 92, 4, (2020), 433-440 https://doi.org/10.1002/jmv.25682
  2. Jun He, Lijun Hu, Xiaojun Huang, Chenran Wang, Zhimin Zhang, Ying Wang, Dongmei Zhang, Wencai Ye, Potential of coronavirus 3C-like protease inhibitors for the development of new anti-SARS-CoV-2 drugs: Insights from structures of protease and inhibitors, International Journal of Antimicrobial Agents, 56, 2, (2020), 106055 https://doi.org/10.1016/j.ijantimicag.2020.106055
  3. World Health Organization, Coronavirus disease (COVID-19) pandemic Dashboard, WHO, 2020
  4. Christian A. Devaux, Jean-Marc Rolain, Philippe Colson, Didier Raoult, New insights on the antiviral effects of chloroquine against coronavirus: what to expect for COVID-19?, International Journal of Antimicrobial Agents, 55, 5, (2020), 105938 https://doi.org/10.1016/j.ijantimicag.2020.105938
  5. Thanigaimalai Pillaiyar, Sangeetha Meenakshisundaram, Manoj Manickam, Recent discovery and development of inhibitors targeting coronaviruses, Drug Discovery Today, 25, 4, (2020), 668-688 https://doi.org/10.1016/j.drudis.2020.01.015
  6. Atala B. Jena, Namrata Kanungo, Vinayak Nayak, G. B. N. Chainy, Jagneshwar Dandapat, Catechin and curcumin interact with S protein of SARS-CoV2 and ACE2 of human cell membrane: insights from computational studies, Scientific Reports, 11, 1, (2021), 2043 https://doi.org/10.1038/s41598-021-81462-7
  7. Yum Eryanti, Adel Zamri, Neni Frimayanti, Hilwan Yuda Teruna, Unang Supratmman, Tati Herlina, Yoshihito Shiono, Synthesis, structure-activity relationship, docking and molecular dynamic simulation of curcumin analogues against HL-60 for anticancer agents (leukemia), Oriental Journal of Chemistry, 33, 5, (2017), 2164-2172 https://doi.org/10.13005/ojc/330503
  8. Bodee Nutho, Panupong Mahalapbutr, Kowit Hengphasatporn, Nawanwat Chainuwong Pattaranggoon, Nattapon Simanon, Yasuteru Shigeta, Supot Hannongbua, Thanyada Rungrotmongkol, Why Are Lopinavir and Ritonavir Effective against the Newly Emerged Coronavirus 2019? Atomistic Insights into the Inhibitory Mechanisms, Biochemistry, 59, 18, (2020), 1769-1779 https://doi.org/10.1021/acs.biochem.0c00160
  9. Jasril Jasril, New Fluorinated Chalcone and Pyrazolines Analogues: Synthesis, Docking and Molecular Dynamic Studies as Anticancer Agents, Thai Journal of Pharmaceutical Sciences (TJPS), 41, 3, (2017), 93-98
  10. Neni Frimayanti, Marzieh Yaeghoobi, Hamid Namavar, Ihsan Ikhtiarudin, Meysam Afzali, In silico studies and biological evaluation of chalcone-based 1, 5-benzothiazepines as new potential H1N1 neuraminidase inhibitors, Journal of Applied Pharmaceutical Science, 10, 10, (2020), 86-94 https://doi.org/10.7324/JAPS.2020.1010010
  11. Akihiro Okamoto, Yoshihide Tokunou, Junki Saito, Cation-limited kinetic model for microbial extracellular electron transport via an outer membrane cytochrome C complex, Biophysics and physicobiology, 13, (2016), 71-76 https://doi.org/10.2142/biophysico.13.0_71
  12. Mohd Shahbaaz, Mohd Amir, Safikur Rahman, Gulam Mustafa Hasan, Ravins Dohare, Krishna Bisetty, Faizan Ahmad, Jihoe Kim, Md Imtaiyaz Hassan, Structural insights into Rab21 GTPase activation mechanism by molecular dynamics simulations, Molecular Simulation, 44, 3, (2018), 179-189 https://doi.org/10.1080/08927022.2017.1357813

Last update: 2021-04-21 10:59:24

No citation recorded.

Last update: 2021-04-21 10:59:24

No citation recorded.
Copyright 2021 Jurnal Kimia Sains dan Aplikasi
License URL: http://creativecommons.org/licenses/by-sa/4.0

As an article writer, the author has the right to use their articles for various purposes, including use by institutions that employ authors or institutions that provide funding for research. Author rights are granted without special permission.

Author who publishes a paper at JKSA has the broad right to use their work for teaching and scientific purposes without the need to ask permission, including: used for (i) teaching in the author's class or institution, (ii) presentation at meetings or conferences and distributing copies to participants ; (iii) training conducted by the author or author's institution; (iv) distribution to colleagues for research use; (v) use in the compilation of subsequent authors' works; (vi) inclusion in a thesis or dissertation; (vi) reuse of part of the article in another work (with citation); (vii) preparation of derivative works (with citation); (viii) voluntary posting on open websites operated by authors or author institutions for scientific purposes (follow the CC BY-SA License).

Authors and readers can copy and redistribute material in any media or format, and mix, modify, and build material for any purpose but they must provide appropriate credit (provide article citation or content), providing links to the license, and indicate if there are changes.

The authors submitting a manuscript do so on the understanding that if accepted for publication, copyright of the article shall be assigned to Jurnal Kimia Sains dan Aplikasi (JKSA). Copyright encompasses rights to reproduce and deliver the article in all form and media, including reprints, photographs, microfilms and any other similar reproductions, as well as translations.

Reproduce any part of this journal, its storage in the database or its transmission by all forms or media is permitted does not need for written permission from JKSA. However, it should be cited as an honor in academic manners

JKSA and the Chemistry Department of Diponegoro University and the Editor make every effort to ensure that there are no data, opinions, or false or misleading statements published in JKSA. However, the content of the article is the sole and exclusive responsibility of each author.

The Copyright Transfer Form can be downloaded here: [Copyright Transfer Form - Indonesian] [Copyright Transfer Form - English]. The copyright form should be signed originally and send to the Editor in the form of printed letters, scanned documents sent via email or fax.

 

Adi Darmawan, Ph.D (Editor in Chief)

Editor in chief of Jurnal Kimia Sains dan Aplikasi (JKSA)

Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Jl. Prof. Soedarto, Kampus Undip Tembalang, Semarang, Central Java, Indonesia 50275
Email: jksa@live.undip.ac.id