DOI: https://doi.org/10.14710/jksa.24.3.85-90

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

1Sekolah Tinggi Ilmu Farmasi (STIFAR), Pekanbaru, Riau, Indonesia

2Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Riau, Riau, 28293, Indonesia

3Study 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 under 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.
Fulltext View|Download
Keywords: coronavirus; docking; molecular dynamic; curcumin; lopinavir
Funding: Sekolah Tinggi Ilmu Farmasi Riau

Article Metrics:

Article Info
Section: Research Articles
Language : EN
Recent articles
Molecular Docking of Red Betel (Piper crocatum Ruiz & Pav) Bioactive Compounds as HMG-CoA Reductase Inhibitor Docking and Molecular Dynamic Simulations Study to Search Curcumin Analogue Compounds as Potential Inhibitor Against SARS-CoV-2: A Computational Approach Addition of Calcined Na2B4O7 on the Synthesis of Li7La3Zr2O12 More recent articles
Most cited articles
Skrining Metabolit Sekunder Bakteri Endofit yang Berfungsi sebagai Antidiabetes dari Daun Mimba (Azadirachta Indica) Interlayer-free Silica Pectin Membrane for Wetland Saline Water via Pervaporation Pengaruh Serbuk Kaca dan Variasi Suhu Pembakaran pada Pembuatan Genteng Lempung Sedimentasi Banjir Kanal Timur Kota Semarang terhadap Kuat Tekan serta Daya Serapnya terhadap Air Sintesis 3-(3,4-Dimetoksi Fenil)-1-Propanol Melalui Hidroborasi Metileugenol Menggunakan H3B:Dietileter Pengaruh Pemerangkapan Enzim Alkalin Fosfatase ke dalam Silika dari Abu Sekam Padi terhadap Aktivitas Enzimatiknya More cited articles
  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:

  1. Synthesis and Tyrosinase Inhibitory Activity of (E)-5-Benzyl-7- (3-Bromobenzylidene)-3-(3-Bromophenyl)-2-Phenyl-3,3a, 4,5,6,7-Hexahydro-2H-Pyrazolo[4,3-c]Pyridine

    Nelly Oscifiani, Noval Herfindo, Rahayu Rahayu, Neni Frimayanti, Adel Zamri. Jurnal Kimia Sains dan Aplikasi, 25 (5), 2022. doi: 10.14710/jksa.25.5.185-191

  2. In Silico Analysis of Inhibitor Potential of Punicalagin Compound in Pomegranate (Punica granatum) Against NS5 DENV-3 Protein

    Radinal Kautsar, Yuanita Rachmawati, Saiku Rokhim, Teguh Hari Sucipto, Mamik Damayanti, Aisyah Hadi Ramadhani. Indonesian Journal of Tropical and Infectious Disease, 12 (1), 2024. doi: 10.20473/ijtid.v12i1.52320

  3. Molecular docking analysis of seagrass (Enhalus acoroides) phytochemical compounds as an antidiabetic

    Yayuk Fatmawati, Sophi Sandrina, Richca Nur Aina, Erlia Narulita. Journal of Biological Research - Bollettino della Società Italiana di Biologia Sperimentale, 95 (1), 2022. doi: 10.4081/jbr.2022.10224

  4. An Insight of Co-Encapsulation Nigella sativa and Cosmos caudatus Kunth Extracts as Anti-Inflammatory Agent Through In Silico Study

    Nadiyah Zuhroh, Zubaidah Ningsih, Anna Safitri. Jurnal Kimia Sains dan Aplikasi, 24 (5), 2021. doi: 10.14710/jksa.24.5.152-160

Last update: 2024-11-23 09:34:12

No citation recorded.