In silico targeting DENV2's prefusion envelope protein by several natural products' bioactive compounds

Hidayatullah, Arief and Putra, Wira Eka and Sustiprijatno, Sustiprijatno and Permatasari, Galuh Wening and Salma, Wa Ode and Widiastuti, Diana and Susanto, Hendra and Muchtaromah, Bayyinatul and Sari, Dewi Ratih Tirto and Ningsih, Febby Nurdiya and Heikal, Muhammad Fikri and Yusuf, Alyana Mahdavikia Rosyada and Arizona, Aliyya Suci (2021) In silico targeting DENV2's prefusion envelope protein by several natural products' bioactive compounds. Journal of Natural Science, 20 (4). pp. 1-20. ISSN 16851994

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Abstract

Dengue caused by the dengue virus (DENV) is a severe health problem in tropical regions such as Southeast Asia, especially Indonesia. Indonesian have used rhizome as traditional medicine for 1300 years. This study investigated the compounds from Kaempferia galanga, Curcuma longa, Zingiber officinale, Curcuma aeruginosa, Curcuma zanthorrhiza, Alpinia galanga, and Allium sativum as antivirals agents, explicitly targeting the DENV envelope protein to inhibit viral fusion. This study involved 121 bioactive compounds and DENV2's prefusion envelope protein. The virtual screening and molecular docking were done through occupied the Lipinski rule of five checker (http://www.scfbio-iitd.res.in/software/drugdesign/lipinski.jsp) and AutoDock Vina (https://pyrx.sourceforge.io/) respectively. The top nine compounds with the strongest binding affinity were galangin, kampferide, demetoxy curcumin, bisdemethoxycurcumin, β-selinene, 6-(hydroxymethyl)-1,4,4-trimethylbicyclo[3.1.0]hexan-2-ol, piperine, estra-1,3, 5(10)-trien-17β-ol, and curcumin. These compounds' affinity values were significantly lower, around 45-62%, than chloroquine. Most of them interact with the kl hairpin and hydrophobic pocket formed by residues Val130, Leu135, Phe193, Leu198, and Phe279of critical domains that can interfere with the conformational change and rearrangement of protein dimer in the post-fusion stage. This study suggested that the galangin, demethoxycurcumin, and bisdemethoxycurcumin are considered the most potential compounds to be developed as anti-prefusion E DENV2 low-affinity and intense interaction with those.

Item Type: Journal Article
Keywords: DENV2; envelope protein; in silico; viral fusion; viral infection
Subjects: 06 BIOLOGICAL SCIENCES > 0601 Biochemistry and Cell Biology > 060102 Bioinformatics
06 BIOLOGICAL SCIENCES > 0601 Biochemistry and Cell Biology > 060108 Protein Trafficking
06 BIOLOGICAL SCIENCES > 0604 Genetics > 060406 Genetic Immunology
06 BIOLOGICAL SCIENCES > 0605 Microbiology > 060506 Virology
06 BIOLOGICAL SCIENCES > 0699 Other Biological Sciences > 069999 Biological Sciences not elsewhere classified
06 BIOLOGICAL SCIENCES > 0699 Other Biological Sciences
Divisions: Faculty of Mathematics and Sciences > Department of Biology
Depositing User: Bayyinatul Muchtaromah
Date Deposited: 24 May 2021 11:38

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