Recent progress on drugs discovery study for treatment of COVID-19: repurposing existing drugs and current natural bioactive molecules

Oktavianawati, Ika; Santoso, Mardi; Bakar, Mohd Fadzelly Abu; Kim, Yong-Ung; Fatmawati, Sri

doi:10.1186/s13765-023-00842-x

Applied Biological Chemistry

Table 4 Antiviral drugs/compounds that have been assessed using in silico approach against SARS-CoV-2 proteins

From: Recent progress on drugs discovery study for treatment of COVID-19: repurposing existing drugs and current natural bioactive molecules

Compounds	Antiviral activities	Molecular docking tools	Refs.
40 triterpenoids, flavonol glycosides, anthocyanidins	SARS-CoV-2 Mpro (pdb id: 6LU7), RBD (pdb id: 6M0J), RdRp (YP_009725307.1), human trans-membrane serine protease 2 TMPRSS2 (NP_001128571.1)	AutoDock Vina	[164]
51 alkaloids, terpenoids, polyphenols, peptides	SARS-CoV-2 Mpro (pdb id: 6LU7)	AutoDock 4.2.0	[165]
19 hydrolyzable tannins	SARS-CoV-2 Mpro (pdb id: 6Y84)	Molecular Operating Environment (MOE 09)	[166]
24 natural plant-based compounds, 22 antiviral drugs, 16 anti-malarial drugs	SARS-CoV-2 Mpro (pdb id: 6LU7)	Virtual screening followed with SP and XP docking modes using GLIDE module MD simulations using GROMACS-2019	[167]
Four tropane alkaloids from Schizanthus porrigens	SARS-CoV-2 PLpro (pdb id: 6WX4)	Autodock Vina Molecular dynamic simulations using NAMD v.2.14	[168]
21 flavonoids	SARS-CoV-2 Mpro (pdb id: 6YNQ)	AutoDock Vina and Swiss dock Molecular dynamic simulations using CABS Flex 2.0	[169]
66 active flavonoids were selected from 2030 natural compounds	SARS-CoV-2 Mpro (pdb id: 6LU7)	GLIDE module	[170]
80 flavonoids	SARS-CoV-2 Mpro (pdb id: 6LU7)	Molegro Virtual Docker 7	[171]
23 flavonoids and 25 indole chalcones	SARS-CoV-2 Mpro (pdb id: 6YB7), RdRp (pdb id: 6M71), spike protein (pdb id: 6LZG)	AutoDock Vina v.1.1.2	[172]
458 flavonoids	SARS-CoV-2 Mpro (pdb id: 6LU7), RdRp (pdb id: 6M71), spike protein (pdb id: 6VW1)	AutoDock 4.1	[173]
12 triterpenoids isolated from Calendula officinalis L	SARS-CoV-2 Mpro (pdb id: 6LU7)	MOE 2019 Suite Molecular dynamic simulation using GROMACS-2019	[174]
14 limonoids and terpenoids	SARS-CoV-2 RBD (pdb id: 6M0J)	AutoDock 4.2 Molecular dynamic simulation using Desmond MD System	[175]
218 coumarins	SARS-CoV-2 Mpro (pdb id: 6LU7), viral methyltransferase (nsp16/10 complex, pdb id: 6W4H), RBD (pdb id: 6M0J), human ACE2 (pdb id: 6VW1)	AutoDock Vina	[176]
78 secoiridoids	SARS-CoV-2 Mpro (pdb id: 6LU7), and S protein (6LZG)	AutoDock Vina Molecular dynamic simulation using Desmond MD System	[177]
6 phenyl propanoids	SARS-CoV-2 Mpro (pdb id: 6Y2F); PLpro (pdb id: 6WX4); RdRp (pdb id: 6M71)	Genetic optimization of ligand docking (GOLD v5.2.2) Groningen machine for chemical simulations (GROMACS v5.15)	[178]

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