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.jpg): Failed to open stream: No such file or directory in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 117 ä-/-ä 2022 ; 22
(1
): 107-23
Nephropedia Template TP
gab.com Text
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English Wikipedia
In silico molecular docking and molecular dynamic simulation of potential
inhibitors of 3C-like main proteinase (3CLpro) from severe acute respiratory
syndrome coronavirus-2 (SARS-CoV-2) using selected african medicinal plants
#MMPMIDC7676093
Isa MA
; Mustapha A
; Qazi S
; Raza K
; Allamin IA
; Ibrahim MM
; Mohammed MM
ä-/-ä 2022[]; 22
(1
): 107-23
PMIDC7676093
show ga
The Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is an infectious virus that
causes mild to severe life-threatening upper respiratory tract infection. The
virus emerged in Wuhan, China in 2019, and later spread across the globe. Its
genome has been completely sequenced and based on the genomic information, the
virus possessed 3C-Like Main Protease (3CLpro), an essential multifunctional
enzyme that plays a vital role in the replication and transcription of the virus
by cleaving polyprotein at eleven various sites to produce different
non-structural proteins. This makes the protein an important target for drug
design and discovery. Herein, we analyzed the interaction between the 3CLpro and
potential inhibitory compounds identified from the extracts of Zingiber offinale
and Anacardium occidentale using in silico docking and Molecular Dynamics (MD)
Simulation. The crystal structure of SARS-CoV-2 main protease in complex with 02J
(5-Methylisoxazole-3-carboxylic acid) and PEJ (composite ligand) (PDB Code: 6LU7,
2.16 Å) retrieved from Protein Data Bank (PDB) and subject to structure
optimization and energy minimization. A total of twenty-nine compounds were
obtained from the extracts of Z. offinale and the leaves of A. occidentale. These
compounds were screened for physicochemical (Lipinski rule of five, Veber rule,
and Egan filter), Pan-Assay Interference Structure, and pharmacokinetic
properties to determine the Pharmaceutical Active Ingredients. Of the 29
compounds, only nineteen (19) possessed drug-likeness properties with efficient
oral bioavailability and less toxicity. These compounds subjected to molecular
docking analysis to determine their binding energies with the 3CLpro. The result
of the analysis indicated that the free binding energies of the compounds ranged
between ??5.08 and ??10.24 kcal/mol, better than the binding energies of 02j
(??4.10 kcal/mol) and PJE (??5.07 kcal/mol). Six compounds
(CID_99615?=???10.24 kcal/mol, CID_3981360?=?9.75 kcal/mol,
CID_9910474?=???9.14 kcal/mol, CID_11697907?=???9.10 kcal/mol,
CID_10503282?=???9.09 kcal/mol and CID_620012?=???8.53 kcal/mol) with good
binding energies further selected and subjected to MD Simulation to determine the
stability of the protein?ligand complex. The results of the analysis indicated
that all the ligands form stable complexes with the protein, although,
CID_9910474 and CID_10503282 had a better stability when compared to other
selected phytochemicals (CID_99615, CID_3981360, CID_620012, and CID_11697907).