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OJBTM
Online Journal of Bioinformatics ©
Volume 11 (1):103-124, 2009
Phylogenetic
analysis, homology modeling, molecular dynamics, docking and structure based
designing of new inhibitors against cinnamyl
alcohol dehydrogenase (CAD) cloned and sequenced
from a leguminous
tree subabul (Leucaena
leucocephala)
Sekhar NP1, Kumar RD2, Sirisha VL2, Prashant S2, Kavi Kishor PB1
Department of
Genetics,
Sekhar NP, Kumar RD, Sirisha
VL, Prashant S, Kavi Kishor
PB, Phylogenetic analysis, homology modeling, molecular dynamics, docking and
structure based designing of new inhibitors against cinnamyl
alcohol dehydrogenase (CAD) cloned and sequenced from a leguminous tree subabul (Leucaena leucocephala), Onl J Bioinform., 11 (1):103-124, 2009. Cinnamyl-alcohol dehydrogenase (CAD; EC
1.1.1.195) catalyzes the final step in the branch of phenylpropanoid
synthesis specific for production of lignin monomers. The homology model of CAD
enzyme cloned and sequenced by us from subhabul was build by energy minimization and molecular dynamics in a
solvated water layer. The refined protein showed that the enzyme have 11 a-helices
and 20 β-sheets with a catalytic and nucleotide binding domains forming a rossmanfold. Superimposition of the refined model with the
template showed 1.38Å. Structural analysis of CAD with the templates revealed
highly conserved GHE pattern. Docking studies show that NADPH acts a cofactor
for the enzyme CAD from subhabul. In the presence of
co-factor, 5-hydroxy coniferyl aldehyde binds with
high affinity with the enzyme predicting to be the major substrate for the
enzyme CAD. Pharmacophore based docking of 5-hydroxy coniferyl
aldehyde show that 5-(2-hydroxyethyl)-6-methyl-pyrimidine-2,
4-diol inhibitor binds with high affinity compared to the natural substrates.
Docking studies also shows that His48, Ser49 and His52 plays
an important role in binding of the substrates, products and inhibitors.
Keywords: Cinamyl alcohol dehydrogenase, homology
modeling, docking
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