full issue - Association of Biotechnology and Pharmacy

Current Trends in Biotechnology and Pharmacy
Vol. 5 (3) 1318 -1324 July 2011, ISSN 0973-8916 (Print), 2230-7303 (Online)
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by using Bioedit (Fig.3). Pre-ADME properties
envisaged that among the chosen ligand
molecules, ampicillin fulfilled the requirements
for the drug solubility, distribution and
elimination (Table- 2).
Fig. 3. Amino Acid Composition by Bioedit. Protein: gi|68249040|ref|YP_248152.1| penicillin-binding protein
1A [Haemophilus influenzae 86-028NP]. Length = 864 amino acids. Molecular Weight = 95630.89 Daltons
Discussion
The proteomic analysis of PBP-1A revealed
its primary properties and secondary structural
information and they are essential to understand
its structure, function and nature of interaction.
The stereochemistry evaluation of predicted 3D
structure of the drug target suggested that the
proposed model is of a good quality. The most
common goal of protein-drug (small molecule)
docking relates to drug design (5, 10). Moreover,
the interaction between the target and the ligand
proposed in this study (Fig.2) is useful for
understanding the potential mechanism of
enzyme and the substrate binding (11). Hydrogen
bonds play important role for the structure and
function of biological molecules, especially for
the enzyme catalysis (12). In the present study,
it was found that the active site residue of PBP-
1A viz., LEU at the position 159 yielded least
energy viz., -10.233 (Table-1), and formed a
strong hydrogen bond interaction with ampicillin
upon comparison with the remaining six ligands.
GOLD, binding site–dependent software,
showed energy minimization and re-ranking of
the top N poses. The GOLD score fitness was
found to be -16.5690.
PBPs have been shown to catalyse a
number of reactions involved in the process of
synthesising cross-linked peptidoglycan from
lipid intermediates and mediate the removal of
D-alanine from the precursor of peptidoglycan
(13). PBPs are reported to have a penicillininsensitive
transglycosylase N-terminal domain
involved in the formation of linear glycan strands
and a penicillin-sensitive transpeptidase C-
terminal domain involved in cross-linking of the
peptide subunits and the serine at the active site
Ramya Jyothi et al