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)
1319
sensitive transpeptidase EC=3.4.-.- Its location
is in the inner cell membrane as type II
membrane protein and plays a key role in the
biogenesis of cell wall and peptidoglycan (4).
The present article aims at the screening of a few
chosen antibiotics against PBP-1A with the
intention of identifying a lead molecule.
Materials and Methods
The amino acid sequence of PBP-1A of
HI strain 86-028NP was extracted from SWISS
Prot database with ID: Q4QNA5. Later,
submitted to NCBI-BLAST (http://
www.ncbi.nlm.nih.gov/BLAST), searched
against protein data bank (http://www.rcsb.org/
pdb/), extracted suitable templates for the query
sequence and found one of the best templates
viz., peptidoglycan glycosyltransferase (PDB
ID:2OQOa) with 52 % identities (8). The length
of PBP-1A was found to be 864 amino acids and
the source of the template is Aquifex aeolicus
(http://www.rcsb.org/pdb/). The primary
properties of protein sequence was analysed by
using Bioedit and the protein secondary structure
prediction was carried out using SOPMA (Self
Optimized Prediction Method). Both the
sequences were aligned using ICM Molsoft and
the same was employed in the construction of
three dimensional structure of PBP-1A. The
alignment of the sequence to be modeled was
done with known related structure in PDB
format. ICM Molsoft further generated a model
structure by minimizing the side chains. To
correct the geometric inaccuracies the theoretical
model was subjected to Procheck. The program,
Procheck concentrates on the parameters such
as bond length, bond angle, main chain and side
chains parameters, residue properties, rms
distance from planarity and distorted geometry
plots. The Protein ligand interaction was
performed using Argus lab engine with flexible
docking (9). Docking analysis was carried out
using on-line GOLD programme.
Results
The in silico tools as indicated in the
previous section, viz., homology modelling,
active site analysis and docking were employed
in the present study for screening the chosen
drugs to bind to the active site of PBP-1A.
The homology modelling of PBP-1A from
HI was obtained from the protein data bank with
ICM Molsoft software. The final model was
evaluated using Procheck. Further validation
analysis employing Ramachandran plot, revealed
that the PBP-1A model showed 92.0% of
residues lie in the most favoured regions and the
remaining 6.3% in the additional allowed
regions. Thus, 98.3% residues are in the allowed
portions of the plot. Hence, PBP-1A is a potential
target to exploit for drug designing, energy
minimization and molecular dynamic
simulations by means of refining loops and
rotomers, checking bonds and adding hydrogen
atoms. The refined model structure thus obtained
after energy minimization and molecular
Fig. 1. Docking in Argus Lab. Docking studies with
Argus lab engine showed that the active site residue is at
159 LEU in PBP-1A. This made a strong hydrogen bond
interaction with ampicillin and yielded least energy -
10.2333.
Ramya Jyothi et al