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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
Current Trends in Biotechnology and Pharmacy Vol. 5 (3) 1318 -1324 July 2011, ISSN 0973-8916 (Print), 2230-7303 (Online) 1320 dynamic simulations was subjected for docking studies. Docking studies with Argus lab engine gave an insight into the binding modes of the various inhibitors. Out of the seven drugs that were selected in the present study for screening, it was found that the active site residue viz., 159 LEU of PBP-1A forms a strong hydrogen bond interaction with ampicillin and yielded least energy -10.2333 (Table-1; Fig.1). GOLD program uses a genetic algorithm to explore the full range of ligand conformational and the rotational flexibilities of selected receptor hydrogen atoms. The mechanism for ligand placement is based on fitting points. The GOLD score fitness was found to be -16.596 (Fig.2). Amino acid primary structure analysis was done Fig. 2. Protein-Ligand interactions in GOLD. The mechanism for ligand placement is based on fitting points. The GOLD score fitness was found to be -16.569. Docking of the penicillin binding protein of Haemophilus influenzae
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(December 7-9, 2011) Venue: Karunya
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