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In silico approach towards designing virtual oligopeptides for HRSV.

Jain R, Piramanayagam S - ScientificWorldJournal (2014)

Bottom Line: In the present study, in silico docking was performed using motavizumab as a template to design motavizumab derived oligopeptides for developing novel anti-HRSV agents.Our study demonstrated the best specific interaction of GEKKLVEAPKS oligopeptide for glycoprotein strain A among various screened oligopeptides.Encouraged by the results, we expect that the proposed scheme will provide rational choices for antibody reengineering which is useful for systematically identifying the possible ways to improve efficacy of existing antibody drugs.

View Article: PubMed Central - PubMed

Affiliation: DBT-Bioinformatics Centre, Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu 641 046, India.

ABSTRACT
HRSV (human respiratory syncytial virus) is a serious cause of lower respiratory tract illness in infants and young children. Designing inhibitors from the proteins involved in virus replication and infection process provides target for new therapeutic treatments. In the present study, in silico docking was performed using motavizumab as a template to design motavizumab derived oligopeptides for developing novel anti-HRSV agents. Additional simulations were conducted to study the conformational propensities of the oligopeptides and confirmed the hypothesis that the designed oligopeptide is highly flexible and capable of assuming stable confirmation. Our study demonstrated the best specific interaction of GEKKLVEAPKS oligopeptide for glycoprotein strain A among various screened oligopeptides. Encouraged by the results, we expect that the proposed scheme will provide rational choices for antibody reengineering which is useful for systematically identifying the possible ways to improve efficacy of existing antibody drugs.

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Related in: MedlinePlus

Interaction of small hydrophobic protein and motavizumab showing interaction of residues with heavy and light chain through various bonds*.
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Related In: Results  -  Collection


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fig7: Interaction of small hydrophobic protein and motavizumab showing interaction of residues with heavy and light chain through various bonds*.

Mentions: Modeled structures of glycoproteins A and B, matrix protein, and small hydrophobic proteins were represented in Figure 1. All modeled structures were validated through Structural Analysis and Verification Server (SAVES) [19]. Ramachandran plot showed that 90.3% of the residues from glycoprotein A, 83.4% of the residues from glycoprotein B, 86.5% of the residues of matrix protein, and 88.3% of the residues from small hydrophobic protein were present in most favoured regions (Figure 2). Motavizumab was subjected to interact with all surface proteins. Heavy chain (H chain) of motavizumab interacted with glycoprotein A through five hydrogen bonds and nonbond interactions while light chain (L chain) interacted with one hydrogen bond and nonbond interactions (Figure 3). H chain of motavizumab bound with glycoprotein B by four hydrogen bonds and nonbond interactions while no hydrogen bond was found in the interaction with L chain showing all nonbond interactions in Figure 4. H chain of motavizumab formed three hydrogen bonds and nonbonded interaction whereas no hydrogen bond was found when motavizumab interacted with L chain of fusion protein (Figure 5). H chain of motavizumab interacted with matrix protein and formed one hydrogen bond and nonbond interactions whereas L chain of motavizumab interacted with matrix protein and formed eight hydrogen bonds, one salt bridge, and nonbond interaction (Figure 6). Finally H chain of motavizumab bound with small hydrophobic protein with three hydrogen bonds and other nonbond interactions while no hydrogen bond was formed when it interacted with L chain of motavizumab; only nonbonded interactions were seen (Figure 7).


In silico approach towards designing virtual oligopeptides for HRSV.

Jain R, Piramanayagam S - ScientificWorldJournal (2014)

Interaction of small hydrophobic protein and motavizumab showing interaction of residues with heavy and light chain through various bonds*.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4265542&req=5

fig7: Interaction of small hydrophobic protein and motavizumab showing interaction of residues with heavy and light chain through various bonds*.
Mentions: Modeled structures of glycoproteins A and B, matrix protein, and small hydrophobic proteins were represented in Figure 1. All modeled structures were validated through Structural Analysis and Verification Server (SAVES) [19]. Ramachandran plot showed that 90.3% of the residues from glycoprotein A, 83.4% of the residues from glycoprotein B, 86.5% of the residues of matrix protein, and 88.3% of the residues from small hydrophobic protein were present in most favoured regions (Figure 2). Motavizumab was subjected to interact with all surface proteins. Heavy chain (H chain) of motavizumab interacted with glycoprotein A through five hydrogen bonds and nonbond interactions while light chain (L chain) interacted with one hydrogen bond and nonbond interactions (Figure 3). H chain of motavizumab bound with glycoprotein B by four hydrogen bonds and nonbond interactions while no hydrogen bond was found in the interaction with L chain showing all nonbond interactions in Figure 4. H chain of motavizumab formed three hydrogen bonds and nonbonded interaction whereas no hydrogen bond was found when motavizumab interacted with L chain of fusion protein (Figure 5). H chain of motavizumab interacted with matrix protein and formed one hydrogen bond and nonbond interactions whereas L chain of motavizumab interacted with matrix protein and formed eight hydrogen bonds, one salt bridge, and nonbond interaction (Figure 6). Finally H chain of motavizumab bound with small hydrophobic protein with three hydrogen bonds and other nonbond interactions while no hydrogen bond was formed when it interacted with L chain of motavizumab; only nonbonded interactions were seen (Figure 7).

Bottom Line: In the present study, in silico docking was performed using motavizumab as a template to design motavizumab derived oligopeptides for developing novel anti-HRSV agents.Our study demonstrated the best specific interaction of GEKKLVEAPKS oligopeptide for glycoprotein strain A among various screened oligopeptides.Encouraged by the results, we expect that the proposed scheme will provide rational choices for antibody reengineering which is useful for systematically identifying the possible ways to improve efficacy of existing antibody drugs.

View Article: PubMed Central - PubMed

Affiliation: DBT-Bioinformatics Centre, Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu 641 046, India.

ABSTRACT
HRSV (human respiratory syncytial virus) is a serious cause of lower respiratory tract illness in infants and young children. Designing inhibitors from the proteins involved in virus replication and infection process provides target for new therapeutic treatments. In the present study, in silico docking was performed using motavizumab as a template to design motavizumab derived oligopeptides for developing novel anti-HRSV agents. Additional simulations were conducted to study the conformational propensities of the oligopeptides and confirmed the hypothesis that the designed oligopeptide is highly flexible and capable of assuming stable confirmation. Our study demonstrated the best specific interaction of GEKKLVEAPKS oligopeptide for glycoprotein strain A among various screened oligopeptides. Encouraged by the results, we expect that the proposed scheme will provide rational choices for antibody reengineering which is useful for systematically identifying the possible ways to improve efficacy of existing antibody drugs.

Show MeSH
Related in: MedlinePlus