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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 antibody with original and designed oligopeptides; arrow represents binding site of oligopeptide with antibody, as shown in the lower right side of each figure. (a1) represents original PGKYKLAVSEK, (a2) represents designed oligopeptide GEKKLVEAPKS, (b1) represents original SGVQPDAPSNDSKDT, (b2) represents designed oligopeptide PDAPSQNDGKDSSTV, (c1) represents original PSTLSVSSGTVYEKHEGLS, (c2) represents designed oligopeptide YHTGSSVSLTSPSLGEVKE, (d1) represents original KREAKQEE, and (d2) designed oligopeptide AEKREKQE.
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fig10: Interaction of antibody with original and designed oligopeptides; arrow represents binding site of oligopeptide with antibody, as shown in the lower right side of each figure. (a1) represents original PGKYKLAVSEK, (a2) represents designed oligopeptide GEKKLVEAPKS, (b1) represents original SGVQPDAPSNDSKDT, (b2) represents designed oligopeptide PDAPSQNDGKDSSTV, (c1) represents original PSTLSVSSGTVYEKHEGLS, (c2) represents designed oligopeptide YHTGSSVSLTSPSLGEVKE, (d1) represents original KREAKQEE, and (d2) designed oligopeptide AEKREKQE.

Mentions: For further screening among these designed oligopeptides, molecular docking procedure was performed by ZDOCK server for original oligopeptide and designed oligopeptide to check their affinity towards respective proteins (Figure 10) which showed that Z-score of PGKYKLAVSEK is 964.281 and designed oligopeptide (GEKKLVEAPKS) Z-score is 994.764, whereas the Z-score of SGVQPDAPSNDSKDT is 937.834 and designed oligopeptide (PDAPSQNDGKDSSTV) Z-score is 632.903, similarly PSTLSVSSGTVYEKHEGLS Z-score is 868.628 and designed oligopeptide (YHTGSSVSLTSPSLGEVKE) Z-score is 654.164, and finally KREAKQEE Z-score is 576.178 and designed oligopeptide (AEKREKQE) Z-score is 572.8880. Based on the binding efficacy and peptide properties of the designed oligopeptide from PGKYKLAVSEK, GEKKLVEAPKS can be considered for further studies.


In silico approach towards designing virtual oligopeptides for HRSV.

Jain R, Piramanayagam S - ScientificWorldJournal (2014)

Interaction of antibody with original and designed oligopeptides; arrow represents binding site of oligopeptide with antibody, as shown in the lower right side of each figure. (a1) represents original PGKYKLAVSEK, (a2) represents designed oligopeptide GEKKLVEAPKS, (b1) represents original SGVQPDAPSNDSKDT, (b2) represents designed oligopeptide PDAPSQNDGKDSSTV, (c1) represents original PSTLSVSSGTVYEKHEGLS, (c2) represents designed oligopeptide YHTGSSVSLTSPSLGEVKE, (d1) represents original KREAKQEE, and (d2) designed oligopeptide AEKREKQE.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig10: Interaction of antibody with original and designed oligopeptides; arrow represents binding site of oligopeptide with antibody, as shown in the lower right side of each figure. (a1) represents original PGKYKLAVSEK, (a2) represents designed oligopeptide GEKKLVEAPKS, (b1) represents original SGVQPDAPSNDSKDT, (b2) represents designed oligopeptide PDAPSQNDGKDSSTV, (c1) represents original PSTLSVSSGTVYEKHEGLS, (c2) represents designed oligopeptide YHTGSSVSLTSPSLGEVKE, (d1) represents original KREAKQEE, and (d2) designed oligopeptide AEKREKQE.
Mentions: For further screening among these designed oligopeptides, molecular docking procedure was performed by ZDOCK server for original oligopeptide and designed oligopeptide to check their affinity towards respective proteins (Figure 10) which showed that Z-score of PGKYKLAVSEK is 964.281 and designed oligopeptide (GEKKLVEAPKS) Z-score is 994.764, whereas the Z-score of SGVQPDAPSNDSKDT is 937.834 and designed oligopeptide (PDAPSQNDGKDSSTV) Z-score is 632.903, similarly PSTLSVSSGTVYEKHEGLS Z-score is 868.628 and designed oligopeptide (YHTGSSVSLTSPSLGEVKE) Z-score is 654.164, and finally KREAKQEE Z-score is 576.178 and designed oligopeptide (AEKREKQE) Z-score is 572.8880. Based on the binding efficacy and peptide properties of the designed oligopeptide from PGKYKLAVSEK, GEKKLVEAPKS can be considered for further studies.

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