In silico docking of phage-displayed peptides targeting Plasmodium vivax apical membrane antigen 1 (PvAMA1)

Chew, C.H. and Lim, Y.A.L. and Chua, K.H. (2018) In silico docking of phage-displayed peptides targeting Plasmodium vivax apical membrane antigen 1 (PvAMA1). In: 3rd AMDI International Biohealth Science Conference (IBSC) 2018, 18-20 Jan 2018, Sarawak, Malaysia.

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Abstract

Purpose: Plasmodium is an obligate intracellular parasite that rely on the ability in host cell penetration and replication. Apical membrane antigen 1 (AMA1) is one of the most well characterized malarial surface antigen for parasite-host cell invasion and served as a pivotal vaccine candidate and potent antimalarial drug target. The present study aimed to predict the binding sites of three previously selected phage-displayed dodecapeptides, i.e., PdVI (DLTFTVNPLSKA), PdV2 (WHWSWWNPNQLT), and PdV3 (TSVSYTNNRHNL) with affinity to refolded recombinant P. vivax AMA1 (rPvAMA l). Methods: The binding sites of the PdVl , PdV2, and PdVJ peptides to the native PvAMA 1 (PDB TD: IW8K) were predicted in silico using CABs-dock web server /Lbiocomp.chem .uw.edu.pl/CABSdock). The pairs of peptide/receptor residues with 3.5 A contact cutoff were then mapped to the native amino acid residues of PvAMA l (1W8K) and rPvAMA I. Results: The simul ation models of protein-peptide docking indicated that the PdVl and PdV3 peptides were mapped to the similar regions, mainly at domains IT and III with sharing 12 similar binding sites, whereas PdV2 peptide was mapped solely Lo the DI of PvAMAl. Conclusion: Phage display technique was used to screen the phage clones that bind to the rPvAMA I. CABS-dock is a free web server for the flexible docking of peptides to target protein without prior knowledge of the binding site and also allow prediction of complex a1i-angcments close to the native structure. A greater understanding of the molecular interaction between the parasite and its host would assist in the development of new therapeutics and most importantly, a vaccine for long term sustainable reduction in the global burden of malaria.

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