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Advances in Bioinformatics
Volume 2019, Article ID 6912914, 12 pages
https://doi.org/10.1155/2019/6912914
Research Article

In Silico Screening of Aptamers Configuration against Hepatitis B Surface Antigen

1Bioengineering Section, Universiti Kuala Lumpur Malaysian Institute of Chemical and Bioengineering Technology (UniKL MICET), Lot 1988, Bandar Vendor Taboh Naning, 78000 Alor Gajah, Melaka, Malaysia
2Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
3Technical Foundation Section, Universiti Kuala Lumpur Malaysian Institute of Chemical and Bioengineering Technology (UniKL MICET), Lot 1988, Bandar Vendor Taboh Naning, 78000 Alor Gajah, Melaka, Malaysia

Correspondence should be addressed to Mohamad Zulkeflee Sabri; ym.ude.lkinu@eelfekluzm

Received 23 December 2018; Revised 20 April 2019; Accepted 30 April 2019; Published 26 June 2019

Academic Editor: Paul Harrison

Copyright © 2019 Mohamad Zulkeflee Sabri et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Aptamer has been long studied as a substitute of antibodies for many purposes. However, due to the exceeded length of the aptamers obtained in vitro, difficulties arise in its manipulation during its molecular conjugation on the matrix surfaces. Current study focuses on computational improvement for aptamers screening of hepatitis B surface antigen (HBsAg) through optimization of the length sequences obtained from SELEX. Three original aptamers with affinity against HBsAg were truncated into five short hairpin structured aptamers and their affinity against HBsAg was thoroughly studied by molecular docking, molecular dynamics (MD) simulation, and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method. The result shows that truncated aptamers binding on HBsAg “a” determinant region are stabilized by the dynamic H-bond formation between the active binding residues and nucleotides. Amino acids residues with the highest hydrogen bonds hydrogen bond interactions with all five aptamers were determined as the active binding residues and further characterized. The computational prediction of complexes binding will include validations through experimental assays in future studies. Current study will improve the current in vitro aptamers by minimizing the aptamer length for its easy manipulation.