In silico screening of aptamers configuration against hepatitis B surface antigen

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...

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Main Authors:	Sabri, Mohamad Zulkeflee, Abdul Hamid, Azzmer Azzar
Format:	Article
Language:	English English
Published:	Hindawi 2019
Subjects:	QD Chemistry QR Microbiology
Online Access:	http://irep.iium.edu.my/73863/ http://irep.iium.edu.my/73863/ http://irep.iium.edu.my/73863/ http://irep.iium.edu.my/73863/1/Azzmer%20et%20al%202019%20b.pdf http://irep.iium.edu.my/73863/7/73863_In%20silico%20screening%20of%20aptamers_Scopus.pdf

id	iium-73863
recordtype	eprints
spelling	iium-738632019-08-23T02:12:20Z http://irep.iium.edu.my/73863/ In silico screening of aptamers configuration against hepatitis B surface antigen Sabri, Mohamad Zulkeflee Abdul Hamid, Azzmer Azzar QD Chemistry QR Microbiology 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. Hindawi 2019 Article PeerReviewed application/pdf en http://irep.iium.edu.my/73863/1/Azzmer%20et%20al%202019%20b.pdf application/pdf en http://irep.iium.edu.my/73863/7/73863_In%20silico%20screening%20of%20aptamers_Scopus.pdf Sabri, Mohamad Zulkeflee and Abdul Hamid, Azzmer Azzar (2019) In silico screening of aptamers configuration against hepatitis B surface antigen. Advances in Bioinformatics, 2019 (12 pages). pp. 1-12. ISSN 1687-8027 https://www.hindawi.com/journals/abi/2019/6912914/ 10.1155/2019/6912914
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English English
topic	QD Chemistry QR Microbiology
spellingShingle	QD Chemistry QR Microbiology Sabri, Mohamad Zulkeflee Abdul Hamid, Azzmer Azzar In silico screening of aptamers configuration against hepatitis B surface antigen
description	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.
format	Article
author	Sabri, Mohamad Zulkeflee Abdul Hamid, Azzmer Azzar
author_facet	Sabri, Mohamad Zulkeflee Abdul Hamid, Azzmer Azzar
author_sort	Sabri, Mohamad Zulkeflee
title	In silico screening of aptamers configuration against hepatitis B surface antigen
title_short	In silico screening of aptamers configuration against hepatitis B surface antigen
title_full	In silico screening of aptamers configuration against hepatitis B surface antigen
title_fullStr	In silico screening of aptamers configuration against hepatitis B surface antigen
title_full_unstemmed	In silico screening of aptamers configuration against hepatitis B surface antigen
title_sort	in silico screening of aptamers configuration against hepatitis b surface antigen
publisher	Hindawi
publishDate	2019
url	http://irep.iium.edu.my/73863/ http://irep.iium.edu.my/73863/ http://irep.iium.edu.my/73863/ http://irep.iium.edu.my/73863/1/Azzmer%20et%20al%202019%20b.pdf http://irep.iium.edu.my/73863/7/73863_In%20silico%20screening%20of%20aptamers_Scopus.pdf
first_indexed	2023-09-18T21:44:43Z
last_indexed	2023-09-18T21:44:43Z
_version_	1777413373566124032

In silico screening of aptamers configuration against hepatitis B surface antigen

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