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Advances in Bioinformatics
Volume 2014 (2014), Article ID 104823, 10 pages
Research Article

Utilization of Boron Compounds for the Modification of Suberoyl Anilide Hydroxamic Acid as Inhibitor of Histone Deacetylase Class II Homo sapiens

1Bioinformatics Group, Department of Chemistry, Faculty of Mathematics and Science, University of Indonesia, Depok 16424, Indonesia
2Mathematics Computation Group, Department of Mathematics, Faculty of Mathematics and Science, University of Indonesia, Depok 16424, Indonesia

Received 3 June 2014; Revised 12 August 2014; Accepted 12 August 2014; Published 24 August 2014

Academic Editor: Antoine van Kampen

Copyright © 2014 Ridla Bakri 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.


Histone deacetylase (HDAC) has a critical function in regulating gene expression. The inhibition of HDAC has developed as an interesting anticancer research area that targets biological processes such as cell cycle, apoptosis, and cell differentiation. In this study, an HDAC inhibitor that is available commercially, suberoyl anilide hydroxamic acid (SAHA), has been modified to improve its efficacy and reduce the side effects of the compound. Hydrophobic cap and zinc-binding group of these compounds were substituted with boron-based compounds, whereas the linker region was substituted with p-aminobenzoic acid. The molecular docking analysis resulted in 8 ligands with Δ value more negative than the standards, SAHA and trichostatin A (TSA). That ligands were analyzed based on the nature of QSAR, pharmacological properties, and ADME-Tox. It is conducted to obtain a potent inhibitor of HDAC class II Homo sapiens. The screening process result gave one best ligand, Nova2 (513246-99-6), which was then further studied by molecular dynamics simulations.