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Biophysical Mechanism of the SAHA Inhibition of Zn^（2+）-Histone Deacetylase-Like Protein(fb188 hdah)Assessed via Crystal Structure Analysis

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Computational Molecular Bioscience 2018年第2期8卷 91-114页

作者： Cynthia Raquel Trejo-Munoz Ricardo Vázquez-Ramírez Luis Mendoza Carlos Kubli-Garfias Escuela Superior de Medicina Instituto Politécnico NacionalCiudad de MéxicoMéxico Instituto de Investigaciones Biomédicas Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico

The zinc-containing enzyme HDAC-like amidohydrolase (fb188 hdah), identified in the Bordetella alcaligenes bacteria, is similar to enzymes that participate in epigenetic mechanisms such as histone modifications. The X-ray crystal structure of fb188 hdah complexed with the antagonist SAHA (suberoylanilide hydroxamic acid) has been solved (PDB ID: 1ZZ1). Notably, the complex crystallizes as a tetramer in the asymmetric unit cell of the crystal. The crystal yielded a suitable structure to analyze the dynamics of the inhibitory mechanism of SAHA on this histone deacetylase. Applying computational chemistry techniques and quantum mechanics theory, several physicochemical properties were calculated to compare the active site of the enzyme of the four monomers. Significant differences were observed in the areas and volumes of the binding pocket, as well as hydrophobic interactions, dipole moments, atomic charges and electrostatic potential, among other properties. Remarkably, a free-energy curve resulting from the evaluation of the energies of SAHA and the interacting amino acids of the four crystal monomers unveiled the biophysical mechanism of the fb188 hdah inhibition exerted by SAHA to a greater extent. The biophysical mechanism of SAHA inhibition on fb188 deacetylase was clearly observed as a dynamic process. It is possible to define the physicochemical dynamics of the molecular complex by the application of computational chemistry techniques and quantum mechanics theory by studying the crystal structures of the interacting molecules.

关键词： SAHA Deacetylase fb188 hdah Free-Energy Crystal-Analysis

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