title: Structural origin of selectivity in class II-selective histone deacetylase inhibitors.
abstract: The development of class- and isoform-selective histone deacetylase (HDAC) inhibitors is highly desirable for the study of the complex interactions of these proteins central to transcription regulation as well as for the development of selective HDAC inhibitors as drugs in epigenetics. To provide a structural basis for the rational design of such inhibitors, a combined computational and experimental study of inhibition of three different histone deacetylase isoforms, HDAC1, -6, and -8, with three different hydroxamate inhibitors is reported. While SAHA was found to be unselective for the inhibition of class I and class II HDACs, the other inhibitors were found to be selective toward class II HDACs. Molecular dynamics simulations indicate that this selectivity is caused by both the overall shape of the protein surface leading to the active site and specific interactions of an aspartate residue in a polar loop and two phenylalanines and a methionine in a nonpolar loop. Monitoring the specific interactions as a function of the simulation time identifies a key sulfur-pi interaction. The implications of the structural motifs for the design of class II-selective HDAC inhibitors are discussed.
authors.affiliation: Walther Cancer Research Center, Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA.
authors.forename: Guillermina
authors.initials: G
authors.lastname: Estiu
authors.forename: Edward
authors.initials: E
authors.lastname: Greenberg
authors.forename: Christopher B
authors.initials: CB
authors.lastname: Harrison
authors.forename: Nicholas P
authors.initials: NP
authors.lastname: Kwiatkowski
authors.forename: Ralph
authors.initials: R
authors.lastname: Mazitschek
authors.forename: James E
authors.initials: JE
authors.lastname: Bradner
authors.forename: Olaf
authors.initials: O
authors.lastname: Wiest
mesh_terms: D000813:Anilides / Q000737:chemistry; D018360:Crystallography, X-Ray; D056284:Histone Deacetylase 1; D000073864:Histone Deacetylase 6; D056572:Histone Deacetylase Inhibitors; D006655:Histone Deacetylases / Q000737:chemistry; D006877:Hydroxamic Acids / Q000737:chemistry; D007527:Isoenzymes / Q000037:antagonists & inhibitors / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D012097:Repressor Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry; D013329:Structure-Activity Relationship; D000077337:Vorinostat
chemical_list: D000813:Anilides; D056572:Histone Deacetylase Inhibitors; D006877:Hydroxamic Acids; D007527:Isoenzymes; D012097:Repressor Proteins; C474316:tubacin; D000077337:Vorinostat; C110550:HDAC1 protein, human; C433811:HDAC6 protein, human; C409470:HDAC8 protein, human; D056284:Histone Deacetylase 1; D000073864:Histone Deacetylase 6; D006655:Histone Deacetylases