Access Type

Open Access Dissertation

Date of Award

January 2012

Degree Type


Degree Name




First Advisor

Mary Kay H. Pflum


Histone deacetylase (HDAC) proteins are targets for drug design towards the treatment of cancers since overexpression of HDAC is linked to cancer. Several HDAC inhibitors, including the FDA approved drug suberoylanilide hydroxamic acid (SAHA, Vorinostat), have cleared clinical trials and emerged as anti-cancer drugs. However, SAHA inhibits all of the 11 metal ion-dependent HDAC proteins. Therefore, we synthesized several libraries of small molecule HDAC inhibitors based on SAHA to help understand the structural requirements of inhibitory potency and isoform selectivity.

In previous work, SAHA analogues functionalized at the C2 position (C2-SAHA analogues) near the metal binding hydroxamic acid displayed decreased inhibitory activity compared to the parent compound, SAHA. The lack of potency of the C2 library indicated that limited flexibility exists in the HDAC active site near the hydroxamic acid. Therefore, we theorized the substituents on the C3, C4, C5, C6, and C7 positions would display more potent inhibition compared to the C2-SAHA library due to the solvent exposed location. Interestingly, while the C2-SAHA analogues containing any substituents were poor potent, the C3-SAHA analogue with a methyl substituent displayed potency, . The potency of the remaining analogues decreased with increasing size of the C3 substituents. Moreover, the C6-SAHA phenyl analogue even displayed potency in the submicromolar range. Finally, most of the C7-SAHA analogues displayed equal or greater potency compared to SAHA. The results indicate that more flexibility in the HDAC active site exists closer to the capping group region near the C6 and C7 position, while only modest flexibility exists in the bottom of the active site near the C2 and C3 position.

After analyzing the potency of SAHA analogues, isoform selective inhibition of the individual compounds was evaluated. Seven of the SAHA analogues demonstrated selectivity. The C3-SAHA ethyl-substituted analogue showed preference for HDAC6 over HDAC1 and HDAC3 even though it displayed decreased potency. The C6-SAHA analogues displayed diverse selectivity; the C6-SAHA methyl variant displayed preference for class I, t-butyl variant showed a dual-HDAC1 and HDAC6 selectivity, and 2-ethylhexyl variant showed HDAC3-selectivity. The C7-SAHA analogues displayed selective inhibition as well; the C7-SAHA pyridylmethyl and anthracenylmethyl variants displayed a dual-HDAC1 and HDAC6 selectivity, and naphthylmethyl variant showed HDAC3-selectivity. The interesting potency and selectivity of linker-modified SAHA analogues suggest that the linker region substituents can be exploited in the design of new anti-cancer drugs.