Access Type

Open Access Dissertation

Date of Award

January 2013

Degree Type


Degree Name




First Advisor



Histone deacetylase 1 (HDAC1) has been linked to cell growth and cell cycle regulation, which makes it a widely recognized target for anticancer drugs. The 14 Å channel of Class 1 HDAC isotypes has long being hypothesized to be the exit cavity for acetate following deacetylation. The amino acids lining this cavity are very similar among the HDAC isoforms, suggesting the role of the cavity is relevant to all HDACs proteins Importanly, HDAC1 selective inhibitors designed to fit the 14Å channel have been designed. To understand the importance of the 14Å channel to HDAC1 activity, we used an alanine scan to determine the influence of residues in the 14 Å channel of the HDAC1. The mutation of eleven channel residues to alanine led to a significant reduction in deacetylase activity. Acetate competition experiment revealed that, charged residues lining the 14Å affect HDAC1 binding to acetate. The combined results reveal 14Å channel residues critical for HDAC1 activity and acetate escape. With no crystallographic information on HDAC1 available, these findings provide important insight HDAC inhibitor design.

Understanding the involvement of HDAC1 in cancer formation is critical in developing selective inhibitors. Towards this goal, we did extensive studies to create a HDAC1 bump-hole inhibitors pair as an alternative to genetic methods which are limited in their usage to characterize HDAC1 function. We developed and validated a histone deacetylase dependent screen in the yeast Rpd3 protein. Using this screen screened a library of Rpd3 mutants with the aim of isolating active mutants for the bump-hole. Of the 15, 000 colonies screened none had a mutation. We focused on testing the active E98A mutant against SAHA inhibitor analogs present in our lab. C-2, C-3 and N-SAHA analogs were screened using a plate based ELISA assay which we developed and validated. All SAHA analogs screened did not qualify for a HDAC1-bump inhibitor system.

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Biochemistry Commons