This proposal is intended to charter new directions for design of more selective and more active histone deacetylase (HDAC) inhibitors by mapping the binding """"""""fingerprints"""""""" of the HDAC ligands in the different HDAC isoforms using small molecule photoaffinity probes. Since many cancers are associated with aberrant transcriptional activity, and the HDACs can affect transcription factors and gene regulation, these enzymes have been identified as attractive targets for cancer therapy. Indeed, chemical inhibitors of HDACs have been shown to inhibit tumor cell growth and induce differentiation and cell death. At least one non-selective HDAC inhibitor was approved by FDA for cancer and several non-selective HDAC inhibitors are in clinical trials. Multiple studies have shown that therapeutics selective for one or a limited number of specific HDAC isoforms may improve overall efficacy and lower toxicity of these compounds. While some rather limited degree of isoform selectivity has been shown by a few compounds, the problem of identifying selective inhibitors is far from solved. Recent success in the elucidation of the crystal structure of HDAC7, 8 and homologous HDAC proteins has opened a possibility for structure-based drug design. Despite the progress, both ligand-based and structure-based approaches are limited in their applicability to design of isoform selective HDAC inhibitors either because only few isoform selective inhibitors are available as a starting point for ligand based drug design or because high resolution three-dimensional structures are available only for 2 out of 11 class I and II HDAC isoforms. It is also poorly understood how the binding modes of those portions of the HDAC ligands that bind on the surface of the HDAC protein affect the activity of HDAC inhibitors. Clearly, a new approach to this problem is needed. We hypothesize that it will be possible to map the binding modes available to the ligands in different HDAC isoforms by small molecule photoaffinity probes (PAP) and use the resulting knowledge to design isoform selective HDAC inhibitors as potential therapeutics for cancer.
Our specific aims i n this proposal are as follow:
Aim 1 : Design and synthesize at least three series of photoaffinity probes (PAPs) consisting of (1) an HDAC ligand, (2) an aromatic azide group for photoaffinity labeling (PAL) of the protein residues directly involved in the binding of the ligand, and (3) an aliphatic azide (a imaging tag attachment group - imTAG) for attaching a fluorescent or a biotin tag.
Aim 2 : Evaluate the ligands containing either PAL or PAL+imTAG or both groups in photoaffinity labeling experiments with available recombinant purified class I and class II HDACs and determine the modification sites on the proteins using mass-spectrometry proteomics methods. Match the proteomics results with the modeling studies and refine later to better reproduce the experimental findings.
Aim 3. Evaluate the cytotoxicity, selectivity, and binding """"""""fingerprints"""""""" of the most potent photoaffinity probes in live Hela cells.
Aim 4. Incorporate the findings of Aims 1-3 in the structure-based drug design and perform several rounds of CADD, medicinal chemistry, and biological tests to improve the activity and selectivity of the HDAC ligands.

Public Health Relevance

This proposal is intended to charter new directions for design of more selective and more active histone deacetylase (HDAC) inhibitors by mapping the binding """"""""fingerprints"""""""" of the HDAC ligands in the different HDAC isoforms using small molecule photoaffinity probes. The ultimate goal of this proposal is to design HDAC inhibitors suitable as HDAC based therapeutics for cancer and other HDAC relevant diseases and conditions.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
Project #
Application #
Study Section
Drug Discovery and Molecular Pharmacology Study Section (DMP)
Program Officer
Lees, Robert G
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Illinois at Chicago
Schools of Pharmacy
United States
Zip Code
Hanigan, Thomas W; Danes, Jeanne M; Taha, Taha Y et al. (2018) Histone deacetylase inhibitor-based chromatin precipitation for identification of targeted genomic loci. J Biol Methods 5:
Abdelkarim, Hazem; Neelarapu, Raghupathi; Madriaga, Antonett et al. (2017) Design, Synthesis, Molecular Modeling, and Biological Evaluation of Novel Amine-based Histone Deacetylase Inhibitors. ChemMedChem 12:2030-2043
Taha, Taha Y; Aboukhatwa, Shaimaa M; Knopp, Rachel C et al. (2017) Design, Synthesis, and Biological Evaluation of Tetrahydroisoquinoline-Based Histone Deacetylase 8 Selective Inhibitors. ACS Med Chem Lett 8:824-829
Hanigan, Thomas W; Aboukhatwa, Shaimaa M; Taha, Taha Y et al. (2017) Divergent JNK Phosphorylation of HDAC3 in Triple-Negative Breast Cancer Cells Determines HDAC Inhibitor Binding and Selectivity. Cell Chem Biol 24:1356-1367.e8
Patel, Hitisha K; Siklos, Marton I; Abdelkarim, Hazem et al. (2014) A chimeric SERM-histone deacetylase inhibitor approach to breast cancer therapy. ChemMedChem 9:602-13
Abdelkarim, Hazem; Brunsteiner, Michael; Neelarapu, Raghupathi et al. (2013) Photoreactive ""nanorulers"" detect a novel conformation of full length HDAC3-SMRT complex in solution. ACS Chem Biol 8:2538-49
Vaidya, Aditya Sudheer; Neelarapu, Raghupathi; Madriaga, Antonett et al. (2012) Novel histone deacetylase 8 ligands without a zinc chelating group: exploring an 'upside-down' binding pose. Bioorg Med Chem Lett 22:6621-7
Neelarapu, Raghupathi; Petukhov, Pavel A (2012) A One-Pot Selective Synthesis of N-Boc Protected Secondary Amines: Tandem Direct Reductive Amination/N-Boc Protection. Tetrahedron 68:7056-7062
Brunsteiner, Michael; Petukhov, Pavel A (2012) Insights from comprehensive multiple receptor docking to HDAC8. J Mol Model 18:3927-39
Vaidya, Aditya Sudheer; Karumudi, Bhargava; Mendonca, Emma et al. (2012) Design, synthesis, modeling, biological evaluation and photoaffinity labeling studies of novel series of photoreactive benzamide probes for histone deacetylase 2. Bioorg Med Chem Lett 22:5025-30

Showing the most recent 10 out of 13 publications