1. Maxwell Tucker
North Carolina School of Science and Mathematics
DESIGN AND SYNTHESIS OF A NOVEL THIOLATE
HISTONE DEACETYLASE INHIBITOR

2. Introduction | Molecular Modeling | Synthesis | Conclusions
HISTONES AND HISTONE ACETYLATION
• Histones are a major component of chromatin, the skeleton upon which DNA is
stored
• Acetylation and deacetylation of histones affects gene expression
• A number of cancers show excess expression of class I HDACs1
Histone acetylation showing affect on gene expression
Transcriptionally active
Transcriptionally repressed
HAT HDAC
1Dokmanovic, M., Clarke, C., & Marks, P. a. (2007). Histone deacetylase inhibitors: overview and
perspectives. Molecular cancer research : MCR, 5(10), 981–9. 2

3. Introduction | Molecular Modeling | Synthesis | Conclusions
HISTONE DEACETYLASE INHIBITORS (HDACI)
• Competitive inhibitors
• Consist of 3 main groups: surface recognition, linker, and chelating
group
• Act by chelating the zinc ion within metal cofactor-dependent HDACs
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4. Introduction | Molecular Modeling | Synthesis | Conclusions
HYDROXAMIC ACID INHIBITORS
• Hydroxamic acid inhibitors are among the most structurally simple histone
deacetylase inhibitors
• Suberoylanilide hydroxamic acid (vorinostat) is one of only 2 HDACis
currently approved by the FDA
• A host of side effects, including
fatigue, nausea, vomiting, and
anemia2
2Ma, X., Ezzeldin, H. H., & Diasio, R. B. (2009). Histone deacetylase inhibitors: current status and
overview of recent clinical trials. Drugs, 69(14), 1911–34. 4

5. Introduction | Molecular Modeling | Synthesis | Conclusions
DEPSIPEPTIDE/THIOLATE INHIBITORS
• Contain large depsipeptide macrocycles
• Prodrugs which form thiol active metabolite
• Highly selective
Romidepsin and largazole, 2
depsipeptide inhibitors and their
active metabolites3
3Cole, K. E., Dowling, D. P., Boone, M. A., Phillips, A. J., & Christianson, D. W. (2011). Structural basis of
the antiproliferative activity of largazole, a depsipeptide inhibitor of the histone deacetylases. Journal of
the American Chemical Society, (133), 12474–12477. 5

6. Introduction | Molecular Modeling | Synthesis | Conclusions
PROBLEMS WITH CURRENT INHIBITORS
• Hydroxamic acid inhibitors have a host of side affects
• Depsipeptide inhibitors are hard to synthesize and therefore costly
Retrosynthetic
Analysis for
romidepsin4
4Greshock, T., Johns, D., Noguchi, Y., & Williams, R. (2008). Improved total synthesis
of the potent HDAC inhibitor FK228 (FR-901228). Organic letters, 10(4), 613–616. 6

7. Introduction | Molecular Modeling | Synthesis | Conclusions
EXPERIMENTAL DESIGN AND PROJECT GOALS
• Design a synthetic inhibitor with simple synthesis and high anticipated
selectivity and activity
• Adapt simple surface recognition regions from hydroxamic acid
inhibitors
• Aliphatic linker
• Thiol chelating agent
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8. Introduction | Molecular Modeling | Synthesis | Conclusions
MOLEGRO MOLECULAR DOCKING
• Moldock engine uses heuristics with a genetic algorithm for accurate
ligand-protein docking5
• Six novel ligands were tested alongside known hydroxamic acid inhibitors
– TSA and SAHA
5Thomsen, R., & Christensen, M. H. (2006). MolDock: a new technique for high-accuracy molecular docking.
Journal of Medicinal Chemistry, 49(11), 3315–21. 8

9. Introduction | Molecular Modeling | Synthesis | Conclusions
DOCKING RESULTS
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10. Introduction | Molecular Modeling | Synthesis | Conclusions
SYNTHETIC TARGET
The active metabolite, top, and the
synthetic target, a disulfide dimer
• Molecular Weight of 253, 504 for
the dimer
• Few hydrogen bonding sites
• clogP between 3.2 and 3.6
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11. Introduction | Molecular Modeling | Synthesis | Conclusions
SYNTHESIS
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12. Introduction | Molecular Modeling | Synthesis | Conclusions
SYNTHESIS
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13. Introduction | Molecular Modeling | Synthesis | Conclusions
PRODUCT VERIFICATION
• Intermediate products were verified using IR spectroscopy
• Final verification was done using proton and carbon-13 NMR
• C13 NMR shifts were predicted at the B3LYP/6-31G** level on a structure
optimized at the 6-31G* level
C-13 NMR
spectrum of
final product
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14. Introduction | Molecular Modeling | Synthesis | Conclusions
Active metabolite IR spectrum
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15. Introduction | Molecular Modeling | Synthesis | Conclusions
CONCLUSIONS
• Successfully designed and synthesized a novel thiolate histone
deacetylase inhibitor
• Molecule is predicted to have high selectivity and activity, based on
molecular modeling
• May one day prove to be effective for the treatment of cancers
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16. Introduction | Molecular Modeling | Synthesis | Conclusions
FUTURE WORK
• Additional molecular modeling to verify selectivity
• Increased synthetic yields – better catalysis and optimized reaction
conditions
• Preliminary biological assays, first on enzyme samples in vitro, then
established cell lines
DMAP, a potential
catalyst for the
esterification
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17. Introduction | Molecular Modeling | Synthesis | Conclusions
ACKNOWLEDGMENTS
Special Thanks to:
Dr. Myra Halpin
Dr. Darrell Spells
The Research in Chemistry Program and Students
The NCSSM Science Department
Dr. W. Andrew Tucker of Queens University
Additional Thanks to the Following:
Dr. Amy Sheck, NCSSM
Mr. John Woodmansee, NCSSM
Ms. Leslie Brinson, NCSSM
My Family
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