Maxwell Tucker

North Carolina School of Science and Mathematics

DESIGN AND SYNTHESIS OF A NOVEL THIOLATE

HISTONE DEACETYLASE INHIBITOR

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

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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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

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

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

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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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

Introduction | Molecular Modeling | Synthesis | Conclusions

DOCKING RESULTS

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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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Introduction | Molecular Modeling | Synthesis | Conclusions

SYNTHESIS

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Introduction | Molecular Modeling | Synthesis | Conclusions

SYNTHESIS

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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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Introduction | Molecular Modeling | Synthesis | Conclusions

Active metabolite IR spectrum14

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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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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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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