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The Design and Synthesis of Peptidomimetic Serine-Based Prodrugs As 14-3-3 Inhibitors

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The Design and Synthesis of Peptidomimetic Serine-Based Prodrugs As 14-3-3 Inhibitors Purdue University Purdue e-Pubs Open Access Theses Theses and Dissertations 2013 The esiD gn And Synthesis Of Peptidomimetic Serine-Based Prodrugs As 14-3-3 Inhibitors Eric Drake Jones Purdue University, [email protected] Follow this and additional works at: https://docs.lib.purdue.edu/open_access_theses Part of the Chemistry Commons Recommended Citation Jones, Eric Drake, "The eD sign And Synthesis Of Peptidomimetic Serine-Based Prodrugs As 14-3-3 Inhibitors" (2013). Open Access Theses. 46. https://docs.lib.purdue.edu/open_access_theses/46 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. Graduate School ETD Form 9 (Revised 12/07) PURDUE UNIVERSITY GRADUATE SCHOOL Thesis/Dissertation Acceptance This is to certify that the thesis/dissertation prepared By Eric Drake Jones Entitled The Design and Synthesis of Peptidomimetic Serine-Based Prodrugs as 14-3-3 Inhibitors. Master of Science For the degree of Is approved by the final examining committee: Richard F. Borch Chair Mark S. Cushman Robert L. Geahlen To the best of my knowledge and as understood by the student in the Research Integrity and Copyright Disclaimer (Graduate School Form 20), this thesis/dissertation adheres to the provisions of Purdue University’s “Policy on Integrity in Research” and the use of copyrighted material. Approved by Major Professor(s): ____________________________________Richard F. Borch ____________________________________ Approved by: Richard F. Borch 11/5/2013 Head of the Graduate Program Date THE DESIGN AND SYNTHESIS OF PEPTIDOMIMETIC SERINE-BASED PRODRUGS AS 14-3-3 INHIBITORS A Thesis Submitted to the Faculty of Purdue University by Eric Drake Jones In Partial Fulfillment of the Requirements for the Degree of Masters of Science December 2013 Purdue University West Lafayette, Indiana ii ACKNOWLEDGMENTS First, I would like to thank Dr. Richard F. Borch for the opportunity which he gave me to take on this project in his laboratory. His gentle guidance, commitment to active communication, and patience has made working for him a pleasurable experience in sometimes trying times. Next, I would like to thank my committee members Dr. Mark Cushman, Dr. Robert Geahlen, and Dr. Alexander Wei. Their comments and questions over the course of many imperfect presentations have helped me to grow as a person and a scientist. I have also been fortunate to experience this journey with many people. I would like to acknowledge my current labmates Irene George, Christina Marian, and Mark Westbroek for the great conversation while here and their everyday help. There are also many former labmates, but I should especially thank Bidyut Biswas and Daniel Nicponski for helping to mold me into a competent chemist. Purdue has offered many great departments and facilities which I have benefited from. The PULSe program’s acceptance and the office staff who helped me consistently. There were many people throughout the chemistry department that were valuable throughout my time there, but particularly I’d like to thank Rob McCormick for many understanding conversations and his infectiously cheerful mood. Last but not least, I should thank my loved ones. The unconditional support of my parents, Floyd and Cynthia Jones, has been instrumental in decompressing some days and always gives me a place to vent. Thanks to my brother, Floyd J. Jones for conversations that expand my horizons and increase my mindfulness. Additionally, thanks to Dr. Maris Cinelli who is my dearest love, an inspiration, offers more guidance than can be adequately described, and makes each day more enjoyable than the last. iii TABLE OF CONTENTS Page LIST OF SCHEMES ..................................................................................................................... iv LIST OF CHARTS AND FIGURES .............................................................................................. v LIST OF SYMBOLS AND ABBREVIATIONS .......................................................................... vi ABSTRACT ................................................................................................................................... ix CHAPTER 1. CHARACTERIZATION OF 14-3-3 PROTEIN ..................................................... 1 CHAPTER 2. INTRODUCTION TO THE 14-3-3 PROTEIN’S BIOLOGICAL FUNCTIONS .. 3 CHAPTER 3. CURRENT PROTEIN STABILIZING/DISRUPTINGMOLECULES .................. 7 CHAPTER 4. RATIONALE AND FORMATION OF COMPOUNDS FOR SYNTHESIS ...... 10 CHAPTER 5. SYNTHESIS OF MODELED COMPOUNDS ..................................................... 19 CHAPTER 6. FUTURE DIRECTIONS/DISCUSSIONS ............................................................ 25 CHAPTER 7. PROCEDURES ..................................................................................................... 26 LIST OF REFERENCES .............................................................................................................. 57 iv LIST OF SCHEMES Scheme Page 1. In vivo removal of prodrugs used for proposed synthesis and cellular access. .......................... 9 2. Synthesis of chiral aziridine as a precursor of difluoromethylenephosphonate serine. ............ 19 3. Opening of the aziridine and subsequent preparation of 17 for prodrug modification. ............ 20 4. Preparation of prodrugs. …........................................................................................................ 20 5. Prodrug coupling to create a phosphoramidate from serinol-like difluorophosphonate 17....... 21 6. Oxidation of serinol-like difluorophosphonate, amide formation, and amine deprotection ..... 21 7. Formation of glycine amides of carboxyl substituted quinoline and isoquinolines .................. 22 8. Boc-protected indole/indolines as precursors to final peptidomimetics. .................................. 22 9. Amide-based protections formed to release the indoline in vivo. ............................................ 23 10. Synthesis of indole and indoline of glycine amides precursors. ............................................. 24 11. Synthesis of final products from amide coupling. .................................................................. 24 v LIST OF CHARTS AND FIGURES Chart/Figure Page 1. Monomer of 14-3-3 structure bound to mode 1 consensus sequence. ........................................ 2 2. Known molecular inhibitors and molecular stabilizers of 14-3-3. ............................................. 7 3. Linear (magenta) and bent (cyan) modes of Compound 1. ..................................................... 11 4. Consensus sequence mode I binding and major interactions. ................................................... 12 5. Chart of G-scores of synthesized compounds. .......................................................................... 14 6. Proposed compounds for synthesis and corresponding G-Scores/C logP. ............................... 15 7. The reverse linear phase binding mode of N-formyl indoline with low C log P. ..................... 16 8. Comparison of indoline and isoquinoline binding mode on the formation of an H-bond to GLU182. ....................................................................................................................................... 17 9. Quinoline and isoquinoline binding modes which demonstrate the comparative input of binding the hydrophobic pocket in helices three and five. ......................................................................... 18 10. Proposed final compounds for synthesis. ................................................................................ 19 vi LIST OF SYMBOLS AND ABBREVIATIONS 19F NMR Fluorine nuclear magnetic resonance 31P NMR Phosphorous nuclear magnetic resonance 1H NMR Proton nuclear magnetic resonance Å Angstrom µM Micromolar Ac2O Acetic anhydride aq. Aqueous Bn Benzyl Boc N-tert-Butoxycarbonyl BOP Benzotriazol-1-yloxytris(Demtheylamino)phosphonium hexafluorophosphate br d Broad doublet br m Broad multiplet br s Broad singlet CI Chemical Ionization cm-1 Wavenumber d Doublet DBU 1,8-Diazabicyclo[5.4.0]undec-7-ene DCC N,N'-Dicyclohexylcarbodiimide DCM Dichloromethane DEAD Diethyl azodicarboxylate dd Doublet of doublets DIC N,N′-Diisopropylcarbodiimide DIPA Diisopropylamine DIPEA Diisopropylethylamine DMF N,N-Dimethylformamide DMAP N,N-(Dimethylamino)pyridine vii dt Doublet of triplets ER Enantiomeric ratio ESI Electrospray ionization EtOAc Ethyl acetate EtOH Ethanol Fmoc (9H-Fluoren-9-yl)methyl carbonyl G score Score output by glide© FT-IR Fourier transform infrared H2O Water H2SO4 Sulfuric acid H-Bond Hydrogen bond HCl Hydrochloric acid HMPA Hexamethylphosphoramide HPLC High performance liquid chromatography HOBt Hydroxybenzotriazole i-PrOH i-Propanol IC50 Concentration with a 50% inhibition of normal function K2CO3 Potassium carbonate kDa Kilodalton KOH Potassium hydroxide LHMDS Lithium bis(trimethylsilyl)amide lit Literature m Multiplet M Molar Mg Milligram(s) MHz Megahertz mL Milliliter(s) mmol Millimole(s) mp Melting point MeOH Methanol MS Mass spectrometry m/z Mass-to-charge ratio n-BuLi n-Butyllithium viii NaBH4 Sodium borohydride Na2CO3 Sodium carbonate Na2SO4 Sodium sulfate NH4Cl Ammonium chloride NaHCO3 Sodium bicarbonate p-TsOH para-Tolunesulfonic acid Pd/C Palladium on carbon PDB Protein data bank PPA Polyphosphoric acid PPh3 Triphenylphosphine PPI Protein-protein interaction ppm Parts per million PyBOP (Benzotriazole-1-yl-oxy-tris-(dimethylamino)-phosphonium
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