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 Entitled For the degree of Is approved by the final examining committee: Chair 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 R esearch” and the use of copyrighted material. Approved by Major Professor(s): ____________________ ________________ ____________________________________ Approved by: Head of the Graduate Program Date Lindsey Gayle Fischer Solid-Phase Synthesis of N-Carboxyalkyl Unnatural Amino Acids Master of Science Martin J. O'Donnell Robert E. Minto William L. Scott Martin J. O'Donnell Martin J. O'Donnell 6/29/10 Graduate School Form 20 (Revised 1/10 ) PURDUE UNIVERSITY GRADUATE SCHOOL Research Integrity an d Copyright Disclaimer Title of Thesis/Dissertation: For the degree of ________________________________________________________________ I certify that in the preparation of this thesis, I have observed the provisions of Purdue University Teaching, Research, and Outreach Policy on Research Misconduct (VIII.3.1) , October 1, 2008.* Further, I certify that this work is free of plagiarism and all materials appearing in this thesis/dissertation have been properly quoted and attributed. I certify that all copyrighted materi al incorporated into this thesis/dissertation is in compliance with the United States’ copyright law and that I have received written permission from the copyright owners for my use of their work, which is beyond the scope of the law. I agree to indemnify and save harmless Purdue University from any and all claims that may be asserted or that may arise from any copyright violation. ______________________________________ Printed Name and Signature of Candidate ______________________________________ Date (month/day/year) *Located at http://www.purdue.edu/policies/pages/ teach_res_outreach/viii_3_1 .html Solid-Phase Synthesis of N-Carboxyalkyl Unnatural Amino Acids Master of Science Lindsey Gayle Fischer 6/30/2010 S OLID - P HASE S Y NTHESIS OF N - C ARBOXYALKYL U NNATURAL A MINO A CIDS A Thesis Submitted to the Faculty of Purdue University by Lindsey Gayle Fischer In Partial Fulfillment of the Requirements for the Degree of Master of Science August 2010 Purdue University Indianapolis, Indiana ii To my beloved grandmother, Phyllis Leidolf, who passed away on August 10, 2009 from congestive heart failure. I will see you again one day. iii ACKNOWLEDGMENTS I would like to acknowledge with thanks the assistance and encouragement from my two mentors,  0   !02)-     > % ++ !-$   0   )++)!,      #.22 . Thank you to my group members Geno Samaritoni, Zin iu Zhou and Jim McCarthy for their advice and input into my project. T he assistance from Dr. Karl Dria with the instrumentation and Dr. Robert Minto w ith NMR interpretations is greatly appreciated . Thank you to Dr. Michael VanNieuwehnze at Indiana University for assistance with optical rotations and to all of my previous co - workers at Dow AgroSciences and Eli Lilly for their instruction in making me the research chemist I am today. Thank you to my family and friends for their love and support. Lastly, a grateful thank you to the Lord who has brought me to places in life I nev er dreamed imaginable. iv TABLE OF CONTENTS Page               : : : : : : : : : : : : : : : : : : : : : : : : : : : : : :  vii LIST OF FIGURES viii LIST OF SCHEME <ZZZZZZZZZZZZZZZZZZZZZZZZZZZZ' Z ix LIST OF ABBREVIA TIONS ZZZZZZZZZZZZZZZZZZZZZZZZZZ x ii ABSTRACT xiv CH APTER 1. BACKGROUND 1 1.1. Introduction 1 1.2. Examples of Solution - Phase Synthesis of N - Carboxyalkyl Dipeptides and Amino Acids in the Chemical Literature: Introducing the N - Carboxyalkyl Group onto Nitrogen 6 1.2.1. Solution - Phase Synthesis of ACE Inhibitor Analogs by N - Alkylation with % - Halocarbonyl C NLONSMDQZZZZZZZZZZZZZZ'' ZZZZ . ZZ' 7 1.2.2. Solution - Phase Synthesis of ACE Inhibitor Analogs by Reductive Amination with % - Ketoca rbonyl Compounds ZZZZZ'ZZZZZ'ZZZZZ'ZZZ' 11 1.2.3 . Solution - Phase Synthesis of Substituted Amines by N - Alkylation with % - Halocarbonyl C NLONSMDQZZZZZZZZZZZZZZZZZZZZ''' 13 1.3. Examples of Solid - Phase Synthesis of Substituted Amines ZZZZZZ'ZZZ . 18 1.3.1. Solid - Phase Synthesis of ACE Inhibitors with % - Ketocarbonyl Compounds . . 18 1.3.2. N - Alkylation of a Re sin - Bound Nucleo phile with % - Bromocarbonyl Compounds Z ZZZZZZZZZZZZZZZZZZZZZZZZ'''ZZ 19 1.3.3. Resin - Bound Electrophilic % - Bromocarbonyl Compounds in Reaction with Excess Amines in Solu RINMZZZZZZZZZZZZZZZZZZZ . ZZ . 19 1.3.4. Synthesis of Peptoids from Resin - Bo und % - Bromoesters and ,LIMEQZ . Z 21 1.4. The Mechanism of the N - Alkylation with % -  !+.#!0" 7+  ., /.3-$ 1: Z ZZZ 22 CHAPTER 2. PLAN OF STUDY 24 v Page CHAPTER 3. RESULTS AND DISCUSSION 28 3 . 1 . Experiments to Optimize the N -  +*7+!2)   % !# 2) : : : :    28 3.1 .1. Optimization of the N - Alkylation of Phe - Wang with Ethyl 2 - Bromo - propanoate 28 3.1 .2. Synthesis of Benzyl % - Bromoesters as Reagents for the N - Alkylation Reaction ZZ'' 32 3.1 .3. N - Alkylation of Phe - Wang with Benzyl 2 - Bromo - 3 - OHEMWKOPNOAMNAREZ . . . Z 33 3 . 1 . 4 . N - Alkylation of Phe - Wang with Benzyl 2 - Bromo - 4 - phenylbutanoate 36 3.1.5 . N - Alkylation of Fmoc - Phe - Wang with Benzyl 2 - Bromopropanoate 40 3. 2. Evaluation of Alkyl Halides in the Synthesis of Unnatural Amino Acids 43 3 . 3 . Combinatorial Synthesis of N - Carbox yalkyl Amino Acid Analogs 44 3. 4 . Deprotection of Benzyl - Protected N - Carboxyalkyl Amino Acids to the Diacid 51 3.5. Synthesis of an Ethyl Ester Analog and Subsequent Hydrolysis to the Amino Diacid ZZZZZZZZZZZZZZZZZZZZZZZZZZZ'''Z'' 56 CHAPTER 4. CONCLU SION <ZZZZZZZZZZZZZZZZZZZZZZZZ'' 58                                   : : : : : : : : : : : : : : : Z ZZ . 59 5.1 . General Methods . 59 5 . 2. General Procedure for the Optimization of N - Alkylation of Resin - Bound Amino Acids with Ethyl 2 - Bromopropanoate: N - [1 - Methyl - 2 - oxo - 2 - (eth oxy)ethyl - ( S ) - phenylalanine ( 131 ) 62 5 .3. General Procedure for the Conversion of Amino Acids to % - B romoacids ( 133 b - d ) 63 5.4. General Procedure for Conversion of % - Bromoacids to Benzyl % - Bromo e sters ( 125 a - d %Z Z ZZZZZZZZZZZZZZ Z Z ZZZZZZZZ . ZZZ'Z' 64 5.5. General Procedure for the Optimization of the N - Alkylation of Resin - Bound Amino A cids with Benzyl % - -PNLNEQREPQZZZZZZZZZZZZZZZZZ' 6 6 5.6. General Procedure for the Evaluation of Alkylating Agents in the Synthesis of  !230!+  , )   # )$ 1: : : : : : : : : : : : : : : : : : : : : : : :    68 5 .7. General Procedure for the Synthesis of N - Carb oxyalkyl Amino Acid Analogs . Z 69 5.8.  % -% 0!+  0.# % $ 30%  &.0 2( %   7$ 0.+71)1 .& 2( %   % -87+  12% 0  -2% 0, % $ )!2% 1: . Z Z 91 5.9 . General Procedure for the Preparation of Ethyl Ester Intermediate 209 and  7$ 0.+71)1 2. 2( %   , )   )!# )$ : : : : : : : : : : : : : : : : : : : : . 101 vi Page BIBLIOGRAPHY ZZZZZZZZZZZZZZ ZZZZZZ . . . 10 3 APPENDICES Appendix A. NMR S pectra. 107 Appendix B.         6/% 0), % -21: Z Z Z' ZZZZZZZZZ Z Z Z'' Z 24 0 vii L IST OF TABLES Table Page Table 1. Results from the N - Alkylation of Phe - Wang with Benzyl 2 - Br omo - 3 - phenyl OPNOAMNAREZZZZZ ZZZZZ ZZZZZZZ' ZZZ''ZZZZZZ Z 3 4 Table 2. Results from the N - Alkylation of Phe - Wang with Be nzyl 2 - Bromo - 4 - phenyl butanoate ZZ ZZZZZZZ Z Z ZZZZZZZZZZZZZZZZZ'Z 37 Table 3. Results from the N - Alkylation of Phe - Wang with Benzyl 2 - Bromo - propanoate ZZZZZZZZZZZZZZZZZZZZZZZZZZZZ''' 41 T able 4. Results of C - Alkylation with Alkylating Reagents 1 41 - 1 50 Followed by N - Alkylation ZZZZZZZZZZZZZZZ ZZZZZZZZZZZZ''' 43 Table 5. Results of the Combinatorial Synthesis of N - Carboxyalkyl Amino Acid Analogs ZZ'' . . 46 Table 6. Results from the Hydrolysis of the Benzyl Est er Intermediates to the Diacids ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ'Z' 54 Table 7. Correla tion of Proton and Carbon Shifts from the 2D NMR Experiments 24 0 viii LIST OF FIGURES Figure Page Figure 1. Commercially Available ACE Inhibitors and Gene ric Structure of Drug Analogs ZZZZZZZZZZZZZZZZZZZZZZZZZZZZ' 'Z' 1 Figure 2. The Binding I nteractions of Captopril and Enala pril at within the ACE Active <IREZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 3 Figure 3. Carboxyalkanoyl and Mercaptoa +*! 7+  0.+)-%   -!+.' 1: : : : : : : :  : 3 Figure 4. Ornithine - based Tripeptidom ), % 2)#   -!+.' 1: : : : : : : : : : : :    : : 5 Figu re 5. Structures of 4 - Substituted Pr .+)-%   -!+.' 1: : : : : : : : : : : : :    : 5 Figure 6. Fused Ring Structures of ACE Inhibitor A MAKNGQZZZZZZZZZZZ'''Z 6 Figure 7. Synthetic Methods for Preparing N - Carboxyalkyl Amino Acids through t he Use of % - Haloesters or % - K ERNEQREPQZZZZZZZZ ZZZZ''''' . Z 7 Figure 8. Possible Transition States for N - Acylalkylation with Ammonia Z . ZZZZZ 22 [...]... University, August 2010, Solid-Phase Synthesis of N-Carboxyalkyl Unnatural Amino Acids Major Professor: Martin J 9^/NMMEKl, Ph.D A novel route has been developed for the solid-phase synthesis of Ncarboxyalkyl unnatural amino acids as potential metalloprotease inhibitors The key step involves a nitrogen alkylation of resin-bound amino acids with %-bromoesters Alkylation of the benzophenone imine of glycine on... Optimized N-Alkylation of Phe-Wang with Benzyl 2 PNLNOPNOAMNARE'Z42 Scheme 53 Synthesis of Unnatural Amino Acids by C-Alkylation of GlWCIMEZZ''ZZ43 Scheme 54 Combinatorial Synthesis of N-Carboxyalkyl Amino Acid Analogs 126ZZ45 Scheme 55 Combinatorial Set-Up for Synthesizing N-Carboxyalkyl Amino Acid Analogs 126ZZZZZZZZZZZZZZZZZZZZZZZZZZ' 45 Scheme 56 Mechanism of the Formation of the Dialkylated By-Product... 136Z''ZZ'''50 Scheme 57 Hydrogenolysis of Benzyl Ester Intermediates to the N-Carboxyalkyl Amino AcIDQZZZZZZZZZZZZZZZZZZZZZZZZ'ZZ 51 Scheme 58 Hydrolysis of Benzyl Ester Intermediates to the N-Carboxyalkyl Amino Aci$ 1: : : : : : : : : : : : : : : : : : : : : : : : : : : : :  53 Scheme 59 Use of Alkyl %-Bromoesters to Prepare Amino Diacids 185ZZZZ''Z'' 56 Scheme 60 Synthesis of Amino Diacid 186 through Ethyl... SCHEMES Scheme Page Scheme 1 Synthesis of 24 as an Important Intermediate for Synthesis of ACE 4MHIBIRNPQZZZZZZZZZZZZZZZZZZZZZZZZ''ZZ'7 Scheme 2 Diastereoselective Synthesis of ACE 4MHIBIRNPQZZZZZZZZZZ''''''Z8 Scheme 3 Synthesis of Unsubstituted N-Carboxyalkyl Dipeptides via N-,KJWKARINMZZ 8 Scheme 4 Synthesis of ECPPA by N-AlkylaRINMZZZZZZZZZZZZZZZZZ 8 Scheme 5 Synthesis of ACE Inhibitor Analogs by N-A+... 5.5 General Procedure for the Optimization of the N-Alkylation of Resin-Bound Amino Acids with Benzyl % PNLNEQREPQZZZZZZZZZZZZZZZZZ' 66 5.6 General Procedure for the Evaluation of Alkylating Agents in the Synthesis of  !2 !+ , ) 30 - # ) 1: : : : : : : : : : : : : : : : : : : : : : : :    68 $ 5.7 General Procedure for the Synthesis of N-Carboxyalkyl Amino Acid Analogs Z69 5.8  % -% 0  0 % $... Scheme 17 Use of N-Alkylation in the Total Synthesis of Ecteinascidin 743ZZ''ZZ14 Scheme 18 Microwave Synthesis of N-Alkylated CarbazolesZZZZZZZZ'''ZZ14 Scheme 19 The Synthesis of Bifunctional Chelating Agents by N-,KJWKARINMZZZ 15 Scheme 20 Synthesis of N-3-Chloropropylglycine Ethyl Ester and N-3-Chloropropylalanine Ethyl Ester as Precursors to 1,2-AzaphospholanesZZZ' 15 Scheme 21 Synthesis of Isoindolones... AmidesZ'Z21 Scheme 32 Synthesis of Peptoid Oligomers using Bromoacetic Acid and Primary AminesZZZZZZZZZZZZZZZZZZZZZZZZ''' 22 Scheme 33 SNAdE Mechanism of N-,CWKAKJWKARINMZZZZZZZZZZZZZZZ 23 Scheme 34 Proposed Synthesis of N-Carboxyalkyl Unnatural Amino AcidsZZ''ZZ24 Scheme 35 Proposed Reaction Sequence to Find Optimal Conditions for N-AlkylationZZZZZZZZZZZZZZZZZZZZZZZZZZ'' 25 Scheme 36 Synthesis of Benzyl %-Bromoesters... introduce unnatural amino acid side chains onto the resin-bound glycine The benzyl %-bromoesters [BrCH(R2)CO2Bn], starting materials for the C-N bond construction, were prepared in solution by diazotization of naturally-occurring amino acids to form the %-bromoacids, followed by benzylation of the carboxylic acid to form the benzyl %-bromoesters NAlkylation of the resin-bound, unnatural amino acids with... Scheme Page Scheme 22 Synthesis of Olefin-Containing Phthalimidines as Precursors for Grubbs Ring  + -'  % 2 ( % 1)  % !# 2 1) !2 1 ) -1: : : ZZZZZ''ZZZ'ZZZZ'' 16 Scheme 23 Synthesis of Phthlamidine Compounds for Synthesis of Spirolactones'Z 16 Scheme 24 Synthesis of Azetidines as Precursors to Carbapenicillanic Acid AnalogsZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 17 Scheme 25 Synthesis of 2,4-Disubstituted... 59 5.2 General Procedure for the Optimization of N-Alkylation of Resin-Bound Amino Acids with Ethyl 2-Bromopropanoate: N-[1-Methyl-2-oxo-2-(ethoxy)ethyl-(S)phenylalanine (131) 62 5.3 General Procedure for the Conversion of Amino Acids to %-Bromoacids (133b-d) 63 5.4 General Procedure for Conversion of %-Bromoacids to Benzyl %-Bromoesters (125a-d%ZZZZZZZZZZZZZZZZZZ