PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher's version. For additional information about this publication click this link. http://hdl.handle.net/2066/83181 Please be advised that this information was generated on 2021-09-23 and may be subject to change. Cyclic Enediyne-Containing Amino Acids Een wetenschappelijke proeve op het gebied van de Natuurwetenschappen, Wiskunde en Informatica Proefschrift ter verkrijging van de graad van doctor aan de Radboud Universiteit Nijmegen op gezag van de rector magnificus prof. mr. S. C. J. J. Kortmann, volgens besluit van het College van Decanen in het openbaar te verdedigen op vrijdag 4 februari 2011 om 15.30 uur precies d o o r Jasper Kaiser geboren op 27 december 1977 te Heidelberg (Duitsland) P r o m o t o r : Prof. dr. Floris P. J. T. Rutjes Copromotor: Dr. Floris L. van Delft Manuscriptcom m issie: Prof. dr. ir. Jan C. M. van Hest Dr. Dennis W. P. M. Löwik Dr. Sape S. Kinderman (Universiteit van Amsterdam) Paranim fen: Danny Gerrits M a r k D a m e n Kaftontwerp: Studio Appeltje-S D r u k k e r ij: Ipskamp Drukkers ISBN/EAN: 978-90-9025901-7 Die gefährlichste Weltanschauung ist die Weltanschauung derer, weiche die Weit nie angeschaut haben. Alexander von Humboldt However beautiful the strategy, you should occasionally look at the results. Winston Churchill Table of Contents List of Abbreviations vi C hap ter 1: Introduction 1 1.1 General introduction 2 1.2 Naturally occurring enediynes 2 1.3 Terminal acetylenic amino acids 10 1.4 Purpose and outline of the thesis 17 1.5 Acknowledgement 17 1.6 References and notes 17 C hap ter 2: Synthesis of Cyclic Enediyne-Containing Amino Acids 21 2.1 Introduction 22 2.2 Previous work in our group 23 2.3 Enediynes based on propargylglycine 25 2.4 Eleven-membered cyclic enediynes from homopropargylglycine 31 2.5 Pyridine-fused enediynes 32 2.6 Conclusion 37 2.7 Acknowledgements 38 2.8 Experimental section 38 2.9 References and notes 51 C hap ter 3: Characterization and Reactivity of Cyclic Enediyne-Containing Amino Acids 53 3.1 Introduction 54 3.2 Structural description of the cyclic enediyne-containing amino acids 57 3.3 Kinetics and half-life determinations 60 3.4 Peptide couplings involving cyclic enediyne-containing amino acids 65 3.5 Bergman Cyclizations of the nosyl variant, the free amine and the dipeptides 70 3.6 The Bergman Cyclization as synthetic tool 73 3.7 Conclusion 74 3.8 Acknowledgement 74 3.9 Experimental section 74 3.10 References and notes 83 C hap ter 4: Ca-Tetrasubstituted Enediyne Amino Acids Based on a-Methyl-a-Propargylglycine 85 4.1 Introduction 86 4.2 Towards enantiopure a-propargylalanine 88 4.3 Cyclic enediyne-containing a-methyl amino acids 91 4.4 Towards peptide couplings of a-Me enediynic amino acids 93 4.5 Kinetics and half-life determinations 96 4.6 Conclusion 98 4.7 Outlook 99 iv 4.8 Acknowledgements 99 4.9 Experimental section 99 4.10 References and notes 108 C hap ter 5: Preparation and Evaluation of a-CF3-Containing Acetylenic Amino Acids 111 5.1 Introduction 112 5.2 Towards a-CF3-a-amino acids via trifluoromethyl ketones 114 5.3 Preparation of acetylene-containing a-CF3-a-amino acids 117 5.4 Enzymatic resolution of TfmPG 119 5.5 Coupling reactions of TfmPG 120 5.6 Miscellaneous reactions of TfmPG 122 5.7 Towards cyclic CF3-containing enediyne amino acids 123 5.8 Conclusion 124 5.9 Acknowledgements 125 5.10 Experimental section 125 5.11 References and notes 135 C hapter 6: Towards Enediynes Linked to Plasmonically Heated Nanoparticles: a Possible Future Direction for Enediyne-Based Therapies 137 6.1 Introduction 138 6.2 Plasmonically heated nanoparticles linked to enediynes 139 6.3 Synthesis 140 6.4 Discussion and conclusion 141 6.5 Acknowledgements 142 6.6 Experimental section 142 6.7 References and notes 143 Summary / Samenvatting 145 1.1 Summary 146 J..2 Samenvatting 150 Dankwoord / Danksagung / Acknowledgements 155 About the Author 159 Appendix: Color Illustrations 160 v List of Abbreviations AA amino acid ETFAA ethyl 4,4,4-trifluoro- AMAA a-methyl-a-amino acid acetoacetate AuNP gold nanoparticle Fmoc 9-fluorenylmethoxycarbonyl B base HATU 0-(7-azabenzotriazol-1-yl)- BC Bergman Cyclization N,N,N' ,N' -tetramethyl- uronium hexafluorophosphate Boc t-butoxycarbony HOAt 1 -hydroxy-7-azabenzotriazole i 1 1 1 di - bi s( P3 P3 N o 0 u 0 yl) BOP-Cl 2 x x HOBt 1 -hydroxybenzotriazole p phosphinich o s ph hin ic chloridech br HPLC high pressure liquid chromatography BSA N,0-bis(trimethylsilyl)- acetamide HRMS high resolution mass spectroscopy CAL calicheamicin IR infrared cat catalytic / catalyst coupling constant (NMR) Cbz benzyloxycarbonyl J KHMDS potassium CHD cyclohexa-1,4-diene bis(trimethylsilyl)amide CI chemical ionization LCMS liquid chromatography - mass Cy cyclohexyl spectrometry d doublet (NMR) LiHMDS lithium 6 chemical shift (NMR) bis(trimethylsilyl)amide DBU 1,8-diazabicyclo[5.4.0]undec- m multiplet (NMR) 7-ene MS molecular sieves DAST (diethylamino)sulfur Ms mesyl; methanesulfonyl trifluoride MSC Myers-Saito cyclization DCC N,N' -dicyclohexyl- m/z mass-to-charge ratio carbodiimide NaHM DS sodium DDQ 2,3-dichloro-5,6-dicyano-1,4- bis(trimethylsilyl)amide benzoquinone NCS neocarzinostatin DEAD diethyl azodicarboxylate Ns nosyl; DIAD diisopropyl azodicarboxylate 2-nitrobenzenesulfonyl d iad - h 2 diisopropyl hydrazine-1,2- nonaflyl; dicarboxylate N f nonafluorobutanesulfonyl D IPCD I diisopropyl carbodiimde NMO N-methylmorpholine-N-oxide DiPEA diisopropylethylamine NMR nuclear magnetic resonance DMAP 4-dimethylaminopyridine Nu nucleophile DME 1, 2 -dimethoxyethane PG protecting group DMF N,N-dimethylformamide PPAA propylphosphonic acid DMAD dimethyl acetylene- anhydride; dicarboxylate 2,4,6-tripropyl-1,3,5,2,4,6- DMSO dimethyl sulfoxide trioxatriphosphorinane-2,4,6- d.r. diastereomeric ratio trioxide EDC 1-ethyl-3-(3-dimethyl- Piv pivaloyl aminopropyl)-carbodiimide py pyridine hydrochloride PyBrO P bromotripyrrolidino- Edy See Chapter 3, Figure 9 phosphonium hexafluoro- ee enantiomeric excess phosphate EI electron impact ionization q quartet (NMR) equiv equivalents quant quantitative ESI electrospray ionization rac racemic ESP esperamicin RCM ring closing metathesis vi R/ retention factor rfx reflux rt room temperature s singlet (NMR) ssp. subspecies (taxonomy) t triplet (NMR) t l/2 half life time TBAF tetra-n-butylammonium fluoride TBAI tetra-n-butylammonium iodide TBDMS t-butyldimethylsilyl TEM transition electron microscopy THF tetrahydrofuran Tf trifluoromethanesulfonyl TFA trifluoroacetic acid TFAA trifluoroacetic anhydride Tfm trifluoromethyl TfmPG a-trifuoromethyl-a- propargylglycine TLC thin layer chromatography TMEDA N,N,N' ,N' -tetramethylethane- 1,2-diamine TMS trimethylsilyl / trimethylsilane tol toluyl Ts tosyl, 4-toluenesulfonyl var. variant (taxonomy) vii viii Introduction Abstract The concept of cyclic enediyne-containing amino acids is introduced, followed by a synopsis covering the most relevant elements of the history, chemistry and biology of naturally occurring enediynes. In addition, a concise overview of applications of acetylenic amino acids relevant to this thesis is provided. An outline of the thesis concludes the chapter. 1 Chapter 1 1.1 General introduction Natural enediynes are compounds containing a (Z)-hexa-3-en-1,5-diyne (1, Figure 1) or a closely related structural motif, and they rank among the most powerful antitumor and antibiotic agents found in Nature. Their active principle relies on the thermal generation of radicals. These are capable of damaging nearby DNA by abstraction of hydrogen atoms from deoxyribose units of the sugar phosphate backbone, causing single- and double-strand scissions and ultimately cell death. Furthermore, naturally occurring enediynes belong - from a scientist's point of view - to the most fascinating chemical entities ever isolated; their chemistry, mode of action and probably also their structural complexity have bewitched and intrigued many a chemist. Considering the tremendous cytotoxic properties of the natural compounds, making available simplified enediynes endowed with versatile handles for derivatization or for accommodation in functional complexes is of general interest. The incorporation of amino acids into enediynes would meet the demands for such versatility by virtue of the amino and the carboxylic acid functionalities. In line with our longstanding experience in the application of acetylenic amino acids ,2,3 we envisaged that this class of amino acids would make for suitable building blocks for enediyne-containing amino acids. Finally, as the activity of the enediyne core benefits from confinement into a cyclic s tr u c tu r e (vide infra), the idea of cyclic enediyne-containing amino acids was conceived (2, Figure 1). 1 2 (Z)-hexa-3-en-1,5-diyne cyclic enediyne-containing amino acids F ig u re 1 1.2 Naturally occurring enediynes 1.2.1 History The story of the natural enediynes, as far as humankind is concerned, began in 1965 when Ishida et al. reported the isolation of neocarzinostatin (NCS), an "antitumor antibiotic of high molecular weight" as they put it, from Streptomyces carzinostaticus var. F-41.4 This compound was later characterized as a 1:1 complex of a protein 2 Introduction component (apoprotein) and a chromophoric molecule, and it was established that the cytotoxicity of neocarzinostatin mainly resided on the chromophore .5 Despite the interesting biological activity, twenty years had to pass before the structure of the chromophore was elucidated by E d o et al. in 1985 (3, Figure 2 ).6 NCS neocarzinostatin chromophore Figure 2 The neocarzinostatin chromophore. Even after the elucidation of the intriguing enyne-cumulene moiety, the interest of the synthetic community in neocarzinostatin remained lukewarm. Aside from the then unresolved absolute stereochemistry, the structure quite possibly seemed too unlikely to the majority of chemists.