Photopharmacology Willem Arend Velema
First edition, November 2014 The work described in this thesis was carried out at the Stratingh Institute for Chemistry, Groningen, The Netherlands. The work was financially supported by the Netherlands Organization for Scientific Research (NWOCW), the European Research Council and the Ministry of Education, Culture and Science. Cover art by Arie van t Riet: www.xrays.nl Printed by Ipskamp Drukkers BV, Enschede, The Netherlands ISBN: 9789036773577 (Printed version) ISBN: 9789036773560 (Electronic version) 2 4 6 8 10 9 7 5 3 1
Photopharmacology PhDThesis toobtainthedegreeofphdatthe UniversityofGroningen ontheauthorityofthe RectorMagnificusProf.E.Sterken andinaccordancewith thedecisionbythecollegeofdeans. Thisthesiswillbedefendedinpublicon Friday21November2014at16:15hours by WillemArendVelema bornon2august1986 ingroningen
Supervisor Prof.B.L.Feringa Assessmentcommittee Prof.A.J.M.Driessen Prof.A.J.Minnaard Prof.D.Trauner
And now, said Julian, when everything was quiet, I hope we are all ready to leave the phenomenal world and enter into the sublime? Donna Tartt in The Secret History
Table of Contents Chapter 1: An Introduction to Photopharmacology 1 1.1 Introduction. 2 1.2 Using light for controlling biological processes. 4 1.3 Design principles for creating photocontrolled drugs.. 8 1.3.1 Pharmacological considerations... 8 1.3.2 Photoisomer ratio at photostationary state 10 1.3.3 Wavelength tuning..12 1.3.4 The halflife of thermodynamically unstable isomer... 15 1.3.5 Stability in the cellular environment. 17 1.3.6 Toxicity.. 18 1.3.7 Design principles: concluding remarks 19 1.4 Photopharmacology: Illustrative examples. 19 1.5 Phototethered ligands 28 1.6 Outlook. 36 1.7 References 38 Chapter 2: Design, Synthesis and Inhibitory Activity of Potent, Photoswitchable Mast Cell Activation Inhibitors 45 2.1 Introduction. 46 2.2 Results... 47 2.2.1 Design of photoswitchable inhibitors.. 47 2.2.2 Synthesis... 48 2.2.3 Photoswitchable behavior of designed mast cell activation inhibitors. 50 2.2.4 Inhibitory activity. 52 2.3 Discussion. 55 2.4 Conclusions.. 56 2.5 Experimental section.. 57 2.5.1 LAD2 Cell culture 57 2.5.2 βhexosaminidase assay. 57
2.5.3 Histamine assay... 57 2.5.4 Inhibitory activity tests 57 2.5.5 Photoswitching experiments. 58 2.5.6 Synthesis... 58 2.5.6.1 General information 58 2.5.6.2 Synthesis of DAC. 58 2.5.6.3 Synthesis of MAC and PAC... 61 2.6 References 66 Chapter 3: Lighttriggered Self Assembly of a Dichromonyl Compound in Water 69 3.1 Introduction. 70 3.2 Results and discussion... 70 3.2.1 Design of photoswitchable hydrogelator 70 3.2.2 Photoswitchable behavior of compound 1. 71 3.2.3 Aggregation studies of compound 1.. 72 3.2.4 Photoswitchable hydrogelation of compound 1 75 3.3 Conclusion 78 3.4 Experimental section.. 78 3.4.1 Photoswitching experiments. 78 3.4.2 cryotem.. 78 3.4.3 Synthesis.. 78 3.5 References 79 Chapter 4: Optical Control of Antibacterial Activity 81 4.1 Introduction. 82 4.2 Results and Discussion.. 83 4.2.1 Design and synthesis of photoswitchable antibiotic.. 83 4.2.2 Photoswitchable behavior of compound 19... 85 4.2.3 Antibacterial activity of compound 19... 86 4.2.4 Thermal inactivation 88
4.2.5 Studying pharmacodynamics using cistrans isomerization 89 4.2.6 Bacterial patterning 91 4.3 Conclusion 92 4.4 Experimental section.. 92 4.4.1 Photoswitching experiments. 92 4.4.2 Bacterial strains and growth conditions.. 92 4.4.3 Antibacterial activity and bacterial growth curves.. 92 4.4.4 Bacterial patterning experiments. 93 4.4.5 Synthesis.. 93 4.5 References 107 Chapter 5: Proteasome Inhibitors with Photocontrolled Activity 109 5.1 Introduction. 110 5.2 Results and Discussion... 112 5.2.1 Design and synthesis of photoswitchable proteasome inhibitors 112 5.2.2 Photochemical properties of photoswitchable proteasome inhibitors 114 5.2.3 Biological activity of photoswitchable proteasome inhibitors 116 5.3 Conlusion. 119 5.4 Experimental section.. 120 5.4.1 Photoswitching experiments. 120 5.4.2 Competition experiments.. 120 5.4.3 Cell culture... 121 5.4.4 Cytotoxicity assay 121 5.4.5 Synthesis... 121 5.5 References 135
Chapter 6: LightControlled Bacterial Communication 139 6.1 Introduction. 140 6.2 Results and Discussion... 141 6.2.1 Design and synthesis of photoswitchable homoserine lactones.. 141 6.2.2 Photoswitchable behavior of compound 24 143 6.2.3 Biological activity of compound 24... 144 6.3 Conclusion 148 6.4 Experimental section.. 149 6.4.1 Photoswitching experiments. 149 6.4.2 Bacterial strains and growth conditions.. 149 6.4.3 Bioluminescence assay.. 149 6.4.4 RNA isolation and cdna synthesis.. 150 6.4.5 Gene expression with qpcr.. 150 6.4.6 Synthesis... 150 6.5 References 154 Chapter 7: Orthogonal Control of Antibacterial Activity with Light 157 7.1 Introduction. 158 7.2 Results and Discussion... 159 7.2.1 Design of photocleavable antibiotics.. 159 7.2.2 Synthesis of photocleavable antibiotics.. 161 7.2.3 Photochemical properties of FQNC and BPOC 163 7.2.4 Antibacterial properties of FQNC and BPOC 165 7.2.5 Bacterial selection using photocleavable antibiotics. 167 7.3 Conclusion 169 7.4 Experimental section.. 169 7.4.1 Photoswitching experiments. 169 7.4.2 Bacterial strains and growth conditions.. 169 7.4.3 Antibacterial activity and bacterial growth curves.. 169 7.4.4 Synthesis... 170
7.4.4.1 General information 170 7.4.4.2 Synthesis of FQNC and BPOC.. 170 7.5 References 176 Samenvatting 179 Summary 181 Acknowledgements 184