Impact of amino acid side chain fluorination on proteolytic stability of peptides Inaugural-Dissertation to obtain the academic degree Doctor rerum naturalium (Dr. rer. nat.) Submitted to the Department of Biology, Chemistry and Pharmacy of Freie Universität Berlin By Vivian Asante From Koforidua, Ghana November 2014 1st Reviewer: Prof. Dr. Beate Koksch (Freie Universität Berlin) 2nd Reviewer: Prof. Dr. Rainer Haag (Freie Universität Berlin) Date of defense: 10.02.2015 Erklärung Die vorliegende Arbeit wurde auf Anregung und unter Anleitung von Frau Prof. Dr. Beate Koksch in der Zeit von Oktober 2009 bis November 2014 an dem Institut für Chemie und Biochemie des Fachbereichs Biologie, Chemie, Pharmazie der Freien Universität Berlin angefertigt. Hiermit versichere ich, dass ich die vorliegende Arbeit mit dem Titel “Impact of amino acid side chain fluorination on proteolytic stability of peptides”, ohne Benutzung anderer als der zugelassenen Hilfsmittel selbstständig angefertigt habe. Alle angeführten Zitate sind als solche kenntlich gemacht. Die vorliegende Arbeit wurde in keinem früheren Promotionsverfahren angenommen oder als ungenügend beurteilt. Berlin, November 2014, Vivian Asante Publication List Peer-reviewed Major Publications: Journal Articles and Conference Proceedings 1. Asante, V., Mortier, J., Wolber, G., Koksch, B. (2014): Impact of fluorination on proteolytic stability of peptides: a case study with α-chymotrypsin and pepsin. Amino acids. DOI: http://dx.doi.org/10.1007/s00726-014-1819-7 2. Asante, V., Mortier, J., Schlüter, H., Koksch B., (2013): Impact of fluorination on proteolytic stability of peptides in human blood plasma. Bioorganic & Medicinal Chemistry 21: 3542-3546. DOI:10.1016/j.bmc.2013.03.051 3. Cadicamo, D.C., Asante, V., Ammar, A.M., Borelli, C., Korting, C.H., Koksch, B., (2009): Investigation of the synthetic route to pepstatin analogues by SPPS using O- protected and O-unprotected statine as building blocks. Journal of Peptide Science, 15: 272-277. DOI:10.1002/psc.1111 4. Asante, V., Koksch, B., (2013): Impact of fluorination on proteolytic stability of peptides; a case study using α‑chymotrypsin and pepsin. 4th Annual Workshop of the Fluorine Graduate School “Fluorine as a Key Element” Potsdam, Germany, 10-11. 10.2013. 5. Asante, V., (2012): Investigating the impact of side-chain fluorinated amino acids on proteolytic stability of peptides, Promotion Seminar of Rosa Luxemburg Stiftung, Berlin, Germany, 14-15.06. 2012. 6. Asante, V., Koksch, B., (2012): Impact of fluorination on the proteolytic stability of peptides towards alpha- chymotrypsin and pepsin, International Symposium on Fluorine Chemistry Kyoto, Japan, 22-27. 07.2012. 7. Asante, V., Koksch, B., (2012): Investigating the impact of side-chain fluorinated amino acids on proteolytic stability, 15. Deutschen Fluorotagung (15th German Fluorine day) Schmitten, Germany, 24-26. 09.2012. 8. Asante, V., Koksch, B., (2012): Impact of fluorination on proteolytic stability of peptides in human blood plasma, 3rd Annual Workshop of the Fluorine Graduate School “Fluorine as a Key Element” Spreewald, Germany, 22-23. 10.2012. 9. Asante, V., Koksch, B., (2012): Impact of fluorination on the proteolytic stability of peptides towards proteolytic enzymes and human blood plasma, Fluorine Graduate School Winter Semester 12/13 Berlin, Germany, 22-23. 11.2012. *Aus dieser Dissertation gingen bisher die Veröffentlichungen 1&2 hervor* Acknowledgements I wish to express my utmost sincere gratitude and appreciation to Prof. Dr. Beate Koksch who has been a friend and mentor, for the supervision of this study. I would like to thank her for her guidance, advice, support and comprehensive encouragement that enabled me to pursue my study to completion. I also wish to thank my second supervisor, Prof. Dr. R. Haag, for his support towards my study. I am greatly indebted to him for all the time and effort he committed to this study. My sincere gratitude goes to Prof. Dr. Beate Röder of Humboldt-University of Berlin, Germany, for her motherly love and kindness. I also appreciate the continuous advice and assistance from Dr. Cosimo D. Cadicamo in the course of my study and Dr. Allison Ann Berger for her suggestions and careful editing of this thesis. I would like to also express my sincere gratitude to Dr. Jérémie Mortier of FU Berlin, for the molecular modeling study which provided the in-depth interpretation of the results. I am grateful to Prof. Dr. Hartmut Schlüter and his group (University of Hamburg) for their collaboration and the supply of human blood plasma used in this study. My special thanks go to Dipl.-Biochem. Matthias Hakelberg for introducing me to this topic. I am grateful to Dr. Mario Salwiczek for his continuous advice and support in the course of my research. I also wish to thank all the members of the AG Koksch group, for the competent advice and for the motivating working atmosphere in the laboratory. I highly appreciate the support and advice from Prof Dr. Daniel Obeng-Ofori, Ghana and Mr. Udo Kummerrow, Berlin. Most of all, I would like to express special thanks to my husband (Dr. Charles Adarkwah, University of Development Studies, Temale, Ghana), our lovely children, Crystal and Jayson, my extended family members and all my friends for their love, care, support and understanding throughout my study. I am also grateful to my only brother Dr. Freeman Adane, Canada, for his support, advice and his brotherly love. I am highly indebted to the Rosa Luxemburg Stiftung (RLS) for granting me a Ph.D. scholarship that supported my living in Germany. I also acknowledge the financial support extended to me by the Deutsche Forschungsgemeinschaft (Research Training Group “Fluorine as Key Element”). Finally, I wish to thank all that I may not have mentioned, who supported me in many different ways for their material and moral support, advice and criticisms. Dedication This thesis is dedicated to all my family members who assisted me in my education especially Madam Theresa Osei-Nyarko (New York), Mr. Adjekum Asante (Nkawkaw) and the late Mr. Charles Baffour Anim (Nkawkaw). “Life is like a book, each day is a new page.” Abstract Protease stability is a pivotal consideration in the development of peptide-based drugs. Improving the bioavailability of pharmacologically active peptides requires in-depth investigation into the noncovalent interactions between the protease and the peptide substrate under consideration. To this end, different strategies such as the use of unnatural building blocks and fluorinated amino acids have become standard approaches in protein engineering. The incorporation of fluorine into amino acids has attracted much interest in recent years due to the unique stereoelectronic properties of fluorine, which have already proven useful in the development of therapeutically active small molecules. In this manner, the current thesis presents data on the systematic investigation of the influence of side chain fluorination on proteolytic stability of peptide sequences that are based on ideal protease substrates. Several model peptides were designed according to the specificities of serine and aspartic proteases; three different control sequences were modified by introducing either 2-aminobutyric acid (Abu) or one of its fluorinated derivatives at the P2, P1'or P2' positions. Through the use of an RP- HPLC assay with fluorescence detection, the proteolytic stabilities of these peptides toward α- chymotrypsin, pepsin, elastase, proteinase K and human blood plasma proteases were determined. Molecular modeling was used to support the interpretation of the structure-activity relationship based on the analysis of potential ligand-enzyme interactions. In all cases, increases and decreases in proteolytic stability were observed for the different isolated enzymes and the human blood plasma, and these effects depend upon the particular peptide sequence, the fluorine content of the side chain, and the position of substitution relative to the cleavage site. Interestingly, in some cases fluorination leads to dramatic improvements in resistance to degradation: namely, TfeGly and DfeGly at the P2’ position with pepsin; DfeGly at the P2 position with chymotrypsin; TfeGly and DfeGly at the P2 and P2’ positions with proteinase K; and TfeGly at the P2 and P1’ positions with elastase. Our observations indicate that although the fluorination of peptide substrates does not always have predictable effects on proteolytic stability, this strategy for developing more bioavailable peptide therapies is promising; in particular, part of this thesis was devoted to establishing an analytical approach for the identification of fluorinated peptide-based HIV-1 entry inhibitors. I II Kurzzusammenfassung Die Proteasestabilität ist ein wichtiges Kriterium bei der Erntwicklung von Peptid-basierten Medikamenten. Daher umfasst die Verbesserung der Bioverfügbarkeit von pharmakologisch aktiven Peptiden eine gründliche Untersuchung der nichtkovalenten Interaktionen zwischen Protease und Peptidsubstrat. In diesem Zusammenhang gehören verschiedene Strategien, wie beispielsweise die Verwendung von nicht-natürlichen Aminosäuren mittlerweile zu etablierten Methoden im Protein Engineering. Der Einbau fluorierte Aminosäuren hat in den letzten Jahren besonders an Bedeutung gewonnen, da das Element Fluor über einzigartige stereoelektroische Eigenschaften verfügt, die sich bei der Entwicklung von Pharmazeutikern als nützlich erwiesen haben. Die vorliegende Arbeit beschreibt die systematische Untersuchung