Design, Synthesis and Evaluation of Peptide-Based Affinity
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Design, Synthesis and Evaluation of Peptide-Based Affinity Labels for Mu Opioid Receptors By C2009 Bhaswati Sinha Submitted to the Department of Medicinal Chemistry and the Faculty of the Graduate School of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy. Dissertation Committee: ____________________________________ Chairperson: Dr. Jane V. Aldrich ____________________________________ Dr. Michael F. Rafferty ____________________________________ Dr. Teruna J. Siahaan ____________________________________ Dr. Emily E. Scott ____________________________________ Dr. David S. Moore Dissertation Defended __________________ The Dissertation Committee for Bhaswati Sinha certifies that this is the approved version of the following dissertation: Design, Synthesis and Evaluation of Peptide-Based Affinity Labels for Mu Opioid Receptors ____________________________________ Chairperson: Dr. Jane V. Aldrich ____________________________________ Dr. Michael F. Rafferty ____________________________________ Dr. Teruna J. Siahaan ____________________________________ Dr. Emily E. Scott ____________________________________ Dr. David S. Moore Date Approved _________________ ii Dedicated to: My parents Kumkum DattaChowdhury Prithwish Chandra DattaChowdhury My brother Atish DattaChowdhury My husband Sandipan Sinha iii Acknowledgements I would like to take this opportunity to thank all those who have helped me earn the doctorate degree from the University of Kansas. First and foremost, I would like to thank my advisor Prof. Jane V. Aldrich for her excellent mentorship, support and guidance through out my graduate career at the University of Kansas. I was fortunate to have some great colleagues to work with and I would like to thank all of them for their co-operation, encouragement and helpful inputs. They are Anand Joshi, Wendy Hartsock, Kendra Dresner, Katherine Smith, Angela Peck, Dr. Wei-Jie Fang, Dr. Xin Wang, Dr. Santosh Kukarni, Dr. Mark Del Borgo, Dr. Kshitij Patkar, Dr. Nicolette Ross, Dr. Tatyana Yakovleva and Dr. Sandra Barlett. Special thanks to Wendy for always being so friendly and helpful. I am grateful to Prof. Mike Rafferty, Prof. Teruna Siahaan, Dr. Emily Scott and Dr. David Moore for being in my thesis committee. I would like to specially thank Dr. Rafferty for his valuable suggestions. I made some wonderful friends in Lawrence and life here would not have been so much enjoyable without them. Rashida, Deb, Mrinal, Barnali, Sumit M, Deepti, Sasi, Aparna, Nadim, Vinya, Naveen, Anurupa, Gagandeep, Diptesh, Ramu and Sanjibani thank you all for your friendship. I express my deepest gratitude to my old friends: Soma, Dhriti, Peuli, Prajna, Pranamita, Iman, Abira, Indranil, Arpana, Pinaki, Sumit G, Paroma and Suchitra for their constant encouragement. Sandipan, my husband has been a pillar of support for me. His love, motivation and patience were instrumental behind my success. I am grateful to my parents-in-law Ashoka Sinha and Salil Kumar Sinha for their affection and encouragement. My brothers- in-law Suman and Sovan Sinha, my sisters-in-law Paromita and Bhaswati iv Sinha have always had faith in my ability. I am fortunate to have such a supportive family including my two cute nephew and niece: Ayush and Ashmita Sinha. Words can not do justice to express my indebtedness to my father Prithwish Chandra DattaChowdhury and my mother Kumkum DattaChowdhury. My father has always been a source of inspiration. Whatever I achieved today is because of their constant motivation, love and trust. My caring and loving brother Atish DattaChowdhury has been equally instrumental towards my achievement through his unconditional support. I am grateful to my sister-in-law Anindita DattaChowdhury for her friendship and affection and my sweet nephew Arnab DattaChowdhury- a bundle of joy. Finally I owe my success to my entire family and would like to thank you all from the bottom of my heart. v Table of Contents Page Acknowledgements………………………………………………………………….iv List of Tables………………………………………………………………………..xii List of Figures………………………………………………………………………xiv List of Schemes……………………………………………………………………xviii Abbreviations………………………………………………………………………xix Abstract………………………………………………………………………………..1 Chapter 1 Summary of Thesis Projects…………………………………………………………3 1.1.Background and Significance……………………………………………………..4 1.2. Research Projects…………………………………………………………………8 1.2.1. Project 1: Discovery of Dermorphin-Based Affinity Labels with Subnanomolar Affinity for Mu Opioid Receptors (Chapter 3)…………………8 1.2.2. Project 2: Synthesis and Evaluation of DAMGO-Based Affinity Labels for MOR and Discovery of an Unexpected Side Reaction (Chapter 4)……….10 1.2.3. Project 3: Design, Synthesis and Evaluation of a Dermorphin-Based Multifunctional Affinity Label Probe for Mu Opioid Receptors (Chapter 5)...12 1.3. Conclusions……………………………………………………………………...14 1.4. Bibliography…………………………………………………………………….14 vi Chapter 2 Literature Review…………………………………………………………………. 22 2.1. Opioid Receptors………………………………………………………………..23 2.1.1. Structure and Function of Opioid Receptors…………………………...24 2.2. Mu Opioid Receptors (MOR)…………………………………………………...25 2.2.1. Mutagenesis Studies of MOR…………………………………………27 2.2.2. Computational Studies on MOR………………………………………30 2.3. Ligands for MOR………………………………………………………………..33 2.3.1. Small Molecule Ligands for MOR……………………………………….33 2.3.2. Opioid Peptides…………………………………………………………...34 2.3.2.1. Endogenous Opioid Peptides Interacting with MOR……………34 2.3.2.2. MOR selective Linear Enkephalin Analogs ……………………36 2.3.2.3. MOR Selective Conformationally Constrained Enkephalin Analogs…………………………………………………………………..37 2.3.2.4. MOR Selective Peptides from Amphibian Skin ………………..38 2.3.2.4.1. SAR Study of Dermorphins………………………...40 2.4. Affinity Labels…………………………………………………………………..44 2.4.1. Photoaffinity Labels………………………………………………………46 2.4.2. Electrophilic Affinity Labels……………………………………………..49 2.4.2.1. Small Molecule-Based Electrophilic Affinity Labels: β- Funaltrexamine and Other Analogs………………………………………50 vii 2.4.2.2. Peptide-Based Electrophilic Affinity Labels……………………54 2.5. Significance: Peptide vs. Small Molecule-Based Affinity Labels………………57 2.6. Bibliography……………………………………………………………………..58 Chapter 3 Discovery of Dermorphin-Based Affinity Labels with Subnanomolar Affinity for Mu Opioid Receptors……………………………………………………………….84 3.1. Introduction……………………………………………………………………...85 3.2. Background……………………………………………………………………...87 3.3. Dermorphin and Previous Dermorphin-Based Analogs………………………...88 3.3.1. Dermorphin-Based Affinity Labels……………………………………....90 3.4. Rationale for the Design of New Affinity Labels……………………………….92 3.5. Results and Discussion………………………………………………………….93 3.6. Conclusions……………………………………………………………………...99 3.7. Experimental…………………………………………………………………...100 3.7.1. Solid Phase peptide Synthesis (SPPS) of Dermophin-Based Affinity Labels ………………………………………………………………………….100 3.7.2. Cleavage from Resin…………………………………………………….102 3.7.3. Purification and Analysis………………………………………………..103 3.7.4. Pharmacological Assays………………………………………………...104 3.7.4.1. Radioligand Binding Assays…………………………………...104 3.7.4.2. Wash-Resistant Inhibition of Binding Assays…………………105 viii 3.8. Bibliography…………………………………………………………………...105 Chapter 4 Synthesis and Evaluation of DAMGO-Based Affinity Labels for MOR and Discovery of an Unexpected Side Reaction………………………………………113 4.1. Introduction…………………………………………………………………….114 4.2. DAMGO-Based Affinity Labels: Design Strategy………………………….....118 4.3. Results and Discussion………………………………………………………...120 4.3.1. Loading of Fmoc-Gly-ol onto DHP-HM Resin and Synthesis of DAMGO Analogs……………………………………………………………121 4.3.2. Side Reaction: Formation of Cyclic O-Alkyl Thiocarbamates………..122 4.3.2.1. Proposed Side Reaction………………………………………125 4.3.2.2. Characterization of the Side Products: FTIR of Fr A and Fr B………………………………………………………….126 4.3.2.3. Characterization of the Products by Proton NMR……………..................................................................................127 4.3.3. Radioligand Binding and Wash-resistant Inhibition of Binding Assays………………………………………………………………………..128 4.3.4. Overcoming the Side Reaction: Design and Synthesis of DAMGA ([D- Ala2,N-MePhe4,Gly5]enkephalinamide) Analogs…………………………....131 4.4. Conclusions…………………………………………………………………….136 4.5. Experimental…………………………………………………………………...138 ix 4.5.1. Loading of Fmoc-Gly-ol onto DHP-HM Resin and SPPS of DAMGO Analogs……………………………………………………………………….140 4.5.2. Solid Phase Peptide Synthesis of the DAMGA Derivatives…………..140 4.5.3. Cleavage from Resin…………………………………………………...140 4.5.4. Purification and Analysis………………………………………………141 4.5.5. Instrumentation………………………………………………………...141 4.5.6. Pharmacological Assays……………………………………………….141 4.6. Bibliography…………………………………………………………………...142 Chapter 5 Design, Synthesis and Evaluation of a Dermorphin-Based Multifunctional Affinity Label Probe for Mu Opioid Receptors…………………………………148 5.1. Introduction……………………………………………………………………149 5.2. Design of a Dermorphin-Based Affinity Labels: Design Strategy……………155 5.3. Results and Discussion………………………………………………………...157 5.3.1 Synthesis of the Multifunctional [D-Lys(=C=S)2]dermorphin Derivative………………………………………157 5.3.2. Results from Preliminary Microscopy Experiments ……………….. …162 5.4. Conclusions……………………………………………………………………164 5.5. Experimental…………………………………………………………………...165 5.5.1 Synthesis of Dermorphin-based Multifunctional Affinity Label…………………………………………………………………165 x 5.5.2 Cleavage from Resin……………………………………………………168 5.5.3 Purification and Analysis………………………………………………..168