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LIBRARIESI ,ARGHC$ES This Doctoral Thesis Has Been Examined by a Committee of the Department of Chemistry As Follows Solution-Phase and Automated Solid-Phase Synthesis of High-Mannose Oligosaccharides: Application to Carbohydrate Microarrays and Biological Studies by Daniel Martin Ratner B.A., Chemistry (1999) Pomona College Submitted to the Department of Chemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology September, 2004 © 2004 Massachusetts Institute of Technology All Rights Reserved Signatureof Author ( Department of Chemistry August 19, 2004 / Certified -, By Pete/H. Seeberger Visiting Profesor of Chemistry, MIT Professor of Chemistry, ETH Zurich, CH Thesis Supervisor Accepted By _,. Robert W. Field MASSACHUSETTS INSTITUTE Professor of Chemistry OF TECHNOLOGY Chairman, Departmental Committee on Graduate Students LIBRARIESSEP15 204 LIBRARIESI ,ARGHC$ES This doctoral thesis has been examined by a committee of the Department of Chemistry as follows: Professor Daniel S. Kemp . = __ Chair / Professor Peter H. Seeberger - r / Thesis Supervisor / Professor Barbara Imperiali Department of Chemistry 2 Solution-Phase and Automated Solid-Phase Synthesis of High-Mannose Oligosaccharides: Application to Carbohydrate Microarrays and Biological Studies by Daniel Martin Ratner Submitted to the Department of Chemistry on August 19, 2004 in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy ABSTRACT Glycosylation is critical to cellular function in eukaryotic systems. N-linked modification of asparagine residues within nascent proteins is involved in numerous folding and processing pathways. N-linked glycans are also a common feature of viral- associated envelope glycoproteins, including gpl20 and gp41 of the human immunodeficiency virus (HIV-1). These glycans are attractive targets for therapy and prophylaxis due to their numerous roles in HIV infectivity and immunoevasion. This thesis describes the solution-phase synthesis of a series high-mannose type glycans using a linear synthetic approach. The synthetic mannans are used to study the potent anti-HIV microbicide cyanovirin-N, a novel 11 kDa protein isolated from the cyanobacterium (blue-green algae) Nostoc ellipsosporum. These studies established the structural basis for carbohydrate-binding by cyanovirin-N, which is responsible for its HIV inactivating properties. Automated solid-phase synthesis and microfluidic reactors were employed in the development of new technologies for synthetic carbohydrate chemistry. Utilizing a carbohydrate synthesizer, the first automated solid-phase synthesis of the N-linked core pentasaccharide is detailed. In addition, the design, fabrication and application of a microreactor for optimizing the glycosylation reaction is described. Utilizing a novel tri(ethylene glycol) linker with a reactive thiol handle, the fabrication of carbohydrate microarrays is depicted. A panel of oligosaccharides was selected to represent the major structural determinants of high-mannose type glycans on a single microarray. These microarrays were used study the glycan-dependent binding interactions of four gpl20-binding proteins: the dendritic cell lectin DC-SIGN, the antibody 2G12, cyanovirin-N, and a recently identified anti-HIV protein, scytovirin. Thesis Supervisor: Peter H. Seeberger Title: Visiting Professor of Chemistry, MIT Professor of Chemistry, ETH Zurich, CH 3 In my view, all that is necessaryforfaith is the belief that by doing our best we shall come nearerto success,and that success in our aims (the improvementof the lot of mankind, present andfuture) is worth attaining. Rosalind Franklin (1920-1958) Letter to her father Summer, 1940 4 Acknowledgements This thesis documents my serendipitous journey into synthetic carbohydrate chemistry. There many who deserve acknowledgement. I apologize in advance to those I neglect to mention on this page. I met Peter Seeberger while visiting MIT as a prospective graduate student. Peter's vision, enthusiasm, and salesmanship drew me to MIT, and ultimately to his research group. My passion for carbohydrate chemistry was lit while working alone at night creating the world's first automated solid-phase oligosaccharide synthesizer (the Emil Fischer -2000) out of space parts and a used peptide synthesizer donated by the Kemp group. Along the way, I met a number of extraordinary people in the Seeberger Laboratory. I had the pleasure of publishing collaboratively with several of them, including Obadiah Plante, Erika Swanson, Matt Disney, Dan Snyder and Eddie Adams. In addition, I was fortunate to have the guidance of two fine mentors, Rodrigo Bohn Andrade and the 'teacher,' Hernan Orgueira. Beyond the confines of the Building 18, I had the opportunity to collaborate with Drs. Barry O'Keefe, Angela Gronenborn and Pradman Qasba of the National Cancer Institute of Frederick, MD; Prof. David Walt of Tufts University; Prof. Milan Mrksich and his student Jing Su of the University of Chicago; and Prof. Klavs Jensen and his student Eddie Murphy of MIT's Dept. of Chemical Engineering. These collaborations shaped my thesis, and gave meaning to my molecules. While studying at MIT, I met a living legend - a Gandalf for my academic journey. As both my thesis committee chair and acting research advisor (2003-2004), Professor Daniel S. Kemp is the most extraordinary individual I have ever worked with, and likely ever will. His generosity is largely responsible for my ability to finish this doctoral work at MIT. To all those mentioned above, I owe many thanks. To my readers, Diana, Sharon and Ed, I thank you for wading through countless pages while catching my many mistakes (except for thiss one). To Bob, my lone labmate, I thank you for putting up with 15 months of non-stop National Public Radio (NPR). And to Sharon, thanks for the smiles and the Peet's French Roast. Most of all, my deepest debt of gratitude is owed to my family. To my parents, who entrusted my elementary education to a bunch of hippies known collectively as Room Nine. I may have never learned my multiplication tables, or how to spell, but I was instilled with the sense that learning is fun. To Shannon and Philip. There are no words to express my thanks. I love you both. 5 For Jan "The Geeze" Jessen 6 List of Abbreviations Ac Acetyl All Allyl Asn Asparagine Bn Benzyl Bu Butyl Bz Benzoyl calcd Calculated CVN Cyanovirin-N DBU 1,8-Diazabicyclo-undec-7-ene DDQ 2,3-Dichloro-5,6-dicyano-1,4-benzoquinone DMAP 4-(Dimethylamnino)pyridine DMDO Dimethyldioxirane DMF N,N-Dimethylformamide DTBP Di-t-butyl pyridine ESI MS Electrospray ionization mass spectrometry Et Ethyl equiv Equivalent(s) Gal Galactose GAPS Gamma amino propyl silane gCOSY IH, H Gradient correlation spectroscopy Glc Glucose GlcNAc N-Acetyl glucosamine h Hour(s) HPLC Highh performance liquid chromatography HRMS High resolution mass spectrometry HSQC Heteronuclear Single Quantum Coherence spectroscopy Hz Hertz IR Infrared Lev Levulinoyl 7 MALDI-TOF Matrix assisted laser desorption ionization - time of flight Man Mannose Me Methyl mm Minute(s) MS Mass spectrometry ms molecular sieves NMR Nuclear magnetic resonance obsd Observed Pent 4-pentenyl Ph Phenyl Phth Phthaloyl PMB p-methoxylbenzyl ppm Parts per million S second(s) SPR Surface plasmon resonance TBAF tetra-n-Butylammonium flouride TBS tert-Butyldimethylsilyl TBSOTf tert-Butyldimethylsilyl trifuoromethanesulfonate TCA Trichloroacetyl TCEP Tris(2-Carboxyethyl) Phosphine Hydrochloride TES Triethylsilane TIPS Triisopropylsilane Tf Trifluoromethanesulfonyl TFA Trifluoroacetic acid TFAA Trifluoroacetic anhydride THF Tetrahydrofuran TLC Thin-layer chromatography TMSOTf Trimethylsilyl trifuoromethanesulfonate TROC 2,2,2-Trichloroethoxycarbonyl V Volume 8 Portions of this thesis were adopted with permission from the following journal articles, co-written by the author. Rather, D. M.; Adams, E. W.; Disney, M. D.; Seeberger, P. H. Tools for Glycomics: Mapping Interactions of Carbohydrates in Biological Systems. ChemBioChem, 2004, In Press. Adams,* E. W.; Ratner,* D. M.; Bokesh, H. R; McMahon, J. B.; O'Keefe, B. R.; Seeberger, P.H. Oligosaccharide and Glycoprotein Microarrays as Tools in HIV- Glycobiology: A Detailed Analysis of Glycan Dependent gpl20 / Protein Interactions. Chem. Biol. 2004, 11,875-881.. Ratner, D. M.; Adams, E. W.; Su, J.; O'Keefe, B. R.; Mrksich, M.; Seeberger, P. H. Probing Protein-Carbohydrate Interactions with Microarrays of Synthetic Oligosaccharides. ChemBioChem. 2004, 5, 379-383. Ratner, D. M.; Swanson, E. R.; Seeberger, P. H. Automated Synthesis of the N-linked Core Pentasaccharide. Org. Let. 2003, 5, 4717-4720. Adams, E. W.; Uberfeld, J.; Ratner, D. M.; O'Keefe, B. R.; Walt, D, R.; Seeberger, P. H. Encoded Fiber-Optic Microsphere Arrays for Probing Protein-Carbohydrate Interactions. Angew. Chem. Int. Ed 2003, 42, 5317-5320. Barrientos, L. G.; Louis, J. M.; Ratner, D. M.; Seeberger, P. H.; Gronenborn, A. M. Solution Structure of a Circular-permuted Variant of the Potent HIV-inactivating Protein Cyanovirin-N: Structural Basis for Protein Stability and Oligosaccharide Interaction. J Mol. Biol. 2003, 325, 211-223. Shenoy, S. R.; Barrientos, L. G.; Ratner, D. M.; O'Keefe, B. R.; Seeberger, P. H.; Gronenborn, A. M.; Boyd, M. R. Multisite and Multivalent Binding Between Cyanovirin-N and Branched Oligomannosides: Calorimetric and NMR Characterization. Chem. Biol. 2002, 9, 1109-1118. Botos, I.; O'Keefe, B. R.; Shenoy S. R.; Cartner, L. K.; Ratner, D. M.; Seeberger, P. H.; Boyd, M. R.; Wlodawer, A. Structures of the Complexes of a Potent Anti-HIV Protein Cyanovirin-N
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