Chemistry
Coiled and extended sodium dodecyl sulfate conformations in the water-soluble cavitand. Nuclear magnetic
resonance evidence supports the "strained" structure
in which 8 carbon atoms adopt a coiled conformation
to maximize interaction with the host. Artwork was
done by Michael P. Schramm, Ph.D., The Skaggs
Institute for Chemical Biology.
Julius Rebek, Jr., Ph.D.
Professor, Department of Chemistry
Director, The Skaggs Institute for Chemical Biology
CHEMISTRY
DEPAR TMENT OF
CHEMISTRY
S TA F F
K.C. Nicolaou, Ph.D.*
Professor and Chairman
Aline W. and L.S. Skaggs
Professor of Chemical Biology
Darlene Shiley Chair in
Chemistry
Phil Baran, Ph.D.
Associate Professor
Dale L. Boger, Ph.D.*
Richard and Alice Cramer
Professor of Chemistry
Tobin J. Dickerson, Ph.D.
Assistant Professor
Albert Eschenmoser, Ph.D.*
Professor
Sheng Ding, Ph.D.
Assistant Professor
M.G. Finn, Ph.D.*
Associate Professor
Valery Fokin, Ph.D.
Associate Professor
M. Reza Ghadiri, Ph.D.*
Professor
William A. Greenberg, Ph.D.
Assistant Professor
Inkyu Hwang, Ph.D.
Assistant Professor
Hayato Ishikawa, Ph.D.
Assistant Professor
Kim D. Janda, Ph.D.**
Professor
Ely R. Callaway, Jr., Chair in
Chemistry
Director, The Worm Institute
for Research and Medicine
Jeffery W. Kelly, Ph.D.*
Lita Annenberg Hazen
Professor of Chemistry
Dean, Graduate and
Postgraduate Studies
2006
Ramanarayanan
Krishnamurthy, Ph.D.
Associate Professor
Richard A. Lerner, M.D.***
President, The Scripps
Research Institute
Lita Annenberg Hazen
Professor of
Immunochemistry
Cecil H. and Ida M. Green
Chair in Chemistry
Masayuki Matsushita,
Ph.D.****
Chugai Pharmaceutical Co.,
LTD.
Tokyo, Japan
Michael Meijler, Ph.D.
Assistant Professor
Jorge J. Nieva, M.D.
Assistant Professor
Evan Powers, Ph.D.
Assistant Professor
Julius Rebek, Jr., Ph.D.*
Professor
Director, The Skaggs Institute
for Chemical Biology
Ed Roberts, Ph.D.
Professor
THE SCRIPPS RESEARCH INSTITUTE
Andrew Bin Zhou, Ph.D.
Assistant Professor
S TA F F S C I E N T I S T S
Byeong D. Song, Ph.D.
Lubica Supekova, Ph.D.
Peter G. Schultz, Ph.D.*
Professor
Scripps Family Chair
K. Barry Sharpless, Ph.D.*
Professor
W.M. Keck Professor of
Chemistry
Vaughn Smider, Ph.D.
Assistant Professor
Anita Wentworth, Ph.D.
Assistant Professor
Paul Wentworth, Jr., Ph.D.
Professor
Chi-Huey Wong, Ph.D.*
Ernest W. Hahn Professor
and Chair in Chemistry
Stellios Arseniyadis, Ph.D.****
Ecole Supérieure de
Physique et de Chimie
Industrielle
Paris, France
Gonen Ashkenasy, Ph.D.****
Ben-Gurion University of the
Negev
Beer-Sheeva, Israel
Wen Xiong, Ph.D.
I N S T R U M E N TAT I O N /
SERVICE FACILITIES
Raj K. Chadha, Ph.D.
Director, X-Ray
Crystallography Facility
Dee H. Huang, Ph.D.
Director, Nuclear Magnetic
Resonance Facility
Gary E. Siuzdak, Ph.D.
Director, Mass Spectrometry
Facility
SENIOR RESEARCH
A S S O C I AT E S
Ashraf Brik, Ph.D.
Yanping Chen, Ph.D.
Floyd E. Romesberg, Ph.D.
Associate Professor
63
Gunnar Kaufmann, Ph.D.
Nurit Ashkenasy, Ph.D.****
Ben-Gurion University of the
Negev
Beer-Sheva, Israel
Masato Atsumi, Ph.D.****
Kyocera JMM
Osaka, Japan
Elizabeth Barrett, Ph.D.
Christoph Behrens, Ph.D.****
University of Gottingen
Gottingen, Germany
Clay Bennett, Ph.D.
Jan Bieschke, Ph.D.****
Max Delbrück Center for
Molecular Medicine
Berlin, Germany
Babu Boga, Ph.D.****
Schering Plough
Redminster, New Jersey
Anthony Boitano, Ph.D.
R E S E A R C H A S S O C I AT E S
Ramzey Abujarour, Ph.D.****
Genomics Institute of the
Novartis Research Foundation
San Diego, California
Venkataiah Bollu, Ph.D.
Brant Boren, Ph.D.
Dariush Ajami, Ph.D.
Daryl Bosco, Ph.D.****
Serono, Inc.
Boston, Massachusetts
Lital Alfonta, Ph.D.
Andrew Brogan, Ph.D.
Xaiver Alvarez-Mico, Ph.D.
Adrian Brunkhorst,
Ph.D.*****
Rahesh Ambasudhan, Ph.D.
Paul Bulger, Ph.D.
Narendra B. Ambhaikar,
Ph.D.****
Vertex Pharmaceuticals
San Diego, California
Kevin Bunker, Ph.D.
Antonio Burtoloso, Ph.D.
64 CHEMISTRY
2006
THE SCRIPPS RESEARCH INSTITUTE
Steven Johnson, Ph.D.
Nil Emre, Ph.D.
Sayam Sen Gupta, Ph.D.****
Technical University Munich
Munich, Germany
Alexandre Carella, Ph.D.
Lisa Eubanks, Ph.D.
Richard Guy, Ph.D.
Michael Cassidy, Ph.D.****
Bristol-Myers Squibb
New Brunswick, New Jersey
Cyrine Ezzili, Ph.D.
Clemens Haas, Ph.D.*****
Michael Kelso, Ph.D.****
University of Wollongong
Wollongong, Australia
Akiyuki Hamasaki, Ph.D.
Sukbok Chang, Ph.D.
Raffaella Faraoni, Ph.D.****
Ambit Biosciences
San Diego, California
Shuo Chen, Ph.D.
Simon Ficht, Ph.D.
Yanping Chen, Ph.D.*****
Laura Flatauer, Ph.D.****
Genomics Institute of the
Novartis Research Foundation
San Diego, California
Mark Bushey, Ph.D.
Jan Elsner, Ph.D.
Sara Butterfield, Ph.D.
Jodie Chin, Ph.D.
Charles Cho, Ph.D.
Wooseok Han, Ph.D.****
Chiron
Emeryville, California
Frank Hauke, Ph.D.****
University of Erlangen
Erlangen, Germany
Antonella Converso, Ph.D.****
Merck & Co., Inc.
West Point, Pennsylvania
Jeromy Cottell, Ph.D.
James Crawford, Ph.D.
Matthew Cremeens, Ph.D.
Jesse Dambacher, Ph.D.
Sandra De Lamo Marin, Ph.D.
Ross Denton, Ph.D.
Caroline Desponts, Ph.D.
David Diaz-Diaz, Ph.D.****
Universidad Autónoma de
Madrid
Madrid, Spain
F. Scott Kimball, Ph.D.
Ravinder Reddy Kondreddi,
Ph.D.
Larisa Krasnova, Ph.D.
Ted Foss, Ph.D.
Kevin Cole, Ph.D.
Gyungyoun Kim, Ph.D.****
SK Biopharmaceuticals
Fairfield, New Jersey
Jason Hein, Ph.D.
So-Hye Cho, Ph.D.
Scott Cockroft, Ph.D.
Jaroslaw Kalisiak, Ph.D.
Jane Kuzelka, Ph.D.
Joseph Rodolph Fotsing,
Ph.D.
Mark Hixon, Ph.D.****
Takeda
San Diego, California
Rebecca Fraser, Ph.D.****
Novartis Pharma AG
Horsham, England
Jiyong Hong, Ph.D.****
Duke University
Durham, North Carolina
Graeme Freestone, Ph.D.
Jim Fuchs, Ph.D.
Sukwon Hong, Ph.D.****
University of Florida
Gainsville, Florida
Amelia Fuller, Ph.D.
Zhangyong Hong, Ph.D.
Jianmin Gao, Ph.D.
Richard Hooley, Ph.D.
Muyun Gao, Ph.D.
Ola Ghoneim, Ph.D.
Daniel Horne, Ph.D.****
Amgen
Thousand Oaks, California
Nathan Gianneschi, Ph.D.
Tsui-Ling Hsu, Ph.D.
Romelo Gibe, Ph.D.
Institute of Chemical and
Engineering Sciences
Jurong Island, Singapore,
China
Zheng-Zheng Huang, Ph.D.
Andreas Lanver, Ph.D.
Brian Lawhorn, Ph.D.
Jinq-Chyi Lee, Ph.D.
Jongkook Lee, Ph.D.
JongSeok Lee, Ph.D.
Ki-Bum Lee, Ph.D.
Kooyeon Lee, Ph.D.
Sang Hyup Lee, Ph.D.****
LG Life Sciences
Daejeon, South Korea
Sejin Lee, Ph.D.
Lucas Leman, Ph.D.
Alexandre Lemire, Ph.D.
Amy Hurshman, Ph.D.****
Joint Science Department of
the Claremont Colleges
Claremont, California
Edward Lemke, Ph.D.
Achim Lenzin, Ph.D.
Christine Dierks, Ph.D.****
Genomics Institute of the
Novartis Research Foundation
San Diego, California
Christina Gil-Lamaignere,
Ph.D.
Der-Ren Hwang, Ph.D.
Hongming Li, Ph.D.
Neill Gingles, Ph.D.
Giltae Hwang, Ph.D.
Ke Li, Ph.D.
David Edmonds, Ph.D.
Naran Gombosuren, Ph.D.
Tetsuo Iwasawa, Ph.D.
Pi-Hui Liang, Ph.D.
Greg Elliott, Ph.D.****
Moore Cancer Center
La Jolla, California
Rajesh K. Grover, Ph.D.
Michael Jahnz, Ph.D.
Jan Grunewald, Ph.D.
Wei Jin, Ph.D.
Jiayu Liao, Ph.D.****
University of California
Riverside, California
CHEMISTRY
Yeon-Hee Lim, Ph.D.
2006
Troy Lister, Ph.D.
Robert Milburn, Ph.D.****
Amgen
Thousand Oaks, California
Chris Liu, Ph.D.
Kyung-Hoon Min, Ph.D.*****
THE SCRIPPS RESEARCH INSTITUTE
Charles Papageorgiou,
Ph.D.****
Amgen
Cambridge, Massachusetts
65
F. Anthony Romero, Ph.D.
Youngha Ryu, Ph.D.
Riccardo Salvio, Ph.D.
Doron Pappo, Ph.D.
Haitian Liu, Ph.D.****
Senomyx, Inc.
La Jolla, California
Jun Liu, Ph.D.****
Genomics Institute of the
Novartis Research Foundation
San Diego, California
Christos A. Mitsos, Ph.D.****
Athens, Greece
Junguk Park, Ph.D.
Gopi Kumar Mittapalli, Ph.D.
Laxman Pasunoori, Ph.D.
Lionel Moisan, Ph.D.
Richard Payne, Ph.D.
Ana Montero, Ph.D.
Murali Peram Surakattula,
Ph.D.
Lei Liu, Ph.D.
Miguel Morales, Ph.D.
Wenshe Liu, Ph.D.
Tingwei Mu, Ph.D.
Yi Liu, Ph.D.****
Lawrence Berkeley National
Laboratory
Berkeley, California
Mridul Mukherji, Ph.D.
Ying (Cindy) Liu, Ph.D.
Dimitrios Lizos, Ph.D.****
Novartis Pharmaceuticals
Basil, Switzerland
Jon Loren, Ph.D.****
Genomics Institute of the
Novartis Research Foundation
San Diego, California
Hongzheng (Eric) Ma, Ph.D.
Roman Manetsch, Ph.D.****
University of South Florida
Tampa, Florida
Enrique Mann, Ph.D.
Felix Marr, Ph.D.*****
Carol Lamenca Martinez,
Ph.D.****
Berlin, Germany
Roshan Perera, Ph.D.
Goran Petrovic, Ph.D.
Andrew Myles, Ph.D.****
University of Alberta
Edmonton, Canada
Jared Piper, Ph.D.****
Eli Lilly
Indianapolis, Indiana
Suresh Pitram, Ph.D.
Kenichiro Nagai, Ph.D.
Tülay Polat, Ph.D.
Yuya Nakai, Ph.D.
Damien Poliet, Ph.D.
Joonwoo Nam, Ph.D.
Anu Sawkar, Ph.D.****
Ropes & Gray
New York, New York
Patrick Schanen, Ph.D.****
ETH Zürich, Laboratory of
Organic Chemistry
Zurich, Switzerland
Stefan Schiller, Ph.D.
Daniel Schlawe, Ph.D.****
Syncom BV
Groningen, the Netherlands
Michael Schramm, Ph.D.
Laura Segatori, Ph.D.
Mary Sever, Ph.D.
Alex Shaginian, Ph.D.
Guido Pontremoli, Ph.D.
David Shaw, Ph.D.
Sridhar Narayan, Ph.D.****
Eisai Research Institute
Wilmington, Massachusetts
Mariceli Puga, Ph.D.
Daniel Nicoletti, Ph.D.
Sreenivas Punna, Ph.D.****
ChemoCentryx, Inc.
Mountain View, California
Junhwa Shin, Ph.D.****
Korea Atomic Energy
Research Institute
Seoul, Korea
Alain Noncovich, Ph.D.****
Senomyx Inc.
La Jolla, California
Yasuo Norikane, Ph.D.****
Nanotechnology Research
Institute, AIST
Tsukuba, Japan
Mehdi Numa, Ph.D.****
Vertex Pharmaceuticals
Incorporated
San Diego, California
Shigeo Matsuda, Ph.D.
Severin Odermatt, Ph.D.
Klaus-Dieter Michael Maue,
Ph.D.
Barun Okram, Ph.D.
Laura McAllister, Ph.D.
Peter Orahovats, Ph.D.
Kathleen McKenzie, Ph.D.
Yazmin Osornio, Ph.D.
Sebastian Steiniger, Ph.D.
Daniela Radu, Ph.D.
Nicole Rahe, Ph.D.****
Tesa AG
Hamburg, Germany
Shai Rahimipour, Ph.D.****
Bar-Ilan University
Ramat-Gan, Isreal
Shula Stokols, Ph.D.****
W. L. Gore & Associates
Flagstaff, Arizona
Ji Young Suk, Ph.D.****
Merck Research Laboratories
Boston, Massachusetts
Daniel Summerer, Ph.D.
Praveen Rao, Ph.D.
Takahiro Suzuki, Ph.D.
Dalit Rechavi-Robinson,
Ph.D.****
University of Geneva
Geneva, Switzerland
Stefanie Roeper, Ph.D.*****
Vertex Pharmaceuticals
Cambridge, Massachusetts
Leo Takaoka, Ph.D.
Eric Tippmann, Ph.D.
Jonathan Tripp, Ph.D.
Meng-Lin Tsao, Ph.D.
66 CHEMISTRY
2006
THE SCRIPPS RESEARCH INSTITUTE
Craig Turner, Ph.D.
Heiko Wurdak, Ph.D.
V I S I T I N G I N V E S T I G AT O R S
Jim Turner, Ph.D.****
Fish & Richardson P.C.
San Diego, California
Jian Xie, Ph.D.
Mohammad Al-Sayah, Ph.D.
American University of
Sharjah
Sharjah, United Arab
Emirates
Andrew Udit, Ph.D.
Yue Xu, Ph.D.
Ryu Yamasaki, Ph.D.
Taiki Umezawa, Ph.D.
Yasuyuki Ura, Ph.D.
Shuyan Yao, Ph.D.****
Sangamo BioScience, Inc.
Richmond, California
Kenji Usui, Ph.D.
Juraj Velcicky, Ph.D.****
Novartis
Basel, Switzerland
Alessandro Volonterio,
Ph.D.****
Politencino di Milano
Milano, Italy
Robert Yeh, Ph.D. ****
Siemens
Torrance, California
Yong Sik Yoo, Ph.D.****
Cheil Industries, Inc.
Seoul, Korea
Zhanqian Yu, Ph.D.
Hong Wang, Ph.D.
Jiangyun Wang, Ph.D.
Weidong Wang, Ph.D.
Mark Zak, Ph.D.****
Genentech
San Francisco, California
Xiaolong Wang, Ph.D.
Felix Zelder, Ph.D.****
Timo Weide, Ph.D.
Huaqiang Zeng, Ph.D.****
National University of
Singapore
Singapore
Lisa Whalen, Ph.D.****
University of New Mexico
Albuquerque, New Mexico
Matthew Whiting, Ph.D.
Aarron Willingham, Ph.D.****
Affymetrix
Santa Clara, California
Albert Willis, Ph.D.
Chung-Yi Wu, Ph.D.****
Academia Sinica
The Genomics Research
Institute
Taipei, Taiwan
Qisheng Zhang, Ph.D.
Yingchao Zhang, Ph.D.
Yuanxiang Zhao, Ph.D.****
Cellular Dynamics
International Inc.
Madison, Wisconsin
Heyue Henry Zhou, Ph.D.
Min Zhou, Ph.D.
Douglass Wu, Ph.D.
Optimer Pharmaceuticals
San Diego, California
Xiuwen Zhu, Ph.D.
Margarita Wuchrer, Ph.D.****
Merck KgaA
Frankfurt, Germany
Caterina Zoni, Ph.D.
Masaaki Sawa, Ph.D. ****
Dainippon Pharmaceuticals
Co., Ltd
Osaka, Japan
Masakazu Sugiyama, Ph.D.
Ajinomoto Co., Inc.
Kawasaki-Shi, Japan
Luda Bazhenova, Ph.D.****
University of California
San Diego, California
Shin-Ichi Takanashi,
Ph.D.****
Sheila Fleming, Ph.D.****
University of California
Los Angeles, California
Erich Uffelman, Ph.D.****
Washington and Lee
University
Lexington, Virginia
Masakazu Fujio, Ph.D.
Mitsubishi Pharma
Corporation
Yokohama, Japan
Luigi Gomez Paloma,
Ph.D.****
University di Salerno
Fisciano, Italy
Andrew S. Grant, Ph.D.****
Mount Allison University
Sackville, New Brunswick,
Canada
Yoshiyuki Hari, Ph.D.
Nagoya City University
Nagoya, Japan
Akira Ino, Ph.D.
Shionogi & Co., LTD.
Osaka, Japan
Lisa Landino, Ph.D.
College of William and Mary
Williamsburg, Virginia
Jason Moss, Ph.D.****
PDL BioPharma, Inc.
Fremont, California
Poul Nielsen, Ph.D.
University of Southern
Denmark
Odense, Denmark
Joerg Zimmermann, Ph.D.
Manuela Rodriguez,
Ph.D.****
University di Salerno
Fisciano, Italy
Makoto Yamashita,
Ph.D.****
Takeda Chemical Industries,
Ltd.
Osaka, Japan
S C I E N T I F I C A S S O C I AT E S
Jon Ashley
Gina Dendle
Suresh Mahajan, Ph.D.
* Joint appointment in The Skaggs
Institute for Chemical Biology
** Joint appointments in the
Skaggs Institute for Chemical
Biology and the Department of
Immunology
*** Joint appointments in The
Skaggs Institute for Chemical
Biology and the Department of
Molecular Biology
**** Appointment completed; new
location shown
***** Appointment completed
CHEMISTRY
2006
K.C. Nicolaou, Ph.D.
Chairman's Overview
s the "central science," chemistry stands between
biology and medicine and between physics and
materials science and provides the crucial bridge
for drug discovery and development. But chemistry has
a much more profound and useful role in science and
society. It is the discipline that continually creates the
myriad of new materials that we all encounter in our
everyday lives: pharmaceuticals, high-tech materials,
polymers and plastics, insecticides and pesticides, fabrics and cosmetics, fertilizers, and vitamins—basically
everything we can touch, feel, and smell.
Chemists at Scripps Research focus on chemical synthesis and chemical biology, the areas most relevant to
biomedical research and materials science. The members of our faculty are distinguished teacher-scholars
who maintain highly visible and independent research
programs in areas as diverse as biological and chemical
catalysis, synthesis of natural products, combinatorial
chemistry, molecular design, supramolecular chemistry,
chemical evolution, materials science, and chemical
biology. The chemistry graduate program attracts some
of the best-qualified candidates from both the United
States and abroad. Our major research facilities, under
the direction of Dee H. Huang (nuclear magnetic resonance), Gary Siuzdak (mass spectrometry), and Raj
A
THE SCRIPPS RESEARCH INSTITUTE
67
Chadha (x-ray crystallography), are second to none and
continue to provide crucial support to our research programs. In addition, the Mabel and Arnold Beckman Center for the Chemical Sciences constantly receives high
praise from visitors from around the world for its architectural design and operational aspects, both highly
conducive to research.
Research in the Department of Chemistry goes on
unabated, establishing international visibility and attracting attention as evidenced by numerous lecture invitations, visits by outside scholars, and headline news in
the media. As of 2005, the Institute for Scientific Information ranked 3 members of our department as highly
cited researchers (in the top 100 worldwide); 2 of the 3
are among the top 51 positions.
Richard Lerner and his group continue to make
advances in catalytic antibodies, with new antibodies
that catalyze important synthetic and biological reactions
and novel applications in chemical synthesis. The group’s
research has recently expanded to include the fundamental chemistry of the polyoxygen species.
Barry Sharpless and his group continue endeavors to
discover and develop better catalysts for organic synthesis
and to construct, through innovative chemistry and biology, libraries of novel compounds for biological screening.
Scientists in Albert Eschenmoser’s La Jolla-based
group advance their experimental studies on the chemical
etiology of nucleic acid structure by investigating nucleic
acid alternatives that have novel backbones and recognition elements unrelated to the canonical phophodiesterbased oligonucleotide systems.
Members of my own group continue explorations of
chemical synthesis and chemical biology, focusing on the
total synthesis of new anticancer agents, antibiotics,
marine-derived neurotoxins, antimalarial compounds,
antifeedant agents, and other biologically active natural
and designed molecules.
The members of Julius Rebek’s group devise biomimetic receptors for studies in molecular recognition.
These include molecules that bind neurotransmitters and
membrane components. Larger host receptors can surround 3 or more molecular guests and act as chambers
where the chemical reactions of the guests are accelerated. The group synthesizes small molecules that act as
protein helix mimetics for pharmaceutical applications.
Peter Schultz and his group have continued to expand
the number of genetically encoded amino acids to include
fluorescent, photocaged, metal binding, thioester, sulfated, and long-chain alkane side chains. They have
68 CHEMISTRY
2006
also adapted this technology to mammalian cells and
are applying it to a number of basic and applied problems in cell biology. In addition, they have used cell-based
screens to identify small molecules that selectively differentiate and expand embryonic and adult stem cells
and reprogram lineage-committed cells, as well as novel
genes that control cell cycle, cell migration, and developmental pathways.
Chi-Huey Wong and his group further advance the
fields of chemoenzymatic organic synthesis, chemical glycobiology, and the development of enzyme inhibitors. A
new strategy for the synthesis of glycoproteins has been
developed. The programmable 1-pot synthesis of oligosaccharides developed by this group has been further used in
the assembly of glycoarrays for study of saccharides that
bind to proteins. This group also developed new probes
to study glycosyltransferases and their role in cancer.
Members of Dale Boger’s group continue their work
on chemical synthesis; combinatorial chemistry; heterocycle synthesis; anticancer agents such as vinblastine,
fostriecin, and yatakemycin; and antibiotics such as
vancomycin, teicoplanin, and ramoplanin.
Scientists in Kim Janda’s laboratory are focusing on
the impact of organic chemistry in specific biological
systems. Their targeted programs span a wide range of
interests from immunopharmacotherapy to biological
and chemical warfare agents to filarial infections, such
as "river blindness," to quorum sensing in bacteria. Their
recent achievements include the discovery of a secondary
nicotine metabolite that alters retinoid homeostasis, a
critical component of vision and growth; small molecules
that "superactivate" botulinum neurotoxin; and a virusbased system that can degrade cocaine in the central
nervous system.
Reza Ghadiri and his group are making significant
contributions in the design and study of a new generation of antimicrobial agents, based on self-assembling
peptide nanotube architecture, to combat multidrugresistant infections. In addition, they continue to make
novel contributions in several ongoing basic research
endeavors, such as biosensor designs, molecular computation, design of self-reproducing systems, understanding the origins of life, and design of emergent
chemical systems.
M.G. Finn and his group have pioneered the use of
virus particles as chemical reagents and building blocks
for nanochemical structures. This effort is directed toward
the development of new diagnostics for disease and catalysts for organic reactions. Members of Dr. Finn’s labo-
THE SCRIPPS RESEARCH INSTITUTE
ratory also develop and investigate new organic and
organometallic reactions and use these processes to
synthesize biologically active compounds.
Jeffery Kelly and his group are exploring the interface between chemistry, biology, and medicine. Their
projects aim to understand the physical and biological
basis of protein folding, and the misfolding and aggregation processes leading to age-onset neurodegenerative diseases. Comprehension of the latter processes is
used to develop new small-molecule therapeutic strategies for a variety of neurodegenerative diseases.
Anita Wentworth and her group are investigating
the chemical basis of complex disease states and are
synthesizing peptide and small molecule–based therapeutics. Their research is focused on disease states
that have a prominent inflammatory and reactive oxygen-species chemical component, such as atherosclerosis, Alzheimer's disease, and other diseases of aging.
Researchers in Floyd Romesberg’s laboratory are
using diverse techniques ranging from bioorganic and
biophysical chemistry to bacterial and yeast genetics to
understand and manipulate the process of evolution.
Major efforts include designing unnatural base pairs and
the directed evolution of DNA polymerases to efficiently
synthesize unnatural DNA containing the base pairs;
using spectroscopy to understand biological function and
how it evolves; and understanding how induced and
adaptive mutations contribute to evolution in eukaryotic
and prokaryotic cells.
Dr. Baran and his group have recently developed
extremely concise chemical solutions to the synthetic
challenges posed by numerous marine natural product
families, including sceptrin, ageliferin, chartelline, haouamine, welwitindolinones, and the stephacidins. These
syntheses are characterized by striking brevity, new
biosynthetic postulates, the invention of a new methodology, and a minimum use or complete absence of protecting groups and superfluous oxidation-state manipulations.
The Frontiers in Chemistry Lecturers (17th Annual
Symposium) for the 2005–2006 academic year were
Richard Lerner, Scripps Research; Peter Vollhardt, University of California, Berkeley; Dieter Enders, Institute
of Organic Chemistry, RWTH Aachen, Germany; and
K.C. Nicolaou, Scripps Research. Thomas Scanlan
(University of California, San Francisco) also visited
Scripps this year as the Novartis Lecturer in Organic
Chemistry, 2005.
CHEMISTRY
2006
THE SCRIPPS RESEARCH INSTITUTE
69
INVESTIGATORS’ R EPORTS
Practical Total Synthesis of
Natural Products
P.S. Baran, N.Z. Burns, M.P. DeMartino, C.A. Guerrero,
B.D. Hafensteiner, P.J. Krawczuk, K. Li, D.W. Lin,
T.J. Maimone, M.K.-D. Maue, S. Nguyen, D.P. O’Malley,
J.M. Richter, R.A. Shenvi, B. Whitefield
rom penicillin to paclitaxel (Taxol), natural products have an unparalleled track record in the
betterment of human health. In fact, 9 of the top
20 best-selling drugs were either inspired by or derived
from natural products. Even the best-selling drug of all
time, atorvastatin (Lipitor), was based on a natural
product lead. Total synthesis, the art and science of
recreating these entities in the laboratory, invariably
leads to fundamental discoveries in chemistry, biology,
and medicine.
We focus on solving interesting challenges in the
total synthesis of natural products and on bridging gaps
in synthetic capabilities by inventing new reactions.
Through judicious target selection and creative retrosynthetic analyses, total synthesis becomes an engine for
discovery that drives the field of organic chemistry to
new levels of sophistication and practicality. Synthetic
organic chemistry requires tremendous ingenuity, artistic taste, experimental acumen, persistence, and character. Not surprisingly, drug development relies on the
expertise of researchers who have these characteristics.
Although we focus entirely on educating students in
fundamental chemistry, we also collaborate with expert
biologists to explore the medicinal potential of newly
synthesized natural products and the products’ analogs.
Recently completed total syntheses (Fig. 1) include
the anticancer agents stephacidins A and B and avrainvillamide; the antibacterial agents sceptrin and ageliferin; members of the bioactive fischerindole, hapalindole,
and welwitindolinone indole alkaloid family; and the
anticancer agent haouamine A. Current natural product targets (Fig. 2) include chartelline C, axinellamine,
strictamine, and sarcodonin.
F
F i g . 1 . Recently completed total syntheses.
Baran, P.S., Li, K., O’Malley, D.P., Mitsos, C. Short, enantioselective total synthesis of sceptrin and ageliferin by programmed oxaquadricyclane fragmentation.
Angew. Chem. Int. Ed. 45:249, 2006.
PUBLICATIONS
Baran, P.S., Burns, N.Z. Total synthesis of (±)-haouamine A. J. Am. Chem. Soc.
128:3908, 2006.
Baran, P.S., Richter, J.M. Enantioselective total syntheses of welwitindolinone A
and fischerindoles I and G. J. Am. Chem. Soc. 127:15394, 2005.
Baran, P.S., Hafensteiner, B.D., Ambhaikar, N.B., Guerrero, C.A., Gallagher, J.D.
Enantioselective total synthesis of avrainvillamide and the stephacidins. J. Am.
Chem. Soc. 128:8678, 2006.
Northrop, B.H., O’Malley, D.P., Zografos, A.L., Baran, P.S., Houk, K.N. The mechanism of the vinylcyclobutane rearrangement of sceptrin to ageliferin and nagelamide E. Angew. Chem. Int. Ed. 45:4126, 2006.
70 CHEMISTRY
2006
THE SCRIPPS RESEARCH INSTITUTE
SYNTHETIC METHODS
Central to much of our work are investigations to
develop and apply the hetero Diels-Alder reaction, including the use of heterocyclic and acyclic azadienes (Fig. 1),
F i g . 1 . N-Sulfonyl-1-aza-1,3-butadiene Diels-Alder reaction.
the thermal reactions of cyclopropenone ketals, intermolecular and intramolecular acyl radical–alkene addition
reactions, medium- and large-ring cyclization technology,
and solution-phase combinatorial chemistry. In each
instance, the development of the methods represents
the investigation of chemistry projected as a key element in the synthesis of a natural or designed agent.
T O TA L S Y N T H E S I S O F N AT U R A L P R O D U C T S
F i g . 2 . Ongoing natural product total syntheses.
Synthetic and
Bioorganic Chemistry
D.L. Boger, S.B. Boga, K. Bunker, R. Clark, D. Colby,
J. Cottell, B. Crowley, J. DeMartino, G. Elliott, J. Elsner,
C. Ezzili, J. Fuchs, J. Garfunkle, A. Hamasaki, W. Han,
N. Haq, S. Hong, D. Horne, I. Hwang, H. Ishikawa, W. Jin,
D. Kato, D. Kastrinsky, M. Kelso, G. Kim, F.S. Kimball,
B. Lawhorn, S. Lee, C. Liu, K. MacMillan, J. Nam, P. Patel,
A. Romero, M. Schnermann, A. Shaginian, C. Slown,
L. Takaoka, H. Tao, M. Tichenor, J. Trzupek, J. Velcicky,
L. Whiby, Y. Zhang
he research interests of our group include the total
synthesis of natural products, development of new
synthetic methods, heterocyclic chemistry, bioorganic and medicinal chemistry, the study of DNA-agent
interactions, and the chemistry of antitumor antibiotics.
We place a special emphasis on investigations to define
the structure-function relationships of natural or designed
organic agents.
T
Efforts are under way on the total synthesis of a
number of natural products that constitute agents in
which we have a specific interest. Representative agents
currently under study include (+)-CC-1065 and functional analogs; the duocarmycin class of antitumor
antibiotics, including yatakemycin; tropoloalkaloids;
prodigiosin and roseophilin; the deoxybouvardin and
RA-I class of antitumor agents; vancomycin, teicoplanin,
ristocetin, chloropeptins and related agents; ramoplanin; the luzopeptins, quinoxapeptins, thiocoraline,
BE-22179 and sandramycin; bleomycin A2 and functional analogs; HUN-7293; chlorofusin; CI-920 (fostriecin) and cytostatin; the combretastatins; storniamide
A; phomazarin; ningalins; lamellarin O; lukianol A;
piericidins; nothapodytine and mappicine; rubrolone;
vindoline; and vinblastine (Figs. 2 and 3).
BIOORGANIC CHEMISTRY
The agents listed in the previous paragraph were
selected on the basis of their properties; in many
instances, they are agents related by a projected property. For example, (+)-CC-1065, the duocarmycins,
and yatakemycin are antitumor antibiotics and related
sequence-selective DNA minor groove alkylating agents.
Representative of such efforts, studies to determine
the structural features of yatakemycin and the duocarmycins that contribute to the sequence-selective
DNA alkylation properties of these agents have resulted
CHEMISTRY
2006
THE SCRIPPS RESEARCH INSTITUTE
71
F i g . 2 . Recent total syntheses.
Fig. 3. Additional recent total syntheses.
in the identification of a unique source of catalysis for
the DNA alkylation reaction. Efforts are under way to
develop DNA cross-linking agents of a predefined crosslink, to further understand the nature of the noncovalent
and covalent interactions between agents and DNA, and
to apply this understanding to the de novo design of
DNA-binding and DNA-effector agents. Techniques for
the evaluation of the agent-DNA binding and alkylation
properties, collaborative efforts in securing biological
data, nuclear magnetic resonance structures of DNAagent complexes, molecular modeling, and studies of
DNA-agent interactions are integral parts of the program.
72 CHEMISTRY
2006
Additional ongoing studies include efforts to define
the fundamental basis of the DNA-binding or cleavage
properties of bleomycin A2, sandramycin, and the luzopeptins; to design inhibitors of the folate-dependent
enzymes glycinamide ribonucleotide transformylase and
aminoimidazole carboxamide ribonucleotide transformylase as potential antineoplastic agents; to establish
the chemical and biological characteristics responsible
for the sleep-inducing properties of the endogenous
lipid oleamide; to inhibit tumor growth through inhibition of angiogenesis; to inhibit aberrant gene transcription associated with cancer; and to control intracellular
signal transduction through the discovery of antagonists or agonists that affect protein-protein interactions,
including receptor dimerization.
PUBLICATIONS
Boger, D.L., Miyauchi, H., Du, W., Hardouin, C., Fecik, R.A., Cheng, H., Hwang,
I., Hedrick, M.P., Leung, D., Acevedo, O., Guimarães, C.R.W., Jorgensen, W.L.,
Cravatt, B.F. Discovery of a potent, selective, and efficacious class of reversible
α-ketoheterocycle inhibitors of fatty acid amide hydrolase effective as analgesics. J.
Med. Chem. 48:1849, 2005.
Capps, K.J., Humiston, J., Dominique, R., Hwang, I., Boger, D.L. Discovery of
AICAR Tfase inhibitors that disrupt requisite enzyme dimerization. Bioorg. Med.
Chem. Lett. 15:2840, 2005.
Cheng, H., Chong, Y., Hwang, I., Tavassoli, A., Zhang, Y., Wilson, I.A., Benkovic,
S.J., Boger, D.L. Design, synthesis, and evaluation of 10-methanesulfonyl-DDACTHF, 10-methanesulfonyl-5-DACTHF, and 10-methylthio-DDACTHF as potent
inhibitors of GAR Tfase and the de novo purine biosynthetic pathway. Bioorg. Med.
Chem. 13:3577, 2005.
Cheng, H., Hwang, I., Chong, Y., Tavassoli, A., Webb, M.E., Zhang, Y., Wilson,
I.A., Benkovic, S.J., Boger, D.L. Synthesis and biological evaluation of N-{4-[5(2,4-diamino-6-oxo-6-dihydropyrimidin-5-yl)-2-(2,2,2-trifluoroacetyl)pentyl]benzoyl}-L-glutamic acid as a potential inhibitor of GAR Tfase and the de novo purine
biosynthetic pathway. Bioorg. Med. Chem. 13:3593, 2005.
Choi, Y., Ishikawa, H., Velcicky, J., Elliott, G.I., Miller, M.M., Boger, D.L. Total
synthesis of (–)- and ent-(+)-vindoline. Org. Lett. 7:4539, 2005.
Chong, Y., Hwang, I., Tavassoli, A., Zhang, Y., Wilson, I.A., Benkovic, S.J, Boger,
D.L. Synthesis and biological evaluation of α- and γ-carboxamide derivatives of 10CF3CO-DDACTHF. Bioorg. Med. Chem. 13:3587, 2005.
Chou, T.-C., Gaun, Y., Soenen, D.R., Danishefsky, S.J., Boger, D.L. Potent reversal of
multidrug resistance by ningalin and its use in drug combinations against human colon
carcinoma xenografts in nude mice. Cancer Chemother. Pharmacol. 56:379, 2005.
Du, W., Hardouin, C., Cheng, H., Hwang, I., Boger, D.L. Heterocyclic sulfoxide
and sulfone inhibitors of fatty acid amide hydrolase. Bioorg. Med. Chem. Lett.
15:103, 2005.
Guimarães, C.R.W., Boger, D.L., Jorgensen, W.L. Elucidation of fatty acid amide
hydrolase inhibition by potent α-ketoheterocycle derivatives from Monte Carlo simulations. J. Am. Chem. Soc. 127:17377, 2005.
Hamasaki, A., Zimpleman, J.M., Hwang, I., Boger, D.L. Total synthesis of ningalin D.
J. Am. Chem. Soc. 127:10767, 2005.
Leung, D., Du, W., Hardouin, C., Cheng, H., Hwang, I., Cravatt, B.F., Boger, D.L.
Discovery of an exceptionally potent and selective class of fatty acid amide hydrolase
inhibitors enlisting proteome-wide selectivity screening: concurrent optimization of
enzyme inhibitor potency and selectivity. Bioorg. Med. Chem. Lett. 15:1423, 2005.
Schnermann, M.J., Boger, D.L. Total synthesis of piercidin A1 and B1. J. Am.
Chem. Soc. 127:15704, 2005.
THE SCRIPPS RESEARCH INSTITUTE
Tse, W.C., Boger, D.L. A fluorescent intercalator displacement (FID) assay for
establishing DNA binding selectivity and affinity. In: Current Protocols in Nucleic
Acid Chemistry. Beaucage, S.L., et al. (Eds.). Wiley & Sons, New York, in press.
Walker, S., Chen, L., Hu, Y., Rew, Y., Shin, D., Boger, D.L. Chemistry and biology
of ramoplanin: a lipoglycodepsipeptide with potent antibiotic activity. Chem. Rev.
105:449, 2005.
Yuan, Z., Ishikawa, H., Boger, D.L. Total synthesis of natural (+)- and ent-(–)-4desacetoxy-6,7-dihydrovindorosine [corrected] and natural and ent-minovine: oxadiazole tandem intramolecular Diels-Alder/1,3-dipolar cycloaddition reaction [published
correction appears in Org. Lett. 7:2079, 2005]. Org. Lett. 7:741, 2005.
Chemical and Functional
Genomic Approaches to
Regenerative Medicine
S. Ding, R. Abu-Jarour, R. Ambasudhan, C. Desponts,
N. Emre, H.S. Hahm, S. Hilcove, J. Hsu, M. Kim, Y. Shi,
S. Takanashi, W. Xiong, Y. Xu, S. Yao, D. Yue, Y. Zhao, X. Zhu
ecent advances in stem cell biology may make
possible new approaches for the treatment of a
number of diseases, including cardiovascular
disease, neurodegenerative disease, musculoskeletal
disease, diabetes, and cancer. These approaches could
involve cell replacement therapy and/or drug treatment
to stimulate the body’s own regenerative capabilities
by promoting survival, migration/homing, proliferation,
and differentiation of endogenous stem/progenitor cells.
However, such approaches will require identification of
renewable cell sources of engraftable functional cells, an
improved ability to manipulate proliferation and differentiation of the cells, and a better understanding of the
signaling pathways that control the fate of the cells.
Equipped with large arrayed molecular libraries—
combinatorial chemical libraries (>100,000 discrete
and diverse small molecules), cDNA overexpression
libraries (>30,000 human and mouse genes) and
small interfering RNA libraries (targeting >20,000
human and mouse genes)—and a high-throughput
screening platform, we are developing and integrating
chemical and functional genomic tools to study stem
cell biology and regeneration. We screen these libraries
to identify small molecules and genes that can control
the fate of stem cells in various systems, including (1)
self-renewal, as well as directed neuronal, cardiac, and
pancreatic differentiations of pluripotent mouse and
human embryonic stem cells; (2) directed neuronal
differentiation and subtype neuron specification of
human and rodent neural stem cells; (3) directed dif-
R
CHEMISTRY
2006
ferentiation of mesenchymal stem cells to osteogenic,
adipogenic, chondrogenic, and myogenic lineages; (4)
functional proliferation of cardiomyocytes and islets/beta
cells in adults; (5) cellular plasticity and dedifferentiation of lineage-restricted somatic cells; and (6) developmental signaling pathways.
In addition, we are doing systemic biochemical
and cellular studies, including detailed investigations
of structure-activity relationships, affinity chromatography for target identification, genome-wide expression
analysis with microarrays, and cDNA and/or RNA interference complementation screens to map signaling pathways to characterize the molecular mechanism of these
identified small molecules and genes.
Recent examples of small molecules of interest
include neuropathiazol, which can direct differentiation
of primary rat adult neural stem cells selectively toward
neurons; pluripotin, which can sustain self-renewal of
murine embryonic stem cells in a chemically defined
medium; and a purine analog that functions as a synergistic Wnt pathway agonist and can induce Xenopus
axis duplication in combination with Wnt8. These studies may ultimately facilitate the therapeutic application
of stem cells and the development of small-molecule
drugs to stimulate tissue and organ regeneration in vivo.
PUBLICATIONS
Warashina, M., Min, K.H., Kuwabara, T., Huynh, A., Gage, F.H., Schultz, P.G.,
Ding, S. A synthetic small molecule that induces neuronal differentiation of adult
hippocampal neural progenitor cells. Angew. Chem. Int. Ed. 45:591, 2006.
Zhao, Y., Clark J., Ding, S. Genomic studies in stem cell systems. Curr. Opin. Mol.
Ther. 7:43, 2005.
Chemical Etiology of the
Structure of Nucleic Acids
A. Eschenmoser, R. Krishnamurthy, G. Kumar, F. De
Riccardis, R. Kondreddi, Y. Osornio, M. Guerrero
D
uring the past year we worked on the following
projects.
O L I G O M E R S B A S E D O N T R I A Z I N E - TA G G E D
OLIGODIPEPTIDE AND OLIGODIPEPTOID BACKBONES
We continued our studies on the self- and crosspairing properties of triazine-tagged oligodipeptides consisting of alternating aspartic acid (Asp) and glutamic
acid (Glu) residues (Fig. 1). Although the oligo-(AspGlu)dipeptides tagged with 2,4-diaminotriazine had strong
THE SCRIPPS RESEARCH INSTITUTE
73
F i g . 1 . Formulas of triazine-tagged oligomers. IDA indicates
iminodiacetic acid.
cross-pairing with complementary RNA and DNA
oligonucleotide sequences, the corresponding oligo(AspGlu)-dipeptides tagged with 2,4-dioxotriazine,
much to our surprise, showed only weak pairing with
the natural oligonucleotides. The intrasystem self-pairing of 2,4-diaminotriazine–, 2,4-dioxotriazine–, and 2amino-4-oxo-triazine–tagged oligo-(AspGlu)-dipeptides
was equally weak.
The base-pairing properties of triazine-tagged oligo(AspAsp)-dipeptides paralleled the trends observed in
the oligo-(AspGlu)-dipeptide series, but, as expected,
were consistently weaker in base-pairing strength.
A variation of the oligo-(AspAsp)-dipeptide shown
in Figure 1B is the achiral oligodipeptoid derived from
iminodiacetic acid units (Fig. 1C). Again, oligodipeptoids containing 2,4-diaminotriazines cross-paired with
RNA and DNA oligonucleotides, but no discernible
pairing occurred with the 2,4-dioxotriazine–tagged
oligodipeptoids.
Our studies indicate that the family of triazine-based
recognition elements lacks the balance in pairing strength
characteristic of the purine-pyrimidine combination in
the natural series, presumably because of the imbalance in protophilicity of dioxotriazines (pKa about 6)
vs diaminotriazines (pKa about 3.9), in an aqueous
environment. Such imbalance in pairing potential leads
to the conclusion that triazines, irrespective of their
generational simplicity, would have been functionally
incapable of fulfilling the role of recognition elements
in a primordial genetic system. This realization has led
us pursue the following project.
74 CHEMISTRY
2006
O L I G O M E R S B A S E D O N 5 - A M I N O P Y R I M I D I N E – TA G G E D
OLIGODIPEPTIDE BACKBONES
Oligomerization of hydrogen cyanide, a potentially
prebiotic reaction generally assumed to have acted as
the primordial source of the canonical nucleobases adenine and guanine, produces in addition pyrimidines, not
the canonical ones, but mostly 5-aminopyrimidines,
which do not play a role in contemporary biology (Fig. 2).
THE SCRIPPS RESEARCH INSTITUTE
Mittapalli, G.K., Osornio, Y.M., Guererro, M.A., Reddy, K.R., Krishnamurthy, R.,
Eschenmoser, A. Mapping the landscape of potentially primordial informational
oligomers: oligodipeptides and oligodipeptoids tagged with 2,4-disubstituted-5amino-pyrimidines as recognition elements. Angew. Chem. Int. Ed., in press.
Wagner, T., Han, B., Koch, G., Krishnamurthy, R., Eschenmoser, A. Tautomerism in
5,8-diaza-7,9-dicarbaguanine (“alloguanine”). Helv. Chim. Acta 88:1960, 2005.
Organic, Materials, and
Analytical Chemistry
M.G. Finn, J. Kuzelka, D. Prasuhn, S. Presolski, V. Rodionov,
Y.-H. Lim, B. Venkataiah
n addition to synthetic chemistry research on viruses,
our program encompasses organic, organometallic,
and materials chemistry. Special emphasis is placed
on methods of chemical synthesis, the discovery of
functional molecules, and catalysis.
I
M E C H A N I S M S A N D A P P L I C AT I O N S O F C L I C K
CHEMISTRY
F i g . 2 . Top, Formulas of 5-aminopyrimidine heterocycles. Bottom,
Also shown, as a representative example, is the 5-amino-2,4-dioxo–
tagged oligomer containing alternating residues of aspartic and glutamic acid.
Chemical reasoning makes a study of the base-pairing
properties of the members of this family highly desirable; they not only can potentially act as substitutes
in the 2 canonical Watson-Crick base pairs but also
offer a unique opportunity to tag polypeptide chains
bearing recurring carboxyl groups by using simple
(regioselective) amide formation. We have synthesized
5-aminopyrimidine–tagged oligo-(AspGlu)-dipeptides
(up to hexadecamers) by using all 4 members of the
family and have explored base-paring properties of the
tagged dipeptides. Preliminary results indicated crosspairing between all of these recognition elements with
the corresponding complementary RNA and DNA oligonucleotides, although the 5-aminopyrimidine heterocycles have stark differences in base-pairing strength.
Also, cross-pairing occurs between the 2,4-diaminotriazine–tagged oligo-(AspGlu)-dipeptides and 5-amino2,4-dioxopyrimidine–tagged oligo-(AspGlu)-dipeptides.
PUBLICATIONS
Eschenmoser, A. Searching for nucleic acid alternatives. Chimia 59:836, 2005.
Mittapalli, G.K., Reddy, K.R., Xiong, H., Munoz, O., Han, B., De Riccardis, F.,
Krishnamurthy, R., Eschenmoser, A. Mapping the landscape of potentially primordial informational oligomers: oligodipeptides and oligodipeptoids tagged with triazines as recognition elements. Angew. Chem. Int. Ed., in press.
The copper-catalyzed azide-alkyne cycloaddition
reaction, discovered in 2002 by V.V. Fokin and
K.B. Sharpless, Department of Chemistry, has been
adopted by chemists all over the world for organic
synthesis, drug development, and materials science.
We have continued our mechanistic studies of the
reaction and our efforts to apply the reaction to the
synthesis of biologically active compounds, materials,
and bioconjugates.
A protocol for using the reaction in the polyvalent
decoration of scaffolds has been optimized (Fig. 1). In
F i g . 1 . Bioconjugation of alkynes to polyvalent azides via the
copper complex of bathophenanthroline ligand 1.
the most demanding situations, with sensitive proteins
at micromolar concentrations, the use of sulfonated
bathophenanthroline (compound 1 in Fig. 1) is vital.
We continue to develop new catalysts to remove the
last barrier to convenient application of the method,
the need to perform the reaction in an inert atmosphere
when protein instability prevents the simultaneous use
of a reducing agent. In addition, a variation of the
CHEMISTRY
2006
standard copper-catalyzed process has been uncovered
in which aromatic azides react with alkynes to give the
1,5-triazole isomer rather than the customary 1,4-triazole. Last, mechanistic studies have revealed changes
in the rate-limiting steps when certain copper-binding
ligands and substrates are used.
SYNTHESIS AND USE OF FORMAMIDINE COMPOUNDS
We synthesized amidines, including formamidines
and formamidine ureas, and tested them for binding
to the acetylcholine-binding proteins of Lymnaea stagnalis and Aplysia californica, soluble homologs of the
nicotinic acetylcholine receptor. Compounds 2, 3, and 4
(Fig. 2) have moderate to high affinities for the target
THE SCRIPPS RESEARCH INSTITUTE
75
Díaz, D.D., Rajagopal, K., Strable, E., Schneider, J., Finn, M.G. “Click” chemistry
in a supramolecular environment: stabilization of organogels by copper(I)-catalyzed
azide-alkyne [3 + 2] cycloaddition. J. Am. Chem. Soc. 128:6056, 2006.
Díaz, D.D., Ripka, A.S., Finn, M.G. 1-(tert-Butyl-imino-methyl)-1,3-dimethyl-urea
hydrochloride. Org. Synth. 82:59, 2005.
Johnson, J.A., Lewis, D.R., Díaz, D.D., Finn, M.G., Koberstein, J.T., Turro, N.J.
Synthesis of degradable model networks via ATRP and click chemistry. J. Am.
Chem. Soc. 128:6564, 2006.
Meng, J., Fokin, V.V., Finn, M.G. Kinetic resolution by copper-catalyzed azidealkyne cycloaddition. Tetrahedron Lett. 46:4543, 2005.
Punna, S., Kaltgrad, E., Finn, M.G. “Clickable” agarose for affinity chromatography. Bioconjug. Chem. 16:1536, 2005.
Punna, S., Meunier, S., Sen Gupta, S., Venkataiah, B., Truong, P., McGavern, D.,
Finn, M.G. Polyvalent inhibition of the LFA-ICAM interaction. J. Am. Chem. Soc.,
in press.
Rae, C.S., Khor, I.W., Wang, Q., Destito, G., Gonzalez, M.J., Singh, P.R., Thomas,
D.M., Estrada, M.N., Powell, E., Finn, M.G., Manchester, M. Systemic trafficking
of plant virus nanoparticles in mice via the oral route. Virology 343:224, 2005.
Sen Gupta, S., Kuzelka, J., Singh, P., Lewis, W.G., Manchester, M., Finn, M.G.
Accelerated bioorthogonal conjugation: a practical method for the ligation of
diverse functional molecules to a polyvalent virus scaffold. Bioconjug. Chem.
16:1572, 2005.
F i g . 2 . Amidine derivatives that bind to nicotinic receptor proteins.
proteins, representing a new class of receptor ligands.
Whereas amidines such as compound 4 are relatively
stable, formamidine ureas such as compounds 2 and 3
are deactivated during a period of approximately 1 hour
by hydrolysis when not bound. Using fluorescence
spectroscopy and x-ray crystallography, we showed
that the bound molecules reside in the canonical hydrophobic pocket. Electrophysiologic measurements indicated that compound 4 is a nicotinic receptor agonist,
consistent with its observed binding behavior. We are
extending this research to molecules specific for subtypes of the nicotinic receptor family. These studies
are conducted in collaboration with P. Taylor, University of California, San Diego, and A. Markou, Molecular
and Integrative Neurosciences Department.
Sen Gupta, S., Raja, K.S., Kaltgrad, E., Strable, E., Finn, M.G. Virus-glycopolymer conjugates by copper(I) catalysis of atom transfer radical polymerization and
azide-alkyne cycloaddition. Chem. Commun. (Camb.) 4315, 2005, Issue 34.
Whiting, M., Muldoon, J., Lin, Y.-C., Silverman, S.M., Lindstrom, W., Olson, A.J.,
Kolb, H.C., Finn, M.G., Sharpless, K.B., Elder, J.H., Fokin, V.V. Inhibitors of HIV-1
protease via in situ click chemistry. Angew. Chem. Int. Ed. 45:1435, 2006.
Wu, P., Malkoch, M., Hunt, J.N., Vestberg, R., Kaltgrad, E., Finn, M.G., Fokin,
V.V., Sharpless, K.B., Hawker, C.J. Multivalent, bifunctional dendrimers prepared
by click chemistry. Chem. Commun. (Camb.) 5775, 2005, Issue 46.
Design of Functional
Synthetic Systems
M.R. Ghadiri, G. Ashkenasy, N. Ashkenasy, J. Beierle,
A. Chavochi, N. Gianneschi, W.S. Horne, Z.-Z. Huang,
P. Imming, L. Leman, A. Loutchnikov, A. Montero, L. Motiei,
D. Nicoletti, Y. Norikane, J. Picuri, N. Rahe, D. Radu,
S. Rahimipour, J. Shin, R. Yamasaki, Y.S. Yoo
PUBLICATIONS
Díaz, D.D., Converso, A., Sharpless, K.B., Finn, M.G. 2,6-Dichloro-9-thiabicyclo[3.3.1]nonane: multigram display of azides and cyanides components on a versatile scaffold. Molecules 11:212, 2006.
Díaz, D.D., Finn, M.G. Facile synthesis of N,N′-bis[formamidine]ureas and symmetrical N,N′-dsubstituted formamidines. Lett. Org. Chem. 2:621, 2005.
Díaz, D.D., Finn, M.G., Mishima, M. Substituent effects on the gas-phase basicity
of formamidine ureas. Eur. J. Org. Chem. 235, 2006, Issue 1.
Díaz, D.D., Lewis, W.G., Finn, M.G. Acid-mediated amine exchange of N,Ndimethylformamidines: preparation of electron-rich formamidines. Synlett 2214,
2005, Issue 14.
Díaz, D.D., Lewis, W.G., Finn, M.G. Activation of urea as a leaving group in substitution reactions of formamidine ureas. Chem. Lett. 34:78, 2005.
e are engaged in a multidisciplinary research
effort to uncover new chemical and biochemical approaches for the design of functional
molecular, supramolecular, and complex self-organized
systems. Our endeavors span disciplines ranging from
synthetic organic, bioorganic, and physical organic chemistry to nanotechnology, biophysics, enzymology, and
molecular biology. Current research includes the design of
synthetic peptide catalysts, antimicrobial self-assembling
peptide nanotubes, semisynthetic allosteric enzymes,
self-replicating molecular systems and emergent net-
W
76 CHEMISTRY
2006
THE SCRIPPS RESEARCH INSTITUTE
works, single-molecule stochastic DNA sensing, molecular computation, and prebiotic chemistry.
ANTIMICROBIAL PEPTIDE NANOTUBES
We showed that appropriately designed cyclic peptide subunits can self-assemble through hydrogen
bond–directed ring stacking into open-ended hollow
tubular structures that have marked antibacterial and
antiviral activities in vitro. The effectiveness of this novel
supramolecular class of bioactive species as selective
antibacterial agents was highlighted by the high efficacy of one of these antimicrobials against lethal methicillin-resistant Staphylococcus aureus infections in mice.
Currently, we are exploring rational design of cyclic
glycopeptides and selections from combinatorial libraries to discover novel antiviral and anticancer supramolecular compounds (Fig. 1).
F i g . 2 . Schematic representation of an intrasterically inactivated
inhibitor-DNA-enzyme construct (left) and the DNA hybridization–triggered enzyme activation (right). The construct can be used to sense
low concentrations of cDNA because of its built-in capacity for signal amplification via rapid turnover of substrate.
membrane protein α-hemolysin as a rapid and highly
sensitive sensor element for stochastic analysis of the
molecules lodged or trapped inside the protein pore;
the analysis relies on detecting the perturbations in
the conductance levels produced in the ion channel in
the native protein. Using this technique, we developed
an approach by which a single-stranded DNA molecule
can be trapped in a specific configuration inside an αhemolysin channel (Fig. 3), manipulated, and studied
F i g . 1 . Antiviral agents based on self-assembling cyclic peptide
nanotubes. Cyclic D,L-α-peptides act on endosomal membranes to prevent the development of low pH in endocytic vesicles, arrest the escape
of virions from the endosome, and abrogate adenovirus infection.
DESIGN OF SIGNAL SELF-AMPLIFYING DNA SENSORS
We constructed a novel sequence-specific DNA
detection system based on rationally designed semisynthetic enzymes. The system is composed of covalently
associated inhibitor-DNA-enzyme modules that function
via DNA hybridization–triggered allosteric enzyme activation and signal amplification through substrate turnover
(Fig. 2). The functional capacity of the system is highlighted by the sequence-specific detection of approximately 10 fmol of DNA in less than 3 minutes under
physiologic conditions. Our studies suggest that rationally designed intrasterically regulated enzymes may be
a promising new class of reagents for highly sensitive,
rapid, 1-step detection of label-free DNA sequences that
does not depend on polymerase chain reactions.
with high sensitivity at the single-molecule level. Moreover, a single adenine nucleotide at a specific location
on a strand of polydeoxycytidine can be detected by
its characteristic effect in reducing the ion conductance in α-hemolysin. We are extending this approach
to the design of rapid single-molecule DNA sensing
and sequencing.
S T O C H A S T I C A N A LY S I S O F S I N G L E - M O L E C U L E D N A
SYNTHETIC NETWORKS
R O TA X A N E S
Living cells use complex networks of evolutionarily
selected biomolecular interactions and chemical transformations to process multiple extracellular input signals
We are interested in the study of matter at the level
of single molecules. For these studies we use the trans-
F i g . 3 . Functional supramolecular chemistry at the single-mole-
cule level. Single strands of DNA can be captured inside an αhemolysin transmembrane pore protein to form single-species
pseudorotaxanes composed of α-hemolysin and DNA. This process
can be used to identify a single adenine nucleotide at a specific
location on a strand of DNA on the basis of the characteristic
reductions in the α-hemolysin ion conductance.
CHEMISTRY
2006
rapidly and simultaneously. We are interested in understanding and experimentally modeling the organizational and functional properties of biological networks.
We have developed a general strategy for the design
and construction of self-organized synthetic peptide
networks based on the sequence-selective autocatalytic
and cross-catalytic template-directed coiled coil peptide fragment condensation reactions in aqueous solutions. The synthetic networks have some of the basic
architectural and dynamic features of the living networks, reorganize in response to changes in environmental conditions and inputs (Fig. 4), and perform
THE SCRIPPS RESEARCH INSTITUTE
77
marginally prebiotic. We showed that carbonyl sulfide,
a simple gas present in the emissions from present-day
volcanoes, is a condensing agent that brings about the
formation of peptides from amino acids under mild conditions in aqueous solution (Fig. 5). We have studied the
F i g . 5 . Peptide formation under plausibly prebiotic reaction con-
ditions. Carbonyl sulfide, a volcanic gas, is the most simple and
effective amino acid–condensing agent for the formation of peptides
in aqueous solutions.
F i g . 4 . Adaptive reorganization in a synthetic peptide network.
The graph structure or wiring of a synthetic peptide network
responds dramatically to changes in the environmental stimuli (pH
or salt content).
basic Boolean logic functions such as OR, NOR, and
NOTIF logic. We suggest that the ability to rationally
construct predictable chemical circuitry might be useful
in advancing the modeling and better understanding
of some of the basic dynamic information-processing
characteristics of the more complex cellular networks.
PREBIOTIC CHEMISTRY
In almost all discussions of prebiotic chemistry, it
is assumed that amino acids, nucleotides, and possibly
other monomers were first formed on Earth or brought
to it in comets and meteorites and that the monomers
subsequently condensed nonenzymatically to form
oligomeric products. Unfortunately, attempts to create
plausibly prebiotic polymerization reactions have met
with limited success. Direct heating of solid mixtures
leads to nonspecific products, and the condensing agents
that have been studied, with the possible exception of
inorganic polyphosphates, are relatively inefficient and/or
carbonyl sulfide–mediated condensations of α-amino
acids under aerobic and anaerobic conditions in the
absence of any added reagents and in the presence
of metal ions, oxidizing agents, or alkylating agents.
Depending on the reaction conditions and additives
used, exposure of α-amino acids to carbonyl sulfide
generates peptides in yields of up to 80% in minutes
to hours at room temperature.
PUBLICATIONS
Askkenasy, N., Sánchez-Quesada, J., Bayley, H., Ghadiri, M.R. Recognizing a single base in an individual DNA strand: a step toward DNA sequencing in nanopores.
Angew. Chem. Int. Ed. 44:1401, 2005.
Horne, S.W., Ashkenasy, N., Ghadiri, M.R. Modulating charge transfer through
cyclic D,L-α-peptide self-assembly. Chemistry 11:1137, 2005.
Horne, S.W., Wiethoff, C.M., Cui, C., Wilcoxen, K.M., Amorin, M., Ghadiri, M.R.,
Nemerow, G.R. Antiviral cyclic D,L-α-peptides: targeting a general biochemical
pathway in viral infections. Bioorg. Med. Chem. 13:5145, 2005.
Yadav, M.K., Redman, J.E., Leman, L.J., Alvarez-Gutiérrez, J.M., Zhang, Y.,
Stout, C.D., Ghadiri, M.R. Structure-based engineering of internal cavities in
coiled-coil peptides. Biochemistry 44:9723, 2005.
78 CHEMISTRY
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THE SCRIPPS RESEARCH INSTITUTE
A Merging of Chemistry
and Biology
K.D. Janda, J. Ashley, C. Berndt, G. Boldt, A. Brogan,
C. Chung, S. De Lamo Marin, T. Dickerson, L. Eubanks,
M. Hixon, A. Ino, G. Kaufmann, J. Kennedy, Y. Kim, J. Liu,
Y. Liu, C. Lowery, H. Ma, S. Mahajan, L. McAllister,
G. McElhaney, K. McKenzie, J. Mee, M. Meijler, J. Park,
S. Steiniger, J. Treweek, A. Willis, Y. Xu, B. Zhou, H. Zhou
uring the past year, we explored various applications of organic chemistry at the interface of
chemistry and biology. Representative examples
of our results were obtained in 3 research programs:
catalysis of retinal isomerization by the nicotine metabolite nornicotine, “superactivation” of botulinum neurotoxin by small molecules, and the development of a
cocaine esterase–bacteriophage construct with suitable
kinetics for the degradation of cocaine in humans.
D
A LT E R E D R E T I N O I D H O M E O S TA S I S C ATA LY Z E D B Y
A N I C O T I N E M E TA B O L I T E
In recent years, we have been studying the role of
long-lived drugs of abuse and their metabolites in drugrelated diseases. Much of this effort has centered on
the Maillard reaction, a process by which amine-containing molecules irreversibly react with proteins through
the intermediacy of glucose, the dominant serum monosaccharide. The mechanism of the Maillard reaction
parallels that of amine organocatalysts; iminium and/or
enamine intermediates are necessary for rate enhancement. In the past year, we expanded our studies beyond
the Maillard reaction to other biological processes in
which iminium ion intermediates are critical.
Retinoids (vitamin A) play 2 major roles in higher
animals: light absorption in vision and gene regulation
in growth and development. Specifically, these processes
are regulated by the conformation of the double bonds
in the polyunsaturated hydrocarbon chain. For example,
in the visual cycle, 11-Z-retinal is converted to all-Eretinal by a photon of light, ultimately leading to the
perception of vision. Much of the biosynthetic pathways leading up to this reaction are controlled by the
formation of iminium ions between the retinal terminal
aldehyde group and a lysine side chain from an appropriate enzyme.
We hypothesized that nornicotine, a metabolite of
nicotine, could also perform this type of chemistry
(Fig. 1) and thus alter the concentrations of retinal intermediates. This reaction would provide an intriguing
F i g . 1 . Mechanism of nornicotine-catalyzed Z-to-E isomerization.
mechanism for the pathologic changes in key smoking-related diseases, because the accumulation of
compounds such as all-E-retinal feeds the N-retinylidene-N-retinylethanolamine biosynthetic pathway,
forming an undigestible byproduct of the visual cycle
and a fluorescent chromophore characteristic of the
pathologic changes in age-related macular degeneration, a leading cause of blindness. Smoking is accepted
as the primary environmental factor contributing to agerelated macular degeneration, and thus elucidating the
molecular mechanism of this contribution is clinidand
retinal compounds, we conclusively showed that nornicotine can indeed catalyze the Z-to-E isomerization
of unsaturated compounds at rates that could have
biological significance in the context of disease.
S U P E R A C T I VAT I O N O F B O T U L I N U M N E U R O T O X I N
S E R O T Y P E A L I G H T - C H A I N M E TA L L O P R O T E A S E
The 7 neurotoxins (A–G) of the bacterium Clostridium botulinum are the most lethal poisons known.
Exposure to these toxins leads to progressive flaccid
paralysis resulting from cleavage of proteins critical
for proper release of neurotransmitters from peripheral
nerve cells. Despite their potent toxicity, botulinum
neurotoxins are widely used in medicine, as well as
cosmetically for treating facial wrinkles. Conditions
including multiple sclerosis, stroke, cerebral palsy,
migraine, and backache can all be treated with the
neurotoxins. Yet, repeated exposure to the toxins can
result in the development of a marked immune response
to them, thereby compromising their efficacy. Tolerance
develops most rapidly when patients are treated frequently with high doses of the toxins. We speculated
that the coadministration of a botulinum neurotoxin
with a molecule that can “activate” the catalytic activ-
CHEMISTRY
2006
ity of the toxin would lead to lower doses, thus reducing the unintended immune response.
In recent investigations of light-chain metalloprotease inhibitors of botulinum neurotoxin A, we discovered that the molecule arginine hydroxamic acid is a
modest inhibitor. Using this compound as a guide, we
prepared a small collection of compounds containing a
zinc-binding motif (2-acylthiophene) combined with an
arginine-side-chain mimetic (acylguanidine). To our surprise, although no inhibition occurred, one compound
(compound 1 in Fig. 2) consistently produced a 2-fold
THE SCRIPPS RESEARCH INSTITUTE
79
the importance of botulinum neurotoxins continues to
expand, methods such as this may ultimately provide
a method for minimizing dosage of the toxins and
thereby increase the clinical efficacy of the molecules.
DEGRADING COCAINE WITH VIRUSES
Cocaine is a powerful stimulant and among the most
reinforcing of all drugs. Consequently, abuse of cocaine
continues to be a major problem. Cocaine acts as an
indirect dopamine agonist by blocking the dopamine
transporter in the pleasure-reward center of the brain.
This obstruction leads to an excess of dopamine in the
synapses, amplifying the sensation of pleasure. Despite
intensive efforts, no effective pharmacotherapy for
cocaine abuse exists. The inherent difficulties in antagonizing a blocker have led to the development of proteinbased therapeutics designed to treat cocaine abuse. In
an approach termed immunopharmacotherapy, we have
devoted extensive efforts to the use of antibodies to
cocaine that can sequester cocaine, retarding its ability to enter the CNS. We have also developed a parallel strategy that involves use of catalytic antibodies
specific for the hydrolysis of the benzoyl ester of cocaine
to give the nonpsychoactive products benzoate and
methyl ecgonine (Fig. 3).
F i g . 2 . Chemical structures of molecules that can superactivate
botulinum neurotoxin serotype A. The specific motifs used in the
design of these compounds are highlighted.
enhancement of activity. Further structure-activity relationship studies revealed that specific features of this
compound were critical for activation, such as the thiophene sulfur atom and the acylguanidine group. When
these initial screening efforts were completed, compound 2 (Fig. 2) was the most potent activator.
Because of the clinical promise of an activator of
botulinum neurotoxin, we further examined the mechanism of this phenomenon. Extensive kinetic characterization indicated that these compounds operate primarily
by reducing the Michaelis constant (Km), not by altering the turnover number (k cat). In this context, compound 2 is the most potent small-molecule activator
of a protease reported to date, with up to 14-fold rate
enhancement at limiting concentrations of substrate.
Indeed, as little as 2-fold enzyme activation has previously been reported as a state of superactivation.
In total, the activation profile and structure-activity
relationship for activation suggests the presence of a
specific “activation domain” on the enzyme. Because
F i g . 3 . Hydrolysis products resulting from cleavage of cocaine
esters. Both the uncatalyzed reaction (path a) and the cocaine
esterase–catalyzed hydrolysis (path b) pathways are shown.
Although the potential of this method has been
demonstrated in rodent models of cocaine overdose
and reinforcement, the kinetic constants of these antibodies must be improved before the method will be
practical as a clinical treatment. Furthermore, these
approaches are only effective in the periphery, whereas
a pharmacotherapy that could act in both the CNS and
the periphery is desirable.
Bacteriophages are viruses that infect bacteria yet
lack intrinsic tropism for eukaryotic cells. Because of
80 CHEMISTRY
2006
the genetic flexibility of bacteriophages, a wide range
of proteins and peptides can be expressed on the phage
coat in an approach termed phage display. Furthermore,
phage molecules can penetrate virtually all tissues,
including the CNS.
We recently reported that cocaine-binding antibodies displayed on the surface of bacteriophages can be
administered intranasally and that the treated animals
are protected from the locomotor stimulation associated
with exposure to cocaine. However, because of the requisite 1:1 stoichiometry of any traditional antibody pharmacotherapy, obtaining a meaningful concentration of
the therapeutic agent in vivo is difficult. We envisioned
that this limitation could be overcome by displaying a
catalyst on the phage surface that can degrade cocaine,
yielding a therapeutically practical approach for treating cocaine abuse.
For these studies, we used cocaine esterase, a
globular bacterial enzyme that is the most efficient
protein catalyst for cocaine hydrolysis reported to
date. We displayed this enzyme on the phage coat
and then used high-performance liquid chromatography to determine the kinetic parameters. We found
that the catalytic efficiency of cocaine esterase–phage
constructs was reduced relative to the efficiency of the
native enzyme yet exceeded the postulated therapeutically relevant threshold. No reported catalytic antibody capable of cocaine hydrolysis achieves this value,
and indeed, only recently described “designer” mutants
of the enzyme butyrylcholinesterase are comparable to
our cocaine esterase–phage constructs.
These results indicate that phage display of clinically relevant enzymes can be achieved without compromising the catalytic efficacy of the desired enzyme.
We envision that this new technology will stimulate
further development of other protein-based treatments
for CNS-related disorders and will lead to powerful
tools to combat drug abuse.
PUBLICATIONS
Boldt, G.E., Dickerson, T.J., Janda, K.D. Emerging chemical and biological approaches
for the preparation of discovery libraries. Drug Discov. Today 11:143, 2006.
Boldt, G.E., Eubanks, L.M., Janda, K.D. Identification of a botulinum neurotoxin A
protease inhibitor displaying efficacy in a cellular model. Chem. Commun. (Camb.)
3063, 2006, Issue 29.
Boldt, G.E., Kennedy, J.P., Hixon, M.S., McAllister, L.A., Barbieri, J.T., Tzipori,
S., Janda, K.D. Synthesis, characterization and development of a high-throughput
methodology for the discovery of botulinum neurotoxin A inhibitors. J. Comb.
Chem. 8:513, 2006.
Boldt, G.E., Kennedy, J.P., Janda, K.D. Identification of a potent botulinum neurotoxin A protease inhibitor using in situ lead identification chemistry. Org. Lett.
8:1729, 2006.
THE SCRIPPS RESEARCH INSTITUTE
Brogan, A.P., Dickerson, T.J., Boldt, G.E., Janda, K.D. Altered retinoid homeostasis catalyzed by a nicotine metabolite: implications in macular degeneration and
normal development. Proc. Natl. Acad. Sci. U. S. A. 102:10433, 2005.
Carrera, M.R.A., Trigo, J.M., Wirsching, P., Roberts, A.J., Janda, K.D. Evaluation
of the anticocaine monoclonal antibody GNC92H2 as an immunotherapy for
cocaine overdose. Pharmacol. Biochem. Behav. 81:709, 2005.
Dickerson, T.J., Beuscher, A.E. IV, Rogers, C.J., Hixon, M.S., Yamamoto, N., Xu, Y.,
Olson, A.J., Janda, K.D. Discovery of acetylcholinesterase peripheral anionic site
ligands through computational refinement of a directed library. Biochemistry
44:14845, 2005.
Dickerson, T.J., Janda, K.D. Recent advances for the treatment of cocaine abuse:
central nervous system immunopharmacotherapy. AAPS J. 7:E579, 2005.
Eubanks, L.M., Dickerson, T.J., Janda, K.D. Vitamin B2-mediated cellular photoinhibition of botulinum neurotoxin A. FEBS Lett. 579:5361, 2005.
Kaufmann, G.F., Sartorio, R., Lee, S.H., Mee, J.M., Altobell, L.J. III, Kujawa,
D.P., Jeffries, E., Clapham, B., Meijler, M.M., Janda, K.D. Antibody interference
with N-acyl homoserine lactone-mediated bacterial quorum sensing. J. Am. Chem.
Soc. 128:2802, 2006.
Kim, Y., Lillo, A., Moss, J.A., Janda, K.D. A contiguous stretch of methionine residues mediates the energy-dependent internalization mechanism of a cell-penetrating peptide. Mol. Pharm. 2:528, 2005.
Lee, B.S., Mahajan, S., Janda, K.D. Asymmetric dihydroxylation catalyzed by ionic
polymer-supported osmium tetroxide. Tetrahedron Lett. 46:4491, 2005.
Lee, B.S., Mahajan, S., Janda, K.D. Molecular iodine-catalyzed imine activation
for three-component nucleophilic addition reactions. Synlett 1325, 2005, Issue 8.
Lillo, A.M., McKenzie, K.M., Janda, K.D. Phage-displayed antibody libraries. In:
Cell Biology: A Laboratory Handbook, 3rd ed. Celis, J., et al. (Eds.). Academic
Press, San Diego, 2006, p. 491.
Ma, H., Zhou, B., Kim, Y., Janda, K.D. A cyclic peptide-polymer probe for the
detection of Clostridium botulinum neurotoxin serotype A. Toxicon 47:401, 2006.
Matsushita, M., Meijler, M.M., Wirsching, P., Lerner, R.A., Janda, K.D. A blue fluorescent antibody-cofactor sensor for mercury. Org. Lett. 7:4943, 2005.
McAllister, L.A., Hixon, M.S., Kennedy, J.P., Dickerson, T.J., Janda, K.D. Superactivation of the botulinum neurotoxin serotype A light chain metalloprotease: a new
wrinkle in botulinum neurotoxin. J. Am. Chem. Soc. 128:4176, 2006.
McKenzie, K.M., Meijler, M.M., Lowery, C.A., Boldt, G.E., Janda, K.D. A furanosyl-carbonate autoinducer in cell-to-cell communication of V. harveyi. Chem.
Commun. (Camb.) 4863, 2005, Issue 38.
Moss, J.A, Stokols, S., Hixon, M.S., Ashley, F.T., Chang, J.Y., Janda, K.D. Solidphase synthesis and kinetic characterization of fluorogenic enzyme-degradable
hydrogel cross-linkers. Biomacromolecules 7:1011, 2006.
Qi, L., Yamamoto, N., Meijler, M.M., Altobell, L.J. III, Koob, G.F., Wirsching, P.,
Janda, K.D. ∆9-Tetrahydrocannabinol immunochemical studies: haptens, monoclonal antibodies, and a convenient synthesis of radiolabeled ∆9-tetrahydrocannabinol. J. Med. Chem. 48:7389, 2005.
Rogers, C.J., Dickerson, T.J., Janda, K.D. Kinetic isotope and thermodynamic analysis of the nornicotine-catalyzed aqueous aldol reaction. Tetrahedron 62:352, 2006.
Rogers, C.J., Dickerson, T.J., Wentworth, P., Jr., Janda, K.D. A high-swelling
reagent scaffold suitable for use in aqueous and organic solvents. Tetrahedron
61:12140, 2005.
Rogers, C.J., Mee, J.M., Kaufmann, G.F., Dickerson, T.J., Janda, K.D. Toward
cocaine esterase therapeutics J. Am. Chem. Soc. 127:10016, 2005.
Shimomura, O., Lee, B.S., Meth, S., Suzuki, H., Mahajan, S., Nomura, R.,
Janda, K.D. Synthesis and application of polytetrahydrofuran-grafted polystyrene
(PS-PTHF) resin supports for organic synthesis. Tetrahedron 61:12160, 2005.
CHEMISTRY
2006
Shute, T.S., Matsushita, M., Dickerson, T.J., La Clair, J.J., Janda, K.D., Burkart,
M.D. A site-specific bifunctional protein labeling system for affinity and fluorescent
analysis. Bioconjug. Chem. 16:1352, 2005.
Toker, J.D., Tremblay, M.R., Yli-Kauhaluoma, J., Wentworth, A.D., Zhou, B.,
Wentworth, P., Jr., Janda, K.D. Exploring the scope of the 29G12 antibody catalyzed 1,3-dipolar cycloaddition reaction. J. Org. Chem. 70:7810, 2005.
Wu, W., Luo, Y., Sun, C., Liu, Y., Kuo, P., Varga, J., Xiang, R., Reisfeld, R.,
Janda, K.D., Edgington, T.S., Liu, C. Targeting cell-impermeable prodrug activation
to tumor microenvironment eradicates multiple drug-resistant neoplasms. Cancer
Res. 66:970, 2006.
Xu, Y., Shi, J., Yamamoto, N., Moss, J.A., Vogt, P.K., Janda, K.D. A credit-card
library approach for disrupting protein-protein interactions. Bioorg. Med. Chem.
14:2660, 2006.
Xu, Y., Yamamoto, N., Ruiz, D.I., Kubitz, D.S., Janda, K.D. Squaric monoamide
monoester as a new class of reactive immunization hapten for catalytic antibodies
Bioorg. Med. Chem. Lett. 15:4304, 2005.
Yamashita, M., Lee, S.-H., Koch, G., Zimmermann, J., Clapham, B., Janda, K.D.
Solid-phase synthesis of oxazolones and other heterocycles via Wang resin-bound
diazocarbonyls. Tetrahedron Lett. 46:5495, 2005.
Yao, Y., Martinez-Yamout, M., Dickerson, T.J., Brogan, A.P., Wright, P.E., Dyson,
H.J. Structure of the Escherichia coli quorum sensing protein SdiA: activation of
the folding switch by acyl homoserine lactones. J. Mol. Biol. 355:262, 2006.
Zhang, L., Long, H., Boldt, G.E., Janda, K.D., Schatz, G.C., Lewis, F.D. α- and
β-Stilbenosides as base-pair surrogates in DNA hairpins. Org. Biomol. Chem.
4:314, 2006.
Zhu, X., Dickerson, T.J., Rogers, C.J., Kaufmann, G.F., Mee, J.M., McKenzie,
K.M., Janda, K.D., Wilson, I.A. Complete reaction cycle of a cocaine catalytic antibody at atomic resolution. Structure 14:205, 2006.
Strategies to Ameliorate Protein
Misfolding Diseases
J.W. Kelly, J. Bieschke, D.A. Bosco, E. Culyba, M.T.A. Dendle,
W. D’Haeze, T.R. Foss, D.M. Fowler, Y. Fu, J. Gao, M.-Y. Gao,
S.M. Johnson, T. Mu, E.T. Powers, A.R. Sawkar, L. Segatori,
S. Siegel, J.Y. Suk, R.L. Wiseman, I. Yonemoto, Z. Yu
ur goal is to better understand the molecular
mechanisms that lead to protein misfolding
diseases, including Alzheimer ’s, Parkinson’s,
and Gaucher diseases, so that we can design new strategies to ameliorate such maladies. To accomplish this
goal, we use organismal and cell biological disease
models and spectroscopic and biophysical approaches
in combination with chemical synthesis and molecular
biology techniques. Successful collaborations with
W.E. Balch, Department of Cell Biology, P. Wentworth,
Jr., Department of Chemistry, and A. Dillin, the Salk
Institute for Biological Studies, La Jolla, California, are
critical to achieve our goals.
O
TRANSTHYRETIN AMYLOIDOGENESIS
Transthyretin is a 55-kD homotetrameric protein
that transports holo-retinol binding protein and L-thy-
THE SCRIPPS RESEARCH INSTITUTE
81
roxine in the blood and cerebrospinal fluid. More than
99.5% of the transthyretin binding sites for L-thyroxine remain unoccupied in blood, and only about 50%
of transthyretin tetramers in plasma are bound to a
single holo-retinol binding protein. As a consequence
of a mutation or denaturation stress associated with
aging and/or oxidative stress, dissociation of the native
transthyretin tetramer, the rate-limiting step for amyloidogenesis, followed by changes in the tertiary structure of the monomer make the monomeric subunits
competent to misassemble into aggregates, including
amyloid fibrils. The deposition of transthyretin amyloid
is linked with a number of human diseases, including
senile systemic amyloidosis, familial amyloid polyneuropathy (FAP), familial amyloid cardiomyopathy, and
CNS-selective amyloidosis.
A suitable strategy to slow or prevent the formation
of aggregates is to inhibit the rate-limiting dissociation
of the transthyretin tetramer by making the native state
more stable than the dissociative transition state. We
have designed, synthesized, and characterized several
classes of structurally distinct small molecules that bind
to and stabilize the transthyretin tetramer. One of these
molecules is being tested in phase 2/3 clinical trials
for treatment of FAP. Compounds discovered in highthroughput screening tests, such as genistein, a natural compound present in soy products, also inhibit
formation of fibrils of wild-type amyloid, as well as amyloidogenesis by the transthyretin variants V30M and
V122I, 2 of the most common disease-associated variants. Furthermore, a clinical study in healthy human
subjects indicated that kinetic stabilization of transthyretin mediated by orally administered diflunisal, a
nonsteroidal anti-inflammatory agent also discovered
by screening, should ameliorate transthyretin amyloidosis. The effect of diflunisal on FAP is currently being
evaluated in a phase 3 clinical study.
Most likely the age-associated nature of neurodegenerative diseases such as the transthyretin amyloidoses
can be explained by a shift from efficient to inefficient
aggregate clearance, leading to increasing concentrations
of the aggregates and proteotoxic effects. We showed
that the reassembly of transthyretin homotetramers
occurs via a monomer-dimer-trimer-tetramer pathway
in which each step depends on the concentration of
folded transthyretin monomers. This finding suggests
that partitioning of transthyretin monomers between
transthyretin tetramer reassembly and the aggregation
pathway is correlated with the relative concentrations
82 CHEMISTRY
2006
of reassembly intermediates and aggregates. The concentration of the aggregates presumably increases with
aging because of inefficient aggregate clearance.
In another study, we found that subunits of the
transthyretin variant R104H most likely act as an in
vivo trans-suppressor of amyloidogenesis associated
with the V30M variant. Compound heterozygotes with
genes for the V30M and R104H variants did not show
signs of the pathologic changes associated with FAP
typical of heterozygotes with genes for the V30M variant and wild-type transthyretin; however, compound
heterozygotes with genes for R104H and the aggressive mutation T59K on their second allele did have
pathologic FAP effects similar to those of compound
heterozygotes with genes for wild-type transthyretin
and the T59K mutation.
We investigated the energetics of R104H homotetramers and mixed tetramers in a fashion analogous to
that used to elucidate the mechanism of T119M transthyretin interallelic trans-suppression. We found that
in contrast to T119M, R104H does not suppress aggregation by a kinetic stabilization mechanism. We showed
that R104H may trans-suppress transthyretin aggregation by subtle thermodynamic stabilization of the transthyretin quaternary structure. This discovery suggests
that R104H could protect compound heterozygotes
from transthyretin aggregation in situations in which
the mutation is mildly destabilizing. This finding supports the current clinical data associated with R104H
in compound heterozygotes.
A B E R R A N T O X I D AT I V E M E TA B O L I T E S A F F E C T
α- S Y N U C L E I N O PAT H I E S
The α-synucleinopathies are characterized by cytoplasmic α-synuclein-rich aggregates within degenerating
dopaminergic neurons in the substantia nigra. Clinical
observations suggest a correlation between oxidative
stress/inflammation and protein misfolding diseases.
We wished to determine whether oxidized metabolites
accelerate the aggregation of α-synuclein, research that
would shed light on the correlation between oxidative
stress and sporadic α-synucleinopathies.
We found that overexpression of α-synuclein in a
neuronal cell line is sufficient to increase the production of oxidative metabolites derived from the oxidation
of cholesterol, presumably due to the production of
reactive oxygen species. We showed that these oxidative metabolites are cytotoxic and that they significantly
accelerate aggregation of α-synuclein in vitro. The experimental data suggest that the acceleration in aggrega-
THE SCRIPPS RESEARCH INSTITUTE
tion occurs predominantly via a noncovalent mechanism. Overexpression of α-synuclein may lead to the
production of reactive oxygen species, which stimulates
the production of oxidative cholesterol metabolites that
then accelerate α-synuclein aggregation. This acceleration may enhance local oxidative stress, resulting in
a vicious cycle that eventually leads or contributes to
α-synucleinopathies.
Although the exact role of α-synuclein in Lewy body
disease and Parkinson’s disease remains to be elucidated, our findings add to an understanding of how
aldehyde-based organic compounds formed as a result
of aging and inflammation may contribute to neurodegenerative diseases.
GELSOLIN AMYLOIDOSIS
Gelsolin amyloidogenesis occurs in persons who produce D187N/Y plasma gelsolin variants. This disease
is characterized by amyloid deposits composed of 5and 8-kD fragments of plasma gelsolin. The D187N/Y
mutation abrogates calcium binding in domain 2, allowing aberrant furin cleavage in the Golgi apparatus during
trafficking and yielding a 68-kD fragment. The fragment
is then cleaved by the membrane type matrix metalloproteinase 1 (MT1-MMP), resulting in 5- and 8-kD
fragments that are deposited as amyloid fibrils in the
extracellular matrix. Fibroblasts from animals lacking
the gene for MT1-MMP are incapable of generating 8and 5-kD fragments from the 68-kD gelsolin fragment.
Biophysical studies indicated that gelsolin amyloid
formation is substantially accelerated in the presence
of the extracellular matrix component heparin. The
extent of sulfation and the location and relative orientation of sulfate residues and the molecular weight are
important factors in the heparin-mediated acceleration
of gelsolin amyloidogenesis, possibly explaining the heavy
deposition of gelsolin amyloid in the extracellular matrix.
Most likely tissue-selective deposition of gelsolin amyloid is correlated with the localization of extracellular
sulfated glycosaminoglycans, a notion supported by the
colocalization of glycosaminoglycans with gelsolin amyloid in the extracellular space of gelsolin amyloidosis
transgenic mice. These transgenic mice will be used
to evaluate the effect of MT1-MMP inhibitors and glycosaminoglycan amyloid antagonists on gelsolin amyloidosis in vivo.
CHEMICAL CHAPERONES AND GAUCHER DISEASE
Mutations in glucocerebrosidase, a lysosomal hydrolase, lead to an accumulation of glucosylceramide in the
lysosome, causing Gaucher disease, the most common
CHEMISTRY
2006
lysosomal storage disorder. Previously, we showed that
N-(n-nonyl)deoxynojirimycin increases the activity of the
glucocerebrosidase variant N370S in a cell line derived
from tissue from a patient with Gaucher disease. This
“chemical chaperoning” effect most likely is due to the
binding of N-(n-nonyl)deoxynojirimycin to the native state
of N370S, allowing the glucocerebrosidase to be trafficked from the endoplasmic reticulum to the lysosomes.
Interestingly, the activity of G202R glucocerebrosidase,
a variant retained in the endoplasmic reticulum, is also
increased in the presence of chemical chaperones, suggesting that those chemical chaperones stimulated
transport to the lysosomes.
Our results indicate that some chemical chaperones enhance the activity of distinct glucocerebrosidase variants to an extent thought to be sufficient to
ameliorate Gaucher disease. Preliminary data suggest
that certain glucocerebrosidase mutants most likely
will need specifically designed chemical chaperones
that target the compromised domain in order to facilitate proper trafficking and partial restoration of the
function of the glucocerebrosidase.
PUBLICATIONS
Bosco, D.A., Fowler, D.M., Zhang, Q., Nieva, J., Powers, E.T., Wentworth, P., Jr.,
Lerner, R.A., Kelly, J.W. Elevated levels of oxidized cholesterol metabolites in Lewy
body disease brains accelerate α-synuclein fibrilization [published correction
appears in Nat. Chem. Biol. 2:346, 2006]. Nat. Chem. Biol. 2:249, 2006.
THE SCRIPPS RESEARCH INSTITUTE
83
Powers, E.T., Deechongkit, S., Kelly, J.W. Backbone-backbone H-bonds make context-dependent contributions to protein folding kinetics and thermodynamics:
lessons from amide-to-ester mutations. Adv. Protein Chem. 72:39, 2005.
Premkumar, L., Sawkar, A.R., Boldin-Adamsky, S., Toker, L., Silman, I., Kelly,
J.W., Futerman, A.H., Sussman, J.L. X-ray structure of human acid-β-glucosidase
covalently bound to conduritol-B-epoxide: implications for Gaucher disease. J. Biol.
Chem. 280:23815, 2005.
Sawkar, A.R., Adamski-Werner, S.L., Cheng, W.-C., Wong, C.-H., Beutler, E.,
Zimmer, K.-P., Kelly, J.W. Gaucher disease-associated glucocerebrosidases show
mutation-dependent chemical chaperoning profiles. Chem. Biol. 12:1235, 2005.
Sawkar, A.R., D’Haeze, W., Kelly, J.W. Therapeutic strategies to ameliorate lysosomal
storage disorders: a focus on Gaucher disease. Cell. Mol. Life Sci. 63:1179, 2006.
Sekijima, Y., Dendle, M.T., Wiseman, R.L., White, J.T., D’Haeze, W., Kelly, J.W.
R104H may suppress transthyretin amyloidogenesis by thermodynamic stabilization,
but not by the kinetic mechanism characterizing T119 trans-suppression. Amyloid
13:57, 2006.
Sörgjerd, K., Ghafouri, B., Jonsson, B.-H., Kelly, J.W., Blond, S.Y., Hammarström, P.
Retention of misfolded mutant transthyretin by the chaperone BiP/GRP78 mitigates
amyloidogensis. J. Mol. Biol. 356:469, 2006.
Suk, J.Y., Zhang, F., Balch, W.E., Linhardt, R.J., Kelly, J.W. Heparin accelerates
gelsolin amyloidogenesis. Biochemistry 45:2234, 2006.
Wiseman, R.L., Powers, E.T., Kelly, J.W. Partitioning conformational intermediates
between competing refolding and aggregation pathways: insights into transthyretin
amyloid disease. Biochemistry 44:16612, 2005.
Total Synthesis, New
Synthetic Technologies,
and Chemical Biology
Deechongkit, S., Nguyen, H., Jäger, M., Powers, E.T., Gruebele, M., Kelly, J.W.
β-Sheet folding mechanisms from perturbation energetics. Curr. Opin. Struct. Biol.
16:94, 2006.
K.C. Nicolaou, S. Arseniyadis, W. Brenzovich, P. Bulger,
Foss, T.R., Wiseman, R.L., Kelly, J.W. The pathway by which the tetrameric protein transthyretin dissociates. Biochemistry 44:15525, 2005.
P. Dagneau, R. Denton, A. Estrada, D. Edmonds, C. Fang,
Fowler, D.M., Koulov, A.V., Alory-Jost, C., Marks, M.S., Balch, W.E., Kelly, J.W.
Functional amyloid formation within mammalian tissue. PLoS Biol. 4:e6, 2006.
V. Jeso, A. Johnson, D. Kim, A. Kislukhin, A. Lanver, K. Lee,
Fu, Y., Bieschke, J., Kelly, J.W. E-Olefin dipeptide isostere incorporation into a
polypeptide backbone enables hydrogen bond perturbation: probing the requirements for Alzheimer’s amyloidogenesis. J. Am. Chem. Soc. 127:15366, 2005.
D. Lizos, E. Loizidou, N. Mainolfi, C. Mathison, X. Mico-Alvarez,
Green, N.S., Foss, T.R., Kelly, J.W. Genistein, a natural product from soy, is a
potent inhibitor of transthyretin amyloidosis. Proc. Natl. Acad. Sci. U. S. A.
102:14545, 2005.
Johnson, S.M., Wiseman, R.L., Sekijima, Y., Green, N.S., Adamski-Werner, S.L.,
Kelly, J.W. Native state kinetic stabilization as a strategy to ameliorate protein misfolding diseases: a focus on the transthyretin amyloidoses. Acc. Chem. Res.
38:911, 2005.
Kelly, J.W., Balch, W.E. The integration of cell and chemical biology in protein
folding. Nat. Chem. Biol. 2:224, 2006.
Nguyen, H., Jäger, M., Kelly, J.W., Gruebele, M. Engineering a β-sheet protein
toward the folding speed limit. J. Phys. Chem. B Condens. Matter Mater. Surf.
Interfaces Biophys. 109:15182, 2005.
Page, L.J., Suk, J.Y., Huff, M.E., Lim, H.-J., Venable, J., Yates, J. III, Kelly, J.W.,
Balch, W.E. Metalloendoprotease cleavage triggers gelsolin amyloidogenesis.
EMBO J. 24:4124, 2005.
A. Burtoloso, J. Chen, K. Cole, A. Converso, J. Crawford,
R. Faraoni, M. Frederick, M. Freestone, R. Gibe, S. Harrison,
S. Lee, A. Lemire, A. Lenzen, A. Li, H. Li, Y. Lim, T. Lister,
R. Milburn, A. Nold, A. Noncovich, R. de Noronha, A. Ortiz,
C. Papageorgiou, D. Pappo, L. Pasunoori, G. Petrovic,
J. Piper, D. Polet, G. Pontremoli, B. Pratt, D. Sarlah,
D. Shaw, C. Stathakis, C. Solorio-Alvarado, T. Suzuki,
G. Tria, C. Turner, T. Umezawa, J. Wang, H. Xu, M. Zak
e focus on the total synthesis of natural products, the discovery and development of new
synthetic technologies, and chemical biology.
Naturally occurring substances are selected as synthetic
targets because of their novel molecular architectures,
important biological properties, and interesting mechanisms of action. The projects are designed to optimize
the opportunities for discovery and invention in the areas
of chemistry, biology, and medicine. The drug pacli-
W
84 CHEMISTRY
2006
taxel (Taxol), the antitumor epothilones, the neurotoxins
brevetoxins A and B, the antibiotic vancomycin, the
cholesterol-lowering CP-molecules, the antibiotic everninomicin, the TNF α–associated trichodimerol, the
tetrahydropyran class of natural products, apoptolidin,
diazonamide A, thiostrepton, and the azaspiracids exemplify this philosophy. Current projects include studies
of the antibiotics nocathiacin and abyssomicin C, the
antifeedant azadirachtin, and the antitumor agents
marinomycin and A lomaiviticin B (Fig. 1).
THE SCRIPPS RESEARCH INSTITUTE
Nicolaou, K.C. Joys of molecules, 1: campaigns in total synthesis. J. Org. Chem.
70:7007, 2005.
Nicolaou, K.C. Joys of molecules, 2: endeavors in chemical biology and medicinal
chemistry. J. Med. Chem. 48:5613, 2005.
Nicolaou, K.C., Brenzovich, W.E., Bulger, P.G., Francis, T.M. Synthesis of isoepoxy-amphidinolide N and des-epoxy-caribenolide I structures: initial forays. Org.
Biomol. Chem. 4:2119, 2006
Nicolaou, K.C., Bulger, P.G., Brenzovich, W.E. Synthesis of iso-epoxy-amphidinolide N and des-epoxy-caribenolide I structures: revised strategy and final stages.
Org. Biomol. Chem. 4:2158, 2006.
Nicolaou, K.C., Chen, D.Y.-K., Li, Y., Uesaka, N., Petrovic, G., Koftis, T.V.,
Bernal, F., Frederick, M.O., Govindasamy, M., Ling, T., Pihko, P.M., Tang, W.,
Vyskocil, S. Total synthesis and structural elucidation of azaspiracid-1: synthesisbased analysis of originally proposed structures and indication of their non-identity
to the natural product. J. Am. Chem. Soc. 128:2258, 2006.
Nicolaou, K.C., Denton, R.M., Lenzen, A., Li, A., Edmonds, D.J., Milburn, R.R.,
Harrison, S.T. Stereocontrolled synthesis of model core systems of lomaiviticins A
and B. Angew. Chem. Int. Ed. 45:2076, 2006.
Nicolaou, K.C., Frederick, M.O., Loizidou, E.Z., Petrovic, G., Cole, K.P., Koftis,
T.V., Yamada, Y.M.A. Second-generation total synthesis of azaspiracids-1, -2, and 3. Chem. Asian J. 1:245, 2006.
Nicolaou, K.C., Frederick, M.O., Petrovic, G., Cole, K.P., Loizidou, E. Total synthesis and confirmation of the revised structures of azaspiracid-2 and azaspiracid3. Angew. Chem. Int. Ed. 45:2609, 2006.
Nicolaou, K.C., Harrison, S.T. Total synthesis of abyssomicin C and atrop-abyssomicin
C. Angew. Chem. Int. Ed. 45:3256, 2006.
Nicolaou, K.C., Kim, D.W., Schlawe, D., Lizos, D.E., de Noronha, R.G., Longbottom, D.A. Total synthesis of halipeptins A and D and analogues. Angew. Chem. Int.
Ed. 44:4925, 2005.
Nicolaou, K.C., Koftis, T.V., Vyskocil, S., Petrovic, G., Tang, W., Frederick, M.O.,
Chen, D.Y.-K., Li, Y., Ling, T., Yamada, Y.M.A. Total synthesis and structural elucidation of azaspiracid-1: final assignment and total synthesis of the correct structure
of azaspiracid-1. J. Am. Chem. Soc. 128:2859, 2006.
Nicolaou, K.C., Lim, Y.H., Papageorgiou, C.D., Piper, J.L. Total synthesis of (+)rugulosin and (+)-2,2′-epi-cytoskyrin A through cascade reactions. Angew. Chem.
Int. Ed. 44:7917, 2005.
Nicolaou, K.C., Lizos, D.E., Kim, D.W., Schlawe, D., de Noronha, R.G., Longbottom, D.A., Rodriquez, M., Bucci, M., Cirino, G. Total synthesis and biological evaluation of halipeptins A and D and analogues. J. Am. Chem. Soc. 128:4460, 2006.
Nicolaou, K.C., Mathison, C.J.N. Synthesis of imides, N-acyl vinylogous carbamates and ureas, and nitriles with Dess-Martin periodinane. Angew. Chem. Int. Ed.
44:5992, 2005.
Nicolaou, K.C., Papageorgiou, C.D., Piper, J.L., Chadha, R.K. The cytoskyrin cascade: a facile entry into cytoskyrin A, deoxyrubroskyrin, rugulin, skyrin and
flavoskyrin model systems. Angew. Chem. Int. Ed. 44:5846, 2005.
F i g . 1 . Selected target molecules.
In addition, we are developing synthetic technologies and strategies for chemical synthesis and chemical biology studies. Our overall aims are to advance
the art and science of chemical synthesis and to develop
enabling technologies for biology and medicine while
maximizing educational opportunities and training of
young men and women in chemistry.
PUBLICATIONS
Ito, E., Frederick, M.O., Koftis, T.V., Tang, W., Petrovic, G., Ling, T., Nicolaou,
K.C. Structure toxicity relationships of synthetic azaspiracid-1 and analogs in mice.
Harmful Algae. 5:586, 2006.
Nicolaou, K.C., Pihko, P.M., Bernal, F., Frederick, M.O., Qian, W., Uesaka, N.,
Diedrichs, N., Hinrichs, J., Koftis, T.V., Loizidou, E., Petrovic, G., Rodriquez, M.,
Sarlah, D., Zou, N. Total synthesis and structural elucidation of azaspiracid-1: construction of key building blocks for originally proposed structure. J. Am. Chem.
Soc. 128:2244, 2006.
Nicolaou, K.C., Pratt, B.A., Arseniyadis, S., Wartmann, M., O’Brate, A., Giannakakou, P. Molecular design and chemical synthesis of a highly potent epothilone.
Chemmedchem 1:41, 2006.
Nicolaou, K.C., Safina, B.S., Zak, M., Lee, S.H., Nevalainen, M., Bella, M.,
Estrada, A.A., Funke, C., Zécri, F., Bulat, S. Total synthesis of thiostrepton: retrosynthetic analysis and construction of key building blocks. J. Am. Chem. Soc.
127:11159, 2005.
Nicolaou, K.C., Schlawe, D., Kim, D.W., Longbottom, D.A., de Noronha, R.G., Lizos,
D.E., Manan, R.R., Faulkner, D.J. Total synthesis of halipeptins: isolation of halipeptin
D and synthesis of oxazoline halipeptin analogues. Chemistry 11:6197, 2005.
CHEMISTRY
2006
THE SCRIPPS RESEARCH INSTITUTE
Nicolaou, K.C., Xu, H. Total synthesis of floresolide B and ∆6,7-Z-floresolide B.
Chem. Commun. (Camb.) 600, 2006, Issue 6.
DUAL OPIOID AGONISTS–CHOLECYSTOKININ
Nicolaou, K.C., Zak, M., Rahimipour, S., Estrada, A.A., Lee, S.H., O’Brate, A.,
Giannankakou, P., Ghadiri, M.R. Discovery of a biologically active thiostrepton
fragment. J. Am. Chem. Soc. 127:15042, 2005.
N E U R O PAT H I C PA I N
Nicolaou, K.C., Zak, M., Safina, B.S., Estrada, A.A., Lee, S.H., Nevalainen, M.
Total synthesis of thiostrepton: assembly of key building blocks and completion of
the synthesis. J. Am. Chem. Soc. 127:11176, 2005.
Translational Chemistry
and Medicine
E. Roberts, Z.Y. Chen, O. Ghoneim, C. Martinez, S. Sinha,
C. Zoni
iscovery and development of new medicines
require the integration of several scientific disciplines. For example, medicinal chemistry relies
on iterative in vitro and in vivo biological testing of molecules. These biological investigations, in turn, rely on
the design and synthesis of new molecules with therapeutic potential to delineate and validate pathways
for therapeutic intervention. The primary focus of our
research is to identify potential new medicines for the
treatment of diseases that currently have inadequate
or no current therapy.
D
G A L A N I N L I G A N D S F O R T H E T R E AT M E N T O F
NEUROLOGIC DISEASES
Epilepsy is a disease in which a hyperexcited state
of the CNS is caused by an imbalance between inhibitory and excitatory neurotransmission. Current epilepsy
therapy focuses on modulating the classical neurotransmitters glutamate and γ-aminobutyric acid. The neuropeptide galanin antagonizes excitatory glutaminergic
neurotransmission in the hippocampus, suggesting that
galanin may have a role in seizure activity. Galanin
and its receptors may be useful in developing novel
antidepressant pharmacotherapies. In a recent study
in humans with depression, intravenously administered
galanin had a rapid and strong antidepressant effect.
To identify new nonpeptidic ligands for galanin
receptors, we are using a small set of known molecules
that can potently displace the peptide galanin from its
binding site on the R3 receptor subtype. Selectivity and
potency can then be established by appending appropriate accessory binding motifs selective for the desired
protein. This research is being done in collaboration
with T. Bartfai, Molecular and Integrative Neurosciences
Department, and A.M. Mazarati, University of California, Los Angeles.
85
A N TA G O N I S T S F O R T R E AT M E N T O F C H R O N I C A N D
Nociception, or the perception of pain, and its modulation depend on the interaction of many endogenous
neurotransmitters in the spinal cord. The interaction
of endogenous peptides such as cholecystokinin with
exogenously administered opioids markedly alters activity in acute and chronic pain states. Cholecystokinin
antagonizes the analgesic effects of morphine, whereas
cholecystokinin antagonists enhance them. The interplay between cholecystokinin antagonists and opiates
may lead to the development of novel medications
that are more effective and safer than currently used
opioids alone.
Molecules with both opioid agonist and cholecystokinin antagonist properties would be useful in conditions in which the effectiveness of opioids is reduced,
as in the development of tolerance to opiate pain relievers in chronic pain associated with cancer. The molecules might also be useful in neuropathic pain conditions
in which opioids are ineffective. Thus, because of the
prevention (or reversal) of tolerance, the possibility of
physical dependence on opioids might be diminished or
inhibited. The advantages of developing a single compound with dual opioid agonist–cholecystokinin antagonist activity rather than a combination of an opioid
agonist taken with a separate cholecystokinin antagonist are clear. Development of a single compound
involves only a single set of parameters, such as toxicology, pharmacokinetics, and formulation, rather than 2
independent and often unrelated sets of data.
In collaboration with F. Porreca and J. Lai, University of Arizona, Tucson, we are using a limited set of
molecular templates that have affinity across a wide
range of type 1 G protein–coupled receptors. The 3
cloned opiate receptors (µ, δ, and κ) and the cholecystokinin 1/(A) and 2/(B) receptors are all members of
this subclass of G protein–coupled receptors. Ligands
are known for both sets of receptors that contain the
diphenylmethyl moiety as a privileged or biased template.
Other critical elements for activity may be appended to
chemically “silent” sites (Fig. 1).
NEUROPHARMACOLOGIC APPROACHES FOR
P R E V E N T I O N A N D T R E AT M E N T O F A U T I S M
Autism is a bioneurologic developmental disability
that generally appears before the age of 3 years. This
disability affects the normal development of the brain
in the areas of social interaction, communication skills,
86 CHEMISTRY
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THE SCRIPPS RESEARCH INSTITUTE
F i g . 3 . A, Known mixed vasopressin V1a/V2 receptor antagoF i g . 1 . Proposed opioid agonist–cholecystokinin antagonist hybrids.
and cognitive function. The prevalence of autistic diseases has reached pandemic proportions. In the United
States, autism occurs in an estimated 1 in 166 births,
and roughly 1.5 million persons have some form of
autism. This rate is increasing significantly and now
surpasses that of all types of cancer combined.
No drug is consistently effective in treating the signs
and symptoms of autism. Vasopressin and oxytocin are
2 nonapeptides (Fig. 2) secreted by the hypothalamus.
nists. B, Known vasopressin V1a receptor antagonists.
F i g . 4 . Known oxytocin receptor agonists.
and A. Roberts, Molecular and Integrative Neurosciences Department.
PUBLICATIONS
Roberts, E., Sancon, J.P., Sweeney, J.B. A new class of ammonium ylid for [2,3]sigmatropic rearrangement reactions: end-endo-spiro ylids. Org. Lett. 7:2075, 2005.
F i g . 2 . Structures of vasopressin and oxytocin.
They differ in only 2 amino acids, and both exert their
effects at protein receptors that belong to the G protein–coupled receptor superfamily, namely vasopressin
V1a, V1b, and V2 receptors and oxytocin receptors.
When oxytocin and vasopressin exert their agonist
effects at the oxytocin and vasopressin V1a receptors,
respectively, in rodents, marked effects occur in the CNS.
These effects include behaviors associated with autism,
such as social behaviors (e.g., bonding, aggression);
cognition (e.g., memory and active-passive avoidance);
and repetitive, patterned movements (e.g., grooming
or social interaction). Antagonists reverse or have no
effect on the observed behaviors.
We are designing and developing small-molecule
oxytocin agonists that can penetrate the CNS and previously unknown vasopressin V1a receptor agonists to
establish the potential roles for these molecules in the
treatment of autism (Figs. 3 and 4). This research is
being done in collaboration with T. Bartfai, G.F. Koob,
Workman, J.A., Garrido, N.P., Sancon, J., Roberts, E., Wessel, H.P., Sweeney,
J.B. Asymmetiric [2,3]-rearrangement of glycine-derived allyl ammonium ylids. J.
Am. Chem. Soc. 127:1066, 2005.
Chemical, Biological, and
Biophysical Approaches to
Understanding Evolution
F.E. Romesberg, D.A. Bachovchin, J.K. Chin, R.T. Cirz,
M.E. Cremeens, C. Gil-Lamaignere, N. Gingles, D.A. Harris,
A.A. Henry, G.T. Hwang, A.M. Leconte, E.T. Lis, S. Matsuda,
E.L. Oakman, B.A. O’Neill, T.C. Roberts, L.B. Sagle,
P.A. Smith, M.C. Thielges, P. Weinkam, W. Yu,
J. Zimmermann
he molecules of biology are unique because they
have been evolved for function. We take a unique
and multidisciplinary approach to understanding
and manipulating these processes.
T
CHEMISTRY
2006
INCREASING THE CHEMICAL AND GENETIC
POTENTIAL OF DNA
Biological information storage is based on the natural genetic alphabet, composed of the 2 base pairs
guanine-cytosine and adenine-thymine. We are interested in increasing the information potential of DNA
by expanding the genetic alphabet with a third base
pair composed of unnatural nucleobases. Using hydrophobicity, polarity, shape complementarity, and hydrogen bonding, we are developing novel unnatural base
pairs, including several that are replicable in vitro.
Nature developed the natural genetic code, not only
by optimizing DNA and RNA but also by evolving the
polymerases that synthesize these nucleic acids. We
developed an activity-based selection system (Fig. 1) to
THE SCRIPPS RESEARCH INSTITUTE
87
malian cells will revolutionize our understanding of
cancer and aging and identify drug targets whose inhibition might actually inhibit these processes.
In bacteria, induced mutation can lead to antibiotic resistance. We have fully characterized the mechanism of induced mutation and antibiotic resistance in
Escherichia coli (Fig. 2), and we are characterizing
F i g . 2 . Induced mutation in E coli is controlled by the transcrip-
tional regulator LexA. Duplex DNA is shown in black; each gray box
indicates a double-strand break. The breaks can be repaired
through pathway A, B, or C. Derepression of the error-prone polymerases Pol IV and Pol V leads to mutations (pathway D).
these pathways in other bacterial pathogens. We are
also designing a drug that inhibits bacterial mutation
and thus evolution.
F i g . 1 . Activity-based phage display selection system for evolv-
EVOLUTION OF PROTEIN DYNAMICS
ing polymerases with novel activity. Infection of phage (B) with the
polymerase library (A) leads to production of phage particles that
The products of evolution are molecules with unique
vibrational dynamics. The study of vibrational dynamics in proteins and nucleic acids has been limited by
spectral complexity, but selective deuteration of a protein or a nucleic acid results in a carbon-deuterium
oscillator that absorbs light in an otherwise transparent region of the infrared spectrum. The synthesis of
selectively deuterated proteins has provided us with a
residue-specific probe of flexibility, function, and folding. We are also using multidimensional femtosecond
spectroscopy to characterize how protein motion is
evolved during the somatic evolution of antibodies.
We discovered that the immune system can manipulating protein dynamics, a finding that suggests a role
for these dynamics in molecular recognition.
display 0–1 copies of the polymerase and 3–5 copies of the acidic
peptide. Phage particles are combined with DNA primer–template
(C) and incubated with the desired nucleoside triphosphates. Active
mutants are isolated (D) and characterized.
evolve polymerases for any desired function. Using this
system, we have already evolved polymerases with a
variety of novel functions, including the synthesis of
DNA containing one of the unnatural base pairs. We are
optimizing these polymerases and evolving new ones.
DNA DAMAGE RESPONSE
Evolution requires mutation, but mutations also make
cells susceptible to aging and cancer. It is now understood that at times of sufficient stress, cells induce
error-prone replication to facilitate their own evolution.
We used genome-wide high-throughput methods to identify genes involved in both error-free and error-prone
responses to DNA stress in budding yeast. Characterization of the proteins required for mutation in mam-
PUBLICATIONS
Chin, J.K., Bashkirov, V.I., Heyer, W.D., Romesberg, F.E. Esc4/Rtt107 and the
control of recombination during replication. DNA Repair (Amst.) 5:618, 2006.
Cirz, R.T., Gingles, N., Romesberg, F.E. Side effects may include evolution. Nat.
Med. 8:890, 2006.
88 CHEMISTRY
2006
Cirz, R.T., O’Neill, B.M., Hammond, J.A., Head, S.R., Romesberg, F.E. Defining
the Pseudomonas aeruginosa SOS response and its role in the global response to
the antibiotic ciprofloxacin. J. Bacteriol. 188:7101, 2006.
Cirz, R.T., Romesberg, F.E. Induction and inhibition of ciprofloxacin resistance-conferring mutations in hypermutator bacteria. Antimicrob. Agents Chemother.
50:220, 2006.
Cremeens, M., Fujisaki, H., Zhang, Y., Zimmermann, J., Sagle, L.B., Matsuda, S.,
Dawson, P.E., Straub, J.E., Romesberg, F.E. Efforts toward developing direct
probes of protein dynamics. J. Am. Chem. Soc. 128:6028, 2006.
Dupradeau, F.-Y., Case, D.A., Yu, C., Jimenez, R., Romesberg, F.E. Differential
solvation and tautomer stability of a model base pair within the minor and major
grooves of DNA. J. Am. Chem. Soc. 127:15612, 2005.
Henry, A.A., Romesberg, F.E. Evolution of DNA polymerases with novel activities.
Curr. Opin. Biotechnol. 16:370, 2005.
Hwang, G.T., Romesberg, F.E. Substituent effects on the pairing and polymerase
recognition of simple unnatural base pairs. Nucleic Acids Res. 34:2037, 2006.
Kim, Y., Leconte, A.M., Hari, Y., Romesberg, F.E. Stability and polymerase recognition of pyridine nucleobase analogues: role of minor-groove H-bond acceptors.
Angew. Chem. Int. Ed., in press.
Leconte, A.M., Chen, L., Romesberg, F.E. Polymerase evolution: efforts toward
expansion of the genetic code. J. Am. Chem. Soc. 127:12470, 2005.
Leconte, A.M., Matsuda, S., Hwang, G., Romesberg, F.E. Efforts towards expansion of the genetic alphabet: pyridone and methyl pyridone nucleobases. Angew.
Chem. Int. Ed. 45:4326, 2006.
Leconte, A.M., Matsuda, S., Romesberg, F.E. An efficiently extended class of
unnatural base pairs. J. Am. Chem. Soc. 128:6780, 2006.
Leconte, A.M., Romesberg, F.E. Amplify this! DNA and RNA get a third base pair.
Nat. Methods 3:667, 2006.
Lis, E.T., Romesberg, F.E. Role of Doa1 in the Saccharomyces cerevisiae DNA
damage response. Mol. Cell. Biol. 26:4122, 2006.
Matsuda, S., Henry, A.A., Romesberg, F.E. Optimization of unnatural base pair
packing for polymerase recognition. J. Am. Chem. Soc. 128:6369, 2006.
Sagle, L.B., Zimmermann, J., Dawson, P.E., Romesberg, F.E. Direct and high-resolution characterization of cytochrome c equilibrium folding. J. Am. Chem. Soc., in press.
Sagle, L.B., Zimmermann, J., Matsuda, S., Dawson, P.E., Romesberg, F.E. Redoxcoupled dynamics and folding in cytochrome c. J. Am. Chem. Soc. 128:7909, 2006.
Zimmermann, J., Oakman, E.L., Thorpe, I.F., Shi, X., Abbyad, P., Brooks, C.L. III,
Boxer, S.G., Romesberg, F.E. Antibody evolution constrains conformational hetereogeneity by tailoring protein dynamics. Proc. Natl. Acad. Sci. U. S. A.
103:13722, 2006.
Biological Chemistry
P.G. Schultz, A. Boitano, E. Brustad, M. Bushey, S. Chen,
J. Guo, J. Grbic, D. Groff, J. Grünewald, W.Y. Hur, M. Jahnz,
T. Kuo, J. Lee, J.-S. Lee, K.-B. Lee, E. Lemke, C. Liu,
W. Liu, C. Lyssiotis, J. Mills, M. Mukherji, T. Nom, B. Okram,
R. Perera, F. Peters, Y. Ryu, S. Schiller, M. Sever,
D. Summerer, L. Supekova, E. Tippmann, M.-L. Tsao,
J. Wang, T. Young, Q. Zhang, S. Zhu
A
lthough chemists are remarkably adept at synthesizing molecular structures, they are far less
sophisticated in designing and synthesizing
THE SCRIPPS RESEARCH INSTITUTE
molecules with defined biological or chemical functions.
Nature, on the other hand, has produced an array of
molecules with remarkably complex functions, ranging
from photosynthesis and signal transduction to molecular recognition and catalysis. Our aim is to combine the
synthetic strategies and biological processes of Nature
with the tools and principles of chemistry to create new
molecules with novel chemical and biological functions.
By studying the properties of the resulting molecules,
we can gain new insights into the molecular mechanisms of complex biological and chemical systems.
For example, we have shown that the tremendous
combinatorial diversity of the immune response can be
chemically reprogrammed to generate selective enzymelike catalysts. We have developed antibodies that catalyze a wide array of chemical and biological reactions,
from acyl transfer to redox reactions. Characterization
of the structure and mechanisms of these catalytic antibodies has led to important new insights into the mechanisms of biological catalysis. In addition, the detailed
characterization of the properties and structures of
germ-line and affinity-matured antibodies has revealed
fundamental new aspects of the evolution of binding
and catalytic function, in particular, the role of structural plasticity in the immune response. Most recently,
we have focused on in vitro evolution methods that
involve the development of novel chemical screens
and selections for identifying metalloantibodies with
proteolytic activity.
Our work on catalytic antibodies redirects natural
combinatorial diversity to produce new function. We
are extending this combinatorial approach to many
other problems, including the generation of genetic
“microcalorimetes” and yeasts lacking mitochondrial
genomes and the ab initio evolution of novel protein
domains. We are also generating structure-based combinatorial libraries of small heterocycles that are being
used in conjunction with novel cellular and organismal
screens to identify important proteins involved in such
cellular processes as differentiation, proliferation, and
signaling. Indeed, we have identified molecules that
control both adult and embryonic stem cell differentiation and self-renewal and that reprogram lineage-committed cells. We are using x-ray crystallographic and
biochemical studies, together with genomics technologies, to characterize the mode of action of these compounds and to study their effects on cellular processes.
We are also applying genomics tools (cell-based phenotypic screens of arrayed genomic cDNA and small
CHEMISTRY
2006
interfering RNA libraries) and proteomics tools (mass
spectrometric phosphoprotein profiling) to a variety of
important biomedical problems in cancer biology, neurodegenerative and autoimmune diseases, and virology.
In addition, we are investigating the role and regulation
of noncoding RNAs.
We have also developed a general biosynthetic
method that can be used to site specifically incorporate
unnatural amino acids into proteins in vitro and in vivo.
Using this method, we effectively expanded the genetic
codes of both prokaryotic and eukaryotic organisms by
adding new components to the biosynthetic machinery
of living cells. We have genetically encoded amino acids
with novel spectroscopic and chemical properties (e.g.,
metal-binding, glycosylated, and fluorescent amino acids
and photocross-linking and photoisomerizable amino
acids) in response to unique 3- and 4-base codons.
These amino acids are being used to explore protein
structure and function both in vitro and in vivo and to
evolve proteins with novel properties. Our results have
removed a billion-year constraint imposed by the genetic
code on the ability to chemically manipulate the structures of proteins.
PUBLICATIONS
Bose, M., Groff, D., Xie, J., Brustad, E., Schultz, P.G. The incorporation of a photoisomerizable amino acid into proteins in E. coli. J. Am. Chem. Soc. 128:388, 2006.
Chen, S., Do, J., Zhang, Q., Yao, S., Yan, F., Peters, E., Scholer, H., Schultz,
P.G., Ding, S. Self-renewal of embryonic stem cells by a small molecule. Proc.
Natl. Acad. Sci. U. S. A., in press.
Mukherji, M., Cho, C., Supekova, L., Wang, Y., Batalov, S., Bell, R., Martin, C.,
Sahasrabuhde, S., Orth, A.P., Chanda, S.K., Schultz, P.G. Functional analysis of
human genome for cell-cycle regulators. Proc. Natl. Acad. Sci. U. S. A., in press.
Summerer, D., Chen, S., Wu, N., Deiters, A., Chin, J.W., Schultz, P.G. A genetically
encoded fluorescent amino acid. Proc. Natl. Acad. Sci. U. S. A. 103:9785, 2006.
Turner, J.M., Graziano, J., Spraggon, G., Schultz, P.G. Structural characterization
of a p-acetylphenylalanyl aminoacyl-tRNA synthetase. J. Am. Chem. Soc.
127:14976, 2005.
Warashina, M., Min, K.H., Kuwabara, T., Huynh, A., Gage, F.H., Schultz, P.G.,
Ding, S. A synthetic small molecule that induces neuronal differentiation of adult
hippocampal neural progenitor cells. Angew. Chem. Int. Ed. 45:591, 2006.
Willingham, A.T., Orth, A.P., Batalov, S., Peters, E.C., Wen, B.G., Aza-Blanc, P.,
Hogenesch, J.B., Schultz, P.G. A strategy for probing the function of noncoding
RNAs finds a repressor of NFAT. Science 309:1570, 2005.
THE SCRIPPS RESEARCH INSTITUTE
89
Powerful Click Processes for
Organic Synthesis, Chemical
Biology, and Materials Research
K.B. Sharpless, V.V. Fokin, M. Ahlquist, B. Boren, M. Cassidy,
S. Chang, A. Feldman, J. Fotsing, R. Fraser, A. Grant, J. Hein,
J. Kalisiak, L. Krasnova, S.-W. Kwok, Y. Liu, J. Loren,
R. Manetsch, K. Nagai, S. Narayan, S. Pitram,
L.K. Rasmussen, J. Raushel, S. Roeper, W. Sharpless,
A. Sugawara, J. Tripp, X. Wang, J. Wassenaar, T. Weide,
M. Whiting, P. Wu
he driving forces in our research are the discovery and understanding of chemical reactivity, the
harbingers of all new reactions. Our main goal
is to develop practical transformations that facilitate
synthesis of novel molecules with desired functions and
allow manipulation of complex biological systems at the
molecular level.
T
CLICK CHEMISTRY
Among the many factors that determine the success of a search for compounds with desired properties, 2 stand out: the degree of diversity of the building
blocks that can be used and the speed with which
synthesis, screening for the desired function, and lead
optimization can be performed. The greater the variety
of scaffolds and functional groups that can be used in
the rapid construction of candidate compounds, the more
likely it is that new and useful function will be discovered. Because of the enormous number of compounds
to explore (the number of small druglike compounds
may be as high as 1064), the size of a given collection
becomes much less important than the ability to rapidly
probe the collection for a desired activity. However,
many chemical methods often have restrictions such as
limited scope, inaccessibility of starting materials,
requirements for protecting groups, and difficult purifications. In addition, inert atmospheres and anhydrous solvents are usually required, a situation that makes these
methods impractical for manipulating biological molecules in the molecules’ natural, aqueous environment.
In the past several years, we have sought to develop
and use only the best reactions for the synthesis of
functional molecules. The reactions that fulfill the most
stringent criteria of usefulness and convenience have
been grouped under the name click chemistry. Most
click reactions form carbon-heteroatom bonds, are tolerant of water, and are often accelerated when water
90 CHEMISTRY
2006
is used as the sole medium, even if the reagents are
not soluble in water.
C O P P E R - C ATA LY Z E D C Y C L O A D D I T I O N S
The copper-catalyzed 1,3-dipolar cycloaddition of
azides and alkynes has emerged as a premiere click reaction that enables reliable assembly of complex molecules
by means of the 1,2,3-triazole heterocycle. Although
both alkynes and azides are highly reactive, their reactivity profiles are quite narrow, that is, “orthogonal” to
an unusually broad range of reagents, solvents, and other
functional groups. These features allow clean sequential transformations of broad scope without the need
for protecting groups, even if the reactions are performed
under physiologic conditions.
The 1,2,3-triazoles have the advantageous properties of high chemical stability (in general, being inert to
severe hydrolytic, oxidizing, and reducing conditions,
even at high temperatures), strong dipole moment,
presence of aromatic groups, and the ability to accept
hydrogen bonds. Thus, they can interact productively
in several ways with biological molecules. For example,
1,2,3-triazoles can replace the amide bond in peptides,
preventing proteolytic degradation of the peptides.
The fundamental thermal reaction, involving terminal or internal alkynes (Fig. 1, top), has been known
F i g . 1 . Thermal cycloaddition of azides and alkynes (top)
requires prolonged heating and results in mixtures of both 1,4- and
1,5-regioisomers, whereas the copper-catalyzed 1,3-dipolar
cycloaddition of azides and alkynes produces only 1,4-disubstituted-1,2,3-triazoles at room temperature (bottom).
for more than a century and has been thoroughly investigated. Although the process is strongly thermodynamically favored, it has a relatively high kinetic barrier
that makes the reaction slow at room temperature for
unactivated reactants and results in the formation of
regioisomers. Copper(I) catalysis dramatically accelerates
the reaction, by a factor of up to 107, and regiospecifically produces only 1,4-disubstituted-1,2,3-triazoles
(Fig. 1, bottom). Because of its experimental simplicity
and unusually broad scope, this process has been used
in a number of applications in synthesis, medicinal
chemistry, molecular biology, and materials science.
THE SCRIPPS RESEARCH INSTITUTE
Although a number of copper(I) complexes can be
used to catalyze the reaction, we found that the catalyst is often better prepared in situ by reduction of
copper(II) salts, which are readily available and are
easier to handle than most copper(I) salts. As the
reductant, ascorbic acid (vitamin C) or sodium ascorbate is excellent. Remarkably, even copper metal can
be used as a source of the catalytic species, making
the experimental procedure even simpler: a small piece
of copper metal (wire or turning) is all that is added to
the reaction mixture, which is then shaken or stirred
for 12–48 hours. This protocol is particularly convenient
in parallel synthesis, because triazole products are
generally isolated in high yields and can often be submitted for screening without further purification.
Our studies of reactivity of sulfonyl azides in the
copper-catalyzed cycloaddition of azides and alkynes
resulted in the development of an experimentally simple catalytic procedure for the highly selective conversion of alkynes to N-sulfonyl azetidin-2-imines under
mild conditions. This 3-component process is thought
to proceed via initial reaction of in situ generated copper(I) acetylides with sulfonyl azides, resulting in transient (1-sulfonyltriazolyl) copper intermediates that upon
extrusion of dinitrogen generate N-sulfonyl keteneimines.
The azetidinimine products are remarkably stable in a
wide range of reaction conditions, and other functional
groups can be easily added (Fig. 2). This newly dis-
F i g 2 . Synthesis of azetidinimines from alkynes, sulfonyl azides,
and imines.
covered reaction sequence rapidly produces densely
functionalized azetidine derivatives from readily available terminal alkynes in just 2 or 3 simple steps and
should be useful for exploring the usefulness of these
4-atom heterocycles.
Although useful because of its rate and functional
group tolerance, the copper-catalyzed 1,3-dipolar
cycloaddition of azides and alkynes cannot produce
1,5-disubstituted 1,2,3-triazoles, and it is not effective with internal alkynes. Therefore, the recent discovery of ruthenium(II) catalysts that are active in
azide-alkyne cycloaddition and result in the formation
of the complementary 1,5-regioisomers of 1,2,3-tria-
CHEMISTRY
2006
zoles was a welcome advance. Pentamethyl cyclopentadienyl ruthenium(II) complexes are active and easy to
handle and provide triazole products in good to excellent yields (Fig. 3). In addition, these catalysts are active
F i g . 3 . Ruthenium-catalyzed synthesis of fully substituted
1,2,3-triazoles.
with internal alkynes, allowing easy synthesis of fully
substituted triazoles.
S Y N T H E S I S O F P O LY F U N C T I O N A L D E N D R I M E R S
Dendrimers are highly ordered, regularly branched
globular macromolecules of defined structure; dendrimers are ideal building blocks for creating bioactive
macromolecules and nanomaterials. Previously, we
exploited the high fidelity of the copper-catalyzed 1,3
dipolar cycloaddition of azides and alkynes in the efficient synthesis of dendrimers. We used procedures that
involved little more than mixing stoichiometric quantities
of reactants, stirring, and isolating dendrimer products.
In collaboration with M.G. Finn, Department of
Chemistry, and C.J. Hawker, University of California,
Santa Barbara, we have extended this approach to
synthesize chemically heterogeneous dendrimers (Fig. 4)
THE SCRIPPS RESEARCH INSTITUTE
91
binding protein concanvalin A and rabbit red blood
cells. The dendrimer had 240-fold greater potency
than monomeric mannose, a difference that translates
to a 15-fold increase in activity per unit. Additionally,
our preliminary experiments indicate that this dendrimer
binds to the modified surface of Escherichia coli, producing detectable fluorescent signals. These results
are a significant advance in dendrimer chemistry and
illustrate an evolving synergy between organic chemistry and functional materials.
Studies of other applications, ranging from biology
to materials science, are currently underway in our laboratories and in collaboration with M.G. Finn, P.K. Vogt,
C.-H. Wong, J.H. Elder, and others at Scripps Research.
PUBLICATIONS
Bourne, Y., Radic, Z., Kolb, H.C., Sharpless, K.B., Taylor, P., Marchot, P. Structural insights into conformational flexibility at the peripheral site and within the
active center gorge of AChE. Chem. Biol. Interact. 157-158:159, 2005.
Cassidy, M.P., Raushel, J., Fokin, V.V. Practical synthesis of amides from in situ
generated copper(I) acetylides and sulfonyl azides. Angew. Chem. Int. Ed.
45:3154, 2006.
Hansen, T.V., Wu, P., Fokin, V.V. One-pot copper(I)-catalyzed synthesis of 3,5-disubstituted isoxazoles. J. Org. Chem. 70:7761, 2005.
Loren, J.C., Krasinski, A., Fokin, V.V., Sharpless, K.B., NH-1,2,3-triazoles from
azidomethyl pivalate and carbamates: base-labile N-protecting groups. Synlett
2847, 2005, Issue 18.
Malkoch, M., Schleicher, K., Drockenmuller, E., Hawker, C.J., Russell, T.P., Wu,
P., Fokin, V.V. Structurally diverse dendritic libraries: a highly efficient functionalization approach using click chemistry. Macromolecules 38:3663, 2005.
Meng, J.-C., Fokin, V.V., Finn, M.G. Kinetic resolution by copper-catalyzed azidealkyne cycloaddition. Tetrahedron Lett. 46:4543, 2005.
Petasis, N.A., Akritopoulou-Zanze, I., Fokin, V.V., Bernasconi, G., Keledjian, R.,
Yang, R., Uddin, J., Nagulapalli, K.C., Serhan, C.N. Design, synthesis and bioactions of novel stable mimetics of lipoxins and aspirin-triggered lipoxins.
Prostaglandins Leukot. Essent. Fatty Acids 73:301, 2005.
Radic, Z., Manetsch, R., Krasinski, A., Raushel, J., Yamauchi, J., Garcia, C., Kolb,
H.C., Sharpless, K.B., Taylor, P. Molecular basis of interactions of cholinesterases
with tight binding inhibitors. Chem. Biol. Interact. 157-158:133, 2005.
Rodionov, V.O., Fokin, V.V., Finn, M.G. Mechanism of the ligand-free Cu(I)-catalyzed azide-alkyne cycloaddition reaction. Angew. Chem. Int. Ed. 44:2210, 2005.
Whiting, M., Fokin, V.V. Copper-catalyzed reaction cascade: direct conversion of
alkynes to N-sulfonylazetidin-2-imines. Angew. Chem. Int. Ed. 45:3157, 2006.
Whiting, M., Muldoon, J., Lin, Y.-C., Silverman, S.M., Lindstrom, W., Olson, A.J.,
Kolb, H.C., Finn, M.G., Sharpless, K.B., Elder, J.H., Fokin, V.V. Inhibitors of HIV1 protease by using in situ click chemistry. Angew. Chem. Int. Ed. 45:1435,
2006.
F i g . 4 . Synthesis of polyfunctional dendrimers via copper-catalyzed 1,3-dipolar cycloaddition of azides and alkynes.
that have multiple recognition functions (such as 16
α-d-mannose units) and detection elements (2 coumarinderived fluorescent chromophores). The performance
of one such bifunctional dendrimer was evaluated in a
standard hemagglutination assay with the mannose-
Wu, P., Hilgraf, R., Fokin, V.V. Osmium-catalyzed olefin dihydroxylation and aminohydroxylation in the second catalytic cycle. Adv. Synth. Catal. 348:1079, 2006.
Wu, P., Malkoch, M., Hunt, J., Vestberg, R., Kaltgrad, E., Finn, M.G., Fokin, V.V.,
Sharpless, K.B., Hawker, C.J. Multivalent, bifunctional dendrimers prepared by
click chemistry. Chem. Commun. (Camb.) 5775, 2005, Issue 46.
Zhang, L., Chen, X., Xue, P., Sun, H.H.Y., Williams, I.D., Sharpless, K.B., Fokin,
V.V., Jia, G. Ruthenium-catalyzed cycloaddition of alkynes and organic azides. J.
Am. Chem. Soc. 127:15998, 2005.
92 CHEMISTRY
2006
THE SCRIPPS RESEARCH INSTITUTE
Chemistry, Biology, and
Inflammatory Disease
P. Wentworth, Jr., J.Y. Chang, Y.P. Chen, J. Dambacher,
L. Eltepu, R.K. Grover, J. Nieva, M. Puga, A. Shafton,
B.D. Song, M.M.R. Peram, J. Rogel, S. Tripurenani,
R. Troseth, H. Wang, A.D. Wentworth
ur research is interdisciplinary and involves bioorganic, biophysical, physical organic, synthetic,
and analytical chemistry coupled with biochemical techniques, cell-based assays, and animal models.
These diverse approaches are combined to facilitate a
better understanding of and generate new therapeutic
approaches to complex disease states. Ongoing projects
include studies on atherosclerosis, neurodegeneration,
ischemia-reperfusion injury, macular degeneration, cancer, inflammation, and infectious diseases.
O
T H E A N T I B O D Y - C ATA LY Z E D WAT E R O X I D AT I O N
PAT H WAY
Our discovery that all antibody molecules, regardless of source or antigenic specificity, can catalyze the
reaction between singlet oxygen and water to give hydrogen peroxide is causing a revision of the axiom that
antibodies are the classical adapter molecule of the
immune system, linking recognition and killing of foreign pathogens. Both the chemical and biological aspects
of this pathway are being explored extensively, and
intriguing new insights into how this pathway may
play a role in immune defense and inflammatory damage are emerging.
We recently showed that flavins, biologically relevant photoactive molecules, can act as efficient triggers
for the antibody-catalyzed water oxidation pathway at
physiologically relevant concentrations and a certain
amount of visible light radiation. This observation indicates that immune defense and damage may be linked
to an association of flavins, such as riboflavin or flavin
mononucleotide, with immunoglobulins. The trigger
would be antibody-antigen binding on cells exposed to
visible light, such as the skin or retina.
In collaboration with I.A. Wilson, Department of
Molecular Biology, we recently studied, at atomic resolution, an antibody, IgGGAR, that has riboflavin bound
in the complementarity-determining regions (Fig. 1). Of
interest, the bound riboflavin is essentially photochemically inert. The x-ray structure of the IgGGAR-flavin
complex offers an insight into the lack of photochemical activity; the isoalloxazine ring is effectively sand-
F i g . 1 . Schematic presentation of riboflavin within the binding
site of IgGGAR. Residues that form van der Waals interactions with
riboflavin are indicated; those that participate in the hydrogen
bonds with the riboflavin are shown in ball-and-stick representations. Hydrogen bonds are illustrated as dotted lines.
wiched between several aromatic side chains. Binding
of riboflavin occurs in a narrow cleft with the isoalloxazine ring stacked between parallel aromatic groups of
tyrosine at position H33 (with the re face of riboflavin),
phenylalanine at position H58, and tyrosine at position
H100A (both associated with the si face of the flavin);
the distances between the isoalloxazine ring and the
respective aromatic rings from these 3 residues are
about 3.2, 3.5. and 3.4 Å, respectively. Such π stacking is known to quench the excited state of riboflavin,
a feature that a number of flavin-binding proteins
have also evolved, presumably to protect themselves
from the intrinsic photochemistry of the flavin moiety.
We are searching for the active site for the antibodycatalyzed water oxidation pathway within the antibody
structure. We have cloned and expressed soluble individual domains of the murine Fab 4C6. Initial attempts
to efficiently express wild-type domains were unsuccessful, but by mutating hydrophobic residues involved
in interdomain interactions into soluble hydrophilic residues, we prepared folded domains. All the domains we
cloned and expressed have been successfully purified
to homogeneity from the periplasm of Escherichia coli
transformed with plasmids encoding individual domains.
In addition, to assess the critical nature of tryptophan
residues in the photosensitization of antibody-bound
triplet oxygen to singlet oxygen, we mutated 2 tryptophan residues within domain CH1 to leucine. Interest-
CHEMISTRY
2006
ingly, neither the single nor the double mutation affected
the ability of ultraviolet-irradiated CH1 to generate
hydrogen peroxide.
C H O L E S T E R O L S E C O - S T E R O L S A N D I N F L A M M AT O R Y
DISEASE
We recently discovered that the 5,6-seco-sterols
atheronal-A and atheronal-B (Fig. 2), compounds of a
class of cholesterol ozonolysis products, are present in
F i g . 2 . The cholesterol seco-sterols atheronal-A (top) and
atheronal-B (bottom).
human atherosclerotic plaques and plasma. In addition,
we found that the atheronals are present in murine models of atherosclerosis, in a rabbit model of acute respiratory distress syndrome (studies done in collaboration
with C. Cochrane, Department of Molecular and Experimental Medicine), and in brain tissue from patients with
Lewy body dementia (studies done in collaboration with
J. Kelly, Department of Chemistry).
The atheronals have a range of biological properties
that in combination would increase the number of macrophages at sites of vascular inflammation. When cultured macrophage cells were incubated with atheronal-A
and atheronal-B complexed with low-density lipoprotein (LDL), marked upregulation of scavenger receptor
class A, but not CD36, occurred, showing that cultured
macrophages respond to complexes of atheronals and
LDL in a manner highly analogous to the response to
acetylated LDL. Both atheronal-A and atheronal-B induce
chemotaxis of cultured macrophages in a dose-dependent manner. When complexed with LDL, atheronal-A,
but not atheronal-B, induces a dose-dependent upregulation of the cell-surface adhesion molecule E-selectin
on vascular endothelial cells. When complexed with
THE SCRIPPS RESEARCH INSTITUTE
93
LDL, atheronal-B, but not atheronal-A, induces cultured human monocytes to differentiate into macrophage cell lineage.
These in vitro data and the effects of cholesterol
5,6-seco-sterols on the formation of foam cells and
the cytotoxic effects of macrophages indicate that the
atheronals have biological effects that could lead in
vivo to the recruitment, entrapment, dysfunction, and
ultimate destruction of macrophages, the major leukocytes in inflammatory artery disease.
The ultimate goals of research for genetic and environmental factors that increase the propensity of a
specific protein to misfold are the understanding and
treatment of disease states as diverse as atherosclerosis, light-chain deposition disease, systemic amyloidosis, Alzheimer’s disease, and Parkinson’s disease. We
showed that the inflammation-derived atheronal-A and
atheronal-B trigger a deformation in the secondary
structure of the normally folded protein apolipoprotein
B-100 into a proamyloidogenic form.
In collaboration with Dr. Kelly, we extended this
model and showed that these cholesterol seco-sterols
also trigger the misfolding of amyloid β-peptide(1–40),
leading to formation of fibrils similar to those observed in
patients with Alzheimer’s disease. Interestingly, analysis
of the structure-activity relationship revealed that among
a panel of aldehydes, only atheronal-A, atheronal-B, and
4-hydroxynonenal trigger misfolding of amyloid β-peptide, suggesting that structural aspects of the aldehyde
and not simple protein adduction were critical to this
misfolding. More recently, using mutated synthetic
sequences of amyloid β-peptide(1–40), we found that
the accelerated aggregation of this protein only occurs
when a particular lysine of the sequence is modified.
We have also shown that atheronals and other lipid
aldehydes accelerate the aggregation of several wild-type
amyloidogenic proteins, including immunoglobulin light
chains, mouse prions, and the tumor suppressor protein p53. The generality and specificity of this process
suggest that inflammatory aldehydes and their posttranslational modification of amyloidogenic peptides
may be the chemical link between the known associations of inflammation, oxidative damage, and various
protein misfolding diseases.
INTERACTION BETWEEN PROTOZOAN J-BINDING
P R O T E I N 1 A N D G LY C O S Y L AT E D D N A
Current treatments of parasitic infections such as
leishmaniasis, African trypanosomiasis, and American
trypanosomiasis are limited in terms of their effective-
94 CHEMISTRY
2006
ness, increasing drug resistance and the inherent toxic
effects of the drugs. Thus, an elucidation of new parasite-specific biological targets for new therapeutic agents
is needed. In this regard, the discovery that DNA from
members of the order Kinetoplastida, but not from other
eukaryotes, contains an unusual modified base, β-D glucosyl(hydroxymethyl)uracil, called base J (compound
1a in Fig. 3) was a breakthrough. Extracts of several
kinetoplastids contain a J-binding protein (JBP) that
THE SCRIPPS RESEARCH INSTITUTE
that some loci around the glycan are essential for binding
and some are not. This information is being translated
into structure-based design of chemical libraries as
inhibitors of JBP-1 binding.
PUBLICATIONS
Bielsch, J., Wang, Q.T., Bosco, D., Powers, E.T., Wentworth, P., Jr., Kelly, J.
Inflammatory metabolite-initiated protein misfolding. Acc. Chem. Res., in press.
Bosco, D.A., Fowler, D.M., Zhang, Q., Nieva, J., Powers, E.T., Wentworth, P., Jr.,
Lerner, R.A., Kelly, J.W. Elevated levels of oxidized cholesterol metabolites in Lewy
body disease accelerate α-synuclein fibrilization [published correction appears in
Nat. Chem. Biol. 2:346, 2006]. Nat. Chem. Biol. 2:249, 2006.
Nieva, J., Kerwin, L., Wentworth, A.D., Lerner, R.A., Wentworth, P., Jr.
Immunoglobulins can utilize riboflavin (vitamin B2) to activate the antibody-catalyzed water oxidation pathway. Immunol. Lett. 103:33, 2006.
Rogers, C.J., Dickerson, T.J., Wentworth, P., Jr., Janda, K.D. A high-swelling
reagent scaffold suitable for use in aqueous and organic solvents. Tetrahedron
61:12140, 2005.
Takeuchi, C., Galve, R., Nieva, J., Witter, D.P., Wentworth, A.D., Troseth, R.P.,
Lerner, R.A., Wentworth, P., Jr. Proatherogenic effects of the cholesterol ozonolysis
products, atheronal-A and atheronal-B. Biochemistry 45:7162, 2006.
Toker, J.D., Tremblay, M., Yli-Kauhaluoma, J., Wentworth, A.D., Zhou, B., Wentworth, P., Jr., Janda, K.D. Exploring the scope of the 29G12 antibody catalyzed
1,3-dipolar cycloaddition reaction. J. Org. Chem. 70:7810, 2005.
Witter, D., Wentworth, P., Jr. The antibody-catalyzed water-oxidation pathway from
discovery to an emerging role in health and disease. Antioxid. Redox Signal., in press.
F i g . 3 . Base J (1a) and base J analogs (1b–1g) synthesized and
used as probes for studying JBP-1–J-DNA recognition. Inset, Image
Zhu, X., Wentworth, P., Jr., Kyle, R.A., Lerner, R.A., Wilson, I.A. Cofactor-containing antibodies: crystal structure of the original yellow antibody. Proc. Nat. Acad.
Sci. U. S. A. 103:3581., 2006.
of base J in doubled-stranded DNA shows how glucose sits in the
major groove.
specifically binds to J-containing duplex DNA. JBP-1
is essential in Leishmania.
As a drug target, JBP has merit. The protein shares
little homology with other proteins in the Protein Data
Bank, and it has a unique ligand, J-DNA containing
telomeric stretches of double-stranded DNA, that does
not occur in other eukaryotes. However, a preliminary
high-throughput screen, focused on disrupting binding
between JBP-1 and J-DNA, with a library of compounds
consisting of all the major drug pharmacophoric groups
revealed no compounds of interest.
In parallel, we have studied the nature of the molecular recognition that underpins JBP-1 recognition of
glycosylated DNA. We synthesized a panel of modified
J-containing bases (compounds 1b–1g in Fig. 3) and
incorporated them into a 16-nucleotide telomeric stretch
of double-stranded DNA. In collaboration with D. Millar, Department of Molecular Biology, we determined
the dissociation constants of these analogs for JBP-1
and generated a ∆G of binding assessment of each
hydroxyl around the glucosyl core. This analysis revealed
Bioorganic and
Synthetic Chemistry
C.-H. Wong, C. Bennett, A. Brik, Y.-H. Chen, S. Dean,
S. Ficht, M. Fujio, W. Greenberg, R. Guy, S. Hanson, Z. Hong,
T.-L. Hsu, D.-R. Hwang, J.-C. Lee, P.-H. Liang, L. Liu,
T. Polat, M. Sawa, M. Sugiyama, D. Thayer, S.-K. Wang,
L. Whalen, C.-Y. Wu, D. Wu, M. Wuchrer, Y.-Y. Yang
ur research programs involve development of
new chemical and enzymatic strategies and
methods for the synthesis of biologically active
compounds. We use the synthesized compounds as
molecular probes to explore carbohydrate-mediated
biological recognition events and enzymatic reactions.
O
ORGANIC AND BIOORGANIC SYNTHESIS
Our work in organic and bioorganic synthesis includes
the development of new chemical reactions and the
exploitation of native and engineered enzymes for
organic synthesis. In the past year, we developed new
methods for making glycopeptides and glycoproteins
via native chemical ligation methods. We will use these
CHEMISTRY
2006
methods to synthesize homogenous glycoproteins that
are important therapeutic agents in humans. We continue to develop covalent glycoarrays for high-throughput analysis of protein-carbohydrate interactions and
the use of aldolases in the synthesis of glycosyltransfer enzyme inhibitors. Using directed evolution, we
developed new aldolase variants capable of making
both enantiomers of sugars.
DEVELOPMENT OF INHIBITORS OF ENZYMES AND
RECEPTORS
Our goals in the area of enzyme and receptor inhibitors are to develop new strategies to discover inhibitors
and ligands with high selectivity as potential therapeutic
agents. Current strategies involve the design and synthesis of structure- and mechanism-based inhibitors of
enzymes associated with a variety of diseases. Targets
for investigation include bacterial transglycosidase, sulfotransferases, retroviral proteases, lethal factor of Bacillus anthracis, and enzymes involved in the biosynthesis
of carbohydrates essential for biological functions.
We have developed new iminocyclitols and derivatives
as inhibitors of glycosidases and glycosyltransferases
for potential treatment of inflammatory diseases. In addition, using a new strategy based on a rapid microscale
synthesis coupled with in situ high-throughput screening,
we developed new tight-binding inhibitors of anthrax
lethal factor, a sulfotransferase, and drug-resistant HIV
proteases. We also developed new reactions based on
tetrabutylammonium fluoride–mediated N- and O-alkylation and epoxide opening in aqueous solution and
used the reactions to identify potent enzyme inhibitors.
C A R B O H Y D R AT E C H E M I S T R Y A N D M O L E C U L A R
G LY C O B I O L O G Y
We continue to improve the programmable 1-pot
oligosaccharide synthesis method for convenient and
rapid preparation of oligosaccharides. So far, we have
designed approximately 600 building blocks and measured the anomeric reactivity of each building block.
Using the computer program OptiMer, developed in
our laboratory, we rapidly assembled a number of
oligosaccharides. We are using this method to define
the specificity of interactions between carbohydrates
and their receptors, with particular focus on optimization of the cancer antigen Globo H and HIV gp120
oligomannose as vaccine candidates. In collaboration
with D.R. Burton, Department of Immunology, and I.A.
Wilson, Department of Molecular Biology, we are evaluating a designed oligomannose-protein conjugate as
an antigen to elicit antibodies for neutralizing HIV gp120
and variants.
THE SCRIPPS RESEARCH INSTITUTE
95
We synthesized a series of bacterial glycolipids and
analogs and found that they are active ligands for CD
cell markers involved in activation of human natural
killer T cells. These compounds may be useful as
immunotherapeutic agents for the treatment of bacterial and viral infections, as well as cancer, and we are
elucidating the structural basis for their activity. In
collaboration with Dr. Wilson, we are determining the
structures of the complexes formed by these glycolipids
and CD1d; the results will assist in designing ligands
with improved therapeutic potential. In collaboration
with J.C. Paulson, Department of Molecular Biology,
we developed new methods for microfabrication of
saccharides on glass slides or microtiter plates for use
in high-throughput analysis of sugar-protein interactions.
PUBLICATIONS
Brigl, M., van den Elzen, P., Chen, X., Meyers, J.H., Wu, D., Wong, C.-H., Reddington, F., Illarianov, P.A., Besra, G.S., Brenner, M.B., Gumperz, J.E. Conserved
and heterogeneous lipid antigen specificities of CD1d-restricted NKT cell receptors.
J. Immunol. 176:3625, 2006.
Brik, A., Ficht, S., Wong, C.-H. Strategies for the preparation of homogenous glycoproteins. Curr. Opin. Chem., in press.
Brik, A., Wu, C.-Y., Wong, C.-H. Microtiter plate based chemistry and in situ
screening: a useful approach for enzymatic inhibitor discovery. Org. Biomol. Chem.
4:1446, 2006.
Brik, A., Yang, Y.-Y., Ficht, S., Wong, C.-H. Sugar-assisted glycopeptide ligation. J.
Am. Chem. Soc. 128:5626, 2006.
Calarese, D.A., Lee, H.-K, Huang, C.-Y., Best, M.D., Astronomo, R.D., Stanfield,
R.L., Katinger, H., Burton, D.R., Wong, C.-H., Wilson I.A. Dissection of the carbohydrate specificity of the broadly neutralizing anti-HIV-1 antibody 2G12. Proc.
Natl. Acad. Sci. U. S. A. 102:13372, 2005.
Cheng, Y.-S.E., Lo, K.-H., Hsu, H.-H., Shao, Y.-M., Yang, W.-B., Lin, C.-H.,
Wong, C.-H. Screening for HIV protease inhibitors by protection against activitymediated cytotoxicity in Escherichia coli. J. Virol. Methods 137:82, 2006.
Chuang, M.-H., Wu, M.-S., Lo, W.-L., Lin, J.-T., Wong, C.-H., Chiou, S.-H. The
antioxidant protein alkylhydroperoxide reductase of Helicobacter pylori switches
from a peroxide reductase to a molecular chaperone function. Proc. Natl. Acad.
Sci. U. S. A. 103:2552, 2006.
Fujio, M., Wu, D., Garcia-Navarro, R., Ho, D.D., Tsuji, M., Wong, C.-H. Structurebased discovery of glycolipids for CD1d-mediated NKT cell activation: tuning the
adjuvant versus immunosuppression activity. J. Am. Chem. Soc. 128:9022, 2006.
Hong, Z.-Y., Liu, L., Hsu, C.-C., Wong, C.-H. Three-step synthesis of sialic acids
and derivatives. Angew. Chem. Int. Ed., in press.
Hsu, H.-Y., Hua, K.-F., Su, Y.-C., Chu, L.-C., Su, S.-C., Chiu, H.-W., Wong, C.-H.,
Chen, S.-T., Shieh, C.-W., Yang, S.-S., Chen, Y.-M., Chao, L.K. Alkali-soluble polysaccharides of Rhizoclonium riparium alga induces IL-1 gene expression via protein kinase signaling pathways. J. Agric. Food Chem. 54:3558, 2006.
Huang, C.-Y., Thayer, D.A., Chang, A.Y., Best, M.D., Hoffmann, J., Head, S.,
Wong, C.-H. Carbohydrate microarray for profiling the antibodies interacting with
Globo H tumor antigen. Proc. Natl. Acad. Sci. U. S. A. 103:15, 2006.
Huang, K.-T., Wu, B.-C., Lin, C.-C., Luo, S.-C., Chen, C., Wong, C.-H., Lin, C.-C.
Multi-enzyme one-pot strategy for the synthesis of sialyl Lewis X-containing PSGL-1
glycopeptide. Carbohydr. Res. 341:2151, 2006.
96 CHEMISTRY
2006
Kinjo, Y., Tupin, E., Wu, D., Fujio, M., Garcia-Navarro, R., Benhnia, M.R.E.I.,
Zajonc, D.M., Ben-Menachem, G., Ainge, G.D., Painter, G.F., Khurana, A.,
Hoebe, K., Behar, S.M., Beutler, B., Wilson, I.A., Tsuji, M., Sellati, T.J., Wong,
C-H., Kronenberg, M. Natural killer T cells recognize diacylglycerol antigens from
pathogenic bacteria. Nat. Immunol. 7:978, 2006.
Lee, J.-C., Wu, C.-Y., Apon, J.V., Siuzdak, G., Wong, C.-H. Reactivity-based onepot synthesis of the tumor-associated antigen N3 minor octasaccharide for the
development of a photocleavable DIOS-MS sugar array. Angew. Chem. Int. Ed.
45:2753, 2006.
Liang, F.-S., Brik, A., Lin, Y.-C., Elder, J.H., Wong, C.-H. Epoxide opening in
water and screening in situ for rapid discovery of enzyme inhibitors in microtiter
plates. Bioorg. Med. Chem. 14:1058, 2006.
Liang, P.-H., Cheng, W.-C., Lee, Y.-L., Yu, H.-P. Wu, Y.-T., Lin, Y.-L., Wong, C.-H.
Novel five-membered iminocyclitol derivatives as selective and potent glycosidase
inhibitors: new structures for antivirals and osteoarthritis. Chembiochem 7:165, 2006.
Liang, F.-S., Greenberg, W.A., Hammond, J.A., Hoffmann, J., Head, S.R., Wong,
C.-H. Evaluation of RNA-binding specificity of aminoglycosides with DNA microarrays. Proc. Natl. Acad. Sci. U. S. A. 103:12311, 2006.
Lin, K.-I., Kao, Y.-Y., Kuo, H.-K., Yang, W.-B., Chou, A., Lin, H.-H., Yu, A.L-T.,
Wong, C.-H. Reishi polysaccharides induce immunoglobulin production through the
TLR4/TLR2-mediated induction of transcription factor Blimp-1. J. Biol. Chem.
281:24111, 2006.
Lin, Y.-C., Brik, A., de Parseval, A., Tam, K., Torbett, B.E., Wong, C.-H., Elder,
J.H. Altered gag polyprotein cleavage specificity of feline immunodeficiency
virus/human immunodeficiency virus mutant proteases as demonstrated in a cellbased expression system. J. Virol. 80:7832, 2006.
Liu, L., Bennett, C.S., Wong, C.-H. Advances in glycoprotein synthesis. Chem.
Commun. (Camb.) 21, 2006, Issue 1.
Liu, L., Hong, Z.-Y., Wong, C.-H. Convergent glycopeptide synthesis by traceless
Staudinger ligation and enzymatic coupling. Chembiochem 7:429, 2006.
Liu, H., Wong, C.-H. Characterization of a transglycosylase domain of Streptococcus pneumoniae PBP1b. Bioorg. Med. Chem. 14:7187, 2006.
Qiul, H., Gabrielsen, A., Agardh, H.E., Wan, M., Wetterholm, A., Wong, C.-H.,
Hedin, U., Swedenborg, J., Hansson, G.K., Samuelsson, B., Paulsson-Berne, G.,
Haeggstrom, J.Z. Expression of 5-lipoxygenase and leukotriene A4 hydrolase in
human atherosclerotic lesions correlates with symptoms of plaque instability. Proc.
Natl. Acad. Sci. U. S. A. 103:8161, 2006.
Sanna, M.G., Wang, S.-K., Gonzalez-Cabrera, P.J., Don, A., Marsolais, D.,
Matheu, M.P., Wei, S.H., Parker, I., Jo, E., Cheng, W.-C., Cahalan, M.D., Wong,
C.-H., Rosen, H. Enhancement of capillary leakage and restoration of lymphocyte
egress by a chiral S1P1 antagonist in vivo. Nat. Chem. Biol. 2:434, 2006.
Sawa, M., Hsu, T.-L., Itoh, T., Sugiyama, M., Hanson, S.R., Vogt, P.K., Wong,
C.-H. Glycoproteomic probes for fluorescent imaging of fucosylated glycans in vivo.
Proc. Natl. Acad. Sci. U. S. A. 103:12371, 2006.
Sawkar, A.R., Adamski-Werner, S.L., Cheng, W.-C., Wong, C.-H., Beutler, E.,
Zimmer, K.-P., Kelly, J.W. Gaucher disease-associated glucocerebrosidases show
mutation-dependent chemical chaperoning profiles. Chem. Biol. 12:1235, 2005.
Scanlan, C., Calarese, D., Lee, H.K., Blixt, O., Wong, C.-H., Wilson, I., Burton,
D., Dwek, R., Rudd P. Antibody recognition of a carbohydrate epitope: a template
for HIV vaccine design. Adv. Exp. Med. Biol. 564:7, 2005.
Shie, J.-J., Fang, J.-M., Kuo, T.-H., Kuo, C.-J., Liang, P.-H., Huang, H.-J., Wu, Y.-T.,
Jan, J.-T., Cheng, Y.-S.E., Wong, C.-H. Inhibition of the severe acute respiratory
syndrome 3CL protease by peptidomimetic α,β-unsaturated esters. Bioorg. Med.
Chem. 13:5240, 2005.
Thayer, D., Wong, C.-H. Vancomycin analogs with improved biological activity: a
combined one-pot enzymatic glycosylation and chemical diversification strategy.
Chem. Asian J., in press.
Wei, S.H., Rosen, H., Matheu, M.P., Sanna, M.G., Wang, S.-K., Jo, E., Wong, C.-H.,
Parker, I., Cahalan, M.D. Sphingosine 1-phosphate type 1 receptor agonism inhibits
transendothelial migration of medullary T cells to lymphatic sinuses. Nat. Immunol.
6:1228, 2005.
THE SCRIPPS RESEARCH INSTITUTE
Whalen, L.J., Wong, C.-H. Enzymes in organic synthesis: aldolase-mediated synthesis of iminocyclitols and novel heterocycles. Aldrichim. Acta 39:63, 2006.
Wu, C.-Y., Brik, A., Wang, S.-K., Chen, Y.-H., Wong, C.-H. Tetrabutylammonium
fluoride-mediated rapid alkylation reaction in microtiter plates for the discovery of
enzyme inhibitors in situ. Chembiochem 6:2176, 2005.
Wu, C.-Y., King, K.-Y., Kuo, C.-J., Fang, J.-M., Wu, Y.-T., Ho, M.-Y., Liao, C.-L.,
Shie, J.-J., Liang, P.-H., Wong, C.-H. Stable benzotriazole esters as mechanismbased inactivators of the severe acute respiratory syndrome 3CL protease. Chem.
Biol. 13:261, 2006.
Wu, D., Zajonc, D.M., Fujio, M., Sullivan, B.A., Kinjo, Y., Kronenberg, M., Wilson,
I.A., Wong, C.-H. Design of natural killer T cell activators: structure and function of
a microbial glycosphingolipid bound to mouse CD1d. Proc. Natl. Acad. Sci. U. S.
A. 103:3972, 2006.
Zajonc, D.M., Maricic, I., Wu, D., Halder, R., Roy, K., Wong, C.-H., Kumar, V.,
Wilson, I.A. Structural basis for CD1d presentation of a sulfatide derived from
myelin and its implications for autoimmunity. J. Exp. Med. 202:1517, 2005.