Chemistry
Click chemistry: Diverse function from a few good reactions. Work done in
the laboratories of K. Barry Sharpless, Ph.D., professor, and Valery V. Fokin,
Ph.D., associate professor.
K. Barry Sharpless, Ph.D., Professor,
Jason Hein and Jonathan Tripp,
Research Associates
CHEMISTRY
DEPAR TMENT OF
CHEMISTRY
S TA F F
2007
Kim D. Janda, Ph.D.***
Professor
Ely R. Callaway, Jr., Chair in
Chemistry
Director, Worm Institute for
Research and Medicine
K.C. Nicolaou, Ph.D.*
Chairman
Aline W. and L.S. Skaggs
Professor of Chemical Biology
Darlene Shiley Chair in
Chemistry
Jeffery W. Kelly, Ph.D.*
Lita Annenberg Hazen
Professor of Chemistry
Dean, Kellogg School of
Science and Technology
Phil Baran, Ph.D.
Associate Professor
Ramanarayanan
Krishnamurthy, Ph.D.
Associate Professor
Dale L. Boger, Ph.D.*
Richard and Alice Cramer
Professor of Chemistry
Sydney Brenner, Ph.D.
Adjunct Professor
Charles Cho, Ph.D.
Adjunct Assistant Professor
Tobin J. Dickerson, Ph.D.
Assistant Professor
Albert Eschenmoser, Ph.D.*
Professor
Sheng Ding, Ph.D.
Associate 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
Donald Hilvert, Ph.D.
Adjunct Professor
THE SCRIPPS RESEARCH INSTITUTE
Vaughn Smider, Ph.D.
Assistant Professor
Anita Wentworth, Ph.D.
Assistant Professor
Paul Wentworth, Jr., Ph.D.
Professor
Chi-Huey Wong, Ph.D.*
Professor
Ernest W. Hahn Professor
and Chair in Chemistry
Xu Wu, Ph.D.
Adjunct Assistant Professor
77
R E S E A R C H A S S O C I AT E S
Xaiver Alvarez-Mico, Ph.D.**
Institute of Chemical and
Engineering Sciences
Biopolis, Singapore
Lital Alfonta, Ph.D.**
Ben Gurion University of the
Negev
Be’er-Sheva, Israel
Rajesh Ambasudhan, Ph.D.
Manuel Amorin Lopez, Ph.D.
Yoshio Ando, Ph.D.
Deboshri Banerjee, Ph.D.
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
Evan Powers, Ph.D.
Assistant Professor
Andrew Bin Zhou, Ph.D.
Assistant Professor
Moritz Biskup, Ph.D.
S TA F F S C I E N T I S T S
Anthony Boitano, Ph.D.
Lisa Eubanks, Ph.D
Brant Boren, Ph.D.**
Exelixis, Inc.
San Diego, California
Rajesh Grover, Ph.D.
Byeong D. Song, Ph.D.
Lubica Supekova, Ph.D.
Julius Rebek, Jr., Ph.D.*
Professor
Director, The Skaggs Institute
for Chemical Biology
Wen Xiong, Ph.D.
I N S T R U M E N TAT I O N
Ed Roberts, Ph.D.
Professor
Floyd E. Romesberg, Ph.D.
Assistant Professor
William R. Roush,
Ph.D.*****
Professor
Associate Dean, Kellogg
School of Science and
Technology
Executive Director of
Medicinal Chemistry,
Scripps Florida
Peter G. Schultz, Ph.D.*
Professor
Scripps Family Chair
Hayato Ishikawa, Ph.D.**
Assistant Professor
Tokyo University of Science
Tokyo, Japan
K. Barry Sharpless, Ph.D.*
Professor
W.M. Keck Professor of
Chemistry
Andrew Brogan, Ph.D.**
RTI Health Solutions
Research Triangle Park,
North Carolina
Paul Bulger, Ph.D.**
Merck & Co., Inc.
Rahway, New Jersey
FACILITIES
Raj K. Chadha, Ph.D.
Director, X-ray
Crystallography Facility
Kevin Bunker, Ph.D.**
Pfizer Inc.
La Jolla, California
Antonio Burtoloso, Ph.D.
Dee H. Huang, Ph.D.
Director, Nuclear Magnetic
Resonance Facility
Mark Bushey, Ph.D.
Gary E. Siuzdak, Ph.D.
Director, Mass Spectrometry
Facility
Petr Capek, Ph.D.
Darren Bykowski, Ph.D.
Katerina Capkova, Ph.D.
Arani Chanda, Ph.D.
SENIOR RESEARCH
Inkyu Hwang, Ph.D.
Assistant Professor
Clay Bennett, Ph.D.
A S S O C I AT E S
Ashraf Brik, Ph.D.**
Ben Gurion University of the
Negev
Be’er-Sheva, Israel
Gunnar Kaufmann, Ph.D.
Sukbok Chang, Ph.D.**
Korea Advanced Institute of
Science and Technology
Daejeon, South Korea
Ke Chen, Ph.D.
Shuo Chen, Ph.D.**
Ohio University
Athens, Ohio
78 CHEMISTRY
Govardhan Cherukupalli,
Ph.D.
2007
THE SCRIPPS RESEARCH INSTITUTE
Nil Emre, Ph.D.**
Millipore
Temecula, California
Neill Gingles, Ph.D.
Jaroslaw Kalisiak, Ph.D.
Neil Grimster, Ph.D.
Kwang Mi Kim, Ph.D.
Cyrine Ezzili, Ph.D.
Jan Grunewald, Ph.D.
Mihyong Kim, Ph.D.
Raffaella Faraoni, Ph.D.**
Ambit Biosciences
San Diego, California
Jiantao Guo, Ph.D.
F. Scott Kimball, Ph.D.
Richard Guy, Ph.D.
Simon Ficht, Ph.D.
Akiyuki Hamasaki, Ph.D.**
UNITECH Co., Ltd.
Chiba, Japan
Ravinder Reddy Kondreddi,
Ph.D.**
Novartis, Inc.
Keppel Towers, Singapore
Jodie Chin, Ph.D.
Charles Cho, Ph.D.
So-Hye Cho, Ph.D.
Sungwook Choi, Ph.D.
Scott Cockroft, Ph.D.
David Colby, Ph.D.
Ted Foss, Ph.D.**
U.S. Genomics, Inc.
Woburn, Massachusetts
Keith Korthals, Ph.D.
Masaki Handa, Ph.D.
Larisa Krasnova, Ph.D.
Kevin Cole, Ph.D
Jeromy Cottell, Ph.D.**
Gilead Science, Inc.
Foster City, California
Christine Crane, Ph.D.
James Crawford, Ph.D.**
AstraZeneca
Cheshire, England
Matthew Cremeens, Ph.D.
Jesse Dambacher, Ph.D.**
Infineum
Linden, New Jersey
Etzer Darout, Ph.D.
Sandra De Lamo Marin,
Ph.D. †
Joseph Rodolph Fotsing,
Ph.D.
Bozena Frackowiak, Ph.D.
Graeme Freestone, Ph.D.
Yu Fu, Ph.D.
Jim Fuchs, Ph.D.**
Ohio State University
Columbus, Ohio
Amelia Fuller, Ph.D.
Doug Fowler, Ph.D.**
University of Washington
Seattle, Washington
Jianmin Gao, Ph.D.
Yuanjun He, Ph.D.
Tsun-Hun Kuo, Ph.D.
Jason Hein, Ph.D
Rodriguez Marcos
Hernandez, Ph.D.
Par Holmberg, Ph.D.
Zhangyong Hong, Ph.D.
Tamara Hopkins, Ph.D.
Tsui-Ling Hsu, Ph.D.**
Genomics Research Center
Academia Sinica
Taipei, Taiwan
Fang Hu, Ph.D.
Xiaoyi Hu, Ph.D.
Jane Kuzelka, Ph.D.**
Calmune, Corp.
San Diego, California
Andreas Lanver, Ph.D.**
BASF AG
Ludwigshafen, Germany
Brian Lawhorn, Ph.D.**
GlaxoSmithKline
King of Prussia, Pennsylvania
Jae Wook Lee, Ph.D.
Jinq-Chyi Lee, Ph.D.
Jongkook Lee, Ph.D.
Judith Denery, Ph.D.
Muyun Gao**
Genomics Institute of the
Novartis Research
Foundation
San Diego, California
Ross Denton, Ph.D.
Haibo Ge, Ph.D.
Benjamin Hutchins, Ph.D.
Sejin Lee, Ph.D.
Caroline Desponts, Ph.D.
Savvas Georgiades, Ph.D.
Der-Ren Hwang, Ph.D.
Lucas Leman, Ph.D.
Deguo Du, Ph.D.
Ola Ghoneim, Ph.D.
Giltae Hwang, Ph.D.
Alexandre Lemire, Ph.D.
Anna Dubrovska, Ph.D.
Nathan Gianneschi, Ph.D.
Michael Jahnz, Ph.D.
Edward Lemke, Ph.D.
Joshua Dunetz, Ph.D.
Romelo Gibe, Ph.D.**
Institute of Chemical and
Engineering Sciences
Biopolis, Singapore
Rong Jiang, Ph.D.
Achim Lenzin, Ph.D. †
Steven Johnson, Ph.D.**
Department of Molecular
Biology, Scripps Research
Christophe Letondor, Ph.D.
Chuang-Chuang Li, Ph.D
Hiroyuki Kakei, Ph.D.
Fangzheng Li, Ph.D.
Amy DeBaillie, Ph.D.
Kyle Eastman, Ph.D.
David Edmonds, Ph.D.
Jan Elsner, Ph.D.
Christina Gil-Lamaignere,
Ph.D.
JongSeok Lee, Ph.D.
Zheng-Zheng Huang, Ph.D.**
Department of Molecular
Biology, Scripps Research
Ki-Bum Lee, Ph.D.
Kooyeon Lee, Ph.D. †
CHEMISTRY
2007
THE SCRIPPS RESEARCH INSTITUTE
Hongming Li, Ph.D.
Adam Morgan, Ph.D. †
Richard Payne, Ph.D.
David Shaw, Ph.D.
Ke Li, Ph.D.
Tingwei Mu, Ph.D.
Xuemei Peng, Ph.D.
Michael Smolinski, Ph.D.
Pi-Hui Liang, Ph.D.
Mridul Mukherji, Ph.D. †
Murali Peram Surakattula,
Ph.D.
Alex Shaginian, Ph.D.
Yeon-Hee Lim, Ph.D.
Kenichiro Nagai, Ph.D.**
Kitasato University
Tokyo, Japan
Roshan Perera, Ph.D.
Tongxiang Lin, Ph.D.
Suresh Pitram, Ph.D.
Troy Lister, Ph.D.
Chris Liu, Ph.D.
Yuya Nakai, Ph.D.
Joonwoo Nam, Ph.D.
Lei Liu, Ph.D.**
Tsinghua University
Beijing, China
Tae-gyu Nam, Ph.D.
Wenshe Liu, Ph.D.
Daniel Nicoletti, Ph.D. †
Ying (Cindy) Liu, Ph.D.**
Catalyst Biosciences, Inc.
South San Francisco,
California
George Nora, Ph.D.
Hongzheng (Eric) Ma,
Ph.D.**
Pioneer Hi-Bred
International, Inc.
Johnston, Iowa
Nello Mainolfi, Ph.D.**
Novartis Pharmaceuticals
Cambridge, Massachusetts
Andrew Nguyen, M.D., Ph.D.
Michael Ober, Ph.D.**
DuPont Virginia
Richmond, Virginia
Barun Okram, Ph.D.**
Genomics Institute of the
Novartis Research
Foundation
San Diego, California
Alexander Mayorov, Ph.D.
Laura McAllister, Ph.D.**
Novartis
Horsham, England
Kathleen McKenzie, Ph.D. †
Gopi-Kumar Mittapalli,
Ph.D.**
Immusol, Inc.
San Diego, California
Yan Shi, Ph.D.
Rituparna Sinha Roy, Ph.D.
Xinyi Song, Ph.D.
Tülay Polat, Ph.D.**
Abraxis Bioscience, Inc.
Los Angeles, California
Simon Stamm, Ph.D.
Praveen Rao, Ph.D.
Antonia Stepan, Ph.D.
Daniela Radu, Ph.D.
James Stover, Ph.D.
Ronald Rahaim, Ph.D.
Shun Su, Ph.D.
Fatima Rivas, Ph.D.
Daniel Summerer, Ph.D.**
Febit Biomed GmbH
Heidelberg, Germany
F. Anthony Romero, Ph.D.**
Merck Research Laboratories
Rahway, New Jersey
Joshua Roth, Ph.D.
Troy Ryba, Ph.D.
Yazmin Osornio, Ph.D.
Youngha Ryu, Ph.D.
Doron Pappo, Ph.D.**
Institute of Chemical and
Engineering Sciences
Biopolis, Singapore
Vasudeva Naidu Sagi, Ph.D.
Sebastian Steiniger, Ph.D.
Takahiro Suzuki, Ph.D.**
Institute of Chemical and
Engineering Sciences
Biopolis, Singapore
Leo Takaoka, Ph.D.**
Schering-Plough Research
Institute
Cambridge, Massachusetts
Alain Salameh, Ph.D. †
Shinobu Takizawa, Ph.D.
Antonio Sanchez-Ruiz, Ph.D.
Junguk Park, Ph.D.
Adam Talbot, Ph.D.
Nicholas Salzameda, Ph.D.
Laxman Pasunoori, Ph.D. †
Yoshikazu Sasaki, Ph.D.
Johan Paulsson, Ph.D.
Stefan Schiller, Ph.D.
Charles Melancon, Ph.D.
Weijun Shen, Ph.D.
Jonathan Pokorski, Ph.D.
Christian Olsen, Ph.D.
Shigeo Matsuda, Ph.D.
Michael Maue, Ph.D. †
Ramulu Poddutoori, Ph.D.
Goran Petrovic, Ph.D.**
Senomyx, Inc.
San Diego, California
Ana Montero, Ph.D.
Damien Polet, Ph.D.**
Institute of Chemical and
Engineering Sciences
Biopolis, Singapore
Miguel Morales, Ph.D.
Guido Pontremoli, Ph.D. †
79
Laura Segatori, Ph.D.**
Rice University
Houston, Texas
Yefeng Tang, Ph.D.
Eric Tippmann, Ph.D.**
Cardiff University
London, England
Mariola Tortosa, Ph.D.
Edward Sessions, Jr., Ph.D.
Vincent Trepanier, Ph.D
Shigeki Seto, Ph.D.
Jonathan Tripp, Ph.D.
Mary Sever, Ph.D.
Craig Turner, Ph.D. †
80 CHEMISTRY
2007
Meng-Lin Tsao, Ph.D.**
University of California
Merced, California
Ryu Yamasaki, Ph.D.**
Tokyo University of Science
Tokyo, Japan
Andrew Udit, Ph.D.
Taiki Umezawa, Ph.D.
Lei Yao, Ph.D.**
Harvard Medical School
Boston, Massachusetts
Kenji Usui, Ph.D.
Ura Yasuyuki, Ph.D.
Carlos Valdez, Ph.D.
Zhanqian Yu, Ph.D.
Bo Wang, Ph.D. †
Hongjun Zhang, Ph.D.
Hong Wang, Ph.D.**
Miami University
Oxford, Ohio
Jian Wang, Ph.D.
THE SCRIPPS RESEARCH INSTITUTE
Masakazu Imamura, Ph.D.
Astellas Pharmaceutical Inc.,
Co., Ltd.
Ushiku-shi, Japan
Qisheng Zhang, Ph.D.**
University of North Carolina
Chapel Hill, North Carolina
Michael Meijler, Ph.D.
Ben Gurion University of the
Negev
Be’er-Sheeva, Israel
Poul Nielsen, Ph.D.
University of Southern
Denmark
Odense M, Denmark
Masakazu Sugiyama, Ph.D.**
Ajinomoto Co., Inc.
Kawasaki, Japan
Heyue Henry Zhou, Ph.D.
Lin Wang, Ph.D.
Xiuwen Zhu, Ph.D.
Weidong Wang, Ph.D.
Takayoshi Suzuki, Ph.D.
Nagoya City University
Nagoya, Japan
Joerg Zimmermann, Ph.D.
Xiaolong Wang, Ph.D.**
Pfizer Inc.
La Jolla, California
Caterina Zoni, Ph.D. †
Timo Weide, Ph.D.
VISITING
I N V E S T I G AT O R S
Albert Willis, III, Ph.D.
Douglass Wu, Ph.D.**
Optimer Pharmaceuticals, Inc.
San Diego, California
Tao Wu, Ph.D.
Heiko Wurdak, Ph.D.
Mohammad Al-Sayah,
Ph.D.**
American University of
Sharjah
Sharjah, United Arab Emirates
Masakazu Fujio, Ph.D.**
Mitsubishi Pharma
Corporation
Yokohama, Japan
Junichiro Yamaguchi, Ph.D.
Shin-Ichi Takanashi, Ph.D.**
Mitsubishi
Kawasaki, Japan
Ken-ichi Takao, Ph.D.**
Keio University
Yokohama, Japan
Yoshiyuki Yoneda, Ph.D.
Daiichi Pharmaceutical Co.,
Ltd.
Tokyo, Japan
S C I E N T I F I C A S S O C I AT E S
Jon Ashley
Keisuke Fukuchi, Ph.D.
Sankyo Co., Ltd.
Tokyo, Japan
Gina Dendle
Yoshiyuki Hari, Ph.D.
Nagoya City University
Nagoya, Japan
Jonathan Zhu, Ph.D.
Jian Xie, Ph.D.
Yue Xu, Ph.D.
Biology
** Appointment completed; new
location shown
Kuniyuki Kishikawa, Ph.D.
Kyowa Hakko Kogyo Co., Ltd.
Sunto-gun, Japan
Xuejun Zhang, Ph.D.
Jiangyun Wang, Ph.D.
Amie Williams, Ph.D.**
GlaxoSmithKline
Durham, North Carolina
Skaggs Institute for Chemical
*** 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
Yingchao Zhang, Ph.D.
Matthew Whiting, Ph.D.**
GlaxoSmithKline
Stevenage, England
* Joint appointment in The
Christine Hernandez, Ph.D.
University of the Philippines,
Diliman
Quezon City, Philippines
Suresh Mahajan, Ph.D.
***** Scripps Florida
†
Appointment completed
CHEMISTRY
2007
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 bestqualified 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 Chadha (x-ray
A
THE SCRIPPS RESEARCH INSTITUTE
81
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 2006, the Institute for Scientific Information ranked 3 members of our department as highly
cited researchers (in the top 100 worldwide).
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 California-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 to explore chemical synthesis and chemical biology, with a focus on the
total synthesis of new anticancer agents, antibiotics,
marine-derived neurotoxins, antimalarial compounds,
antifeedant agents, and other biologically active natural
and designed molecules.
Julius Rebek and his group devise biomimetic receptors, including molecules that bind neurotransmitters and
membrane components, for studies in molecular recognition. Larger host receptors surround 3 or more molecular guests and act as chambers where the chemical
reactions of the guests are accelerated. Members of the
group also synthesize small molecules that act as protein helix mimetics for pharmaceutical applications.
Peter Schultz and researchers in his laboratory continue to expand the number of genetically encoded amino
acids to include fluorescent, photocaged, metal-binding,
chemically reactive, and posttranslationally modified
amino acids. These scientists have also adapted this
technology to mammalian cells and are using these
82 CHEMISTRY
2007
tools in a number of basic and applied problems in cell
biology. In addition, members of the group 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 and small molecules that affect a number
of physiologic and disease processes.
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. Members of this group
also developed new probes to study glycosyltransferases
and the roles of these enzymes in cancer.
Researchers in Dale Boger’s laboratory continue their
work on chemical synthesis; combinatorial chemistry;
heterocycle synthesis; anticancer agents, such as vinblastine, cytostatin, chlorofusion, and yatakemycin; and antibiotics, such as vancomycin, teicoplanin, and ramoplanin.
Scientists in Kim Janda’s laboratory focus on the
impact of organic chemistry in specific biological systems.
The targeted programs span a wide range of interests from
immunopharmacotherapy to biological and chemical warfare to filarial infections such as “river blindness” to
quorum sensing in bacteria. Recent achievements include
in vivo detection of antagonists of botulinum neurotoxins, the development of a cyclic peptide that homes to
cancer cells as a drug delivery module, and the discovery of antibodies that can degrade the active component
of marijuana.
M. Reza Ghadiri and his group are making important
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, members of the group
continue to make novel contributions in several ongoing
basic research endeavors, such as designing biosensors,
developing molecular computation, designing self-reproducing systems, understanding the origins of life, and
creating 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 laboratory also develop and investigate new organic and
THE SCRIPPS RESEARCH INSTITUTE
organometallic reactions and use these reactions to synthesize biologically active compounds.
Jeff Kelly and his group are exploring the interface
between chemistry, biology, and medicine. The aim of
their projects is to understand the physical and biological
basis of protein folding and the misfolding and aggregation
processes that lead to age-associated neurodegenerative
diseases. This information is used to develop new smallmolecule therapeutic strategies for a variety of neurodegenerative diseases.
Anita Wentworth and the researchers in her laboratory are investigating the chemical basis of complex
disease states and are synthesizing peptide- and small
molecule–based therapeutic agents. These scientists
focus on disease states in which inflammation and reactive oxygen species are prominent, 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 using 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.
Phil Baran and his group recently developed extremely
concise chemical solutions to the synthetic challenges
posed by numerous families of marine natural products,
including sceptrin, ageliferin, chartelline, haouamine, welwitindolinone, and the stephacidins. These syntheses are
characterized by striking brevity, new biosynthetic postulates, the invention of new methods, and a minimum
use or complete absence of protecting groups and superfluous oxidation-state manipulations.
The Frontiers in Chemistry Lecturers (18th Annual
Symposium) for the 2006–2007 academic year were
Brian M. Stoltz, California Institute of Technology; Dean
Toste, University of California, Berkeley; Colin Nuckolls,
Columbia University; and Eric T. Kool, Staford University.
John Montgomery, University of Michigan, also visited
Scripps as the 2006 Bristol-Myers Squibb Lecturer.
CHEMISTRY
2007
THE SCRIPPS RESEARCH INSTITUTE
83
INVESTIGATORS’ R EPORTS
Practical Total Synthesis of
Natural Products
P.S. Baran, M.B. Biskup, N.Z. Burns, K. Chen,
M.P. DeMartino, K.J. Eastman, S.N. Georgiades,
C.A. Guerrero, B.D. Hafensteiner, P.J. Krawczuk, C. Li,
K. Li, D.W. Lin, J.W. Lockner, T.J. Maimone, M.K.-D. Maue,
T.R. Newhouse, D.P. O’Malley, J.M. Richter, I.B. Seiple,
R.A. Shenvi, J. Shi, S. Su, B. Whitefield, J. Yamaguchi
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
(1) the anticancer agents stephacidin A and B and
avrainvillamide; (2) the antibacterial agents sceptrin
and ageliferin; (3) members of the bioactive fischerindole, hapalindole, and welwitindolinone indole alkaloid
family; (4) the anticancer agent haouamine A; and (5)
the structurally exotic marine alkaloid chartelline C.
Current natural product targets (Fig. 2) include stylissadine A and sarcodonin.
F
F i g . 1 . Recently completed total syntheses.
PUBLICATIONS
Baran, P.S., DeMartino, M.P. Intermolecular oxidative enolate heterocoupling.
Angew. Chem. Int. Ed. 45:7083, 2006.
Baran, P.S., Maimone, T.J., Richter, J.M. Total synthesis of marine natural products without using protecting groups. Nature 446:404, 2007.
Baran, P.S., Shenvi, R.A. Total synthesis of (±)-chartelline C. J. Am. Chem. Soc.
128:14028, 2006.
Baran, P.S., Shenvi, R.A., Nguyen, S.A. One-step synthesis of 4,5-disubstituted
pyrimidines using commercially available and inexpensive reagents. Heterocycles
70:581, 2006.
84 CHEMISTRY
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THE SCRIPPS RESEARCH INSTITUTE
to define the structure-function relationships of natural
or designed organic agents.
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.
F i g . 2 . Recent natural product targets.
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
Maimone, T.J., Baran, P.S. Modern synthetic efforts toward biologically active terpenes. Nat. Chem. Biol. 3:396, 2007.
O’Malley, D.P., Li, K., Maue, M., Zografos, A.L., Baran, P.S. Total synthesis of
dimeric pyrrole-imidazole alkaloids: sceptrin, ageliferin, nagelamide E, oxysceptrin,
nakamuric acid, and the axinellamine carbon skeleton [published correction appears
in J. Am. Chem. Soc. 129:7702, 2007]. J. Am. Chem. Soc. 129:4762, 2007.
Synthetic and Bioorganic
Chemistry
D.L. Boger, R. Clark, D. Colby, J. Cottell, C. Crane,
J. DeMartino, J. Elsner, C. Ezzili, J. Fuchs, J. Garfunkle,
H. Ge, N. Haq, I. Hwang, H. Ishikawa, W. Jin, R. Jones,
H. Kakei, D. Kato, F.S. Kimball, B. Lawhorn, S. Lee, C. Liu,
K. MacMillan, J. Nam, P. Patel, T. Rayl, W. Robertson,
A. Romero, Y. Sasaki, M. Schnermann, A. Shaginian, C. Slown,
S. Stamm, J. Stover, L. Takaoka, S. Takizawa, H. Tao,
M. Tichenor, J. Trzupek, L. Whiby, J. Xie, Y. Zhang, A. Zuhl
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 DNAagent interactions, and the chemistry of antitumor antibiotics. We place a special emphasis on investigations
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 duo-
CHEMISTRY
2007
THE SCRIPPS RESEARCH INSTITUTE
85
F i g . 3 . Additional recent total syntheses.
F i g . 2 . Recent total syntheses.
carmycins that contribute to the sequence-selective
DNA alkylation properties of these agents have resulted
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.
86 CHEMISTRY
2007
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
Clark, R.C., Pfeiffer, S.S., Boger, D.L. Diastereoselective Diels-Alder reactions of
N-sulfonyl-1-aza-1,3-butadienes with optically active enol ethers: an asymmetric variant of the 1-azadiene Diels-Alder reaction. J. Am. Chem. Soc. 128:2587, 2006.
Crowley, B.M., Boger, D.L. Total synthesis and evaluation of [ψ[CH2NH]Tpg4]vancomycin aglycon: reengineering vancomycin for dual D-Ala-D-Ala and D-Ala-D-Lac
binding. J. Am. Chem. Soc. 128:2885, 2006.
DeMartino, J.K., Hwang, I., Xu, L., Wilson, I.A., Boger, D.L. Discovery of a potent,
nonpolyglutamatable inhibitor of glycinamide ribonucleotide transformylase. J. Med.
Chem. 49:2998, 2006.
THE SCRIPPS RESEARCH INSTITUTE
Worm Institute for Research
and Medicine
T.J. Dickerson, J. Denery, L. Eubanks, A. Hoyt, S. Mahajan,
A. Moreno, J. Park, N. Salzameda, K.D. Janda
lthough rare in the United States, in many other
parts of the world, infections caused by filarial
worms (nematodes) afflict hundreds of millions
of people with painful, disfiguring, and debilitating
diseases, including onchocerciasis, lymphatic filariasis,
and dracunculiasis. Through the generous donation of
John J. Moores, the Worm Institute for Research and
Medicine was established to investigate the basic science needed for the development of diagnostic tools to
efficiently detect the presence of parasitic worms in a
person’s body. These new diagnostic tests will be a
powerful tool for public health practitioners and may
ultimately lead to unique approaches for the treatment
of filiarial infections throughout the world.
Onchocerciasis, or river blindness, is caused by the
nematode Onchocerca volvulus (Fig. 1). In severe infec-
A
Elliott, G.I., Fuchs, J.R., Blagg, B.S.J., Ishikawa, H., Tao, H., Yuan, Z.-Q., Boger,
D.L. Intramolecular Diels-Alder/1,3-dipolar cycloaddition cascade of 1,3,4-oxadiazoles. J. Am. Chem. Soc. 128:10589, 2006.
Elliott, G.I., Velcicky, J., Ishikawa, H., Li, Y., Boger, D.L. Total synthesis of (–)and ent-(+)-vindorosine: tandem intramolecular Diels-Alder/1,3-dipolar cycloaddition of 1,3,4-oxadiazoles. Angew. Chem. Int. Ed. 45:620, 2006.
Fang, X., Tiyanont, K., Zhang, Y., Wanner, J., Boger, D., Walker, S. The mechanism of action of ramoplanin and enduracidin, Mol. Biosyst. 2:69, 2006.
Hamasaki, A., Ducray, R., Boger, D.L. Two novel 1,2,4,5-tetrazines that participate in inverse electron demand Diels-Alder reactions with an unexpected regioselectivity. J. Org. Chem. 71:185, 2006.
Ishikawa, H., Elliott, G.I., Velcicky, J., Choi, Y., Boger, D.L. Total synthesis of (–)and ent-(+)-vindoline and related alkaloids. J. Am. Chem. Soc. 128:10596, 2006.
Lawhorn, B.G., Boga, S.B., Wolkenberg, S.E., Boger, D.L. Total synthesis of cytostatin. Heterocycles 70:65, 2006.
Lawhorn, B.G., Boga, S.B., Wolkenberg, S.E., Colby, D.A., Gauss, C.-M., Swingle,
M.R., Amable, L., Honkanen, R.E., Boger, D.L. Total synthesis of cytostatin, its
C10-C11 diastereomers and additional key analogues: impact on PP2A inhibition.
J. Am. Chem. Soc. 128:16720, 2006.
Romero, F.A., Hwang, I., Boger, D.L. Delineation of a fundamental α-ketoheterocycle substituent effect for use in the design of enzyme inhibitors. J. Am. Chem. Soc.
128:14004, 2006.
Schnermann, M.J., Romero, F.A., Hwang, I., Nakamaru-Ogiso, E., Yagi, T., Boger,
D.L. Total synthesis of piericidin A1 and B1 and key analogues. J. Am. Chem. Soc.
128:11799, 2006.
Tichenor, M.S., Trzupek, J.D., Kastrinsky, D.B., Shiga, F., Hwang, I., Boger, D.L.
Asymmetric total synthesis of (+)- and ent-(–)-yatakemycin and duocarmycin SA:
evaluation of yatakemycin key partial structures and its unnatural enantiomer. J.
Am. Chem. Soc. 128:15683, 2006.
Trzupek, J.D., Gottesfeld, J.M., Boger, D.L. Alkylation of duplex DNA in nucleosome
core particles by duocarmycin SA and yatakemycin. Nat. Chem. Biol. 2:79, 2006.
F i g . 1 . A live female O volvulus worm extracted from a human
nodule.
tions, the worms can cause lesions and massive inflammation in the eyes, ultimately leading to blindness.
Onchocerciasis is a major problem in many African
nations, where 99% of all cases occur. Although much
effort has been devoted to regional programs to reduce
the risk for this disease, significant obstacles, including improvement of current diagnostic methods, must
CHEMISTRY
2007
be overcome before eradication is successful. Great
strides in detection have been made by using various
assays, including skin biopsies, detection of O volvulus
DNA, and antibody-based strategies for detecting specific O volvulus proteins. However, none of the current
methods can be used to detect sexually mature worms.
Major sperm protein (MSP) is the main component
of nematode sperm and is critical for sperm motility.
Because MSP is a unique feature of nematode reproduction, we propose that it is a potential target for diagnosis
of nematode infections. In addition, antibody-mediated
disruption of MSP polymerization may inhibit nematode
reproduction. During the past year, we successfully
cloned and expressed MSP from O volvulus and confirmed the dimeric character of the protein in solution.
This recombinant MSP has been used both in screens
of phage-displayed combinatorial antibody libraries and
in traditional immunization procedures to isolate antibody reagents that can be used to detect MSP in the
serum of patients with onchocerciasis.
Using serum samples collected from individuals of
the Northwest Province of Cameroon, we determined
that MSP is indeed released from the worm and that
the protein is recognized by the immune system, resulting in significant antibody titers against MSP. We are
optimizing the assay conditions to detect MSP directly
by using our monoclonal antibodies.
Chemical and Functional
Genomic Approaches to
Regenerative Medicine
S. Ding, R. Abu-Jarour, R. Ambasudhan, R. Coleman,
C. Desponts, H.S. Hahm, S. Hilcove, J. Hsu, T. Lin, Y. Shi,
W. Xiong, Y. Xu, X. Zhu
ecent advances in stem cell biology may make
possible new approaches for the treatment of a
number of illnesses, 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 dif-
R
THE SCRIPPS RESEARCH INSTITUTE
87
ferentiation of the cells, and a better understanding of
the signaling pathways that control the fate of the cells.
Equipped with a high-throughput screening platform
and large arrayed molecular libraries—combinatorial
chemical libraries, genome-scale cDNA libraries, and
small interfering RNA libraries—we are developing and
integrating chemical and functional genomic tools to
study stem cell biology and regeneration. We screen
these libraries to identify and further characterize small
molecules and genes that can control stem cell fate in
various systems, including (1) self-renewal regulation of
embryonic and adult stem cells; (2) directed and stepwise differentiation of embryonic stem cells toward neuronal, cardiac, and pancreatic lineages; (3) directed
neuronal differentiation and subtype neuronal specification of human and rodent neural stem cells; (4) cellular plasticity and reprogramming of lineage-restricted
somatic cells to more primitive precursor cells; (5) functional proliferation of adult cardiomyocytes and pancreatic beta cells; (6) developmental signaling pathways
and epigenetic mechanisms (histone and DNA de/methylation); and (7) development of new technologies for
stem cell derivation and gene targeting.
In addition, we are characterizing the molecular
mechanism of these identified small molecules and
genes by using various approaches, including detailed
investigations of structure-activity relationship, affinity
chromatography for target identification, transcriptome
profiling, proteomics analysis, chemical/genetic epistasis,
and biochemical and functional assays in vitro and in
vivo. So far, we have identified and are characterizing
functional small molecules and/or genes in each of the
distinct biological processes previously mentioned that
involve regulation of stem/progenitor cells.
More recent examples include identification and
characterization of distinct small molecules for selfrenewal of human embryonic stem cells and clonal
expansion/survival; dopaminergic neuron specification
from mouse embryonic stem cells; derivation of rat
embryonic stem cells; reprogramming of neural cells
to a pluripotent state; definitive endoderm and pancreatic induction; chemically defined monolayer conditions for self-renewal of embryonic stem cells and
their directed differentiation to cardiac lineages; proliferation of human beta cells; and regulating Wnt signaling. 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.
88 CHEMISTRY
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THE SCRIPPS RESEARCH INSTITUTE
PUBLICATIONS
Chen, S., Do, J.-T., Zhang, Q., Yao, S., Yan, F., Peters, E.C., Schöler, H.R.,
Schultz, P.G., Ding, S. Self-renewal of embryonic stem cells by a small molecule.
Proc. Natl. Acad. Sci. U. S. A. 103:17266, 2006.
Emre, N., Coleman, R., Ding, S. A chemical approach to stem cell biology. Curr.
Opin. Chem. Biol. 11:252, 2007.
Yao, S., Chen, S., Clark, J., Hao, E., Beattie, G.M., Hayek, A., Ding, S. Long-term
self-renewal and directed differentiations of human embryonic stem cells in chemically defined conditions. Proc. Natl. Acad. Sci. U. S. A. 103:6907, 2006.
Zhang, Q., Major, M.B., Takanashi, S., Camp, N.D., Nishiya, N., Peters, E.C.,
Ginsberg, M.H., Jian, X., Randazzo, P.A., Schultz, P.G., Moon, R.T., Ding, S.
Small-molecule synergist of the Wnt/β-catenin signaling pathway. Proc. Natl. Acad.
Sci. U. S. A. 104:7444, 2007.
Zhao, Y., Ding, S. A high-throughput siRNA library screen identifies osteogenic
suppressors in human mesenchymal stem cells. Proc. Natl. Acad. Sci. U. S. A.
104:9673, 2007.
Chemical Etiology of the
Structure of Nucleic Acids
A. Eschenmoser, R. Krishnamurthy, G.K. Mittapalli,
R.R. Kondreddi, Y. Osornio, M. Guerrero, J. Xie
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 5 - A M I N O P Y R I M I D I N E – TA G G E D
F i g . 1 . Top, Formulas of 5-aminopyrimidine heterocycles. Bottom,
Also shown, as a representative example, is the 5-amino-2,4-dioxo–
tagged oligomer containing alternating Asp and Glu residues.
oxo-amino-5-aminopyrimidine members, (APON) and
(APNO), experiments indicate that 1 of the 2 isomeric
oxo-aminopyrimidine bases can exist as its NH-3 tautomer to accommodate base pairing.
The most accessible chemical property that parallels the incongruity of pairing behavior of the 2,4-disubstituted triazines and 5-aminopyrimidines relative to
the standard of the canonical nucleobases is the pKa
value (Fig. 2). The juxtaposition points to a correlation
OLIGODIPEPTIDE BACKBONES
We continued our studies on the self- and crosspairing properties of triazine- and 5-aminopyrimidine–
tagged oligodipeptides consisting of alternating glutamic
(Glu) and aspartic acid (Asp) residues (Fig. 1). We
observed that the homododecamer tagged with the
2,4-dioxopyrimidine nucleus (APOO) cross-paired strongly
with complementary DNA sequences, whereas the
analogous homododecamer tagged with the 2,4-diaminopyrimidine nucleus (APNN) cross-paired weakly. This
finding was exactly the opposite of that observed in the
corresponding oligomers tagged with the complementary 2,4-dioxotrizines (TOO) and 2,4-diaminotriazines
(TNN) as nucleobases, which we had studied earlier.
Therefore, not surprisingly, the intrasystem combination
of the two 5-aminopyrimidine–tagged homo-oligodipeptide dodecamers AspGlu(APO,O)12 and AspGlu(APN,N)12
results in only very weak intrasystem pairing. The intersystem combination of 2 complementary homobasic
oligo-(Asp-Glu)-dipeptide dodecamers, one tagged with
the 2,4-dioxopyrimidine nucleus and the other with the
2,4-diaminotriazine nucleus had reasonably strong intersystem cross-pairing, whereas the inverse combination
showed no pairing at all. In the case of the 2 isomeric
F i g . 2 . Correlation between base-pairing strength with ∆-pK a
values of pairs of complementary bases in aqueous solution at neutral
pH. Reprinted with permission from Mittapalli, G.K., Osornio, Y.M.,
Guerrero, M.A., Kondreddi, R.R., Krishnamurthy, R., Eschenmoser, A.
Mapping the landscape of potentially primordial informational oligomers: oligodipeptides tagged with 2,4-disubstituted 5-aminopyrimidines as recognition elements. Angew. Chem. Int. Ed. 46:2478, 2007.
between differences in pKa values (∆-pKa) of pairs of
complementary bases and the pairing strength of the
bases: the smaller the ∆-pKa value of a pair of complementary 2,4-dioxo and 2,4-diamino pairing partners (compared with the standard difference of about
CHEMISTRY
2007
5 pKa units for the canonical pair of bases), the weaker
is the pairing (in aqueous solution at neutral pH). The
trend of this correlation points in the opposite direction
of the one described in the literature for ∆-pKa values
of the relative strengths of hydrogen bonds in nonaqueous media.
Our observations indicate that 2,4-disubstituted1,3,5-triazines and 2,4-disubstituted-5-aminopyrimidines,
2 families of heterocycles deemed to be of generational simplicity comparable to that of the canonical
nucleobases, yet offering chemically wider opportunities for backbone tagging, are functionally inferior to
the family of Watson-Crick bases because of reasons
that seem intrinsically chemical. The findings provide
a chemical illustration of the view that the canonical
nucleobases represent a functional optimum in informational base pairing in aqueous solution.
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
2 ′ g 3 ′ - P H O S P H O D I E S T E R – L I N K E D G LY C E R I C A C I D
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89
oligomer synthesis of 2,4-dioxo-5-aminopyrimidine
(5-aminouracil)–tagged nucleic acid with a glyceric
acid backbone. We have made the oligomer containing
six 5-aminouracil units and have begun to explore its
base-pairing properties. Preliminary results validate our
expectations; we found a strong base pairing between
this oligomer and polydeoxyadenosine.
PUBLICATIONS
Egli, M., Pallan, P.S., Pattanayek, R., Wilds, C.J., Lubini, P., Minasov, G., Dobler,
M., Leumann, C.J., Eschenmoser, A. Crystal structure of homo-DNA and Nature’s
choice of pentose over hexose in the genetic system. J. Am. Chem. Soc.
128:10847, 2006.
Mittapalli, G.K., Kondreddi, R.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. 46:2470, 2007.
Mittapalli, G.K., Osornio, Y.M., Guerrero, M.A., Kondreddi, R.R., Krishnamurthy,
R., Eschenmoser, A. Mapping the landscape of potentially primordial informational
oligomers: oligodipeptides tagged with 2,4-disubstituted 5-aminopyrimidines as
recognition elements. Angew. Chem. Int. Ed. 46:2478, 2007.
BACKBONES
We are continuing our search for structurally and
generationally simpler informational systems, that is,
systems considered to have the capability of being
assembled from potentially prebiotic source molecules.
Recently, we synthesized oligomers derived from a
2′,3′-phosphodiester–linked glyceric acid backbone that
has 2,4-disubsituted 5-aminopyrimidines attached to the
carboxyl group via an amide bond at the 5 amino position as recognition elements (Fig. 3), and we are exam-
Organic, Organometallic, and
Medicinal Chemistry
M.G. Finn, S. Brown, S.-H. Cho, V. Hong, J. Kuzelka,
J. Lau, S. Lee, Y.-H. Lim, S. Presolski, V. Rodionov
n addition to our work on biological polyvalency
with engineered virus particles, supported by the
Skaggs Institute of Chemical Biology, we focus on
the development of catalysts and the synthesis of biologically useful structures. Three of these projects are
described in the following sections.
I
C O P P E R - C ATA LY Z E D A Z I D E - A L K Y N E C Y C L O A D D I T I O N
F i g . 3 . 5-Aminouracil–tagged 2′,3′-phosphodiester–linked glyc-
eric acid backbone.
ining the base-pairing properties of the synthesized
molecules. We expect that these systems will show
base pairing because systems with similar backbone
connections, namely, 2′ g 3′-phosphodiester–linked
β-D -lyxopyranosyl nucleic acids and 2′g 3′-phosphodiester–linked α-D -threofuranosyl nucleic acids can show
Watson-Crick base pairing.
We have completed the synthesis of the requisite
building block and the machine-assisted automated
We have continued our development of new catalysts for the azide-alkyne cycloaddition reaction, which
has become a principal tool for the synthesis of possible drugs, dendrimers, polymers, and functionalized
surfaces in laboratories around the world. Using quantitative kinetics measurements and reaction calorimetry, we screened more than 200 candidate compounds
as catalysts this past year. We found that tris(benzimidazole-methyl)amine ligands are strong accelerators of
the cycloaddition, allowing the use of small amounts
of catalyst for the quantitative conversion of complex
azides and alkynes into linked triazoles. A mechanistic
investigation revealed that the reaction is quite complex,
but several key hypotheses have emerged. Figure 1
shows one of the best new ligands, which bears an alkylcarboxylate group on each of the benzimidazole arms.
90 CHEMISTRY
2007
THE SCRIPPS RESEARCH INSTITUTE
F i g . 2 . Examples of electron-dense labeling reagents for electron
cryomicroscopy.
lysine residues. Derivatives bearing maleimides (for
labeling cysteine) and alkynes (for labeling azide-containing unnatural amino acids) are also in hand. Currently, we are evaluating such compounds in electron
cryomicroscopy analyses of cowpea mosaic virus, bacteriophage Qβ, and other proteins from collaborators.
F i g . 1 . Proposed mechanistic details of the copper-catalyzed
azide-alkyne cycloaddition reaction involving a new benzimidazolebased ligand.
Although the ligand is tetradentate, the acetylide
complex (compound 1 in Fig. 1) is bound by 3 of the
4 ligand-binding atoms, leaving 1 benzimidazole “arm”
free. A second arm can be released to allow the organic
azide to bind in structure 2. Kinetics measurements
indicate that the reaction requires 2 copper centers,
and so π-coordination to the alkyne by a second metal
center is proposed to speed the bond-forming event,
leading to intermediate 3. The pendant carboxylate
arm may assist in the last step of the process, hydrolysis of the copper-carbon bond to release the product
triazole. A complex such as 4 may result, which can
be quickly converted back to the starting acetylide 1,
completing the catalytic cycle. To further improve the
reaction, we are testing this mechanistic scheme by
constructing a variety of new ligands and substrates.
SYNTHESIS OF NEW ELECTRON-DENSE LABELING
REAGENTS FOR STRUCTURAL BIOLOGY
Our work with viruses has highlighted a need for
new reagents that contain clusters of heavy atoms and
reactive functional groups that allow for site-specific
attachment to proteins. Such compounds are of great
use in labeling complex structures to aid in structure
determination by electron cryomicroscopy. In collaboration with the automated molecular imaging group at
Scripps Research, we have developed reagents such as
compounds 1 and 2 in Figure 2. These compounds contain 3 and 6 osmium atoms, respectively, as well as
an N-hydroxysuccinimide ester group for attachment to
I N H I B I T O R S O F M U LT I D R U G - R E S I S TA N C E E N Z Y M E S
Membrane-bound proteins of the ATP-binding lipid
flippase family are often mutated in cancer cells and
result in removal of cytotoxic anticancer drugs before the
drugs can work, leading to broad multidrug resistance.
Using both structure-guided design, in collaboration with
G. Chang and coworkers, Department of Molecular Biology, and in situ assembly of fragments in the target
enzymes themselves, we are developing new families of
molecules that inhibit these enzymes. Steroidal derivatives that strongly inhibit bacterial (MDR3) and human
(P-gp) homologs have been synthesized, as well as several that unexpectedly enhance activity. Both types of
compounds are important for an improved understanding of the mechanism of drug transport.
PUBLICATIONS
Bourne, C.R., Finn, M.G., Zlotnick A. Global structural changes in hepatitis B virus
capsids induced by the assembly effector HAP1. J. Virol. 80:11055, 2006.
Díaz, D.D., Sen Gupta, S., Kuzelka, J., Cymborowski, M., Sabat, M., Finn, M.G.
Bis(formamidine-urea) cmplexes of NiII and CuII: synthesis, characterization, and
reactivity. Eur. J. Inorg. Chem. 4489, 2006, Issue 22.
Finn, M.G. Emerging high-throughput screening methods for asymmetric induction.
In: Chiral Analysis. Busch, K.W., Busch, M.A. (Eds.). Elsevier, Amsterdam, the
Netherlands, 2006, p. 79.
Hawker, C.J., Fokin, V.V., Finn, M.G., Sharpless, K.B. Bringing efficiency to materials synthesis: the philosophy of click chemistry. Aust. J. Chem. 60:381, 2007.
Johnson, J.A., Finn, M.G., Koberstein, J.T., Turro, N.J. Synthesis of photocleavable linear macromonomers by ATRP and star macromonomers by a tandem ATRPclick reaction: precursors to photodegradable model networks. Macromolecules
40:3589, 2007.
Le Baut, N., Díaz, D.D., Punna, S., Finn, M.G., Brown, H.R. Study of high glass
transition temperature thermosets made from the copper(I)-catalyzed azide-alkyne
cycloaddition reaction. Polymer 48:239, 2007.
CHEMISTRY
2007
Li, C., Finn, M.G. Click chemistry in materials synthesis, 2: acid-swellable crosslinked polymers made by copper-catalyzed azide-alkyne cycloaddition. J. Polym.
Sci. A Polym. Chem. 44:5513, 2006.
Prasuhn, D.E., Jr., Yeh, R.M., Obenaus, A., Manchester, M., Finn, M.G. Viral MRI
contrast agents: coordination of Gd by native virions and attachment of Gd complexes
by azide-alkyne cycloaddition. Chem. Commun. (Camb.) 1269, 2007, Issue 12.
Singh, P., Prasuhn, D., Yeh, R.M., Destito, G., Rae, C.S., Osborn, K., Finn, M.G.,
Manchester, M. Bio-distribution, toxicity, and pathology of cowpea mosaic virus
nanoparticles in vivo. J. Control. Release 120:41, 2007.
Yang, H.B., Das, N., Huang, F., Hawkridge, A.M., Díaz, D.D., Arif, A.M., Finn, M.G.,
Muddiman, D.C., Stang, P.J. Incorporation of 2,6-di(4,4′-dipyridyl)-9-thiabicyclo[3.3.1]nonane into discrete 2D supramolecules via coordination-driven selfassembly. J. Org. Chem. 71:6644, 2006.
Organometallic Catalysis in
Synthesis, Bioorganic Chemistry,
and Materials Research
V.V. Fokin, B. Boren, A. Chanda, S. Chang, J. Fotsing,
L. Krasnova, S.-W. Kwok, J. Raushel, T. Weide, M. Whiting
ur goals are to discover new reactivities and to
develop their practical applications in organic
synthesis, chemical biology, and materials science. Transformations catalyzed by transition metals are
of particular importance, because they often have many
variables that can be optimized to make the transformations useful on both laboratory and industrial scales.
Although we often use automation techniques to screen
extensive sets of catalysts, ligands, and conditions (often
on the basis of just a hunch that “it should work”),
mechanistic studies of the initial reactivity are prominent
in our research. Analysis of reaction kinetics, in situ
infrared monitoring, microcalorimetry, and other physicochemical methods are routinely used to understand the
mechanistic underpinning of the processes under investigation. This approach also offers excellent training
opportunities for graduate students and postdoctoral
researchers, preparing these scientists for successful
careers in pharmaceutical and chemical industries.
Although high-throughput biology, genetics tools,
robotics, and information technology have progressed
with lightning speed since the late 1980s, the demands
on the chemical methods made by these advances
remain largely unmet. Many “conventional” transformations have been successfully adopted to parallel
synthesis of chemical libraries of significant size (but
not necessarily of significant diversity), but reactions
that allow selective manipulation of biological targets,
both in vitro and in vivo, are still scarce. Indeed, the
O
THE SCRIPPS RESEARCH INSTITUTE
91
development of chemical tools to selectively address
desired molecules in the complex biological milieu is
still a formidable task: at the very least, the reactants
must be tolerant to protic, nucleophilic, and electrophilic
functional groups and must be reactive, yet tame, to
perform efficiently, reliably, and selectively in the presence of water, oxygen, and proteins. Organic azides
seem to fulfill most of these criteria.
Two reactions discovered in our laboratories, the
copper- and ruthenium-catalyzed cycloadditions of
azides and alkynes, provide ready access to 1,2,3-triazoles of various substitution patterns. The coppercatalyzed variant has become a premier click reaction
and has been adopted by chemists working in organic
synthesis, medicinal chemistry, chemical biology, and
materials science. In addition to its excellent reliability
and tolerance to a wide range of functional groups, the
copper-catalyzed reaction has provided valuable insights
into the unique and, until recently, unexplored reactivity
of organic azides and in situ generated copper acetylides.
The ruthenium-catalyzed reaction, although not yet as
widely accepted as the copper-catalyzed one, enables
“fusion” of organic azides and both terminal and internal alkynes with a complementary regioselectivity
and appears to proceed through a completely different
mechanism (Fig. 1).
F i g . 1 . Copper- and ruthenium-catalyzed azide-alkyne cycloadditions.
Both reactions and their applications to the synthesis of biologically active compounds and novel materials
have been the subject of our intense attention during
92 CHEMISTRY
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the past few years. We have investigated the mechanism
of these processes and endeavored to develop new
ligands to make the reactions more biocompatible. In
addition, we have used the reactions to synthesize libraries of compounds for HIV protease inhibition (Fig. 2A),
THE SCRIPPS RESEARCH INSTITUTE
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., Tripp, J.C., Lin, Y.-C., Lindstrom, W., Olson, A.J., Elder, J.H., Sharpless, K.B., Fokin, V.V. Rapid discovery and structure-activity profiling of novel
inhibitors of human immunodeficiency virus type 1 protease enabled by the copper(I)-catalyzed synthesis of 1,2,3-triazoles and their further functionalization. J.
Med. Chem. 49:7697, 2006.
Wu, P., Fokin, V.V. Catalytic azide-alkyne cycloadditions: reactivity and applications. Aldrichim. Acta 40:7, 2007.
Yoo, E.J., Ahlquist, M., Kim, S.H., Bae, I., Fokin, V.V., Sharpless, K.B., Chang, S.
Copper-catalyzed synthesis of N-sulfonyl-1,2,3-triazoles: controlling selectivity.
Angew. Chem. Int. Ed. 46:1730, 2007.
A Merging of Chemistry
and Biology
K.D. Janda, J. Ashley, A. Brogan, C. Carney, K. Capkova,
C. Chung, S. De Lamo Marin, J. Denery, T. Dickerson,
L. Eubanks, K. Fukuchi, C. Hernandez, A. Hoyt, A. Ino,
G. Kaufmann, J. Liu, Y. Liu, C. Lowery, S. Mahajan,
A. Mayorov, G. McElhaney, K. McKenzie, J. Mee, A. Moreno,
Y. Nakai, J. Park, N. Salzameda, S. Steiniger, J. Treweek,
A. Willis, Y. Xu, Y. Yoneda, B. Zhou, H. Zhou
uring the past year, we used various applications
of organic chemistry to address biological problems. The results of 3 research programs—in
vivo identification of botulinum neurotoxin antagonists,
development of a cyclic peptide as a drug delivery module, and discovery of antibodies capable of degrading
the active component of marijuana—are highlighted in
the following sections.
D
F i g . 2 . A, New nicotinic acetylcholine receptor ligands (Kd <1
nm). B, Polyvalent fluorescent dendrimer.
in collaboration with J.H. Elder and A.J. Olson, Department of Molecular Biology; β-secretase inhibition and
nicotinic receptor agonists and antagonists, in studies
with P. Taylor, University of California, San Diego; and
polymeric materials and dendritic constructs for polyvalent display and imaging applications (Fig. 2B), in
research with C. Hawker, University of California, Santa
Barbara, and M.G. Finn, Department of Chemistry.
PUBLICATIONS
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.
Fokin, V.V, Wu, P. Epoxides and aziridines in click chemistry. In: Aziridines and
Epoxides in Organic Synthesis. Yudin, A.K. (Ed.). Wiley-VCH, Weinheim, Germany,
2006, p. 443.
Kade, M., Vestberg, R., Malkoch, M., Wu, P., Fokin, V.V., Finn, M.G. Sharpless,
K.B., Hawker, C. A covalently bonded layer-by-layer assembly of dendrimers by
‘click’ chemistry. Polymer Preprints (Am. Chem. Soc.) 47:376, 2006.
Narayan, S., Fokin, V.V., Sharpless, K.B. Chemistry ‘on water’: organic synthesis
in aqueous suspension. In: Organic Synthesis in Water: Principles, Strategies and
Applications. Lindström, U.M. (Ed.). Blackwell Publishing, Oxford, England, 2007,
p. 350.
I D E N T I F I C AT I O N O F A N TA G O N I S T S O F B O T U L I N U M
NEUROTOXIN A
The neurotoxins produced by the bacteria Clostridium
botulinum, Clostridium butyricum, and Clostridium
barati are the most toxic proteins known; the toxins are
classified as 1 of the 6 highest-risk agents for bioterrorism (category A agent). These proteins (serotypes
A–G) are the agents responsible for botulism, a disease
characterized by peripheral neuromuscular blockade
and a characteristic flaccid paralysis. Botulinum neurotoxins cause the paralysis by entering neuronal cells
and cleaving soluble N-ethylmaleimide-sensitive–factor
attachment protein receptors, thereby blocking fusion
of synaptic vesicles to the plasma membrane and the
release of the neurotransmitter acetylcholine at neuromuscular junctions. Interestingly, this same property
has led to the use of the neurotoxins for therapeutic
and cosmetic purposes, such as treatment of strabismus, hemifacial spasms, and wrinkles.
CHEMISTRY
2007
Although no approved pharmacologic treatments
exist, current strategies to combat the effects of the
neurotoxins rely mainly on vaccination or passive administration of antibodies derived from either immunized
personnel or equine sources. Both vaccines and antibodies are effective only if administered before the
neurotoxins enter neurons. Because of their potential
to enter cells, small molecules provide an opportunity
to combat botulism both before and after entry of the
toxins into neurons. Published studies on small-molecule antagonists of the botulinum neurotoxins have relied
on in vitro methods; therefore, to establish a model for
predicting in vivo efficacy, we recently identified several compounds that extend the time of death in mice
exposed to lethal doses of botulinum neurotoxin A.
The mechanism of action of botulinum neurotoxin
A is a series of protein-protein interactions that culminate in a catalytic event. Accordingly, we hypothesized
that screening a library of compounds known to disrupt
protein-protein interactions would yield antagonists of
the neurotoxin. Initially, we used a high-throughput
screening method with purified neurotoxin A metalloprotease to detect possible antagonists, and then we
verified the effects of the putative antagonists in a
neuroblastoma cell–based assay. On the basis of the
data obtained from the 2 initial screens, several compounds were advanced to animal trials. Two of the
compounds (Fig. 1) significantly extended the time of
THE SCRIPPS RESEARCH INSTITUTE
93
CYCLIC PEPTIDES AS LIGANDS OF CANCER
CELL-SURFACE RECEPTORS
Currently available therapeutic agents for cancer
often are not specific for cancer cells and are associated
with severe side effects and distress for patients. Peptidic ligands of cellular receptors have gained attention
for their ability to recognize specific receptors and thus
penetrate cells to deliver a “payload.” With this information in mind, we used whole-cell phage-panning technology to screen a library of cyclic peptides against 2
melanoma cell lines, the highly metastatic Me6652/4
and the low metastatic clone Me5552/56, to identify
cyclic peptides with specificity for highly metastatic cells.
DNA sequencing of the peptides specific for melanoma cells in the panning revealed a cyclic 13mer
peptide, Pep42, with a novel sequence (Fig. 2A). For
F i g . 2 . A, Structure of the cyclic peptide Pep42 with conjugated
payload. B, Localization of Pep42 to highly metastatic cancer cells
Me6652/4.
F i g . 1 . Chemical structures of molecules that can inhibit botu-
linum neurotoxin serotype A in animal models.
death in mice given botulinum neurotoxin A. These 2
compounds were unlikely candidates after the first
2 rounds of screening; NA-A1B2C10 showed poor protection in cellular assays, and 2,4-dichlorocinnamic
hydroxamic acid, originally included simply for comparison, was cytotoxic in the cellular assays. The emergence
of these 2 antagonists only after 3 rounds of screening
highlights the importance of a multidisciplinary approach
involving both in vivo and in vitro approaches in the
development of therapies for botulism.
further biological analysis, a synthetic analog of Pep42,
which had the same activity as the originally isolated
peptide, was designed and prepared for future conjugation with a desired payload. Using fluorescein-labeled
Pep42 and confocal microscopy, we found that internalization of the peptide by the highly metastatic
Me6652/4 cell line was more efficient than internalization by the control Me6652/56 cell line (Fig. 2B),
validating our phage-panning approach.
To elucidate the mechanism of Pep42 internalization, we constructed a Pep42 variant incorporating a
photoaffinity label. Incubation of this peptide with cells
revealed that the molecular target of Pep42 is glucose-
94 CHEMISTRY
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regulated protein 78 (GRP78). Expression of GRP78
increases in response to stressful conditions, and upregulation of GRP78 has been correlated with an increase
in malignancy of cancer cells, making this protein an
attractive target as a drug delivery receptor. To demonstrate the usefulness of GRP78-targeted peptides, we
conjugated Pep42 to the anticancer drug paclitaxel
(Taxol) and tested the conjugate for the ability to induce
apoptosis in melanoma cells. The Pep42-paclitaxel conjugate was 2-fold more potent than paclitaxel alone
because of the efficient delivery of the drug to tumor
cells by Pep42. Importantly, incubation of cells with
Pep42 resulted in minimal cell death, paralleling the
amount of death in the presence of growth medium
alone. Taken together, these results establish Pep42
as a candidate for the construction of drug conjugates
to deliver anticancer agents to malignant cells while
reducing undesirable side effects.
C ATA LY T I C A N T I B O D I E S A G A I N S T
THE SCRIPPS RESEARCH INSTITUTE
We examined 2 previously generated panels of
antibodies for the capacity to degrade
∆9-THC. In the presence of singlet oxygen, generated
by riboflavin and sunlight, all tested antibodies oxidatively degraded ∆9-THC to form a single major product
and several minor products. Exhaustive spectroscopic
analyses indicated that the major product of the antibody-catalyzed reaction was cannabitriol, in which
the C9-C10 olefin of ∆9-THC has essentially undergone
dihydroxylation (Fig. 3). On the basis of the regiochem∆9-THC–binding
F i g . 3 . Antibody-catalyzed conversion of ∆9-THC to cannabitriol.
∆9-TETRAHYDROCANNABINOL
Marijuana is the most commonly abused illicit drug
in the United States and often leads to the abuse of
other illicit drugs, as postulated by the “cannabis gateway
hypothesis.” Recently, it was shown that ∆9-tetrahydrocannabinol (∆9-THC) increases opiate self-administration in mice by altering the endogenous opioid system,
providing a molecular basis for the gateway hypothesis. Despite the dangers posed by marijuana abuse,
currently no clinical treatments for abuse of this drug
are available.
During the past several years, researchers in our
laboratory have advanced a tactic known as immunopharmacotherapy to combat drugs of abuse. This technique hinges on the administration of an antibody to
bind a drug before the drug reaches its cognate receptor. Using this strategy, we have developed approaches
to treat cocaine, nicotine, and methamphetamine abuse.
One drawback to this approach is the need for stoichiometric amounts of antibody to bind the target drug;
alternatively, we envisioned a catalytic antibody capable of decomposing ∆9-THC as a promising approach
for therapies that require substoichiometric amounts
of antibody.
Despite the absence of any obvious candidate bonds
for antibody-promoted degradation, we reasoned that
the C9-C10 olefin would be susceptible to oxidation.
Additionally, recent research has shown that antibodies have the intrinsic ability to perform oxidative degradations by generating reactive oxygen species from
singlet oxygen.
istry and stereochemistry of the product and our knowledge of antibody-catalyzed reactions, we have proposed
a mechanism for this conversion that involves oxidation, epoxide opening, and elimination.
Pharmacologically, the cytotoxicity of cannabitriol is
similar to that of ∆9-THC, but the addition of 2 hydroxyl
groups leads us to expect that the increase in polarity
will aid in the elimination of cannabitriol through natural
metabolic pathways. These findings not only reveal the
usefulness of a catalytic antibody–based therapy for
drugs of abuse but also illustrate the inherent potential
of all antibodies to catalyze complex chemical reactions.
PUBLICATIONS
Brogan, A.P., Dickerson, T.J., Janda, K.D. Catalytic antibodies: past, present, and
future. In: Wiley Encyclopedia of Chemical Biology. Wiley, New York, in press.
Brogan, A.P., Dickerson, T.J., Janda, K.D. Enamine-based aldol organocatalysis in
water: are they really “all wet”? Angew. Chem. Int. Ed. 45:8100, 2006.
Brogan, A.P., Eubanks, L.M., Koob, G.F., Dickerson, T.J., Janda, K.D. Antibody-catalyzed oxidation of ∆9-tetrahydrocannabinol. J. Am. Chem. Soc. 129:3698, 2007.
De Lamo Marin, S., Xu, Y., Meijler, M.M., Janda, K.D. Antibody catalyzed hydrolysis of a quorum sensing signal found in gram-negative bacteria. Bioorg. Med.
Chem. Lett. 17:1549, 2007.
Debler, E.W., Kaufmann, G.F., Kirchdoerfer, R.N., Mee, J.M., Janda, K.D., Wilson, I.A. Crystal structures of a quorum-quenching antibody. J. Mol. Biol.
368:1392, 2007.
Dickerson, T.J., Janda, K.D. The use of small molecules to investigate molecular
mechanisms and therapeutic targets for treatment of botulinum neurotoxin A intoxication. ACS Chem. Biol. 2:359, 2007.
Eubanks, L.M., Dickerson, T.J., Janda, K.D. Technological advancements for the
detection of and protection against biological and chemical warfare agents. Chem.
Soc. Rev. 36:458, 2007.
CHEMISTRY
2007
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95
Eubanks, L.M., Hixon, M.S., Jin, W., Hong, S., Clancy, C.M., Tepp, W.H., Baldwin, M.R., Malizio, C.J., Goodnough, M.C., Barbieri, J.T., Johnson, E.A., Boger,
D.L., Dickerson, T.J., Janda, K.D. An in vitro and in vivo disconnect uncovered
through high-throughput identification of botulinum neurotoxin A antagonists. Proc.
Natl. Acad. Sci. U. S. A. 104:2602, 2007.
Strategies to Ameliorate Protein
Misfolding Diseases
Eubanks, L.M., Rogers, C.J., Beuscher, A.E. IV, Koob, G.F., Olson, A.J., Dickerson, T.J., Janda, K.D. A molecular link between the active component of marijuana
and Alzheimer’s disease pathology. Mol. Pharm. 3:773, 2006.
J.W. Kelly, J. Bieschke, S. Choi, E. Culyba, M.T.A. Dendle,
Fu, Z., Chen, S., Baldwin, M.R., Boldt, G.E., Crawford, A., Janda, K.D., Barbieri,
J.T., Kim, J.J. Light chain of botulinum neurotoxin serotype A: structural resolution
of a catalytic intermediate. Biochemistry 45:8903, 2006.
Kim, Y., Lillo, A.M., Steiniger, S.C., Liu, Y., Ballatore, C., Anichini, A., Mortarini,
R., Kaufmann, G.F., Zhou, B., Felding-Habermann, B., Janda, K.D. Targeting heat
shock proteins on cancer cells: selection, characterization, and cell-penetrating
properties of a peptidic GRP78 ligand. Biochemistry 45:9434, 2006.
Kravchenko, V.V., Kaufmann, G.F., Mathison, J.C., Scott, D.A., Katz, A.Z., Wood,
M.R., Brogan, A.P., Lehmann, M., Mee, J.M., Iwata, K., Pan, Q., Fearns, C.,
Knaus, U.G., Meijler, M.M., Janda, K.D., Ulevitch R.J. N-(3-oxo-acyl)homoserine
lactones signal cell activation through a mechanism distinct from the canonical
pathogen-associated molecular pattern recognition receptor pathways. J. Biol.
Chem. 281:28822, 2006.
Liu, Y., Steiniger, S.C., Kim, Y., Kaufmann, G.F., Felding-Habermann, B., Janda,
K.D. Mechanistic studies of a peptidic GRP78 ligand for cancer cell-specific drug
delivery. Mol. Pharm. 4:435, 2007.
McAllister, L.A., Hixon, M.S., Schwartz, R., Kubitz, D.S., Janda, K.D. Synthesis
and application of a novel ligand for affinity chromatography based removal of
endotoxin from antibodies. Bioconjug. Chem. 18:559, 2007.
McKenzie, K.M., Mee, J.M., Rogers, C.J., Hixon, M.S., Kaufmann, G.F., Janda,
K.D. Identification and characterization of single chain anti-cocaine catalytic antibodies. J. Mol. Biol. 365:722, 2007.
Rogers, C.J., Eubanks, L.M., Dickerson, T.J., Janda, K.D. Unexpected acetylcholinesterase activity of cocaine esterases. J. Am. Chem. Soc. 128:15364, 2006.
Shigenaga, A., Moss, J.A., Janda, K.D. New synthetic methodology for the synthesis of cyclic depsipeptides employing acylphenyldiazene activation. In: Peptide Science 2005: Proceedings of the 42nd Japanese Peptide Symposium. Wakamiya, T.
(Ed.). Protein Research Foundation, Osaska, Japan, 2006, p. 137.
Silvaggi, N.R., Boldt, G.E., Hixon, M.S., Kennedy, J.P., Tzipori, S., Janda, K.D.,
Allen, K.N. Structures of Clostridium botulinum neurotoxin serotype A light chain
complexed with small-molecule inhibitors highlight active-site flexibility. Chem.
Biol. 14:533, 2007.
Steiniger, S.C., Altobell, L.J. III, Zhou, B., Janda, K.D. Selection of human antibodies against cell surface-associated oligomeric anthrax protective antigen. Mol.
Immunol. 44:2749, 2007.
Xu, Y., Hixon, M.S., Yamamoto, N., McAllister, L.A., Wentworth, A.D., Wentworth, P., Jr., Janda, K.D. Antibody-catalyzed anaerobic destruction of methamphetamine. Proc. Natl. Acad. Sci. U. S. A. 104:3681, 2007.
Xu, Y., Lu, H., Kennedy, J.P., Yan, X., McAllister, L.A., Yamamoto, N., Moss, J.A.,
Boldt, G.E., Jiang, S., Janda, K.D. Evaluation of “credit card” libraries for inhibition of HIV-1 gp41 fusogenic core formation. J. Comb. Chem. 8:531, 2006.
Zorrilla, E.P., Iwasaki, S., Moss, J.A., Chang, J., Otsuji, J., Inoue, K., Meijler,
M.M., Janda, K.D. Vaccination against weight gain. Proc. Natl. Acad. Sci. U. S. A.
103:13226, 2006.
W. D’Haeze, D. Du, T.R. Foss, D.M. Fowler, A. Fuller,
J. Gao, M.-Y. Gao, S.M. Johnson, T. Mu, A. Murray,
E.T. Powers, P. Rao, L. Segatori, S. Siegel, J.Y. Suk, K. Usui,
Y. Wang, I. Yonemoto, Z. Yu
ur goal is to better understand the molecular
mechanisms that lead to compromised protein
homeostasis, resulting in illnesses that include
Alzheimer ’s, Parkinson’s, and Gaucher diseases and
type 2 diabetes. Protein homeostasis refers to the maintenance of functional proteins both inside and outside
human cells, which is essential for development, reproduction, and successful aging, consistent with the central role of proteins as the workhorses in the physiology
of all organisms. Understanding the mechanisms of
protein homeostasis, especially the defects in these
pathways associated with aging, enables us to design
new strategies to ameliorate protein misfolding diseases,
a main goal of our research. We use organismal and cell
biological disease models and biophysical approaches in
combination with medicinal chemistry and structurebased drug design. Successful collaborations with
W.E. Balch, Department of Cell Biology, J. Buxbaum,
Department of Molecular and Experimental Medicine,
and A. Dillin, 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-thyroxine 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 a protein homeostasis stress associated
with aging and/or oxidative stress, dissociation of the
native transthyretin tetramer and subsequent changes
in the tertiary structure of the monomer make the
monomeric subunits competent to misassemble into
cytotoxic aggregates, including amyloid fibrils. Deposition of transthyretin amyloid is linked with a number
of human diseases, including senile systemic amyloidosis, familial amyloid polyneuropathy, familial amyloid cardiomyopathy, and CNS-selective amyloidosis.
96 CHEMISTRY
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A suitable strategy to slow or prevent the formation
of aggregates is to inhibit the rate-limiting dissociation
of the transthyretin tetramer by using small molecules,
which we discovered, to stabilize the normal functional
state. Two of these molecules are in placebo-controlled
clinical trials for treatment of familial amyloid polyneuropathy, a disease similar to Alzheimer ’s that attacks
the peripheral nervous system instead of the brain. This
year we determined the mechanism behind the efficacy
of one of these compounds. We also synthesized and
identified even more potent native-state kinetic stabilizers of transthyretin for the amelioration of familial
amyloid cardiomyopathy, a disease leading to congestive
heart failure. We anticipate that trials of the stabilizers
for treatment of cardiomyopathy will begin after the
results of the peripheral neuropathy trials are known.
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 N D T H E
ONSET OF SPORADIC PARKINSON’S AND
ALZHEIMER’S DISEASES
Understanding the molecular or mechanistic basis for
the age-associated onset of Alzheimer’s and Parkinson’s
diseases is one of our key goals. The α-synucleinopathies, including Parkinson’s disease, 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 found that overexpression of α-synuclein
in a neuronal cell line is sufficient to increase the production of oxidative metabolites that, in turn, significantly accelerate aggregation of α-synuclein in vitro.
The data suggest that the acceleration of aggregation
occurs predominantly via a noncovalent mechanism.
We recently found that a prominent oxidative metabolite, 4-hydroxynonenal, long correlated with Alzheimer’s
disease, covalently modifies amyloid β-peptide (Aβ),
whose aggregation is thought to cause Alzheimer ’s
disease. This covalent modification makes amyloid
formation much more efficient. Thus, we continue to
explore the hypothesis that enhanced local oxidative
stress, perhaps as a result of aging, results in a vicious
cycle that forms reactive oxidative metabolites that
exacerbate aggregation of α-synuclein and Aβ, resulting in even more oxidative stress and higher concentrations of oxidative metabolites that enable even more
aggregation and proteotoxic effects, causing sporadic
Alzheimer’s and Parkinson’s disease.
DIMINISHING PROTEOTOXIC EFFECTS LEADING TO
ALZHEIMER’S DISEASE
Aberrant protein aggregation is a common feature
of late-onset neurodegenerative diseases, including
THE SCRIPPS RESEARCH INSTITUTE
Alzheimer’s disease, which is associated with the misassembly of the Aβ1-42 peptide. In collaboration with
Dr. Dillin and coworkers, we found that the aggregationmediated proteotoxic effects of Aβ1-42 in a Caenorhabditis elegans model of Alzheimer’s disease were reduced
when aging was slowed by a decrease in insulin/insulin
growth factor-1–like signaling (IIS). We discovered that
the downstream transcription factors heat-shock factor-1 and DAF 16 regulate opposing disaggregation
and aggregation activities to promote cellular survival
and protein homeostasis in response to constitutive
aggregation that can become toxic. Because the IIS
pathway is central to the regulation of longevity and
youthfulness in worms, flies, and mammals, these
results suggest a mechanistic link between the aging
process and aggregation-mediated proteotoxic effects
that we strive to manipulate with small-molecule drugs
as a fundamentally new approach to ameliorate Alzheimer’s disease.
Of note, the IIS pathway plays a role in modulating other forms of toxic protein aggregation, such as in
the aggregation of the huntingtin protein leading to
Huntington’s disease, suggesting that the aggregation/
disaggregation activities we discovered in the past year
may be quite general. Additionally, it is becoming clear
that small perturbations in the activities responsible
for protein homeostasis have a profound impact on
organismal integrity, suggesting that the protective mechanisms regulated by the IIS pathway may link longevity
to protein homeostasis, enabling new therapeutic strategies to be conceived.
N E W T H E R A P E U T I C S T R AT E G I E S T O A M E L I O R AT E
LY S O S O M A L S T O R A G E D I S E A S E S
Mutations in glucocerebrosidase lower the concentration and activity of this lysosomal glycolipid hydrolase,
lead to an accumulation of the glucocerebrosidase
substrate, glucosylceramide, in the lysosome, and
cause Gaucher disease, the most common lysosomal
storage disorder. We showed previously that administration of 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 is due to
the binding of N-(n-nonyl)deoxynojirimycin to the native
state N370S, allowing the glucocerebrosidase to fold
properly within the cell and be trafficked from the
endoplasmic reticulum to lysosomes.
We are now seeking compounds that can be used
in combination with these protein- and disease-specific
small molecules to enhance the cellular protein folding
CHEMISTRY
2007
and trafficking capacity. Compounds that influence the
cellular folding and trafficking of classes of glycolipid
hydrolases have the potential to be useful for more than
a single lysosomal storage disease. Recently, we discovered molecules of this type, drug candidates that offer
the potential to change the economics of health care by
treating multiple diseases in a family of diseases with
a single compound.
PUBLICATIONS
Bieschke, J., Zhang, Q., Bosco, D.A., Lerner, R.A., Powers, E.T., Wentworth, P.,
Jr., Kelly, J.W. Small molecule oxidation products trigger disease-associated protein
misfolding. Acc. Chem. Res. 39:611, 2006.
Cohen, E., Bieschke, J., Perciavalle, R., Kelly, J.W., Dillin, A. Opposing activities
protect against age-onset proteotoxicity. Science 313:1604, 2006.
Cordeiro, Y., Kraineva, J., Suarez, M.-C., Tempesta, A.-G., Kelly, J.W., Silva, J.L.,
Winter, R., Foguel, D. Fourier transform infrared spectroscopy provides a fingerprint
for the tetramer and for aggregates of transthyretin. Biophys. J. 91:957, 2006.
Fu, Y., Gao, J., Bieschke, J., Dendle, M.A., Kelly, J.W. Amide-to-E-olefin versus
amide-to-ester backbone H-bond perturbations: evaluating the O-O repulsion for
extracting H-bond energies. J. Am. Chem. Soc. 128:15948, 2006.
Jager, M., Zhang, Y., Bieschke, J., Nguyen, H., Dendle, M., Bowman, M.E., Noel,
J.P., Gruebele, M., Kelly, J.W. The structure-function-folding relationship in a WW
domain. Proc. Natl. Acad. Sci. U. S. A. 103:10648, 2006.
Kelly, J.W. Structural biology: proteins downhill all the way. Nature 442:255, 2006.
Reixach, N., Adamanski-Werner, S.L., Kelly, J.W., Koziol, J., Buxbaum, J.N. Cell
based screening of inhibitors of transthyretin aggregation. Biochem. Biophys. Res.
Commun. 348:889, 2006.
Sawkar, A.R., Schmitz, M., Zimmer, K.-P., Reczek, D., Edmunds, T., Balch, W.E.,
Kelly, J.W. Chemical chaperones and permissive temperatures alter localization of
Gaucher disease associated glucocerebrosidase variants. ACS Chem. Biol. 1:235,
2006.
Sekijima, Y., Kelly, J.W. Orally administered diflunisal stabilizes transthyretin
against dissociation required for amyloidogenesis. Amyloid 13:236, 2006.
Siegel, S.J., Bieschke, J., Powers, E.T., Kelly, J.W. The oxidative stress metabolite
4-hydroxynonenal promotes Alzheimer protofibril formation. Biochemistry
46:1503, 2007.
Tojo, K., Sekijima, Y., Kelly, J.W., Ikeda, S.-I. Diflunisal stabilizes familial amyloid
polyneuropathy-associated transthyretin variant tetramers in serum against dissociation required for amyloidogenesis. Neurosci. Res. 56:441, 2006.
Wang, X., Venable, J., LaPointe, P., Hutt, D.M., Koulov, A.V., Coppinger, J., Gurkan,
C., Kellner, W., Matteson, J., Plutner, H., Riordan, J.R., Kelly, J.W., Yates, J.R.
III, Balch, W.E. Hsp90 cochaperone Aha1 downregulation rescues misfolding of
CFTR in cystic fibrosis. Cell 127:803, 2006.
Yu, Z., Sawkar, A.R., Whalen, L.J., Wong, C.-H., Kelly, J.W. Isofagamine- and
2,5-anhydro-2,5-imino-D-glucitol-based glucocerebrosidase pharmacological chaperones for Gaucher disease intervention. J. Med. Chem. 50:94, 2007.
Zhang, Y., Kim, Y., Genoud, N., Gao, G., Kelly, J.W., Pfaff, S.N., Gill, G., Dixon, J.E.,
Noel, J.P. Determinants for dephosphorylation of the RNA polymerase II C-terminal
domain by Scp1. Mol. Cell 24:759, 2006.
THE SCRIPPS RESEARCH INSTITUTE
97
Total Synthesis, New Synthetic
Technologies, and Chemical
Biology
K.C. Nicolaou, X. Alvarez-Mico, R. Aversa, W. Brenzovich,
P. Bulger, A. Burtoloso, J. Chen, K. Cole, J. Crawford,
P. Dagneau, R. Denton, D. Edmonds, S. Ellery, A. Estrada,
C. Fang, R. Faraoni, M. Frederick, M. Freestone, R. Gibe,
S. Harrison, V. Jeso, A. Johnson, A. Kislukhin, A. Lanver,
K. Lee, A. Lemire, A. Lenzen, A. Li, H. Li, Y. Lim, T. Lister,
N. Mainolfi, C. Mathison, A. Morgan, A. Nold, A. Ortiz,
K. Pendri, G. Petrovic, D. Polet, G. Pontremoli, B. Pratt,
F. Rivas, A. Sanchez Ruiz, D. Sarlah, D. Shaw, A. Stepan,
T. Suzuki, A. Talbot, Y. Tang, V. Trepanier, G. Tria, C. Turner,
T. Umezawa, J. Wang, T. Wu, H. Xu, H. Zhang
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 for 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 drugs diazonamide A, thiostrepton, azaspiracid-1–azaspiracid-3,
abyssomycin C, the bisanthraquinones, and the marinomycins exemplify this philosophy. Current projects
include studies on the antibiotics nocathiacin I and platensimycin, the antifeedant azadirachtin, the antitumor
agents lomaiviticin B and unicalamycin, and the antiHIV agent biyouyanagin (Fig. 1).
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.
W
PUBLICATIONS
Alfonso, A., Vieytes, M.R., Ofuji, K., Satake, M., Nicolaou, K.C., Frederick, M.O.,
Botana, L.M. Azaspiracids modulate intracellular pH levels in human lymphocytes.
Biochem. Biophys. Res. Commun. 346:1091, 2006.
Altmann, K.-H., Pfeiffer, B., Arseniyadis, S., Pratt, B.A., Nicolaou, K.C. The
chemistry and biology of epothilones: the wheel keeps turning. ChemMedChem
2:396, 2007.
Hamel, E., Day, B.W., Miller, J.H., Jung, M.K., Northcote, P.T., Ghosh, A.K., Curran, D.P., Cushman, M., Nicolaou, K.C., Paterson, I., Sorensen, E.J. Synergistic
effects of peloruside A and laulimalide with taxoid site drugs, but not with each
other, on tubulin assembly. Mol. Pharmacol. 70:1555, 2006.
98 CHEMISTRY
2007
THE SCRIPPS RESEARCH INSTITUTE
Nicolaou, K.C., Tang, Y., Wang, J. Formal synthesis of (±)-platensimycin. Chem.
Commun. (Camb.) 1922, 2007, Issue 19.
Nicolaou, K.C., Zhang, H., Chen, J.S., Crawford, J.J., Pasunoori, L. Total synthesis and stereochemistry of uncialamycin. Angew. Chem. Int. Ed. 46:4704, 2007.
Nicolaou, K.C., Zou, B., Dethe, D.H., Li, D.B., Chen, D.Y.-K. Total synthesis of
antibiotics GE2270A and GE2270T. Angew. Chem. Int. Ed. 45:7786, 2006.
Vale, C., Nicolaou, K.C., Frederick, M.O., Gomez-Limia, B., Alfonso, A., Vieytes,
M.R., Botana, L.M. Effects of azaspiracid-1, a potent cytotoxic agent, in primary neuronal cultures: a structure-activity relationship study. J. Med. Chem. 50:356, 2007.
Vilariño, N., Nicolaou, K.C., Frederick, M.O., Cagide, E., Ares, I.M., Louzao,
M.C., Vieytes, M.R., Botana, L.M. Cell growth inhibition and actin cytoskeleton
disorganization induced by azaspiracid-1: structure-activity studies. Chem. Res.
Toxicol. 19:1459, 2006.
Translational Chemistry
and Medicine
E. Roberts, G. Cherukupalli, O. Ghoneim, M. Morales,
X. Peng, C. Zoni, S. Sinha, K. Reynolds, R. Poddutoori,
Y. Wang
F i g . 1 . Selected target molecules.
Nicolaou, K.C., Edmonds, D.J., Bulger, P.G. Cascade reactions in total synthesis.
Angew. Chem. Int. Ed. 45:7134, 2006.
Nicolaou, K.C., Edmonds, D.J., Li, A., Tria, G.S. Asymmetric syntheses of platensimycin. Angew. Chem. Int. Ed. 46:3942, 2007.
Nicolaou, K.C., Estrada, A.A., Freestone, G.C., Lee, S.H., Alvarez, X.M. New synthetic technology for the construction of N-hydroxyindoles and synthesis of
nocathiacin I model systems. Tetrahedron 63:6088, 2007.
Nicolaou, K.C., Estrada, A.A., Lee, S.H., Freestone, G.C. Synthesis of highly substituted N-hydroxyindoles through 1,5-addition of carbon nucleophiles to in situ
generated unsaturated nitrones. Angew. Chem. Int. Ed. 45:5364, 2006.
Nicolaou, K.C., Frederick, M.O. On the structure of maitotoxin. Angew. Chem. Int.
Ed. 46:5278, 2007.
Nicolaou, K.C., Harrison, S.T. Total synthesis of abyssomicin C, atrop-abyssomicin C,
and abyssomicin D: implications for natural origins of atrop-abyssomicin C. J. Am.
Chem. Soc. 129:429, 2007.
Nicolaou, K.C., Li, A., Edmonds, D.J. Total synthesis of platensimycin. Angew.
Chem. Int. Ed. 45:7086, 2006.
Nicolaou, K.C., Lim, Y.H., Piper, J.L., Papageorgiou, C.D. Total synthesis of
2,2′-epi-cytoskyrin A, rugulosin, and the alleged structure of rugulin. J. Am. Chem.
Soc. 129:4001, 2007.
Nicolaou, K.C., Lister, T., Denton, R.M., Montero, A., Edmonds, D.J. Adamantaplatensimycin: a bioactive analogue of platensimycin. Angew. Chem. Int. Ed.
46:4712, 2007.
Nicolaou, K.C., Nold, A.L., Milburn, R.R., Schindler, C.S. Total synthesis of marinomycins A-C. Angew. Chem. Int. Ed. 45:6527, 2006.
Nicolaou, K.C., Nold, A.L., Milburn, R.R., Schindler, C.S., Cole, K.P., Yamaguchi, J.
Total synthesis of marinomycins A-C and of their monomeric counterparts monomarinomycin A and iso-monomarinomycin A. J. Am. Chem. Soc. 129:1760, 2007.
Nicolaou, K.C., Sarlah, D., Shaw, D. Total synthesis and revised structure of
biyouyanagin A. Angew. Chem. Int. Ed. 46:4708, 2007.
iscovery and development of new medicines
require the integration of several scientific disciplines. 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 enhance
and cooperate in applied scientific efforts with clear goals
and milestones to identify potential new medicines for
the treatment of diseases that currently have inadequate
or no therapy.
D
T R E AT M E N T O F N E U R O L O G I C D I S E A S E S
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.
In collaboration with T. Bartfai, Molecular and Integrative Neurosciences Department, and A.M. Mazarati,
University of California, Los Angeles, we have identified
new nonpeptidic ligands for the galanin receptors GalR1
and GalR2. This set of small, druglike molecules can
displace the peptide galanin from its protein binding
site. Selectivity and potency of these initial molecular
starting points are being optimized.
CHEMISTRY
2007
THE SCRIPPS RESEARCH INSTITUTE
99
DUAL OPIOID AGONISTS–CHOLECYSTOKININ
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
N E U R O PAT H I C PA I N
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 the effects. The
interaction between cholecystokinin antagonists and
opiates may lead to the development of novel medications that are more effective and safer than currently
available 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 and in neuropathic pain conditions
in which opioids are ineffective. Thus, because of the
prevention (or reversal) of tolerance, physical dependence
on opioids may 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 (Fig. 1).
NEUROPHARMACOLOGIC APPROACHES FOR
T R E AT M E N T O F P E R VA S I V E D E V E L O P M E N TA L
DISORDERS
Autism is a bioneurologic developmental disability
that affects the normal development of the brain in the
areas associated with social interaction, communication
skills, 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. This rate is increasing significantly and now surpasses that of all types of cancer combined.
F i g . 1 . Opioid agonist–cholecystokinin antagonist hybrids.
No drug is consistently effective in treating the signs
and symptoms of autism. The neuropeptides vasopressin
and oxytocin (Fig. 2) have profound effects in rodent
F i g . 2 . Structures of vasopressin and oxytocin.
and sheep models of social behavior. These models are
being used to understand more fully human social
deficit disorders such as the pervasive development
disorders of autism and Asperger’s syndrome and the
effects of stress on women. The lack of CNS-accessible
and subtype-selective ligands has hindered drug research
and development in these areas. We are developing
small-molecule, druglike agonists for the oxytocin and
vasopressin V1a receptors that are selective and able
to penetrate the blood-brain barrier and are testing the
agonists in these models of social behavior. Our goal is
to identify validated lead compounds for further preclinical development (Figs. 3 and 4). This research is
done in collaboration with T. Bartfai, G.F. Koob, and
A. Roberts, Molecular and Integrative Neurosciences
Department.
I M M U N O M O D U L AT I N G C O M P O U N D S F O R T H E
T R E AT M E N T O F D I S E A S E S W I T H U N C O N T R O L L E D
I N F L A M M AT I O N
In collaboration with H. Rosen and coworkers,
Department of Immunology, we are investigating the
sphingosine phosphate family of G protein–coupled
receptors. Iterative screening/design and synthesis
100 CHEMISTRY
2007
THE SCRIPPS RESEARCH INSTITUTE
lating without compromising the immune response. Such
molecules may find use in organ transplantation, tissue
grafts, neoplastic diseases, and autoimmune disorders.
PUBLICATIONS
Don, A.S., Martinez-Lamenca, C., Webb, W.R., Proia, R.L., Roberts, E., Rosen,
H. Essential requirement for sphingosine kinase 2 in a sphingolipid apoptosis pathway activated by FTY720 analogs. J. Biol. Chem. 282:15833, 2007.
Chemical, Biological, and
Biophysical Approaches to
Understanding Evolution
F i g . 3 . A, Known mixed vasopressin V1a/V2a receptor antagonists. B, Known vasopressin V1a antagonists.
F.E. Romesberg, D.A. Bachovchin, P. Capek, J.K. Chin,
R.T. Cirz, M.E. Cremeens, C. Gil-Lamaignere, N. Gingles,
Y. Hari, D.A. Harris, G.T. Hwang, A.M. Leconte, E.T. Lis,
S. Matsuda, B.A. O’Neill, M.E. Powers, 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 evolutionary processes.
T
INCREASING THE CHEMICAL AND GENETIC
F i g . 4 . Known oxytocin receptor agonists.
POTENTIAL OF DNA
have yielded several extremely potent sphingosine
1-phosphate subtype agonists with low molecular
weights and druglike properties (Table 1). The best
of these are being characterized in in vivo models and
for absorption, distribution, metabolism, excretion, and
pharmacokinetic properties. These compounds are
designed to be orally active and to be immunomodu-
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 bond-
T a b l e 1 . Agonists of sphingosine 1-phosphates.
Compound
Molecular
weight, kD
Total polar
surface area,
Å2
Calculated logP
EC 50, nM
Sphingosine 1phosphate 1
Sphingosine 1phosphate 3
CYM5196
297
64.8
2.6
64
2700
CYM5200
337
64.8
3.5
72
322
CYM5202
305
46.3
4.9
83
Not applicable
CYM5178
325
64.8
3.3
0.15
397
CYM5180
311
64.8
3.3
8.8
Not applicable
CYM5181
311
64.8
3.3
3.7
661
CYM5182
326
90.8
2.9
1.7
387
CHEMISTRY
2007
THE SCRIPPS RESEARCH INSTITUTE
101
ing, 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)
F i g . 2 . Induced mutation in E coli is controlled by the transcriptional 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 (denoted by xxx; pathway D).
are also designing a drug that inhibits bacterial mutation and thus evolution.
F i g . 1 . Activity-based phage display selection system for evolv-
ing polymerases with novel activity. Infection of phage (B) with the
polymerase library (A) leads to production of phage particles that
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.
to 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 damage stress in budding yeast.
Characterization of the proteins required for mutation
in mammalian 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 these
pathways in other bacterial pathogens, including Staphylococcus aureus and Pseudomonas aeruginosa. We
EVOLUTION OF PROTEIN DYNAMICS
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 manipulate protein dynamics, a finding that suggests a role
for these dynamics in molecular recognition.
PUBLICATIONS
Cirz, R.T., Romesberg, F.E. Controlling mutation: intervening in evolution as a therapeutic strategy. Crit. Rev. Biochem. Mol. Biol. 42:341, 2007.
Goodman, M.F., Scharff, M.D., Romesberg, F.E. AID-initiated purposeful mutations
in immunoglobulin genes. Adv. Immunol. 94:127, 2007.
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. 45:7809, 2006.
Kinnaman, C.S., Cremeens, M.E., Romesberg, F.E., Corcelli, S.A. Infrared line
shape of an α-carbon deuterium-labeled amino acid. J. Am. Chem. Soc.
128:13334, 2006.
Matsuda, S., Leconte, A.M., Romesberg, F.E. Minor groove hydrogen bonds and
the replication of unnatural base pairs. J. Am. Chem. Soc. 129:5551, 2007.
O’Neill, B.M., Szyjka, S.J., Lis, E.T., Bailey, A.O., Yates, J.R. III, Aparicio, O.M.,
Romesberg, F.E. Pph3-Psy2 is a phosphatase complex required for Rad53 dephosphorylation and replication fork restart during recovery from DNA damage. Proc.
Natl. Acad. Sci. U. S. A. 104:9290, 2007.
102 CHEMISTRY
2007
THE SCRIPPS RESEARCH INSTITUTE
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.
128:14232, 2006.
Synthesis of Natural Products,
Development of Synthetic
Methods, and
Medicinal Chemistry
W.R. Roush, R. Bates, D. Bykowski, Y.-T. Chen, E. Darout,
A. DeBaillie, J. Dunetz, G. Halvorsen, M. Handa, J. Hicks,
T. Hopkins, C.-W. Huh, F. Li, R. Lira, C. Nguyen, M. Ober,
R. Pragani, J. Roth, T. Ryba, M. Tortosa, P. Va, A. Williams,
S. Winbush
ur research has 2 major themes. One is the synthesis of structurally complex, biologically active
natural products such as those shown in Figure 1.
These efforts in total synthesis are pursued in parallel
with reaction design, stereochemical studies, and the
development of new synthetic methods. We have been
particularly interested in stereochemical aspects of
intramolecular and transannular Diels-Alder reactions,
in the development of methods for the diastereoselective and enantioselective reactions of allylmetal compounds with carbonyl compounds.
Recently, we have focused on the Diels-Alder reactions of siloxacyclopentene-constrained trienes, development of new versions of the double allylboration
reactions of aldehydes with γ-boryl–substituted allylboranes for stereocontrolled synthesis of 1,5-endiols,
synthesis of highly substituted tetrahydrofurans via
[3 + 2]-annulation reactions of highly functionalized
allylsilanes, and development of phosphine-mediated
organocatalytic reactions.
Natural products of current interest to us include
amphidinolides C and F, amphidinol 3, angelmicin B,
annonaceous acetogenin analogs, durhamycin A and
analogs, integramicin, lomaiviticin A, peloruside A,
quartromicin D1, reidispongiolide A, spinosyn A biosynthetic intermediates, scytophycin C, superstolide A,
tedanolide, and tetrafibricin. We selected these molecules as targets because of their biological properties
and their interesting and complex structures. We place
a significant emphasis on the discovery, development,
and/or illustration of new reactions and synthetic methods for achieving high levels of stereochemical control
in each of these synthesis efforts.
O
F i g . 1 . Structures of recently synthesized natural products.
Our second area of major interest involves problems
in bioorganic chemistry and medicinal chemistry. One
long-term project is the design and synthesis of inhibitors of cysteine proteases isolated from tropical parasites, such as Trypanosoma cruzi, the causative agent
of Chagas disease, and Plasmodium falciparum, the
most virulent of the malaria parasites. This research is
performed in collaboration with colleagues at the Uni-
CHEMISTRY
versity of California, San Francisco. In collaboration
with S. Reed, University of California, San Diego, we
recently developed a cysteine protease inhibitor with
remarkable ability to prevent Entamoeba histolytica
from invading human intestinal tissue. New projects
at Scripps Florida involve discovery of small molecules that affect cancer and other targets, studies of
the structure-activity relationship of certain natural
products, and optimization of the pharmacologic profile of certain natural products.
PUBLICATIONS
Goetz, D.H., Choe, T., Hansell, E., Chen, Y.T., McDowell, M., Jonsson, C.B.,
Roush, W.R., McKerrow, J., Craik, C.S. Substrate specificity profiling and identification of a new class of inhibitor for the major protease of the SARS coronavirus.
Biochemistry 46:8744, 2007.
Halvorsen, G.T., Roush, W.R. Intramolecular Diels-Alder reactions of siloxacyclopentene constrained trienes. Org. Lett. 9:2243, 2007.
Lira, R., Roush, W.R. Stereoselective synthesis of the C(1)-C(19) fragment of
tetrafibricin. Org. Lett. 9:533, 2007.
Meléndez-López, S.G., Herdman, S., Hirata, K., Choi, M.-H., Choe, Y., Craik, C.,
Caffrey, C.R., Chávez-Munguía, B., Chen, Y.T., Roush, W.R., McKerrow, J., Eckmann, L., Guo, J., Stanley, S.L., Jr., Reed, S.L. Use of recombinant Entamoeba
histolytica cysteine proteinase 1 to identify a potent inhibitor of amebic invasion in
a human colonic model. Eucaryot. Cell 6:1130, 2007.
Qi, J., Roush, W.R. Synthesis of precursors of the agalacto (exo) fragment of the
quartromicins via an auxiliary-controlled exo-selective Diels-Alder reaction. Org.
Lett. 8:2795, 2006.
Trullinger, T.K., Qi, J., Roush, W.R. Studies on the synthesis of quartromicins A3
and D3: synthesis of the vertical and horizontal bis-spirotetronate fragments. J.
Org. Chem. 71:6915, 2006.
Va, P., Roush, W.R. Synthesis of 2-epi-amphidinolide E: an unexpected and highly
selective C(2) inversion during an esterification reaction. Org. Lett. 9:307, 2007.
Va, P., Roush, W.R. Total synthesis of amphidinolide E. J. Am. Chem. Soc.
128:15960, 2006.
Va, P., Roush, W.R. Total synthesis of amphidinolide E and amphidinolide E
stereoisomers. Tetrahedron 63:5768, 2007.
Biological Chemistry
P.G. Schultz, A. Boitano, E. Brustad, M. Bushey,
C. Dambacher, J. Grbic, D. Groff, J. Grünewald, J. Guo,
B. Hutchins, M. Jahnz, H. Lee, J. Lee, J.-S. Lee, K.-B. Lee,
C. Liu, W. Liu, C. Lyssiotis, J. Mills, M. Mukherji, R. Perera,
F. Peters, Y. Ryu, S. Schiller, M. Sever, V. Smider,
L. Supekova, M.-L. Tsao, J. Wang, T. Young
lthough chemists are remarkably adept at synthesizing molecular structures, they are far less
sophisticated in designing and synthesizing molecules with defined biological or chemical functions.
Nature, on the other hand, has produced an array of
molecules with remarkably complex functions, ranging
A
2007
THE SCRIPPS RESEARCH INSTITUTE
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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.
In addition, we are extending this combinatorial
approach to many other problems, including the generation of novel cellular reporters, the ab initio evolution
of novel protein domains, and the synthesis of structurebased combinatorial libraries of small heterocycles.
The libraries of small heterocycles are being used in
conjunction with novel cellular and organismal screens
to identify molecules that modulate the activity of key
proteins involved in cellular processes such as differentiation, proliferation, and apoptosis. Indeed, we have
identified molecules that both control adult and embryonic stem cell differentiation and stem cell self-renewal
and that reprogram lineage committed cells to alternative cell fates. We are using biochemical and genomics
experiments (e.g., mRNA profiling technology, affinity
chromatography, genetic complementation) to characterize the mode of action of these compounds and to
study their effects in vitro and in animal models of
regeneration. We have extended this approach to a variety of genetic and neglected diseases (e.g., malaria,
type 1 diabetes, spinal muscular atrophy, childhood
cancers). We are also developing and applying modern
genomics tools (e.g., cell-based phenotypic screens of
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arrayed genomic cDNA and small interfering RNA libraries) and proteomics tools (mass spectrometric phosphoprotein profiling) to a variety of important biomedical
problems in cancer biology, neurodegenerative 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 code of living organisms by adding new
components to the existing biosynthetic machinery. We
have genetically encoded amino acids with novel spectroscopic and chemical properties (e.g., metal-binding,
sulfated, fluorescent, chemically reactive, photocrosslinking, and photoisomerizable) 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, create novel therapeutic agents and
biomaterials, and evolve proteins with novel properties.
Recently, we have extended this approach to yeast and
mammalian cells, and we are attempting to adapt this
approach to multicellular organisms. Our results have
removed a billion-year constraint imposed by the genetic
code on the ability to chemically manipulate the structures of proteins.
PUBLICATIONS
Chen, S., Do, J.T., Zhang, Q., Yao, S., Yan, F., Peters, E.C., Schöler, H.R.,
Schultz, P.G., Ding, S. Self-renewal of embryonic stem cells by a small molecule.
Proc. Natl. Acad. Sci. U. S. A. 103:17266, 2006.
Chen, S., Takanashi, S., Zhang, Q., Xiong, W., Peters, E.C., Ding, S., Schultz,
P.G. Reversine increases the plasticity of lineage-committed mammalian cells. Proc.
Natl. Acad. Sci. U. S. A. 104:10482, 2007.
Deiters, A., Groff, D., Ryu, Y., Xie, J., Schultz, P.G. A genetically encoded photocaged tyrosine. Angew. Chem. Int. Ed. 45:2728, 2006.
Liu, C., Schultz, P.G. Recombinant expression of selectively sulfated proteins in
Escherichia coli. Nat. Biotechnol. 24:1436, 2006.
Liu, W., Brock, A., Chen, S., Chen, S., Schultz, P.G. Genetic incorporation of unnatural amino acids into proteins in mammalian cells. Nat. Methods 4:239, 2007.
Luesch, H., Chanda, S.K., Raya, R.M., DeJesus, P.D., Orth, A.P., Walker, J.R.,
Izpisúa Belmonte, J.C., Schultz, P.G. A functional genomics approach to the mode
of action of apratoxin A. Nat. Chem. Biol. 2:158, 2006.
Mukherji, M., Bell, R., Supekova, L., Wang, Y., Orth, A.P., Batalov, S., Miraglia,
L., Huesken, D., Lange, J., Martin, C., Sahasrabudhe, S., Reinhardt, M., Natt, F.,
Hall, J., Mickanin, C., Labow, M., Chanda, S.K., Cho, C.Y., Schultz, P.G. Genomewide functional analysis of human cell-cycle regulators. Proc. Natl. Acad. Sci. U. S. A.
103:14819, 2006.
Turner, J.M., Graziano, J., Spraggon, G., Schultz, P.G. Structural plasticity of an
aminoacyl-tRNA synthetase active site. Proc. Natl. Acad. Sci. U. S. A. 103:6483,
2006.
Wang, J., Xie, J., Schultz, P.G. A genetically encoded fluorescent amino acid. J.
Am. Chem. Soc. 128:8738, 2006.
THE SCRIPPS RESEARCH INSTITUTE
Xie, J., Liu, W., Schultz, P.G. A genetically encoded bidentate, metal-binding
amino acid. Angew. Chem. Int. Ed., in press.
Xie, J., Schultz, P.G. A chemical toolkit for proteins: an expanded genetic code.
Nat. Rev. Mol. Cell Biol. 7:775, 2006.
Zhang, Q., Major, M., Takanashi, S., Camp, N.D., Peters, E.C., Ginsberg, M.H.,
Jian, X., Randazzo, P.A., Schultz, P.G., Moon, R.T., Ding, S. Small-molecule synergist of the Wnt/β-catenin signaling pathway. Proc. Natl. Acad. Sci. U. S. A.
104:7444, 2007.
Click Chemistry and
Biological Activity
K.B. Sharpless, M. Ahlquist, A. Feldman, J. Fotsing,
N. Grimster, J. Hein, J. Kalisiak, K. Korthals, S.-W. Kwok,
K. Nagai, S. Pitram, J. Raushel, A. Salameh, J. Tripp,
C. Valdez, X. Wang, T. Weide
he driving forces in our research are the discovery and understanding of new chemical reactivity,
the harbingers of all new reactions. Our main
goal is to develop chemical transformations that facilitate rapid synthesis of compounds with desired properties. The degree of diversity of the building blocks
and the speed with which synthesis, screening for the
desired function, and lead optimization can be performed are important factors in the search for the new
function. 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 duglike 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 difficult to implement for synthesis and scale-up
of chemical libraries.
In the past several years, we have sought to develop
and use only the best reactions for the synthesis of functional molecules. Inspired by the natural synthesis of
myriad functional molecules (nucleic acids, proteins, and
carbohydrates) from just a handful of building blocks,
we devised a fast, reliable, and highly modular style
of organic synthesis, which we termed click chemistry.
T
CHEMISTRY
2007
Click reactions fulfill the most stringent criteria of usefulness and convenience (Fig. 1), they are highly ener-
F i g . 1 . Click chemistry: molecular diversity from a handful of
near-perfect reactions.
getically driven, and the majority of them form carbonheteroatom bonds. We use click reactions to assemble
molecules with diverse properties. The new organic
substances are obtained in short reaction sequences
that establish stable heteroatom links between building blocks. We contend that a wide variety of interesting and useful molecules can be easily made in this
way and that the chances for achieving desirable biological activity with such compounds are at least as
good as chances with the traditional target structures
now favored by medicinal chemists.
Recently, we realized that many of the click reactions work as well as, or better, in water as they do in
the organic solvents most commonly used. The second
realization, which has shaped our research program in
the past several years, was that although olefins, through
their selective oxidative functionalization, provide convenient access to reactive modules, the assembly of
these energetic blocks into the final structures is best
achieved by cycloaddition reactions involving the formation of bonds between carbons and heteroatoms,
such as 1,3-dipolar cycloadditions and hetero DielsAlder reactions.
The 1,3-dipolar cycloaddition of azides and alkynes,
most extensively studied by R. Huisgen in the 1960s,
and its copper-catalyzed version, recently discovered
by V.V. Fokin, Department of Chemistry, take a prominent place in click reactions. These transformations
enable reliable assembly of complex molecules by means
of the 1,2,3-triazole heterocycle. Experimental simplicity
and the unusually broad scope of this process enabled
a number of applications in synthesis, medicinal chemistry, molecular biology, and materials science.
Although both alkynes and azides are highly energetic, they are quite unreactive to an unusually broad
range of reagents, solvents, and other functional groups.
THE SCRIPPS RESEARCH INSTITUTE
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This inertness allows clean sequential transformations
of broad scope without the need for protecting groups,
even if the reactions are performed in aqueous solvent
in the presence of atmospheric oxygen. 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.
In addition to developing new click reactions, we
are currently engaged in a number of collaborative projects with scientists at Scripps Research and other institutions. The targets include HIV protease, in studies
with J.H. Elder and A.J. Olson, Department of Molecular Biology, and B.E. Torbett, Department of Molecular
and Experimental Medicine; acetylcholinesterase, in collaboration with P.W. Taylor and Z. Radic, University of
California, San Diego; and development of new antibacterial agents (Fig. 2), in research with S. Omura and
T. Sunazuka, Kitasato Institute, Tokyo, Japan.
F i g . 2 . Spiramycin analogs for antibacterial profiling.
PUBLICATIONS
Díaz, D.D., Converso, A., Sharpless, K.B., Finn, M.G. 2,6-Dichloro-9-thiabicyclo[3.3.1]nonane: multigram display of azide and cyanide components on a versatile scaffold. Molecules 11:212, 2006.
Hirose, T., Sunazuka, T., Noguchi, Y., Yamaguchi, Y., Hanaki, H., Sharpless, K.B.,
Omura, S. Rapid ‘SAR’ via click chemistry: an alkyne-bearing spiramycin is fused
with diverse azides to yield new triazole-antibacterial candidates. Heterocycles
69:55, 2006.
Narayan, S., Fokin, V.V., Sharpless, K.B. Chemistry ‘on water’: organic synthesis
in aqueous suspension. In: Organic Synthesis in Water: Principles, Strategies and
Applications. Lindström, U.M. (Ed.). Blackwell Publishing, Oxford, England, 2007,
p. 350.
Sharpless, K.B., Manetsch, R. In situ click chemistry: a powerful means for lead
discovery. Expert Opin. Drug Discov. 1:525, 2006.
Whiting, M., Tripp, J., Lin, Y.-C., Lindstrom, W., Olson, A.J., Elder, J.H., Sharpless, K.B., Fokin, V.V. Rapid discovery and structure-activity profiling of novel
inhibitors of human immunodeficiency virus type 1 protease enabled by the copper(I)-catalyzed synthesis of 1,2,3-triazoles and their further functionalization. J.
Med. Chem. 49:7697, 2006.
106 CHEMISTRY
2007
THE SCRIPPS RESEARCH INSTITUTE
Yoo, E.J., Ahlquist, M., Kim, S.H., Bae, I., Fokin, V.V., Sharpless, K.B., Chang, S.
Copper-catalyzed synthesis of N-sulfonyl-1,2,3-triazoles: controlling selectivity.
Angew. Chem. Int. Ed. 46:1730, 2007.
Chemistry, Biology, and
Inflammatory Disease
P. Wentworth, Jr., J.Y. Chang, Y.P. Chen, J. Dambacher,
R.K. Grover, J. Nieva, M. Puga, B.D. Song, M.M.R. Peram,
J. Rogel, S.R. Troseth, H. Wang, A.D. Wentworth
ur research is interdisciplinary and involves
aspects of bioorganic, biophysical, physical
organic, synthetic, and analytical chemistry
coupled with biochemical techniques, cell-based assays,
and animal models. Ongoing projects include studies
on atherosclerosis, neurodegenerative diseases, ischemiareperfusion 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 the 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 are searching for the active site for the antibodycatalyzed water oxidation pathway within the antibody
structure. We have cloned and expressed soluble individual domains (VHV L, CH1CL, VH, VL, CH 1, CL) of the
mouse Fab 4C6. All the domains have been successfully purified to homogeneity from the periplasm of
Escherichia coli transformed with plasmids encoding
individual domains. All the domains are folded, as
indicated by ultraviolet circular dichroism. These findings indicate that all these immunoglobulin domains
can participate in the antibody-catalyzed water oxidation pathway when activated with singlet dioxygen.
I N F L A M M AT O R Y A L D E H Y D E S A N D P R O T E I N
MISFOLDING
We have shown that the inflammation-derived
cholesterol seco-sterols atheronal-A and atheronal-B
(Fig. 1) trigger a deformation in the secondary struc-
F i g . 1 . The cholesterol seco-sterols atheronal-A (top) and
atheronal-B (bottom).
ture of the normally folded low-density lipoprotein
apoB-100 into a proamyloidogenic form. In collaboration with J.W. Kelly and colleagues, Department of
Chemistry, we extended this model and showed that
these cholesterol seco-sterols also trigger the misfolding of amyloid β-peptide1–40, leading to formation of
fibrils similar to those observed in patients with Alzheimer’s disease. More recently, using mutated synthetic
sequences of amyloid β-peptide1–40, 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 (cutaneous or visceral, Leishmania species), African trypanosomiasis (sleeping sickness, Trypanosoma brucei), and American trypanosomiasis
(Chagas disease, Trypanosoma cruzi) have limited effectiveness, increasing drug resistance and the inherent
toxic effects of the drugs. Thus, an elucidation of new
parasite-specific biological targets for therapeutic agents
is needed. In this regard, the discovery that DNA from
CHEMISTRY
2007
members of the order Kinetoplastida, but not from other
eukaryotes, contains an unusual modified base, β-D-glucosyl(hydroxymethyl)uracil, called base J was a breakthrough. Extracts of several kinetoplastids contain a
J-binding protein (JBP) that 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
has revealed no compounds of interest.
In parallel, we have studied the molecular recognition that underlies JBP-1 recognition of glycosylated
DNA. In collaboration with D.P. Millar and D.A. Case,
Department of Molecular Biology, we found that JBP-1
interacts with the J-containing DNA only when a critical conformation of the glucose within the major groove
is established (Fig. 2).
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107
Xu, Y., Hixon, M.S., Yamamoto, N., McAllister, L.A., Wentworth, A.D., Wentworth, P., Jr., Janda, K.D. Antibody-catalyzed anaerobic destruction of methamphetamine. Proc. Natl. Acad. Sci. U. S. A. 104:3681, 2007.
Bioorganic and
Synthetic Chemistry
C.-H. Wong, C. Bennett, A. Brik, S. Dean, S. Ficht, Y. Fu,
M. Fujio, W. Greenberg, R. Guy, S. Hanson, Z. Hong,
T.-L. Hsu, H.-S. Huang, D.-R. Hwang, M. Imamura,
K. Kishikawa, J.-C. Lee, P.-H. Liang, L. Liu, R.J. Payne,
T. Polat, M. Sawa, M. Sugiyama, S.-K. Wang, Y.-Y. Yang
e develop new chemical and enzymatic strategies for synthesis of bioactive small molecules
and biomolecules. We use the methods to
probe carbohydrate-mediated recognition events important in cancer, bacterial infections, inflammation, and
viral infections such as influenza and HIV.
W
SYNTHETIC METHODS
We have developed a new method, sugar-assisted
ligation, for synthesis of homogenous glycoproteins
(Fig. 1). The method makes possible the assembly of
F i g . 1 . Sugar-assisted ligation for synthesis of glycoproteins.
F i g . 2 . Surface rendering of a molecular dynamics snapshot of the
critical “edge-on” conformation of glucose (stick representation) within
the major groove essential for recognition of J-DNA by JBP-1.
PUBLICATIONS
Bieschke, J., Zhang, Q., Bosco, D.A., Lerner, R.A., Powers, E.T., Wentworth, P.,
Jr., Kelly, J.W. Small molecule oxidation products trigger disease-associated protein
misfolding. Acc. Chem. Res. 39:611, 2006.
Grover, R.K., Pond, S.J., Cui. Q., Subramanian, P., Case, D.A., Millar, D.P., Wentworth, P., Jr. O-Glycoside orientation is an essential aspect of base J recognition by
the kinetoplastid DNA-binding protein JBP1. Angew. Chem. Int. Ed. 46:2839, 2007.
Nieva, J., Shafton, A., Altobell, L.J. III, Tripurenani, S., Lerner, R.A., Wentworth,
P., Jr. Inflammatory aldehydes accelerate antibody light chain aggregation. Biochemistry, in press.
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.
complex glycoproteins via chemical synthesis, and we
are optimizing the techniques to achieve the total synthesis of therapeutic glycoproteins. Using programmable
1-pot oligosaccharide synthesis methods developed in
our laboratory, we create glycoarrays on glass slides for
high-throughput quantitative analysis of protein-carbohydrate interactions. Using enzymes as synthetic catalysts,
we have developed practical new methods of synthesizing molecules such as iminocyclitols, which are inhibitors of glycosidases and other enzymes. Using directed
evolution, we are evolving these enzymes to catalyze
new reactions and synthesize new molecules, such as
the enantiomeric form of naturally occurring sugars.
108 CHEMISTRY
2007
C A R B O H Y D R AT E - M E D I AT E D R E C O G N I T I O N I N
DISEASE
We are using our synthetic methods to discover
inhibitors and therapeutic agents in several areas. Current targets include bacterial transglycosidase, sulfotransferases, and glycoprocessing enzymes involved in the
biosynthesis of carbohydrates that mediate cancer metastasis, inflammation, and viral infections. Enzymatically
synthesized iminocyclitols are being investigated as
treatments for osteoarthritis and Gaucher disease. In
collaboration with I.A. Wilson, Department of Molecular
Biology, we are developing ligands for CD1 for activation
of natural killer T cells. These compounds represent a
promising new immunotherapeutic approach to treatment of bacterial and viral infections and of cancer. In
collaboration with D.R. Burton, Department of Immunology, we are synthesizing multivalent oligomannose antigens for use in development of an HIV vaccine.
G LY C O P R O T E O M I C S A N D M O L E C U L A R
G LY C O B I O L O G Y
Using metabolic oligosaccharide engineering, we
have developed methods for incorporating tagged sugars
into glycans expressed on mammalian cells (Fig. 2).
THE SCRIPPS RESEARCH INSTITUTE
Brik, A., Wong, C.-H. Sugar-assisted ligation for the synthesis of glycopeptides.
Chem. Eur. J. 13:5670, 2007.
Chang, Y.-J., Huang, J.-R., Tsai, Y.-C., Wu, D., Fujio, M., Wong, C.-H., Yu, A.L.
Potent immune-modulating and anticancer effects of novel NKT stimulatory glycolipids. Proc. Natl. Acad. Sci. U. S. A. 104:10299, 2007.
Dean, S.M., Greenberg, W.A., Wong, C.-H. Recent advances in aldolase-catalyzed
asymmetric synthesis. Adv. Synth. Catal. 349:1308, 2007.
Ficht, S., Payne, R.J., Brik, A., Wong, C.-H. Second-generation sugar-assisted
ligation: a method for the synthesis of cysteine-containing glycopeptides. Angew.
Chem. Int. Ed. 46:5975, 2007.
Hanson, S.R., Hsu, T.L, Weerapana, E., Kishikawa, K., Simon, G.M., Cravatt,
B.F., Wong, C.-H. Tailored glycoproteomics and glycan site mapping using saccharide-selective bioorthogonal probes. J. Am. Chem. Soc. 129:7266, 2007.
Hanson, S., Whalen, L., Wong, C.-H. Synthesis and evaluation of general mechanism-based inhibitors of sulfatases based on (difluoro)methyl phenol sulfate and
phenol cyclic sulfamate motifs. Bioorg. Med. Chem. 14:8386, 2006.
Hong, Z.-Y., Liu, L., Hsu, C.-C., Wong, C.-H. Three-step synthesis of sialic acids
and derivatives. Angew. Chem. Int. Ed. 45:7417, 2006.
Hsu, T.-L., Hanson, S.R., Kishikawa, K., Wang, S.-K., Sawa, M., Wong, C.-H.
Alkynyl sugar analogs for the labeling and visualization of glycoconjugates in cells.
Proc. Natl. Acad. Sci. U. S. A. 104:2614, 2007.
Kaltgrad, E., Sen Gupta, S., Punna, S., Huang, C.-Y., Chang, A., Wong, C.-H.,
Finn, M.G., Blixt, O. Anti-carbohydrate antibodies elicited by polyvalent display on
a viral scaffold. Chembiochem 8:1455, 2007.
Lee, J.-C., Greenberg, W.A., Wong, C.-H. Programmable reactivity-based one-pot
oligosaccharide synthesis. Nat. Protoc. 1:3143, 2006.
Liang, P.-H., Wang, S.-K., Wong, C.-H. Quantification of carbohydrate-protein
interactions using glycan microarrays: determination of surface and solution dissociation constants. J. Am. Chem. Soc. 129:11177, 2007.
Michel, M.-L., Keller, A.C., Paget, C., Fujio, M., Trottein, F., Savage, P.B., Wong,
C.-H., Schneider, E., Dy, M., Leite-de-Moraes, M.C. Identification of an IL-17-producing NK1.1NEG cell population involved in airway neutrophilia. J. Exp. Med.
204:995, 2007.
Payne, R.J., Ficht, S. Tang, S., Brik, A., Yang, Y.-Y., Case, D.A., Wong, C.-H.
Extended sugar-assisted ligations: development, scope, and applications. J. Am.
Chem. Soc. 129:13527, 2007.
Polat, T., Wong, C.-H. Anomeric reactivity-based one-pot synthesis of heparin-like
oligosaccharides. J. Am. Chem. Soc. 129:12795, 2007.
F i g . 2 . Metabolic oligosaccharide engineering and click-activated
fluorescent imaging.
Using click chemistry, we can label the engineered glycans and use fluorescent imaging to compare glycosylation patterns of different cells, such as normal vs
cancerous cells or cancer cells vs cancer stem cells.
Using tandem mass spectrometry, we are extending
this technology to proteome-wide glycoproteomic analysis, to catalog new glycoproteins and identify the effect
of different glycans on cellular function.
Sugiyama, M., Hong, Z., Liang, P.-H., Whalen, L.J., Greenberg, W.A., Wong, C.H. D-Fructose-6-phosphate aldolase catalyzed one-pot synthesis of iminocyclitols.
J. Am. Chem. Soc., in press.
Sugiyama, M., Hong, Z.-Y., Greenberg, W.A., Wong, C.-H. In vivo selection for the
directed evolution of L-rhamnulose aldolase from L-rhamnulose-1-phosphate aldolase (RhaD). Bioorg. Med. Chem. 15:5905, 2007.
Sugiyama, M., Hong, Z.-Y., Whalen, L.J., Greenberg, W.A., Wong, C.-H. Borate as
a phosphate ester mimic in aldolase-catalyzed reactions: practical syntheses of
L-fructose and L-iminocyclitols. Adv. Synth. Catal. 348:2555, 2006.
Thayer, D., Wong, C.-H. Vancomycin analogues containing monosaccharides
exhibit improved antibiotic activity: a combined one-pot enzymatic glycosylation
and chemical diversification strategy. Chem. Asian J. 1:445, 2006.
Wong, C.-H., Greenberg, W.A. Asymmetric synthesis using deoxyribose-5-phosphate aldolase. In: Asymmetric Synthesis: The Essentials. Christmann, M., Bräse,
S. (Eds.). Wiley-VCH, New York, 2007, p. 217.
PUBLICATIONS
Bennett, C.S., Wong, C.-H. Chemoenzymatic approaches to glycoprotein synthesis.
Chem. Soc. Rev. 36:1227, 2007.
Wu, D., Fujio, M., Wong, C.-H. Glycolipids as immunostimulating agents. Bioorg.
Med. Chem., in press.
Brik, A., Ficht, S., Wong, C.-H. Strategies for the preparation of homogenous glycoproteins. Curr. Opin. Chem. Biol. 10:638, 2006.
Yang, Y.-Y., Ficht, S., Brik, A., Wong, C.-H. Sugar-assisted ligation in glycoprotein
synthesis. J. Am. Chem. Soc. 129:7690, 2007.
Brik, A., Ficht, S., Yang, Y.-Y., Bennett, C., Wong, C.-H. Sugar-assisted ligation of
N-linked glycopeptides with broad sequence tolerance at the ligation junction. J.
Am. Chem. Soc. 128:15026, 2006.
Yu, Z., Sawkar, A.R., Whalen, L.J., Wong, C.-H., Kelly, J.W. Isofagomine- and
2,5-anhydro-2,5-imino-D-glucitol-based glucocerebrosidase pharmacological chaperones for Gaucher disease intervention. J. Med. Chem. 50:94, 2007.