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The Skaggs Institute
for Chemical Biology

Scientific Report 2008

Synthetic, Medicinal, and Bioorganic Chemistry

D.L. Boger, E. Anderson, Y. Ando, K. Boyle, C. Burke, R. Clark, D. Colby, C. Crane, J. DeMartino, K. Duncan, C. Ezzili, J. Garfunkle, H. Ge, D. Hochstatter, I. Hwang, R. Jones, H. Kakei, D. Kato, F.S. Kimball, J. Lajiness, S. Lee, K. MacMillan, K. Otrubova, P. Patel, W. Robertson, R. Rodriguez, Y. Sasaki, M. Schnermann, S. Seto, H. Shimamura, C. Slown, S. Stamm, J. Stover, D. Swingle, S. Takizawa, A. Tam, P. Va, L. Whitby, A. Wolfe, J. Xie, A. Zuhl

The research interests of our group include the total synthesis of biologically active natural products, the development of new synthetic methods, heterocyclic chemistry, bioorganic and medicinal chemistry, combinatorial chemistry, the study of DNA-agent interactions, and the chemistry of antitumor antibiotics. We place a special emphasis on investigations to define the structure-function relationships of natural or designed agents in efforts to understand the origin of the biological properties.

Fatty Acid Amide Hydrolase Inhibitors

Inhibiting fatty acid amide hydrolase (FAAH) increases endogenous levels of anandamide, which in turn leads to analgesia in models of neuropathic and chronic pain. Extending studies conducted in collaboration with R.A. Lerner and B.F. Cravatt, the Skaggs Institute, that led to the identification, isolation, characterization, and delineation of the functional role of FAAH, we have developed a series of exceptionally potent and selective inhibitors of FAAH ( α-ketoheterocycles) that are active in vivo in all rodent models of pain examined. The most extensively studied of the inhibitors to date (e.g., OL-135 at 20 mg/kg) are as efficacious as morphine (at 1—3 mg/kg), ibuprofen (at 100 mg/kg), and gabapentin (at 500 mg/kg) and, unlike ibuprofen and gabapentin, maintain activity across all rodent pain models (Fig. 1). This research constitutes a well-defined translation of basic science (target discovery, target structure) into useful tools (inhibitors of enzyme for target validation) and their further development into potential therapeutic agents (optimization for in vivo efficacy).
Fig. 1.Profile of a prototypical FAAH inhibitor.

DNA-Binding Agents

Our continuing examination of naturally occurring antitumor agents that derive their biological properties through sequence-selective DNA binding resulted in a detailed study of yatakemycin. We defined the exceptional potency of the natural material; characterized its DNA alkylation properties, consisting of an adenine N3 alkylation central to a 5-bp adenine-thymine–rich site; and conducted first- and second-generation syntheses of the natural product in efforts that provided both the natural and the unnatural enantiomers. The unnatural enantiomer was just as effective and potent as the natural product itself.

These efforts not only provided a sufficient amount of the scarce natural product for detailed studies of its properties but also enabled the assignment of its unknown absolute configuration. Unexpectedly, these efforts also led to a reassignment of the structure of the natural product and revealed a new group (thiomethyl ester) in the molecule that contributes to the properties of yatakemycin. With the systematic preparation of more than 70 analogs, we have defined key structural features responsible for the biological properties of this antitumor agent.

Vancomycin and Related Glycopeptide Antibiotics

Vancomycin and its family of related naturally occurring glycopeptides, which include teicoplanin and ristocetin, are potent antibiotics used to treat infections caused by microorganisms resistant to other antibiotics. Antibiotics in the vancomycin family inhibit the synthesis of bacterial cell walls by binding to the terminal D-Ala-D-Ala of the precursor cell wall peptidoglycan, thereby inhibiting the action of transpeptidases and transglycosylases required to complete the cell wall synthesis.

As part of a program to define the structural features that contribute to the activity of members of the vancomycin family and to explore approaches to improve the biological properties of the drugs, we developed an efficient de novo synthesis of the aglycons of these antibiotics. The emergence of vancomycin resistance is associated with an alteration of the bacterial cell wall precursor to D-Ala-D-Lac, resulting in a 1000-fold loss in vancomycin binding affinity and antimicrobial activity.

We showed experimentally that this loss in binding affinity is due primarily to destabilizing lone-pair interactions (100-fold) rather than to the simple loss of a single hydrogen bond (10-fold) in the bound complex (Fig. 2). This finding has consequences on the reengineering of vancomycin to bind D-Ala-D-Lac so that antimicrobial activity against vancomycin-resistant bacteria can be restored. We recently completed the total synthesis of the [ ψ[CH2NH]Tpg4]vancomycin aglycon in which the residue 4 carbonyl and its destabilizing lone pairs have been removed from the vancomycin structure. Examination of this aglycon revealed that such a reengineering of vancomycin provides antibiotics active against vancomycin-sensitive and vancomycin-resistant bacteria.
Fig. 2. Origin of vancomycin-destabilized binding to D-Ala-D-Lac.

Ramoplanin, a naturally occurring complex of 3 components, represents a new and potent antibiotic effective against antibiotic-resistant bacteria, including vancomycin-resistant strains. As a complement to our studies on the reengineering of vancomycin, we are examining this new class of antibiotics. To date, this research has resulted in the total synthesis of the ramoplanin A2 aglycon (major component of the complex), the total synthesis and structural reassignment of the ramoplanin A1 and A3 aglycons (minor components), and the preparation of a series of key analogs. One analog, [Dap2]ramoplanin A2 aglycon in which the labile depsipeptide ester is replaced by a stable amide, was slightly more potent and much more stable than the natural product and provided a stable template for detailed structure-function studies.


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 [published correction appears in Proc. Natl. Acad. Sci. U. S. A. 104:6490, 2008]. Proc. Natl. Acad. Sci. U. S. A. 104:2602, 2007.

Hardouin, C., Kelso, M.J., Romero, F.A., Rayl, T.J., Leung, D., Hwang, I., Cravatt, B.F., Boger, D.L. Structure-activity relationships of the α-ketooxazole inhibitors of fatty acid amide hydrolase. J. Med. Chem. 50:3359, 2007.

Ishikawa, H., Boger, D.L. Total synthesis of (–)- and ent-(+)-4-desacetoxy-5-desethylvindoline. Heterocycles 72:95, 2007.

Jin, W., Trzupek, J.D., Rayl, T.J., Broward, M.A., Vielhauer, G.A., Weir, S.J., Hwang, I., Boger, D.L. A unique class of duocarmycin and CC-1065 analogues subject to reductive activation. J. Am. Chem. Soc. 129:15391, 2007.

Lee, S.Y., Clark, R.C., Boger, D.L. Total synthesis, stereochemical reassignment, and absolute configuration of chlorofusin. J. Am. Chem. Soc. 129:9860, 2007.

Nam, J., Shin, D., Rew, Y., Boger, D.L. Alanine scan of [L-Dap2]ramoplanin A2 aglycon: assessment of the importance of each residue. J. Am. Chem. Soc. 129:8747, 2007.

Romero, F.A., Du, W., Hwang, I., Rayl, T.J., Kimball, F.S., Leung, D., Hoover, H.S., Apodaca, R.L., Breitenbucher, J.G., Cravatt, B.F., Boger, D.L. Potent and selective α-ketoheterocycle-based inhibitors of the anandamide and oleamide catabolizing enzyme, fatty acid amide hydrolase. J. Med. Chem. 50:1058, 2007.

Tichenor, M.S., MacMillan, K.S., Stover, J.S., Wolkenberg, S.E., Pavani, M.G., Zanella, L., Zaid, A.N., Spalluto, G., Rayl, T.J., Hwang, I., Baraldi, P.G., Boger, D.L. Rational design, synthesis, and evaluation, of key analogues of CC-1065 and the duocarmycins. J. Am. Chem. Soc. 129:14092, 2007.

Tichenor, M.S., MacMillan, K.S., Trzupek, J.D., Rayl, T.J., Hwang, I., Boger, D.L. Systematic exploration of the structural features of yatakemycin impacting DNA alkylation and biological activity. J. Am. Chem. Soc. 129:10858, 2007.

Xu, L., Chong, Y., Hwang, I., D'Onofrio, A., Amore, K., Beardsley, G.P., Li, C., Olson, A.J., Boger, D.L., Wilson, I.A. Structure-based design, synthesis, evaluation, and crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase. J. Biol. Chem. 282:13033, 2007.


Dale L. Boger, Ph.D.
Richard and Alice Cramer Professor of Chemistry of Molecular and Experimental Medicine

Boger Web Site