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The Skaggs Institute
for Chemical Biology

Scientific Report 2005

Synthetic, Medicinal, and Bioorganic Chemistry

D.L. Boger, S.B. Boga, K. Bunker, K. Capps, Y. Choi, Y. Chong, R. Clark, J. Cottell, B. Crowley, J. DeMartino, R. Dominique, W. Du, G. Elliott, J. Fuchs, J. Garfunkle, Y.W. Ham, A. Hamasaki, N. Haq, S. Hong, D. Horne, I. Hwang, H. Ishikawa, W. Jin, D. Kastrinsky, M. Kelso, G. Kim, B. Lawhorn, S. Lee, Y. Li, K. MacMillan, J. Nam, S. Pfeiffer, Y. Rew, A. Romero, M. Schnermann, A. Shaginian, D. Shin, C. Slown, L. Takaoka, H. Tao, M. Tichenor, J. Trzupek

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.

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 exploration of yatakemycin. In the course of these studies, 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 a total synthesis of the natural product in efforts that provided both the natural product and the unnatural enantiomer. The unnatural enantiomer was just as effective and as potent as the natural product itself. These efforts not only provided a sufficient amount of the scarce natural product for more detailed studies of its properties but also allowed the assignment of its previously 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 the product (Fig. 1).

Fig. 1. Structure reassignment of yatakemycin based on total synthesis of the natural product.

Vancomycin and Related Glycopeptide Antibiotics

Vancomycin and its family of related naturally occurring glycopeptides, which include teicoplanin and ristocetin, are used to treat bacterial infections caused by microorganisms that are 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 of the 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 properties of members of the vancomycin family and to explore approaches to improvements in their biological properties, we developed an efficient de novo synthesis of the aglycons of these antibiotics. This research recently culminated in the first total synthesis of the ristocetin A aglycon (Fig. 2A).

Fig. 2. A, Structure of ristocetin A aglycon. B, Structure of [ψ[CH2NH]Tpg4]vancomycin aglycon.

The emergence of vancomycin resistance is associated with an alteration of the precursor in the bacterial wall 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 principally to destabilizing lone pair interactions (100-fold) rather than to the simple loss of a single hydrogen bond (10-fold) in the bound complex. In turn, 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 (Fig. 2B). Examination of this aglycon will reveal whether such a reengineering of vancomycin will provide antibiotics active against vancomycin-sensitive or vancomycin-resistant bacteria.

Ramoplanin, a naturally occurring complex of 3 components, is emerging as a new and potent agent 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 both the ramoplanin A1 and A3 aglycons, 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, is slightly more potent and much more stable than the natural product and provides a stable template for detailed structure-function studies (Fig. 3).

Fig. 3. Structures of ramoplanins.


Chen, L., Yuan, Y., Helm, J.S., Hu, Y., Rew, Y., Shin, D., Boger, D.L., Walker, S. Dissecting ramoplanin: mechanistic analysis of synthetic ramoplanin analogues as a guide to the design of improved antibiotics. J. Am. Chem. Soc. 126:7462, 2004.

Crowley, B.M., Mori, Y., McComas, C.C., Tang, D., Boger D.L. Total synthesis of the ristocetin aglycon. J. Am. Chem. Soc. 126:4310, 2004.

Ham, Y.W., Boger, D.L. A powerful selection assay for mixture libraries of DNA alkylating agents. J. Am. Chem. Soc. 126:9194, 2004.

Kastrinsky, D.B., Boger, D.L. Effective asymmetric synthesis of 1,2,9,9a-tetrahydrocyclopropa[c]benzo[e]indol-4-one (CBI). J. Org. Chem. 69:2284, 2004.

Lee, P.S., Du, W., Boger, D.L., Jorgensen, W.L. Energetic preferences for α,β versus β,γ unsaturation. J. Org. Chem. 69:5448, 2004.

Lichtman, A.H., Leung, D., Shelton, C.C., Saghatelian, A., Hardouin, C., Boger, D.L., Cravatt, B.F. Reversible inhibitors of fatty acid amide hydrolase that promote analgesia: evidence for an unprecedented combination of potency and selectivity. J. Pharmacol. Exp. Ther. 311:441, 2004.

Lillo, A.M., Sun, C., Gao, C., Ditzel, H., Parrish, J., Gauss, C.-M., Moss, J., Felding-Habermann, B., Wirsching, P., Boger, D.L., Janda, K.D. A human single-chain antibody specific for integrin α3β 1 capable of cell internalization and delivery of antitumor agents. Chem. Biol. 11:897, 2004.

Parrish, J.P., Hughes, T.V., Hwang, I., Boger, D.L. Establishing the parabolic relationship between reactivity and activity for derivatives and analogues of the duocarmycin and CC-1065 alkylation subunits. J. Am. Chem. Soc. 126:80, 2004.

Parrish, J.P., Trzupek, J.D., Hughes, T.V., Hwang, I., Boger, D.L. Synthesis and evaluation of N-aryl and N-alkenyl CBI derivatives. Bioorg. Med. Chem. 12:5845, 2004.

Rew, Y., Shin, D., Hwang, I., Boger D.L. Total synthesis and examination of three key analogues of ramoplanin: a lipoglycodepsipeptide with potent antibiotic activity. J. Am. Chem. Soc. 126:1041, 2004.

Shin, D., Rew, Y., Boger, D.L. Total synthesis and structure of the ramoplanin A1 and A3 aglycons: two minor components of the ramoplanin complex. Proc. Natl. Acad. Sci. U. S. A. 101:11977, 2004.

Tao, H., Hwang, I., Boger, D.L. Multidrug resistance reversal activity of permethyl ningalin B amide derivatives. Bioorg. Med. Chem. Lett. 14:5979, 2004.

Tichenor, M.S., Kastrinsky, D.B., Boger, D.L. Total synthesis, structure revision, and absolute configuration of (+)-yatakemycin. J. Am. Chem. Soc. 126:8396, 2004.

Tse, W.C., Boger, D.L. A fluorescent intercalator displacement assay for establishing DNA binding selectivity and affinity. Acc. Chem. Res. 37:61, 2004.

Tse, W.C., Boger, D.L. Sequence-selective DNA recognition: natural products and Nature’s lessons. Chem. Biol. 11:1607, 2004.


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

Boger Web Site