Small Molecules and Proteins: Targeting Cancer
In targeting cancer, we take a multidisciplinary approach that involves gene regulation, catalytic antibodies, drug design, and combinatorial antibody libraries. Using a chemically programmed antibody strategy, we recently showed the power of combining small-molecule chemistry with immunochemistry. We designed small-molecule integrin antagonists to self-assemble into a covalent complex with antibody 38C2. The resulting chemically programmed antibody had significant advantages compared with small molecules or antibody alone in studies of metastatic melanoma (Fig. 2) and breast cancer. With catalytic antibodies, we are also developing strategies to activate drugs in a highly specific fashion at the site of cancer.
Designer Transcription Factors and Recombinases
From the simplest to the most complex, proteins that bind nucleic acids are involved in orchestrating gene expression. The nucleic acids DNA and RNA are the molecules that store the recipes of all life forms. The fertilized egg of a human contains the genetic recipe for the development and differentiation of a single cell into 2 cells, 4 cells, and so on, finally yielding a complete individual. The coordinated expression or reading of the recipes for life allows cells containing the same genetic information to perform different functions and to have distinctly different physical characteristics. Proteins that bind nucleic acids enable this coordinated control of the genetic code. Lack of coordination due to genetic defects or to viral seizure of control of the cell results in disease.
In one project, we are developing methods to produce proteins that bind to specific DNA sequences to control specified genes. As we showed earlier, these proteins can be used as specific genetic switches to turn on or turn off genes on demand, creating an operating system for genomes. To this end, we selected and designed specific zinc finger domains that will constitute an alphabet of 64 domains that will allow any DNA sequence to be bound selectively. The prospects for this second genetic code are fascinating and should have a major impact on basic and applied biology.
Billions of transcription factors can now be prepared by using our approach. Our goal is to develop a new class of therapeutic proteins that inhibit or enhance the synthesis of proteins, providing a new strategy for fighting diseases of either somatic or viral origin.
Using a novel library of transcription factors, we developed a strategy that effectively allows us to turn on and turn off every gene in the genome. We recently extended this approach to enable us to endow enzymes with sequence specificity of our own design through the creation of zinc finger recombinases (Fig. 3). We think these new enzymes will allow us to insert or delete genes with surgical precision within the genome.
Cheong, P.H-Y., Zhang, H., Thayumanavan, R., Tanaka, F., Houk, K.N., Barbas, C.F. III. Pipecolic acid-catalyzed direct asymmetric Mannich reactions. Org. Lett. 8:811, 2006.
Chowdari, N.S., Ahmad, M., Albertshofer, K., Tanaka, F., Barbas, C.F. III. Expedient synthesis of chiral 1,2- and 1,4-diamines: protecting group dependent regioselectivity in direct organocatalytic asymmetric Mannich reactions. Org. Lett. 8:2839, 2006.
Eberhardy, S.R., Goncalves, J., Coelho, S., Segal, D.J., Berkhout, B., Barbas, C.F. III. Inhibition of human immunodeficiency virus type 1 replication with artificial transcription factors targeting the highly conserved primer-binding site. J. Virol. 80:2873, 2006.
Gordley, R.M., Smith, J.D., Graslund, T., Barbas, C.F. III. Evolution of programmable zinc finger recombinases with activity in human cells. J. Mol. Biol., in press.
Guo, F., Das, S., Mueller, B.M., Barbas, C.F. III, Lerner, R.A., Sinha, S.C. Breaking the one antibody-one target axiom. Proc. Natl. Acad. Sci. U. S. A. 103:11009, 2006.
Mandell, J., Barbas, C.F. III. Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Res. 34(Web server issue):516, 2006.
Mase, N., Nakai, Y., Ohara, H., Yoda, H., Takabe, K., Tanaka, F., Barbas, C.F. III. Organocatalytic direct asymmetric aldol reactions in water. J. Am. Chem. Soc. 128:734, 2006.
Mase, N., Watanabe, K., Yoda, H., Takabe, K., Tanaka, F., Barbas, C.F. III. Organocatalytic direct Michael reaction of ketones and aldehydes with β-nitrostyrene in brine. J. Am. Chem. Soc. 128:4966, 2006.
Mitsumori, S., Zhang, H., Cheong, P.H-Y., Houk, K.N., Tanaka, F., Barbas, C.F. III. Direct asymmetric anti-Mannich-type reactions catalyzed by a designed amino acid. J. Am. Chem. Soc. 128:1040, 2006.
Nathan, S., Rader, C., Barbas, C.F. III. Neutralization of Burkholderia pseudomallei protease by Fabs generated through phage display. Biosci. Biotechnol. Biochem. 69:2302, 2005.
Popkov, M., Rader, C., Gonzalez, B., Sinha, S.C., Barbas, C.F. III. Small molecule drug activity in melanoma models may be dramatically enhanced with an antibody effector. Int. J. Cancer 119:1194. 2006.
Segal, D.J., Crotty, J.W., Barbas, C.F. III, Horton, N.C. Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA. J. Mol. Biol. 363:405, 2006.
Suri, J.T., Mitsumori, S., Albertshofer, K., Tanaka, F., Barbas, C.F. III. Dihydroxyacetone variants in the organocatalytic construction of carbohydrates: mimicking tagatose and fuculose aldolases. J. Org. Chem. 71:3822, 2006.
Swan, C.H., Buhler, B., Tschan, M.P., Barbas, C.F. III, Torbett, B.E. T-cell protection and enrichment through lentiviral CCR5 intrabody gene delivery. Gene Ther. 13:1480, 2006.
Tan, W., Dong, Z., Wilkinson, T.A., Barbas, C.F. III, Chow, S.A. Human immunodeficiency virus type 1 incorporated with fusion proteins consisting of integrase and the designed polydactyl zinc finger protein E2C can bias integration of viral DNA into a predetermined chromosomal region in human cells. J. Virol. 80:1939, 2006.
Zhang, H., Mifsud, M., Tanaka, F., Barbas, C.F. III. 3-Pyrrolidinecarboxylic acid for direct catalytic asymmetric anti-Mannich-type reactions of unmodified ketones. J. Am. Chem. Soc. 128:9630, 2006.