Using this method, we directly synthesized a wide variety of α and β amino acids, carbohydrates, and lactams. Stereochemically complex molecules can now be assembled by using small molecules in a manner analogous to that of natural enzymes. Novel catalyst designs have enabled us to synthesize particular diastereoisomers previously not accessible with proline, and we envision that this approach will largely replace the use of aldolase enzymes in synthesis.
Chemically Programmed Antibodies
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, colon, and breast cancer. We recently developed a powerful new approach to a programmable vaccine strategy based on a universal vaccination that elicits programmable antibodies (Fig. 2).
Designer Transcription Factors and Enzymes
From the simplest to the most complex, proteins that bind nucleic acids are involved in orchestrating gene expression. 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. 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 a variety of enzymes with sequence specificity of our own design (Fig. 3). In the future, these new enzymes will enable us to insert, delete, or otherwise modify genes with surgical precision within any genome.
Abraham, S., Guo, F., Li, L.-S., Rader, C., Liu, C., Barbas, C.F. III, Lerner, R.A., Sinha, S.C. Synthesis of the next-generation therapeutic antibodies that combine cell targeting and antibody-catalyzed prodrug activation. Proc. Natl. Acad. Sci. U. S. A. 104:5584, 2007.
Albertshofer, K., Thayumanavan, R., Utsumi, N., Tanaka, F., Barbas, C.F. III. Amine-catalyzed Michael reactions of an aminoaldehyde derivative to nitroolefins. Tetrahedron Lett. 48:693, 2007.
Barbas, C.F. III. Organocatalysis lost: modern chemistry, ancient chemistry, and an unseen biosynthetic apparatus. Angew. Chem. Int. Ed. 47:42, 2008.
Doppalapudi, V.R., Tryder, N., Li, L., Aja, T., Griffith, D., Liao, F.F., Roxas, G., Ramprasad, M.P., Bradshaw, C., Barbas, C.F. III. Chemically programmed antibodies: endothelin receptor targeting CovX-Bodies. Bioorg. Med. Chem. Lett. 17:501, 2007.
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. 367:802, 2007.
Nomura, W., Barbas, C.F. III. In vivo site-specific DNA methylation with a designed sequence-enabled DNA methylase. J. Am. Chem. Soc. 129:8676, 2007.
Rader, C., Barbas, C.F. III. Synthetic antibodies prey on B cells. Blood 108:2889, 2006.
Ramasastry S.S.V., Albertshofer, A., Utsumi, N., Tanaka, F., Barbas, C.F. III. Mimicking fructose and rhamnulose aldolases: organocatalytic syn-aldol reactions with unprotected dihydroxyacetone. Angew. Chem. Int. Ed. 46:5572, 2007.
Ramasastry, S.S.V., Zhang, H., Tanaka, F., Barbas, C.F. III. Direct catalytic asymmetric synthesis of anti-1,2-amino alcohols and syn-1,2-diols through organocatalytic anti-Mannich and syn-aldol reactions. J. Am. Chem. Soc. 129:288, 2007.
Shamis, M., Barbas, C.F. III, Shabat, D. A new visual screening assay for catalytic antibodies with retro-aldol retro-Michael activity. Bioorg. Med. Chem. Lett. 17:1172, 2006.
Sinha, S.C., Das, S., Li, L.-S., Lerner, R.A., Barbas, C.F. III. Preparation of integrin αβ3-targeting Ab 38C2 constructs. Nat. Protoc. 2:449, 2007.
Tanaka, F., Barbas, C.F. III. Aldol and Mannich-type reactions. In: Enantioselective Organocatalysis: Reactions and Experimental Procedures. Dalko, P.I. (Ed.). Wiley-VCH, Weinheim, Germany, 2007, p. 19.
Tanaka, F., Fuller, R.P., Asawapornmongkol, L., Warsinke, A., Gobuty, S., Barbas, C.F. III. Development of a small peptide tag for covalent labeling of proteins. Bioconjug. Chem. 18:1318, 2007.
Utsumi, N., Imai, M., Tanaka, F., Ramasastry, S.S.V., Barbas, C.F. III. Mimicking aldolases through organocatalysis: syn-selective aldol reactions with protected dihydroxyacetone. Org. Lett. 9:3445, 2007.
Utsumi, N., Zhang, H., Tanaka, F., Barbas, C.F. III. A way to highly enantiomerically enriched aza-Morita-Baylis-Hillman-type products. Angew. Chem. Int. Ed. 46:1878, 2007.
Zhang, H., Mitsumori, S., Utsumi, N., Imai, M., Garcia-Delgado, N., Mifsud, M., Albertshofer, K., Cheong, P.H., Houk, K.N., Tanaka, F., Barbas, C.F. III. Catalysis of 3-pyrrolidinecarboxylic acid and related pyrrolidine derivatives in enantioselective anti-Mannich-type reactions: importance of the 3-acid group on pyrrolidine for stereocontrol. J. Am. Chem. Soc. 130:875, 2008.