• Carlos F. Barbas, III, Ph.D.

    Kellogg Professor and Chair in Molecular Biology
    The Skaggs Institute for Chemical Biology
    and the Departments of Chemistry and Cell & Molecular Biology

  •   The Scripps Research Institute
    10550 North Torrey Pines Rd.
    La Jolla, CA 92037

  • Carlos F. Barbas, III, Ph.D. 
    Roberta  Fuller, Sr. Res. Assistant 
    Thom  Gaj, Ph.D. 
    Jarlath  Garcia 
    Xianxing  Jiang, Ph.D. 
    Brian  Lamb, Ph.D. 
    Robyn  Leary, Ph.D. 
    Jia  Liu, Ph.D. 
  • Mishelle  McClanahan-Shinn 
    Pedro  Perdigão 
    Bianca  Romana 
    Jingjing  Song 
    Mark  Wallen 
    Wei  Zhang, Ph.D. 
    Michael  Zorniak, Ph.D. 
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    The Barbas Laboratory Research


    pComb3X is the newest of the pComb vectors. Improvements over pComb3 include increased stability and introduction of SfiI cassette for cloning of full Fab, scFv, peptide and other protein for phage display. 6xHis and HA tags allow for purification and detection. An amber stop codon was introduced to turn-off expression of the pIII fusion protein by switching to a non-supressor strain of E. coli allowing production of soluble protein without subcloning. Alternatively, the gene for phage protein pIII can be removed by SpeI/NheI digest. pComb3XSS is the vector we normally ship. The “SS” refers to the double stuffer, a 1200bp stuffer in the Fab light chain cloning region bounded by SacI and XbaI restriction sites and a 300bp stuffer in Fab heavy chain cloning region bound by XhoI and SpeI restriction sites. Also, the 1600bp double stuffer (both stuffer plus the leader sequence between the Fab light chain and heavy chain cloning regions) can be removed by SfiI digest so that non-Fab genes of interest can also by cloned. pComb3XTT and pComb3XLambda are only needed for the construction of chimeric Fab libraries as described in Phage Display: A Laboratory Manual. The “TT” refers to the human Fab to tetanus toxin from which the kappa light chain constant region and Fd can be amplified. pComb3XLambda contains a non-functional Fab from which the lambda light chain constant region can be amplified.

    ZF Tools was created by Jeff Mandell for the Barbas Laboratory at TSRI. The purpose of the site is to assist researchers who want to design zinc finger proteins (ZFPs). Although the rules describing how ZFPs recognizing a specific DNA sequence can be constructed are well described, their application is not always straightforward. ZF Tools can save researchers the substantial time and effort required to design ZFPs. ZF Tools will also identify DNA sites that can be targeted by ZFPs, thus making it possible to quickly scan any DNA sequence for potential target sites.

    The ability to directly design proteins that efficiently perform predefined tasks would have a profound impact on science and on the everyday life of human beings. Designer proteins might enable us to dissect biological pathways and mechanisms, rapidly create and synthesize new drugs, use natural resources efficiently, and create new agricultural products. These proteins might help explain our past and define our future.

    If you have a dream of developing a new therapeutic approach, you should see the 1940 Warner Brothers film entitled "Dr. Ehrlich's Magic Bullet". The film chronicles the life of Paul Erhlich and his development of both antibody therapeutics in serum therapy and the first targeted small molecule therapeutic, Salvarson or "606" for the treatment of syphilis. Everything from 'high-throughput' screening leading to the identification of compound number 606 as the lead molecule, to the tribulations of 'phase 4' studies and the realization that drugs can have unexpected side effects in certain individuals are recounted.

    Since Ehrlich's recognition of the potential of antibodies as therapeutic agents in the early twentieth century, the development of monoclonal antibody (mAb) technology in the 1970s, and more recently the development of antibody phage libraries, mAbs have gained importance for the treatment of a variety of diseases. In addition to a dozen mAbs approved by the US Food and Drug Administration, a considerable number of biotechnology drugs in development are mAbs and recent IND applications for mAbs have eclipsed those filed for small molecules. The mounting success of the antibody molecule as a therapeutic agent is based on at least three properties; (i) an Fab moiety that permits antigen binding with high specificity and affinity, (ii) an Fc moiety that mediates effector functions, such as antibody-dependent cellular cytotoxicity (ADCC), and (iii) a molecular weight of at least 150 kD that permits a circulatory half-life of up to 21 days. By contrast, conventional therapeutic agents based on small synthetic molecules and peptides are clearly limited with respect to their short half-life in circulation, particularly in chronic treatment regimens like those needed in cancer therapy, and their inability to mediate effector functions. Unlike therapeutic antibody development that faces limitations in terms of manufacturing due to bioreactor requirements, industry has proven itself capable of manufacturing a very large diversity of small molecule drugs in large-scale and most drugs are small molecules.

    Our development of Chemically Programmed Antibodies is based on recognition of both the strengths and weaknesses of small molecule and antibody approaches and the development of an approach that creates new immunotherapeutics by drawing on the relative strengths of both. We suggest that a blend of the unlimited chemical diversity of small synthetic molecules with the longer serum half-life and the effector function of an antibody molecule will lead to therapeutic agents with superior properties. Inspired by Ehrlich, we aim to test this hypothesis with this new class of Magic Bullets.

    In Search of Beautiful Reactions: Organocatalysis


    Beautiful Reaction- a reaction facilitated by an environmentally safe catalyst in an environmentally safe solvent. Ideally, multiple reaction components are assembled in a diastereo- and enantiospecific fashion to furnish stereochemically complex products in a single step without by products.


    Our interest in organocatalysis was piqued in 1997 when we initiated comparative studies of aldolase antibodies with L-Proline, the well-known catalyst of the intramolecular Hajos-Eder-Sauer-Wiechert reaction, an enantiogroup-differentiating aldol cyclodehydration reaction. Evidence suggested that this intramolecular proline-catalyzed reaction proceeds via an enamine reaction mechanism much like our aldolase antibodies. Mechanistically then, catalysis with antibody aldolases and the simple amino acid proline are very similar. We then demonstrated that our aldolase antibodies were actually better catalysts than proline in the intramolecular Hajos-Eder-Sauer-Wiechert reaction and in fact could catalyze the Michael step as well as the aldol step of this annulation reaction. Empowered by our findings with aldolase antibodies, we screened a wide variety of amino acids and chiral amines with and without additives for catalysis of the U.V. active retro-aldol reaction we developed to facilitate reaction screening with aldolase antibodies under the premise that catalysts better than proline might be readily discovered. In late 1998, after performing several hundreds of assays in order to best the known catalyst proline, the technician assigned to this project, Tommy Bui*, reported that despite his efforts proline and hydroxyproline remained most active catalysts in the aldol reaction and organocatalysis with proline was reborn. Proline provided us with the open active-site catalyst we had been searching for in our promiscuous aldolase antibodies and it allowed us to catalyze reactions that failed with aldolase antibodies due to substrate restrictions.

    Nucleic acid libraries provide tremendous opportunities for the selection of novel ligands and catalysts since the polymerase chain reaction, PCR, allows for the synthesis and selection of libraries containing more than 1014 different molecules. There are now many examples of nucleic acids that have been selected to bind proteins and small molecules and to catalyze a limited set of reactions. The catalytic and mechanistic scope of nucleic acids is limited since the natural nucleotide monomers possess minimal functionality compared to the repertoire available to Nature's dominant catalytic biopolymers, proteins. In recognition of this shortcoming, much attention has been focused on the development of functionalized nucleotides suitable for in vitro selection with the hope of increasing the potential of nucleic acids for binding and catalysis. Functionalized nucleotide triphosphates have been shown to be substrates for RNA polymerases and catalytic RNA's dependent on the modified base for their activity have been selected. Like RNA, DNA has also been selected to bind proteins and small molecules and more recently to catalyze reactions. While DNA possesses enhanced stability as compared to RNA, the lack of a 2'-hydroxyl group which provides for the enhanced stability of this molecule further reduces the functionality available to this molecule for chemistry. In contrast to the success achieved in identifying modified nucleotide triphosphates for RNA libraries, prior to our work there was but a single a deoxynucleotide triphosphate, 5-(1-pentynyl)-2'deoxyuridine triphosphate, that had been demonstrated to be a good substrate for a thermostable DNA polymerase and utilized in an in vitro DNA selection study. Indeed, difficulties in identifying modified deoxynucleotide triphophates substrates for the thermostable polymerases required for PCR have led recently to the development of novel strategies for in vitro selection without enzymatic amplification.

    The major focus and driving vision of our laboratory concerns learning nature's strategies or improving upon them to develop new therapeutic approaches to human diseases through studies at the interface of synthetic organic chemistry, molecular biology, and medicine. Key accomplishments pioneered by us and our colleagues include the development of the first human and synthetic antibody phage libraries, the development of the first artificial transcription factors capable of regulating endogenous genes, and chemically programmed antibodies. Each of these approaches, first developed in this laboratory, has resulted in a new drug class that is currently in clinical trials for the treatment of a variety of diseases and in some cases validated with approved drugs created using these approaches. Several antibody drugs created using our methods are now approved drugs and many new antibody drugs are advancing in clinical studies. Sangamo Biosciences Inc. is advancing our zinc finger transcription factors in several clinical trials through a license to our patents in this area. CovX Inc., of which Professor Barbas is the founder, is advancing chemically programmed antibodies in clinical trials as well.

    In all organisms, from the simplest to the most complex, proteins that bind nucleic acids control the expression of genes. 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 two cells, four 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.

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