Rubedo is the transcendence, the final achievement of the goal. As an organic chemist and molecular biologist, my rubedo crystallizes in the purity of a cure: a cure for a disease. A rubedo envisioned since I was a child. My course has not been direct, but has taken a number of turns. Sometimes we are distracted. Serendipity has stepped in on occasion and directed me to my path. The path to a rubedo may be long, it may be endless. I may never reach it, but a cure for a disease is the goal of my quest nonetheless. In order to create drugs, I became an organic chemist and then became a molecular biologist.

Over the years this quest has led my colleagues and me to a few albedos and we have been highly cited in the literature. We demonstrated that proteins as large and complex as antibody Fab fragments (50kD heterodimers) could be displayed on the surface of phage at a time when it was believed that the phage-display approach would be limited to peptides or cDNA fragments. Fab fragments are the portions of antibodies that bind antigen. We created the first human antibody Fab fragment libraries on phage, allowing us to rapidly isolate human monoclonal antibodies directly from humans and subsequently create the first synthetic human antibodies directly. These methodologies and the pComb3 vector system now facilitate the development of antibody therapeutics in laboratories around the world. I adapted this approach to evolve in vitro the activity of a unique anti-HIV antibody. I had the pleasure of isolating this antibody, IgG1-b12, with my own hands. The evolved progeny of IgG1-b12 show improved anti-viral potency and may soon be tested in patients as immunotoxins aimed at eliminating HIV-1 infected cells. The affinity maturation of antibodies can now be readily performed using the methodologies we have established as we probed the chemistry of the antibody binding-site. We hope that the large number of anti-HIV antibodies that we have described will also aid in the development of an HIV vaccine. I also isolated a human antibody known as RSV-19, with the hope of treating respiratory syncitial virus-induced pneumonia, a disease that kills more then a million children every year. A CDR-grafted anti-RSV antibody beat our RSV-19 into clinical development, but our human antibody may one day be tested in patients.

I can’t refer to the singular "I" when I discuss the work of my laboratory any longer, since I now live through the experimental hands of my colleagues. I enjoy it just the same, but it is not as simple as performing experiments with your own hands. Recently, we developed a novel antibody against the colon antigen A33. This antibody is now in clinical development for the treatment of colon cancer. We have also studied methods of expressing antibodies in cells and engineering novel forms of antibodies. We have demonstrated that such antibodies can inhibit HIV entry while others can inhibit the growth of tumors. We have also shown that peptide ligands can be grafted into the CDR’s of antibodies to create ligand-mimetic antibodies that display numerous advantages over the starting peptide ligand. Like the ancient alchemists who attempted again and again to transmute base metal into gold, we seek to develop new therapies, hopefully with a much greater success rate. Along the way, we learn the secrets of biology, the negredo, and refine our approaches to therapeutics in the albedo.

Sometimes a scientist can find results that are so compelling in their potential to have an impact on disease that a moral imperative results. The moral imperative, an albedo in its own right, requires the scientist to push the idea to maturity either through finding a partner to develop the drug or technology or by founding a company themselves. In an attempt to facilitate the translation of our phage-display antibody studies into clinical reality, I co-founded a biotechnology company named Prolifaron, Inc., now known as Alexion Antibody Technology. The quest for clinical success with antibody-based therapeutics continues today.

Not content with examining a single approach to my envisioned rubedo, in the early 1990’s I developed a research course aimed at reaching into genomes to turn genes on or off using proteins. The hypothesis here is that we have within our genomes the cures to many diseases. If we can learn to orchestrate gene expression, we may be able to treat disease. If we can control the genomes of viruses, we can control the fate of the virus as well. My colleagues and I have learned to create proteins that could be shaped to bind virtually any DNA sequence. We also achieved, for the first time, the directed regulation of endogenous human and plant genes. Polydactyl zinc finger transcription factors, the approach we envisioned, actually worked. Of course, it had to. Nature had shown us the way and we found the path. Endogenous genes can now be turned on or up or off or down using our zinc finger transcription factor technology. The negredo of this study was learning how these proteins recognize DNA specifically and how we might best place them in the genome to control genes. We have also designed novel approaches that allow our designed transcription factors to be regulated by small molecules. Significantly, we were the first to patent this approach to control genes, a process that actually facilitates drug development rather than hindering it. The first entry of this technology into the clinic is due at the end of 2004, led by a biotechnology company that licensed our patents in this area. My laboratory moved from the basic study of protein-DNA interactions and transcription to an attempt at having an impact on human disease. That is how I like to envision research projects: learning nature’s secrets, and hoping to use them to treat disease.

My colleagues and I created a unique class of catalytic antibodies known as aldolase antibodies. By recreating proteins with the functions of natural enzymes we have teased out some of the secrets of nature’s methods of catalysis. With these antibodies we have prepared, in chiral form, a large number of synthons that may one day be pieced into a drug that sits on a shelf in a pharmacy. That’s the dream, a vision of a rubedo. We have also crafted a suite of anti-cancer drugs that can be selectively activated by these special antibodies and we have shown in animal models of cancer that we can effectively treat cancer with them. We aim to create a new approach to chemotherapy that is more effective and less limited by side effects. We continue today to further refine this approach, and perhaps one day will develop an effective prodrug therapy for cancer and HIV-1.

Drawing our catalytic antibody studies together with our knowledge of drug design and its inherent limitations, we have recently created a new class of therapeutic molecules called chemically programmed antibodies. Chemically programmed antibodies build on the chemistry of aldolase antibodies and their intrinsic activity with beta-diketones. We have demonstrated that by finding permissible sites on drugs for attachment of a beta-diketone linker, we can simply and site-specifically label the active sites of catalytic antibodies with receptor-binding drugs. The antibody is then effectively reprogrammed to bind the receptor that the original drug bound. Through this linkage, the antibody brings to the drug the antibody’s favorable characteristics of a long and predictable half-life in the body, valency that effectively boosts binding, and ability to interact with the immune system through the constant region of the antibody. Thus antibody effector functions like antibody dependent cellular cytotoxicity (ADCC) are added to the intrinsic activity of the drug. We have demonstrated in multiple models of cancer that we can take a poorly active drug and boost its activity using this approach to achieve impressive therapeutic results in preclinical studies. The promise of this approach created a moral imperative that led me to found my second biotechnology company, known as CovX Pharmaceuticals, to develop this approach into the rubedo I envision.

Our studies in catalytic antibodies and our attempts to learn nature’s secrets to catalyzing chemical reactions has led not only to the creation of the most highly efficient class of antibody catalysts known but also to the rediscovery and rebirth of a fundamental area of chemistry known as organocatalysis. We approach the problem of catalytic asymmetric synthesis by attempting to unveil the strategies that nature has hidden over the millennia in the form of enzymes. I believe the synthesis of stereochemically complex molecules is a rather simple feat. We simply don’t know enough chemistry yet to carry out stereochemically challenging syntheses in a straightforward fashion. Since asymmetric synthesis has led the pharmaceutical industry to many successful drugs, we need to know how to achieve this feat more effectively, how to make such molecules efficiently and in a diversity sufficient to allow us to find more drugs.

We have sprung from salty ponds of molecules, somehow organizing ourselves from rather simple starting materials to a point where we actually act, dream, and create. My assumption is that we are molecules in a sack, born under simple conditions. By learning from nature and drawing on the negredo of our antibody studies, we have created highly efficient catalytic asymmetric variants of the aldol, Mannich, Michael, Diels-Alder, and a wide variety of assembly reactions. By studying how nature’s complex aldolase enzymes catalyze reactions, we were able to recapitulate many features of this class of large protein catalysts with the simple amino acid L-proline. Using L-proline we have developed a number of practical enantioselective reactions. Who could have imagined that an amino acid as simple as L-proline and its derivatives might be such fantastic catalysts for so many asymmetric reactions? Aldehydes can now be directly and readily harnessed by chemists to act as efficient nucleophiles. Amino acids, amines, and simple reactions conditions now make it possible. Asymmetric molecules that once required many chemical steps to synthesize can now be created using a very simple and environmentally sound chemistry. By facilitating the synthesis of asymmetric molecules we hope that we are providing others with the building blocks for their own rubedo of new drugs.

I want to close this dialogue with a brief tribute to those who have served as my mentors over the years. Alchemy, of course, is passed on by a master to an apprentice. As an undergraduate I majored in both chemistry and physics, a path that arose due to great teachers in both areas. Great teachers and mentors can have a tremendous impact on a student. As an undergraduate, my mentors were Wayne Guida in chemistry and Harry Ellis in physics. These two men led me to complicate my life a bit more with a double major. My road to graduate studies was ahead of me but its path was not set. On one fateful trip to a graduate school interview, the police intervened and ticketed my roommate and me on the way to the airport causing me to miss my flight. That was actually a great traffic ticket. When I finally arrived, most of the faculty members I had requested to meet with were unavailable. I was given an interview schedule with names and areas of research that were unfamiliar to me. One of those individuals would pick up where Guida and Ellis left off. My next "master" was Chi-Huey Wong. Under Chi-Huey I began to mix synthetic chemistry with molecular biology and a whole new horizon opened for me. I received my Ph.D. in 1989 and moved to The Scripps Research Institute. At Scripps, Richard Lerner became my mentor and instilled in me his drive for fearless exploration of diverse areas of science and medicine. Following my postdoctoral studies with him, I remained at Scripps and was promoted to Assistant Professor in 1991. Now as a Full Professor I am no less hungry for discovery and my quest for the rubedo continues. Of course I must credit all of my achievements to the collective wisdom and efforts of my mentors and the students, postdoctoral fellows, and technicians that have joined me on this quest over the years.

The end of science? Bully!