Programmable Antibodies—A Hybrid Cancer Therapy Described by TSRI Scientists

By Jason Socrates Bardi

Exploring the interface between organic chemistry and antibody engineering, a team of scientists from the Department of Molecular Biology and The Skaggs Institute for Chemical Biology at The Scripps Research Institute (TSRI) has designed a "hybrid" anticancer compound that physically combines the potent punch of a cancer cell-targeting agent with the long-lasting dose of an antibody.

Much as a hybrid bicycle is a cross between two bikes—a road bike frame with mountain bike handlebars, for instance—this hybrid compound is a cross between two molecules. One is a traditional anticancer drug, a small molecule that targets cancer tumors. The other is a type of antibody, which is a protein produced in great abundance by the body's immune system and found naturally in the bloodstream.

The hybrid of the two, described in an upcoming issue of the journal Proceedings of the National Academy of Sciences, was found to have a profound effect on the size of tumors in mouse models—shrinking tumors of both Kaposi's sarcoma and colon cancers in these preclinical studies. Moreover, this approach is general enough that it could be used to design hybrids against any number of cancers.

"A single antibody can become a whole multiplicity of therapeutics simply by mixing it with the desired small molecule," says TSRI Professor Carlos F. Barbas III, who is Janet and W. Keith Kellogg II Chair in Molecular Biology.

Barbas and several other scientists at TSRI collaborated in the interdisciplinary research, which one of them described as existing at the interface of organic chemistry, biochemistry, and immunology.

This team included Assistant Professor Christoph Rader, Associate Professor and Skaggs Investigator Subhash Sinha, postdoctoral fellow Mikhail Popkov, and TSRI President and Skaggs Investigator Richard A. Lerner, who is Lita Annenberg Hazen Professor of Immunochemistry and Cecil H. and Ida M. Green Chair in Chemistry.

"The beauty of this [approach] is its generic design," says Rader. "You have one antibody molecule and you can blend it with the whole diversity of the organic chemistry world."

Steering and Support, Joined at the Hip

The TSRI team built the hybrid molecule with a "catalytic" antibody, a small drug molecule, and a linker molecule that joins the two. The hybrid thus formed borrows the wheels and the frame of the antibody for supports and the handlebars of the small drug molecule for steering ability.

Also called immunoglobulins, antibodies are proteins produced by immune cells that are designed to recognize a wide range of foreign pathogens. After a bacterium, virus, or other pathogen enters the bloodstream, antibodies target antigens—proteins, carbohydrate molecules, and other pieces of the pathogen—specific to that foreign invader. These antibodies then alert the immune system to the presence of the invaders and attract lethal "effector" immune cells to the site of infection.

Antibodies have for many years been seen as useful therapeutics for a number of human diseases ranging from rheumatoid arthritis to leukemia because they are designed to target particular cells and attract other parts of the immune system to the site. There are a dozen antibodies that are approved as therapeutics by the U.S. Food and Drug Administration, and many more under development.

The hybrid the TSRI team created does not use the antibody's targeting ability but rather its other properties—namely its ability to stay around in the bloodstream. While many small-molecule drugs are cleared from the blood by the kidneys in a matter of minutes or hours, the large, soluble antibody molecules are designed by the body to remain in the bloodstream for long periods of time. In fact, in their experiments, Barbas and his colleagues observed that their hybrid antibodies remained in circulation for a week, while the small-molecule drug was cleared in minutes.

Barbas and his colleagues used a catalytic antibody, since these have the ability to react with other molecules like a catalytic enzyme. In particular, the antibody they used has a lysine residue at a key location. This lysine residue allowed them to react the antibody with the small drug molecule and "covalently" attach the two with a diketone linker.

"The diketone reacts with the reactive lysine residues in the binding sites of the aldolase monoclonal antibody 38C2, that we used, and you get the [hybrid] molecule," says Sinha.

This was more difficult than it sounds, however, since the small molecule also had to be linked to the diketone without disturbing the binding of the molecule to its receptor and at the same time the diketone also reacts with the antibody. "We had to build [from scratch] a molecule that we could link," says Sinha, who produced such a molecule in a 13-step organic synthesis, starting with the chemical 4-bromo-3-methyl anisole.

Circulating and Guiding

The beauty of the hybrid is that while the antibody portion keeps the hybrids circulating, the small-molecule portion guides them towards cancer cells. In this case, the small molecule they used guided the hybrids to target two molecules known as the integrins alpha(v)beta(3) and alpha(v)beta(5).

Cancerous cells activate endothelial cells to express integrins like alpha(v)beta(3) and alpha(v)beta(5) to promote the process of angiogenesis, the formation of new blood vessels that bring necessary nutrients and oxygen to hungry tumor cells. Block angiogenesis, the thinking goes, and you can starve a tumor—like drying out a lake by diverting all its tributaries. Many cancer cells like breast, ovarian and prostate cancer also express these integrins on their surface, providing for a potential double-strike against the tumor itself as well as its key blood supply.

In its study, the TSRI team found that the affinity of the small molecule for the alpha(v)beta(3) and alpha(v)beta(5) on the surfaces of the tumor cells steered the hybrids towards the tumors. And once there, the antibody part of the hybrid would activate other parts of the immune system—like macrophages and the "complement" system—that recognize the antibody and destroy the cells to which they are attached.

This proved to work well in the pre-clinical studies performed by the TSRI team. In addition, the use of the targeting molecule allowed the researchers to avoid one common difficulty with developing antibody therapeutics—monoclonal mouse antibodies don't normally target mouse antigens, which makes doing preclinical studies tricky.

Moreover, say the authors, this hybrid approach could be used as a broad drug-design strategy to rescue compounds that are able to kill cancerous cells in the test tube but have proven ineffective in human trials because they have a very short half-life in the bloodstream. Alternatively, the technique could provide killing function to drugs that may only bind the tumor cells.

"There is a whole world of small molecules that have been developed and tested in the clinic but have failed because of low half-life or poor efficacy," says Barbas. "A single antibody can be used [as a vehicle for many of these small molecules]."

"In essence," says Popkov, "we have replaced the antibody diversity with a chemical diversity. We can use this single antibody as a template to recognize all the other molecules [we desire]."

The article, "Chemically programmed monoclonal antibodies for cancer therapy: Adaptor immunotherapy based on a covalent antibody catalyst," authored by Christoph Rader, Subhash C. Sinha, Mikhail Popkov, Richard A. Lerner, and Carlos F. Barbas, III, is available online at: and will be published in an upcoming issue of the journal Proceedings of the National Academy of Sciences.

This work was supported by funds from The Skaggs Institute for Research and an Investigator Award from the Cancer Research Institute.



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A team of TSRI scientists, including (left to right) Mikhail Popkov, Christoph Rader, and Subhash C. Sinha, explored the interface between organic chemistry and antibody engineering in a new study. On the team but not pictured are Carlos Barbas III and Richard A. Lerner. Photo by Jason S. Bardi.














A targeting module derivatized with a 1,3-diketone linker can program the specificity of an aldolase antibody through reaction with its reactive lysine residue. As shown in this crystal structure obtained in Ian A. Wilson's laboratory, the reactive lysine residue is deeply buried, yet accessible at the base of a hydrophobic pocket in the antibody binding site.