Super-drugs of the future will be bound to DNA

Disease and treatment 3. sep 2020 9 min PhD, Professor Kurt Vesterager Gothelf Written by Kristian Sjøgren

Researchers from Aarhus University and others are collaborating on a major research project to design new multifunctional drugs that can potentially be much more effective against cancer and other diseases and can be optimized for each individual.

Drugs have traditionally been small molecules that can travel easily around the body and affect it. However, they have some limitations, since targeting them to individual cells is difficult.

In recent years, the pharmaceutical industry has therefore strongly focused on creating biological drugs, including antibodies and proteins, which are more specifically targeted to the diseased cells, but they also have their own challenges.

The biological drug molecules are often large, making it difficult for them to penetrate the cells and tissues they are intended to affect. They are also often expensive to produce.

However, a new solution may be on the way. Researchers from Aarhus University and others have been devising a new way of designing drugs that could revolutionize the pharmaceutical industry. Using synthetic molecules similar to the DNA in our genome, researchers bind several molecules of active ingredient, combining several activation mechanisms into one conjugate drug that is both specific and effective.

In addition to making the drugs much more effective, mechanisms can be incorporated so that the drugs can reach places in the body that biological drugs have not yet been able to reach, such as crossing the blood–brain barrier. Further, researchers can also incorporate markers into the drugs so that they can be tracked and used for both diagnosis and treatment.

“An increasingly large part of the pharmaceutical industry is oriented towards developing biological drugs, but there are some major challenges in the way they are constructed. We can address these challenges by binding the active ingredients to DNA,” explains Kurt Gothelf, Professor, Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University.

The Novo Nordisk Foundation awarded Kurt Gothelf and collaborators a major Challenge Programme grant of DKK 60 million to create the basis for opening completely new avenues in the pharmaceutical industry over 6 years.

DNA assembles the drugs

Kurt Gothelf has focused on synthesizing DNA into various structures for many years.

He and his colleagues have constructed a nanoscale DNA box with a controllable lid that can be opened and closed.

In the new project, the researchers combine the technology to get DNA to self-assemble into some specific structures that bind to antibodies, proteins and other drugs. The snippets of DNA then act as a kind of programmable glue that assembles the desired drug components into a complex molecule called a conjugate. However, the researchers do not use natural DNA in their drug conjugates, since this rapidly degrades in the body, but rather DNA-like chains that do not degrade.

“First, we place a snippet of DNA on various proteins, and the pieces of DNA are then programmed to self-assemble the proteins in a predetermined structure, simply by mixing them,” says Kurt Gothelf.

Kurt Gothelf explains that DNA is extremely good at very precisely positioning the various substances in a three-dimensional structure, so that the active ingredients that need to interact with, for example, cancer cells, are positioned exactly where they will be most effective. They may bind to several receptors on the surface of cancer cells simultaneously or position the immune system’s cells in relation to the cancer cells so that they do as much damage as possible.

“We make DNA the architect that assembles the final drug, and in designing the DNA we can very accurately ensure that two or more molecules of active ingredient are positioned relative to each other to optimize effectiveness,” says Kurt Gothelf.

Combining different ingredients in one drug

There are many ways of assembling various ingredients in large biological drug conjugates in which DNA is the glue.

• Researchers can bind active ingredients such as anticancer drugs to the DNA.

• In addition, researchers can bind one or more antibodies that recognize and bind to various receptors on the surface of the cancer cells to the DNA.

• If the researchers also want to be able to determine where the drug ends up in the body to ensure that the drug is used both actively and diagnostically, they can also put dyes or radioactive isotopes on the DNA and subsequently locate the drug through a body scan.

• If the active ingredient needs to be delivered to parts of the body by crossing various barriers, such as the intestinal wall or the blood–brain barrier, the researchers can bind peptides to the DNA and ensure that the body’s transport mechanisms move the large drug molecule to the target location.

• Finally, the researchers can also attach molecules that ensure that the drug is stable and is not excreted by the body again. These may include albumin-binding substances that bind the active ingredient to albumin so that the kidneys do not filter it from the blood.

“Connecting this many components is very difficult with other methods. However, if we use DNA, the DNA just assembles the structure for which it is programmed. Furthermore, there are almost no limitations to synthesizing drugs with DNA,” explains Kurt Gothelf.

Cancer is the target

In the Challenge Programme project, the researchers are examining several existing drugs that they would like to combine into new drugs to more effectively attack cancer cells.

These include the three chemotherapy drugs rituximab, cetuximab and trastuzumab, which are all antibodies. They bind to three different receptors on the surface of cancer cells, and Kurt Gothelf and his colleagues will try to combine them using DNA into one drug, which should be more effective than the three drugs individually or combined without being bound together.

However, this is not as easy as it may sound. Kurt Gothelf is developing new methods for binding DNA to proteins and other substances that are cost-effective and easy to scale up, and these qualities are necessary for the technology to ultimately succeed.

For example, he says that an antibody that can bind to DNA via an amine on the surface (an amine is a reactive group on the surface of proteins) may well contain 90 different amines, and the DNA and antibody must bind through the specific amine that will be most effective pharmaceutically.

“The binding must not interfere with the function of the antibody, and we need to determine which binding method is most effective and how we ensure that the DNA binds the antibody exactly where it should and that the resulting drug is as uniform and pure as possible. My task in the project is to develop methods to enable this,” says Kurt Gothelf.

Each researcher has a specialty

The researchers in this major research project are like a four-stage rocket.

• Kurt Gothelf focuses on the organic chemistry element of the project, such as developing effective methods to bind DNA and proteins.

• Jørgen Kjems, a Professor from iNANO and the Department of Molecular Biology and Genetics at Aarhus University, is an expert in molecular biology and can progress the project from the chemical to the biological. For example, Jørgen Kjems has patented a method for binding four drugs or active ingredients.

• Ken Howard, Associate Professor at iNANO, can take the designed molecules one step further and turn them into actual drugs. Ken Howard works on binding albumin to the drugs to make them last longer in the body.

• Finally, Tony Lahoutte, Professor at Vrije Universiteit Brussel in Belgium, is in charge of the clinical trials of the drug candidates, which will be tested in cells, mice and hopefully also people in the last stage of the research project.

“Overall, the research project is structured so that we must first further develop the chemistry for binding biological molecules. Then we need to collect molecules that may be potential active ingredients, and finally we need to test whether the drugs can help people with disease,” says Kurt Gothelf.

Making anticancer drugs more effective

The research has been underway since 2018, and it has already yielded some promising results.

The researchers carried out a proof-of-concept study in which they bound eight molecules of doxorubicin, used to combat lung cancer by killing the cancer cells, with a DNA carrier.

The researchers also bound the antibody cetuximab to their drug. Cetuximab is used for people with cancer when the epidermal growth factor receptor is overexpressed on the surface of the cancer cells. Cetuximab binds to this receptor.

The researchers experimented with the new drug and found that it was only taken up by the cells that had epidermal growth factor receptor overexpressed on the cell surface – such as cancer cells – whereas all cells take up doxorubicin, including healthy cells.

“This has enabled us to make a far more selective drug that better targets cancer cells and thereby spares the healthy cells,” explains Kurt Gothelf.

The researchers have also carried out another proof-of-concept study in which they demonstrated that five antibodies can be synthesized into one drug complex by using DNA.

Finding high-risk atherosclerotic lesions

Although the entire research project may seem to focus on cancer, this is far from the case.

The technology can be used to develop drugs to combat many diseases, and the researchers are also focusing on atherosclerosis.

Specifically, the researchers would like to develop better diagnostic tools to identify atherosclerotic lesions.

The problem with atherosclerosis is that we all have it to a greater or lesser extent, and the goal is to be able to identify the atherosclerotic lesions in which part of the plaque risks loosening and becoming a blood clot that can get stuck elsewhere in the body.

However, experience has shown that especially atherosclerotic lesions surrounded by necrotic tissue have the greatest risk of sending potential plaques into circulation. New diagnostic tools to identify these high-risk atherosclerotic lesions are precisely what researchers want to develop.

“In this situation, we will combine some antibodies that can identify atherosclerotic lesions, bind to receptors in necrotic tissue and be equipped with an isotope, so doctors can find the critical atherosclerotic lesions by scanning,” says Kurt Gothelf.

Most advanced with anticancer drugs

Kurt Gothelf says that the two main targets, cancer and atherosclerosis, represent two different problems.

The advantage of having to identify atherosclerotic lesions is that everything occurs in the blood vessels, so the DNA conjugate developed does not have to cross any barriers.

Conversely, most anticancer drugs have to overcome barriers, and in addition to killing the cancer cells, the researchers will also equip their drug with isotopes to determine the location of the cancer cells.

“We are at a very early stage, so we cannot cure anyone yet, but that is where we want to go,” says Kurt Gothelf, who also states that the researchers are more advanced in developing anticancer drugs than they are with new diagnostic tools to localize atherosclerotic lesions.

The technology can be used to make personalized medicine

The technology has far-reaching implications if Kurt Gothelf and his colleagues succeed.

In this context, personalized medicine is an obvious goal.

We all differ in blood type, metabolism and many other parameters, and this makes some drugs work better on some people than on others.

If the researchers can realize their goal of being able to design more effective drugs from scratch, it will open up the future prospect of creating personalized medicine by combining the effects of different drugs based on an individual’s unique biology.

“Imagine being able to examine in cell experiments which drugs work best on an individual person with a given tumour and being able to use DNA as glue to combine the antibodies that can best recognize the cancer to optimize effectiveness,” says Kurt Gothelf.

Problems, but surmountable ones

Nevertheless, the researchers need to overcome several obstacles to achieve their goal.

Kurt Gothelf identifies several problems that may arise, and the researchers need to find ways to solve them if they occur.

• The new drugs combine DNA and proteins, and the immune system may not like to have these flowing around the body. Maybe the immune system will go crazy and degrade the DNA and proteins furiously. However, Kurt Gothelf says that their initial investigations indicate that this does not happen.

• Another challenge is finding the right DNA-like molecule to bind the drugs. The researchers are working with both known DNA analogues and are also developing new types that are not degraded in the body. The researchers are also developing methods of packing the DNA tightly so that it becomes more compact and surrounded by many proteins. This appears to prolong the life of the DNA and the drug.

• Finally, the whole procedure needs to be made scalable so that it can become commercially viable. Modified DNA and biological drugs are expensive components. However, this must all be done cost-effectively to become a viable alternative to traditional medicine.

“However, none of these problems are insurmountable,” says Kurt Gothelf.

Developing pioneering diagnostic methods for identifying blood clots

Kurt Gothelf hopes and expects that in 4 years, when the project ends, the researchers will have demonstrated a clear clinical benefit of combining drugs with DNA as the researchers propose.

He also hopes and thinks that researchers have shown that drugs can be designed in a way that mimics nature, because this is neither too expensive nor complicated.

Finally, he hopes that both the anticancer drugs and the drugs for diagnosing atherosclerotic lesions will be so advanced that they can be tested in human clinical trials.

“In terms of atherosclerotic lesions, I hope we find new groundbreaking ways of identifying and diagnosing people at risk of a blood clot. There is a clear commercial interest in this, which we can also sense from our industrial collaborators. Some of the chemistry we have developed is already being used today in various commercial fields, such as making biosensors, and more people will probably begin to examine this,” says Kurt Gothelf.

The Novo Nordisk Foundation awarded Kurt Gothelf a Challenge Programme grant in 2017 for the Center for Multifunctional Biomolecular Drug Design (CEMBID) project.

Kurt Gothelf’s research is founded upon organic chemistry and branches out into DNA nanotechnology, bioconjugation, nucleic acid chemistry, medicinal...

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