Small-Molecule Probes: Bridging the gap between understanding and curing disease

by Michael Vinyard
figures by Jovana Andrejevic and Michael Vinyard

Why do we have cures and medicines for some diseases but not others? Surprisingly, it is not because we cannot make the medicines; it is because we do not know enough about the diseases that need new medicines. To span the chasm between understanding the biology of a disease and successfully treating patients, we must foster collaborative efforts between biology and chemistry. The hope is that such cross-field cooperation will enable insights into disease biology by using chemical compounds that could lead to FDA-approved therapeutics.

What are drugs and where do they come from?

Many drugs are small molecules (tiny, carbon-based chemical compounds) designed to treat disease. Different drugs work in different ways, but the general goal of most drugs is to somehow disrupt the biological process that causes the disease. An example of this is vemurafenib, a small-molecule drug used to treat melanoma patients whose tumors contain a genetic mutation (or “typo” in its genetic code) that corresponds to a protein called BRAF (Figure 1). BRAF is a protein involved in cell growth, and when this protein is mutated, it can drive melanoma by allowing the cancer cells to grow uncontrollably and form tumors. Vemurafenib blocks BRAF activity, thereby halting the previously unrestrained growth of cancer cells and causing the tumors to shrink.

Although chemists have succeeded in creating drugs like vemurafenib that effectively treat disease, many such drugs were discovered by accident. Most disease-relevant drugs arose because chemists were attempting to re-create complex, beautiful compounds known as natural products. These molecules, created entirely by nature with no input from mankind, range from simple constructions of atoms to arrangements that are so geometrically intricate that scientists puzzle over how they could have been assembled.

In the past 100 years or so, chemists have learned how to make increasingly complex molecules and natural products. While attempting to re-create natural molecules in the lab, chemists have “accidentally” generated many compounds capable of treating disease. Although this unintentional drug discovery process has been successful in the past, drugs could be developed more efficiently if chemists did so in a targeted fashion, making drugs specifically for the purpose of treating a disease. Unfortunately, though, this goal is complicated by the fact that many diseases are poorly understood.

Figure 1: An example of a targeted therapy. Vemurafenib targets a mutant form of BRAF. When vemurafenib binds BRAF, growth and proliferation of the melanoma cells that harbor this mutant protein (roughly 60% of this type of melanoma) is halted, killing the cancer. — **Figure 1: An example of a targeted therapy.** Vemurafenib targets a mutant form of BRAF. When vemurafenib binds BRAF, growth and proliferation of the melanoma cells that harbor this mutant protein (found in roughly half of melanoma patients) is halted, killing the cancer.

The process of drug discovery

Drug discovery can be thought of as a “lock and key” problem in which the biological target of interest is the lock and the key is a small-molecule drug. To extend this analogy, think of the key maker as a scientist who makes molecules that are tested as drugs in clinical trials. Now imagine that there is a specific lock (disease) for which the key maker wants to make a key (drug). Unfortunately, the key maker doesn’t have the best idea of what the tumblers look like inside of the lock she needs to open. One option involves the key maker creating many different keys and seeing which designs enable her to fit the groove of certain tumblers, eventually finding the best fit. Alternatively, she can study the lock and learn everything about its internal shape to design the perfect key.

To bring this analogy back to drug discovery, scientists, as “key makers,” generally take one of two approaches. They can either make a large number of molecules with various shapes, which can then be tested for biological activity. Or, they can study the disease, learning all they can about its potential molecular targets, and then create the perfect designer molecule to modulate that disease. Although these two approaches are the most common, there is a third strategy that may be more fruitful: design molecules that can be used to both learn about diseases and enable the development of drugs for those diseases.

Using molecular probes to learn about disease

In modern-day medicine, only a small fraction of molecules created by chemists are put through clinical trials, and an even smaller fraction become drugs that help patients. Why is there such a low success rate in these clinical trials? Oftentimes, this is because we do not truly understand how the molecules we make are working in the human body. We can gain a better foothold on developing drugs for diseases through the development of probe molecules that can simultaneously be used to study disease in a research laboratory setting and serve as starting points for drug development.

Finding such starting points, however, is a resource-intensive and time-consuming process. To know if a molecule might be used to treat a disease, we must first introduce it into a disease model, such as a model organism (e.g., a mouse) or group of cells that have been isolated from patients. During the process of cell-based screening, for example, scientists put molecules into cells and see if the cells change (e.g., stop a cancer cell in its tracks while leaving healthy cells alone). Compounds of particular biological interest can be referred to as probes. As the name implies, we can use these probe molecules to poke and prod diseased cells to learn more about how they work.

Since probe molecules tend to fit a particular biological lock, per our analogy above, they tend to serve as fantastic starting points for drug discovery. As an example, vemurafenib, the melanoma drug discussed above, began as a collection of probe molecules at the drug discovery company, Plexxikon. These molecules were identified in biological activity screens for their ability to manipulate the target of interest (mutant BRAF). Chemists at Plexxikon were then able to “fine-tune” the structure of the molecule so that it was effective in patients. This highlights an important difference between a probe and a drug: a probe is a small molecule that is selective (your molecule interacts with your desired target and nothing else), while a drug does everything that a probe can do in a research lab, except it does so in people. In the research setting, vemurafenib has been used as a probe to understand drug resistance in melanoma and has aided our general understanding of the disease.

Closing the gap between chemistry and biology

We need more probe molecules that are both useful for studying disease and can serve as starting points for making drugs. How can we do this? Laboratories must act collaboratively through investigations that involve chemists who make probes and drugs cooperating with biologists who attempt to understand disease. These two groups must work side-by side with a majority of researchers falling somewhere in between those two flavors of science. The ability to both study disease and make probe molecules for this purpose, preferably under one roof, is in dire need. The term for this method of scientific inquiry is called chemical biology: using chemistry to study biology.

Drug development and advancements in medicine, while not entirely dependent on small-molecule-based drugs, rely heavily on the past efforts of chemists and their abilities to make molecules that biologists have characterized in the context of disease. In order to push medicine forward, it is imperative that we understand the biology of the disease that we wish to drug. This should serve as a call for chemists and biologists to merge their investigations and collaborate as often as possible. These needs may also be met by researchers who both construct new molecules and subsequently characterize them in disease models like human cells or animals. We are no longer performing science in an age of isolation—making medicines for diseases that afflict people worldwide is a large-scale problem. Coordination between the fields of biology and chemistry will better enable us to systematically develop therapies for diseases like cancer, Alzheimer’s disease, and many others.

Michael Vinyard is a Ph.D. student in the Department of Chemistry & Chemical Biology at Harvard University.

For more information:

Here is a perspective on the development of probe molecules and their implications for drug discovery.
Check out this commentary and this review for more information on vemurafenib and targeted therapies in cancer.
Lastly, and perhaps most pertinent to this article, check out this New York Times article that illustrates both the hopes and struggles of targeted therapies, and how understanding biology can help us to find new medicines.