The Importance of Understanding Target–Protein Interactions in Drug Discovery

You’re unwell, you see a doctor, they prescribe you a medicine… and you take it. But how exactly is that drug having an effect? What is its mechanism of action? Drugs exhibit their effects through specific protein-target interactions.

But in some cases, there may not be a treatment available. In approximately 30% of cases, drugs fail during clinical development, and toxicity – which can be caused by “off-target” binding – is often to blame.

Andrew Lynn, Chief Executive Officer at Fluidic Analytics discusses why understanding protein–target interactions is so important, the common challenges researchers face when attempting to determine these interactions, and touches on the relationship between the drug "attrition rate" crisis and the off-target effects of drugs.

Laura Lansdowne (LL): Could you discuss the importance of understanding protein–target interactions in drug discovery, and the implications of not knowing your target?

Andrew Lynn (AL): Understanding protein–target interactions is crucial — we are talking about the difference between finding a lifesaving drug/therapy and wasting hundreds of millions of dollars developing a drug with the wrong mechanism of action.

A recent paper from Jason Sheltzer’s group showed that ten anticancer drugs undergoing clinical trials had a completely different mechanism of action from the one originally attributed to them. Briefly, when the protein targeted by each of the drugs was removed from cancer cells, the group expected the drugs to stop working. But what they found was that the drugs continued to work as normal and thus had to be working through off-target binding.

This is crucial because it means potentially there are many more drugs out there that are working through off-target binding; it also means that many other drug candidates that have previously been disregarded may have unrecognized promise. This problem is about to become even more acute as research expands into conditions with difficult targets like Alzheimer's disease.

The way in which we discover the exact mechanism of action between proteins and potential drug candidates needs better technologies for characterizing on-target and off-target interactions. We cannot discover new information relying solely on technologies that have fallen short for decades.

LL: What challenges do drug discovery researchers face when trying to identify target–protein interactions?

AL: Drug discovery and development is a lengthy, complex and costly process with a high degree of uncertainty whether a drug will succeed. The two biggest challenges are: First, not understanding the pathophysiology of many disorders, such as neurodegenerative disorders, which makes target identification challenging. Second, the lack of validated diagnostic and therapeutic biomarkers to objectively detect and measure biological states.

At the heart of both challenges is the ability to characterize protein-drug target interactions. Unfortunately, the methods currently employed by researchers to do this research are outdated.

An example of this can be seen when scientists try to characterize interactions involving intrinsically disordered proteins (IDPs) such as the ones associated with Parkinson’s disease. Current characterization methods modify proteins by fixing them to a surface or putting them in artificial environments. So, it’s no surprise that many drugs are great at targeting proteins with these modifications but poor at targeting these same proteins as they exist in vivo – in solution and not tethered to an artificial surface.

This is why we’re building new tools and methods for researchers to more accurately characterize binding events in solution: to better understand how drugs interact with their protein targets in their native environment.

LL: What is microfluidic diffusional sizing and how can this be used to measure the binding affinity of protein–protein interactions?

AL: Microfluidic diffusional sizing (MDS) characterizes proteins and their interactions in solution based on the size (or more specifically hydrodynamic radius) of proteins and protein complexes as they diffuse within a microfluidic laminar flow. Characterizing in solution avoids artefacts from surfaces or matrices; gathering information about size to give crucial insights into stoichiometry, on- and off-target binding, oligomerization and folding.

MDS can be used to measure binding affinity by tracking changes in the size of a protein as it binds at different concentrations. The size of the complex can also give a strong indication of whether the protein is forming a protein-target complex at the expected size (on-target binding) or something with a completely different or unexpected size (off-target binding). A major additional advantage of MDS is that, because of the absence of surfaces or matrices, it can be used to characterize binding involving difficult targets such as intrinsically disordered proteins and membrane proteins.

LL: Could you discuss the relationship between the drug "attrition rate" crisis and the off-target effects of drugs?

AL: Compound failure rates due to toxicity before human testing is very high. A recent review from a top-20 pharma company cited toxicity as the reason why, between 2005-2010, 82% of drugs were rejected at the preclinical stage and 35% in phase 2a. Overall, concerns surrounding toxicity account for as much as 30% of drug attrition occurring during the clinical stage of development.

For many potential drugs, toxicity is due to off-target binding. By employing new methods to characterize drug candidates binding to protein targets in native conditions, we can identify off-target binding more effectively. This could help save billions of dollars in development costs and reduce the attrition rate we are currently facing.

LL: There has currently been very limited success in the development of effective therapies for Alzheimer’s disease (AD). Could you touch on some of the “successes” and highlight the molecules of interest in AD as well as the challenges related to their study.

AL: One recent success is the anti-amyloid drug, aducanumab. After Biogen re-examined the data from the clinical trials, they found that exposure to high doses of Aducanumab reduced clinical decline in patients exhibiting early stages of Alzheimer’s disease.

If approved, aducanumab would become the first therapy to slow the cognitive decline that accompanies Alzheimer's disease. This a massive step forward and a much-needed source of hope for patients and their families.

But aducanumab doesn’t cure Alzheimer’s disease. A major challenge impeding the development of further AD drugs is the ability to understand the mechanism of action via which candidate drugs interact with targets. Amyloid-β is known to be a particularly difficult-to-characterize peptide, and even aducanumab doesn’t have a well-understood mechanism of action. Any breakthroughs in being able to characterize how it or other Alzheimer’s disease drugs interact with difficult targets would be a major breakthrough in drug development.

However, the majority of Alzheimer’s patients do not carry the dominantly inherited genetic mutation for the disease, and we don’t know why amyloid proteins aggregate within their brains.

It follows that there won’t be a single cause but rather many causes. Thus, the common consensus is that there won’t be a single miracle drug that cures Alzheimer’s disease for everyone.

Andrew Lynn was speaking with Laura Elizabeth Lansdowne, Senior Science Writer, Technology Networks.