In the search for effective and safe drugs for patients, it’s vital to understand the full mechanism of action of both the compound and therapeutic target. However, forming this complex picture can be challenging, particularly if you’re not using the most effective tools to quantify compound-target binding from the start of your target identification studies.

In our new eBook, we discuss how the early adoption of CETSA MS  has the potential to expedite target identification research and help you gain a richer understanding of your compound’s efficacy and safety to enhance clinical success.

Download our new eBook: “Right tools, right time: How adopting CETSA-MS earlier in target identification could boost your drug discovery success”

As with any exploration of unknown territory, using the most efficient and reliable approach from the start will increase your chances of obtaining the information you need, when you need it. Read on to learn more about where MS-based proteomics methods fit into the modern landscape of target- and phenotypic-based drug discovery, and how adopting one approach can overcome the limitations of traditional methods to drive the success of your target identification research.

Target- versus phenotypic-based drug discovery

Let’s start with a bit of context and remind ourselves of the two main approaches currently helping to advance drug discovery: target-based and phenotypic-based drug discovery strategies.

Target-based drug discovery

Target-based drug discovery starts with the search for a specific molecular target, usually a protein, that has an assumed or known role in the disease of interest. Having identified the target, compound libraries are then screened to find a drug that not only successfully engages with the target but also modifies it to have the intended therapeutic effect (i.e., ‘hit’ identification).

Such hypothesis-driven drug discovery is a highly valuable approach for uncovering not only small-molecule compounds but also antibody drugs and other protein biologics. For example, out of 113 first-in-class drugs approved by the US FDA from 1999 to 2013, 70% were identified through target-based drug discovery.

Phenotypic-based drug discovery

The alternative phenotypic-based approach is the original drug screening paradigm, which has recently made a comeback in drug discovery after losing momentum in the past. In contrast to the target-based approach, the phenotypic-based strategy is empirically driven and identifies drugs without knowledge of or bias towards a specific target.

The first step in phenotypic-based drug discovery is to identify a suitable assay that measures the drug’s pharmacological action in cells, tissues, or animal models to yield a response readout, such as changes in cell death or cytokine release. Next, this assay is used to screen a compound library for hits, although the targets of these hits are unknown at first. As such, target deconvolution and validation studies are performed to retrospectively identify the target as well as understand how the compound exerts its pharmacological effect in a specific cellular context (i.e., the mechanism of action, or MoA).

Now that we’ve recapped these two main approaches to drug discovery, let’s delve deeper into the key challenges you can encounter in your target identification studies and how certain methods can help you overcome them.

Tackling challenges in target identification to advance drug discovery

Regardless of whether you use a target- or phenotypic-based approach in your research, there’s one major challenge you will need to address: forming a rich understanding of your compound’s MoA. This includes identifying the primary target of your compound (i.e., binding with the intended target) but also any off-target effects associated with potential toxicity in patients. As most compounds in clinical trials fail due to toxicity or lack of efficacy, improving the characterization of the MoA is likely to enhance success in drug discovery—but this is proving to be a tough challenge.

One promising solution is to use CETSA MS. These powerful tools enable the direct quantification of in vitro compound-protein binding to gain insights into the effects of the compound on the entire disease pathway, including on- and off-target effects. This method is having great success in elucidating compound MoA and target validation in the preclinical stages of small molecule drug discovery, as well as in clinical applications, such as for biomarker discovery.

Mass spectrometry (MS)-based proteomics: Which approach to use?

There are different MS-based proteomics methods you can use in your research. One option is chemoproteomics, which involves chemically labelling ligands or proteins. The alternative is label-free functional screening approaches, which use compound-induced protein expression changes to deconvolute targets and/or MoA via several methods, such as thermal profiling, chemical denaturation, and limited proteolysis.

However, these two approaches have various pros and cons. For example, although chemoproteomics has yielded proof-of-relevance chemical probes for a large portion of the human proteome, the chemical probes can take 6-12 months to develop and the artificial modification of the ligand or protein target limits physiological relevance. Instead, a label-free method, such as CETSA MS (also known as ‘thermal proteome profiling’), is not only immediately available to use but also enables unbiased measurement of drug-target binding in unmodified, disease-relevant systems, among various other advantages.

It can, therefore, be valuable to consider using CETSA MS before chemoproteomics. The early adoption of the highly efficient and reliable CETSA MS method could expedite your target identification studies while ensuring you fully understand the efficacy and safety of your compound. 

Are you using the method that quickly explores the full target landscape?

Several leading research groups are gaining significant benefits from implementing CETSA MS. For example, a recent study used CETSA MS to elucidate the molecular effects of palbociclib (Ibrance®, a CDK4/6 inhibitor approved for metastatic breast cancer). The research confirmed the known CDK4/6 targets as well as identified a new target: the 20S proteasome (a protein complex which degrades unneeded or damaged proteins via proteolysis). Palbociclib induced the ECM29 protein to dissociate from the proteasome, which caused proteasomal activation and the subsequent cellular senescence and cell cycle arrest associated with palbociclib. What’s more, in a follow-up study, the same researchers revealed that ECM29 levels were predictive of relapse-free survival in breast cancer patients treated with endocrine therapy.

As well as identifying predictive biomarkers and obtaining a clearer understanding of the wider biological impact of drugs, CETSA MS has helped make significant progress in other areas. For example, the approach has been used to reveal previously unknown causes of toxicity (such as how FECH inhibition by vemurafenib and alecitinib underpins photoxicity and skin rashes in patients) to enhance safety assessments.

Unlocking the benefits of CETSA MS can help you to better predict the efficacy and safety of your compounds and drive their successful progression through both pre-clinical and clinical stages of drug development. Indeed, choosing the most efficient and reliable approach for prosecuting targets from the earliest stages of your studies is critical for minimizing risk to your drug discovery pipeline and protecting your investments. As we take these and other critical steps to drive drug discovery forward, there is renewed hope that more patients will gain access to new and life-changing medicines.