Editorial Article: Chemical probes, degraders, and chemogenomic libraries accelerate rational drug discovery

The drug discovery field is changing, find out how to keep up with the evolving landscape, from chemogenomic libraries to new modality drugs

15 Aug 2023

A photo of Susanne Müller-Knapp discussing the chemogenomic libraries to accelerate rational drug discovery
Susanne Müller-Knapp, COO, SGC, and Director of Operations, Chemical Probes Portal

Targeted approaches in drug discovery need well-validated small molecules. Collaborations between industry and academia are becoming commonplace in order to establish open access small molecule libraries. In addition, chemists now place a focus to develop new modality drugs.

We speak with Susanne Müller-Knapp, Chief Operating Officer at the Structural Genomics Consortium (SGC), Frankfurt, and Director of Operations of the Chemical Probes Portal, about the new approach of chemogenomic libraries to drug discovery and the important research she has been carrying out at the SGC. Müller-Knapp also shares her view on the importance of an Open Science policy to further discovery.

The SGC is a global public-private partnership with the aim to unravel the structures and functions of medically important human proteins. The SGC is dedicated to an Open Science policy and makes the generated data and tools, such as pharmacological modulators, freely accessible in the public domain. The SGC focuses its research on various areas, including human protein kinases, metabolism-related proteins, integral membrane proteins, and proteins involved in epigenetics with the final goal to understand the function(s) of all proteins encoded by the human genome and accelerate the discovery of new medicines1.

Shift the focus to explore new modalities

One of the major developments in drug discovery is the shift from a traditional trial-and-error approach to a more targeted process thanks to new technologies which reduce the cost and time of early drug discovery2. Druggability is an important pillar of new drug development, with druggable targets being biological targets, such as a protein, peptide, or nucleic acid, that possesses activity that can be modulated by a drug.

Previously, researchers relied heavily on screening large libraries of compoundsin relevant phenotypic screens—in the hope of finding a hit, which could be further developed into a high-affinity compound and ultimately optimized into a drug. Today, scientists have a better understanding of the molecular targets involved in diseases, allowing for more focused efforts in designing drugs that interact with these targets, and creating chemogenomic libraries.

Müller-Knapp’s group at the SGC establishes cellular model systems to evaluate the effectiveness of (novel) inhibitors of interest. The aim of the Frankfurt team is to develop potent, selective, and cell-active inhibitors, so-called chemical probes that can be used to interrogate the biological activity of a protein in a cell and evaluate these proteins as potential targets in drug discovery.

Müller-Knapp explains the team’s methodology, “there are different aspects to how we characterize chemical modulators. We have a particular focus on cellular target engagement i.e., the ability of an inhibitor to bind to the protein/target of interest in a cellular context. In addition, we use cellular selectivity assays to ensure that only this and no other target is engaged. We also screen for other off-target effects by monitoring the effect of the inhibitors in cellular health assays using high-content imaging techniques”.

Müller-Knapp shares how new bioluminescence resonance energy transfer (BRET)-based technologies enabled a considerably higher throughput to assess a compound’s binding to a target in living cells. This increased throughput with automated technologies is not only seen in the industry but also now in the academic sector and this represents a transformation in the field.

There is a growing focus on exploring new modalities beyond traditional small-molecule drugs. Müller-Knapp highlights the team’s recent efforts on the development of assays to characterize novel proteolysis targeting chimeras (PROTACs), a project that Ph.D. student Martin Schwalm is focused on. PROTACs are a new modality that facilitates the targeted degradation of a protein of interest. Müller-Knapp explains, “this novel modality of protein inhibitors is bispecific, simultaneously binding a target and an E3 ligase which ubiquitinates the protein and targets it for degradation by the proteasome”. The suite of assays the group has developed is designed to characterize the steps in protein degradation in order to assess at which step a PROTAC may fail when tested as a degrader.

Towards targeting the human proteome

Well plates used to help generate chemogenomic libraries to accelerate rational drug discovery
Well-plates: A pioneer in drug discovery enabling higher throughput

Advancements in genomics and high-throughput screening techniques have played a crucial role in how drug discovery has evolved. The completion of the Human Genome Project in 2003 opened up new opportunities to identify disease-associated genes and their corresponding proteins. This knowledge has led to the development of targeted therapies, personalized medicine approaches, and the emergence of precision medicine. Additionally, the rise of innovative technologies such as CRISPR-Cas9 gene editing, organ-on-a chip-systems, and advanced imaging techniques have expanded our understanding of disease biology and provided new tools for drug discovery. Nevertheless, drug discovery projects still fail because there is a lack of understanding of the underlying disease mechanism and the biology of the proteins involved. The most versatile way to interrogate the function of a protein is the use of highly characterized selective small molecule modulators and chemical probes.

“However, the generation of chemical probes is a long, tedious, and costly process. So-called chemogenomic libraries, i.e., libraries of well-validated compounds binding to a small number of targets, complement the effort to target specific proteins with small molecules. This can be achieved using a set of pharmacological agents with overlapping profiles so that from a phenotypic screen one or a small number of targets can be identified.” Annotating the libraries required the establishment of higher-throughput cellular assays. “For this, my team has developed a suite of assays to annotate the compounds in the library” describes Müller-Knapp.

The generation of chemical probes is a long, tedious, and costly process.

Susanne Müller-Knapp 

SGC and the Chemical Probes Portal

Müller-Knapp explains how her laboratory uses a modular high-content image screen developed by the Ph.D. student, Amelie Tjaden, combining a nuclear stain to determine cell viability, and complemented by different markers to analyze the effect of small molecules on cellular health. An important example is to assess the effect on tubulin as many compounds are non-specific tubulin binders. Tubulin is essential for cellular viability, as it is one of the main components responsible for maintaining cell shape and mitotic spindle functionality. “Some molecules bind non-specifically to tubulin, thereby inhibiting cell viability or cell division. This assay enables us to see if the compound affects cell health parameters and therefore contributes to its potential as a drug.”

Müller-Knapp’s team also profiles chemogenomic compounds for their capabilities to induce phospholipidosis. Drug-induced phospholipidosis (DIPL), an excessive accumulation of phospholipids in lysosomes, can have significant implications for drug safety, potentially causing toxicity and this property should therefore be identified early on in the development of small molecule drug candidates. In addition, DIPL may alter phenotypic readouts in functional assays using chemical probes or other tool compounds. Müller-Knapp went on to work closely with a team in Barcelona led by Albert Antolin to set up a high-content image screen complete with machine learning for phospholipidosis, highlighting the importance of collaboration in novel drug discoveries.

Looking to the future

Looking ahead, drug discovery holds several exciting prospects. Artificial intelligence (AI) and machine learning are expected to play an increasingly important role in analyzing vast amounts of data, predicting drug-target interactions, and accelerating the identification of potential drug candidates. AI-driven algorithms can analyze large datasets and identify patterns that humans may overlook, leading to more efficient and targeted drug discovery efforts. Furthermore, the focus on exploring new modalities offers promising approaches to address diseases that were previously challenging to target effectively3.

Collaboration and data sharing among academia, pharmaceutical companies, and regulatory agencies are also crucial for future advancements. By pooling resources, expertise, and data, researchers can tackle complex diseases more effectively and accelerate the drug discovery process. During the interview, Müller-Knapp shared the goal of the EUbOPEN project, which is the first step towards the goals of Target 2035, a movement initiated by the SGC. This phase involves assembling and characterizing libraries of compounds covering a thousand targets. “The engagement of the scientific community within the movement has enabled that already more than half of the compounds to be characterized have been assembled at the present date, with data published and accessible in the EUbOPEN repository”. This milestone highlights the importance of such collaboration in furthering drug discovery.

From serendipitous discoveries to a more rational and targeted approach, the field of discovery has witnessed momentous transformations in the past few decades. With ongoing technological advancements, computational tools, and innovative modalities, the field is poised to make further strides in developing safe, effective, and personalized medicines for a wide range of diseases.


  1. About SGC [Internet]. 2023 [cited 2023 Jul 7]. Available from: https://www.thesgc.org/about
  2. Berdigaliyev N., Aljofan M. An overview of drug discovery and development. Future Medicinal Chemistry. 2020 May; 12(10):939–947. doi: 10.4155/fmc-2019-0307.
  3. D1. Devereson A, Idoux E, Macak M, Nagra N, Stanzl E. Ai in biopharma research: A Time to focus and scale [Internet]. McKinsey & Company; 2022 [cited 2023 Jul 7]. Available from: https://www.mckinsey.com/industries/life-sciences/our-insights/ai-in-biopharma-research-a-time-to-focus-and-scale