Chemical Biology and Target-Based Drug Design

Contact: Dr Jean Bertoldo, jbertoldo@ccia.org.au 

RNA-binding proteins (RBPs) are directly involved in all aspects of the RNA life cycle and, as such, play a pivotal role in gene expression regulation and cancer. By forming ribonucleoprotein complexes, RBPs dictate the fate of RNAs, most importantly their translation or degradation. Despite significant advancements in methods for RBP biology investigation, our understanding of RNA-protein interactions remains poor.

The use of chemical probes (small molecules that bind to RBPs) can facilitate this endeavour by providing a tool for RBP function interrogation and targeted inhibition, especially if focused on covalent probes that irreversibly bind to RBPs, which are known to enhance selectivity. However, most available RBP-targeting small molecules lack selectivity and there are no covalent probes available.

This project aims to address these hurdles by leveraging cutting-edge chemical biology tools to develop selective covalent chemical probes for RBP biology interrogation, thus expanding our knowledge of this important and often neglected class of non-catalytic proteins in childhood cancer. In addition, this project will lay the foundations for the development of potent RBP inhibitors with long-term health benefits and wide-ranging applications.

Contact: Dr Jean Bertoldo, jbertoldo@ccia.org.au

Despite advances in cancer treatment, childhood cancers remain neglected and are often treated with adult drugs, leading to suboptimal efficacy and adverse effects. Addressing the urgent need for effective and safer treatments for children requires overcoming two major challenges: a lack of druggable targets in childhood cancer and lack of drugs specifically developed for the paediatric population.

To address these needs, the objective of this project is to develop a pipeline that integrates chemoproteomics (which explores interactions between chemical probes and protein targets) with functional genomics data. This approach aims to uncover targets specific to childhood malignancies and discover promising chemical probes targeting these.

Contact: Dr Jean Bertoldo, jbertoldo@ccia.org.au

Despite intensive treatment modalities such as radiation therapy and chemotherapy, the prognosis for children diagnosed with diffuse midline gliomas (DMG), particularly diffuse intrinsic pontine glioma (DIPG), remains bleak.

DIPG is an epigenetic-driven cancer marked by alterations in genes such as ACVR1, PDGFRA, PIK3CA, TP53 and MYC, alongside the histone H3 mutation H3K27M, which serves as a pivotal oncogenic driver influencing patient outcomes. The H3K27M mutation causes a widespread loss of the repressive trimethylated H3K27me3 mark, thereby promoting a pro-oncogenic transcriptional reprogramming. While inhibitors targeting ACVR1 and PIK3CA may offer potential therapeutic avenues for DIPG, the primary driver H3K27M, MYC and TP53 remain undruggable. This is because non-catalytic proteins like H3K27M lack well-defined binding pockets, presenting a challenge for traditional drug discovery.

In this project we aim to overcome these challenges and develop cysteine-directed chemical probes targeting these oncogenic drivers, using a combination of computational chemistry, machine learning, chemoproteomics and pre-clinical models of DIPG. Restoring H3K27me3 levels to normalise the aberrant epigenome through inhibition of H3K27M, while simultaneously targeting other undruggable oncogenic drivers, might be the key to eradicating DIPG tumours.

Developing safer and more effective treatments remains a central challenge in modern drug discovery, particularly in oncology. Addressing the urgent need for effective and safer treatments requires overcoming two major challenges: a lack of druggable targets in cancer, and the lack of drugs specifically developed for these targets.   

Therefore, we are developing a cancer-agnostic drug discovery pipeline, ChemProTarget. By integrating functional genomics and chemical proteomics, we can uncover tractable cancer-relevant targets and identify promising covalent small molecule binders.

Our preliminary data across multiple paediatric cancer models show that these covalent small molecules are pharmacokinetically ideal candidates for lead optimization, selectively engage their targets, and exhibit anti-cancer properties. These results provide proof-of-concept that functional genomics with chemical proteomics can reveal both strong targets and high-quality drug leads. ChemProTarget is currently being developed into an interactive WebApp, enabling researchers to explore target-ligand interactions and accelerate target identification and therapeutic discovery.  

Diffuse midline gliomas (DMG) are highly aggressive childhood brain cancers that currently lack effective treatment options. Unlike traditional drug discovery, which relies on reversible binding of small molecules to well-defined active sites, our chemoproteomics strategy uses electrophilic compounds that form irreversible covalent bonds with proteins, including those lacking deep or stable binding pockets. A key component of this approach is activity-based protein profiling (ABPP), revealing which cysteine residues across the proteome are covalently engaged by reactive electrophiles. By analysing the labelling patterns of different compounds, we can identify ligandable ‘hotspots’ on proteins and determine each compound’s selectivity. Importantly, the formation of irreversible covalent bonds enables the targeting of reactive cysteines in proteins previously considered “undruggable”. Subsequent chemical elaboration, guided by our collaboration with computational chemists, can enhance the drug-likeness of these molecules, improving their selectivity and preclinical efficacy as lead compounds. Through this approach, we aim to uncover new breakthrough therapeutic strategies against DMG.