Chemical Biology

"Nature is dominated by chemically favoured processes. While biology is prone to evolution, universal principles of physical chemistry are not (at least not on the same time scale). It is my opinion that life has evolved mechanisms to circumvent undesired chemistry’’ -Raphaël Rodriguez-

Our laboratory has adopted ‘the small molecule approach’ to biology. We study cell biology at the molecular and atomic levels using an integrated approach combining synthetic organic chemistry and molecular biology techniques. We custom design our probes to interrogate cell processes relevant to human diseases. For example, we have established protocols based on click chemistry to fluorescently label small molecules in cells with the view to shed light on their mechanisms of action. This, combined with multi-omics has revealed previously uncharted molecular features in cells that promote the disease-state, while offering opportunities for small molecule intervention. For instance, we have discovered a novel mechanism of metal uptake involving the plasma membrane glycoprotein CD44 and its ligands hyaluronates. We have identified an iron-dependency of the mesenchymal state of cancer cells, which confer a vulnerability of this cell state to ferroptosis. More recently, we have uncovered a previously uncharted role of mitochondrial copper in the regulation of immune cell activation and epithelial-mesenchymal transition of cancer cells. We found that targeting these metals in the disease-state with in-house small molecules confers therapeutic benefits in vivo. Thus, our laboratory exploits universal principles of physical chemistry and knowledge of biology to impact human medicine.

Relevant lab findings

• Discovery of a general metal uptake mechanism mediated by the plasma membrane glycoprotein CD44 and its ligands hyaluronates.
• Discovery that copper and iron operate as metal catalysts that regulate cell plasticity at the metabolic and epigenetic levels.
• Discovery that iron regulates epithelial-mesenchymal plasticity. Discovery (concomitantly with the Schreiber lab) that the mesenchymal (persister) cancer cell state is vulnerable to ferroptosis.
• Developed small molecules that mediate their activity through unprecedented mechanisms of action (e.g. lysosomal iron retention triggers ferroptosis, mitochondrial copper(II) inactivation interferes with cell plasticity).

Keywords

Natural products, biologically active small molecules, organic synthesis, iron, copper, endocytosis, signaling, metabolism, epigenetics, cell plasticity, cancer, degenerative diseases.

Figure 1. Total synthesis of Marmycin A, a fluorescent natural product that accumulates in the lysosomal compartment (Cañeque et al. Nat Chem 2015).

Figure 2. Top left: General strategy to fluorescently label small molecules in cells. This methodology can reveal to the subcellular localization of small molecules and provide mechanistic insights. Bottom left: Images of ironomycin labeled in situ by means of click chemistry, illustrating a colocalization with a lysosomal marker (Mai et al. Nat Chem 2017; Cañeque et al, Nat Rev Chem 2018; Rodriguez et al Nat Chem Biol 2012; Larrieu et al Science 2014; Tyler et al Science 2017).

Figure 3. Working model of lysosomal iron retention by small molecules leading to ferroptotic cell death in breast and pancreatic cancer cell (Mai et al. Nat Chem 2017). In contrast, mitochondrial iron depletion triggers a non-canonical Bak/Bax-dependent cell death in acute myeloid leukemia (Garciaz et al. Cancer Discov 2022). Conceptualization that the persister cancer cell state is addicted to iron, which confers a clonal advantage of this cell state over other cancer cells during standard therapy, while conferring vulnerability to ferroptosis (Rodriguez et al Mol Cell 2022). This illuminates a new paradigm whereby it is the state of cells that defines the cell death mechanisms at work.

Figure 4. Discovery of a general metal uptake mechanism that is engaged during cell plasticity. CD44-mediated endocytosis of metal catalysts, which regulate cell plasticity, in particular epithelial-to-mesenchymal transition (EMT) in cancer (Müller et al., Nat Chem 2020). Copper is used in mitochondria for the biosynthesis of metabolites, including a-ketoglutarate and acetyl-CoA, required for epigenetic programming of EMT (bioRcin doi: https://doi.org/10.1101/2022.03.29.486253). In contrast, iron is exploited in the nucleus to promote the activity of a-ketoglutarate-dependent demethylases to program the epigenetic landscape poised for mesenchymal gene expression. This pathway can be exploited for therapeutic benefits by means of small molecule intervention. For instance, salinomycin/ironomycin can sequester iron in lysosome and trigger ferroptosis. Alternatively, metformin can interact with mitochondrial copper and interfere with cell plasticity.