Maurice Michel Team

Welcome to the page of the Chemical Switching Group. We are an independent entity at the Center for Molecular Medicine, the only unit affiliated to the Department of Oncology and Pathology – we are developing our key technology for both basic and clinical research, rewriting human physiology at will.

Although widely used in industry, organocatalysis has classically been limited to ex vivo application. In addition, the small molecule activation of enzymes has so far been exerted by allosteric control. A union of the two concepts has classically been considered unattractive, as partaking in the reaction would require binding to the enzymatic active site. This in turn would render the molecule an inhibitor as desired high compound concentration for high reaction turnover would compete with the originally intended substrate. However, this interpretation ignores enzymes with complex biochemistry, where substrate hydrolysis is achieved by consecutive steps of replacement and cleavage. Here, the inhibition or enhancement of single steps is conceivable with more complex mode of action.

Recently, we reported that small molecules can act as organocatalysts for the DNA repair enzyme 8-oxoguanine DNA glycosylase 1 (OGG1). The underlying principle, termed chemical switching, allows for a full control of enzymatic function with potential for alleviating oxidative stress to the genome or as a new strategy in cancer therapy.

To build on this discovery, we focus on three pillars, leveraging our expertise in medicinal and computational chemistry, biochemistry and biophysics, cell and disease biology.

1. Development of OGG1 activators

In June 2022, we were first to report cellularly active organocatalysts – organocatalytic switches, we call them ORCAs, assist the enzyme in reaction turnover and diversification of substrate and product scope. Based on some of the findings, we continue to drive synthetic chemistry with help of X-Ray co-crystal structures and computational chemistry. Our goals within this context, are the exact control of product scope, the tuning of a defined pH range of OGG1 biochemical reactions and the selective targeting of cellular organelles. With this achieved for lead molecules, we recruit or collaborate with disease experts to reach proof of principle in disease models driven by OGG1 biology or oxidative stress to the genome in general. We also aim to understand the activation of elimination mechanisms in DNA repair by exploiting chemical principles, such as leaving group activation, proton abstraction and aldehyde tuning. Here, we are making great strides in reducing the necessary molecularity, dramatically increasing enzyme turnover.

^{Figure 1: Left: The repair fate for substrates of monofunctional and β,δ-bifunctional DNA glycosylases is either APE1 or PNKP1 dependent. OGG1 as a bifunctional glycosylase with residual product-assisted β-elimination activity recognizes and excises 8-oxoG. Because of the inefficient process, APE1 performs incision of the AP site and excision of PUA to generate a 3′-hydroxyl end compatible with a DNA polymerase. Other DNA glycosylases, such as endonuclease VIII–like proteins 1 and 2 (NEIL1/2), can catalyze an additional β,δ-elimination in addition to the DNA glycosylase function, which includes incision of the AP site and removal of resulting PUA. This generates a 3′-hydroxyl end, which is only compatible with a DNA polymerase after additional elimination of the generated 3′-phosphate by PNKP1. Thus, these enzymes are functioning independently of APE1. OGG1-ORCAs introduce a novel β,δ-elimination, rendering OGG1 initiated BER independent of APE1. Right: close-up view of ligand TH10785 (purple) binding to human OGG1. Important residues in the binding site are marked; a central π-stacking of the quinazoline ring with Phe319 was observed. Further stabilization of the complex is provided by a hydrogen bond between the proton of the secondary amine and Gly42. Notably, in the hOGG1 complex, TH10785 makes a hydrogen bond with the acidic side chain of Asp268, whereas Lys249 is oriented away from the catalytic pocket.}

2. Broadening of the technology base of enzyme activation

Although OGG1 is no significant AP-lyase in cells, DNA glycosylases with pronounced β- or β, δ-AP lyase activity exist in humans and other species. Understanding how these activities are controlled on a molecular level, allows us to alter enzyme function at will and thus generate new DNA repair pathways for the treatment of disease. We call this strategy chemical switching. Along these lines, we have designed bioinformatics workflows that allow us to identify enzymes suitable for artificial functions. We then perform computational calculations to elucidate chemical and biochemical reaction mechanisms, generate amino acid mutants, develop ORCAs and engineer proteins through amino acid selective modifications and bioorthogonal chemistry. The ultimate goal: enabling an array of enzymes to cleave non-natural substrates through previously unreported reaction pathways. To achieve this, we leverage our expertise in computational chem/bioinformatics, the design of bio-macromolecules, gain-of-function enzymes and additional ORCAs. Once a technology is established in vitro, we characterize the consequences of chemical switching in a cellular context. As of now, we employ techniques from DNA repair to quantify the altered physiological state of a several enzymes. Developing the platform further, we will move from DNA repair to other metabolic pathways. Importantly, the implications of this research reach also beyond medicine and thus we also collaborate with industry partners to impact biocatalysis.

^{Figure 2: “Dark activities” of enzymes and virtually all proteins are underlying favoured as wll as unfavoured chemical reactions: A) Activation energies define which enzymatic reactions proceed. Redifining what we treat as enzymatic function, activity and transformation opens the possibility to chemically switch all levels of enzyme control; B) Formerly unfavoured chemical reactions are improved to generate new products, which equals the enhancement of rudimentary or slow reactions; C) The reaction profile may also underlie secondary transformations in which the reaction intermediate may be an additional substrate. Both original substrate and former intermediate may be transformed into an entirely new product, effectively rewiring the reaction pathway; D) A favoured biochemical reaction may indeed only be the first step of a potential and hidden enzymatic cascade; E) Lowering the activation barrier of the following steps successfully rewires the enzymatic cascade by enhancing one transformation.}

3. A Nordic DNA glycosylase platform

Eleven human DNA glycosylases exist and most of them are considered understudied. In extension of the EUbOPEN consortium and the SGC, we have joined forces with partners in Sweden and Norway to assemble all of them physically. We have developed a platform that includes in vitro and cellular assays for selectivity/activity readout and target engagement. In collaboration with partners at the SGC and Target 2035 we perform large scale screens, solve crystal structures, generate selective antibodies and other reagents and enable investigation of the entire protein family – effectively deorphanizing them for investigation. We donate this setup to the scientific community through protocols within EUbOPEN and Target2035. Ultimately, we thrive to combine our work on ORCAs with these novel targets and enable the studying of DNA repair biology.

We are deeply committed to mentoring, coaching, teaching and supporting the next generation of students. Our strategic exchange program with the Universities of St. Andrews and Edinburgh has led to fruitful collaborations and a uniquely educated generation of undergraduate students – their success is our legacy. In addition, we teach in the Biomedicine program across the entire curriculum. Reach out, if you want to work with us and shape the future in protein regulation.

Maurice Michel, PhD, assistant professor, principal investigator, maurice.michel@ki.se

Maurice is a chemist by training and immerged himself in biological questions since his undergraduate studies. He now uses this unique angle to newly interpret enzymatic reactions in DNA repair using informatics, medicinal chemistry, biochemistry, biophysics and cell biology.

Maurice about himself: “When not thinking about science, I love spending time with my family, playing in the garden, reading them the latest books and singing in the absolute worst voice anyone has ever heard. I am a keen swimmer both in pool and fresh water; during winter you might find me online, playing coop survival or strategy games.”      

Alice Eddershaw, PhD, Postdoctoral Researcher, alice.eddershaw@ki.se

Alice joined us from Oxford bringing valuable expertise in assay development and expression of membrane proteins with her. She currently, focuses on creating a platform for the next generation of targets, including chemical matter screens and gain-of-function variants.

Alice about herself: “I enjoy running (mainly to and from cafes for coffee), going to pilates classes and reading. Since moving to Stockholm, I have loved adopting the Swedish practice of bastu/cold dips, as well as trying out the many winter sports on offer (you may see me snow plough-ing my way down the slopes at 1 mph…).”

Natalie Rudolfova, Placement Student, University of Edinburgh

Natalie is at the forefront of our next breakthrough. Before, we have developed the chemical switching concept for small molecules. In her project she focuses on transferring novel function into proteins without the need for small molecules.

Natalie about herself: “I am a big coffee enthusiast that enjoys peculiar coffee drinks (like espresso and tonic) so much that I got a barista certificate. If not sitting in a cafe, you can usually find me reading some historical novel or playing the piano. In winter, my love for skiing makes me overcome my aversion to early mornings, and you can find me skiing down the slopes as soon as they open.”

Rahul Upadhyay, PhD, Postdoctoral Researcher

Rahul is a chemical wizard with vast experience in small molecule synthesis. With an exceptionally productive PhD from CSIR-IHBT in India and a first PostDoc at the University Health Network, Rahul is ready to expand on OGG1-ORCAs and join forces with the biochemists in the team.

Rahul says: “Beyond being a chemist, I find joy in playing and watching cricket, which keeps me active and connected to the sport I love. Gardening also brings a sense of peace and fulfillment as I nurture plants and appreciate nature. Both bring a refreshing balance to my life, blending excitement with tranquility.”

Carlos Benítez-Buelga, PhD, Visiting Researcher

We have been working Carlos for a long time, since when he was instrumental in first discovering ORCAs of OGG1. His expertise on fibrotic conditions and in telomere biology are important cornerstones of our research. He now heads investigations in treatments for rare diseases exploiting our unique collaboration.

When I’m not in the lab, I enjoy spending quality time with my wife, son, and other family members. I love exploring the city with friends, discovering new restaurants, and traveling whenever possible. Also, I am a music lover, so I enjoy listening to my records, and playing the congas.

We strive to place all manuscripts on preprint servers prior to publication. You can find all publications related to the lab at Google Scholar: https://scholar.google.com/citations?user=-_WjEy4AAAAJ&hl=de