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Highly selective covalent chemical probes to explore, track and time intracellular signaling

English title Highly selective covalent chemical probes to explore, track and time intracellular signaling
Applicant Wymann Matthias
Number 204602
Funding scheme Project funding
Research institution Departement Biomedizin Universität Basel
Institution of higher education University of Basel - BS
Main discipline Organic Chemistry
Start/End 01.10.2021 - 30.09.2025
Approved amount 770'374.00
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All Disciplines (2)

Discipline
Organic Chemistry
Biochemistry

Keywords (9)

Chemical biology; Chemical reactivity; Cellular signaling; Medicinal chemistry; Structure function analysis; Covalent inhibitors; Phophoinositide 3-kinase; PI3K; CRM1

Lay Summary (German)

Lead
Einige Moleküle die mit physiologisch wichtigen Signal-Enzymen in unseren Zellen reagieren, werden bereits therapeutisch verwendet. Die Reaktionen, welche zur Bildung von chemischen Bindungen zwischen Ziel-Enzymen und diesen kovalenten Inhibitoren führen, sind quantitativ wenig untersucht worden. Wir präsentieren hier Ideen um Wege zu einer besser verstandenen, «intrazellulären, zielführenden Chemie» entwickeln.
Lay summary

Kleine chemische Moleküle, wie Inhibitoren für zelluläre Enzyme, können benützt werden um Signalübertragungs-Ketten in physiologischen und pathologischen Prozessen zu untersuchen. Leider sind diese Inhibitoren oft zu wenig spezifisch, und führen deshalb zu falschen Interpretationen. Besonders bei Untersuchungen bei denen ähnliche Enzym-Isoformen untersucht werden, können diese nicht selektiv inhibiert werden. Die Selektivität kann verbessert werden, wenn Inhibitoren mit chemisch reaktiven Gruppen versehen werden, sogenannten «warheads». Diese können dann mit nicht konservierten, nukleophilen Aminosäuren-Seitenketten reagieren, und bilden eine kovalente Bindung mit dem Zielenzym aus. Bis heute wurden verschiedene solche Inhibitoren sogar als Medikamente entwickelt. Allerdings wurden diese nicht immer systematisch selektiert. Wird schlagen hier Wege vor, wie kovalente Inhibitoren effizienter validiert werden können, und wie Nebenreaktionen schädliche minimiert werden. Integriert werden auch Methoden der «Chemischen Biologie» und der «Chemischen Genetik».

Als erstes Zielmolekül bearbeiten wir die Lipidkinase «Phophoinositide 3-kinase alfa» (PI3Kalfa), welche bei Zellwachstum, -Proliferation und der Metastasen-Bildung in Tumoren wichtig ist. Die geplanten kovalenten Inhibitoren werden wichtige Werkzeuge sein um zu bestimmen, welche PI3K Isoform im Insulin-abhängigen Glucose Metabolismus wichtig ist.

Direct link to Lay Summary Last update: 27.10.2021

Responsible applicant and co-applicants

Employees

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Associated projects

Number Title Start Funding scheme
189065 Distinct PI3Kg Complexes in Inflammation, Allergy and Metabolic Control 01.11.2019 Project funding

Abstract

Small-molecule chemical probes are excellent tools to interrogate biological systems, but sometimes display insufficient on-target selectivity to functionally dissect structurally related signaling enzymes and enzyme isoforms. A major improvement in selectivity can be achieved using chemically reactive groups - warheads - able to form covalent bonds with non-conserved amino acid side chain nucleophiles in targeted enzymes. Up-to-date, a lack of systematic kinetic investigation of warhead reactivity impairs the rational development of covalent probes and drugs.Herein, we systematically assess novel areas of electrophilic chemical space, explore warheads with undisclosed mechanism of action and propose electrophiles activated by intracellular chemical conditions. We pioneer novel, versatile applications of covalent strategies for intracellular reactions. Our methods allow for a broad applicability to different protein types, providing innovative tools for chemical biology, extendable to chemical genetics.Due to the need for a better understanding of phosphoinositide 3-kinase signaling in cancer and inflammation, and our expertise on lipid kinases, we have selected phosphoinositide 3-kinase alpha (PI3Kalpha) as a first target to validate the proposed chemical concepts. Our main objectives in brief are to(i)investigate and tune warhead reactivity to expand the chemical space of electrophiles,(ii)establish a rational approach and workflow to model and target distal cysteines,(iii)pioneer a strategy for a timed and localized activation of signaling enzymes and(iv)develop targeted intracellular labelling for protein tracking.First, we aim to provide comprehensive knowledge on the effect of the electrophilic character of chemical probes, to control selectivity, potency, tissue distribution, cellular localization, and metabolic stability. Moreover, we will apply a beta-elimination strategy to develop warheads that can be activated intracellularly, minimizing off-target effects due to reaction with extracellular nucleophiles. Second, we will provide a path to optimize warhead/target residue proximity and to set up rational structural activity relationships for covalent inhibitor development. Third, we will combine covalent inhibition and spatiotemporal controlled photo-cleavage to overcome the spatial limitation of current caged compounds.This application of photocleavable modules will enable us to investigate and control the localization of (reactivated) target enzymes. Fourth, we will disclose a conjugate addition-elimination reaction mechanism which will allow to deposit cargo modules, including fluorophores, on a native cellular protein. Finally, our work will also pave the way for the investigation of multifunctional covalent inhibitors with an unprecedented mechanism of action.We expect that the proposed research will provide innovative and versatile applications of covalent warhead chemistry, supporting inhibition, localization and labelling of intracellular proteins.
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