Activity-based Protein Profiling: Druggable Sites Identification

In course

Description

This lecture covers the principles and applications of Activity-based Protein Profiling (ABPP) for identifying potentially druggable sites on proteins, discussing the advantages and limitations of this approach. It introduces tools like peptide digest, affinity pulldown, and quantitative target ID, showcasing competitive ABPP and gel-based ABPP case studies. The instructor presents strategies for minimizing off-target reactivity of covalent inhibitors and demonstrates the use of ABPP in testing these strategies. In-class exercises involve analyzing data from ABPP experiments to determine the target of covalent binding by probes and evaluate the effectiveness of kinetic-selectivity models.

Instructor

Official source

https://mediaspace.epfl.ch/media/0_f5efv8nx

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Drug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that activates or inhibits the function of a biomolecule such as a protein, which in turn results in a therapeutic benefit to the patient. In the most basic sense, drug design involves the design of molecules that are complementary in shape and charge to the biomolecular target with which they interact and therefore will bind to it.

Enzyme inhibitor

An enzyme inhibitor is a molecule that binds to an enzyme and blocks its activity. Enzymes are proteins that speed up chemical reactions necessary for life, in which substrate molecules are converted into products. An enzyme facilitates a specific chemical reaction by binding the substrate to its active site, a specialized area on the enzyme that accelerates the most difficult step of the reaction.

Protein kinase

A protein kinase is a kinase which selectively modifies other proteins by covalently adding phosphates to them (phosphorylation) as opposed to kinases which modify lipids, carbohydrates, or other molecules. Phosphorylation usually results in a functional change of the target protein (substrate) by changing enzyme activity, cellular location, or association with other proteins. The human genome contains about 500 protein kinase genes and they constitute about 2% of all human genes. There are two main types of protein kinase.

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Chemoproteomics (also known as chemical proteomics) entails a broad array of techniques used to identify and interrogate protein-small molecule interactions. Chemoproteomics complements phenotypic drug discovery, a paradigm that aims to discover lead compounds on the basis of alleviating a disease phenotype, as opposed to target-based drug discovery (reverse pharmacology), in which lead compounds are designed to interact with predetermined disease-driving biological targets.