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  • Review Article
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The emerging role of mass spectrometry-based proteomics in drug discovery

Abstract

Proteins are the main targets of most drugs; however, system-wide methods to monitor protein activity and function are still underused in drug discovery. Novel biochemical approaches, in combination with recent developments in mass spectrometry-based proteomics instrumentation and data analysis pipelines, have now enabled the dissection of disease phenotypes and their modulation by bioactive molecules at unprecedented resolution and dimensionality. In this Review, we describe proteomics and chemoproteomics approaches for target identification and validation, as well as for identification of safety hazards. We discuss innovative strategies in early-stage drug discovery in which proteomics approaches generate unique insights, such as targeted protein degradation and the use of reactive fragments, and provide guidance for experimental strategies crucial for success.

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Fig. 1: Mass spectrometry-based proteomics applications in the preclinical drug discovery process.
Fig. 2: Major protein identification and quantification strategies.
Fig. 3: Proteomics strategies to study drug action by the analysis of protein affinity, activity, stability and folding.
Fig. 4: Proteomics strategies to study mechanisms of drug action as well as disease biology by the analysis of protein abundance, localization, interactions and modifications.

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The authors contributed equally to all aspects of the article.

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Correspondence to Felix Meissner or Marcus Bantscheff.

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Related links

Proteomics software tools and databases: https://proteomics.bio.tools

The human protein atlas: https://www.proteinatlas.org/search/protein_class%3AFDA+approved+drug+targets

Glossary

CRISPR interference

(CRISPRi). A genetic perturbation technique that enables sequence-specific repression of transcription.

CRISPR activation

(CRISPRa). A genetic perturbation technique that allows sequence-specific activation of transcription.

Chemoproteomics

A discovery-driven proteomics technology to assess target engagement, mechanism of action and/or nonspecific off-targets by characterizing the interactions between compounds and proteins.

Compound-centric chemoproteomics

(CCCP). A chemical proteomics strategy to assess interacting proteins of bioactive compounds.

Structure–activity relationship

(SAR). Describes the interdependency between compound structures and protein binding affinities.

Photoaffinity labelling

(PAL). A strategy to study protein interaction by use of photocrosslinkers that generate reactive species and react with adjacent molecules, resulting in a direct covalent modification.

Click chemistry

A class of biocompatible reactions commonly used to join small, modular molecule units.

Dissociation constants

Binding affinity is typically reported by the equilibrium dissociation constant (Kd), which measures the strength of interaction between compounds and proteins.

Cheng–Prusoff relationship

Defines the theoretical relationship between the measured IC50 of a competitive inhibitor of a given Ki, the concentration of labelled ligand and the Kd of the ligand–receptor interaction.

Activity-based probe profiling

(ABPP). Uses active-site-targeted chemical probes that react with mechanistically related classes of enzyme and monitor the state of proteins.

Pharmacophores

Description of molecular features that are necessary for molecular recognition of a ligand by a biological macromolecule.

Chaotropes

Disrupt the hydrogen-bonding network between water molecules, thereby perturbing the stability of the native state of other molecules in the solution, in particlular, biological macromolecules.

Thermal proteome profiling

(TPP). Also known as cellular thermal shift assay (CETSA)–MS, a proteomics profiling and target identification approach based on the principle that proteins change their thermal stability and become more resistant to heat-induced unfolding when complexed with a ligand.

2D thermal proteome profiling

(2D-TPP). Monitors changes of protein melting curves over a range of drug concentrations.

Warhead

A chemical group that reacts with adjacent molecules, resulting in a direct covalent modification.

Biased agonism

The ability of a ligand to induce different functional states by activating specific signalling pathways downstream of the same activated receptor.

Prenylated proteins

The addition of a prenyl group (3-methylbut-2-en-1-yl) that facilitates protein attachment to cell membranes.

Secondary pharmacology

Unintended pharmacological activity of a drug.

Drug polypharmacology

The design or use of drugs that act on multiple targets or disease pathways.

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Meissner, F., Geddes-McAlister, J., Mann, M. et al. The emerging role of mass spectrometry-based proteomics in drug discovery. Nat Rev Drug Discov 21, 637–654 (2022). https://doi.org/10.1038/s41573-022-00409-3

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