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Monitoring protein communities and their responses to therapeutics

Nature Reviews Drug Discovery volume 19, pages 414–426 (2020)Cite this article

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Abstract

Most therapeutics are designed to alter the activities of proteins. From metabolic enzymes to cell surface receptors, connecting the function of a protein to a cellular phenotype, to the activity of a drug and to a clinical outcome represents key mechanistic milestones during drug development. Yet, even for therapeutics with exquisite specificity, the sequence of events following target engagement can be complex. Interconnected communities of structural, metabolic and signalling proteins modulate diverse downstream effects that manifest as interindividual differences in efficacy, adverse effects and resistance to therapy. Recent advances in mass spectrometry proteomics have made it possible to decipher these complex relationships and to understand how factors such as genotype, cell type, local environment and external perturbations influence them. In this Review, we explore how proteomic technologies are expanding our understanding of protein communities and their responses to large- and small-molecule therapeutics.

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Fig. 1: Proteins function within multiple protein communities.
Fig. 2: Protein communities from the prism of mass spectrometry-based proteomics.
Fig. 3: Proteomic approaches for basic biology and drug discovery.

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Acknowledgements

The authors thank members of the MPL group for their input and support.

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  1. Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA

    Hanna G. Budayeva & Donald S. Kirkpatrick

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  1. Hanna G. Budayeva
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The authors contributed equally to all aspects of the article.

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Correspondence to Donald S. Kirkpatrick.

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H.G.B. and D.S.K. are employees of Genentech Inc., a wholly owned subsidiary of Roche. D.S.K. is a shareholder in Roche.

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Glossary

Spectral counting

Quantitative analysis based on comparing the total number of spectra identified per protein in a mass spectrometry analysis.

Multiplexed isobaric tagging

Mass spectrometry (MS)-based quantification approach, in which labelled peptides from multiple samples are mixed together and analysed by mass spectrometer. Upon peptide fragmentation, reporter ions of different masses are released from the isobaric tags, and their relative intensities are measured within individual MS2/MS3 scan events.

Chemoproteomics

Proteomics approaches that use chemical probes to elucidate small-molecule–protein interactions in the proteome.

Proximity labelling

Proteomics approaches that use genetically engineered enzymes for the labelling and enrichment of proteins within subcellular regions and protein communities.

Phosphoproteomics

Proteomics approaches used for the characterization of proteins post-translationally modified with a phosphate group by kinase enzymes.

Thermal-shift assay

A method used to quantify changes in protein stability under thermal denaturation in response to different treatments or conditions, such as binding of a small molecule.

Synaptic cleft

Space or gap at the synapse between a neuron and an effector cell (such as a neuron or a muscle cell).

Postsynaptic density

Protein-dense compartment at the postsynaptic membrane of a synapse between two neurons.

Xenobiotics

Substances that are foreign to the biological system.

BioID

A mass spectrometry-based method for studying the associations of a protein of interest fused to a biotin ligase that labels other proteins in its close proximity.

Single-shot mass spectrometry

A mass spectrometry experimental setup wherein single sample injections are performed, as opposed to multiple injections of fractionated peptide mixtures.

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Budayeva, H.G., Kirkpatrick, D.S. Monitoring protein communities and their responses to therapeutics. Nat Rev Drug Discov 19, 414–426 (2020). https://doi.org/10.1038/s41573-020-0063-y

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