Native mass spectrometry can effectively predict PROTAC efficacy

Beveridge, Rebecca; Kessler, Dirk; Rumpel, Klaus; Ettmayer, Peter; Meinhart, Anton; Clausen, Tim

doi:10.1101/851980

Cited by 6 publications

(9 citation statements)

References 30 publications

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“…Assays other than the aforementioned that have also been used to characterize ternary complexes include size exclusive chromatography (SEC) [94,95], crystallography [25,35,74], co-immunoprecipitation (Co-IP) [83,96], mass spectrometry (MS) [61,97] and the NanoBiT R assay [95].…”

Section: Othersmentioning

confidence: 99%

“…MS is another label-free technique that can provide insights into PROTAC degrader-mediated PPI [61,97]. According to the study by Beveridge et al, native MS can preferentially reveal the E3-PROTAC-POI ternary complex in competition experiments with multiple substrate proteins present, thereby suggesting that it is not only an ideal HTS strategy for the development of new PROTACs [97] but also a valuable tool to dissect the mechanism of actions, selectivity and specificity of PROTACs.…”

Section: Othersmentioning

confidence: 99%

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Assays and Technologies for Developing Proteolysis Targeting Chimera Degraders

Liu

Zhang

et al. 2020

Future Med. Chem.

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Targeted protein degradation by small-molecule degraders represents an emerging mode of action in drug discovery. Proteolysis targeting chimeras (PROTACs) are small molecules that can recruit an E3 ligase and a protein of interest (POI) into proximity, leading to induced ubiquitination and degradation of the POI by the proteasome system. To date, the design and optimization of PROTACs remain empirical due to the complicated mechanism of induced protein degradation. Nevertheless, it is increasingly appreciated that profiling step-by-step along the ubiquitin-proteasome degradation pathway using biochemical and biophysical assays are essential in understanding the structure–activity relationship and facilitating the rational design of PROTACs. This review aims to summarize these assays and to discuss the potential of expanding the toolbox with other new techniques.

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Section: Othersmentioning

confidence: 99%

Section: Othersmentioning

confidence: 99%

Assays and Technologies for Developing Proteolysis Targeting Chimera Degraders

Liu

Zhang

et al. 2020

Future Med. Chem.

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“…used native nano‐ESI‐Q‐TOF‐MS to effectively study PROTAC‐mediated protein complexes in a label‐free manner. The use of native MS was demonstrated to be capable of the characterization of PROTAC‐protein complexes, semi‐quantification of their equilibria, insight into PROTAC specificities for substrate proteins and PROTAC cooperativity, and competitive experiments 40 . This work highlights the potential of native‐HRMS for high‐throughput methods in PROTACs development.…”

Section: Hrms Applications In 2020mentioning

confidence: 93%

“…Protein degraders, commonly known as proteolysis targeting chimeras (PROTACs), are small molecule inhibitors that block the activities of intracellular target proteins and interfere with signaling pathways 39,40 . This is an emerging modality that has seen limited growth due to the complexities of the PROTAC‐mediated protein interactions that involve binary and ternary interactions between the components 39,40 . Beveridge et al .…”

Section: Hrms Applications In 2020mentioning

confidence: 99%

Advances in high‐resolution mass spectrometry applied to pharmaceuticals in 2020: A whole new age of information

Géhin

Holman

2021

Analytical Science Advances

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Continuous improvements in mass spectrometry (MS) have resulted in the widespread availability and adoption of high‐resolution mass spectrometry (HRMS) across laboratories worldwide. The capabilities and the associated advantages of HRMS make it an invaluable analytical tool for analyte characterization, screening, and quantification methodologies for a wide scope of applications across pharmaceutical development. These applications include drug discovery, product characterizations of both small molecules and novel drug modalities, in vitro and in vivo metabolism studies, post‐approval quality control, and pharmacovigilance. This review gives an overview of the current capabilities of HRMS and its pharmaceutical applications in 2020, and provides a perspective on the future of HRMS within the pharmaceutical industry.

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“…[28][29][30] (However, it has recently been suggested that such covalent binders are perhaps ill-suited for PROTACs, 31,32 although this finding has itself been questioned. 33 ) Multiple independent research groups have recently developed photoactivated PROTACs, [34][35][36][37] and novel experimental diagnostic techniques [38][39][40] will continue to afford additional insight with both greater accuracy and throughput.…”

Section: Introductionmentioning

confidence: 99%

Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via NewIn SilicoMethodologies

Drummond¹,

Henry²,

Li³

et al. 2020

Preprint

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Extending upon our previous publication (Drummond and Williams, J. Chem. Inf. Model.2019, 59, 1634), in this work two additional computational methods are presented to model PROTAC-mediated ternary complex structures, which are then used to predict the efficacy of any accompanying protein degradation. Method 4B, an extension to one of our previous approaches, incorporates a clustering procedure uniquely suited for considering ternary complexes. Method 4B yields the highest proportion to date of crystal-like poses in modeled ternary complex ensembles, nearing 100% in two cases and always giving a hit rate of at least 10%. Techniques to further improve this performance for particularly troublesome cases are suggested and validated. This demonstrated ability to reliably reproduce known crystallographic ternary complex structures is further established through modeling of a newly released crystal structure. Moreover, for the far more common scenario where the structure of the ternary complex intermediate is unknown, the methods detailed in this work nonetheless consistently yield results that reliably follow experimental protein degradation trends, as established through seven retrospective case studies. These various case studies cover challenging yet common modeling situations, such as when the precise orientation of the PROTAC binding moiety in one (or both) of the protein pockets has not been experimentally established. Successful results are presented for one PROTAC targeting many proteins, for different possible PROTACs targeting the same protein, and even for degradation effected by an E3 ligase that has not been structurally characterized in a ternary complex. Overall, the computational modeling approaches detailed in this work should greatly facilitate PROTAC screening and design efforts, so that the many advantages of a PROTAC-based degradation approach can be effectively utilized both rapidly and at reduced cost.

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Native mass spectrometry can effectively predict PROTAC efficacy

Cited by 6 publications

References 30 publications

Assays and Technologies for Developing Proteolysis Targeting Chimera Degraders

Assays and Technologies for Developing Proteolysis Targeting Chimera Degraders

Advances in high‐resolution mass spectrometry applied to pharmaceuticals in 2020: A whole new age of information

Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via NewIn SilicoMethodologies

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