The promise and peril of chemical probes

Arrowsmith, C.H.; Audia, James E.; Austin, Christopher P.; Baell, Jonathan B.; Bennett, Jonathan P.; Blagg, Julian; Bountra, C.; Brennan, P.E.; Brown, Peter J.; Bunnage, Mark E.; Buser-Doepner, Carolyn; Campbell, Robert M.; Carter, Adrian J.; Cohen, Philip; Copeland, Robert A.; Cravatt, Ben; Dahlin, Jayme L.; Dhanak, Dashyant; Edwards, A.M.; Frederiksen, Mathias; Frye, Stephen V.; Gray, Nathanael S.; Grimshaw, Charles E.; Hepworth, David; Howe, Trevor; Huber, Kilian; Jin, Jian; Knapp, Stefan; Kotz, Joanne; Kruger, Ryan G.; Lowe, Derek; Mader, Mary M.; Marsden, Brian D.; Mueller‐Fahrnow, Anke; Müller, Susanne; O’Hagan, Ronan; Overington, John P.; Owen, Dafydd R.; Rosenberg, Saul H.; Roth, Bryan L.; Ross, Ruth A.; Schapira, Matthieu; Schreiber, Stuart L.; Shoichet, Brian K.; Sundström, M.; Superti‐Furga, Giulio; Taunton, Jack; Toledo-Sherman, Leticia; Walpole, Chris; Walters, Michael A.; Willson, Timothy M.; Workman, Paul; Young, Robert N.; Zuercher, William J.

doi:10.1038/nchembio.1867

Cited by 747 publications

(757 citation statements)

References 39 publications

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“…21 Recent years have witnessed a major effort to raise awareness of PAINS in the scientific literature, so these molecules are not mistakenly applied as highly specific chemical probes. 10,22 Paralleling this effort has been a growing reliance on phenotypic screens to identify inhibitors of challenging to target biological pathways. 23 C646 is a molecule that lies at the intersection of these two paradigms, containing many chemical features of a PAIN compound, while also demonstrating the ability to phenocopy some effects of p300/CBP knockdown.…”

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confidence: 99%

Characterizing the Covalent Targets of a Small Molecule Inhibitor of the Lysine Acetyltransferase P300

Shrimp

Sorum

Garlick

et al. 2015

ACS Med. Chem. Lett.

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C646 inhibits the lysine acetyltransferases (KATs) p300 and CBP and represents the most potent and selective small molecule KAT inhibitor identified to date. To gain insights into the cellular activity of this epigenetic probe, we applied chemoproteomics to identify covalent targets of the C646 chemotype. Modeling and synthetic derivatization was used to develop a clickable analogue (C646-yne) that inhibits p300 similarly to the parent compound and enables enrichment of bound proteins. LC−MS/MS identified the major covalent targets of C646-yne as highly abundant cysteine-containing proteins, and follow-up studies found that C646 can inhibit tubulin polymerization in vitro. Finally, we provide evidence that thiol reactivity of C646 may limit its ability to antagonize acetylation in cells. These findings should enable a more precise interpretation of studies utilizing C646 as a chemical probe of KAT activity and suggest that an underappreciated liability of electrophile-containing inhibitors is a reduction in their cellular potency due to consumption by abundant protein and metabolite thiol sinks.

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confidence: 99%

Characterizing the Covalent Targets of a Small Molecule Inhibitor of the Lysine Acetyltransferase P300

Shrimp

Sorum

Garlick

et al. 2015

ACS Med. Chem. Lett.

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“…When designing, interpreting, and reporting preclinical studies, it is important to fully understand the cellular potencies, selectivity, and PK of the tool compound selected, as recently stated by a crossacademic/pharmaceutical working group (Arrowsmith et al, 2015). BI 1002494 fulfills these criteria; it is more selective than fostamatinib (Braselmann et al, 2006), cerdulatinib (Coffey et al, 2014), R343 , and LAS189386 (Ramis et al, 2015) and has better rodent PK compared with BAY 61-3606 (Bhagwat, 2009).…”

Section: Discussionmentioning

confidence: 99%

BI 1002494, a Novel Potent and Selective Oral Spleen Tyrosine Kinase Inhibitor, Displays Differential Potency in Human Basophils and B Cells

Lamb

Wollin

Schnapp

et al. 2016

Journal of Pharmacology and Experimental Therapeutics

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BI 1002494 [(R)-4-{(R)-1- [7-(3,4,5-trimethoxy-phenyl)- [1,6] napthyridin-5-yloxy]-ethyl}pyrrolidin-2-one] is a novel, potent, and selective spleen tyrosine kinase (SYK) inhibitor with sustained plasma exposure after oral administration in rats, which qualifies this molecule as a good in vitro and in vivo tool compound. BI 1002494 exhibits higher potency in inhibiting highaffinity IgE receptor-mediated mast cell and basophil degranulation (IC 50 5 115 nM) compared with B-cell receptor-mediated activation of B cells (IC 50 5 810 nM). This may be explained by lower kinase potency when the physiologic ligand B-cell linker was used, suggesting that SYK inhibitors may exhibit differential potency depending on the cell type and the respective signal transduction ligand. A 3-fold decrease in potency was observed in rat basophils (IC 50 5 323 nM) compared with human basophils, but a similar species potency shift was not observed in B cells. The lower potency in rat basophils was confirmed in both ex vivo inhibition of bronchoconstriction in precision-cut rat lung slices and in reversal of anaphylaxis-driven airway resistance in rats. The different cellular potencies translated into different in vivo efficacy; full efficacy in a rat ovalbumin model (that contains an element of mast cell dependence) was achieved with a trough plasma concentration of 340 nM, whereas full efficacy in a rat collageninduced arthritis model (that contains an element of B-cell dependence) was achieved with a trough plasma concentration of 1400 nM. Taken together, these data provide a platform from which different estimates of human efficacious exposures can be made according to the relevant cell type for the indication intended to be treated.

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“…Contributions to irreproducible results, artifactual bioactivity, and poorly tractable bioactivity can include assay reagents, data analysis methods, test compounds, instrumentation, and contaminants. Compound‐mediated assay interferences can be highly reproducible yet intractable sources of bioactivity due to either nonspecific compound mechanisms of action or to compound interference with assay readouts 44, 45. The amount of time and resources invested in follow‐up studies of irreproducible false‐positives as well as intractable or artifactual mechanisms of bioactivity can substantially reduce the productivity of a discovery program, but more importantly represents lost opportunity costs.…”

Section: Current Contents and Usage In The Public Domainmentioning

confidence: 99%

Assay Guidance Manual: Quantitative Biology and Pharmacology in Preclinical Drug Discovery

Coussens

Sittampalam

Guha

et al. 2018

Clinical Translational Sci

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The Assay Guidance Manual (AGM) is an eBook of best practices for the design, development, and implementation of robust assays for early drug discovery. Initiated by pharmaceutical company scientists, the manual provides guidance for designing a “testing funnel” of assays to identify genuine hits using high‐throughput screening (HTS) and advancing them through preclinical development. Combined with a workshop/tutorial component, the overall goal of the AGM is to provide a valuable resource for training translational scientists.

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The promise and peril of chemical probes

Cited by 747 publications

References 39 publications

Characterizing the Covalent Targets of a Small Molecule Inhibitor of the Lysine Acetyltransferase P300

Characterizing the Covalent Targets of a Small Molecule Inhibitor of the Lysine Acetyltransferase P300

BI 1002494, a Novel Potent and Selective Oral Spleen Tyrosine Kinase Inhibitor, Displays Differential Potency in Human Basophils and B Cells

Assay Guidance Manual: Quantitative Biology and Pharmacology in Preclinical Drug Discovery

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