Remodelin Is a Cryptic Assay Interference Chemotype That Does Not Inhibit NAT10-Dependent Cytidine Acetylation

Jonathan H. Shrimp; Yihang Jing; Supuni Thalalla Gamage; Kathryn M. Nelson; Joseph Han; Keri M. Bryson; David C. Montgomery; Justin M. Thomas; Kellie D. Nance; Sunny Sharma; Stephen D. Fox; Thorkell Andressen; Wilson R. Sinclair; Hong Wu; Abdellah Allali-Hassani; Guillermo Senisterra; Masoud Vedadi; Denis Lafontaine; Jayme L. Dahlin; Ronen Marmorstein; Michael A. Walters; Jordan L. Meier

doi:10.1021/acsmedchemlett.0c00193

Remodelin Is a Cryptic Assay Interference Chemotype That Does Not Inhibit NAT10-Dependent Cytidine Acetylation

Jonathan H. Shrimp, Yihang Jing, Supuni Thalalla Gamage, Kathryn M. Nelson, Joseph Han, Keri M. Bryson, David C. Montgomery, Justin M. Thomas, Kellie D. Nance, Sunny Sharma, Stephen D. Fox, Thorkell Andressen, Wilson R. Sinclair, Hong Wu, Abdellah Allali-Hassani, Guillermo Senisterra, Masoud Vedadi, Denis Lafontaine, Jayme L. Dahlin, Ronen MarmorsteinMichael A. Walters, Jordan L. Meier

Institute for Therapeutics Discovery and Development

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16 Scopus citations

Abstract

Remodelin is a putative small molecule inhibitor of the RNA acetyltransferase NAT10 which has shown preclinical efficacy in models of the premature aging disease Hutchinson-Gilford Progeria Syndrome (HGPS). Here we evaluate remodelin's assay interference characteristics and effects on NAT10-catalyzed RNA cytidine acetylation. We find the remodelin chemotype constitutes a cryptic assay interference compound, which does not react with small molecule thiols but demonstrates protein reactivity in ALARM NMR and proteome-wide affinity profiling assays. Biophysical analyses find no direct evidence for interaction of remodelin with the NAT10 acetyltransferase active site. Cellular studies verify that N4-acetylcytidine (ac4C) is a nonredundant target of NAT10 activity in human cell lines and find that this RNA modification is not affected by remodelin treatment in several orthogonal assays. These studies display the potential for remodelin's chemotype to interact with multiple protein targets in cells and indicate remodelin should not be applied as a specific chemical inhibitor of NAT10-catalyzed RNA acetylation.

Original language	English (US)
Pages (from-to)	887-892
Number of pages	6
Journal	ACS Medicinal Chemistry Letters
Volume	12
Issue number	6
DOIs	https://doi.org/10.1021/acsmedchemlett.0c00193
State	Published - Jun 10 2021

Bibliographical note

Funding Information:
We thank Martin Schnermann (Chemical Biology Laboratory, NCI), Drs. Brian Shoichet, and Parnian Lak for performing dynamic light scattering experiments, and our anonymous reviewers for helpful suggestions regarding potential degradation products of remodelin mentioned in the Supplementary Discussion . This work was supported by the Intramural Research Program of NIH, the National Cancer Institute, The Center for Cancer Research (ZIA BC011488-04), the NHLBI (JLD T32HL007627), and NIGMS (R35 GM118090). The SGC is a registered charity (number 1097737) that receives funds from AbbVie, Bayer Pharma AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genome Canada through Ontario Genomics Institute [OGI-055], Innovative Medicines Initiative (EU/EFPIA) [ULTRA-DD grant no. 115766], Janssen, Merck KGaA, Darmstadt, Germany, MSD, Novartis Pharma AG, Pfizer, São Paulo Research Foundation-FAPESP, Takeda, and Wellcome. This project has also been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under contract number HHSN261200800001E.

Publisher Copyright:
© 2020 American Chemical Society.

Keywords

Acetyltransferase
Hutchinson-Gilford Progeria Syndrome
NAT10
RNA modification
chemical probes
pan-assay interference

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Shrimp, J. H., Jing, Y., Gamage, S. T., Nelson, K. M., Han, J., Bryson, K. M., Montgomery, D. C., Thomas, J. M., Nance, K. D., Sharma, S., Fox, S. D., Andressen, T., Sinclair, W. R., Wu, H., Allali-Hassani, A., Senisterra, G., Vedadi, M., Lafontaine, D., Dahlin, J. L., ... Meier, J. L. (2021). Remodelin Is a Cryptic Assay Interference Chemotype That Does Not Inhibit NAT10-Dependent Cytidine Acetylation. ACS Medicinal Chemistry Letters, 12(6), 887-892. https://doi.org/10.1021/acsmedchemlett.0c00193

Shrimp, JH, Jing, Y, Gamage, ST, Nelson, KM, Han, J, Bryson, KM, Montgomery, DC, Thomas, JM, Nance, KD, Sharma, S, Fox, SD, Andressen, T, Sinclair, WR, Wu, H, Allali-Hassani, A, Senisterra, G, Vedadi, M, Lafontaine, D, Dahlin, JL, Marmorstein, R, Walters, MA & Meier, JL 2021, 'Remodelin Is a Cryptic Assay Interference Chemotype That Does Not Inhibit NAT10-Dependent Cytidine Acetylation', ACS Medicinal Chemistry Letters, vol. 12, no. 6, pp. 887-892. https://doi.org/10.1021/acsmedchemlett.0c00193

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title = "Remodelin Is a Cryptic Assay Interference Chemotype That Does Not Inhibit NAT10-Dependent Cytidine Acetylation",

abstract = "Remodelin is a putative small molecule inhibitor of the RNA acetyltransferase NAT10 which has shown preclinical efficacy in models of the premature aging disease Hutchinson-Gilford Progeria Syndrome (HGPS). Here we evaluate remodelin's assay interference characteristics and effects on NAT10-catalyzed RNA cytidine acetylation. We find the remodelin chemotype constitutes a cryptic assay interference compound, which does not react with small molecule thiols but demonstrates protein reactivity in ALARM NMR and proteome-wide affinity profiling assays. Biophysical analyses find no direct evidence for interaction of remodelin with the NAT10 acetyltransferase active site. Cellular studies verify that N4-acetylcytidine (ac4C) is a nonredundant target of NAT10 activity in human cell lines and find that this RNA modification is not affected by remodelin treatment in several orthogonal assays. These studies display the potential for remodelin's chemotype to interact with multiple protein targets in cells and indicate remodelin should not be applied as a specific chemical inhibitor of NAT10-catalyzed RNA acetylation.",

keywords = "Acetyltransferase, Hutchinson-Gilford Progeria Syndrome, NAT10, RNA modification, chemical probes, pan-assay interference",

author = "Shrimp, {Jonathan H.} and Yihang Jing and Gamage, {Supuni Thalalla} and Nelson, {Kathryn M.} and Joseph Han and Bryson, {Keri M.} and Montgomery, {David C.} and Thomas, {Justin M.} and Nance, {Kellie D.} and Sunny Sharma and Fox, {Stephen D.} and Thorkell Andressen and Sinclair, {Wilson R.} and Hong Wu and Abdellah Allali-Hassani and Guillermo Senisterra and Masoud Vedadi and Denis Lafontaine and Dahlin, {Jayme L.} and Ronen Marmorstein and Walters, {Michael A.} and Meier, {Jordan L.}",

note = "Funding Information: We thank Martin Schnermann (Chemical Biology Laboratory, NCI), Drs. Brian Shoichet, and Parnian Lak for performing dynamic light scattering experiments, and our anonymous reviewers for helpful suggestions regarding potential degradation products of remodelin mentioned in the Supplementary Discussion . This work was supported by the Intramural Research Program of NIH, the National Cancer Institute, The Center for Cancer Research (ZIA BC011488-04), the NHLBI (JLD T32HL007627), and NIGMS (R35 GM118090). The SGC is a registered charity (number 1097737) that receives funds from AbbVie, Bayer Pharma AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genome Canada through Ontario Genomics Institute [OGI-055], Innovative Medicines Initiative (EU/EFPIA) [ULTRA-DD grant no. 115766], Janssen, Merck KGaA, Darmstadt, Germany, MSD, Novartis Pharma AG, Pfizer, S{\~a}o Paulo Research Foundation-FAPESP, Takeda, and Wellcome. This project has also been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under contract number HHSN261200800001E. Publisher Copyright: {\textcopyright} 2020 American Chemical Society.",

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AU - Jing, Yihang

AU - Gamage, Supuni Thalalla

AU - Nelson, Kathryn M.

AU - Han, Joseph

AU - Bryson, Keri M.

AU - Montgomery, David C.

AU - Thomas, Justin M.

AU - Nance, Kellie D.

AU - Sharma, Sunny

AU - Fox, Stephen D.

AU - Andressen, Thorkell

AU - Sinclair, Wilson R.

AU - Wu, Hong

AU - Allali-Hassani, Abdellah

AU - Senisterra, Guillermo

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AU - Lafontaine, Denis

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AU - Walters, Michael A.

AU - Meier, Jordan L.

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PY - 2021/6/10

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N2 - Remodelin is a putative small molecule inhibitor of the RNA acetyltransferase NAT10 which has shown preclinical efficacy in models of the premature aging disease Hutchinson-Gilford Progeria Syndrome (HGPS). Here we evaluate remodelin's assay interference characteristics and effects on NAT10-catalyzed RNA cytidine acetylation. We find the remodelin chemotype constitutes a cryptic assay interference compound, which does not react with small molecule thiols but demonstrates protein reactivity in ALARM NMR and proteome-wide affinity profiling assays. Biophysical analyses find no direct evidence for interaction of remodelin with the NAT10 acetyltransferase active site. Cellular studies verify that N4-acetylcytidine (ac4C) is a nonredundant target of NAT10 activity in human cell lines and find that this RNA modification is not affected by remodelin treatment in several orthogonal assays. These studies display the potential for remodelin's chemotype to interact with multiple protein targets in cells and indicate remodelin should not be applied as a specific chemical inhibitor of NAT10-catalyzed RNA acetylation.

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KW - RNA modification

KW - chemical probes

KW - pan-assay interference

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Remodelin Is a Cryptic Assay Interference Chemotype That Does Not Inhibit NAT10-Dependent Cytidine Acetylation

Abstract

Bibliographical note

Keywords

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