A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes

Huarui Cui; Anand Divakaran; Zachariah Hoell; Mikael O. Ellingson; Cole R. Scholtz; Huda Zahid; Jorden A Johnson; Elizabeth C. Griffith; Clifford T. Gee; Amani L. Lee; Shalil Khanal; Ke Shi; Hideki Aihara; Vijay H. Shah; Richard E. Lee; Daniel A. Harki; William C.K. Pomerantz

doi:10.1021/acs.jmedchem.1c01779

A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes

Huarui Cui, Anand Divakaran, Zachariah Hoell, Mikael O. Ellingson, Cole R. Scholtz, Huda Zahid, Jorden A Johnson, Elizabeth C. Griffith, Clifford T. Gee, Amani L. Lee, Shalil Khanal, Ke Shi, Hideki Aihara, Vijay H. Shah, Richard E. Lee, Daniel A. Harki, William C.K. Pomerantz

Research output: Contribution to journal › Article › peer-review

17 Scopus citations

Abstract

Chemical probes for epigenetic proteins are essential tools for dissecting the molecular mechanisms for gene regulation and therapeutic development. The bromodomain and extra-terminal (BET) proteins are master transcriptional regulators. Despite promising therapeutic targets, selective small molecule inhibitors for a single bromodomain remain an unmet goal due to their high sequence similarity. Here, we address this challenge via a structure-activity relationship study using 1,4,5-trisubstituted imidazoles against the BRD4 N-terminal bromodomain (D1). Leading compounds 26 and 30 have 15 and 18 nM affinity against BRD4 D1 and over 500-fold selectivity against BRD2 D1 and BRD4 D2 via ITC. Broader BET selectivity was confirmed by fluorescence anisotropy, thermal shift, and CETSA. Despite BRD4 engagement, BRD4 D1 inhibition was unable to reduce c-Myc expression at low concentration in multiple myeloma cells. Conversely, for inflammation, IL-8 and chemokine downregulation were observed. These results provide new design rules for selective inhibitors of an individual BET bromodomain.

Original language	English (US)
Pages (from-to)	2342-2360
Number of pages	19
Journal	Journal of medicinal chemistry
Volume	65
Issue number	3
DOIs	https://doi.org/10.1021/acs.jmedchem.1c01779
State	Published - Feb 10 2022

Bibliographical note

Funding Information:
This work was funded by Office of Discovery and Translation Grant at UMN, UL1 TR002494 (W.C.K.P), Center for Regenerative Medicine (V.S.), and the NIH MIRA awards, R35 GM140837-01 (W.C.K.P.) and R35 GM118047 (H.A.) A.D. was supported by the UMN Doctoral Dissertation Fellowship and a NIH chemistry–biology interface training grant (T32-GM008700/T32-GM132029-01). H.Z. was supported by UMN IEM Engineering in Medicine Doctoral Fellowship 2020. D.H. acknowledges funding from the Masonic Cancer Center at the University of Minnesota with resources from Minnesota Masonic Charities. R.L. is supported in part by St. Jude Cancer Center Support grant CA21765 and by the American Lebanese Syrian Associated Charities (ALSAC). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Health or other funding agencies. X-ray diffraction data were collected at the Northeastern Collaborative Access Team beamlines, which are supported by NIGMS P30 GM124165. The Pilatus 6 M detector on 24-ID-C beamline is funded by a NIH-ORIP HEI grant (S10 RR029205).

Publisher Copyright:
© 2022 American Chemical Society.

Keywords

Binding Sites
Cell Cycle Proteins/antagonists & inhibitors
Cell Line, Tumor
Drug Design
Humans
Imidazoles/chemistry
Molecular Structure
Protein Binding
Protein Domains
Proto-Oncogene Proteins c-myc/metabolism
Structure-Activity Relationship
Transcription Factors/antagonists & inhibitors

PubMed: MeSH publication types

Research Support, Non-U.S. Gov't
Journal Article
Research Support, N.I.H., Extramural

Publisher link

10.1021/acs.jmedchem.1c01779

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Cui, H., Divakaran, A., Hoell, Z., Ellingson, M. O., Scholtz, C. R., Zahid, H., Johnson, J. A., Griffith, E. C., Gee, C. T., Lee, A. L., Khanal, S., Shi, K., Aihara, H., Shah, V. H., Lee, R. E., Harki, D. A., & Pomerantz, W. C. K. (2022). A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes. Journal of medicinal chemistry, 65(3), 2342-2360. https://doi.org/10.1021/acs.jmedchem.1c01779

Cui, H, Divakaran, A, Hoell, Z, Ellingson, MO, Scholtz, CR, Zahid, H, Johnson, JA, Griffith, EC, Gee, CT, Lee, AL, Khanal, S, Shi, K , Aihara, H, Shah, VH, Lee, RE, Harki, DA & Pomerantz, WCK 2022, 'A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes', Journal of medicinal chemistry, vol. 65, no. 3, pp. 2342-2360. https://doi.org/10.1021/acs.jmedchem.1c01779

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title = "A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes",

abstract = "Chemical probes for epigenetic proteins are essential tools for dissecting the molecular mechanisms for gene regulation and therapeutic development. The bromodomain and extra-terminal (BET) proteins are master transcriptional regulators. Despite promising therapeutic targets, selective small molecule inhibitors for a single bromodomain remain an unmet goal due to their high sequence similarity. Here, we address this challenge via a structure-activity relationship study using 1,4,5-trisubstituted imidazoles against the BRD4 N-terminal bromodomain (D1). Leading compounds 26 and 30 have 15 and 18 nM affinity against BRD4 D1 and over 500-fold selectivity against BRD2 D1 and BRD4 D2 via ITC. Broader BET selectivity was confirmed by fluorescence anisotropy, thermal shift, and CETSA. Despite BRD4 engagement, BRD4 D1 inhibition was unable to reduce c-Myc expression at low concentration in multiple myeloma cells. Conversely, for inflammation, IL-8 and chemokine downregulation were observed. These results provide new design rules for selective inhibitors of an individual BET bromodomain.",

keywords = "Binding Sites, Cell Cycle Proteins/antagonists & inhibitors, Cell Line, Tumor, Drug Design, Humans, Imidazoles/chemistry, Molecular Structure, Protein Binding, Protein Domains, Proto-Oncogene Proteins c-myc/metabolism, Structure-Activity Relationship, Transcription Factors/antagonists & inhibitors",

author = "Huarui Cui and Anand Divakaran and Zachariah Hoell and Ellingson, {Mikael O.} and Scholtz, {Cole R.} and Huda Zahid and Johnson, {Jorden A} and Griffith, {Elizabeth C.} and Gee, {Clifford T.} and Lee, {Amani L.} and Shalil Khanal and Ke Shi and Hideki Aihara and Shah, {Vijay H.} and Lee, {Richard E.} and Harki, {Daniel A.} and Pomerantz, {William C.K.}",

note = "Funding Information: This work was funded by Office of Discovery and Translation Grant at UMN, UL1 TR002494 (W.C.K.P), Center for Regenerative Medicine (V.S.), and the NIH MIRA awards, R35 GM140837-01 (W.C.K.P.) and R35 GM118047 (H.A.) A.D. was supported by the UMN Doctoral Dissertation Fellowship and a NIH chemistry–biology interface training grant (T32-GM008700/T32-GM132029-01). H.Z. was supported by UMN IEM Engineering in Medicine Doctoral Fellowship 2020. D.H. acknowledges funding from the Masonic Cancer Center at the University of Minnesota with resources from Minnesota Masonic Charities. R.L. is supported in part by St. Jude Cancer Center Support grant CA21765 and by the American Lebanese Syrian Associated Charities (ALSAC). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Health or other funding agencies. X-ray diffraction data were collected at the Northeastern Collaborative Access Team beamlines, which are supported by NIGMS P30 GM124165. The Pilatus 6 M detector on 24-ID-C beamline is funded by a NIH-ORIP HEI grant (S10 RR029205). Publisher Copyright: {\textcopyright} 2022 American Chemical Society.",

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doi = "10.1021/acs.jmedchem.1c01779",

language = "English (US)",

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AU - Divakaran, Anand

AU - Hoell, Zachariah

AU - Ellingson, Mikael O.

AU - Scholtz, Cole R.

AU - Zahid, Huda

AU - Johnson, Jorden A

AU - Griffith, Elizabeth C.

AU - Gee, Clifford T.

AU - Lee, Amani L.

AU - Khanal, Shalil

AU - Shi, Ke

AU - Aihara, Hideki

AU - Shah, Vijay H.

AU - Lee, Richard E.

AU - Harki, Daniel A.

AU - Pomerantz, William C.K.

N1 - Funding Information: This work was funded by Office of Discovery and Translation Grant at UMN, UL1 TR002494 (W.C.K.P), Center for Regenerative Medicine (V.S.), and the NIH MIRA awards, R35 GM140837-01 (W.C.K.P.) and R35 GM118047 (H.A.) A.D. was supported by the UMN Doctoral Dissertation Fellowship and a NIH chemistry–biology interface training grant (T32-GM008700/T32-GM132029-01). H.Z. was supported by UMN IEM Engineering in Medicine Doctoral Fellowship 2020. D.H. acknowledges funding from the Masonic Cancer Center at the University of Minnesota with resources from Minnesota Masonic Charities. R.L. is supported in part by St. Jude Cancer Center Support grant CA21765 and by the American Lebanese Syrian Associated Charities (ALSAC). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Health or other funding agencies. X-ray diffraction data were collected at the Northeastern Collaborative Access Team beamlines, which are supported by NIGMS P30 GM124165. The Pilatus 6 M detector on 24-ID-C beamline is funded by a NIH-ORIP HEI grant (S10 RR029205). Publisher Copyright: © 2022 American Chemical Society.

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N2 - Chemical probes for epigenetic proteins are essential tools for dissecting the molecular mechanisms for gene regulation and therapeutic development. The bromodomain and extra-terminal (BET) proteins are master transcriptional regulators. Despite promising therapeutic targets, selective small molecule inhibitors for a single bromodomain remain an unmet goal due to their high sequence similarity. Here, we address this challenge via a structure-activity relationship study using 1,4,5-trisubstituted imidazoles against the BRD4 N-terminal bromodomain (D1). Leading compounds 26 and 30 have 15 and 18 nM affinity against BRD4 D1 and over 500-fold selectivity against BRD2 D1 and BRD4 D2 via ITC. Broader BET selectivity was confirmed by fluorescence anisotropy, thermal shift, and CETSA. Despite BRD4 engagement, BRD4 D1 inhibition was unable to reduce c-Myc expression at low concentration in multiple myeloma cells. Conversely, for inflammation, IL-8 and chemokine downregulation were observed. These results provide new design rules for selective inhibitors of an individual BET bromodomain.

AB - Chemical probes for epigenetic proteins are essential tools for dissecting the molecular mechanisms for gene regulation and therapeutic development. The bromodomain and extra-terminal (BET) proteins are master transcriptional regulators. Despite promising therapeutic targets, selective small molecule inhibitors for a single bromodomain remain an unmet goal due to their high sequence similarity. Here, we address this challenge via a structure-activity relationship study using 1,4,5-trisubstituted imidazoles against the BRD4 N-terminal bromodomain (D1). Leading compounds 26 and 30 have 15 and 18 nM affinity against BRD4 D1 and over 500-fold selectivity against BRD2 D1 and BRD4 D2 via ITC. Broader BET selectivity was confirmed by fluorescence anisotropy, thermal shift, and CETSA. Despite BRD4 engagement, BRD4 D1 inhibition was unable to reduce c-Myc expression at low concentration in multiple myeloma cells. Conversely, for inflammation, IL-8 and chemokine downregulation were observed. These results provide new design rules for selective inhibitors of an individual BET bromodomain.

KW - Binding Sites

KW - Cell Cycle Proteins/antagonists & inhibitors

KW - Cell Line, Tumor

KW - Drug Design

KW - Humans

KW - Imidazoles/chemistry

KW - Molecular Structure

KW - Protein Binding

KW - Protein Domains

KW - Proto-Oncogene Proteins c-myc/metabolism

KW - Structure-Activity Relationship

KW - Transcription Factors/antagonists & inhibitors

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SN - 0022-2623

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JO - Journal of medicinal chemistry

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A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes

Abstract

Bibliographical note

Keywords

PubMed: MeSH publication types

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