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Article: Ribosome subunit attrition and activation of the p53-MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition.

bioRxiv : the preprint server for biology

2024

Abstract: The chromatin-associated protein WD Repeat Domain 5 (WDR5) is a promising target for cancer drug discovery, with most efforts blocking an arginine-binding cavity on the protein called the "WIN" site that tethers WDR5 to chromatin. WIN site inhibitors ( ... ...

Abstract	The chromatin-associated protein WD Repeat Domain 5 (WDR5) is a promising target for cancer drug discovery, with most efforts blocking an arginine-binding cavity on the protein called the "WIN" site that tethers WDR5 to chromatin. WIN site inhibitors (WINi) are active against multiple cancer cell types in vitro, the most notable of which are those derived from MLL-rearranged (MLLr) leukemias. Peptidomimetic WINi were originally proposed to inhibit MLLr cells via dysregulation of genes connected to hematopoietic stem cell expansion. Our discovery and interrogation of small molecule WIN site inhibitors, however, revealed that they act in MLLr cell lines to suppress ribosome protein gene (RPG) transcription, induce nucleolar stress, and activate p53. Because there is no precedent for an anti-cancer strategy that specifically targets RPG expression, we took an integrated multi-omics approach to further interrogate the mechanism of action of WINi in MLLr cancer cells. We show that WINi induce depletion of the stock of ribosomes, accompanied by a broad yet modest translational choke and changes in alternative mRNA splicing that inactivate the p53 antagonist MDM4. We also show that WINi are synergistic with agents including venetoclax and BET-bromodomain inhibitors. Together, these studies reinforce the concept that WINi are a novel type of ribosome-directed anti-cancer therapy and provide a resource to support their clinical implementation in MLLr leukemias and other malignancies.
Language	English
Publishing date	2024-01-10
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.26.550648
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Article ; Online: Myeloid cell leukemia-1 is an important apoptotic survival factor in triple-negative breast cancer.

Goodwin, C M / Rossanese, O W / Olejniczak, E T / Fesik, S W

Cell death and differentiation

2015 Volume 22, Issue 12, Page(s) 2098–2106

Abstract: Breast cancer is the second-most frequently diagnosed malignancy in US women. The triple-negative breast cancer (TNBC) subtype, which lacks expression of the estrogen receptor, progesterone receptor and human epidermal growth factor receptor-2, afflicts ... ...

Abstract	Breast cancer is the second-most frequently diagnosed malignancy in US women. The triple-negative breast cancer (TNBC) subtype, which lacks expression of the estrogen receptor, progesterone receptor and human epidermal growth factor receptor-2, afflicts 15% of patients and is refractory to current targeted therapies. Like many cancers, TNBC cells often deregulate programmed cell death by upregulating anti-apoptotic proteins of the B-cell CLL/lymphoma 2 (Bcl-2) family. One family member, myeloid cell leukemia-1 (Mcl-1), is commonly amplified in TNBC and correlates with a poor clinical prognosis. Here we show the effect of silencing Mcl-1 and Bcl-2-like protein 1 isoform 1 (Bcl-xL) expression on viability in a panel of seventeen TNBC cell lines. Cell death was observed in a subset upon Mcl-1 knockdown. In contrast, Bcl-xL knockdown only modestly reduced viability, indicating that Mcl-1 is a more important survival factor. However, dual silencing of both Mcl-1 and Bcl-xL reduced viability in most cell lines tested. These proliferation results were recapitulated by BH3 profiling experiments. Treatment with a Bcl-xL and Bcl-2 peptide had only a moderate effect on any of the TNBC cell lines, however, co-dosing an Mcl-1-selective peptide with a peptide that inhibits Bcl-xL and Bcl-2 was effective in each line tested. Similarly, the selective Bcl-xL inhibitor WEHI-539 was only weakly cytotoxic across the panel, but sensitization by Mcl-1 knockdown markedly improved its EC50. ABT-199, which selectively inhibits Bcl-2, did not synergize with Mcl-1 knockdown, indicating the relatively low importance of Bcl-2 in these lines. Mcl-1 sensitivity is not predicted by mRNA or protein levels of a single Bcl-2 family member, except for only a weak correlation for Bak and Bax protein expression. However, a more comprehensive index composed of Mcl-1, Bcl-xL, Bim, Bak and Noxa protein or mRNA expression correlates well with Mcl-1 sensitivity in TNBC and can also predict Mcl-1 dependency in non-small cell lung cancer cell lines.
MeSH term(s)	Apoptosis/drug effects ; Apoptosis Regulatory Proteins/genetics ; Apoptosis Regulatory Proteins/metabolism ; Bcl-2-Like Protein 11 ; Bridged Bicyclo Compounds, Heterocyclic/pharmacology ; Cell Line, Tumor ; Cell Survival/drug effects ; Female ; Humans ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Myeloid Cell Leukemia Sequence 1 Protein/antagonists & inhibitors ; Myeloid Cell Leukemia Sequence 1 Protein/genetics ; Myeloid Cell Leukemia Sequence 1 Protein/metabolism ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins/metabolism ; Proto-Oncogene Proteins c-bcl-2/genetics ; Proto-Oncogene Proteins c-bcl-2/metabolism ; RNA Interference ; RNA, Small Interfering/metabolism ; Sulfonamides/pharmacology ; Triple Negative Breast Neoplasms/metabolism ; Triple Negative Breast Neoplasms/pathology ; bcl-2 Homologous Antagonist-Killer Protein/genetics ; bcl-2 Homologous Antagonist-Killer Protein/metabolism ; bcl-2-Associated X Protein/genetics ; bcl-2-Associated X Protein/metabolism ; bcl-X Protein/antagonists & inhibitors ; bcl-X Protein/genetics ; bcl-X Protein/metabolism
Chemical Substances	Apoptosis Regulatory Proteins ; BCL2L11 protein, human ; Bcl-2-Like Protein 11 ; Bridged Bicyclo Compounds, Heterocyclic ; MCL1 protein, human ; Membrane Proteins ; Myeloid Cell Leukemia Sequence 1 Protein ; PMAIP1 protein, human ; Proto-Oncogene Proteins ; Proto-Oncogene Proteins c-bcl-2 ; RNA, Small Interfering ; Sulfonamides ; bcl-2 Homologous Antagonist-Killer Protein ; bcl-2-Associated X Protein ; bcl-X Protein ; venetoclax (N54AIC43PW)
Language	English
Publishing date	2015-06-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1225672-9
ISSN	1476-5403 ; 1350-9047
ISSN (online)	1476-5403
ISSN	1350-9047
DOI	10.1038/cdd.2015.73
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Article: Insights into programmed cell death through structural biology.

Fesik, S W

Cell

2000 Volume 103, Issue 2, Page(s) 273–282

MeSH term(s)	Apoptosis ; Mitochondria ; Models, Biological ; Models, Molecular ; Protein Conformation ; Protein Structure, Tertiary ; Receptors, Cell Surface ; Signal Transduction
Chemical Substances	Receptors, Cell Surface
Language	English
Publishing date	2000-10-13
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/s0092-8674(00)00119-7
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Article ; Online: Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models.

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 120, Issue 1, Page(s) e2211297120

Abstract: WD repeat domain 5 (WDR5) is a core scaffolding component of many multiprotein complexes that perform a variety of critical chromatin-centric processes in the nucleus. WDR5 is a component of the mixed lineage leukemia MLL/SET complex and localizes MYC to ...

Abstract	WD repeat domain 5 (WDR5) is a core scaffolding component of many multiprotein complexes that perform a variety of critical chromatin-centric processes in the nucleus. WDR5 is a component of the mixed lineage leukemia MLL/SET complex and localizes MYC to chromatin at tumor-critical target genes. As a part of these complexes, WDR5 plays a role in sustaining oncogenesis in a variety of human cancers that are often associated with poor prognoses. Thus, WDR5 has been recognized as an attractive therapeutic target for treating both solid and hematological tumors. Previously, small-molecule inhibitors of the WDR5-interaction (WIN) site and WDR5 degraders have demonstrated robust in vitro cellular efficacy in cancer cell lines and established the therapeutic potential of WDR5. However, these agents have not demonstrated significant in vivo efficacy at pharmacologically relevant doses by oral administration in animal disease models. We have discovered WDR5 WIN-site inhibitors that feature bicyclic heteroaryl P
MeSH term(s)	Animals ; Humans ; Mice ; Chromatin ; Intracellular Signaling Peptides and Proteins/antagonists & inhibitors ; Intracellular Signaling Peptides and Proteins/metabolism ; Models, Animal ; WD40 Repeats ; Neoplasms/drug therapy ; Cell Line, Tumor
Chemical Substances	Chromatin ; Intracellular Signaling Peptides and Proteins ; WDR5 protein, human
Language	English
Publishing date	2022-12-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2211297120
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Article: NMR structure-based drug design.

Fesik, S W

Journal of biomolecular NMR

1993 Volume 3, Issue 3, Page(s) 261–269

Abstract: NMR is a useful tool for rapidly determining the conformations of receptor-bound ligands and identifying those portions of the ligand in contact with the receptor. In addition, the complete 3D structures of receptors and ligand/receptor complexes can be ... ...

Abstract	NMR is a useful tool for rapidly determining the conformations of receptor-bound ligands and identifying those portions of the ligand in contact with the receptor. In addition, the complete 3D structures of receptors and ligand/receptor complexes can be obtained using recently developed heteronuclear multi-dimensional NMR techniques. This NMR-derived structural information is potentially useful for aiding in The design of improved pharmaceutical agents. Approaches for utilizing the NMR-derived structural information along with the computational tools that facilitate this process are discussed.
MeSH term(s)	Carrier Proteins/metabolism ; Databases, Bibliographic ; Drug Design ; HIV Protease Inhibitors/chemical synthesis ; HIV Protease Inhibitors/chemistry ; Ligands ; Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; Protein Conformation ; Receptors, Cell Surface/metabolism ; Structure-Activity Relationship ; Tacrolimus/analogs & derivatives ; Tacrolimus/metabolism ; Tacrolimus Binding Proteins
Chemical Substances	Carrier Proteins ; HIV Protease Inhibitors ; Ligands ; Receptors, Cell Surface ; immunomycin (AUF4U5NSJK) ; Tacrolimus Binding Proteins (EC 5.2.1.-) ; Tacrolimus (WM0HAQ4WNM)
Language	English
Publishing date	1993-05
Publishing country	Netherlands
Document type	Comparative Study ; Journal Article
ZDB-ID	1081696-3
ISSN	0925-2738
ISSN	0925-2738
DOI	10.1007/bf00212513
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Article: NMR studies of molecular complexes as a tool in drug design.

Fesik, S W

Journal of medicinal chemistry

1991 Volume 34, Issue 10, Page(s) 2937–2945

MeSH term(s)	Drug Design ; Magnetic Resonance Spectroscopy/methods ; Molecular Conformation ; Molecular Structure ; Receptors, Drug
Chemical Substances	Receptors, Drug
Language	English
Publishing date	1991-10
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/jm00114a001
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Article ; Online: Discovery of WD Repeat-Containing Protein 5 (WDR5)-MYC Inhibitors Using Fragment-Based Methods and Structure-Based Design.

Chacón Simon, Selena / Wang, Feng / Thomas, Lance R / Phan, Jason / Zhao, Bin / Olejniczak, Edward T / Macdonald, Jonathan D / Shaw, J Grace / Schlund, Caden / Payne, William / Creighton, Joy / Stauffer, Shaun R / Waterson, Alex G / Tansey, William P / Fesik, Stephen W

Journal of medicinal chemistry

2020 Volume 63, Issue 8, Page(s) 4315–4333

Abstract: The frequent deregulation of MYC and its elevated expression via multiple mechanisms drives cells to a tumorigenic state. Indeed, MYC is overexpressed in up to ∼50% of human cancers and is considered a highly validated anticancer target. Recently, we ... ...

Abstract	The frequent deregulation of MYC and its elevated expression via multiple mechanisms drives cells to a tumorigenic state. Indeed, MYC is overexpressed in up to ∼50% of human cancers and is considered a highly validated anticancer target. Recently, we discovered that WD repeat-containing protein 5 (WDR5) binds to MYC and is a critical cofactor required for the recruitment of MYC to its target genes and reported the first small molecule inhibitors of the WDR5-MYC interaction using structure-based design. These compounds display high binding affinity, but have poor physicochemical properties and are hence not suitable for
MeSH term(s)	Cell Line, Tumor ; Drug Design ; Drug Discovery/methods ; HEK293 Cells ; Humans ; Intracellular Signaling Peptides and Proteins/antagonists & inhibitors ; Intracellular Signaling Peptides and Proteins/metabolism ; Protein Structure, Tertiary ; Proto-Oncogene Proteins c-myc/antagonists & inhibitors ; Proto-Oncogene Proteins c-myc/metabolism ; Structure-Activity Relationship ; Sulfonamides/chemical synthesis ; Sulfonamides/pharmacology
Chemical Substances	Intracellular Signaling Peptides and Proteins ; MYC protein, human ; Proto-Oncogene Proteins c-myc ; Sulfonamides ; WDR5 protein, human
Language	English
Publishing date	2020-04-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.0c00224
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Article: Structural biology. Controlling the caspases.

Fesik, S W / Shi, Y

Science (New York, N.Y.)

2001 Volume 294, Issue 5546, Page(s) 1477–1478

MeSH term(s)	Amino Acid Motifs ; Animals ; Apoptosis ; Binding Sites ; Carrier Proteins/chemistry ; Carrier Proteins/metabolism ; Caspase Inhibitors ; Caspases/chemistry ; Caspases/metabolism ; Crystallography, X-Ray ; Cysteine Proteinase Inhibitors/chemistry ; Cysteine Proteinase Inhibitors/metabolism ; Dimerization ; Humans ; Hydrogen Bonding ; Intracellular Signaling Peptides and Proteins ; Mitochondria/metabolism ; Mitochondrial Proteins/chemistry ; Mitochondrial Proteins/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/chemistry ; Proteins/metabolism ; X-Linked Inhibitor of Apoptosis Protein
Chemical Substances	Carrier Proteins ; Caspase Inhibitors ; Cysteine Proteinase Inhibitors ; DIABLO protein, human ; Intracellular Signaling Peptides and Proteins ; Mitochondrial Proteins ; Proteins ; X-Linked Inhibitor of Apoptosis Protein ; XIAP protein, human ; Caspases (EC 3.4.22.-)
Language	English
Publishing date	2001-11-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.1062236
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Article ; Online: Impact of WIN site inhibitor on the WDR5 interactome.

Guarnaccia, Alissa D / Rose, Kristie L / Wang, Jing / Zhao, Bin / Popay, Tessa M / Wang, Christina E / Guerrazzi, Kiana / Hill, Salisha / Woodley, Chase M / Hansen, Tyler J / Lorey, Shelly L / Shaw, J Grace / Payne, William G / Weissmiller, April M / Olejniczak, Edward T / Fesik, Stephen W / Liu, Qi / Tansey, William P

Cell reports

2021 Volume 34, Issue 3, Page(s) 108636

Abstract: The chromatin-associated protein WDR5 is a promising pharmacological target in cancer, with most drug discovery efforts directed against an arginine-binding cavity in WDR5 called the WIN site. Despite a clear expectation that WIN site inhibitors will ... ...

Abstract	The chromatin-associated protein WDR5 is a promising pharmacological target in cancer, with most drug discovery efforts directed against an arginine-binding cavity in WDR5 called the WIN site. Despite a clear expectation that WIN site inhibitors will alter the repertoire of WDR5 interaction partners, their impact on the WDR5 interactome remains unknown. Here, we use quantitative proteomics to delineate how the WDR5 interactome is changed by WIN site inhibition. We show that the WIN site inhibitor alters the interaction of WDR5 with dozens of proteins, including those linked to phosphatidylinositol 3-kinase (PI3K) signaling. As proof of concept, we demonstrate that the master kinase PDPK1 is a bona fide high-affinity WIN site binding protein that engages WDR5 to modulate transcription of genes expressed in the G2 phase of the cell cycle. This dataset expands our understanding of WDR5 and serves as a resource for deciphering the action of WIN site inhibitors.
MeSH term(s)	3-Phosphoinositide-Dependent Protein Kinases/chemistry ; 3-Phosphoinositide-Dependent Protein Kinases/genetics ; 3-Phosphoinositide-Dependent Protein Kinases/metabolism ; Amino Acid Sequence ; Binding Sites ; Drug Discovery ; G2 Phase/genetics ; Gene Expression Regulation ; HEK293 Cells ; Humans ; Immunoprecipitation ; Intracellular Signaling Peptides and Proteins/antagonists & inhibitors ; Intracellular Signaling Peptides and Proteins/chemistry ; Intracellular Signaling Peptides and Proteins/genetics ; Models, Molecular ; Molecular Targeted Therapy ; Protein Binding
Chemical Substances	Intracellular Signaling Peptides and Proteins ; WDR5 protein, human ; 3-Phosphoinositide-Dependent Protein Kinases (EC 2.7.11.1) ; PDPK1 protein, human (EC 2.7.11.1)
Language	English
Publishing date	2021-01-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2020.108636
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Article ; Online: Fragment Optimization of Reversible Binding to the Switch II Pocket on KRAS Leads to a Potent, In Vivo Active KRAS

Bröker, Joachim / Waterson, Alex G / Smethurst, Chris / Kessler, Dirk / Böttcher, Jark / Mayer, Moriz / Gmaschitz, Gerhard / Phan, Jason / Little, Andrew / Abbott, Jason R / Sun, Qi / Gmachl, Michael / Rudolph, Dorothea / Arnhof, Heribert / Rumpel, Klaus / Savarese, Fabio / Gerstberger, Thomas / Mischerikow, Nikolai / Treu, Matthias /

Herdeis, Lorenz / Wunberg, Tobias / Gollner, Andreas / Weinstabl, Harald / Mantoulidis, Andreas / Krämer, Oliver / McConnell, Darryl B / W Fesik, Stephen

Journal of medicinal chemistry

2022 Volume 65, Issue 21, Page(s) 14614–14629

Abstract: Activating mutations in KRAS are the most frequent oncogenic alterations in cancer. The oncogenic hotspot position 12, located at the lip of the switch II pocket, offers a covalent attachment point for ... ...

Abstract	Activating mutations in KRAS are the most frequent oncogenic alterations in cancer. The oncogenic hotspot position 12, located at the lip of the switch II pocket, offers a covalent attachment point for KRAS
MeSH term(s)	Humans ; Proto-Oncogene Proteins p21(ras)/genetics ; Genes, ras ; Mutation ; Neoplasms/genetics ; Cysteine
Chemical Substances	Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2) ; Cysteine (K848JZ4886) ; KRAS protein, human
Language	English
Publishing date	2022-10-27
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.2c01120
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