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Potjewyd FM, Foley CA, Ong HW, Rectenwald JM, Hanley RP, Norris-Drouin JL, Cholensky SH, Mills CA, Pearce KH, Herring LE, Kireev D, Frye SV, James LI. PROTAC Linkerology Leads to an Optimized Bivalent Chemical Degrader of Polycomb Repressive Complex 2 (PRC2) Components. ACS Chem Biol 2023; 18:494-507. [PMID: 36877831 PMCID: PMC10023369 DOI: 10.1021/acschembio.2c00804] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Bivalent chemical degraders, otherwise known as proteolysis-targeting chimeras (PROTACs), have proven to be an efficient strategy for targeting overexpressed or mutated proteins in cancer. PROTACs provide an alternative approach to small-molecule inhibitors, which are restricted by occupancy-driven pharmacology, often resulting in acquired inhibitor resistance via compensatory increases in protein expression. Despite the advantages of bivalent chemical degraders, they often have suboptimal physicochemical properties and optimization for efficient degradation remains highly unpredictable. Herein, we report the development of a potent EED-targeted PRC2 degrader, UNC7700. UNC7700 contains a unique cis-cyclobutane linker and potently degrades PRC2 components EED (DC50 = 111 nM; Dmax = 84%), EZH2WT/EZH2Y641N (DC50 = 275 nM; Dmax = 86%), and to a lesser extent SUZ12 (Dmax = 44%) after 24 h in a diffuse large B-cell lymphoma DB cell line. Characterization of UNC7700 and related compounds for ternary complex formation and cellular permeability to provide a rationale for the observed improvement in degradation efficiency remained challenging. Importantly, UNC7700 dramatically reduces H3K27me3 levels and is anti-proliferative in DB cells (EC50 = 0.79 ± 0.53 μM).
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Affiliation(s)
- Frances M. Potjewyd
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Caroline A. Foley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Han Wee Ong
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Justin M. Rectenwald
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ronan P. Hanley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jacqueline L. Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie H. Cholensky
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christine A. Mills
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kenneth H. Pearce
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura E. Herring
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Drewry DH, Potjewyd FM, Bayati A, Smith JL, Dickmander RJ, Howell S, Taft-Benz S, Min SM, Hossain MA, Heise M, McPherson PS, Moorman NJ, Axtman AD. Identification and Utilization of a Chemical Probe to Interrogate the Roles of PIKfyve in the Lifecycle of β-Coronaviruses. J Med Chem 2022; 65:12860-12882. [PMID: 36111834 PMCID: PMC9574855 DOI: 10.1021/acs.jmedchem.2c00697] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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From a designed library of indolyl pyrimidinamines, we
identified
a highly potent and cell-active chemical probe (17) that
inhibits phosphatidylinositol-3-phosphate 5-kinase (PIKfyve). Comprehensive
evaluation of inhibitor selectivity confirmed that this PIKfyve probe
demonstrates excellent kinome-wide selectivity. A structurally related
indolyl pyrimidinamine (30) was characterized as a negative
control that lacks PIKfyve inhibitory activity and exhibits exquisite
selectivity when profiled broadly. Chemical probe 17 disrupts
multiple phases of the lifecycle of β-coronaviruses: viral replication
and viral entry. The diverse antiviral roles of PIKfyve have not been
previously probed comprehensively in a single study or using the same
compound set. Our scaffold is a distinct chemotype that lacks the
canonical morpholine hinge-binder of classical lipid kinase inhibitors
and has a non-overlapping kinase off-target profile with known PIKfyve
inhibitors. Our chemical probe set can be used by the community to
further characterize the role of PIKfyve in virology.
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Affiliation(s)
- David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Frances M. Potjewyd
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Armin Bayati
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Jeffery L. Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Rebekah J. Dickmander
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefanie Howell
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sharon Taft-Benz
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sophia M. Min
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Mark Heise
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Peter S. McPherson
- Structural Genomics Consortium, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Nathaniel J. Moorman
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, North Carolina 27599, United States
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alison D. Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Agajanian MJ, Potjewyd FM, Bowman BM, Solomon S, LaPak KM, Bhatt DP, Smith JL, Goldfarb D, Axtman AD, Major MB. Protein proximity networks and functional evaluation of the casein kinase 1 gamma family reveal unique roles for CK1γ3 in WNT signaling. J Biol Chem 2022; 298:101986. [PMID: 35487243 PMCID: PMC9157009 DOI: 10.1016/j.jbc.2022.101986] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/25/2022] Open
Abstract
Aberrant activation or suppression of WNT/β-catenin signaling contributes to cancer initiation and progression, neurodegeneration, and bone disease. However, despite great need and more than 40 years of research, targeted therapies for the WNT pathway have yet to be fully realized. Kinases are considered exceptionally druggable and occupy key nodes within the WNT signaling network, but several pathway-relevant kinases remain understudied and "dark." Here, we studied the function of the casein kinase 1γ (CSNK1γ) subfamily of human kinases and their roles in WNT signaling. miniTurbo-based proximity biotinylation and mass spectrometry analysis of CSNK1γ1, CSNK1γ2, and CSNK1γ3 revealed numerous components of the β-catenin-dependent and β-catenin-independent WNT pathways. In gain-of-function experiments, we found that CSNK1γ3 but not CSNK1γ1 or CSNK1γ2 activated β-catenin-dependent WNT signaling, with minimal effect on other signaling pathways. We also show that within the family, CSNK1γ3 expression uniquely induced low-density lipoprotein receptor-related protein 6 phosphorylation, which mediates downstream WNT signaling transduction. Conversely, siRNA-mediated silencing of CSNK1γ3 alone had no impact on WNT signaling, though cosilencing of all three family members decreased WNT pathway activity. Finally, we characterized two moderately selective and potent small-molecule inhibitors of the CSNK1γ family. We show that these inhibitors and a CSNK1γ3 kinase-dead mutant suppressed but did not eliminate WNT-driven low-density lipoprotein receptor-related protein 6 phosphorylation and β-catenin stabilization. Our data suggest that while CSNK1γ3 expression uniquely drives pathway activity, potential functional redundancy within the family necessitates loss of all three family members to suppress the WNT signaling pathway.
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Affiliation(s)
- Megan J Agajanian
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, Missouri, USA
| | - Frances M Potjewyd
- Division of Chemical Biology and Medicinal Chemistry, Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brittany M Bowman
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, Missouri, USA
| | - Smaranda Solomon
- Institute for Informatics, School of Medicine, Washington University in St Louis, St Louis, Missouri, USA
| | - Kyle M LaPak
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, Missouri, USA
| | - Dhaval P Bhatt
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, Missouri, USA
| | - Jeffery L Smith
- Division of Chemical Biology and Medicinal Chemistry, Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dennis Goldfarb
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, Missouri, USA; Institute for Informatics, School of Medicine, Washington University in St Louis, St Louis, Missouri, USA
| | - Alison D Axtman
- Division of Chemical Biology and Medicinal Chemistry, Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael B Major
- Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, Missouri, USA; Department of Otolaryngology, School of Medicine, Washington University in St Louis, St Louis, Missouri, USA.
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Potjewyd FM, Annor‐Gyamfi JK, Aubé J, Chu S, Conlon IL, Frankowski KJ, Guduru SKR, Hardy BP, Hopkins MD, Kinoshita C, Kireev DB, Mason ER, Moerk CT, Nwogbo F, Pearce KH, Richardson TI, Rogers DA, Soni DM, Stashko M, Wang X, Wells C, Willson TM, Frye SV, Young JE, Axtman AD. AD Informer Set: Chemical tools to facilitate Alzheimer's disease drug discovery. Alzheimers Dement (N Y) 2022; 8:e12246. [PMID: 35475262 PMCID: PMC9019904 DOI: 10.1002/trc2.12246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/29/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Introduction The portfolio of novel targets to treat Alzheimer's disease (AD) has been enriched by the Accelerating Medicines Partnership Program for Alzheimer's Disease (AMP AD) program. Methods Publicly available resources, such as literature and databases, enabled a data-driven effort to identify existing small molecule modulators for many protein products expressed by the genes nominated by AMP AD and suitable positive control compounds to be included in the set. Compounds contained within the set were manually selected and annotated with associated published, predicted, and/or experimental data. Results We built an annotated set of 171 small molecule modulators targeting 98 unique proteins that have been nominated by AMP AD consortium members as novel targets for the treatment of AD. The majority of compounds included in the set are inhibitors. These small molecules vary in their quality and should be considered chemical tools that can be used in efforts to validate therapeutic hypotheses, but which will require further optimization. A physical copy of the AD Informer Set can be requested on the Target Enablement to Accelerate Therapy Development for Alzheimer's Disease (TREAT-AD) website. Discussion Small molecules that enable target validation are important tools for the translation of novel hypotheses into viable therapeutic strategies for AD.
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Affiliation(s)
- Frances M. Potjewyd
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryStructural Genomics ConsortiumChapel HillNorth CarolinaUSA
| | - Joel K. Annor‐Gyamfi
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryStructural Genomics ConsortiumChapel HillNorth CarolinaUSA
| | - Jeffrey Aubé
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Shaoyou Chu
- Department of MedicineDivision of Clinical PharmacologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Ivie L. Conlon
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Kevin J. Frankowski
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Shiva K. R. Guduru
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Brian P. Hardy
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Megan D. Hopkins
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Chizuru Kinoshita
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Dmitri B. Kireev
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Emily R. Mason
- Department of MedicineDivision of Clinical PharmacologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Charles T. Moerk
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Felix Nwogbo
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Kenneth H. Pearce
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Timothy I. Richardson
- Department of MedicineDivision of Clinical PharmacologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - David A. Rogers
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Disha M. Soni
- Department of MedicineDivision of Clinical PharmacologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Michael Stashko
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Xiaodong Wang
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Carrow Wells
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryStructural Genomics ConsortiumChapel HillNorth CarolinaUSA
| | - Timothy M. Willson
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryStructural Genomics ConsortiumChapel HillNorth CarolinaUSA
| | - Stephen V. Frye
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryCenter for Integrative Chemical Biology and Drug DiscoveryChapel HillNorth CarolinaUSA
| | - Jessica E. Young
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
- Institute for Stem Cell and Regenerative MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Alison D. Axtman
- UNC Eshelman School of PharmacyDivision of Chemical Biology and Medicinal ChemistryStructural Genomics ConsortiumChapel HillNorth CarolinaUSA
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5
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Potjewyd FM, Annor‐Gyamfi JK, Aubé J, Chu S, Conlon IL, Frankowski KJ, Guduru SKR, Hardy BP, Hopkins MD, Kinoshita C, Kireev DB, Mason ER, Moerk CT, Nwogbo F, Pearce KH, Richardson TI, Rogers DA, Soni DM, Stashko M, Wang X, Wells C, Willson TM, Frye SV, Young JE, Axtman AD. Use of AD Informer Set compounds to explore validity of novel targets in Alzheimer's disease pathology. A&D Transl Res & Clin Interv 2022; 8:e12253. [PMID: 35434254 PMCID: PMC9005681 DOI: 10.1002/trc2.12253] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/29/2021] [Accepted: 12/15/2021] [Indexed: 12/03/2022]
Abstract
Introduction A chemogenomic set of small molecules with annotated activities and implicated roles in Alzheimer's disease (AD) called the AD Informer Set was recently developed and made available to the AD research community: https://treatad.org/data‐tools/ad‐informer‐set/. Methods Small subsets of AD Informer Set compounds were selected for AD‐relevant profiling. Nine compounds targeting proteins expressed by six AD‐implicated genes prioritized for study by Target Enablement to Accelerate Therapy Development for Alzheimer's Disease (TREAT‐AD) teams were selected for G‐protein coupled receptor (GPCR), amyloid beta (Aβ) and tau, and pharmacokinetic (PK) studies. Four non‐overlapping compounds were analyzed in microglial cytotoxicity and phagocytosis assays. Results The nine compounds targeting CAPN2, EPHX2, MDK, MerTK/FLT3, or SYK proteins were profiled in 46 to 47 primary GPCR binding assays. Human induced pluripotent stem cell (iPSC)‐derived neurons were treated with the same nine compounds and secretion of Aβ peptides (Aβ40 and Aβ42) as well as levels of phosphophorylated tau (p‐tau, Thr231) and total tau (t‐tau) peptides measured at two concentrations and two timepoints. Finally, CD1 mice were dosed intravenously to determine preliminary PK and/or brain‐specific penetrance values for these compounds. As a final cell‐based study, a non‐overlapping subset of four compounds was selected based on single‐concentration screening for analysis of both cytotoxicity and phagocytosis in murine and human microglia cells. Discussion We have demonstrated the utility of the AD Informer Set in the validation of novel AD hypotheses using biochemical, cellular (primary and immortalized), and in vivo studies. The selectivity for their primary targets versus essential GPCRs in the brain was established for our compounds. Statistical changes in tau, p‐tau, Aβ40, and/or Aβ42 and blood–brain barrier penetrance were observed, solidifying the utility of specific compounds for AD. Single‐concentration phagocytosis results were validated as predictive of dose–response findings. These studies established workflows, validated assays, and illuminated next steps for protein targets and compounds.
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Affiliation(s)
- Frances M. Potjewyd
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Structural Genomics Consortium Chapel Hill North Carolina USA
| | - Joel K. Annor‐Gyamfi
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Structural Genomics Consortium Chapel Hill North Carolina USA
| | - Jeffrey Aubé
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Shaoyou Chu
- Department of Laboratory Medicine and Pathology University of Washington Seattle Washington USA
| | - Ivie L. Conlon
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Kevin J. Frankowski
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Shiva K. R. Guduru
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Brian P. Hardy
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Megan D. Hopkins
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Chizuru Kinoshita
- Department of Laboratory Medicine and Pathology University of Washington Seattle Washington USA
- Institute for Stem Cell and Regenerative Medicine University of Washington Seattle Washington USA
| | - Dmitri B. Kireev
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Emily R. Mason
- Department of Medicine Division of Clinical Pharmacology Indiana University School of Medicine Indianapolis Indiana USA
| | - Charles T. Moerk
- Department of Laboratory Medicine and Pathology University of Washington Seattle Washington USA
- Institute for Stem Cell and Regenerative Medicine University of Washington Seattle Washington USA
| | - Felix Nwogbo
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Kenneth H. Pearce
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Timothy I. Richardson
- Department of Medicine Division of Clinical Pharmacology Indiana University School of Medicine Indianapolis Indiana USA
| | - David A. Rogers
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Disha M. Soni
- Department of Medicine Division of Clinical Pharmacology Indiana University School of Medicine Indianapolis Indiana USA
| | - Michael Stashko
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Xiaodong Wang
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Carrow Wells
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Structural Genomics Consortium Chapel Hill North Carolina USA
| | - Timothy M. Willson
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Structural Genomics Consortium Chapel Hill North Carolina USA
| | - Stephen V. Frye
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Center for Integrative Chemical Biology and Drug Discovery Chapel Hill North Carolina USA
| | - Jessica E. Young
- Department of Laboratory Medicine and Pathology University of Washington Seattle Washington USA
- Institute for Stem Cell and Regenerative Medicine University of Washington Seattle Washington USA
| | - Alison D. Axtman
- UNC Eshelman School of Pharmacy Division of Chemical Biology and Medicinal Chemistry Structural Genomics Consortium Chapel Hill North Carolina USA
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Potjewyd FM, Annor‐Gyamfi JK, Guduru SKR, Nwogbo F, Rogers DA, Hopkins MD, Conlon I, Wells C, Stashko M, Hardy BP, Wang X, Frankowski K, Kireev DB, Pearce KH, Willson T, Aubé J, Frye SV, Richardson T, Young JE, Axtman AD. Generation of the AD Informer Set: Chemical tools to facilitate Alzheimer’s disease drug discovery. Alzheimers Dement 2021. [DOI: 10.1002/alz.051113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Frances M. Potjewyd
- University of North Carolina at Chapel Hill Chapel Hill NC USA
- Structural Genomics Consortium Chapel Hill NC USA
| | - Joel K. Annor‐Gyamfi
- University of North Carolina at Chapel Hill Chapel Hill NC USA
- Structural Genomics Consortium Chapel Hill NC USA
| | | | - Felix Nwogbo
- University of North Carolina at Chapel Hill Chapel Hill NC USA
| | - David A. Rogers
- University of North Carolina at Chapel Hill Chapel Hill NC USA
| | | | - Ivie Conlon
- University of North Carolina at Chapel Hill Chapel Hill NC USA
| | - Carrow Wells
- University of North Carolina at Chapel Hill Chapel Hill NC USA
- Structural Genomics Consortium Chapel Hill NC USA
| | - Michael Stashko
- University of North Carolina at Chapel Hill Chapel Hill NC USA
| | - Brian P. Hardy
- University of North Carolina at Chapel Hill Chapel Hill NC USA
| | - Xiaodong Wang
- University of North Carolina at Chapel Hill Chapel Hill NC USA
| | | | | | | | - Tim Willson
- University of North Carolina at Chapel Hill Chapel Hill NC USA
- Structural Genomics Consortium Chapel Hill NC USA
| | - Jeff Aubé
- University of North Carolina at Chapel Hill Chapel Hill NC USA
| | - Stephen V. Frye
- University of North Carolina at Chapel Hill Chapel Hill NC USA
| | | | | | - Alison D. Axtman
- University of North Carolina at Chapel Hill Chapel Hill NC USA
- Structural Genomics Consortium Chapel Hill NC USA
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7
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Potjewyd FM, Axtman AD. Exploration of Aberrant E3 Ligases Implicated in Alzheimer's Disease and Development of Chemical Tools to Modulate Their Function. Front Cell Neurosci 2021; 15:768655. [PMID: 34867205 PMCID: PMC8637409 DOI: 10.3389/fncel.2021.768655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/28/2021] [Indexed: 11/24/2022] Open
Abstract
The Ubiquitin Proteasome System (UPS) is responsible for the degradation of misfolded or aggregated proteins via a multistep ATP-dependent proteolytic mechanism. This process involves a cascade of ubiquitin (Ub) transfer steps from E1 to E2 to E3 ligase. The E3 ligase transfers Ub to a targeted protein that is brought to the proteasome for degradation. The inability of the UPS to remove misfolded or aggregated proteins due to UPS dysfunction is commonly observed in neurodegenerative diseases, such as Alzheimer's disease (AD). UPS dysfunction in AD drives disease pathology and is associated with the common hallmarks such as amyloid-β (Aβ) accumulation and tau hyperphosphorylation, among others. E3 ligases are key members of the UPS machinery and dysfunction or changes in their expression can propagate other aberrant processes that accelerate AD pathology. The upregulation or downregulation of expression or activity of E3 ligases responsible for these processes results in changes in protein levels of E3 ligase substrates, many of which represent key proteins that propagate AD. A powerful way to better characterize UPS dysfunction in AD and the role of individual E3 ligases is via the use of high-quality chemical tools that bind and modulate specific E3 ligases. Furthermore, through combining gene editing with recent advances in 3D cell culture, in vitro modeling of AD in a dish has become more relevant and possible. These cell-based models of AD allow for study of specific pathways and mechanisms as well as characterization of the role E3 ligases play in driving AD. In this review, we outline the key mechanisms of UPS dysregulation linked to E3 ligases in AD and highlight the currently available chemical modulators. We present several key approaches for E3 ligase ligand discovery being employed with respect to distinct classes of E3 ligases. Where possible, specific examples of the use of cultured neurons to delineate E3 ligase biology have been captured. Finally, utilizing the available ligands for E3 ligases in the design of proteolysis targeting chimeras (PROTACs) to degrade aberrant proteins is a novel strategy for AD, and we explore the prospects of PROTACs as AD therapeutics.
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