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  1. Artikel ; Online: Targeting epigenetic modulators using PROTAC degraders: Current status and future perspective.

    Webb, Thomas / Craigon, Conner / Ciulli, Alessio

    Bioorganic & medicinal chemistry letters

    2022  Band 63, Seite(n) 128653

    Abstract: Epigenetic modulators perform critical functions in gene expression for rapid adaption to external stimuli and are prevalent in all higher-order organisms. The establishment of a link between dysregulation of epigenetic processes and disease pathogenesis, ...

    Abstract Epigenetic modulators perform critical functions in gene expression for rapid adaption to external stimuli and are prevalent in all higher-order organisms. The establishment of a link between dysregulation of epigenetic processes and disease pathogenesis, particularly in cancer, has led to much interest in identifying drug targets. This prompted the development of small molecule inhibitors, primarily in haematological malignancies. While there have been epigenetic-targeting drugs to receive FDA approval for the treatment of cancers, many suffer from limited applicability, toxicity and the onset of drug resistance, as our understanding of the biology remains incomplete. The recent advent of genome-wide RNAi and CRISPR screens has shed new light on loss of specific proteins causing vulnerabilities of specific cancer types, highlighting the potential for exploiting synthetic lethality as a therapeutic approach. However, small molecule inhibitors have largely been unable to recapitulate phenotypic effects observed using genome-wide knockdown approaches. This mechanistic disconnect and gap are set to be addressed by targeted protein degradation. Degraders such as PROTACs targeting epigenetic proteins recapitulate CRISPR mediated genetic knockdown at the post-translational level and therefore can better exploit target druggability. Here, we review the current landscape of epigenetic drug discovery, the rationale behind and progress made in the development of PROTAC degraders, and look at future perspectives for the field.
    Mesh-Begriff(e) Humans ; Drug Discovery ; Epigenesis, Genetic ; Neoplasms/drug therapy ; Proteolysis
    Sprache Englisch
    Erscheinungsdatum 2022-03-04
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1063195-1
    ISSN 1464-3405 ; 0960-894X
    ISSN (online) 1464-3405
    ISSN 0960-894X
    DOI 10.1016/j.bmcl.2022.128653
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Mechanistic and Structural Features of PROTAC Ternary Complexes.

    Casement, Ryan / Bond, Adam / Craigon, Conner / Ciulli, Alessio

    Methods in molecular biology (Clifton, N.J.)

    2021  Band 2365, Seite(n) 79–113

    Abstract: The rapid and ever-growing advancements from within the field of proteolysis-targeting chimeras (PROTAC)-induced protein degradation have driven considerable development to gain a deeper understanding of their mode of action. The ternary complex formed ... ...

    Abstract The rapid and ever-growing advancements from within the field of proteolysis-targeting chimeras (PROTAC)-induced protein degradation have driven considerable development to gain a deeper understanding of their mode of action. The ternary complex formed by PROTACs with their target protein and E3 ubiquitin ligase is the key species in their substoichiometric catalytic mechanism. Here, we describe the theoretical framework that underpins ternary complexes, including a current understanding of the three-component binding model, cooperativity, hook effect and structural considerations. We discuss in detail the biophysical methods used to interrogate ternary complex formation in vitro, including X-ray crystallography, AlphaLISA, FRET, FP, ITC and SPR. Finally, we provide detailed ITC methods and discuss approaches to assess binary and ternary target engagement, target ubiquitination and degradation that can be used to obtain a more holistic understanding of the mode of action within a cellular environment.
    Mesh-Begriff(e) Proteolysis ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination
    Chemische Substanzen Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Sprache Englisch
    Erscheinungsdatum 2021-08-24
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1665-9_5
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Amide-to-Ester Substitution as a Strategy for Optimizing PROTAC Permeability and Cellular Activity.

    Klein, Victoria G / Bond, Adam G / Craigon, Conner / Lokey, R Scott / Ciulli, Alessio

    Journal of medicinal chemistry

    2021  Band 64, Heft 24, Seite(n) 18082–18101

    Abstract: Criteria for predicting the druglike properties of "beyond Rule of 5" Proteolysis Targeting Chimeras (PROTAC) degraders are underdeveloped. PROTAC components are often combined via amide couplings due to their reliability. Amides, however, can give rise ... ...

    Abstract Criteria for predicting the druglike properties of "beyond Rule of 5" Proteolysis Targeting Chimeras (PROTAC) degraders are underdeveloped. PROTAC components are often combined via amide couplings due to their reliability. Amides, however, can give rise to poor absorption, distribution, metabolism, and excretion (ADME) properties. We hypothesized that a bioisosteric amide-to-ester substitution could lead to improvements in both physicochemical properties and bioactivity. Using model compounds, bearing either amides or esters, we identify parameters for optimal lipophilicity and permeability. We applied these learnings to design a set of novel amide-to-ester-substituted, VHL-based BET degraders with the goal to increase permeability. Our ester PROTACs retained intracellular stability, were overall more potent degraders than their amide counterparts, and showed an earlier onset of the hook effect. These enhancements were driven by greater cell permeability rather than improvements in ternary complex formation. This largely unexplored amide-to-ester substitution provides a simple strategy to enhance PROTAC permeability and bioactivity and may prove beneficial to other beyond Ro5 molecules.
    Mesh-Begriff(e) Amides/chemistry ; Animals ; Cell Membrane Permeability ; Dogs ; Esters/chemistry ; Hydrogen Bonding ; Ligands ; Madin Darby Canine Kidney Cells ; Oligopeptides/chemistry ; Oligopeptides/metabolism ; Oligopeptides/pharmacology ; Proteolysis/drug effects ; Reproducibility of Results ; Ubiquitin-Protein Ligases/metabolism
    Chemische Substanzen Amides ; Esters ; Ligands ; Oligopeptides ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Sprache Englisch
    Erscheinungsdatum 2021-12-09
    Erscheinungsland United States
    Dokumenttyp 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 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.1c01496
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Targeted protein degradation via intramolecular bivalent glues.

    Hsia, Oliver / Hinterndorfer, Matthias / Cowan, Angus D / Iso, Kentaro / Ishida, Tasuku / Sundaramoorthy, Ramasubramanian / Nakasone, Mark A / Imrichova, Hana / Schätz, Caroline / Rukavina, Andrea / Husnjak, Koraljka / Wegner, Martin / Correa-Sáez, Alejandro / Craigon, Conner / Casement, Ryan / Maniaci, Chiara / Testa, Andrea / Kaulich, Manuel / Dikic, Ivan /
    Winter, Georg E / Ciulli, Alessio

    Nature

    2024  Band 627, Heft 8002, Seite(n) 204–211

    Abstract: Targeted protein degradation is a pharmacological modality that is based on the induced proximity of an E3 ubiquitin ligase and a target protein to promote target ubiquitination and proteasomal degradation. This has been achieved either via proteolysis- ... ...

    Abstract Targeted protein degradation is a pharmacological modality that is based on the induced proximity of an E3 ubiquitin ligase and a target protein to promote target ubiquitination and proteasomal degradation. This has been achieved either via proteolysis-targeting chimeras (PROTACs)-bifunctional compounds composed of two separate moieties that individually bind the target and E3 ligase, or via molecular glues that monovalently bind either the ligase or the target
    Mesh-Begriff(e) Bromodomain Containing Proteins/metabolism ; Cell Cycle Proteins/metabolism ; Drug Design ; Proteasome Endopeptidase Complex/metabolism ; Proteolysis ; Proteolysis Targeting Chimera ; Transcription Factors/metabolism ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination ; Protein Binding ; Substrate Specificity ; Protein Domains
    Chemische Substanzen Bromodomain Containing Proteins ; Cell Cycle Proteins ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Proteolysis Targeting Chimera ; Transcription Factors ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Sprache Englisch
    Erscheinungsdatum 2024-02-21
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-024-07089-6
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Development of BromoTag: A "Bump-and-Hole"-PROTAC System to Induce Potent, Rapid, and Selective Degradation of Tagged Target Proteins.

    Bond, Adam G / Craigon, Conner / Chan, Kwok-Ho / Testa, Andrea / Karapetsas, Athanasios / Fasimoye, Rotimi / Macartney, Thomas / Blow, J Julian / Alessi, Dario R / Ciulli, Alessio

    Journal of medicinal chemistry

    2021  Band 64, Heft 20, Seite(n) 15477–15502

    Abstract: Small-molecule-induced protein depletion technologies, also called inducible degrons, allow degradation of genetically engineered target proteins within cells and animals. Here, we design and develop the BromoTag, a new inducible degron system comprising ...

    Abstract Small-molecule-induced protein depletion technologies, also called inducible degrons, allow degradation of genetically engineered target proteins within cells and animals. Here, we design and develop the BromoTag, a new inducible degron system comprising a Brd4 bromodomain L387A variant as a degron tag that allows direct recruitment by heterobifunctional bumped proteolysis targeting chimeras (PROTACs) to hijack the VHL E3 ligase. We describe extensive optimization and structure-activity relationships of our bump-and-hole-PROTACs using a CRISPR knock-in cell line expressing model target BromoTag-Brd2 at endogenous levels. Collectively, our cellular and mechanistic data qualifies bumped PROTAC AGB1 as a potent, fast, and selective degrader of BromoTagged proteins, with a favorable pharmacokinetic profile in mice. The BromoTag adds to the arsenal of chemical genetic degradation tools allowing us to manipulate protein levels to interrogate the biological function and therapeutic potential in cells and
    Mesh-Begriff(e) Cell Cycle Proteins/antagonists & inhibitors ; Cell Cycle Proteins/metabolism ; Dose-Response Relationship, Drug ; Drug Development ; HEK293 Cells ; Humans ; Molecular Structure ; Proteolysis/drug effects ; Structure-Activity Relationship ; Transcription Factors/antagonists & inhibitors ; Transcription Factors/metabolism
    Chemische Substanzen BRD4 protein, human ; Cell Cycle Proteins ; Transcription Factors
    Sprache Englisch
    Erscheinungsdatum 2021-10-15
    Erscheinungsland United States
    Dokumenttyp Journal Article ; 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.1c01532
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity.

    Imaide, Satomi / Riching, Kristin M / Makukhin, Nikolai / Vetma, Vesna / Whitworth, Claire / Hughes, Scott J / Trainor, Nicole / Mahan, Sarah D / Murphy, Nancy / Cowan, Angus D / Chan, Kwok-Ho / Craigon, Conner / Testa, Andrea / Maniaci, Chiara / Urh, Marjeta / Daniels, Danette L / Ciulli, Alessio

    Nature chemical biology

    2021  Band 17, Heft 11, Seite(n) 1157–1167

    Abstract: Bivalent proteolysis-targeting chimeras (PROTACs) drive protein degradation by simultaneously binding a target protein and an E3 ligase and forming a productive ternary complex. We hypothesized that increasing binding valency within a PROTAC could ... ...

    Abstract Bivalent proteolysis-targeting chimeras (PROTACs) drive protein degradation by simultaneously binding a target protein and an E3 ligase and forming a productive ternary complex. We hypothesized that increasing binding valency within a PROTAC could enhance degradation. Here, we designed trivalent PROTACs consisting of a bivalent bromo and extra terminal (BET) inhibitor and an E3 ligand tethered via a branched linker. We identified von Hippel-Lindau (VHL)-based SIM1 as a low picomolar BET degrader with preference for bromodomain containing 2 (BRD2). Compared to bivalent PROTACs, SIM1 showed more sustained and higher degradation efficacy, which led to more potent anticancer activity. Mechanistically, SIM1 simultaneously engages with high avidity both BET bromodomains in a cis intramolecular fashion and forms a 1:1:1 ternary complex with VHL, exhibiting positive cooperativity and high cellular stability with prolonged residence time. Collectively, our data along with favorable in vivo pharmacokinetics demonstrate that augmenting the binding valency of proximity-induced modalities can be an enabling strategy for advancing functional outcomes.
    Mesh-Begriff(e) Humans ; Proteolysis ; Ubiquitin-Protein Ligases/metabolism
    Chemische Substanzen Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Sprache Englisch
    Erscheinungsdatum 2021-10-21
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/s41589-021-00878-4
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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