1
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Thomas AM, Serafini M, Grant EK, Coombs EAJ, Bluck JP, Schiedel M, McDonough MA, Reynolds JK, Lee B, Platt M, Sharlandjieva V, Biggin PC, Duarte F, Milne TA, Bush JT, Conway SJ. Mutate and Conjugate: A Method to Enable Rapid In-Cell Target Validation. ACS Chem Biol 2023; 18:2405-2417. [PMID: 37874862 PMCID: PMC10660337 DOI: 10.1021/acschembio.3c00437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/22/2023] [Accepted: 10/05/2023] [Indexed: 10/26/2023]
Abstract
Target validation remains a challenge in drug discovery, which leads to a high attrition rate in the drug discovery process, particularly in Phase II clinical trials. Consequently, new approaches to enhance target validation are valuable tools to improve the drug discovery process. Here, we report the combination of site-directed mutagenesis and electrophilic fragments to enable the rapid identification of small molecules that selectively inhibit the mutant protein. Using the bromodomain-containing protein BRD4 as an example, we employed a structure-based approach to identify the L94C mutation in the first bromodomain of BRD4 [BRD4(1)] as having a minimal effect on BRD4(1) function. We then screened a focused, KAc mimic-containing fragment set and a diverse fragment library against the mutant and wild-type proteins and identified a series of fragments that showed high selectivity for the mutant protein. These compounds were elaborated to include an alkyne click tag to enable the attachment of a fluorescent dye. These clickable compounds were then assessed in HEK293T cells, transiently expressing BRD4(1)WT or BRD4(1)L94C, to determine their selectivity for BRD4(1)L94C over other possible cellular targets. One compound was identified that shows very high selectivity for BRD4(1)L94C over all other proteins. This work provides a proof-of-concept that the combination of site-directed mutagenesis and electrophilic fragments, in a mutate and conjugate approach, can enable rapid identification of small molecule inhibitors for an appropriately mutated protein of interest. This technology can be used to assess the cellular phenotype of inhibiting the protein of interest, and the electrophilic ligand provides a starting point for noncovalent ligand development.
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Affiliation(s)
- Adam M. Thomas
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Marta Serafini
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Emma K. Grant
- Department
of Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Edward A. J. Coombs
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Joseph P. Bluck
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department
of Biochemistry, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Matthias Schiedel
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A. McDonough
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jessica K. Reynolds
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Bernadette Lee
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael Platt
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Vassilena Sharlandjieva
- MRC
Molecular Haematology Unit, MRC Weatherall Institute of Molecular
Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United
Kingdom
| | - Philip C. Biggin
- Department
of Biochemistry, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Fernanda Duarte
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Thomas A. Milne
- MRC
Molecular Haematology Unit, MRC Weatherall Institute of Molecular
Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United
Kingdom
| | - Jacob T. Bush
- Department
of Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Stuart J. Conway
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department
of Chemistry & Biochemistry, University
of California Los Angeles, 607 Charles E. Young Drive East, P.O. Box 951569, Los Angeles, California 90095-1569, United States
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2
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Kenanova D, Visser EJ, Virta JM, Sijbesma E, Centorrino F, Vickery HR, Zhong M, Neitz RJ, Brunsveld L, Ottmann C, Arkin MR. A Systematic Approach to the Discovery of Protein-Protein Interaction Stabilizers. ACS CENTRAL SCIENCE 2023; 9:937-946. [PMID: 37252362 PMCID: PMC10214524 DOI: 10.1021/acscentsci.2c01449] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Indexed: 05/31/2023]
Abstract
Dysregulation of protein-protein interactions (PPIs) commonly leads to disease. PPI stabilization has only recently been systematically explored for drug discovery despite being a powerful approach to selectively target intrinsically disordered proteins and hub proteins, like 14-3-3, with multiple interaction partners. Disulfide tethering is a site-directed fragment-based drug discovery (FBDD) methodology for identifying reversibly covalent small molecules. We explored the scope of disulfide tethering for the discovery of selective PPI stabilizers (molecular glues) using the hub protein 14-3-3σ. We screened complexes of 14-3-3 with 5 biologically and structurally diverse phosphopeptides derived from the 14-3-3 client proteins ERα, FOXO1, C-RAF, USP8, and SOS1. Stabilizing fragments were found for 4/5 client complexes. Structural elucidation of these complexes revealed the ability of some peptides to conformationally adapt to make productive interactions with the tethered fragments. We validated eight fragment stabilizers, six of which showed selectivity for one phosphopeptide client, and structurally characterized two nonselective hits and four fragments that selectively stabilized C-RAF or FOXO1. The most efficacious fragment increased 14-3-3σ/C-RAF phosphopeptide affinity by 430-fold. Disulfide tethering to the wildtype C38 in 14-3-3σ provided diverse structures for future optimization of 14-3-3/client stabilizers and highlighted a systematic method to discover molecular glues.
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Affiliation(s)
- Dyana
N. Kenanova
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94143, United States
| | - Emira J. Visser
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Johanna M. Virta
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94143, United States
| | - Eline Sijbesma
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Federica Centorrino
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Holly R. Vickery
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94143, United States
| | - Mengqi Zhong
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94143, United States
| | - R. Jeffrey Neitz
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94143, United States
| | - Luc Brunsveld
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94143, United States
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3
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A novel mRNA decay inhibitor abolishes pathophysiological cellular transition. Cell Death Dis 2022; 8:278. [PMID: 35672286 PMCID: PMC9174231 DOI: 10.1038/s41420-022-01076-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022]
Abstract
In cells, mRNA synthesis and decay are influenced by each other, and their balance is altered by either external or internal cues, resulting in changes in cell dynamics. We previously reported that it is important that an array of mRNAs that shape a phenotype are degraded before cellular transitions, such as cellular reprogramming and differentiation. In adipogenesis, the interaction between DDX6 and 4E-T had a definitive impact on the pathway in the processing body (PB). We screened a library of α-helix analogs with an alkaloid-like backbone to identify compounds that inhibit the binding between DDX6 and 4E-T proteins, which occurs between the α-helix of structured and internally disordered proteins. IAMC-00192 was identified as a lead compound. This compound directly inhibited the interaction between DDX6 and 4E-T. IAMC-00192 inhibited the temporal increase in PB formation that occurs during adipogenesis and epithelial-mesenchymal transition (EMT) and significantly suppressed these cellular transitions. In the EMT model, the half-life of preexisting mRNAs in PBs was extended twofold by the compound. The novel inhibitor of RNA decay not only represents a potentially useful tool to analyze in detail the pathological conditions affected by RNA decay and how it regulates the pathological state. The identification of this inhibitor may lead to the discovery of a first-in-class RNA decay inhibitor drug. ![]()
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4
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Modell AE, Marrone F, Panigrahi NR, Zhang Y, Arora PS. Peptide Tethering: Pocket-Directed Fragment Screening for Peptidomimetic Inhibitor Discovery. J Am Chem Soc 2022; 144:1198-1204. [PMID: 35029987 PMCID: PMC8959088 DOI: 10.1021/jacs.1c09666] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Constrained peptides have proven to be a rich source of ligands for protein surfaces, but are often limited in their binding potency. Deployment of nonnatural side chains that access unoccupied crevices on the receptor surface offers a potential avenue to enhance binding affinity. We recently described a computational approach to create topographic maps of protein surfaces to guide the design of nonnatural side chains [J. Am. Chem. Soc. 2017, 139, 15560]. The computational method, AlphaSpace, was used to predict peptide ligands for the KIX domain of the p300/CBP coactivator. KIX has been the subject of numerous ligand discovery strategies, but potent inhibitors of its interaction with transcription factors remain difficult to access. Although the computational approach provided a significant enhancement in the binding affinity of the peptide, fine-tuning of nonnatural side chains required an experimental screening method. Here we implement a peptide-tethering strategy to screen fragments as nonnatural side chains on conformationally defined peptides. The combined computational-experimental approach offers a general framework for optimizing peptidomimetics as inhibitors of protein-protein interactions.
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Affiliation(s)
- Ashley E Modell
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Frank Marrone
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Nihar R Panigrahi
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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5
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Ahmad W, Ahmad Q, Yaseen M, Ahmad I, Hussain F, Mohamed Jan B, Ikram R, Stylianakis MM, Kenanakis G. Development of Waste Polystyrene-Based Copper Oxide/Reduced Graphene Oxide Composites and Their Mechanical, Electrical and Thermal Properties. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:2372. [PMID: 34578688 PMCID: PMC8464779 DOI: 10.3390/nano11092372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022]
Abstract
The current study reports the effect of different wt. ratios of copper oxide nanoparticle (CuO-NPs) and reduced graphene oxide (rGO) as fillers on mechanical, electrical, and thermal properties of waste polystyrene (WPS) matrix. Firstly, thin sheets of WPS-rGO-CuO composites were prepared through solution casting method with different ratios, i.e., 2, 8, 10, 15 and 20 wt.% of CuO-NPs and rGO in WPS matrix. The synthesized composite sheets were characterized by Fourier transform infrared spectroscopy (FTIR), energy dispersive X-ray (EDX), X-ray diffraction (XRD) analysis, scanning electron microscopy (SEM) and thermal gravimetric analysis (TGA). The electrical conductance and mechanical strength of the prepared composites were determined by using LCR meter and universal testing machine (UTM). These properties were dependent on the concentrations of CuO-NPs and rGO. Results display that the addition of both fillers, i.e., rGO and CuO-NPs, collectively led to remarkable increase in the mechanical properties of the composite. The incorporation of rGO-CuO: 15% WPS sample, i.e., WPS-rGO-CuO: 15%, has shown high mechanical strength with tensile strength of 25.282 MPa and Young modulus of 1951.0 MPa, respectively. Similarly, the electrical conductance of the same composite is also enhanced from 6.7 × 10-14 to 4 × 10-7 S/m in contrast to WPS at 2.0 × 106 Hz. The fabricated composites exhibited high thermal stability through TGA analysis in terms of 3.52% and 6.055% wt. loss at 250 °C as compared to WPS.
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Affiliation(s)
- Waqas Ahmad
- Institute of Chemical Sciences, University of Peshawar, Peshawar 25120, Pakistan; (Q.A.); (M.Y.); (I.A.)
| | - Qaizar Ahmad
- Institute of Chemical Sciences, University of Peshawar, Peshawar 25120, Pakistan; (Q.A.); (M.Y.); (I.A.)
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Peshawar, Peshawar 25120, Pakistan; (Q.A.); (M.Y.); (I.A.)
| | - Imtiaz Ahmad
- Institute of Chemical Sciences, University of Peshawar, Peshawar 25120, Pakistan; (Q.A.); (M.Y.); (I.A.)
| | - Fida Hussain
- Department of Chemical and Energy Engineering, Pak-Austria Fachhochschule, Institute of Applied Science & Technology, Haripur 22621, Pakistan;
| | - Badrul Mohamed Jan
- Department of Chemical Engineering, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Rabia Ikram
- Department of Chemical Engineering, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Minas M. Stylianakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas, N. Plastira 100, Vasilika Vouton, GR-700 13 Heraklion, Greece; (M.M.S.); (G.K.)
| | - George Kenanakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas, N. Plastira 100, Vasilika Vouton, GR-700 13 Heraklion, Greece; (M.M.S.); (G.K.)
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6
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Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Visualizing and trapping transient oligomers in amyloid assembly pathways. Biophys Chem 2021; 268:106505. [PMID: 33220582 PMCID: PMC8188297 DOI: 10.1016/j.bpc.2020.106505] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK.
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7
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Sijbesma E, Somsen BA, Miley GP, Leijten-van de Gevel IA, Brunsveld L, Arkin MR, Ottmann C. Fluorescence Anisotropy-Based Tethering for Discovery of Protein-Protein Interaction Stabilizers. ACS Chem Biol 2020; 15:3143-3148. [PMID: 33196173 PMCID: PMC7754187 DOI: 10.1021/acschembio.0c00646] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein-protein interaction (PPI) networks are fundamental for cellular processes. Small-molecule PPI enhancers have been shown to be powerful tools to fundamentally study PPIs and as starting points for potential new therapeutics. Yet, systematic approaches for their discovery are not widely available, and the design prerequisites of "molecular glues" are poorly understood. Covalent fragment-based screening can identify chemical starting points for these enhancers at specific sites in PPI interfaces. We recently reported a mass spectrometry-based disulfide-trapping (tethering) approach for a cysteine residue in the hub protein 14-3-3, an important regulator of phosphorylated client proteins. Here, we invert the strategy and report the development of a functional read-out for systematic identification of PPI enhancers based on fluorescence anisotropy (FA-tethering) with the reactive handle now on a client-derived peptide. Using the DNA-binding domain of the nuclear receptor Estrogen Related Receptor gamma (ERRγ), we target a native cysteine positioned at the 14-3-3 PPI interface and identify several fragments that form a disulfide bond to ERRγ and stabilize the complex up to 5-fold. Crystallography indicates that fragments bind in a pocket comprised of 14-3-3 and the ERRγ phosphopeptide. FA-tethering presents a streamlined methodology to discover molecular glues for protein complexes.
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Affiliation(s)
- Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bente A. Somsen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Galen P. Miley
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Iris A. Leijten-van de Gevel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Michelle R. Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, United States
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Chemistry, University of Duisburg-Essen, Essen, Germany
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8
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Lodge JM, Majmudar CY, Clayton J, Mapp AK. Covalent Chemical Cochaperones of the p300/CBP GACKIX Domain. Chembiochem 2018; 19:1907-1912. [PMID: 29939485 PMCID: PMC10900128 DOI: 10.1002/cbic.201800173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Indexed: 12/28/2022]
Abstract
The GACKIX activator binding domain has been a compelling target for small-molecule probe discovery because of the central role of activator-GACKIX complexes in diseases ranging from leukemia to memory disorders. Additionally, GACKIX is an ideal model to dissect the context-dependent function of activator-coactivator complexes. However, the dynamic and transient protein-protein interactions (PPIs) formed by GACKIX are difficult targets for small molecules. An additional complication is that activator-binding motifs, such as GACKIX, are found in multiple coactivators, making specificity difficult to attain. In this study, we demonstrate that the strategy of tethering can be used to rapidly discover highly specific covalent modulators of the dynamic PPIs between activators and coactivators. These serve as both ortho- and allosteric modulators, enabling the tunable assembly or disassembly of the activator-coactivator complexes formed between the KIX domain and its cognate activator binding partners MLL and CREB. The molecules maintain their function and selectivity, even in human cell lysates and in bacterial cells, and thus, will ultimately be highly useful probes for cellular studies.
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Affiliation(s)
- Jean M Lodge
- University of Michigan, Life Sciences Institute, 210 Washentaw Avenue, Ann Arbor, MI, 48109, USA
| | - Chinmay Y Majmudar
- University of Michigan, Life Sciences Institute, 210 Washentaw Avenue, Ann Arbor, MI, 48109, USA
| | - James Clayton
- University of Michigan, Life Sciences Institute, 210 Washentaw Avenue, Ann Arbor, MI, 48109, USA
| | - Anna K Mapp
- University of Michigan, Life Sciences Institute, 210 Washentaw Avenue, Ann Arbor, MI, 48109, USA
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9
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Breen ME, Mapp AK. Modulating the masters: chemical tools to dissect CBP and p300 function. Curr Opin Chem Biol 2018; 45:195-203. [PMID: 30025258 DOI: 10.1016/j.cbpa.2018.06.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/25/2018] [Accepted: 06/02/2018] [Indexed: 01/07/2023]
Abstract
Dysregulation of transcription is found in nearly every human disease, and as a result there has been intense interest in developing new therapeutics that target regulators of transcription. CREB binding protein (CBP) and its paralogue p300 are attractive targets due to their function as `master coactivators'. Although inhibitors of several CBP/p300 domains have been identified, the selectivity of many of these compounds has remained underexplored. Here, we review recent successes in the development of chemical tools targeting several CBP/p300 domains with selectivity acceptable for use as chemical probes. Additionally, we highlight recent studies which have used these probes to expand our understanding of interdomain interactions and differential coactivator usage.
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Affiliation(s)
- Meghan E Breen
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA
| | - Anna K Mapp
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA.
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10
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Xie F, Li BX, Xiao X. Design, synthesis and biological evaluation of regioisomers of 666-15 as inhibitors of CREB-mediated gene transcription. Bioorg Med Chem Lett 2017; 27:994-998. [PMID: 28073675 PMCID: PMC5296214 DOI: 10.1016/j.bmcl.2016.12.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/28/2016] [Accepted: 12/28/2016] [Indexed: 11/19/2022]
Abstract
cAMP-response element binding protein (CREB) is a nuclear transcription factor that has been implicated in the pathogenesis and maintenance of various types of human cancers. Identification of small molecule inhibitors of CREB-mediated gene transcription has been pursued as a novel strategy for developing cancer therapeutics. We recently discovered a potent and cell-permeable CREB inhibitor called 666-15. 666-15 is a bisnaphthamide and has been shown to possess efficacious anti-breast cancer activity without toxicity in vivo. In this study, we designed and synthesized a series of analogs of 666-15 to probe the importance of regiochemistry in naphthalene ring B. Biological evaluations of these analogs demonstrated that the substitution pattern of the alkoxy and carboxamide in naphthalene ring B is very critical for maintaining potent CREB inhibition activity, suggesting that the unique bioactive conformation accessible in 666-15 is critically important.
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Affiliation(s)
- Fuchun Xie
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - Bingbing X Li
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - Xiangshu Xiao
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA; Knight Cardiovascular Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA.
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11
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Choi S, Choi KY. Screening-based approaches to identify small molecules that inhibit protein–protein interactions. Expert Opin Drug Discov 2017; 12:293-303. [DOI: 10.1080/17460441.2017.1280456] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sehee Choi
- Translational Research Center for Protein Function Control, Yonsei University, Seoul, Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Kang-Yell Choi
- Translational Research Center for Protein Function Control, Yonsei University, Seoul, Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
- CK Biotechnology Inc., 416 Advanced Science and Technology Center, 50 Yonsei-ro, Seoul, Korea
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12
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van der Vlag R, Hirsch A. Analytical Methods in Protein-Templated Dynamic Combinatorial Chemistry. COMPREHENSIVE SUPRAMOLECULAR CHEMISTRY II 2017. [PMCID: PMC7150222 DOI: 10.1016/b978-0-12-409547-2.12559-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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13
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Doak BC, Norton RS, Scanlon MJ. The ways and means of fragment-based drug design. Pharmacol Ther 2016; 167:28-37. [DOI: 10.1016/j.pharmthera.2016.07.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 07/08/2016] [Indexed: 12/21/2022]
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14
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Li BX, Gardner R, Xue C, Qian DZ, Xie F, Thomas G, Kazmierczak SC, Habecker BA, Xiao X. Systemic Inhibition of CREB is Well-tolerated in vivo. Sci Rep 2016; 6:34513. [PMID: 27694829 PMCID: PMC5046085 DOI: 10.1038/srep34513] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/15/2016] [Indexed: 11/30/2022] Open
Abstract
cAMP-response element binding protein (CREB) is a nuclear transcription factor activated by multiple extracellular signals including growth factors and hormones. These extracellular cues activate CREB through phosphorylation at Ser133 by various protein serine/threonine kinases. Once phosphorylated, it promotes its association with transcription coactivators CREB-binding protein (CBP) and its paralog p300 to activate CREB-dependent gene transcription. Tumor tissues of different origins have been shown to present overexpression and/or overactivation of CREB, indicating CREB as a potential cancer drug target. We previously identified 666-15 as a potent inhibitor of CREB with efficacious anti-cancer activity both in vitro and in vivo. Herein, we investigated the specificity of 666-15 and evaluated its potential in vivo toxicity. We found that 666-15 was fairly selective in inhibiting CREB. 666-15 was also found to be readily bioavailable to achieve pharmacologically relevant concentrations for CREB inhibition. Furthermore, the mice treated with 666-15 showed no evidence of changes in body weight, complete blood count, blood chemistry profile, cardiac contractility and tissue histologies from liver, kidney and heart. For the first time, these results demonstrate that pharmacological inhibition of CREB is well-tolerated in vivo and indicate that such inhibitors should be promising cancer therapeutics.
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Affiliation(s)
- Bingbing X Li
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health &Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - Ryan Gardner
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health &Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - Changhui Xue
- Knight Cancer Institute, Oregon Health &Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - David Z Qian
- Knight Cancer Institute, Oregon Health &Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - Fuchun Xie
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health &Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health &Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - Steven C Kazmierczak
- Department of Pathology, Oregon Health &Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - Beth A Habecker
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health &Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA.,Knight Cardiovascular Institute, Department of Medicine, Oregon Health &Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
| | - Xiangshu Xiao
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health &Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA.,Knight Cancer Institute, Oregon Health &Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA.,Knight Cardiovascular Institute, Department of Medicine, Oregon Health &Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
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15
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Gee CT, Arntson KE, Urick AK, Mishra NK, Hawk LML, Wisniewski AJ, Pomerantz WCK. Protein-observed (19)F-NMR for fragment screening, affinity quantification and druggability assessment. Nat Protoc 2016; 11:1414-27. [PMID: 27414758 DOI: 10.1038/nprot.2016.079] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
NMR spectroscopy can be used to quantify the binding affinity between proteins and low-complexity molecules, termed 'fragments'; this versatile screening approach allows researchers to assess the druggability of new protein targets. Protein-observed (19)F-NMR (PrOF NMR) using (19)F-labeled amino acids generates relatively simple spectra that are able to provide dynamic structural information toward understanding protein folding and function. Changes in these spectra upon the addition of fragment molecules can be observed and quantified. This protocol describes the sequence-selective labeling of three proteins (the first bromodomains of Brd4 and BrdT, and the KIX domain of the CREB-binding protein) using commercially available fluorinated aromatic amino acids and fluorinated precursors as example applications of the method developed by our research group. Fragment-screening approaches are discussed, as well as Kd determination, ligand-efficiency calculations and druggability assessment, i.e., the ability to target these proteins using small-molecule ligands. Experiment times on the order of a few minutes and the simplicity of the NMR spectra obtained make this approach well-suited to the investigation of small- to medium-sized proteins, as well as the screening of multiple proteins in the same experiment.
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Affiliation(s)
- Clifford T Gee
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Keith E Arntson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew K Urick
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Neeraj K Mishra
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Laura M L Hawk
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrea J Wisniewski
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
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16
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Modell AE, Blosser SL, Arora PS. Systematic Targeting of Protein-Protein Interactions. Trends Pharmacol Sci 2016; 37:702-713. [PMID: 27267699 DOI: 10.1016/j.tips.2016.05.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/14/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022]
Abstract
Over the past decade, protein-protein interactions (PPIs) have gone from being neglected as 'undruggable' to being considered attractive targets for the development of therapeutics. Recent advances in computational analysis, fragment-based screening, and molecular design have revealed promising strategies to address the basic molecular recognition challenge: how to target large protein surfaces with specificity. Several systematic and complementary workflows have been developed to yield successful inhibitors of PPIs. Here we review the major contemporary approaches utilized for the discovery of inhibitors and focus on a structure-based workflow, from the selection of a biological target to design.
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Affiliation(s)
- Ashley E Modell
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sarah L Blosser
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
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17
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Corbi-Verge C, Kim PM. Motif mediated protein-protein interactions as drug targets. Cell Commun Signal 2016; 14:8. [PMID: 26936767 PMCID: PMC4776425 DOI: 10.1186/s12964-016-0131-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/25/2016] [Indexed: 12/17/2022] Open
Abstract
Protein-protein interactions (PPI) are involved in virtually every cellular process and thus represent an attractive target for therapeutic interventions. A significant number of protein interactions are frequently formed between globular domains and short linear peptide motifs (DMI). Targeting these DMIs has proven challenging and classical approaches to inhibiting such interactions with small molecules have had limited success. However, recent new approaches have led to the discovery of potent inhibitors, some of them, such as Obatoclax, ABT-199, AEG-40826 and SAH-p53-8 are likely to become approved drugs. These novel inhibitors belong to a wide range of different molecule classes, ranging from small molecules to peptidomimetics and biologicals. This article reviews the main reasons for limited success in targeting PPIs, discusses how successful approaches overcome these obstacles to discovery promising inhibitors for human protein double minute 2 (HDM2), B-cell lymphoma 2 (Bcl-2), X-linked inhibitor of apoptosis protein (XIAP), and provides a summary of the promising approaches currently in development that indicate the future potential of PPI inhibitors in drug discovery.
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Affiliation(s)
- Carles Corbi-Verge
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada.
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18
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19
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Rettenmaier TJ, Hudson SA, Wells JA. Site-Directed Fragment Discovery for Allostery. FRAGMENT-BASED DRUG DISCOVERY LESSONS AND OUTLOOK 2016. [DOI: 10.1002/9783527683604.ch11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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20
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Nevola L, Giralt E. Modulating protein-protein interactions: the potential of peptides. Chem Commun (Camb) 2015; 51:3302-15. [PMID: 25578807 DOI: 10.1039/c4cc08565e] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein-protein interactions (PPIs) have emerged as important and challenging targets in chemical biology and medicinal chemistry. The main difficulty encountered in the discovery of small molecule modulators derives from the large contact surfaces involved in PPIs when compared with those that participate in protein-small molecule interactions. Because of their intrinsic features, peptides can explore larger surfaces and therefore represent a useful alternative to modulate PPIs. The use of peptides as therapeutics has been held back by their instability in vivo and poor cell internalization. However, more than 200 peptide drugs and homologous compounds (proteins or antibodies) containing peptide bonds are (or have been) on the market, and many alternatives are now available to tackle these limitations. This review will focus on the latest progress in the field, spanning from "lead" identification methods to binding evaluation techniques, through an update of the most successful examples described in the literature.
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Affiliation(s)
- Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, 08028 Barcelona, Spain.
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21
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Xie F, Li BX, Kassenbrock A, Xue C, Wang X, Qian DZ, Sears RC, Xiao X. Identification of a Potent Inhibitor of CREB-Mediated Gene Transcription with Efficacious in Vivo Anticancer Activity. J Med Chem 2015; 58:5075-87. [PMID: 26023867 PMCID: PMC4493896 DOI: 10.1021/acs.jmedchem.5b00468] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
Recent
studies have shown that nuclear transcription factor cyclic
adenosine monophosphate response element binding protein (CREB) is
overexpressed in many different types of cancers. Therefore, CREB
has been pursued as a novel cancer therapeutic target. Naphthol AS-E
and its closely related derivatives have been shown to inhibit CREB-mediated
gene transcription and cancer cell growth. Previously, we identified
naphthamide 3a as a different chemotype to inhibit CREB’s
transcription activity. In a continuing effort to discover more potent
CREB inhibitors, a series of structural congeners of 3a was designed and synthesized. Biological evaluations of these compounds
uncovered compound 3i (666-15) as a potent
and selective inhibitor of CREB-mediated gene transcription (IC50 = 0.081 ± 0.04 μM). 666-15 also
potently inhibited cancer cell growth without harming normal cells.
In an in vivo MDA-MB-468 xenograft model, 666-15 completely
suppressed the tumor growth without overt toxicity. These results
further support the potential of CREB as a valuable cancer drug target.
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22
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Magee TV. Progress in discovery of small-molecule modulators of protein-protein interactions via fragment screening. Bioorg Med Chem Lett 2015; 25:2461-8. [PMID: 25971770 DOI: 10.1016/j.bmcl.2015.04.089] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 04/21/2015] [Accepted: 04/27/2015] [Indexed: 11/16/2022]
Abstract
Protein-protein interactions (PPIs) present a formidable challenge to medicinal chemistry. The extended and open nature of many binding sites at protein interfaces has made it difficult to find useful chemical matter by traditional screening methods using standard screening libraries. This Digest focuses on the progress that has been made in discovering small-molecule modulators for a diverse selection of PPI targets using fragment screening and highlights the utility of this strategy in this context.
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Affiliation(s)
- Thomas V Magee
- Worldwide Medicinal Chemistry, Pfizer Inc, 610 Main Street, Cambridge, MA 02139, USA.
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23
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Affiliation(s)
- Omar Boutureira
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili , C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
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24
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Gee CT, Koleski EJ, Pomerantz WCK. Fragment screening and druggability assessment for the CBP/p300 KIX domain through protein-observed 19F NMR spectroscopy. Angew Chem Int Ed Engl 2015; 54:3735-9. [PMID: 25651535 DOI: 10.1002/anie.201411658] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Indexed: 11/08/2022]
Abstract
(19)F NMR spectroscopy of labeled proteins is a sensitive method for characterizing structure, conformational dynamics, higher-order assembly, and ligand binding. Fluorination of aromatic side chains has been suggested as a labeling strategy for small-molecule ligand discovery for protein-protein interaction interfaces. Using a model transcription factor binding domain of the CREB binding protein (CBP)/p300, KIX, we report the first full small-molecule screen using protein-observed (19)F NMR spectroscopy. Screening of 508 compounds and validation by (1)H-(15)N HSQC NMR spectroscopy led to the identification of a minimal pharmacaphore for the MLL-KIX interaction site. Hit rate analysis for the CREB-KIX and MLL-KIX sites provided a metric to assess the ligandability or "druggability" of each interface informing future medicinal chemistry efforts. The structural information from the simplified spectra and data collection speed, affords a new screening tool for analysis of protein interfaces and discovery of small molecules.
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Affiliation(s)
- Clifford T Gee
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Twin Cities (USA)
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25
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Gee CT, Koleski EJ, Pomerantz WCK. Fragment Screening and Druggability Assessment for the CBP/p300 KIX Domain through Protein-Observed19F NMR Spectroscopy. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411658] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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26
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Allen CE, Curran PR, Brearley AS, Boissel V, Sviridenko L, Press NJ, Stonehouse JP, Armstrong A. Efficient and facile synthesis of acrylamide libraries for protein-guided tethering. Org Lett 2015; 17:458-60. [PMID: 25582165 DOI: 10.1021/ol503486t] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A kinetic template-guided tethering (KTGT) strategy has been developed for the site-directed discovery of fragments that bind to defined protein surfaces, where acrylamide-modified fragments can be irreversibly captured in a protein-templated conjugate addition reaction. Herein, an efficient and facile method is reported for the preparation of acrylamide libraries from a diverse range of amine fragments using a solid-supported quaternary amine base.
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Affiliation(s)
- Charlotte E Allen
- Global Discovery Chemistry, Novartis Horsham Research Centre , Wimblehurst Road, Horsham RH12 5AB, U.K
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27
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Li BX, Xie F, Fan Q, Barnhart KM, Moore CE, Rheingold AL, Xiao X. Novel Type of Prodrug Activation through a Long-Range O,N-Acyl Transfer: A Case of Water-Soluble CREB Inhibitor. ACS Med Chem Lett 2014; 5:1104-9. [PMID: 25313320 DOI: 10.1021/ml500330n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/22/2014] [Indexed: 11/29/2022] Open
Abstract
CREB (cAMP response element binding protein) has been shown to play an important role in tumor initiation, progression, and metastasis. We discovered that naphthol AS-E, a cell-permeable CREB inhibitor, presented antiproliferative activity in a broad panel of cancer cell lines in vitro. However, it has limited aqueous solubility. In this report, we described a water-soluble inhibitor (compound 6) of CREB-mediated gene transcription with in vivo anticancer activity. Unexpectedly, compound 6 was found to be a prodrug of compound 12 necessitating an unprecedented long-range O,N-acyl transfer. The rate of this transfer was pH- and temperature-dependent. To the best of our knowledge, this is the first time to show that a long-range O,N-acyl transfer could be exploited as a prodrug activation strategy to improve aqueous solubility. This type of prodrug may be applicable to other structures with spatially arranged hydroxyl amide to improve their aqueous solubility.
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Affiliation(s)
| | | | | | | | - Curtis E. Moore
- Department
of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Arnold L. Rheingold
- Department
of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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28
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Dissecting allosteric effects of activator-coactivator complexes using a covalent small molecule ligand. Proc Natl Acad Sci U S A 2014; 111:12061-6. [PMID: 25049401 DOI: 10.1073/pnas.1406033111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Allosteric binding events play a critical role in the formation and stability of transcriptional activator-coactivator complexes, perhaps in part due to the often intrinsically disordered nature of one or more of the constituent partners. The kinase-inducible domain interacting (KIX) domain of the master coactivator CREB binding protein/p300 is a conformationally dynamic domain that complexes with transcriptional activators at two discrete binding sites in allosteric communication. The complexation of KIX with the transcriptional activation domain of mixed-lineage leukemia protein leads to an enhancement of binding by the activation domain of CREB (phosphorylated kinase-inducible domain of CREB) to the second site. A transient kinetic analysis of the ternary complex formation aided by small molecule ligands that induce positive or negative cooperative binding reveals that positive cooperativity is largely governed by stabilization of the bound complex as indicated by a decrease in koff. Thus, this suggests the increased binding affinity for the second ligand is not due to an allosteric creation of a more favorable binding interface by the first ligand. This is consistent with data from us and from others indicating that the on rates of conformationally dynamic proteins approach the limits of diffusion. In contrast, negative cooperativity is manifested by alterations in both kon and koff, suggesting stabilization of the binary complex.
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29
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Abstract
The kinase-inducible domain interacting (KIX) domain of the CREB binding protein (CBP) is capable of simultaneously binding two intrinsically disordered transcription factors, such as the mixed-lineage leukemia (MLL) and c-Myb peptides, at isolated interaction sites. In vitro, the affinity for binding c-Myb is approximately doubled when KIX is in complex with MLL, which suggests a positive cooperative binding mechanism, and the affinity for MLL is also slightly increased when KIX is first bound by c-Myb. Expanding the scope of recent NMR and computational studies, we explore the allosteric mechanism at a detailed molecular level that directly connects the microscopic structural dynamics to the macroscopic shift in binding affinities. To this end, we have performed molecular dynamics simulations of free KIX, KIX-c-Myb, MLL-KIX, and MLL-KIX-c-Myb using a topology-based Gō-like model. Our results capture an increase in affinity for the peptide in the allosteric site when KIX is prebound by a complementary effector and both peptides follow an effector-independent folding-and-binding mechanism. More importantly, we discover that MLL binding lowers the entropic cost for c-Myb binding, and vice versa, by stabilizing the L12-G2 loop and the C-terminal region of the α3 helix on KIX. This work demonstrates the importance of entropy in allosteric signaling between promiscuous molecular recognition sites and can inform the rational design of small molecule stabilizers to target important regions of conformationally dynamic proteins.
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