1
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Stokes ME, Vasciaveo A, Small JC, Zask A, Reznik E, Smith N, Wang Q, Daniels J, Forouhar F, Rajbhandari P, Califano A, Stockwell BR. Subtype-selective prenylated isoflavonoids disrupt regulatory drivers of MYCN-amplified cancers. Cell Chem Biol 2024; 31:805-819.e9. [PMID: 38061356 PMCID: PMC11031350 DOI: 10.1016/j.chembiol.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 07/18/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
Transcription factors have proven difficult to target with small molecules because they lack pockets necessary for potent binding. Disruption of protein expression can suppress targets and enable therapeutic intervention. To this end, we developed a drug discovery workflow that incorporates cell-line-selective screening and high-throughput expression profiling followed by regulatory network analysis to identify compounds that suppress regulatory drivers of disease. Applying this approach to neuroblastoma (NBL), we screened bioactive molecules in cell lines representing its MYC-dependent (MYCNA) and mesenchymal (MES) subtypes to identify selective compounds, followed by PLATESeq profiling of treated cells. This revealed compounds that disrupt a sub-network of MYCNA-specific regulatory proteins, resulting in MYCN degradation in vivo. The top hit was isopomiferin, a prenylated isoflavonoid that inhibited casein kinase 2 (CK2) in cells. Isopomiferin and its structural analogs inhibited MYC and MYCN in NBL and lung cancer cells, highlighting the general MYC-inhibiting potential of this unique scaffold.
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Affiliation(s)
- Michael E Stokes
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Alessandro Vasciaveo
- Department of Systems Biology, Columbia University Medical Center, New York City, NY 10032, USA
| | - Jonnell Candice Small
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Arie Zask
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Eduard Reznik
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Nailah Smith
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Qian Wang
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Jacob Daniels
- Department of Pharmacology, Columbia University Medical Center, New York City, NY 10032, USA
| | - Farhad Forouhar
- Proteomics and Macromolecular Crystallography Shared Resource (PMCSR), Columbia University Medical Center, New York City, NY 10032, USA
| | - Presha Rajbhandari
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Medical Center, New York City, NY 10032, USA.
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York City, NY 10027, USA; Department of Chemistry, Columbia University, New York City, NY 10027, USA; Department of Pathology and Cell Biology and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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2
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Du Y, Taylor CG, Aukema HM, Zahradka P. PD146176 affects human EA.hy926 endothelial cell function by differentially modulating oxylipin production of LOX, COX and CYP epoxygenase. Biochim Biophys Acta Mol Cell Biol Lipids 2022; 1867:159156. [DOI: 10.1016/j.bbalip.2022.159156] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023]
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3
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Klein VG, Townsend CE, Testa A, Zengerle M, Maniaci C, Hughes SJ, Chan KH, Ciulli A, Lokey RS. Understanding and Improving the Membrane Permeability of VH032-Based PROTACs. ACS Med Chem Lett 2020; 11:1732-1738. [PMID: 32939229 PMCID: PMC7488288 DOI: 10.1021/acsmedchemlett.0c00265] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/30/2020] [Indexed: 01/03/2023] Open
Abstract
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Proteolysis targeting
chimeras (PROTACs) are catalytic heterobifunctional
molecules that can selectively degrade a protein of interest by recruiting
a ubiquitin E3 ligase to the target, leading to its ubiquitylation
and degradation by the proteasome. Most degraders lie outside the
chemical space associated with most membrane-permeable drugs. Although
many PROTACs have been described with potent activity in cells, our
understanding of the relationship between structure and permeability
in these compounds remains limited. Here, we describe a label-free
method for assessing the permeability of several VH032-based PROTACs
and their components by combining a parallel artificial membrane permeability
assay (PAMPA) and a lipophilic permeability efficiency (LPE) metric.
Our results show that the combination of these two cell-free membrane
permeability assays provides new insight into PROTAC structure–permeability
relationships and offers a conceptual framework for predicting the
physicochemical properties of PROTACs in order to better inform the
design of more permeable and more effective degraders.
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Affiliation(s)
- Victoria G. Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chad E. Townsend
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Andrea Testa
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Michael Zengerle
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Chiara Maniaci
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Scott J. Hughes
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Kwok-Ho Chan
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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4
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Design and Applications of Bifunctional Small Molecules in Biology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140534. [PMID: 32871274 DOI: 10.1016/j.bbapap.2020.140534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/17/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
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5
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Foley CA, Potjewyd F, Lamb KN, James LI, Frye SV. Assessing the Cell Permeability of Bivalent Chemical Degraders Using the Chloroalkane Penetration Assay. ACS Chem Biol 2020; 15:290-295. [PMID: 31846298 DOI: 10.1021/acschembio.9b00972] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bivalent chemical degraders provide a catalytic route to selectively degrade disease-associated proteins. By linking target-specific ligands with E3 ubiquitin ligase recruiting ligands, these compounds facilitate targeted protein ubiquitination and degradation by the proteasome. Due to the complexity of this multistep mechanism, the development of effective degrader molecules remains a difficult, lengthy, and unpredictable process. Since degraders are large heterobifunctional molecules, the efficacy of these compounds may be limited by poor cell permeability, and an efficient and reliable method to quantify the cell permeability of these compounds is lacking. Herein, we demonstrate that by the addition of a chloroalkane tag on the BRD4 specific degrader, MZ1, cell permeability can be quantified via the chloroalkane penetration assay. By extending this analysis to individual components of the degrader molecule, we have obtained structure-permeability relationships that will be informative for future degrader development, particularly as degraders move into the clinic as potential therapeutics.
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Affiliation(s)
- 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, North Carolina 27599, United States
| | - Frances 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, North Carolina 27599, United States
| | - Kelsey N. Lamb
- 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, North Carolina 27599, United States
| | - 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, North Carolina 27599, United States
| | - 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, North Carolina 27599, United States
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6
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Peraro L, Kritzer JA. Emerging Methods and Design Principles for Cell-Penetrant Peptides. Angew Chem Int Ed Engl 2018; 57:11868-11881. [PMID: 29740917 PMCID: PMC7184558 DOI: 10.1002/anie.201801361] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/24/2018] [Indexed: 12/12/2022]
Abstract
Biomolecules such as antibodies, proteins, and peptides are important tools for chemical biology and leads for drug development. They have been used to inhibit a variety of extracellular proteins, but accessing intracellular proteins has been much more challenging. In this review, we discuss diverse chemical approaches that have yielded cell-penetrant peptides and identify three distinct strategies: masking backbone amides, guanidinium group patterning, and amphipathic patterning. We summarize a growing number of large data sets, which are starting to reveal more specific design guidelines for each strategy. We also discuss advantages and disadvantages of current methods for quantifying cell penetration. Finally, we provide an overview of best-odds approaches for applying these new methods and design principles to optimize cytosolic penetration for a given bioactive peptide.
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Affiliation(s)
- Leila Peraro
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA
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7
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Peraro L, Kritzer JA. Neue Methoden und Designprinzipien für zellgängige Peptide. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801361] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Leila Peraro
- Department of Chemistry Tufts University Medford Massachusetts 02155 USA
| | - Joshua A. Kritzer
- Department of Chemistry Tufts University Medford Massachusetts 02155 USA
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8
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Matthes F, Massari S, Bochicchio A, Schorpp K, Schilling J, Weber S, Offermann N, Desantis J, Wanker E, Carloni P, Hadian K, Tabarrini O, Rossetti G, Krauss S. Reducing Mutant Huntingtin Protein Expression in Living Cells by a Newly Identified RNA CAG Binder. ACS Chem Neurosci 2018; 9:1399-1408. [PMID: 29506378 DOI: 10.1021/acschemneuro.8b00027] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Expanded CAG trinucleotide repeats in Huntington's disease (HD) are causative for neurotoxicity. The mutant CAG repeat RNA encodes neurotoxic polyglutamine proteins and can lead to a toxic gain of function by aberrantly recruiting RNA-binding proteins. One of these is the MID1 protein, which induces aberrant Huntingtin (HTT) protein translation upon binding. Here we have identified a set of CAG repeat binder candidates by in silico methods. One of those, furamidine, reduces the level of binding of HTT mRNA to MID1 and other target proteins in vitro. Metadynamics calculations, fairly consistent with experimental data measured here, provide hints about the binding mode of the ligand. Importantly, furamidine also decreases the protein level of HTT in a HD cell line model. This shows that small molecules masking RNA-MID1 interactions may be active against mutant HTT protein in living cells.
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Affiliation(s)
- Frank Matthes
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Strasse 27, 53127 Bonn, Germany
| | - Serena Massari
- Department of Pharmaceutical Science, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Anna Bochicchio
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Kenji Schorpp
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München für Gesundheit und Umwelt, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Judith Schilling
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Strasse 27, 53127 Bonn, Germany
| | - Stephanie Weber
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Strasse 27, 53127 Bonn, Germany
| | - Nina Offermann
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Strasse 27, 53127 Bonn, Germany
| | - Jenny Desantis
- Department of Pharmaceutical Science, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Erich Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
- JARA-HPC, Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Kamyar Hadian
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München für Gesundheit und Umwelt, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Oriana Tabarrini
- Department of Pharmaceutical Science, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, 52425 Jülich, Germany
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Sybille Krauss
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Strasse 27, 53127 Bonn, Germany
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9
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Development and validation of a high-performance liquid chromatography method for the quantitation of intracellular PARP inhibitor Olaparib in cancer cells. J Pharm Biomed Anal 2018; 152:74-80. [DOI: 10.1016/j.jpba.2018.01.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/12/2018] [Accepted: 01/17/2018] [Indexed: 12/22/2022]
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10
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Vergaro V, Civallero M, Citti C, Cosenza M, Baldassarre F, Cannazza G, Pozzi S, Sacchi S, Fanizzi FP, Ciccarella G. Cell-Penetrating CaCO₃ Nanocrystals for Improved Transport of NVP-BEZ235 across Membrane Barrier in T-Cell Lymphoma. Cancers (Basel) 2018; 10:E31. [PMID: 29370086 PMCID: PMC5836063 DOI: 10.3390/cancers10020031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/15/2018] [Accepted: 01/19/2018] [Indexed: 12/14/2022] Open
Abstract
Owing to their nano-sized porous structure, CaCO₃ nanocrystals (CaCO₃NCs) hold the promise to be utilized as desired materials for encapsulating molecules which demonstrate wide promise in drug delivery. We evaluate the possibility to encapsulate and release NVP-BEZ235, a novel and potent dual PI3K/mTOR inhibitor that is currently in phase I/II clinical trials for advanced solid tumors, from the CaCO₃NCs. Its chemical nature shows some intrinsic limitations which induce to administer high doses leading to toxicity; to overcome these problems, here we proposed a strategy to enhance its intracellular penetration and its biological activity. Pristine CaCO₃ NCs biocompatibility, cell interactions and internalization in in vitro experiments on T-cell lymphoma line, were studied. Confocal microscopy was used to monitor NCs-cell interactions and cellular uptake. We have further investigated the interaction nature and release mechanism of drug loaded/released within/from the NCs using an alternative approach based on liquid chromatography coupled to mass spectrometry. Our approach provides a good loading efficiency, therefore this drug delivery system was validated for biological activity in T-cell lymphoma: the anti-proliferative test and western blot results are very interesting because the proposed nano-formulation has an efficiency higher than free drug at the same nominal concentration.
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Affiliation(s)
- Viviana Vergaro
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento & UdR INSTM di Lecce, Campus Universitario, Via Monteroni, 73100 Lecce, Italy.
| | - Monica Civallero
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Università di Modena & Reggio Emilia, via Campi 287, 41125 Modena, Italy.
| | - Cinzia Citti
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
- CNR NANOTEC-Istituto di Nanotecnologia c/o Campus Ecotekne, Università del Salento, Via Monteroni, 73100 Lecce, Italy.
| | - Maria Cosenza
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Università di Modena & Reggio Emilia, via Campi 287, 41125 Modena, Italy.
| | - Francesca Baldassarre
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento & UdR INSTM di Lecce, Campus Universitario, Via Monteroni, 73100 Lecce, Italy.
- CNR NANOTEC-Istituto di Nanotecnologia c/o Campus Ecotekne, Università del Salento, Via Monteroni, 73100 Lecce, Italy.
| | - Giuseppe Cannazza
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
- CNR NANOTEC-Istituto di Nanotecnologia c/o Campus Ecotekne, Università del Salento, Via Monteroni, 73100 Lecce, Italy.
| | - Samantha Pozzi
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Università di Modena & Reggio Emilia, via Campi 287, 41125 Modena, Italy.
| | - Stefano Sacchi
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Università di Modena & Reggio Emilia, via Campi 287, 41125 Modena, Italy.
| | - Francesco Paolo Fanizzi
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, Via Monteroni, 73100 Lecce, Italy.
| | - Giuseppe Ciccarella
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento & UdR INSTM di Lecce, Campus Universitario, Via Monteroni, 73100 Lecce, Italy.
- CNR NANOTEC-Istituto di Nanotecnologia c/o Campus Ecotekne, Università del Salento, Via Monteroni, 73100 Lecce, Italy.
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11
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Welsch ME, Kaplan A, Chambers JM, Stokes ME, Bos PH, Zask A, Zhang Y, Sanchez-Martin M, Badgley MA, Huang CS, Tran TH, Akkiraju H, Brown LM, Nandakumar R, Cremers S, Yang WS, Tong L, Olive KP, Ferrando A, Stockwell BR. Multivalent Small-Molecule Pan-RAS Inhibitors. Cell 2017; 168:878-889.e29. [PMID: 28235199 DOI: 10.1016/j.cell.2017.02.006] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 10/23/2016] [Accepted: 02/01/2017] [Indexed: 12/30/2022]
Abstract
Design of small molecules that disrupt protein-protein interactions, including the interaction of RAS proteins and their effectors, may provide chemical probes and therapeutic agents. We describe here the synthesis and testing of potential small-molecule pan-RAS ligands, which were designed to interact with adjacent sites on the surface of oncogenic KRAS. One compound, termed 3144, was found to bind to RAS proteins using microscale thermophoresis, nuclear magnetic resonance spectroscopy, and isothermal titration calorimetry and to exhibit lethality in cells partially dependent on expression of RAS proteins. This compound was metabolically stable in liver microsomes and displayed anti-tumor activity in xenograft mouse cancer models. These findings suggest that pan-RAS inhibition may be an effective therapeutic strategy for some cancers and that structure-based design of small molecules targeting multiple adjacent sites to create multivalent inhibitors may be effective for some proteins.
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Affiliation(s)
- Matthew E Welsch
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Anna Kaplan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Jennifer M Chambers
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Michael E Stokes
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Pieter H Bos
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Arie Zask
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Yan Zhang
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Marta Sanchez-Martin
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA
| | - Michael A Badgley
- Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Division of Digestive and Liver Diseases in the Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Christine S Huang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Timothy H Tran
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Hemanth Akkiraju
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY 10027, USA
| | - Lewis M Brown
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY 10027, USA
| | - Renu Nandakumar
- Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY 10032, USA
| | - Serge Cremers
- Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY 10032, USA
| | - Wan Seok Yang
- Department of Biological Sciences, St. John's University, Queens, NY 11439, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Kenneth P Olive
- Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Division of Digestive and Liver Diseases in the Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA; Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Brent R Stockwell
- Department of Chemistry, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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12
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Teuscher KB, Zhang M, Ji H. A Versatile Method to Determine the Cellular Bioavailability of Small-Molecule Inhibitors. J Med Chem 2017; 60:157-169. [PMID: 27935314 PMCID: PMC7771553 DOI: 10.1021/acs.jmedchem.6b00923] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The determination of the cellular bioavailability of small-molecule inhibitors is a critical step for interpreting cell-based data and guiding inhibitor optimization. Herein, a HPLC-MS based protocol was developed to determine inhibitor cellular bioavailability. This generalizable protocol allows determination of the accurate intracellular concentrations and characterization of various properties of inhibitors including the extra- and intracellular stability, the dose- and time-dependence of the intracellular concentrations, the cell permeability, and the nonspecific binding with the cell culture plates, the extracellular matrices, and the cell membrane. The inhibitors of the protein-protein interactions, bromodomains, and the β-catenin/B-cell lymphoma 9 (BCL9) interaction were used to examine the protocol, and the cellular bioavailability of the inhibitors in cancer cells was determined. High nonspecific binding and low cellular uptake were observed for two bromodomain inhibitors. The two β-catenin/BCL9 inhibitors had low nonspecific binding but different cellular uptake. These inhibitors exhibited different stability kinetics in cells.
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Affiliation(s)
- Kevin B Teuscher
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612-9416, United States.,Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Min Zhang
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612-9416, United States
| | - Haitao Ji
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612-9416, United States.,Department of Oncologic Sciences, University of South Florida College of Medicine , Tampa, Florida 33612, United States.,Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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13
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Hoggard LR, Zhang Y, Zhang M, Panic V, Wisniewski JA, Ji H. Rational design of selective small-molecule inhibitors for β-catenin/B-cell lymphoma 9 protein-protein interactions. J Am Chem Soc 2015; 137:12249-60. [PMID: 26352795 DOI: 10.1021/jacs.5b04988] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Selective inhibition of α-helix-mediated protein-protein interactions (PPIs) with small organic molecules provides great potential for the discovery of chemical probes and therapeutic agents. Protein Data Bank data mining using the HippDB database indicated that (1) the side chains of hydrophobic projecting hot spots at positions i, i + 3, and i + 7 of an α-helix had few orientations when interacting with the second protein and (2) the hot spot pockets of PPI complexes had different sizes, shapes, and chemical groups when interacting with the same hydrophobic projecting hot spots of α-helix. On the basis of these observations, a small organic molecule, 4'-fluoro-N-phenyl-[1,1'-biphenyl]-3-carboxamide, was designed as a generic scaffold that itself directly mimics the binding mode of the side chains of hydrophobic projecting hot spots at positions i, i + 3, and i + 7 of an α-helix. Convenient decoration of this generic scaffold led to the selective disruption of α-helix-mediated PPIs. A series of small-molecule inhibitors selective for β-catenin/B-cell lymphoma 9 (BCL9) over β-catenin/cadherin PPIs was designed and synthesized. The binding mode of new inhibitors was characterized by site-directed mutagenesis and structure-activity relationship studies. This new class of inhibitors can selectively disrupt β-catenin/BCL9 over β-catenin/cadherin PPIs, suppress the transactivation of canonical Wnt signaling, downregulate the expression of Wnt target genes, and inhibit the growth of Wnt/β-catenin-dependent cancer cells.
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Affiliation(s)
- Logan R Hoggard
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Yongqiang Zhang
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Min Zhang
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Vanja Panic
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - John A Wisniewski
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Haitao Ji
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
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Gordon LJ, Allen M, Artursson P, Hann MM, Leavens BJ, Mateus A, Readshaw S, Valko K, Wayne GJ, West A. Direct Measurement of Intracellular Compound Concentration by RapidFire Mass Spectrometry Offers Insights into Cell Permeability. ACTA ACUST UNITED AC 2015; 21:156-64. [DOI: 10.1177/1087057115604141] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/06/2015] [Indexed: 11/16/2022]
Abstract
One of the key challenges facing early stage drug discovery is understanding the commonly observed difference between the activity of compounds in biochemical assays and cellular assays. Traditionally, indirect or estimated cell permeability measurements such as estimations from logP or artificial membrane permeability are used to explain the differences. The missing link is a direct measurement of intracellular compound concentration in whole cells. This can, in some circumstances, be estimated from the cellular activity, but this may also be problematic if cellular activity is weak or absent. Advances in sensitivity and throughput of analytical techniques have enabled us to develop a high-throughput assay for the measurement of intracellular compound concentration for routine use to support lead optimization. The assay uses a RapidFire-MS based readout of compound concentration in HeLa cells following incubation of cells with test compound. The initial assay validation was performed by ultra-high performance liquid chromatography tandem mass spectrometry, and the assay was subsequently transferred to RapidFire tandem mass spectrometry. Further miniaturization and optimization were performed to streamline the process, increase sample throughput, and reduce cycle time. This optimization has delivered a semi-automated platform with the potential of production scale compound profiling up to 100 compounds per day.
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Affiliation(s)
- Laurie J. Gordon
- Department of Biological Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - Morven Allen
- Department of Biological Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP) at Chemical Biology Consortium, Uppsala, Sweden
| | - Michael M. Hann
- Department of Chemical Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - Bill J. Leavens
- Department of Chemical Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - André Mateus
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Simon Readshaw
- Department of Chemical Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - Klara Valko
- Department of Chemical Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - Gareth J. Wayne
- Department of Target and Pathway Validation, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
| | - Andy West
- Department of Chemical Sciences, Molecular Discovery Research, GlaxoSmithKline, Stevenage, UK
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15
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Hann MM, Simpson GL. Intracellular drug concentration and disposition – The missing link? Methods 2014; 68:283-5. [DOI: 10.1016/j.ymeth.2014.05.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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16
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Hepatitis C NS5B polymerase inhibitors: Functional equivalents for the benzothiadiazine moiety. Bioorg Med Chem Lett 2011; 21:1876-9. [DOI: 10.1016/j.bmcl.2010.12.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 12/09/2010] [Accepted: 12/15/2010] [Indexed: 11/19/2022]
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