1
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Harnden A, Davis OA, Box GM, Hayes A, Johnson LD, Henley AT, de Haven Brandon AK, Valenti M, Cheung KMJ, Brennan A, Huckvale R, Pierrat OA, Talbot R, Bright MD, Akpinar HA, Miller DSJ, Tarantino D, Gowan S, de Klerk S, McAndrew PC, Le Bihan YV, Meniconi M, Burke R, Kirkin V, van Montfort RLM, Raynaud FI, Rossanese OW, Bellenie BR, Hoelder S. Discovery of an In Vivo Chemical Probe for BCL6 Inhibition by Optimization of Tricyclic Quinolinones. J Med Chem 2023; 66:5892-5906. [PMID: 37026591 PMCID: PMC10150366 DOI: 10.1021/acs.jmedchem.3c00155] [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: 01/27/2023] [Indexed: 04/08/2023]
Abstract
B-cell lymphoma 6 (BCL6) is a transcriptional repressor and oncogenic driver of diffuse large B-cell lymphoma (DLBCL). Here, we report the optimization of our previously reported tricyclic quinolinone series for the inhibition of BCL6. We sought to improve the cellular potency and in vivo exposure of the non-degrading isomer, CCT373567, of our recently published degrader, CCT373566. The major limitation of our inhibitors was their high topological polar surface areas (TPSA), leading to increased efflux ratios. Reducing the molecular weight allowed us to remove polarity and decrease TPSA without considerably reducing solubility. Careful optimization of these properties, as guided by pharmacokinetic studies, led to the discovery of CCT374705, a potent inhibitor of BCL6 with a good in vivo profile. Modest in vivo efficacy was achieved in a lymphoma xenograft mouse model after oral dosing.
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Affiliation(s)
- Alice
C. Harnden
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Owen A. Davis
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Gary M. Box
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Angela Hayes
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Louise D. Johnson
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Alan T. Henley
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Alexis K. de Haven Brandon
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Melanie Valenti
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Kwai-Ming J. Cheung
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Alfie Brennan
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rosemary Huckvale
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Olivier A. Pierrat
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rachel Talbot
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Michael D. Bright
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Hafize Aysin Akpinar
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Daniel S. J. Miller
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Dalia Tarantino
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Sharon Gowan
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Selby de Klerk
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Peter Craig McAndrew
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Yann-Vaï Le Bihan
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Mirco Meniconi
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rosemary Burke
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Vladimir Kirkin
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rob L. M. van Montfort
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Florence I. Raynaud
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Olivia W. Rossanese
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Benjamin R. Bellenie
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Swen Hoelder
- Centre
for Cancer Drug Discovery and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
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2
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Ackloo S, Antolin AA, Bartolome JM, Beck H, Bullock A, Betz UAK, Böttcher J, Brown PJ, Chaturvedi M, Crisp A, Daniels D, Dreher J, Edfeldt K, Edwards AM, Egner U, Elkins J, Fischer C, Glendorf T, Goldberg S, Hartung IV, Hillisch A, Homan E, Knapp S, Köster M, Krämer O, Llaveria J, Lessel U, Lindemann S, Linderoth L, Matsui H, Michel M, Montel F, Mueller-Fahrnow A, Müller S, Owen DR, Saikatendu KS, Santhakumar V, Sanderson W, Scholten C, Schapira M, Sharma S, Shireman B, Sundström M, Todd MH, Tredup C, Venable J, Willson TM, Arrowsmith CH. Target 2035 – an update on private sector contributions. RSC Med Chem 2023. [DOI: 10.1039/d2md00441k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Target 2035, an international federation of biomedical scientists from the public and private sectors, is leveraging ‘open’ principles to develop a pharmacological tool for every human protein.
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Affiliation(s)
- Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Albert A. Antolin
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | | | - Hartmut Beck
- Research and Development, Bayer AG, Pharmaceuticals, 42103 Wuppertal, Germany
| | - Alex Bullock
- Center for Medicines Discovery, Old Road Campus, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | | | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Peter J. Brown
- Structural Genomics Consortium, University of North Carolina at Chapel Hill, USA
| | - Menorca Chaturvedi
- Boehringer Ingelheim International, Binger Str. 173, D-55216 Ingelheim, Germany
| | - Alisa Crisp
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Danette Daniels
- Foghorn Therapeutics, 500 Technology Square, Suite 700, Cambridge, MA 02139, USA
| | - Jan Dreher
- Research and Development, Bayer AG, Pharmaceuticals, 42103 Wuppertal, Germany
| | - Kristina Edfeldt
- Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Aled M. Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Ursula Egner
- Nuvisan Innovation Campus Berlin GmbH, Müllerstraße 178, 13353, Berlin, Germany
| | - Jon Elkins
- Center for Medicines Discovery, Old Road Campus, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Christian Fischer
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, USA
| | - Tine Glendorf
- Research & Early Development, Novo Nordisk A/S, Måløv, Denmark
| | - Steven Goldberg
- Janssen Research and Development LLC, San Diego, California, USA
| | - Ingo V. Hartung
- Medicinal Chemistry, Global R&D, Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Alexander Hillisch
- Research and Development, Bayer AG, Pharmaceuticals, 42103 Wuppertal, Germany
| | - Evert Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Markus Köster
- Boehringer Ingelheim International, Binger Str. 173, D-55216 Ingelheim, Germany
| | - Oliver Krämer
- Boehringer Ingelheim International, Binger Str. 173, D-55216 Ingelheim, Germany
| | - Josep Llaveria
- A Division of Janssen-Cilag S.A., Janssen Research and Development, Toledo, Spain
| | - Uta Lessel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, D-88397 Biberach an der Riss, Germany
| | | | - Lars Linderoth
- Research & Early Development, Novo Nordisk A/S, Måløv, Denmark
| | - Hisanori Matsui
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Maurice Michel
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Florian Montel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, D-88397 Biberach an der Riss, Germany
| | | | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Dafydd R. Owen
- Discovery Network Group, Pfizer Medicine Design, Cambridge, MA 02139, USA
| | - Kumar Singh Saikatendu
- Global Research Externalization, Takeda California, Inc., 9625 Towne Center Drive, San Diego, CA 92121, USA
| | | | - Wendy Sanderson
- Janssen Research & Development, Janssen Pharmaceutica N. V, Beerse, Belgium
| | - Cora Scholten
- Research and Development, Bayer AG, Pharmaceuticals, 13353 Berlin, Germany
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sujata Sharma
- Janssen Research and Development LLC, San Diego, California, USA
| | - Brock Shireman
- Janssen Research and Development LLC, San Diego, California, USA
| | - Michael Sundström
- Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Matthew H. Todd
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Claudia Tredup
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Jennifer Venable
- Janssen Research and Development LLC, San Diego, California, USA
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, M5G 1L7, Canada
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3
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Gu H, He J, Li Y, Mi D, Guan T, Guo W, Liu B, Chen Y. B-cell Lymphoma 6 Inhibitors: Current Advances and Prospects of Drug Development for Diffuse Large B-cell Lymphomas. J Med Chem 2022; 65:15559-15583. [PMID: 36441945 DOI: 10.1021/acs.jmedchem.2c01433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
B-cell lymphoma 6 (BCL6) is a transcriptional repressor that regulates the differentiation of B lymphocytes and mediates the formation of germinal centers (GCs) by recruiting corepressors through the BTB domain of BCL6. Physiological processes regulated by BCL6 involve cell activation, differentiation, DNA damage, and apoptosis. BCL6 is highly expressed when the gene is mutated, leading to the malignant proliferation of cells and drives tumorigenesis. BCL6 overexpression is closely correlated with tumorigenesis in diffuse large B-cell lymphoma (DLBCL) and other lymphomas, and BCL6 inhibitors can effectively inhibit some lymphomas and overcome resistance. Therefore, targeting BCL6 might be a promising therapeutic strategy for treating lymphomas. Herein, we comprehensively review the latest development of BCL6 inhibitors in diffuse large B-cell lymphoma and discuss the overview of the pharmacophores of BCL6 inhibitors and their efficacies in vitro and in vivo. Additionally, the current advances in BCL6 degraders are provided.
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Affiliation(s)
- Haijun Gu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jia He
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yuzhan Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Dazhao Mi
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Tian Guan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Weikai Guo
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Bo Liu
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yihua Chen
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
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4
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Karimi S, Shahabi F, Mubarak SMH, Arjmandi H, Hashemi ZS, Pourzardosht N, Zakeri A, Mahboobi M, Jahangiri A, Rahbar MR, Khalili S. Impact of SNPs, off-targets, and passive permeability on efficacy of BCL6 degrading drugs assigned by virtual screening and 3D-QSAR approach. Sci Rep 2022; 12:21091. [PMID: 36473934 PMCID: PMC9726907 DOI: 10.1038/s41598-022-25587-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
B-cell lymphoma 6 (BCL6) regulates various genes and is reported to be overexpressed in lymphomas and other malignancies. Thus, BCL6 inhibition or its tagging for degradation would be an amenable therapeutic approach. A library of 2500 approved drugs was employed to find BCL6 inhibitory molecules via virtual screening. Moreover, the 3D core structure of 170 BCL6 inhibitors was used to build a 3D QSAR model and predict the biological activity. The SNP database was analyzed to study the impact on the destabilization of BCL6/drug interactions. Structural similarity search and molecular docking analyses were used to assess the interaction between possible off-targets and BCL6 inhibitors. The tendency of drugs for passive membrane permeability was also analyzed. Lifitegrast (DB11611) had favorable binding properties and biological activity compared to the BI-3802. Missense SNPs were located at the essential interaction sites of the BCL6. Structural similarity search resulted in five BTB-domain containing off-target proteins. BI-3802 and Lifitegrast had similar chemical behavior and binding properties against off-target candidates. More interestingly, the binding affinity of BI-3802 (against off-targets) was higher than Lifitegrast. Energetically, Lifitegrast was less favorable for passive membrane permeability. The interaction between BCL6 and BI-3802 is more prone to SNP-derived variations. On the other hand, higher nonspecific binding of BI-3802 to off-target proteins could bring about higher undesirable properties. It should also be noted that energetically less desirable passive membrane translocation of Lifitegrast would demand drug delivery vehicles. However, further empirical evaluation of Lifitegrast would unveil its true potential.
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Affiliation(s)
- Solmaz Karimi
- grid.419305.a0000 0001 1943 2944Laboratory of Mitochondrial Biology and Metabolism, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Farzaneh Shahabi
- grid.411747.00000 0004 0418 0096Faculty of Advanced Technologies in Medical Sciences, Golestan University of Medical Sciences, Gorgan, Iran
| | - Shaden M. H. Mubarak
- grid.442852.d0000 0000 9836 5198Department of Clinical Laboratory Science, Faculty of Pharmacy, University of Kufa, Najaf, Iraq
| | - Hanie Arjmandi
- grid.467532.10000 0004 4912 2930Faculty of Pharmacy, Islamic Azad University of Amol Branch, Amol, Iran
| | - Zahra Sadat Hashemi
- grid.417689.5ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Navid Pourzardosht
- grid.411874.f0000 0004 0571 1549Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran
| | - Alireza Zakeri
- grid.440791.f0000 0004 0385 049XDepartment of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Mahdieh Mahboobi
- grid.411521.20000 0000 9975 294XApplied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Abolfazl Jahangiri
- grid.411521.20000 0000 9975 294XApplied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Rahbar
- grid.412571.40000 0000 8819 4698Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Khalili
- grid.440791.f0000 0004 0385 049XDepartment of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
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5
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Increased slow dynamics defines ligandability of BTB domains. Nat Commun 2022; 13:6989. [PMID: 36384931 PMCID: PMC9668832 DOI: 10.1038/s41467-022-34599-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
Efficient determination of protein ligandability, or the propensity to bind small-molecules, would greatly facilitate drug development for novel targets. Ligandability is currently assessed using computational methods that typically consider the static structural properties of putative binding sites or by experimental fragment screening. Here, we evaluate ligandability of conserved BTB domains from the cancer-relevant proteins LRF, KAISO, and MIZ1. Using fragment screening, we discover that MIZ1 binds multiple ligands. However, no ligands are uncovered for the structurally related KAISO or LRF. To understand the principles governing ligand-binding by BTB domains, we perform comprehensive NMR-based dynamics studies and find that only the MIZ1 BTB domain exhibits backbone µs-ms time scale motions. Interestingly, residues with elevated dynamics correspond to the binding site of fragment hits and recently defined HUWE1 interaction site. Our data argue that examining protein dynamics using NMR can contribute to identification of cryptic binding sites, and may support prediction of the ligandability of novel challenging targets.
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6
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Pierrat OA, Liu M, Collie GW, Shetty K, Rodrigues MJ, Le Bihan YV, Gunnell EA, McAndrew PC, Stubbs M, Rowlands MG, Yahya N, Shehu E, Talbot R, Pickard L, Bellenie BR, Cheung KMJ, Drouin L, Innocenti P, Woodward H, Davis OA, Lloyd MG, Varela A, Huckvale R, Broccatelli F, Carter M, Galiwango D, Hayes A, Raynaud FI, Bryant C, Whittaker S, Rossanese OW, Hoelder S, Burke R, van Montfort RLM. Discovering cell-active BCL6 inhibitors: effectively combining biochemical HTS with multiple biophysical techniques, X-ray crystallography and cell-based assays. Sci Rep 2022; 12:18633. [PMID: 36329085 PMCID: PMC9633773 DOI: 10.1038/s41598-022-23264-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
By suppressing gene transcription through the recruitment of corepressor proteins, B-cell lymphoma 6 (BCL6) protein controls a transcriptional network required for the formation and maintenance of B-cell germinal centres. As BCL6 deregulation is implicated in the development of Diffuse Large B-Cell Lymphoma, we sought to discover novel small molecule inhibitors that disrupt the BCL6-corepressor protein-protein interaction (PPI). Here we report our hit finding and compound optimisation strategies, which provide insight into the multi-faceted orthogonal approaches that are needed to tackle this challenging PPI with small molecule inhibitors. Using a 1536-well plate fluorescence polarisation high throughput screen we identified multiple hit series, which were followed up by hit confirmation using a thermal shift assay, surface plasmon resonance and ligand-observed NMR. We determined X-ray structures of BCL6 bound to compounds from nine different series, enabling a structure-based drug design approach to improve their weak biochemical potency. We developed a time-resolved fluorescence energy transfer biochemical assay and a nano bioluminescence resonance energy transfer cellular assay to monitor cellular activity during compound optimisation. This workflow led to the discovery of novel inhibitors with respective biochemical and cellular potencies (IC50s) in the sub-micromolar and low micromolar range.
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Affiliation(s)
- Olivier A Pierrat
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Manjuan Liu
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Gavin W Collie
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Kartika Shetty
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Matthew J Rodrigues
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Yann-Vaï Le Bihan
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Emma A Gunnell
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - P Craig McAndrew
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Mark Stubbs
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Martin G Rowlands
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Norhakim Yahya
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Erald Shehu
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Rachel Talbot
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Lisa Pickard
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Benjamin R Bellenie
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Kwai-Ming J Cheung
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ludovic Drouin
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Paolo Innocenti
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Hannah Woodward
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Owen A Davis
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Matthew G Lloyd
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ana Varela
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Rosemary Huckvale
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Fabio Broccatelli
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Michael Carter
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - David Galiwango
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Angela Hayes
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Florence I Raynaud
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Christopher Bryant
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Steven Whittaker
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Olivia W Rossanese
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Swen Hoelder
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Rosemary Burke
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Rob L M van Montfort
- Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK.
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK.
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7
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Davis OA, Cheung KMJ, Brennan A, Lloyd MG, Rodrigues MJ, Pierrat OA, Collie GW, Le Bihan YV, Huckvale R, Harnden AC, Varela A, Bright MD, Eve P, Hayes A, Henley AT, Carter MD, McAndrew PC, Talbot R, Burke R, van Montfort RLM, Raynaud FI, Rossanese OW, Meniconi M, Bellenie BR, Hoelder S. Optimizing Shape Complementarity Enables the Discovery of Potent Tricyclic BCL6 Inhibitors. J Med Chem 2022; 65:8169-8190. [PMID: 35657291 PMCID: PMC9234963 DOI: 10.1021/acs.jmedchem.1c02174] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 11/30/2022]
Abstract
To identify new chemical series with enhanced binding affinity to the BTB domain of B-cell lymphoma 6 protein, we targeted a subpocket adjacent to Val18. With no opportunities for strong polar interactions, we focused on attaining close shape complementarity by ring fusion onto our quinolinone lead series. Following exploration of different sized rings, we identified a conformationally restricted core which optimally filled the available space, leading to potent BCL6 inhibitors. Through X-ray structure-guided design, combined with efficient synthetic chemistry to make the resulting novel core structures, a >300-fold improvement in activity was obtained by the addition of seven heavy atoms.
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Affiliation(s)
- Owen A. Davis
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Kwai-Ming J. Cheung
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Alfie Brennan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Matthew G. Lloyd
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Matthew J. Rodrigues
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
- Division
of Structural Biology, The Institute of
Cancer Research, London SM2 5NG, U.K..
| | - Olivier A. Pierrat
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Gavin W. Collie
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
- Division
of Structural Biology, The Institute of
Cancer Research, London SM2 5NG, U.K..
| | - Yann-Vaï Le Bihan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
- Division
of Structural Biology, The Institute of
Cancer Research, London SM2 5NG, U.K..
| | - Rosemary Huckvale
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Alice C. Harnden
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Ana Varela
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Michael D. Bright
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Paul Eve
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Angela Hayes
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Alan T. Henley
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Michael D. Carter
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - P. Craig McAndrew
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Rachel Talbot
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Rosemary Burke
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Rob L. M. van Montfort
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
- Division
of Structural Biology, The Institute of
Cancer Research, London SM2 5NG, U.K..
| | - Florence I. Raynaud
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Olivia W. Rossanese
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Mirco Meniconi
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Benjamin R. Bellenie
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
| | - Swen Hoelder
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K..
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8
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Huckvale R, Harnden AC, Cheung KMJ, Pierrat OA, Talbot R, Box GM, Henley AT, de Haven Brandon AK, Hallsworth AE, Bright MD, Akpinar HA, Miller DSJ, Tarantino D, Gowan S, Hayes A, Gunnell EA, Brennan A, Davis OA, Johnson LD, de Klerk S, McAndrew C, Le Bihan YV, Meniconi M, Burke R, Kirkin V, van Montfort RLM, Raynaud FI, Rossanese OW, Bellenie BR, Hoelder S. Improved Binding Affinity and Pharmacokinetics Enable Sustained Degradation of BCL6 In Vivo. J Med Chem 2022; 65:8191-8207. [PMID: 35653645 PMCID: PMC9234961 DOI: 10.1021/acs.jmedchem.1c02175] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 11/30/2022]
Abstract
The transcriptional repressor BCL6 is an oncogenic driver found to be deregulated in lymphoid malignancies. Herein, we report the optimization of our previously reported benzimidazolone molecular glue-type degrader CCT369260 to CCT373566, a highly potent probe suitable for sustained depletion of BCL6 in vivo. We observed a sharp degradation SAR, where subtle structural changes conveyed the ability to induce degradation of BCL6. CCT373566 showed modest in vivo efficacy in a lymphoma xenograft mouse model following oral dosing.
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Affiliation(s)
- Rosemary Huckvale
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Alice C. Harnden
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Kwai-Ming J. Cheung
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Olivier A. Pierrat
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rachel Talbot
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Gary M. Box
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Alan T. Henley
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | | | - Albert E. Hallsworth
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Michael D. Bright
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Hafize Aysin Akpinar
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Daniel S. J. Miller
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Dalia Tarantino
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Sharon Gowan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Angela Hayes
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Emma A. Gunnell
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
- Division
of Structural Biology, The Institute of
Cancer Research, London SM2 5NG, U.K.
| | - Alfie Brennan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Owen A. Davis
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Louise D. Johnson
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Selby de Klerk
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Craig McAndrew
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Yann-Vaï Le Bihan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
- Division
of Structural Biology, The Institute of
Cancer Research, London SM2 5NG, U.K.
| | - Mirco Meniconi
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rosemary Burke
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Vladimir Kirkin
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rob L. M. van Montfort
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
- Division
of Structural Biology, The Institute of
Cancer Research, London SM2 5NG, U.K.
| | - Florence I. Raynaud
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Olivia W. Rossanese
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Benjamin R. Bellenie
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Swen Hoelder
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
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9
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Pei H, Guo W, Peng Y, Xiong H, Chen Y. Targeting key proteins involved in transcriptional regulation for cancer therapy: Current strategies and future prospective. Med Res Rev 2022; 42:1607-1660. [PMID: 35312190 DOI: 10.1002/med.21886] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/10/2022] [Accepted: 02/22/2022] [Indexed: 12/14/2022]
Abstract
The key proteins involved in transcriptional regulation play convergent roles in cellular homeostasis, and their dysfunction mediates aberrant gene expressions that underline the hallmarks of tumorigenesis. As tumor progression is dependent on such abnormal regulation of transcription, it is important to discover novel chemical entities as antitumor drugs that target key tumor-associated proteins involved in transcriptional regulation. Despite most key proteins (especially transcription factors) involved in transcriptional regulation are historically recognized as undruggable targets, multiple targeting approaches at diverse levels of transcriptional regulation, such as epigenetic intervention, inhibition of DNA-binding of transcriptional factors, and inhibition of the protein-protein interactions (PPIs), have been established in preclinically or clinically studies. In addition, several new approaches have recently been described, such as targeting proteasomal degradation and eliciting synthetic lethality. This review will emphasize on accentuating these developing therapeutic approaches and provide a thorough conspectus of the drug development to target key proteins involved in transcriptional regulation and their impact on future oncotherapy.
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Affiliation(s)
- Haixiang Pei
- Institute for Advanced Study, Shenzhen University and Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China.,Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Weikai Guo
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China.,Joint National Laboratory for Antibody Drug Engineering, School of Basic Medical Science, Henan University, Kaifeng, China
| | - Yangrui Peng
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Hai Xiong
- Institute for Advanced Study, Shenzhen University and Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
| | - Yihua Chen
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
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10
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Xing Y, Guo W, Wu M, Xie J, Huang D, Hu P, Zhou M, Zhang L, Zhang Q, Wang P, Wang X, Wang G, Wu H, Zhou C, Chen Y, Liu M, Yi Z, Sun Z. An orally available small molecule BCL6 inhibitor effectively suppresses diffuse large B cell lymphoma cells growth in vitro and in vivo. Cancer Lett 2022; 529:100-111. [PMID: 34990752 DOI: 10.1016/j.canlet.2021.12.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 12/18/2022]
Abstract
The transcription factor B cell lymphoma 6 (BCL6) is an oncogenic driver of diffuse large B cell lymphoma (DLBCL) and mediates lymphomagenesis through transcriptional repression of its target genes by recruiting corepressors to its N-terminal broad-complex/tramtrack/bric-a-brac (BTB) domain. Blocking the protein-protein interactions of BCL6 and its corepressors has been proposed as an effective approach for the treatment of DLBCL. However, BCL6 inhibitors with excellent drug-like properties are rare. Hence, the development of BCL6 inhibitors is worth pursuing. We screened our internal chemical library by luciferase reporter assay and Homogenous Time Resolved Fluorescence (HTRF) assay and a small molecule compound named WK500B was identified. WK500B engaged BCL6 inside cells, blocked BCL6 repression complexes, reactivated BCL6 target genes, killed DLBCL cells and caused apoptosis as well as cell cycle arrest. In animal models, WK500B inhibited germinal center (GC) formation and DLBCL tumour growth without toxic and side effects. Moreover, WK500B displayed strong efficacy and favourable pharmacokinetics and presented superior druggability. Therefore, WK500B is a promising candidate that could be developed as an effective orally available therapeutic agent for DLBCL.
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Affiliation(s)
- Yajing Xing
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China; Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400030, China
| | - Weikai Guo
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China
| | - Min Wu
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China
| | - Jiuqing Xie
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China
| | - Dongxia Huang
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China
| | - Pan Hu
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China
| | - Miaoran Zhou
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Lin Zhang
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China
| | - Qiansen Zhang
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China
| | - Peili Wang
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China
| | - Xin Wang
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China
| | - Guixue Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400030, China
| | - Huangan Wu
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Cili Zhou
- Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yihua Chen
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China
| | - Mingyao Liu
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China; East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai Key Laboratory of Regulatory Biology Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Zhengfang Yi
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China; East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai Key Laboratory of Regulatory Biology Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Zhenliang Sun
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai University of Medicine & Health Sciences Affiliated Sixth People's Hospital South Campus, 201499, Shanghai, China; East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational Medicine, Shanghai Key Laboratory of Regulatory Biology Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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11
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Lloyd M, Huckvale R, Cheung KMJ, Rodrigues MJ, Collie GW, Pierrat OA, Gatti Iou M, Carter M, Davis OA, McAndrew PC, Gunnell E, Le Bihan YV, Talbot R, Henley AT, Johnson LD, Hayes A, Bright MD, Raynaud FI, Meniconi M, Burke R, van Montfort RLM, Rossanese OW, Bellenie BR, Hoelder S. Into Deep Water: Optimizing BCL6 Inhibitors by Growing into a Solvated Pocket. J Med Chem 2021; 64:17079-17097. [PMID: 34846884 PMCID: PMC8667045 DOI: 10.1021/acs.jmedchem.1c00946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 12/14/2022]
Abstract
We describe the optimization of modestly active starting points to potent inhibitors of BCL6 by growing into a subpocket, which was occupied by a network of five stably bound water molecules. Identifying potent inhibitors required not only forming new interactions in the subpocket but also perturbing the water network in a productive, potency-increasing fashion while controlling the physicochemical properties. We achieved this goal in a sequential manner by systematically probing the pocket and the water network, ultimately achieving a 100-fold improvement of activity. The most potent compounds displaced three of the five initial water molecules and formed hydrogen bonds with the remaining two. Compound 25 showed a promising profile for a lead compound with submicromolar inhibition of BCL6 in cells and satisfactory pharmacokinetic (PK) properties. Our work highlights the importance of finding productive ways to perturb existing water networks when growing into solvent-filled protein pockets.
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Affiliation(s)
| | | | - Kwai-Ming J. Cheung
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Matthew J. Rodrigues
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Gavin W. Collie
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Olivier A. Pierrat
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Mahad Gatti Iou
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Michael Carter
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Owen A. Davis
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - P. Craig McAndrew
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Emma Gunnell
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Yann-Vaï Le Bihan
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rachel Talbot
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Alan T. Henley
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Louise D. Johnson
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Angela Hayes
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Michael D. Bright
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Florence I. Raynaud
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Mirco Meniconi
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rosemary Burke
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rob L. M. van Montfort
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Olivia W. Rossanese
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Benjamin R. Bellenie
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Swen Hoelder
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
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12
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Zacharchenko T, Kalverda AP, Wright SC. Structural basis of Apt48 inhibition of the BCL6 BTB domain. Structure 2021; 30:396-407.e3. [PMID: 34774129 DOI: 10.1016/j.str.2021.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/31/2021] [Accepted: 10/22/2021] [Indexed: 10/19/2022]
Abstract
B cell lymphoma 6 (BCL6) is a transcriptional repressor that is deregulated in diffuse large B cell lymphoma, and the peptide aptamer, Apt48, inhibits BCL6 by an unknown mechanism. We report the crystal structure of BCL6 in complex with an Apt48 peptide, and show that Apt48 binds to a therapeutically uncharacterized region at the bottom of the BCL6 BTB domain. We show that the corepressor binding site of the BTB domain may be divided conceptually into two low-affinity, peptide-binding regions. An upper region, the lateral groove, binds peptides in robust three-dimensional conformations, whereas a lower binding site is permissive to less-specific interactions. We show that, even with little sequence specificity, the interactions of the lower region are required for the high-affinity binding of the SMRT corepressor and other peptides to the BTB domain. This has relevance for the design of new BCL6 inhibitors and for understanding the evolution of corepressor interactions with the BTB domain.
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Affiliation(s)
- Thomas Zacharchenko
- School of Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Arnout P Kalverda
- School of Molecular and Cellular Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Stephanie C Wright
- School of Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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13
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Orth B, Sander B, Möglich A, Diederichs K, Eilers M, Lorenz S. Identification of an atypical interaction site in the BTB domain of the MYC-interacting zinc-finger protein 1. Structure 2021; 29:1230-1240.e5. [PMID: 34186024 DOI: 10.1016/j.str.2021.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/26/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
The repurposing of structurally conserved protein domains in different functional contexts is thought to be a driving force in the evolution of complex protein interaction networks. The BTB/POZ domain is such a versatile binding module that occurs over 200 times in the human proteome with diverse protein-specific adaptations. In BTB-zinc-finger transcription factors, the BTB domain drives homo- and heterodimerization as well as interactions with non-BTB-domain-containing proteins. Which mechanisms encode specificity in these interactions at a structural level is incompletely understood. Here, we uncover an atypical peptide-binding site in the BTB domain of the MYC-interacting zinc-finger protein 1 (MIZ1) that arises from local flexibility of the core BTB fold and may provide a target site for MIZ1-directed therapeutic approaches. Intriguingly, the identified binding mode requires the BTB domain to be in a homodimeric state, thus holding opportunities for functional discrimination between homo- and heterodimers of MIZ1 in the cell.
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Affiliation(s)
- Barbara Orth
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany; Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Bodo Sander
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Andreas Möglich
- Lehrstuhl für Biochemie, University of Bayreuth, 95447 Bayreuth, Germany
| | - Kay Diederichs
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Martin Eilers
- Lehrstuhl für Biochemie, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sonja Lorenz
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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14
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Ai Y, Hwang L, MacKerell AD, Melnick A, Xue F. Progress toward B-Cell Lymphoma 6 BTB Domain Inhibitors for the Treatment of Diffuse Large B-Cell Lymphoma and Beyond. J Med Chem 2021; 64:4333-4358. [PMID: 33844535 DOI: 10.1021/acs.jmedchem.0c01686] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
B-cell lymphoma 6 (BCL6) is a master regulator of germinal center formation that produce antibody-secreting plasma cells and memory B-cells for sustained immune responses. The BTB domain of BCL6 (BCL6BTB) forms a homodimer that mediates transcriptional repression by recruiting its corepressor proteins to form a biologically functional transcriptional complex. The protein-protein interaction (PPI) between the BCL6BTB and its corepressors has emerged as a therapeutic target for the treatment of DLBCL and a number of other human cancers. This Perspective provides an overview of recent advances in the development of BCL6BTB inhibitors from reversible inhibitors, irreversible inhibitors, to BCL6 degraders. Inhibitor design and medicinal chemistry strategies for the development of novel compounds will be provided. The binding mode of new inhibitors to BCL6BTB are highlighted. Also, the in vitro and in vivo assays used for the evaluation of new compounds will be discussed.
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Affiliation(s)
- Yong Ai
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Lucia Hwang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Ari Melnick
- Department of Hematology and Oncology, Weill Cornell Medical College, New York, New York 10021, United States.,Department of Pharmacology, Weill Cornell Medical College, New York, New York 10021, United States
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
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15
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Kosugi Y, Hosea N. Prediction of Oral Pharmacokinetics Using a Combination of In Silico Descriptors and In Vitro ADME Properties. Mol Pharm 2021; 18:1071-1079. [PMID: 33512165 DOI: 10.1021/acs.molpharmaceut.0c01009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate prediction of oral pharmacokinetics remains challenging. This study investigated quantitative approaches for the prediction of the area under the plasma concentration-time curve after oral administration (AUCp,oral) to rats using the in vitro-in vivo extrapolation (IVIVE), in silico model using machine learning approaches and the combination of the in silico model and in vitro data. A set of 595 structurally diverse compounds with determined AUCp,oral at 1 mg/kg, in vitro intrinsic clearance (CLint), an unbound fraction in plasma (fu,p) in rats, and kinetic solubility at pH 6.8 was used for this assessment. Prediction models developed by two different types of machine learning techniques (i.e., random forest regression and Gaussian processes) were evaluated using three validation methods implementing the time and cluster-split training and test set and fivefold cross-validation. The developed machine learning models have a square of correlation coefficient (R2) in the range of 0.381-0.685 with 33-45% of the compounds being predicted within 2-fold of the observed AUCp,oral value. The predictivity was improved by incorporating CLint, fu,p, and solubility as explanatory variables with R2 = 0.554-0.743. In cases where extraction by the liver is the main elimination pathway and intestinal extraction is negligible, AUCp,oral can be expressed by dose, CLint, and fu,p based on a well-stirred model. By using this conventional IVIVE approach, only 1.7-5.0% of compounds were predicted within the 2-fold error with R2 = 0.354-0.487. Two empirical scaling factors (ESFs) determined by linear regression analysis and machine learning approaches improved the predictivity of AUCp,oral with 33-44% predicted within twofold variability. The IVIVE using ESF predicted by random forest regression showed better predictivity of AUCp,oral with R2 = 0.471-0.618, while it still showed lower predictivity than machine learning approaches applied directly to AUCp,oral prediction. This study demonstrated that the combination of in silico and in vitro parameters is useful to improve the predictivity of the machine learning model for rat AUCp,oral and supports consideration for predicting AUCp,oral for human and other non-clinical species in a similar manner.
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Affiliation(s)
- Yohei Kosugi
- Global DMPK, Takeda California Inc., San Diego, California 92121, United States
| | - Natalie Hosea
- Global DMPK, Takeda California Inc., San Diego, California 92121, United States
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16
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Kosugi Y, Hosea N. Direct Comparison of Total Clearance Prediction: Computational Machine Learning Model versus Bottom-Up Approach Using In Vitro Assay. Mol Pharm 2020; 17:2299-2309. [PMID: 32478525 DOI: 10.1021/acs.molpharmaceut.9b01294] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The in vitro-in vivo extrapolation (IVIVE) approach for predicting total plasma clearance (CLtot) has been widely used to rank order compounds early in discovery. More recently, a computational machine learning approach utilizing physicochemical descriptors and fingerprints calculated from chemical structure information has emerged, enabling virtual predictions even earlier in discovery. Previously, this approach focused more on in vitro intrinsic clearance (CLint) prediction. Herein, we directly compare these two approaches for predicting CLtot in rats. A structurally diverse set of 1114 compounds with known in vivo CLtot, in vitro CLint, and plasma protein binding was used as the basis for this evaluation. The machine learning models were assessed by validation approaches using the time- and cluster-split training and test sets, and five-fold cross validation. Assessed by five-fold validation, the random forest regression (RF) and radial basis function (RBF) models demonstrated better prediction performance in eight attempted machine learning models. The CLtot values predicted by the RF and RBF models were within two-fold of the observed values for 67.7 and 71.9% of cluster-split test set compounds, respectively, while the predictivity was worse in the time-split dataset. The predictivity of both models tended to be improved by incorporating in vitro parameters, unbound fraction in plasma (fu,p), and CLint. CLtot prediction utilizing in vitro CLint and the well-stirred model, correcting for the fraction unbound in blood, was substantially worse compared to machine learning approaches for the same cluster-split test set. The reason that CLtot is underestimated by IVIVE is not fully explained by considering the calculated microsomal unbound fraction (cfu,mic), extended clearance classification system (ECCS), and omitting high clearance compounds in excess of hepatic blood flow. The analysis suggests that in silico machine learning models may have the power to reduce reliance on or replace in vitro and in vivo studies for chemical structure optimization in early drug discovery.
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Affiliation(s)
- Yohei Kosugi
- Global DMPK, Takeda California Inc., San Diego, California 92121, United States
| | - Natalie Hosea
- Global DMPK, Takeda California Inc., San Diego, California 92121, United States
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17
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Piepoli S, Alt AO, Atilgan C, Mancini EJ, Erman B. Structural analysis of the PATZ1 BTB domain homodimer. Acta Crystallogr D Struct Biol 2020; 76:581-593. [PMID: 32496219 PMCID: PMC7271949 DOI: 10.1107/s2059798320005355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/16/2020] [Indexed: 11/10/2022] Open
Abstract
PATZ1 is a ubiquitously expressed transcriptional repressor belonging to the ZBTB family that is functionally expressed in T lymphocytes. PATZ1 targets the CD8 gene in lymphocyte development and interacts with the p53 protein to control genes that are important in proliferation and in the DNA-damage response. PATZ1 exerts its activity through an N-terminal BTB domain that mediates dimerization and co-repressor interactions and a C-terminal zinc-finger motif-containing domain that mediates DNA binding. Here, the crystal structures of the murine and zebrafish PATZ1 BTB domains are reported at 2.3 and 1.8 Å resolution, respectively. The structures revealed that the PATZ1 BTB domain forms a stable homodimer with a lateral surface groove, as in other ZBTB structures. Analysis of the lateral groove revealed a large acidic patch in this region, which contrasts with the previously resolved basic co-repressor binding interface of BCL6. A large 30-amino-acid glycine- and alanine-rich central loop, which is unique to mammalian PATZ1 amongst all ZBTB proteins, could not be resolved, probably owing to its flexibility. Molecular-dynamics simulations suggest a contribution of this loop to modulation of the mammalian BTB dimerization interface.
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Affiliation(s)
- Sofia Piepoli
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey
| | - Aaron Oliver Alt
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, United Kingdom
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey
- Sabanci University Nanotechnology Research and Application Center, SUNUM, 34956 Istanbul, Turkey
| | - Erika Jazmin Mancini
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, United Kingdom
| | - Batu Erman
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey
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18
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Bellenie B, Cheung KMJ, Varela A, Pierrat OA, Collie GW, Box GM, Bright MD, Gowan S, Hayes A, Rodrigues MJ, Shetty KN, Carter M, Davis OA, Henley AT, Innocenti P, Johnson LD, Liu M, de Klerk S, Le Bihan YV, Lloyd MG, McAndrew PC, Shehu E, Talbot R, Woodward HL, Burke R, Kirkin V, van Montfort RLM, Raynaud FI, Rossanese OW, Hoelder S. Achieving In Vivo Target Depletion through the Discovery and Optimization of Benzimidazolone BCL6 Degraders. J Med Chem 2020; 63:4047-4068. [PMID: 32275432 PMCID: PMC7184563 DOI: 10.1021/acs.jmedchem.9b02076] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Indexed: 12/22/2022]
Abstract
Deregulation of the transcriptional repressor BCL6 enables tumorigenesis of germinal center B-cells, and hence BCL6 has been proposed as a therapeutic target for the treatment of diffuse large B-cell lymphoma (DLBCL). Herein we report the discovery of a series of benzimidazolone inhibitors of the protein-protein interaction between BCL6 and its co-repressors. A subset of these inhibitors were found to cause rapid degradation of BCL6, and optimization of pharmacokinetic properties led to the discovery of 5-((5-chloro-2-((3R,5S)-4,4-difluoro-3,5-dimethylpiperidin-1-yl)pyrimidin-4-yl)amino)-3-(3-hydroxy-3-methylbutyl)-1-methyl-1,3-dihydro-2H-benzo[d]imidazol-2-one (CCT369260), which reduces BCL6 levels in a lymphoma xenograft mouse model following oral dosing.
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Affiliation(s)
- Benjamin
R. Bellenie
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Kwai-Ming J. Cheung
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Ana Varela
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Olivier A. Pierrat
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Gavin W. Collie
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Gary M. Box
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Michael D. Bright
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Sharon Gowan
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Angela Hayes
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Matthew J. Rodrigues
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Kartika N. Shetty
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Michael Carter
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Owen A. Davis
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Alan T. Henley
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Paolo Innocenti
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Louise D. Johnson
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Manjuan Liu
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Selby de Klerk
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Yann-Vaï Le Bihan
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Matthew G. Lloyd
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - P. Craig McAndrew
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Erald Shehu
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rachel Talbot
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Hannah L. Woodward
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rosemary Burke
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Vladimir Kirkin
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rob L. M. van Montfort
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Florence I. Raynaud
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Olivia W. Rossanese
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Swen Hoelder
- Cancer
Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K.
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19
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Schlager S, Salomon C, Olt S, Albrecht C, Ebert A, Bergner O, Wachter J, Trapani F, Gerlach D, Voss T, Traunbauer A, Jude J, Hinterndorfer M, Minnich M, Schweifer N, Blake SM, Zinzalla V, Drobits B, McConnell DB, Kraut N, Pearson M, Zuber J, Koegl M. Inducible knock-out of BCL6 in lymphoma cells results in tumor stasis. Oncotarget 2020; 11:875-890. [PMID: 32180900 PMCID: PMC7061739 DOI: 10.18632/oncotarget.27506] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 02/08/2020] [Indexed: 02/06/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphomas worldwide and is characterized by a high diversity of genetic and molecular alterations. Chromosomal translocations and mutations leading to deregulated expression of the transcriptional repressor BCL6 occur in a significant fraction of DLBCL patients. An oncogenic role of BCL6 in the initiation of DLBCL has been shown as the constitutive expression of BCL6 in mice recapitulates the pathogenesis of human DLBCL. However, the role of BCL6 in tumor maintenance remains poorly investigated due to the absence of suitable genetic models and limitations of pharmacological inhibitors. Here, we have utilized tetracycline-inducible CRISPR/Cas9 mutagenesis to study the consequences of BCL6 deletion in established DLBCL models in culture and in vivo. We show that BCL6 knock-out in SU-DHL-4 cells in vitro results in an anti-proliferative response 4–7 days after Cas9 induction that was characterized by cell cycle (G1) arrest. Conditional BCL6 deletion in established DLBCL tumors in vivo induced a significant tumor growth inhibition with initial tumor stasis followed by slow tumor growth kinetics. Our findings support a role of BCL6 in the maintenance of lymphoma growth and showcase the utility of inducible CRISPR/Cas9 systems for probing oncogene addiction.
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Affiliation(s)
| | | | - Sabine Olt
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Anja Ebert
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | | | | | | | | | - Tilman Voss
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Anna Traunbauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Matthias Hinterndorfer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Martina Minnich
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | | | - Sophia M Blake
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.,Current address: AstraZeneca AB, Gothenburg, Sweden
| | | | | | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
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20
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Patrício D, Fardilha M. The mammalian two-hybrid system as a powerful tool for high-throughput drug screening. Drug Discov Today 2020; 25:764-771. [PMID: 32032707 DOI: 10.1016/j.drudis.2020.01.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/13/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are the backbone of signaling pathways, responsible for the basis of cell communication and, when deregulated, several diseases. Consequently, identifying and modulating PPIs can unravel the pathophysiological mechanisms of diseases. The two-hybrid system, particularly the mammalian two-hybrid system (MTH), is an efficient technique to validate PPIs ex vivo. Combining MTH with high-throughput screening has a huge advantage in biomedical research. In this review, we describe methodologies developed from MTH and the role of these adaptations in PPI discovery. We also highlight the powerful contribution of MTH to the identification of disease-related PPIs and its use in the development of potential new drug screens.
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Affiliation(s)
- Daniela Patrício
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
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21
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Mabonga L, Kappo AP. Protein-protein interaction modulators: advances, successes and remaining challenges. Biophys Rev 2019; 11:559-581. [PMID: 31301019 DOI: 10.1007/s12551-019-00570-x] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 06/24/2019] [Indexed: 12/12/2022] Open
Abstract
Modulating disease-relevant protein-protein interactions (PPIs) using small-molecule inhibitors is a quite indispensable diagnostic and therapeutic strategy in averting pathophysiological cues and disease progression. Over the years, targeting intracellular PPIs as drug design targets has been a challenging task owing to their highly dynamic and expansive interfacial areas (flat, featureless and relatively large). However, advances in PPI-focused drug discovery technology have been reported and a few drugs are already on the market, with some potential drug-like candidates already in clinical trials. In this article, we review the advances, successes and remaining challenges in the application of small molecules as valuable PPI modulators in disease diagnosis and therapeutics.
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Affiliation(s)
- Lloyd Mabonga
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa, 3886, South Africa
| | - Abidemi Paul Kappo
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa, 3886, South Africa.
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22
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A simple fluorescent assay for the discovery of protein-protein interaction inhibitors. Anal Biochem 2019; 569:46-52. [PMID: 30707898 DOI: 10.1016/j.ab.2019.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022]
Abstract
Due to the therapeutic potential of targeting protein-protein interactions (PPIs) there is a need for easily executed assays to perform high throughput screening (HTS) of inhibitors. We have developed and optimized an innovative and robust fluorescence-based assay for detecting PPI inhibitors, called FluorIA (Fluorescence-based protein-protein Interaction Assay). Targeting the PPI of RAD52 with replication protein A (RPA) was used as an example, and the FluorIA protocol design, optimization and successful application to HTS of large chemical libraries are described. Here enhanced green fluorescent protein (EGFP)-tagged RAD52 detected the PPI using full-length RPA heterotrimer coated, black microtiter plates and loss in fluorescence intensity identified small molecule inhibitors (SMIs) that displaced the EGFP-tagged RAD52. The FluorIA design and protocol can be adapted and applied to detect PPIs for other protein systems. This should push forward efforts to develop targeted therapeutics against protein complexes in pathological processes.
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23
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Cheng H, Linhares BM, Yu W, Cardenas MG, Ai Y, Jiang W, Winkler A, Cohen S, Melnick A, MacKerell A, Cierpicki T, Xue F. Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design. J Med Chem 2018; 61:7573-7588. [PMID: 29969259 PMCID: PMC6334293 DOI: 10.1021/acs.jmedchem.8b00040] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein-protein interactions (PPI) between the transcriptional repressor B-cell lymphoma 6 (BCL6) BTB domain (BCL6BTB) and its corepressors have emerged as a promising target for anticancer therapeutics. However, identification of potent, drug-like inhibitors of BCL6BTB has remained challenging. Using NMR-based screening of a library of fragment-like small molecules, we have identified a thiourea compound (7CC5) that binds to BCL6BTB. From this hit, the application of computer-aided drug design (CADD), medicinal chemistry, NMR spectroscopy, and X-ray crystallography has yielded an inhibitor, 15f, that demonstrated over 100-fold improved potency for BCL6BTB. This gain in potency was achieved by a unique binding mode that mimics the binding mode of the corepressor SMRT in the aromatic and the HDCH sites. The structure-activity relationship based on these new inhibitors will have a significant impact on the rational design of novel BCL6 inhibitors, facilitating the identification of therapeutics for the treatment of BCL6-dependent tumors.
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Affiliation(s)
- Huimin Cheng
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, Maryland, 21201, USA
| | - Brian M. Linhares
- University of Michigan, Department of Pathology, Ann Arbor, Michigan, 48109, USA
| | - Wenbo Yu
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, Maryland, 21201, USA,University of Maryland Computer-Aided Drug Design Center, Baltimore, Maryland, 21201, USA
| | - Mariano G. Cardenas
- Weill Cornell Medical College, Department of Hematology/Oncology, New York, New York, 10021, USA
| | - Yong Ai
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, Maryland, 21201, USA
| | - Wenjuan Jiang
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, Maryland, 21201, USA,University of Maryland Computer-Aided Drug Design Center, Baltimore, Maryland, 21201, USA
| | - Alyssa Winkler
- University of Michigan, Department of Pathology, Ann Arbor, Michigan, 48109, USA
| | - Sandra Cohen
- Weill Cornell Medical College, Department of Hematology/Oncology, New York, New York, 10021, USA
| | - Ari Melnick
- Weill Cornell Medical College, Department of Hematology/Oncology, New York, New York, 10021, USA
| | - Alexander MacKerell
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, Maryland, 21201, USA,University of Maryland Computer-Aided Drug Design Center, Baltimore, Maryland, 21201, USA
| | - Tomasz Cierpicki
- University of Michigan, Department of Pathology, Ann Arbor, Michigan, 48109, USA,Correspondence to: Professor Fengtian Xue at the Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, USA, Phone: 410-706-8521, , Professor Tomasz Cierpicki at the University of Michigan, Department of Pathology, Ann Arbor, Michigan 48109, USA, Phone: 734-615-9324,
| | - Fengtian Xue
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, Maryland, 21201, USA,University of Maryland Computer-Aided Drug Design Center, Baltimore, Maryland, 21201, USA,Correspondence to: Professor Fengtian Xue at the Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, USA, Phone: 410-706-8521, , Professor Tomasz Cierpicki at the University of Michigan, Department of Pathology, Ann Arbor, Michigan 48109, USA, Phone: 734-615-9324,
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24
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Lambert M, Jambon S, Depauw S, David-Cordonnier MH. Targeting Transcription Factors for Cancer Treatment. Molecules 2018; 23:molecules23061479. [PMID: 29921764 PMCID: PMC6100431 DOI: 10.3390/molecules23061479] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022] Open
Abstract
Transcription factors are involved in a large number of human diseases such as cancers for which they account for about 20% of all oncogenes identified so far. For long time, with the exception of ligand-inducible nuclear receptors, transcription factors were considered as “undruggable” targets. Advances knowledge of these transcription factors, in terms of structure, function (expression, degradation, interaction with co-factors and other proteins) and the dynamics of their mode of binding to DNA has changed this postulate and paved the way for new therapies targeted against transcription factors. Here, we discuss various ways to target transcription factors in cancer models: by modulating their expression or degradation, by blocking protein/protein interactions, by targeting the transcription factor itself to prevent its DNA binding either through a binding pocket or at the DNA-interacting site, some of these inhibitors being currently used or evaluated for cancer treatment. Such different targeting of transcription factors by small molecules is facilitated by modern chemistry developing a wide variety of original molecules designed to specifically abort transcription factor and by an increased knowledge of their pathological implication through the use of new technologies in order to make it possible to improve therapeutic control of transcription factor oncogenic functions.
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Affiliation(s)
- Mélanie Lambert
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Samy Jambon
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Sabine Depauw
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Marie-Hélène David-Cordonnier
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
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Sameshima T, Yamamoto T, Sano O, Sogabe S, Igaki S, Sakamoto K, Ida K, Gotou M, Imaeda Y, Sakamoto J, Miyahisa I. Discovery of an Irreversible and Cell-Active BCL6 Inhibitor Selectively Targeting Cys53 Located at the Protein-Protein Interaction Interface. Biochemistry 2018; 57:1369-1379. [PMID: 29293322 DOI: 10.1021/acs.biochem.7b00732] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
B-cell lymphoma 6 (BCL6) is the most frequently involved oncogene in diffuse large B-cell lymphomas (DLBCLs). BCL6 shows potent transcriptional repressor activity through interactions with its corepressors, such as BCL6 corepressor (BCOR). The inhibition of the protein-protein interaction (PPI) between BCL6 and its corepressors suppresses the growth of BCL6-dependent DLBCLs, thus making BCL6 an attractive drug target for lymphoma treatment. However, potent small-molecule PPI inhibitor identification remains challenging because of the lack of deep cavities at PPI interfaces. This article reports the discovery of a potent, cell-active small-molecule BCL6 inhibitor, BCL6-i (8), that operates through irreversible inhibition. First, we synthesized irreversible lead compound 4, which targets Cys53 in a cavity on the BCL6-BTB domain dimer by introducing an irreversible warhead to high-throughput screening hit compound 1. Further chemical optimization of 4 based on kinact/KI evaluation produced BCL6-i with a kinact/KI value of 1.9 × 104 M-1 s-1, corresponding to a 670-fold improvement in potency compared to that of 4. By exploiting the property of irreversible inhibition, engagement of BCL6-i to intracellular BCL6 was confirmed. BCL6-i showed intracellular PPI inhibitory activity between BCL6 and its corepressors, thus resulting in BCL6-dependent DLBCL cell growth inhibition. BCL6-i is a cell-active chemical probe with the most potent BCL6 inhibitory activity reported to date. The discovery process of BCL6-i illustrates the utility of irreversible inhibition for identifying potent chemical probes for intractable target proteins.
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Affiliation(s)
- Tomoya Sameshima
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-higashi 2 chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takeshi Yamamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-higashi 2 chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Osamu Sano
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-higashi 2 chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Sogabe
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-higashi 2 chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Shigeru Igaki
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-higashi 2 chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kotaro Sakamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-higashi 2 chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Koh Ida
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-higashi 2 chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Mika Gotou
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-higashi 2 chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yasuhiro Imaeda
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-higashi 2 chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Junichi Sakamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-higashi 2 chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Ikuo Miyahisa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-higashi 2 chome, Fujisawa, Kanagawa 251-8555, Japan
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Affiliation(s)
- Rebecca J Leeman-Neill
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
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