Increased slow dynamics defines ligandability of BTB domains

Kharchenko, Vladlena; Linhares, Brian M.; Borregard, Megan; Czaban, Iwona; Grembecka, Jolanta; Jaremko, Mariusz; Cierpicki, Tomasz; Jaremko, Łukasz

doi:10.1038/s41467-022-34599-6

Increased slow dynamics defines ligandability of BTB domains

Journal Article · 01 November 2022 · Nat. Commun.

DOI:https://doi.org/10.1038/s41467-022-34599-6· OSTI ID:1901306

Kharchenko, Vladlena; Linhares, Brian M.; Borregard, Megan; Czaban, Iwona; Grembecka, Jolanta; Jaremko, Mariusz; Cierpicki, Tomasz; Jaremko, Łukasz

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; FOREIGN

OSTI ID:: 1901306

Journal Information:: Nat. Commun., Journal Name: Nat. Commun. Vol. 13

Country of Publication:: United States

Language:: ENGLISH

References (65)

FTMove: A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures Egbert, Megan; Jones, George; Collins, Matthew R. Journal of Molecular Biology, Vol. 434, Issue 11 https://doi.org/10.1016/j.jmb.2022.167587	journal	June 2022
Structure-based maximal affinity model predicts small-molecule druggability Cheng, Alan C.; Coleman, Ryan G.; Smyth, Kathleen T. Nature Biotechnology, Vol. 25, Issue 1 https://doi.org/10.1038/nbt1273	journal	January 2007
Practical aspects of NMR signal assignment in larger and challenging proteins Frueh, Dominique P. Progress in Nuclear Magnetic Resonance Spectroscopy, Vol. 78 https://doi.org/10.1016/j.pnmrs.2013.12.001	journal	April 2014
Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery Valkov, Eugene; Sharpe, Tim; Marsh, May Topics in Current Chemistry https://doi.org/10.1007/128_2011_265	book	January 2011
Reaching for high-hanging fruit in drug discovery at protein–protein interfaces Wells, James A.; McClendon, Christopher L. Nature, Vol. 450, Issue 7172 https://doi.org/10.1038/nature06526	journal	December 2007
Protein-protein docking benchmark version 4.0: Protein-Protein Docking Benchmark Version 4.0 Hwang, Howook; Vreven, Thom; Janin, Joël Proteins: Structure, Function, and Bioinformatics, Vol. 78, Issue 15 https://doi.org/10.1002/prot.22830	journal	July 2010
Sequence and structural analysis of BTB domain proteins Stogios, Peter J.; Downs, Gregory S.; Jauhal, Jimmy JS Genome Biology, Vol. 6, Issue 10, p. R82 https://doi.org/10.1186/gb-2005-6-10-r82	journal	January 2005
Development of a Novel B-Cell Lymphoma 6 (BCL6) PROTAC To Provide Insight into Small Molecule Targeting of BCL6 McCoull, William; Cheung, Tony; Anderson, Erica ACS Chemical Biology, Vol. 13, Issue 11 https://doi.org/10.1021/acschembio.8b00698	journal	October 2018
Backbone resonance assignment of the BCL6-BTB/POZ domain Lin, Li-Ying; Evans, S. E.; Fairall, L. Biomolecular NMR Assignments, Vol. 12, Issue 1 https://doi.org/10.1007/s12104-017-9778-z	journal	September 2017
Exploiting structural information for drug-target assessment Volkamer, Andrea; Rarey, Matthias Future Medicinal Chemistry, Vol. 6, Issue 3 https://doi.org/10.4155/fmc.14.3	journal	March 2014
Quantitative metrics for drug–target ligandability Vukovic, Sinisa; Huggins, David J. Drug Discovery Today, Vol. 23, Issue 6 https://doi.org/10.1016/j.drudis.2018.02.015	journal	June 2018
Role of LRF/Pokemon in lineage fate decisions Lunardi, Andrea; Guarnerio, Jlenia; Wang, Guocan Blood, Vol. 121, Issue 15 https://doi.org/10.1182/blood-2012-11-292037	journal	April 2013
Structure-based druggability assessment—identifying suitable targets for small molecule therapeutics Fauman, Eric B.; Rai, Brajesh K.; Huang, Enoch S. Current Opinion in Chemical Biology, Vol. 15, Issue 4 https://doi.org/10.1016/j.cbpa.2011.05.020	journal	August 2011
Simple tests for the validation of multiple field spin relaxation data Morin, Sébastien; M. Gagné, Stéphane Journal of Biomolecular NMR, Vol. 45, Issue 4 https://doi.org/10.1007/s10858-009-9381-4	journal	October 2009
Epidermal growth factor increases LRF/Pokemon expression in human prostate cancer cells Aggarwal, Himanshu; Aggarwal, Anshu; Agrawal, Devendra K. Experimental and Molecular Pathology, Vol. 91, Issue 2 https://doi.org/10.1016/j.yexmp.2011.05.006	journal	October 2011
Current perspectives in fragment-based lead discovery (FBLD) Lamoree, Bas; Hubbard, Roderick E. Essays in Biochemistry, Vol. 61, Issue 5 https://doi.org/10.1042/EBC20170028	journal	November 2017
Born to bind: the BTB protein–protein interaction domain Perez-Torrado, Roberto; Yamada, Daisuke; Defossez, Pierre-Antoine BioEssays, Vol. 28, Issue 12 https://doi.org/10.1002/bies.20500	journal	January 2006
Tumor cell‐specific inhibition of MYC function using small molecule inhibitors of the HUWE 1 ubiquitin ligase Peter, Stefanie; Bultinck, Jennyfer; Myant, Kevin EMBO Molecular Medicine, Vol. 6, Issue 12 https://doi.org/10.15252/emmm.201403927	journal	September 2014
The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins Kozakov, Dima; Grove, Laurie E.; Hall, David R. Nature Protocols, Vol. 10, Issue 5 https://doi.org/10.1038/nprot.2015.043	journal	April 2015
The Interaction of Myc with Miz1 Defines Medulloblastoma Subgroup Identity Vo, BaoHan T.; Wolf, Elmar; Kawauchi, Daisuke Cancer Cell, Vol. 29, Issue 1 https://doi.org/10.1016/j.ccell.2015.12.003	journal	January 2016
Predicting protein druggability Hajduk, Philip J.; Huth, Jeffrey R.; Tse, Christin Drug Discovery Today, Vol. 10, Issue 23-24 https://doi.org/10.1016/S1359-6446(05)03624-X	journal	December 2005
Broad-complex, tramtrack, and bric-à-brac (BTB) proteins: Critical regulators of development: C haharbakhshi and J emc Chaharbakhshi, Edwin; Jemc, Jennifer C. genesis, Vol. 54, Issue 10 https://doi.org/10.1002/dvg.22964	journal	August 2016
Fast evaluation of protein dynamics from deficient 15N relaxation data Jaremko, Łukasz; Jaremko, Mariusz; Ejchart, Andrzej Journal of Biomolecular NMR, Vol. 70, Issue 4 https://doi.org/10.1007/s10858-018-0176-3	journal	March 2018
The Ubiquitin Ligase HectH9 Regulates Transcriptional Activation by Myc and Is Essential for Tumor Cell Proliferation Adhikary, Sovana; Marinoni, Federica; Hock, Andreas Cell, Vol. 123, Issue 3 https://doi.org/10.1016/j.cell.2005.08.016	journal	November 2005
Therapeutic targeting of the BCL6 oncogene for diffuse large B-cell lymphomas Parekh, Samir; Privé, Gilbert; Melnick, Ari Leukemia & Lymphoma, Vol. 49, Issue 5 https://doi.org/10.1080/10428190801895345	journal	January 2008
Structure-based computational analysis of protein binding sites for function and druggability prediction Nisius, Britta; Sha, Fan; Gohlke, Holger Journal of Biotechnology, Vol. 159, Issue 3 https://doi.org/10.1016/j.jbiotec.2011.12.005	journal	June 2012
Principles of protein-protein interactions. Jones, S.; Thornton, J. M. Proceedings of the National Academy of Sciences, Vol. 93, Issue 1 https://doi.org/10.1073/pnas.93.1.13	journal	January 1996
Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation Guvench, Olgun; MacKerell, Alexander D. PLoS Computational Biology, Vol. 5, Issue 7 https://doi.org/10.1371/journal.pcbi.1000435	journal	July 2009
Mechanism of SMRT Corepressor Recruitment by the BCL6 BTB Domain Ahmad, K. Farid; Melnick, Ari; Lax, Stuart Molecular Cell, Vol. 12, Issue 6 https://doi.org/10.1016/S1097-2765(03)00454-4	journal	December 2003
The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht Conte, Loredana Lo; Chothia, Cyrus; Janin, Joël Journal of Molecular Biology, Vol. 285, Issue 5 https://doi.org/10.1006/jmbi.1998.2439	journal	February 1999
Exploring protein–ligand recognition with Binding MOAD Smith, Richard D.; Hu, Liegi; Falkner, Jayson A. Journal of Molecular Graphics and Modelling, Vol. 24, Issue 6 https://doi.org/10.1016/j.jmgm.2005.08.002	journal	May 2006
The druggable genome Hopkins, Andrew L.; Groom, Colin R. Nature Reviews Drug Discovery, Vol. 1, Issue 9 https://doi.org/10.1038/nrd892	journal	September 2002
Discovery of a novel B-cell lymphoma 6 (BCL6)–corepressor interaction inhibitor by utilizing structure-based drug design Yasui, Takeshi; Yamamoto, Takeshi; Sakai, Nozomu Bioorganic & Medicinal Chemistry, Vol. 25, Issue 17 https://doi.org/10.1016/j.bmc.2017.07.037	journal	September 2017
Druggability Indices for Protein Targets Derived from NMR-Based Screening Data Hajduk, Philip J.; Huth, Jeffrey R.; Fesik, Stephen W. Journal of Medicinal Chemistry, Vol. 48, Issue 7 https://doi.org/10.1021/jm049131r	journal	April 2005
The Expanding Role of the BCL6 Oncoprotein as a Cancer Therapeutic Target Cardenas, Mariano G.; Oswald, Erin; Yu, Wenbo Clinical Cancer Research, Vol. 23, Issue 4 https://doi.org/10.1158/1078-0432.CCR-16-2071	journal	November 2016
Targeting epigenetic protein–protein interactions with small-molecule inhibitors Linhares, Brian M.; Grembecka, Jolanta; Cierpicki, Tomasz Future Medicinal Chemistry, Vol. 12, Issue 14 https://doi.org/10.4155/fmc-2020-0082	journal	July 2020
Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N Shen, Yang; Bax, Ad Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-2239-0_2	book	November 2014
Measurement of 15N relaxation rates in perdeuterated proteins by TROSY-based methods Lakomek, Nils-Alexander; Ying, Jinfa; Bax, Ad Journal of Biomolecular NMR, Vol. 53, Issue 3 https://doi.org/10.1007/s10858-012-9626-5	journal	June 2012
Breaking bad in the germinal center: how deregulation of BCL6 contributes to lymphomagenesis Hatzi, Katerina; Melnick, Ari Trends in Molecular Medicine, Vol. 20, Issue 6 https://doi.org/10.1016/j.molmed.2014.03.001	journal	June 2014
Kaiso depletion attenuates the growth and survival of triple negative breast cancer cells Bassey-Archibong, Blessing I.; Rayner, Lyndsay G. A.; Hercules, Shawn M. Cell Death & Disease, Vol. 8, Issue 3 https://doi.org/10.1038/cddis.2017.92	journal	March 2017
The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor Prokhortchouk, A. Genes & Development, Vol. 15, Issue 13 https://doi.org/10.1101/gad.198501	journal	July 2001
High-Resolution NMR Determination of the Dynamic Structure of Membrane Proteins Jaremko, Mariusz; Jaremko, Łukasz; Villinger, Saskia Angewandte Chemie International Edition, Vol. 55, Issue 35 https://doi.org/10.1002/anie.201602639	journal	July 2016
BCL6 as a therapeutic target for lymphoma Leeman-Neill, Rebecca J.; Bhagat, Govind Expert Opinion on Therapeutic Targets, Vol. 22, Issue 2 https://doi.org/10.1080/14728222.2018.1420782	journal	January 2018
Expression of leukemia/lymphoma related factor (LRF/Pokemon) in human benign prostate hyperplasia and prostate cancer Aggarwal, Himanshu; Aggarwal, Anshu; Hunter, William J. Experimental and Molecular Pathology, Vol. 90, Issue 2 https://doi.org/10.1016/j.yexmp.2011.01.003	journal	April 2011
The LRF transcription factor regulates mature B cell development and the germinal center response in mice Sakurai, Nagisa; Maeda, Manami; Lee, Sung-Uk Journal of Clinical Investigation, Vol. 121, Issue 7 https://doi.org/10.1172/JCI45682	journal	July 2011
Fragment screening to predict druggability (ligandability) and lead discovery success Edfeldt, Fredrik N. B.; Folmer, Rutger H. A.; Breeze, Alexander L. Drug Discovery Today, Vol. 16, Issue 7-8 https://doi.org/10.1016/j.drudis.2011.02.002	journal	April 2011
Structure of a BCOR Corepressor Peptide in Complex with the BCL6 BTB Domain Dimer Ghetu, Alexandru F.; Corcoran, Connie M.; Cerchietti, Leandro Molecular Cell, Vol. 29, Issue 3 https://doi.org/10.1016/j.molcel.2007.12.026	journal	February 2008
Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing toward the Reality Arkin, Michelle R.; Tang, Yinyan; Wells, James A. Chemistry & Biology, Vol. 21, Issue 9 https://doi.org/10.1016/j.chembiol.2014.09.001	journal	September 2014
Approaches to target tractability assessment – a practical perspective Brown, Kristin K.; Hann, Michael M.; Lakdawala, Ami S. MedChemComm, Vol. 9, Issue 4 https://doi.org/10.1039/C7MD00633K	journal	January 2018
Dynamic 15N{1H} NOE measurements: a tool for studying protein dynamics Kharchenko, Vladlena; Nowakowski, Michal; Jaremko, Mariusz Journal of Biomolecular NMR, Vol. 74, Issue 12 https://doi.org/10.1007/s10858-020-00346-6	journal	September 2020
Exploring the structural origins of cryptic sites on proteins Beglov, Dmitri; Hall, David R.; Wakefield, Amanda E. Proceedings of the National Academy of Sciences, Vol. 115, Issue 15 https://doi.org/10.1073/pnas.1711490115	journal	March 2018
Hot spot-based design of small-molecule inhibitors for protein–protein interactions Guo, Wenxing; Wisniewski, John A.; Ji, Haitao Bioorganic & Medicinal Chemistry Letters, Vol. 24, Issue 11 https://doi.org/10.1016/j.bmcl.2014.03.095	journal	June 2014
Finding Druggable Sites in Proteins Using TACTICS Evans, Daniel J.; Yovanno, Remy A.; Rahman, Sanim Journal of Chemical Information and Modeling, Vol. 61, Issue 6 https://doi.org/10.1021/acs.jcim.1c00204	journal	June 2021
Expanding the Number of ‘Druggable’ Targets: Non-Enzymes and Protein-Protein Interactions Makley, Leah N.; Gestwicki, Jason E. Chemical Biology & Drug Design, Vol. 81, Issue 1 https://doi.org/10.1111/cbdd.12066	journal	December 2012
The Quest for Simplicity: Remarks on the Free-Approach Models Jaremko, Łukasz; Jaremko, Mariusz; Nowakowski, Michał The Journal of Physical Chemistry B, Vol. 119, Issue 36 https://doi.org/10.1021/acs.jpcb.5b07181	journal	August 2015
The role of the transcription factor Miz-1 in lymphocyte development and lymphomagenesis—Binding Myc makes the difference Möröy, Tarik; Saba, Ingrid; Kosan, Christian Seminars in Immunology, Vol. 23, Issue 5 https://doi.org/10.1016/j.smim.2011.09.001	journal	October 2011
Expression of leukemia/lymphoma-related factor (LRF/POKEMON) in human breast carcinoma and other cancers Aggarwal, Anshu; Hunter, William J.; Aggarwal, Himanshu Experimental and Molecular Pathology, Vol. 89, Issue 2 https://doi.org/10.1016/j.yexmp.2010.05.002	journal	October 2010
Discovery of Pyrazolo[1,5- a ]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors McCoull, William; Abrams, Roman D.; Anderson, Erica Journal of Medicinal Chemistry, Vol. 60, Issue 10 https://doi.org/10.1021/acs.jmedchem.7b00359	journal	May 2017
Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design Cheng, Huimin; Linhares, Brian M.; Yu, Wenbo Journal of Medicinal Chemistry, Vol. 61, Issue 17 https://doi.org/10.1021/acs.jmedchem.8b00040	journal	July 2018
Identification of an atypical interaction site in the BTB domain of the MYC-interacting zinc-finger protein 1 Orth, Barbara; Sander, Bodo; Möglich, Andreas Structure, Vol. 29, Issue 11 https://doi.org/10.1016/j.str.2021.06.005	journal	November 2021
TROSY in triple-resonance experiments: New perspectives for sequential NMR assignment of large proteins Salzmann, M.; Pervushin, K.; Wider, G. Proceedings of the National Academy of Sciences, Vol. 95, Issue 23 https://doi.org/10.1073/pnas.95.23.13585	journal	November 1998
Predicting druggable binding sites at the protein–protein interface Fuller, Jonathan C.; Burgoyne, Nicholas J.; Jackson, Richard M. Drug Discovery Today, Vol. 14, Issue 3-4 https://doi.org/10.1016/j.drudis.2008.10.009	journal	February 2009
Discovery of an Irreversible and Cell-Active BCL6 Inhibitor Selectively Targeting Cys53 Located at the Protein–Protein Interaction Interface Sameshima, Tomoya; Yamamoto, Takeshi; Sano, Osamu Biochemistry, Vol. 57, Issue 8 https://doi.org/10.1021/acs.biochem.7b00732	journal	February 2018
Chemically Induced Degradation of the Oncogenic Transcription Factor BCL6 Kerres, Nina; Steurer, Steffen; Schlager, Stefanie Cell Reports, Vol. 20, Issue 12 https://doi.org/10.1016/j.celrep.2017.08.081	journal	September 2017
A Small-Molecule Inhibitor of BCL6 Kills DLBCL Cells In Vitro and In Vivo Cerchietti, Leandro C.; Ghetu, Alexandru F.; Zhu, Xiao Cancer Cell, Vol. 17, Issue 4 https://doi.org/10.1016/j.ccr.2009.12.050	journal	April 2010

Similar Records

Increased slow dynamics defines ligandability of BTB domains

Journal Article · 2022 · Nat. Commun. · OSTI ID:1902401

Flavonol Activation Defines an Unanticipated Ligand-Binding Site in the Kinase-RNase Domain of IRE1

Journal Article · 2010 · Mol. Cell · OSTI ID:1002467

Insights into Strand Exchange in BTB Domain Dimers from the Crystal Structures of FAZF and Miz1

Journal Article · 2010 · J. Mol. Biol. · OSTI ID:1002720

Increased slow dynamics defines ligandability of BTB domains

Citation Formats

References (65)

Similar Records

Related Subjects