A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo.

The BCL6 transcriptional repressor is the most frequently involved oncogene in diffuse large B cell lymphoma (DLBCL). We combined computer-aided drug design with functional assays to identify low-molecular-weight compounds that bind to the corepressor binding groove of the BCL6 BTB domain. One such compound disrupted BCL6/corepressor complexes in vitro and in vivo, and was observed by X-ray crystallography and NMR to bind the critical site within the BTB groove. This compound could induce expression of BCL6 target genes and kill BCL6-positive DLBCL cell lines. In xenotransplantation experiments, the compound was nontoxic and potently suppressed DLBCL tumors in vivo. The compound also killed primary DLBCLs from human patients.

[1]  Andreas Sewing,et al.  Improving the Design and Analysis of High-Throughput Screening Technology Comparison Experiments Using Statistical Modeling , 2006, Journal of biomolecular screening.

[2]  J. Licht,et al.  Specific peptide interference reveals BCL6 transcriptional and oncogenic mechanisms in B-cell lymphoma cells , 2004, Nature Medicine.

[3]  Alexander D. MacKerell,et al.  Consideration of Molecular Weight during Compound Selection in Virtual Target-Based Database Screening , 2003, J. Chem. Inf. Comput. Sci..

[4]  A. Melnick Reprogramming Specific Gene Expression Pathways in B-Cell Lymphomas , 2005, Cell cycle.

[5]  Alexander D. MacKerell,et al.  Computational identification of inhibitors of protein-protein interactions. , 2007, Current topics in medicinal chemistry.

[6]  P. Stogios,et al.  Sequence and structural analysis of BTB domain proteins , 2005, Genome Biology.

[7]  M. Wientjes,et al.  Computational model of intracellular pharmacokinetics of paclitaxel. , 2000, The Journal of pharmacology and experimental therapeutics.

[8]  L. Staudt,et al.  Control of inflammation, cytokine expression, and germinal center formation by BCL-6. , 1997, Science.

[9]  R L Juliano,et al.  Macromolecular therapeutics: emerging strategies for drug discovery in the postgenome era. , 2001, Molecular interventions.

[10]  B. Shoichet,et al.  Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. , 2002, Journal of medicinal chemistry.

[11]  Todd J. A. Ewing,et al.  DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases , 2001, J. Comput. Aided Mol. Des..

[12]  R. Green,et al.  Bcl-6 mediates the germinal center B cell phenotype and lymphomagenesis through transcriptional repression of the DNA-damage sensor ATR , 2007, Nature Immunology.

[13]  P. Tulkens,et al.  Cellular pharmacokinetics and intracellular activity of torezolid (TR-700): studies with human macrophage (THP-1) and endothelial (HUVEC) cell lines. , 2009, The Journal of antimicrobial chemotherapy.

[14]  Aiman Abrahim,et al.  Combined PET and microdialysis for in vivo assessment of intracellular drug pharmacokinetics in humans. , 2005, Journal of nuclear medicine : official publication, Society of Nuclear Medicine.

[15]  A. Melnick,et al.  A peptomimetic inhibitor of BCL6 with potent antilymphoma effects in vitro and in vivo. , 2009, Blood.

[16]  M. Shipp,et al.  BCL6 programs lymphoma cells for survival and differentiation through distinct biochemical mechanisms. , 2007, Blood.

[17]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[18]  P. Edelstein,et al.  Azithromycin pharmacokinetics and intracellular concentrations in Legionella pneumophila-infected and uninfected guinea pigs and their alveolar macrophages , 1994, Antimicrobial Agents and Chemotherapy.

[19]  K. Audouze,et al.  Emerging classes of protein-protein interaction inhibitors and new tools for their development. , 2004, Current opinion in chemical biology.

[20]  A. Melnick,et al.  BCL6 represses CHEK1 and suppresses DNA damage pathways in normal and malignant B-cells. , 2008, Blood cells, molecules & diseases.

[21]  Qiong Shen,et al.  Deregulated BCL6 expression recapitulates the pathogenesis of human diffuse large B cell lymphomas in mice. , 2005, Cancer cell.

[22]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[23]  Alexander D. MacKerell,et al.  Identification and characterization of small molecule inhibitors of the calcium-dependent S100B-p53 tumor suppressor interaction. , 2004, Journal of medicinal chemistry.

[24]  A. Melnick,et al.  CtBP Is an Essential Corepressor for BCL6 Autoregulation , 2008, Molecular and Cellular Biology.

[25]  Ryan T. Phan,et al.  The BCL6 proto-oncogene suppresses p53 expression in germinal-centre B cells , 2004, Nature.

[26]  C. Lipinski Drug-like properties and the causes of poor solubility and poor permeability. , 2000, Journal of pharmacological and toxicological methods.

[27]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[28]  David L. Jaye,et al.  MTA3 and the Mi-2/NuRD Complex Regulate Cell Fate during B Lymphocyte Differentiation , 2004, Cell.

[29]  Jürgen Bajorath,et al.  Anatomy of Fingerprint Search Calculations on Structurally Diverse Sets of Active Compounds , 2005, J. Chem. Inf. Model..

[30]  I. Kuntz Structure-Based Strategies for Drug Design and Discovery , 1992, Science.

[31]  Alexander D. MacKerell,et al.  Identification of novel extracellular signal-regulated kinase docking domain inhibitors. , 2005, Journal of medicinal chemistry.

[32]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[33]  Wladek Minor,et al.  HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes. , 2006, Acta crystallographica. Section D, Biological crystallography.

[34]  Alexander D. MacKerell,et al.  Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY + 3 binding site. , 2004, Journal of medicinal chemistry.

[35]  R. Gascoyne,et al.  Sequential transcription factor targeting for diffuse large B-cell lymphomas. , 2008, Cancer research.

[36]  Christopher L. McClendon,et al.  Reaching for high-hanging fruit in drug discovery at protein–protein interfaces , 2007, Nature.

[37]  B. H. Ye,et al.  BCL-6 in the Pathogenesis of Non-Hodgkin's Lymphoma , 2000, Cancer investigation.

[38]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[39]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[40]  P. Stogios,et al.  Crystal structure of the BTB domain from the LRF/ZBTB7 transcriptional regulator , 2006, Protein science : a publication of the Protein Society.

[41]  Kenny Q. Ye,et al.  Transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B cell lymphomas , 2007, Proceedings of the National Academy of Sciences.

[42]  Denis Bouchard,et al.  Mechanism of SMRT corepressor recruitment by the BCL6 BTB domain. , 2003, Molecular cell.

[43]  K. Basso,et al.  BCL6 interacts with the transcription factor Miz-1 to suppress the cyclin-dependent kinase inhibitor p21 and cell cycle arrest in germinal center B cells , 2005, Nature Immunology.

[44]  Darko Butina,et al.  Unsupervised Data Base Clustering Based on Daylight's Fingerprint and Tanimoto Similarity: A Fast and Automated Way To Cluster Small and Large Data Sets , 1999, J. Chem. Inf. Comput. Sci..

[45]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[46]  A. Melnick,et al.  Structure of a BCOR corepressor peptide in complex with the BCL6 BTB domain dimer. , 2008, Molecular cell.

[47]  H. Mattie,et al.  Uptake of azithromycin by human monocytes and enhanced intracellular antibacterial activity against Staphylococcus aureus , 1993, Antimicrobial Agents and Chemotherapy.

[48]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[49]  A. Degterev,et al.  Small-Molecule Inhibition of the Interaction between the Translation Initiation Factors eIF4E and eIF4G , 2007, Cell.

[50]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[51]  D. Felsher,et al.  The human BCL6 transgene promotes the development of lymphomas in the mouse. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[52]  P. Pandolfi,et al.  The BCL-6 proto-oncogene controls germinal-centre formation and Th2-type inflammation , 1997, Nature Genetics.

[53]  B. Shoichet,et al.  Molecular docking and ligand specificity in fragment-based inhibitor discovery. , 2009, Nature chemical biology.