Identification of Novel Disruptor of Telomeric Silencing 1-like (DOT1L) Inhibitors through Structure-Based Virtual Screening and Biological Assays

Histone methyltransferases are involved in many important biological processes, and abnormalities in these enzymes are associated with tumorigenesis and progression. Disruptor of telomeric silencing 1-like (DOT1L), a key hub in histone lysine methyltransferases, has been reported to play an important role in the processes of mixed-lineage leukemia (MLL)-rearranged leukemias and validated to be a potential therapeutic target. In this study, we identified a novel DOT1L inhibitor, DC_L115 (CAS no. 1163729-79-0), by combining structure-based virtual screening with biochemical analyses. This potent inhibitor DC_L115 shows high inhibitory activity toward DOT1L (IC50 = 1.5 μM). Through a process of surface plasmon resonance-based binding assays, DC_L115 was founded to bind to DOT1L with a binding affinity of 0.6 μM in vitro. Moreover, this compound selectively inhibits MLL-rearranged cell proliferation with an IC50 value of 37.1 μM. We further predicted the binding modes of DC_L115 through molecular docking analysis and found that the inhibitor competitively occupies the binding site of S-adenosylmethionine. Overall, this study demonstrates the development of potent DOT1L inhibitors with novel scaffolds.

[1]  E. Olhava,et al.  Exploring drug delivery for the DOT1L inhibitor pinometostat (EPZ-5676): Subcutaneous administration as an alternative to continuous IV infusion, in the pursuit of an epigenetic target. , 2015, Journal of controlled release : official journal of the Controlled Release Society.

[2]  Hualiang Jiang,et al.  Discovery and Optimization of Novel, Selective Histone Methyltransferase SET7 Inhibitors by Pharmacophore- and Docking-Based Virtual Screening. , 2015, Journal of medicinal chemistry.

[3]  Scott A Armstrong,et al.  Targeting DOT1L and HOX gene expression in MLL-rearranged leukemia and beyond. , 2015, Experimental hematology.

[4]  Hualiang Jiang,et al.  Virtual screening and biological evaluation of novel small molecular inhibitors against protein arginine methyltransferase 1 (PRMT1). , 2014, Organic & biomolecular chemistry.

[5]  Hualiang Jiang,et al.  Identifying novel selective non-nucleoside DNA methyltransferase 1 inhibitors through docking-based virtual screening. , 2014, Journal of medicinal chemistry.

[6]  Robert A Copeland,et al.  Nonclinical pharmacokinetics and metabolism of EPZ‐5676, a novel DOT1L histone methyltransferase inhibitor , 2014, Biopharmaceutics & drug disposition.

[7]  Yongcheng Song,et al.  A medicinal chemistry perspective for targeting histone H3 lysine-79 methyltransferase DOT1L. , 2013, Journal of medicinal chemistry.

[8]  E. Olhava,et al.  Potent inhibition of DOT1L as treatment of MLL-fusion leukemia. , 2013, Blood.

[9]  Matthieu Schapira,et al.  Bromo-deaza-SAH: a potent and selective DOT1L inhibitor. , 2013, Bioorganic & medicinal chemistry.

[10]  J. Medina-Franco,et al.  Molecular modeling and virtual screening of DNA methyltransferase inhibitors. , 2013, Current pharmaceutical design.

[11]  E. Olhava,et al.  Conformational Adaptation Drives Potent, Selective and Durable Inhibition of the Human Protein Methyltransferase DOT1L , 2012, Chemical biology & drug design.

[12]  Robert A. Copeland,et al.  Protein methyltransferase inhibitors as personalized cancer therapeutics , 2012 .

[13]  Hualiang Jiang,et al.  Pharmacophore-based virtual screening and biological evaluation of small molecule inhibitors for protein arginine methylation. , 2012, Journal of medicinal chemistry.

[14]  Manfred Jung,et al.  New lysine methyltransferase drug targets in cancer , 2012, Nature Biotechnology.

[15]  Michael M. Mysinger,et al.  Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking , 2012, Journal of medicinal chemistry.

[16]  C. Bountra,et al.  Epigenetic protein families: a new frontier for drug discovery , 2012, Nature Reviews Drug Discovery.

[17]  Matthieu Schapira,et al.  Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors , 2012, Nature Communications.

[18]  Yongcheng Song,et al.  Selective inhibitors of histone methyltransferase DOT1L: design, synthesis, and crystallographic studies. , 2011, Journal of the American Chemical Society.

[19]  Lars Bullinger,et al.  MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L. , 2011, Cancer cell.

[20]  S. Armstrong,et al.  Selective killing of mixed lineage leukemia cells by a potent small-molecule DOT1L inhibitor. , 2011, Cancer cell.

[21]  Adrian Whitty,et al.  Growing PAINS in academic drug discovery. , 2011, Future medicinal chemistry.

[22]  Jiaying Tan,et al.  The PAF complex synergizes with MLL fusion proteins at HOX loci to promote leukemogenesis. , 2010, Cancer cell.

[23]  J. Baell,et al.  New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. , 2010, Journal of medicinal chemistry.

[24]  Robert A. Copeland,et al.  Protein methyltransferases as a target class for drug discovery , 2009, Nature Reviews Drug Discovery.

[25]  M. Lazar,et al.  DOT1L/KMT4 Recruitment and H3K79 Methylation Are Ubiquitously Coupled with Gene Transcription in Mammalian Cells , 2008, Molecular and Cellular Biology.

[26]  Scott A. Armstrong,et al.  MLL translocations, histone modifications and leukaemia stem-cell development , 2007, Nature Reviews Cancer.

[27]  Jeremy R. Greenwood,et al.  Epik: a software program for pKa prediction and protonation state generation for drug-like molecules , 2007, J. Comput. Aided Mol. Des..

[28]  R. Pijnenborg,et al.  The use of Alamar Blue assay for quantitative analysis of viability, migration and invasion of choriocarcinoma cells. , 2007, Human reproduction.

[29]  J. Irwin,et al.  Benchmarking sets for molecular docking. , 2006, Journal of medicinal chemistry.

[30]  Matthew P. Repasky,et al.  Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. , 2006, Journal of medicinal chemistry.

[31]  M. D. Boer,et al.  The MLL recombinome of acute leukemias , 2006, Leukemia.

[32]  Tony Kouzarides,et al.  Reversing histone methylation , 2005, Nature.

[33]  J. Hess,et al.  The eleven-nineteen-leukemia protein ENL connects nuclear MLL fusion partners with chromatin , 2005, Oncogene.

[34]  Yi Zhang,et al.  hDOT1L Links Histone Methylation to Leukemogenesis , 2005, Cell.

[35]  C. Peterson,et al.  Histones and histone modifications , 2004, Current Biology.

[36]  Hege S. Beard,et al.  Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. , 2004, Journal of medicinal chemistry.

[37]  Matthew P. Repasky,et al.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.

[38]  Yi Zhang,et al.  Structure of the Catalytic Domain of Human DOT1L, a Non-SET Domain Nucleosomal Histone Methyltransferase , 2003, Cell.

[39]  Kevin Struhl,et al.  Methylation of H3-Lysine 79 Is Mediated by a New Family of HMTases without a SET Domain , 2002, Current Biology.

[40]  Kevin Struhl,et al.  Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. , 2002, Genes & development.

[41]  Philip R. Gafken,et al.  Dot1p Modulates Silencing in Yeast by Methylation of the Nucleosome Core , 2002, Cell.

[42]  D. Reinberg,et al.  Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. , 2001, Genes & development.

[43]  J. Huret,et al.  An Atlas on Chromosomes in Hematological Malignancies. Example: 11q23 and MLL partners , 2001, Leukemia.

[44]  C. Pui,et al.  Biological and therapeutic aspects of infant leukemia. , 2000, Blood.

[45]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[46]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , 1997 .

[47]  P. Domer,et al.  MLL fusion partners AF4 and AF9 interact at subnuclear foci , 2004, Leukemia.

[48]  Yongcheng Song,et al.  Synthesis and Structure−Activity Relationship Investigation of Adenosine-Containing Inhibitors of Histone Methyltransferase DOT1L , 2022 .