2. Academic Validation
  3. Identification of DOT1L inhibitors by structure-based virtual screening adapted from a nucleoside-focused library

Identification of DOT1L inhibitors by structure-based virtual screening adapted from a nucleoside-focused library

  • Eur J Med Chem. 2020 Mar 1;189:112023. doi: 10.1016/j.ejmech.2019.112023.
Garrett S Gibbons 1,  Amarraj Chakraborty 2,  Sierrah M Grigsby 1,  Afoma C Umeano 3,  Chenzhong Liao 4,  Omar Moukha-Chafiq 5,  Vibha Pathak 5,  Bini Mathew 5,  Young-Tae Lee 4,  Yali Dou 4,  Stephan C Schürer 6,  Robert C Reynolds 7,  Timothy S Snowden 8,  Zaneta Nikolovska-Coleska 9
Affiliations

Affiliations

  • 1 Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
  • 2 Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA.
  • 3 Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
  • 4 Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
  • 5 Southern Research Institute, Drug Discovery Division, Birmingham, AL, 35205, USA.
  • 6 Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA; Center for Computational Science, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
  • 7 Division of Hematology and Oncology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
  • 8 Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA. Electronic address: snowden@ua.edu.
  • 9 Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Rogel Cancer Center at University of Michigan Medical School, Ann Arbor, MI, 48109, USA. Electronic address: zanetan@med.umich.edu.
PMID: 31978781 DOI: 10.1016/j.ejmech.2019.112023
Abstract

Disruptor of Telomeric Silencing 1-Like (DOT1L), the sole histone H3 lysine 79 (H3K79) methyltransferase, is required for leukemogenic transformation in a subset of leukemias bearing chromosomal translocations of the Mixed Lineage Leukemia (MLL) gene, as well as Other cancers. Thus, DOT1L is an attractive therapeutic target and discovery of small molecule inhibitors remain of high interest. Herein, we are presenting screening results for a unique focused library of 1200 nucleoside analogs originally produced under the aegis of the NIH Pilot Scale Library Program. The complete nucleoside set was screened virtually against DOT1L, resulting in 210 putative hits. In vitro screening of the virtual hits resulted in validation of 11 compounds as DOT1L inhibitors clustered into two distinct chemical classes, adenosine-based inhibitors and a new chemotype that lacks adenosine. Based on the developed DOT1L ligand binding model, a structure-based design strategy was applied and a second-generation of non-nucleoside DOT1L inhibitors was developed. Newly synthesized compound 25 was the most potent DOT1L Inhibitor in the new series with an IC50 of 1.0 μM, showing 40-fold improvement in comparison with hit 9 and exhibiting reasonable on target effects in a DOT1L dependent murine cell line. These compounds represent novel chemical probes with a unique non-nucleoside scaffold that bind and compete with the SAM binding site of DOT1L, thus providing foundation for further medicinal chemistry efforts to develop more potent compounds.

Keywords

DOT1L; Histone methyltransferase; Molecular modeling; Small-molecule inhibitors; Structure-based virtual screening; Synthesis.

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