Structure-guided DOT1L probe optimization by label-free ligand displacement.
The DOT1L lysine methyltransferase has emerged as a validated therapeutic target in MLL-rearranged (MLLr) acute leukemias. Although S-adenosylmethionine competitive inhibitors have demonstrated pharmacological proof-of-principle in MLLr-leukemia, these compounds require further optimization to improve cellular potency and pharmacokinetic stability. Limiting DOT1L inhibitor discovery and ligand optimization have been complex biochemical methods often using radionucleotides and cellular methods requiring prolonged culture. We therefore developed a new suite of assay technologies that allows comparative assessment of chemical tools for DOT1L in a miniaturized format. Coupling these assays with structural information, we developed new insights into DOT1L ligand binding and identified several functionalized probes with increased cellular potency (IC50 values ∼10 nM) and excellent selectivity for DOT1L. Together these assay technologies define a platform capability for discovery and optimization of small-molecule DOT1L inhibitors.
†Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.|‡Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.|§Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States.
Joanna S
JS
Yi
†Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.
Alexander J
AJ
Federation
†Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.
Jun
J
Qi
∥Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.
Sirano
S
Dhe-Paganon
⊥Human Oncology and Pathogenesis Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States.
Michael
M
Hadler
#Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States.
Xiang
X
Xu
†Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.
Roodolph
R
St Pierre
†Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.
Anthony C
AC
Varca
○Shanghai ChemPartner Co. Ltd., 998 Hailei Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, China.
Lei
L
Wu
†Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.
Jason J
JJ
Marineau
†Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.
William B
WB
Smith
†Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.
Amanda
A
Souza
†Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.
Emma J
EJ
Chory
⊥Human Oncology and Pathogenesis Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States.
Scott A
SA
Armstrong
†Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States.|▽Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States.
James E
JE
Bradner
D000241:Adenosine / Q000031:analogs & derivatives / Q000138:chemical synthesis / Q000494:pharmacology; D000970:Antineoplastic Agents / Q000138:chemical synthesis* / Q000494:pharmacology; D045744:Cell Line, Tumor; D004791:Enzyme Inhibitors / Q000138:chemical synthesis* / Q000494:pharmacology; D004847:Epithelial Cells / Q000187:drug effects / Q000201:enzymology / Q000473:pathology; D015972:Gene Expression Regulation, Neoplastic; D057166:High-Throughput Screening Assays; D011495:Histone-Lysine N-Methyltransferase; D006657:Histones / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008024:Ligands; D008745:Methylation; D008780:Methyltransferases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D010671:Phenylurea Compounds / Q000138:chemical synthesis / Q000494:pharmacology; D011993:Recombinant Fusion Proteins / Q000235:genetics / Q000378:metabolism; D012436:S-Adenosylmethionine / Q000737:chemistry / Q000378:metabolism; D054852:Small Molecule Libraries / Q000138:chemical synthesis / Q000494:pharmacology; D013329:Structure-Activity Relationship
D000970:Antineoplastic Agents; C581325:EPZ004777; D004791:Enzyme Inhibitors; D006657:Histones; D008024:Ligands; D010671:Phenylurea Compounds; D011993:Recombinant Fusion Proteins; D054852:Small Molecule Libraries; D012436:S-Adenosylmethionine; C473477:DOT1L protein, human; D008780:Methyltransferases; D011495:Histone-Lysine N-Methyltransferase; D000241:Adenosine