TY - JOUR
T1 - Identification of DOT1L inhibitors by structure-based virtual screening adapted from a nucleoside-focused library
AU - Gibbons, Garrett S.
AU - Chakraborty, Amarraj
AU - Grigsby, Sierrah M.
AU - Umeano, Afoma C.
AU - Liao, Chenzhong
AU - Moukha-Chafiq, Omar
AU - Pathak, Vibha
AU - Mathew, Bini
AU - Lee, Young Tae
AU - Dou, Yali
AU - Schürer, Stephan C.
AU - Reynolds, Robert C.
AU - Snowden, Timothy S.
AU - Nikolovska-Coleska, Zaneta
N1 - Funding Information:
We are thankful and acknowledge the financial support from the Leukemia Research Foundation and the Cancer Research Committee Fund of the University of Michigan Comprehensive Cancer Center (UMCC) award to Z. Nikolovska-Coleska. The preparation of the reported compounds in this investigation was partially supported by NIH grant No. 1P41 GM086163-01 (entitled: Pilot-Scale Libraries Based on Nucleoside Templates for the ML Initiative, R. C. Reynolds, P.I.). Dr. Robert C. Reynolds would like to thank Drs. Boris Pasche and Ravi Bhatia for support of this research project via start-up funds provided through the Division of Hematology and Oncology at the University of Alabama at Birmingham. Additionally, Judith V. Hobrath of the Drug Discovery Unit in the College of Life Sciences at the University of Dundee gave critical input into manuscript preparation and the DOT1L binding models presented in this work during her time at Southern Research and the University of Alabama at Birmingham. Afoma C. Umeano is supported by the National Cancer Institute, Ruth L. Kirschstein National Research Service Award Individual Predoctoral Fellowship under NIH award number 1F31CA228331-01A1. We would like to thank graduate student Michael Ihde at the University of Alabama who was incredibly helpful with the solubility studies. Dr. Stephan Sch?rer acknowledges support from NIH grants U54HL127624 (Data Coordination and Integration Center for LINCS-BD2K) and U24TR002278 (Illuminating the Druggable Genome Resource Dissemination and Outreach Center, IDG-RDOC). Dr. Sch?rer thanks OpenEye Scientific Software (https://www.eyesopen.com/) and ChemAxon (https://chemaxon.com/) for making their software tools accessible to the research group via their academic software licenses.
Funding Information:
We are thankful and acknowledge the financial support from the Leukemia Research Foundation and the Cancer Research Committee Fund of the University of Michigan Comprehensive Cancer Center (UMCC) award to Z. Nikolovska-Coleska. The preparation of the reported compounds in this investigation was partially supported by NIH grant No. 1P41 GM086163-01 (entitled: Pilot-Scale Libraries Based on Nucleoside Templates for the ML Initiative, R. C. Reynolds, P.I.). Dr. Robert C. Reynolds would like to thank Drs. Boris Pasche and Ravi Bhatia for support of this research project via start-up funds provided through the Division of Hematology and Oncology at the University of Alabama at Birmingham. Additionally, Judith V. Hobrath of the Drug Discovery Unit in the College of Life Sciences at the University of Dundee gave critical input into manuscript preparation and the DOT1L binding models presented in this work during her time at Southern Research and the University of Alabama at Birmingham. Afoma C. Umeano is supported by the National Cancer Institute , Ruth L. Kirschstein National Research Service Award Individual Predoctoral Fellowship under NIH award number 1F31CA228331-01A1 . We would like to thank graduate student Michael Ihde at the University of Alabama who was incredibly helpful with the solubility studies. Dr. Stephan Schürer acknowledges support from NIH grants U54HL127624 (Data Coordination and Integration Center for LINCS-BD2K) and U24TR002278 (Illuminating the Druggable Genome Resource Dissemination and Outreach Center, IDG-RDOC). Dr. Schürer thanks OpenEye Scientific Software ( https://www.eyesopen.com/ ) and ChemAxon ( https://chemaxon.com/ ) for making their software tools accessible to the research group via their academic software licenses. Appendix A
PY - 2020/3/1
Y1 - 2020/3/1
N2 - 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.
AB - 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.
KW - DOT1L
KW - Histone methyltransferase
KW - Molecular modeling
KW - Small-molecule inhibitors
KW - Structure-based virtual screening
KW - Synthesis
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U2 - 10.1016/j.ejmech.2019.112023
DO - 10.1016/j.ejmech.2019.112023
M3 - Article
C2 - 31978781
AN - SCOPUS:85078636539
VL - 189
JO - European Journal of Medicinal Chemistry
JF - European Journal of Medicinal Chemistry
SN - 0223-5234
M1 - 112023
ER -