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Gibbons GS, Chakraborty A, Grigsby SM, Umeano AC, Liao C, Moukha-Chafiq O, Pathak V, Mathew B, Lee YT, Dou Y, Schürer SC, Reynolds RC, Snowden TS, Nikolovska-Coleska Z. Identification of DOT1L inhibitors by structure-based virtual screening adapted from a nucleoside-focused library. Eur J Med Chem 2020; 189:112023. [PMID: 31978781 DOI: 10.1016/j.ejmech.2019.112023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/27/2019] [Accepted: 12/29/2019] [Indexed: 02/07/2023]
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.
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Affiliation(s)
- Garrett S Gibbons
- 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
| | - Amarraj Chakraborty
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA
| | - Sierrah M Grigsby
- 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
| | - Afoma C Umeano
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Chenzhong Liao
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Omar Moukha-Chafiq
- Southern Research Institute, Drug Discovery Division, Birmingham, AL, 35205, USA
| | - Vibha Pathak
- Southern Research Institute, Drug Discovery Division, Birmingham, AL, 35205, USA
| | - Bini Mathew
- Southern Research Institute, Drug Discovery Division, Birmingham, AL, 35205, USA
| | - Young-Tae Lee
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yali Dou
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Stephan C Schürer
- 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
| | - Robert C Reynolds
- Division of Hematology and Oncology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Timothy S Snowden
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA.
| | - Zaneta Nikolovska-Coleska
- 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.
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2
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Moukha-Chafiq O, Reynolds RC, Wilson JC, Snowden TS. Parallel Solution Phase Synthesis and Preliminary Biological Activity of a 5'-Substituted Cytidine Analog Library. ACS COMBINATORIAL SCIENCE 2019; 21:628-634. [PMID: 31365223 DOI: 10.1021/acscombsci.9b00072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A 109-membered library of 5'-substituted cytidine analogs was synthesized, via funding through the NIH Roadmap Initiative and the Pilot Scale Library (PSL) Program. Reaction core compounds contained -NH2 (2) and -COOH (44 and 93) groups that were coupled to a diversity of reactants in a parallel, solution phase format to produce the target library. The assorted reactants included -NH2, -CHO, -SO2Cl, and -COOH functional groups, and condensation with the intermediate core materials 2 and 44 followed by acidic hydrolysis produced 3-91 in good yields and high purity. Linkage of the amino terminus of d-phenylalanine methyl ester to the free 5'-COOH of 44 and NaOH treatment led to core library -COOH precursor 93. In a libraries from libraries approach, compound 93 served as the vital building block for our unique library of dipeptidyl cytidine analogs 94-114 through amide coupling of the -COOH group with numerous commercial amines followed by acidic deprotection. Initial screening of the complete final library through the MLPCN program revealed a modest number of hits over diverse biological processes. These hits might be considered as starting points for hit-to-lead optimization and development studies.
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Affiliation(s)
- Omar Moukha-Chafiq
- Chemistry Department, Drug Discovery Division, Southern Research, 2000 Ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Robert C. Reynolds
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, NP 2540 J, 1720 Second Avenue South, Birmingham, Alabama 35294-3300, United States
| | - Jacob C. Wilson
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, Alabama 35487-0336, United States
| | - Timothy S. Snowden
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, Alabama 35487-0336, United States
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Pathak V, Pathak AK, Reynolds RC. Synthesis of Aza-acyclic Nucleoside Libraries of Purine, Pyrimidine, and 1,2,4-Triazole. ACS COMBINATORIAL SCIENCE 2019; 21:183-191. [PMID: 30653914 DOI: 10.1021/acscombsci.8b00136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Under the aegis of the Pilot Scale Library Program of the NIH Roadmap Initiative, a new library of propan-1-amine containing aza acyclic nucleosides was designed and prepared, and we now report a diverse set of 157 purine, pyrimidine, and 1,2,4-triazole- N-acetamide analogues. These new nucleoside analogues were prepared in a parallel high throughput solution-phase format. A set of diverse amines was reacted with several nucleobase N-propaldehydes utilizing reductive amination with sodium triacetoxyborohydride coupling to produce a small and diverse aza acyclic nucleoside library. All reactions were performed using 24-well reaction blocks and an automatic reagent-dispensing platform under an inert atmosphere. Final targets were purified on an automated system using solid sample loading prepacked cartridges and prepacked silica gel columns. All compounds were characterized by NMR and HRMS and were analyzed for purity by HPLC prior to submission to the Molecular Libraries Small Molecule Repository (MLSMR). Initial screening through the Molecular Libraries Probe Production Centers Network (MLPCN) demonstrated diverse and interesting biological activities.
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Affiliation(s)
- Vibha Pathak
- Chemistry Department, Drug Discovery Division, Southern Research, 2000 Ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Ashish K. Pathak
- Chemistry Department, Drug Discovery Division, Southern Research, 2000 Ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Robert C. Reynolds
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, NP 2540 J, 1720 Second Avenue South, Birmingham, Alabama 35294-3300, United States
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Moukha-Chafiq O, Reynolds RC. Synthesis and general biological activity of a small adenosine-5'-(carboxamide and sulfanilamide) library. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 33:709-29. [PMID: 25295748 DOI: 10.1080/15257770.2014.931588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A small library of fifty-five adenosine peptide analogs was synthesized, under the Pilot Scale Library (PSL) Program of the NIH Roadmap initiative, from 2',3'-O-isopropylideneadenosine-5'-carboxylic acid 2. The coupling of amine or sulfanilamide reactants to the free 5'-carboxylic acid moiety of 2, in automated solution-phase fashion, led after acid-mediated hydrolysis to target compounds 3-57 in good yields and high purity. No marked anticancer or antimalarial activity was noted on preliminary cellular testing. Initial screening through the MLPCN program, however, indicates that these analogs may show diverse and interesting biological activities.
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Affiliation(s)
- Omar Moukha-Chafiq
- a Southern Research Institute , Drug Discovery Division , Birmingham , Alabama , USA
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Moukha-Chafiq O, Reynolds RC. Synthesis of novel peptidyl adenosine antibiotic analogs. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 33:53-63. [PMID: 24660880 DOI: 10.1080/15257770.2013.866243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A small library of peptidyl adenosine antibiotic analogs was synthesized, under the Pilot Scale Library Program of the NIH Roadmap initiative, from 2',3'-O-isoproylideneadenosine-5'-carboxylic acid 2 in excellent yield. The coupling of the amino terminus of L-2-aminophenylbutyric methyl ester to a free 5'-carboxylic acid moiety of 2 followed by sodium hydroxide treatment led to carboxylic acid analog 4. Hydrolysis of this latter gave unprotected nucleoside analog 5. Intermediate 4 served as the precursor for the preparation of novel peptidyl adenosine analogs 6-18 in good yields and high purity through peptide coupling reactions to diverse amine derivatives. No marked anticancer and antimalaria activity was noted on preliminary cellular testing; however these analogs should be useful candidates for other types of biological activity.
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Affiliation(s)
- Omar Moukha-Chafiq
- a Southern Research Institute, Drug Discovery Division , Birmingham , AL 35205 , USA
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Pathak AK, Pathak V, Reynolds RC. Solution-phase parallel synthesis of acyclic nucleoside libraries of purine, pyrimidine, and triazole acetamides. ACS COMBINATORIAL SCIENCE 2014; 16:485-93. [PMID: 24933643 PMCID: PMC4157782 DOI: 10.1021/co500067c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Molecular
diversity plays a pivotal role in modern drug discovery
against phenotypic or enzyme-based targets using high throughput screening
technology. Under the auspices of the Pilot Scale Library Program
of the NIH Roadmap Initiative, we produced and report herein a diverse
library of 181 purine, pyrimidine, and 1,2,4-triazole-N-acetamide analogues which were prepared in a parallel high throughput
solution-phase reaction format. A set of assorted amines were reacted
with several nucleic acid N-acetic acids utilizing
HATU as the coupling reagent to produce diverse acyclic nucleoside N-acetamide analogues. These reactions were performed using
24 well reaction blocks and an automatic reagent-dispensing platform
under inert atmosphere. The targeted compounds were purified on an
automated purification system using solid sample loading prepacked
cartridges and prepacked silica gel columns. All compounds were characterized
by NMR and HRMS, and were analyzed for purity by HPLC before submission
to the Molecular Libraries Small Molecule Repository (MLSMR) at NIH.
Initial screening through the Molecular Libraries Probe Production
Centers Network (MLPCN) program, indicates that several analogues
showed diverse and interesting biological activities.
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Affiliation(s)
- Ashish K. Pathak
- Drug Discovery Division, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Vibha Pathak
- Drug Discovery Division, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Robert C. Reynolds
- Drug Discovery Division, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, Alabama 35205, United States
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Moukha-chafiq O, Reynolds RC. Parallel solution-phase synthesis and general biological activity of a uridine antibiotic analog library. ACS COMBINATORIAL SCIENCE 2014; 16:232-7. [PMID: 24661222 PMCID: PMC4025591 DOI: 10.1021/co4001452] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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A small library of ninety four uridine antibiotic analogs was synthesized,
under the Pilot Scale Library (PSL) Program of the NIH Roadmap initiative,
from amine 2 and carboxylic acids 33 and 77 in solution-phase fashion. Diverse aldehyde, sulfonyl chloride,
and carboxylic acid reactant sets were condensed to 2, leading after acid-mediated hydrolysis, to the targeted compounds 3–32 in good yields and high purity. Similarly,
treatment of 33 with diverse amines and sulfonamides
gave 34–75. The coupling of the amino
terminus of d-phenylalanine methyl ester to the free 5′-carboxylic
acid moiety of 33 followed by sodium hydroxide treatment
led to carboxylic acid analog 77. Hydrolysis of this
material gave analog 78. The intermediate 77 served as the precursor for the preparation of novel dipeptidyl
uridine analogs 79–99 through peptide
coupling reactions to diverse amine reactants. None of the described
compounds show significant anticancer or antimalarial acivity. A number
of samples exhibited a variety of promising inhibitory, agonist, antagonist,
or activator properties with enzymes and receptors in primary screens
supplied and reported through the NIH MLPCN program.
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Affiliation(s)
- Omar Moukha-chafiq
- Southern Research Institute, Drug Discovery Division, Birmingham, Alabama 35205, United States
| | - Robert C. Reynolds
- Southern Research Institute, Drug Discovery Division, Birmingham, Alabama 35205, United States
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