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Matarlo JS, Krumpe LRH, Heinz WF, Oh D, Shenoy SR, Thomas CL, Goncharova EI, Lockett SJ, O'Keefe BR. The Natural Product Butylcycloheptyl Prodiginine Binds Pre-miR-21, Inhibits Dicer-Mediated Processing of Pre-miR-21, and Blocks Cellular Proliferation. Cell Chem Biol 2019; 26:1133-1142.e4. [PMID: 31155509 DOI: 10.1016/j.chembiol.2019.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/15/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022]
Abstract
Identification of RNA-interacting pharmacophores could provide chemical probes and, potentially, small molecules for RNA-based therapeutics. Using a high-throughput differential scanning fluorimetry assay, we identified small-molecule natural products with the capacity to bind the discrete stem-looped structure of pre-miR-21. The most potent compound identified was a prodiginine-type compound, butylcycloheptyl prodiginine (bPGN), with the ability to inhibit Dicer-mediated processing of pre-miR-21 in vitro and in cells. Time-dependent RT-qPCR, western blot, and transcriptomic analyses showed modulation of miR-21 expression and its target genes such as PDCD4 and PTEN upon treatment with bPGN, supporting on-target inhibition. Consequently, inhibition of cellular proliferation in HCT-116 colorectal cancer cells was also observed when treated with bPGN. The discovery that bPGN can bind and modulate the expression of regulatory RNAs such as miR-21 helps set the stage for further development of this class of natural product as a molecular probe or therapeutic agent against miRNA-dependent diseases.
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Affiliation(s)
- Joe S Matarlo
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Lauren R H Krumpe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Daniel Oh
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Shilpa R Shenoy
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Cheryl L Thomas
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ekaterina I Goncharova
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Biomedical Informatics and Data Science Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Stephen J Lockett
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Barry R O'Keefe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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2
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Evans CE, Si Y, Matarlo JS, Yin Y, French JB, Tonge PJ, Tan DS. Structure-Based Design, Synthesis, and Biological Evaluation of Non-Acyl Sulfamate Inhibitors of the Adenylate-Forming Enzyme MenE. Biochemistry 2019; 58:1918-1930. [PMID: 30912442 PMCID: PMC6653581 DOI: 10.1021/acs.biochem.9b00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
N-Acyl sulfamoyladenosines (acyl-AMS) have been used
extensively to inhibit adenylate-forming enzymes that are involved in a wide
range of biological processes. These acyl-AMS inhibitors are nonhydrolyzable
mimics of the cognate acyl adenylate intermediates that are bound tightly by
adenylate-forming enzymes. However, the anionic acyl sulfamate moiety presents a
pharmacological liability that may be detrimental to cell permeability and
pharmacokinetic profiles. We have previously developed the acyl sulfamate
OSB-AMS (1) as a potent inhibitor of the adenylate-forming enzyme
MenE, an o-succinylbenzoate-CoA (OSB-CoA) synthetase that is
required for bacterial menaquinone biosynthesis. Herein, we report the use of
computational docking to develop novel, non-acyl sulfamate inhibitors of MenE. A
m-phenyl ether-linked analogue (5) was found
to be the most potent inhibitor (IC50 = 8 μM;
Kd = 244 nM), and its X-ray co-crystal structure
was determined to characterize its binding mode in comparison to the
computational prediction. This work provides a framework for the development of
potent non-acyl sulfamate inhibitors of other adenylate-forming enzymes in the
future.
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3
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Abstract
MicroRNAs (miRNAs) regulate cell fate selection and cellular differentiation. miRNAs of the miR23b polycistron (miR-23b, miR-27b, and miR-24) target components of the TGF-β signaling pathway and affect murine bile ductular and hepatocyte cell fate selection in vitro. Here we show that miR-23b polycistron miRNAs directly target murine Smad4, which is required for TGF-β signaling. Injection of antagomirs against these miRNAs directly into E16.5 murine fetuses caused increased cytokeratin expression in sinusoids and primitive ductular elements throughout the parenchyma of newborn mice. Similar antagomir injection in newborn mice increased bile ductular differentiation in the liver periphery and reduced hepatocyte proliferation. Antagomir injection in newborn Alb/TGF-β1 transgenic mice that develop fibrosis inhibited the development of fibrosis, and injection of older mice caused the resolution of existing fibrosis. Furthermore, murine stellate cell activation, including ColA1 and ACTA2 expression, is regulated by miR-23b cluster miRNAs. In summary, knockdown of miR-23b cluster miRNAs in fetal and newborn liver promotes bile duct differentiation and can block or revert TGF-β-induced liver fibrosis that is dependent on stellate cell activation. These data may find practical application in the highly needed development of therapies for the treatment of fibrosis.
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Affiliation(s)
- Charles E. Rogler
- Division of Gastroenterology and Liver Disease, Department of Medicine, Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joe S. Matarlo
- Division of Gastroenterology and Liver Disease, Department of Medicine, Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Brian Kosmyna
- Division of Gastroenterology and Liver Disease, Department of Medicine, Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Daniel Fulop
- Division of Gastroenterology and Liver Disease, Department of Medicine, Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Leslie E. Rogler
- Division of Gastroenterology and Liver Disease, Department of Medicine, Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
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Evans CE, Matarlo JS, Tonge PJ, Tan DS. Stereoselective Synthesis, Docking, and Biological Evaluation of Difluoroindanediol-Based MenE Inhibitors as Antibiotics. Org Lett 2016; 18:6384-6387. [PMID: 27978658 PMCID: PMC5171203 DOI: 10.1021/acs.orglett.6b03272] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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A stereoselective
synthesis has been developed to provide all four
side-chain stereoisomers of difluoroindanediol 2, the
mixture of which was previously identified as an inhibitor of the o-succinylbenzoate-CoA synthetase MenE in bacterial menaquinone
biosynthesis, having promising in vitro activity against methicillin-resistant Staphylococcus aureus and Mycobacterium tuberculosis. Only the (1R,3S)-diastereomer
inhibited the biochemical activity of MenE, consistent with computational
docking studies, and this diastereomer also exhibited in vitro antibacterial
activity comparable to that of the mixture. However, mechanism-of-action
studies suggest that this inhibitor and its diastereomers may act
via other mechanisms beyond inhibition of menaquinone biosynthesis.
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Affiliation(s)
- Christopher E Evans
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Joe S Matarlo
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.,Department of Biochemistry and Cell Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Peter J Tonge
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.,Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Derek S Tan
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States.,Chemical Biology Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
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5
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Matarlo JS, Lu Y, Daryaee F, Daryaee T, Ruzsicska B, Walker SG, Tonge PJ. A Methyl 4-Oxo-4-phenylbut-2-enoate with in Vivo Activity against MRSA that Inhibits MenB in the Bacterial Menaquinone Biosynthesis Pathway. ACS Infect Dis 2016; 2:329-340. [PMID: 27294200 DOI: 10.1021/acsinfecdis.6b00023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
4-Oxo-4-phenyl-but-2-enoates inhibit MenB, the 1,4-dihydroxyl-2-naphthoyl-CoA synthase in the bacterial menaquinone (MK) biosynthesis pathway, through the formation of an adduct with coenzyme A (CoA). Here, we show that the corresponding methyl butenoates have MIC values as low as 0.35-0.75 µg/mL against drug sensitive and resistant strains of Staphylococcus aureus. Mode of action studies on the most potent compound, methyl 4-(4-chlorophenyl)-4-oxobut-2-enoate (1), reveal that 1 is converted into the corresponding CoA adduct in S. aureus cells, and that this adduct binds to the S. aureus MenB (saMenB) with a Kd value of 2 µM. The antibacterial spectrum of 1 is limited to bacteria that utilize MK for respiration, and the activity of 1 can be complemented with exogenous MK or menadione. Finally, treatment of methicillin-resistant S. aureus (MRSA) with 1 results in the small colony variant phenotype and thus 1 phenocopies knockout of the menB gene. Taken together the data indicate that the antibacterial activity of 1 results from a specific effect on MK biosynthesis. We also evaluated the in vivo efficacy of 1 using two mouse models of MRSA infection. Notably, compound 1 increased survival in a systemic infection model and resulted in a dose-dependent decrease in bacterial load in a thigh infection model, validating MenB as a target for the development of new anti-MRSA candidates.
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Affiliation(s)
- Joe S. Matarlo
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Yang Lu
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Fereidoon Daryaee
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Taraneh Daryaee
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Bela Ruzsicska
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Stephen G. Walker
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Peter J. Tonge
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, and ‡Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, United States
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6
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Matarlo JS, Evans CE, Sharma I, Lavaud LJ, Ngo SC, Shek R, Rajashankar KR, French JB, Tan DS, Tonge PJ. Mechanism of MenE inhibition by acyl-adenylate analogues and discovery of novel antibacterial agents. Biochemistry 2015; 54:6514-6524. [PMID: 26394156 DOI: 10.1021/acs.biochem.5b00966] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MenE is an o-succinylbenzoyl-CoA (OSB-CoA) synthetase in the bacterial menaquinone biosynthesis pathway and is a promising target for the development of novel antibacterial agents. The enzyme catalyzes CoA ligation via an acyl-adenylate intermediate, and we have previously reported tight-binding inhibitors of MenE based on stable acyl-sulfonyladenosine analogues of this intermediate, including OSB-AMS (1), which has an IC50 value of ≤25 nM for Escherichia coli MenE. Herein, we show that OSB-AMS reduces menaquinone levels in Staphylococcus aureus, consistent with its proposed mechanism of action, despite the observation that the antibacterial activity of OSB-AMS is ∼1000-fold lower than the IC50 for enzyme inhibition. To inform the synthesis of MenE inhibitors with improved antibacterial activity, we have undertaken a structure-activity relationship (SAR) study stimulated by the knowledge that OSB-AMS can adopt two isomeric forms in which the OSB side chain exists either as an open-chain keto acid or a cyclic lactol. These studies revealed that negatively charged analogues of the keto acid form bind, while neutral analogues do not, consistent with the hypothesis that the negatively charged keto acid form of OSB-AMS is the active isomer. X-ray crystallography and site-directed mutagenesis confirm the importance of a conserved arginine for binding the OSB carboxylate. Although most lactol isomers tested were inactive, a novel difluoroindanediol inhibitor (11) with improved antibacterial activity was discovered, providing a pathway toward the development of optimized MenE inhibitors in the future.
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Affiliation(s)
- Joe S Matarlo
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-3400
| | - Christopher E Evans
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Indrajeet Sharma
- Chemical Biology Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Lubens J Lavaud
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Stephen C Ngo
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Roger Shek
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-3400
| | - Kanagalaghatta R Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Building 436E, Argonne National Laboratory, Argonne, IL 60439
| | - Jarrod B French
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400.,Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-3400
| | - Derek S Tan
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065.,Chemical Biology Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Peter J Tonge
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400.,Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
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