1
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Shao Z, Tam KKG, Achalla VPK, Woon ECY, Mason AJ, Chow SF, Yam WC, Lam JKW. Synergistic combination of antimicrobial peptide and isoniazid as inhalable dry powder formulation against multi-drug resistant tuberculosis. Int J Pharm 2024; 654:123960. [PMID: 38447778 DOI: 10.1016/j.ijpharm.2024.123960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/24/2024] [Accepted: 02/28/2024] [Indexed: 03/08/2024]
Abstract
Multidrug-resistant tuberculosis (MDR-TB) has posed a serious threat to global public health, and antimicrobial peptides (AMPs) have emerged to be promising candidates to tackle this deadly infectious disease. Previous study has suggested that two AMPs, namely D-LAK120-A and D-LAK120-HP13, can potentiate the effect of isoniazid (INH) against mycobacteria. In this study, the strategy of combining INH and D-LAK peptide as a dry powder formulation for inhalation was explored. The antibacterial effect of INH and D-LAK combination was first evaluated on three MDR clinical isolates of Mycobacteria tuberculosis (Mtb). The minimum inhibitory concentrations (MICs) and fractional inhibitory concentration indexes (FICIs) were determined. The combination was synergistic against Mtb with FICIs ranged from 0.25 to 0.38. The INH and D-LAK peptide at 2:1 mole ratio (equivalent to 1: 10 mass ratio) was identified to be optimal. This ratio was adopted for the preparation of dry powder formulation for pulmonary delivery, with mannitol used as bulking excipient. Spherical particles with mass median aerodynamic diameter (MMAD) of around 5 µm were produced by spray drying. The aerosol performance of the spray dried powder was moderate, as evaluated by the Next Generation Impactor (NGI), with emitted fraction and fine particle fraction of above 70 % and 45 %, respectively. The circular dichroism spectra revealed that both D-LAK peptides retained their secondary structure after spray drying, and the antibacterial effect of the combination against the MDR Mtb clinical isolates was successfully preserved. The combination was found to be effective against MDR Mtb isolates with KatG or InhA mutations. Overall, the synergistic combination of INH with D-LAK peptide formulated as inhaled dry powder offers a new therapeutic approach against MDR-TB.
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Affiliation(s)
- Zitong Shao
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region; UCL School of Pharmacy, University College London, United Kingdom
| | - Kingsley King-Gee Tam
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - V P K Achalla
- UCL School of Pharmacy, University College London, United Kingdom
| | - Esther C Y Woon
- UCL School of Pharmacy, University College London, United Kingdom
| | - A James Mason
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, King's College London, United Kingdom
| | - Shing Fung Chow
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region; Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong Special Administrative Region
| | - Wing Cheong Yam
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Jenny K W Lam
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region; UCL School of Pharmacy, University College London, United Kingdom; Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong Special Administrative Region.
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2
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Abstract
The AlkB family of nucleic acid demethylases is currently of intense chemical, biological, and medical interest because of its critical roles in several key cellular processes, including epigenetic gene regulation, RNA metabolism, and DNA repair. Emerging evidence suggests that dysregulation of AlkB demethylases may underlie the pathogenesis of several human diseases, particularly obesity, diabetes, and cancer. Hence there is strong interest in developing selective inhibitors for these enzymes to facilitate their mechanistic and functional studies and to validate their therapeutic potential. Herein we review the remarkable advances made over the past 20 years in AlkB demethylase inhibition research. We discuss the rational design of reported inhibitors, their mode-of-binding, selectivity, cellular activity, and therapeutic opportunities. We further discuss unexplored structural elements of the AlkB subfamilies and propose potential strategies to enable subfamily selectivity. It is hoped that this perspective will inspire novel inhibitor design and advance drug discovery research in this field.
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Affiliation(s)
- Gemma S Perry
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Mohua Das
- Lab of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Esther C Y Woon
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
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3
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Ou YH, Zou S, Goh WJ, Chong SY, Venkatesan G, Wacker MG, Storm G, Wang JW, Czarny B, Pastorin G, Woon ECY. Micro cell vesicle technology (mCVT): a novel hybrid system of gene delivery for hard-to-transfect (HTT) cells. Nanoscale 2020; 12:18022-18030. [PMID: 32857097 DOI: 10.1039/d0nr03784b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A hybrid gene delivery platform, micro Cell Vesicle Technology (mCVT), produced from the fusion of plasma membranes and cationic lipids, is presently used to improve the transfection efficiency of hard-to-transfect (HTT) cells. The plasma membrane components of mCVTs impart specificity in cellular uptake and reduce cytotoxicity in the transfection process, while the cationic lipids complex with the genetic material and provide structural integrity to mCVTs.
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Affiliation(s)
- Yi-Hsuan Ou
- Department of Pharmacy, National University of Singapore, Singapore.
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4
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Yang T, Low JJA, Woon ECY. A general strategy exploiting m5C duplex-remodelling effect for selective detection of RNA and DNA m5C methyltransferase activity in cells. Nucleic Acids Res 2020; 48:e5. [PMID: 31691820 PMCID: PMC7145549 DOI: 10.1093/nar/gkz1047] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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] [Received: 07/20/2019] [Revised: 10/07/2019] [Accepted: 10/30/2019] [Indexed: 01/25/2023] Open
Abstract
RNA:5-methylcytosine (m5C) methyltransferases are currently the focus of intense research following a series of high-profile reports documenting their physiological links to several diseases. However, no methods exist which permit the specific analysis of RNA:m5C methyltransferases in cells. Herein, we described how a combination of biophysical studies led us to identify distinct duplex-remodelling effects of m5C on RNA and DNA duplexes. Specifically, m5C induces a C3′-endo to C2′-endo sugar-pucker switch in CpG RNA duplex but triggers a B-to-Z transformation in CpG DNA duplex. Inspired by these different ‘structural signatures’, we developed a m5C-sensitive probe which fluoresces spontaneously in response to m5C-induced sugar-pucker switch, hence useful for sensing RNA:m5C methyltransferase activity. Through the use of this probe, we achieved real-time imaging and flow cytometry analysis of NOP2/Sun RNA methyltransferase 2 (NSUN2) activity in HeLa cells. We further applied the probe to the cell-based screening of NSUN2 inhibitors. The developed strategy could also be adapted for the detection of DNA:m5C methyltransferases. This was demonstrated by the development of DNA m5C-probe which permits the screening of DNA methyltransferase 3A inhibitors. To our knowledge, this study represents not only the first examples of m5C-responsive probes, but also a new strategy for discriminating RNA and DNA m5C methyltransferase activity in cells.
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Affiliation(s)
- Tianming Yang
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543 Singapore
| | - Joanne J A Low
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543 Singapore
| | - Esther C Y Woon
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, 117543 Singapore
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5
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Das M, Yang T, Dong J, Prasetya F, Xie Y, Wong KHQ, Cheong A, Woon ECY. Cover Feature: Multiprotein Dynamic Combinatorial Chemistry: A Strategy for the Simultaneous Discovery of Subfamily-Selective Inhibitors for Nucleic Acid Demethylases FTO and ALKBH3 (Chem. Asian J. 19/2018). Chem Asian J 2018. [DOI: 10.1002/asia.201801029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mohua Das
- Department of Pharmacy; National University of Singapore; 18 Science Drive 4 Singapore 117543 Singapore
| | - Tianming Yang
- Department of Pharmacy; National University of Singapore; 18 Science Drive 4 Singapore 117543 Singapore
| | - Jinghua Dong
- Department of Pharmacy; National University of Singapore; 18 Science Drive 4 Singapore 117543 Singapore
| | - Fransisca Prasetya
- Department of Pharmacy; National University of Singapore; 18 Science Drive 4 Singapore 117543 Singapore
| | - Yiming Xie
- Department of Pharmacy; National University of Singapore; 18 Science Drive 4 Singapore 117543 Singapore
| | - Kendra H. Q. Wong
- Department of Pharmacy; National University of Singapore; 18 Science Drive 4 Singapore 117543 Singapore
| | - Adeline Cheong
- Department of Pharmacy; National University of Singapore; 18 Science Drive 4 Singapore 117543 Singapore
| | - Esther C. Y. Woon
- Department of Pharmacy; National University of Singapore; 18 Science Drive 4 Singapore 117543 Singapore
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6
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Cheong A, Low JJA, Lim A, Yen PM, Woon ECY. A fluorescent methylation-switchable probe for highly sensitive analysis of FTO N 6-methyladenosine demethylase activity in cells. Chem Sci 2018; 9:7174-7185. [PMID: 30288236 PMCID: PMC6149071 DOI: 10.1039/c8sc02163e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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] [Received: 05/16/2018] [Accepted: 08/01/2018] [Indexed: 01/25/2023] Open
Abstract
N 6-Methyladenosine (m6A) is one of the most abundant epigenetic modifications on mRNA. It is dynamically regulated by the m6A demethylases FTO and ALKBH5, which are currently attracting intense medical interest because of their strong association with several human diseases. Despite their clinical significance, the molecular mechanisms of m6A demethylases remain unclear, hence there is tremendous interest in developing analytical tools to facilitate their functional studies, with a longer term view of validating their therapeutic potentials. To date, no method exists which permits the analysis of m6A-demethylase activity in cells. To overcome this challenge, herein, we describe the first example of a fluorescent m6A-switchable oligonucleotide probe, which enables the direct detection of FTO demethylase activity both in vitro and in living cells. The m6A probe provides a simple, yet powerful visual tool for highly sensitive detection of demethylase activity. Through the use of m6A-probe, we were able to achieve real-time imaging and single-cell flow cytometry analyses of FTO activity in HepG2 cells. We also successfully applied the probe to monitor dynamic changes in FTO activity and m6A methylation levels during 3T3-L1 pre-adipocyte differentiation. The strategy outlined here is highly versatile and may, in principle, be adapted to the study of a range of RNA demethylases and, more widely, other RNA modifying enzymes. To the best of our knowledge, the present study represents not only the first assay for monitoring FTO activity in living cells, but also a new strategy for sensing m6A methylation dynamics.
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Affiliation(s)
- Adeline Cheong
- Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . ; ; Tel: +65 6516 2932
| | - Joanne J A Low
- Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . ; ; Tel: +65 6516 2932
| | - Andrea Lim
- Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . ; ; Tel: +65 6516 2932
- Program of Cardiovascular and Metabolic Disorders , Duke-NUS Medical School , 8 College Road , 169857 , Singapore
| | - Paul M Yen
- Program of Cardiovascular and Metabolic Disorders , Duke-NUS Medical School , 8 College Road , 169857 , Singapore
| | - Esther C Y Woon
- Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . ; ; Tel: +65 6516 2932
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7
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Das M, Yang T, Dong J, Prasetya F, Xie Y, Wong KHQ, Cheong A, Woon ECY. Multiprotein Dynamic Combinatorial Chemistry: A Strategy for the Simultaneous Discovery of Subfamily-Selective Inhibitors for Nucleic Acid Demethylases FTO and ALKBH3. Chem Asian J 2018; 13:2854-2867. [PMID: 29917331 DOI: 10.1002/asia.201800729] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/12/2018] [Indexed: 12/18/2022]
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful supramolecular approach for discovering ligands for biomolecules. To date, most, if not all, biologically templated DCC systems employ only a single biomolecule to direct the self-assembly process. To expand the scope of DCC, herein, a novel multiprotein DCC strategy has been developed that combines the discriminatory power of a zwitterionic "thermal tag" with the sensitivity of differential scanning fluorimetry. This strategy is highly sensitive and could differentiate the binding of ligands to structurally similar subfamily members. Through this strategy, it was possible to simultaneously identify subfamily-selective probes against two clinically important epigenetic enzymes: FTO (7; IC50 =2.6 μm) and ALKBH3 (8; IC50 =3.7 μm). To date, this is the first report of a subfamily-selective ALKBH3 inhibitor. The developed strategy could, in principle, be adapted to a broad range of proteins; thus it is of broad scientific interest.
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MESH Headings
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/antagonists & inhibitors
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/chemistry
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics
- AlkB Homolog 5, RNA Demethylase/antagonists & inhibitors
- AlkB Homolog 5, RNA Demethylase/chemistry
- AlkB Homolog 5, RNA Demethylase/genetics
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/antagonists & inhibitors
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/chemistry
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics
- Catalysis
- Combinatorial Chemistry Techniques/methods
- Enzyme Inhibitors/chemistry
- Fluorometry/methods
- Humans
- Hydrazones/chemistry
- Kinetics
- Ligands
- Molecular Structure
- Oxidoreductases, O-Demethylating/antagonists & inhibitors
- Oxidoreductases, O-Demethylating/chemistry
- Oxidoreductases, O-Demethylating/genetics
- Peptides/chemistry
- Peptides/genetics
- Protein Denaturation
- Protein Engineering
- Protein Structure, Secondary
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Transition Temperature
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Affiliation(s)
- Mohua Das
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Tianming Yang
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Jinghua Dong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Fransisca Prasetya
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Yiming Xie
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Kendra H Q Wong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Adeline Cheong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Esther C Y Woon
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
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8
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Zou S, Toh JDW, Wong KHQ, Gao YG, Hong W, Woon ECY. N(6)-Methyladenosine: a conformational marker that regulates the substrate specificity of human demethylases FTO and ALKBH5. Sci Rep 2016; 6:25677. [PMID: 27156733 PMCID: PMC4860565 DOI: 10.1038/srep25677] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [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] [Received: 02/15/2016] [Accepted: 04/21/2016] [Indexed: 01/08/2023] Open
Abstract
N6-Methyladenosine (m6A) is currently one of the most intensively studied post-transcriptional modifications in RNA. Due to its critical role in epigenetics and physiological links to several human diseases, it is also of tremendous biological and medical interest. The m6A mark is dynamically reversed by human demethylases FTO and ALKBH5, however the mechanism by which these enzymes selectively recognise their target transcripts remains unclear. Here, we report combined biophysical and biochemical studies on the specificity determinants of m6A demethylases, which led to the identification of an m6A-mediated substrate discrimination mechanism. Our results reveal that m6A itself serves as a ‘conformational marker’, which induces different conformational outcomes in RNAs depending on sequence context. This critically impacts its interactions with several m6A-recognising proteins, including FTO and ALKBH5. Remarkably, through the RNA-remodelling effects of m6A, the demethylases were able to discriminate substrates with very similar nucleotide sequences. Our findings provide novel insights into the biological functions of m6A modifications. The mechanism identified in this work is likely of significance to other m6A-recognising proteins.
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Affiliation(s)
- Shui Zou
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117 543, Singapore
| | - Joel D W Toh
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117 543, Singapore.,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138 673, Singapore
| | - Kendra H Q Wong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117 543, Singapore
| | - Yong-Gui Gao
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138 673, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637 551, Singapore
| | - Wanjin Hong
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138 673, Singapore
| | - Esther C Y Woon
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117 543, Singapore
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9
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Yang T, Cheong A, Mai X, Zou S, Woon ECY. A methylation-switchable conformational probe for the sensitive and selective detection of RNA demethylase activity. Chem Commun (Camb) 2016; 52:6181-4. [PMID: 27074833 DOI: 10.1039/c6cc01045h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We describe a novel methylation-sensitive nucleic acid (RNA) probe which switches conformation according to its methylation status. When combined with a differential scanning fluorimetry technique, it enables highly sensitive and selective detection of demethylase activity at a single methylated-base level. The approach is highly versatile and may be adapted to a broad range of RNA demethylases.
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Affiliation(s)
- Tianming Yang
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, 117 543, Singapore.
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10
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Toh JDW, Sun L, Lau LZM, Tan J, Low JJA, Tang CWQ, Cheong EJY, Tan MJH, Chen Y, Hong W, Gao YG, Woon ECY. A strategy based on nucleotide specificity leads to a subfamily-selective and cell-active inhibitor of N6-methyladenosine demethylase FTO. Chem Sci 2015; 6:112-122. [PMID: 28553460 PMCID: PMC5424463 DOI: 10.1039/c4sc02554g] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [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] [Received: 08/22/2014] [Accepted: 09/15/2014] [Indexed: 01/30/2023] Open
Abstract
The AlkB family of nucleic acid demethylases are of intense biological and medical interest because of their roles in nucleic acid repair and epigenetic modification. However their functional and molecular mechanisms are unclear, hence, there is strong interest in developing selective inhibitors for them. Here we report the identification of key residues within the nucleotide-binding sites of the AlkB subfamilies that likely determine their substrate specificity. We further provide proof of principle that a strategy exploiting these inherent structural differences can enable selective and potent inhibition of the AlkB subfamilies. This is demonstrated by the first report of a subfamily-selective and cell-active FTO inhibitor 12. The distinct selectivity of 12 for FTO against other AlkB subfamilies and 2OG oxygenases shall be of considerable interest with regards to its potential use as a functional probe. The strategy outlined here is likely applicable to other AlkB subfamilies, and, more widely, to other 2OG oxygenases.
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Affiliation(s)
- Joel D W Toh
- Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . ; ; Tel: +65 6516 2932
- Institute of Molecular and Cell Biology , 61 Biopolis Drive, Proteos , 138673 , Singapore
| | - Lingyi Sun
- Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . ; ; Tel: +65 6516 2932
| | - Lisa Z M Lau
- Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . ; ; Tel: +65 6516 2932
| | - Jackie Tan
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 637551 , Singapore .
| | - Joanne J A Low
- Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . ; ; Tel: +65 6516 2932
| | - Colin W Q Tang
- Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . ; ; Tel: +65 6516 2932
| | - Eleanor J Y Cheong
- Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . ; ; Tel: +65 6516 2932
| | - Melissa J H Tan
- Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . ; ; Tel: +65 6516 2932
| | - Yun Chen
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 637551 , Singapore .
| | - Wanjin Hong
- Institute of Molecular and Cell Biology , 61 Biopolis Drive, Proteos , 138673 , Singapore
| | - Yong-Gui Gao
- Institute of Molecular and Cell Biology , 61 Biopolis Drive, Proteos , 138673 , Singapore
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 637551 , Singapore .
| | - Esther C Y Woon
- Department of Pharmacy , National University of Singapore , 18 Science Drive 4 , 117543 , Singapore . ; ; Tel: +65 6516 2932
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11
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Singh N, Halliday AC, Thomas JM, Kuznetsova OV, Baldwin R, Woon ECY, Aley PK, Antoniadou I, Sharp T, Vasudevan SR, Churchill GC. A safe lithium mimetic for bipolar disorder. Nat Commun 2013; 4:1332. [PMID: 23299882 PMCID: PMC3605789 DOI: 10.1038/ncomms2320] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [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] [Received: 08/14/2012] [Accepted: 11/22/2012] [Indexed: 12/29/2022] Open
Abstract
Lithium is the most effective mood stabilizer for the treatment of bipolar disorder, but it is toxic at only twice the therapeutic dosage and has many undesirable side effects. It is likely that a small molecule could be found with lithium-like efficacy but without toxicity through target-based drug discovery; however, lithium’s therapeutic target remains equivocal. Inositol monophosphatase is a possible target but no bioavailable inhibitors exist. Here we report that the antioxidant ebselen inhibits inositol monophosphatase and induces lithium-like effects on mouse behaviour, which are reversed with inositol, consistent with a mechanism involving inhibition of inositol recycling. Ebselen is part of the National Institutes of Health Clinical Collection, a chemical library of bioavailable drugs considered clinically safe but without proven use. Therefore, ebselen represents a lithium mimetic with the potential both to validate inositol monophosphatase inhibition as a treatment for bipolar disorder and to serve as a treatment itself.
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Affiliation(s)
- Nisha Singh
- University of Oxford, Department of Pharmacology, Mansfield Road, Oxford OX1 3QT, UK
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12
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Yeoh KK, Chan MC, Thalhammer A, Demetriades M, Chowdhury R, Tian YM, Stolze I, McNeill LA, Lee MK, Woon ECY, Mackeen MM, Kawamura A, Ratcliffe PJ, Mecinović J, Schofield CJ. Dual-action inhibitors of HIF prolyl hydroxylases that induce binding of a second iron ion. Org Biomol Chem 2012; 11:732-745. [PMID: 23151668 DOI: 10.1039/c2ob26648b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Inhibition of the hypoxia-inducible factor (HIF) prolyl hydroxylases (PHD or EGLN enzymes) is of interest for the treatment of anemia and ischemia-related diseases. Most PHD inhibitors work by binding to the single ferrous ion and competing with 2-oxoglutarate (2OG) co-substrate for binding at the PHD active site. Non-specific iron chelators also inhibit the PHDs, both in vitro and in cells. We report the identification of dual action PHD inhibitors, which bind to the active site iron and also induce the binding of a second iron ion at the active site. Following analysis of small-molecule iron complexes and application of non-denaturing protein mass spectrometry to assess PHD2·iron·inhibitor stoichiometry, selected diacylhydrazines were identified as PHD2 inhibitors that induce the binding of a second iron ion. Some compounds were shown to inhibit the HIF hydroxylases in human hepatoma and renal carcinoma cell lines.
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Affiliation(s)
- Kar Kheng Yeoh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Mun Chiang Chan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Armin Thalhammer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Marina Demetriades
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Ya-Min Tian
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Ineke Stolze
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Luke A McNeill
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Myung Kyu Lee
- BioNanotechnology Research Centre, Korea Institute of Bioscience & Biotechnology, Yuseong 305-333, Daejeon, Korea
| | - Esther C Y Woon
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Mukram M Mackeen
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Peter J Ratcliffe
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Jasmin Mecinović
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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Rose NR, Woon ECY, Tumber A, Walport LJ, Chowdhury R, Li XS, King ONF, Lejeune C, Ng SS, Krojer T, Chan MC, Rydzik AM, Hopkinson RJ, Che KH, Daniel M, Strain-Damerell C, Gileadi C, Kochan G, Leung IKH, Dunford J, Yeoh KK, Ratcliffe PJ, Burgess-Brown N, von Delft F, Muller S, Marsden B, Brennan PE, McDonough MA, Oppermann U, Klose RJ, Schofield CJ, Kawamura A. Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases. J Med Chem 2012; 55:6639-43. [PMID: 22724510 DOI: 10.1021/jm300677j] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The JmjC oxygenases catalyze the N-demethylation of N(ε)-methyl lysine residues in histones and are current therapeutic targets. A set of human 2-oxoglutarate analogues were screened using a unified assay platform for JmjC demethylases and related oxygenases. Results led to the finding that daminozide (N-(dimethylamino)succinamic acid, 160 Da), a plant growth regulator, selectively inhibits the KDM2/7 JmjC subfamily. Kinetic and crystallographic studies reveal that daminozide chelates the active site metal via its hydrazide carbonyl and dimethylamino groups.
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Affiliation(s)
- Nathan R Rose
- Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
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14
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Demetriades M, Leung IKH, Chowdhury R, Chan MC, McDonough MA, Yeoh KK, Tian YM, Claridge TDW, Ratcliffe PJ, Woon ECY, Schofield CJ. Dynamic Combinatorial Chemistry Employing Boronic Acids/Boronate Esters Leads to Potent Oxygenase Inhibitors. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202000] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Demetriades M, Leung IKH, Chowdhury R, Chan MC, McDonough MA, Yeoh KK, Tian YM, Claridge TDW, Ratcliffe PJ, Woon ECY, Schofield CJ. Dynamic Combinatorial Chemistry Employing Boronic Acids/Boronate Esters Leads to Potent Oxygenase Inhibitors. Angew Chem Int Ed Engl 2012; 51:6672-5. [DOI: 10.1002/anie.201202000] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Indexed: 11/05/2022]
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16
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Woon ECY, Demetriades M, Bagg EAL, Aik W, Krylova SM, Ma JHY, Chan M, Walport LJ, Wegman DW, Dack KN, McDonough MA, Krylov SN, Schofield CJ. Dynamic combinatorial mass spectrometry leads to inhibitors of a 2-oxoglutarate-dependent nucleic acid demethylase. J Med Chem 2012; 55:2173-84. [PMID: 22263962 DOI: 10.1021/jm201417e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2-Oxoglutarate-dependent nucleic acid demethylases are of biological interest because of their roles in nucleic acid repair and modification. Although some of these enzymes are linked to physiology, their regulatory roles are unclear. Hence, there is a desire to develop selective inhibitors for them; we report studies on AlkB, which reveal it as being amenable to selective inhibition by small molecules. Dynamic combinatorial chemistry linked to mass spectrometric analyses (DCMS) led to the identification of lead compounds, one of which was analyzed by crystallography. Subsequent structure-guided studies led to the identification of inhibitors of improved potency, some of which were shown to be selective over two other 2OG oxygenases. The work further validates the use of the DCMS method and will help to enable the development of inhibitors of nucleic acid modifying 2OG oxygenases both for use as functional probes and, in the longer term, for potential therapeutic use.
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Affiliation(s)
- Esther C Y Woon
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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17
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Woon ECY, Tumber A, Kawamura A, Hillringhaus L, Ge W, Rose NR, Ma JHY, Chan MC, Walport LJ, Che KH, Ng SS, Marsden BD, Oppermann U, McDonough MA, Schofield CJ. Linking of 2-oxoglutarate and substrate binding sites enables potent and highly selective inhibition of JmjC histone demethylases. Angew Chem Int Ed Engl 2012; 51:1631-4. [PMID: 22241642 DOI: 10.1002/anie.201107833] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Indexed: 12/19/2022]
Affiliation(s)
- Esther C Y Woon
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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18
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Woon ECY, Tumber A, Kawamura A, Hillringhaus L, Ge W, Rose NR, Ma JHY, Chan MC, Walport LJ, Che KH, Ng SS, Marsden BD, Oppermann U, McDonough MA, Schofield CJ. Linking of 2-Oxoglutarate and Substrate Binding Sites Enables Potent and Highly Selective Inhibition of JmjC Histone Demethylases. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107833] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Contreras-Martel C, Amoroso A, Woon ECY, Zervosen A, Inglis S, Martins A, Verlaine O, Rydzik AM, Job V, Luxen A, Joris B, Schofield CJ, Dessen A. Structure-guided design of cell wall biosynthesis inhibitors that overcome β-lactam resistance in Staphylococcus aureus (MRSA). ACS Chem Biol 2011; 6:943-51. [PMID: 21732689 DOI: 10.1021/cb2001846] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
β-Lactam antibiotics have long been a treatment of choice for bacterial infections since they bind irreversibly to Penicillin-Binding Proteins (PBPs), enzymes that are vital for cell wall biosynthesis. Many pathogens express drug-insensitive PBPs rendering β-lactams ineffective, revealing a need for new types of PBP inhibitors active against resistant strains. We have identified alkyl boronic acids that are active against pathogens including methicillin-resistant S. aureus (MRSA). The crystal structures of PBP1b complexed to 11 different alkyl boronates demonstrate that in vivo efficacy correlates with the mode of inhibitor side chain binding. Staphylococcal membrane analyses reveal that the most potent alkyl boronate targets PBP1, an autolysis system regulator, and PBP2a, a low β-lactam affinity enzyme. This work demonstrates the potential of boronate-based PBP inhibitors for circumventing β-lactam resistance and opens avenues for the development of novel antibiotics that target Gram-positive pathogens.
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Affiliation(s)
| | - Ana Amoroso
- Centre d'Ingénierie des Protéines, Institut de Chimie, B6a, Université de Liège, Sart Tilman, B4000 Liège, Belgium
| | - Esther C. Y. Woon
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Astrid Zervosen
- Centre de Recherches du Cyclotron, B30, Université de Liège, Sart Tilman, B4000 Liège, Belgium
| | - Steven Inglis
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | | | - Olivier Verlaine
- Centre d'Ingénierie des Protéines, Institut de Chimie, B6a, Université de Liège, Sart Tilman, B4000 Liège, Belgium
| | - Anna M. Rydzik
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | | | - André Luxen
- Centre de Recherches du Cyclotron, B30, Université de Liège, Sart Tilman, B4000 Liège, Belgium
| | - Bernard Joris
- Centre d'Ingénierie des Protéines, Institut de Chimie, B6a, Université de Liège, Sart Tilman, B4000 Liège, Belgium
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20
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Chowdhury R, Yeoh KK, Tian YM, Hillringhaus L, Bagg EA, Rose NR, Leung IKH, Li XS, Woon ECY, Yang M, McDonough MA, King ON, Clifton IJ, Klose RJ, Claridge TDW, Ratcliffe PJ, Schofield CJ, Kawamura A. The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep 2011; 12:463-9. [PMID: 21460794 PMCID: PMC3090014 DOI: 10.1038/embor.2011.43] [Citation(s) in RCA: 755] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 02/21/2011] [Accepted: 02/22/2011] [Indexed: 02/07/2023] Open
Abstract
Mutations in isocitrate dehydrogenases (IDHs) have a gain-of-function effect leading to R(-)-2-hydroxyglutarate (R-2HG) accumulation. By using biochemical, structural and cellular assays, we show that either or both R- and S-2HG inhibit 2-oxoglutarate (2OG)-dependent oxygenases with varying potencies. Half-maximal inhibitory concentration (IC(50)) values for the R-form of 2HG varied from approximately 25 μM for the histone N(ɛ)-lysine demethylase JMJD2A to more than 5 mM for the hypoxia-inducible factor (HIF) prolyl hydroxylase. The results indicate that candidate oncogenic pathways in IDH-associated malignancy should include those that are regulated by other 2OG oxygenases than HIF hydroxylases, in particular those involving the regulation of histone methylation.
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Affiliation(s)
- Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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21
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Sunderland PT, Woon ECY, Dhami A, Bergin AB, Mahon MF, Wood PJ, Jones LA, Tully SR, Lloyd MD, Thompson AS, Javaid H, Martin NMB, Threadgill MD. 5-Benzamidoisoquinolin-1-ones and 5-(ω-carboxyalkyl)isoquinolin-1-ones as isoform-selective inhibitors of poly(ADP-ribose) polymerase 2 (PARP-2). J Med Chem 2011; 54:2049-59. [PMID: 21417348 DOI: 10.1021/jm1010918] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PARP-2 is a member of the poly(ADP-ribose) polymerase family, with some activities similar to those of PARP-1 but with other distinct roles. Two series of isoquinolin-1-ones were designed, synthesized, and evaluated as selective inhibitors of PARP-2, using the structures of the catalytic sites of the isoforms. A new efficient synthesis of 5-aminoisoquinolin-1-one was developed, and acylation with acyl chlorides gave 5-acylaminoisoquinolin-1-ones. By examination of isoquinolin-1-ones with carboxylates tethered to the 5-position, Heck coupling of 5-iodoisoquinolin-1-one furnished the 5-CH═CHCO(2)H compound for reduction to the 5-propanoic acid. Alkylation of 5-aminoisoquinolin-1-one under mildly basic conditions, followed by hydrolysis, gave 5-(carboxymethylamino)isoquinolin-1-one, whereas it was alkylated at 2-N with methyl propenoate and strong base. Compounds were assayed in vitro for inhibition of PARP-1 and PARP-2, using FlashPlate and solution-phase assays, respectively. The 5-benzamidoisoquinolin-1-ones were more selective for inhibition of PARP-2, whereas the 5-(ω-carboxyalkyl)isoquinolin-1-ones were less so. 5-Benzamidoisoquinolin-1-one is the most PARP-2-selective compound (IC(50(PARP-1))/IC(50(PARP-2)) = 9.3) to date, in a comparative study.
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Affiliation(s)
- Peter T Sunderland
- Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
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22
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Chang KH, King ONF, Tumber A, Woon ECY, Heightman TD, McDonough MA, Schofield CJ, Rose NR. Inhibition of histone demethylases by 4-carboxy-2,2'-bipyridyl compounds. ChemMedChem 2011; 6:759-764. [PMID: 21412984 DOI: 10.1002/cmdc.201100026] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Kai-Hsuan Chang
- Chemistry Research Laboratory, University of Oxford Oxford, OX1 3TA, United Kingdom
| | - Oliver N F King
- Chemistry Research Laboratory, University of Oxford Oxford, OX1 3TA, United Kingdom
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, United Kingdom
| | - Esther C Y Woon
- Chemistry Research Laboratory, University of Oxford Oxford, OX1 3TA, United Kingdom
| | - Tom D Heightman
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, United Kingdom
| | - Michael A McDonough
- Chemistry Research Laboratory, University of Oxford Oxford, OX1 3TA, United Kingdom
| | | | - Nathan R Rose
- Chemistry Research Laboratory, University of Oxford Oxford, OX1 3TA, United Kingdom
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23
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Woon ECY, Zervosen A, Sauvage E, Simmons KJ, Živec M, Inglis SR, Fishwick CWG, Gobec S, Charlier P, Luxen A, Schofield CJ. Structure guided development of potent reversibly binding penicillin binding protein inhibitors. ACS Med Chem Lett 2011; 2:219-23. [PMID: 24900305 DOI: 10.1021/ml100260x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [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: 10/29/2010] [Accepted: 12/29/2010] [Indexed: 11/28/2022] Open
Abstract
Following from the evaluation of different types of electrophiles, combined modeling and crystallographic analyses are used to generate potent boronic acid based inhibitors of a penicillin binding protein. The results suggest that a structurally informed approach to penicillin binding protein inhibition will be useful for the development of both improved reversibly binding inhibitors, including boronic acids, and acylating inhibitors, such as β-lactams.
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Affiliation(s)
- Esther C. Y. Woon
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Astrid Zervosen
- Centre de Recherches du Cyclotron, B30, Universite de Liège, Sart-Tilman, B-4000 Liège, Belgium
| | - Eric Sauvage
- Centre d’Ingénierie des Protéines, Université de Liège, Institut de Physique B5, B-4000 Liège, Belgium
| | - Katie J. Simmons
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Matej Živec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Steven R. Inglis
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | | | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Paulette Charlier
- Centre d’Ingénierie des Protéines, Université de Liège, Institut de Physique B5, B-4000 Liège, Belgium
| | - André Luxen
- Centre de Recherches du Cyclotron, B30, Universite de Liège, Sart-Tilman, B-4000 Liège, Belgium
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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Inglis SR, Woon ECY, Thompson AL, Schofield CJ. Observations on the deprotection of pinanediol and pinacol boronate esters via fluorinated intermediates. J Org Chem 2010; 75:468-71. [PMID: 20014787 DOI: 10.1021/jo901930v] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [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
Methods for the deprotection of pinanediol and pinacol esters of various boronic acids via fluoroborane intermediates were evaluated. Treatment of the boronate esters with potassium hydrogen difluoride normally gives trifluoroborate salts; in the case of alpha-amido alkyl or o-amido phenyl boronate esters, aqueous workup gives difluoroboranes. Procedures for transformation of both trifluoroborates and difluoroboranes to free boronic acids are described.
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Affiliation(s)
- Steven R Inglis
- The Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
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25
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Rose NR, Woon ECY, Kingham GL, King ONF, Mecinović J, Clifton IJ, Ng SS, Talib-Hardy J, Oppermann U, McDonough MA, Schofield CJ. Selective inhibitors of the JMJD2 histone demethylases: combined nondenaturing mass spectrometric screening and crystallographic approaches. J Med Chem 2010; 53:1810-8. [PMID: 20088513 PMCID: PMC2825117 DOI: 10.1021/jm901680b] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [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: 11/30/2022]
Abstract
Ferrous ion and 2-oxoglutarate (2OG) oxygenases catalyze the demethylation of N(epsilon)-methylated lysine residues in histones. Here we report studies on the inhibition of the JMJD2 subfamily of histone demethylases, employing binding analyses by nondenaturing mass spectrometry (MS), dynamic combinatorial chemistry coupled to MS, turnover assays, and crystallography. The results of initial binding and inhibition assays directed the production and analysis of a set of N-oxalyl-d-tyrosine derivatives to explore the extent of a subpocket at the JMJD2 active site. Some of the inhibitors were shown to be selective for JMJD2 over the hypoxia-inducible factor prolyl hydroxylase PHD2. A crystal structure of JMJD2A in complex with one of the potent inhibitors was obtained; modeling other inhibitors based on this structure predicts interactions that enable improved inhibition for some compounds.
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Affiliation(s)
- Nathan R Rose
- The Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
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26
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Inglis SR, Zervosen A, Woon ECY, Gerards T, Teller N, Fischer DS, Luxen A, Schofield CJ. Synthesis and evaluation of 3-(dihydroxyboryl)benzoic acids as D,D-carboxypeptidase R39 inhibitors. J Med Chem 2009; 52:6097-106. [PMID: 19731939 DOI: 10.1021/jm9009718] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Penicillin binding proteins (PBPs) catalyze steps in the biosynthesis of bacterial cell walls and are the targets for the beta-lactam antibiotics. Non-beta-lactam based antibiotics that target PBPs are of interest because bacteria have evolved resistance to the beta-lactam antibiotics. Boronic acids have been developed as inhibitors of the mechanistically related serine beta-lactamases and serine proteases; however, they have not been explored extensively as PBP inhibitors. Here we report aromatic boronic acid inhibitors of the D,D-carboxypeptidase R39 from Actinomadura sp. strain. Analogues of an initially identified inhibitor [3-(dihydroxyboryl)benzoic acid 1, IC(50) 400 microM] were prepared via routes involving pinacol boronate esters, which were deprotected via a two-stage procedure involving intermediate trifluorborate salts that were hydrolyzed to provide the free boronic acids. 3-(Dihydroxyboryl)benzoic acid analogues containing an amide substituent in the meta, but not ortho position were up to 17-fold more potent inhibitors of the R39 PBP and displayed some activity against other PBPs. These compounds may be useful for the development of even more potent boronic acid based PBP inhibitors with a broad spectrum of antibacterial activity.
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Abstract
We report an efficient and versatile solid-phase synthesis through which two series of chlorofusin analogues, one bearing varying chromophores and the other with various amino acid substitutions in the cyclic peptide, were synthesized. These peptides were prepared using a strategy involving side-chain immobilization, on-resin cyclization, and postcyclization modification. The success of these syntheses demonstrates the broad utility of the method. Both series of analogues were evaluated for their inhibitory activity against the p53/MDM2 interaction but were shown to be inactive in the concentration range tested. This suggests that the full chromophore structure may be required for activity.
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Affiliation(s)
- Esther C Y Woon
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX
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28
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Abstract
The poly(ADP-ribose)polymerases (PARPs) catalyse the transfer of ADP-ribose units from the substrate NAD+ to acceptor proteins, biosynthesising polyanionic poly(ADP-ribose) polymers. A major isoform, PARP-1, has been the target for design of inhibitors for over twenty-five years. Inhibitors of the activity of PARP-1 have been claimed to have applications in the treatment of many disease states, including cancer, haemorrhagic shock, cardiac infarct, stroke, diabetes, inflammation and retroviral infection, but only recently have PARP-1 inhibitors entered clinical trial. Most PARP-1 inhibitors mimic the nicotinamide of NAD+ and the structure-activity relationships are understood in terms of the structure of the catalytic site. However, five questions remain if PARP-1 inhibitors are to realise their potential in treating human diseases. Firstly, the consensus pharmacophore is a benzamide with N-H conformationally constrained anti to the carbonyl-arene bond but this is also a "pharmacophore" for insolubility in water; can water-solubility be designed into inhibitors without loss of potency? Secondly, some potential clinical applications require tissue-selective PARP-1 inhibition; is this possible through prodrug approaches? Thirdly, different diseases may require therapeutic PARP-1 inhibition to be either short-term or chronic; are there potential problems associated with chronic inhibition of this DNA-repair process? Fourthly, PARP-1 is one of at least eighteen isoforms; is isoform-selectivity essential, desirable or even possible? Fifthly, PARP activity can be inhibited in cells by inhibition of poly(ADP-ribose)glycohydrolase (PARG); will this be a viable strategy for future drug design? The answers to these questions will determine the future of disease therapy through inhibition of PARP.
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Affiliation(s)
- Esther C Y Woon
- Department of Pharmaceutical Chemistry, School of Phatmacy, University of London, UK
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