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Ryan P, Shi Y, von Itzstein M, Rudrawar S. Novel bisubstrate uridine-peptide analogues bearing a pyrophosphate bioisostere as inhibitors of human O-GlcNAc transferase. Bioorg Chem 2021; 110:104738. [PMID: 33667901 DOI: 10.1016/j.bioorg.2021.104738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 11/16/2022]
Abstract
Protein O-linked β-D-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), an essential post-translational as well as cotranslational modification, is the attachment of β-D-N-acetylglucosamine to serine and threonine residues of nucleocytoplasmic proteins. An aberrant O-GlcNAc profile on certain proteins has been implicated in metabolic diseases such as diabetes and cancer. Inhibitors of O-GlcNAc transferase (OGT) are valuable tools to study the cell biology of protein O-GlcNAc modification. In this study we report novel uridine-peptide conjugate molecules composed of an acceptor peptide covalently linked to a catalytically inactive donor substrate analogue that bears a pyrophosphate bioisostere and explore their inhibitory activities against OGT by a radioactive hOGT assay. Further, we investigate the structural basis of their activities via molecular modelling, explaining their lack of potency towards OGT inhibition.
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Affiliation(s)
- Philip Ryan
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia; School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia; School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Yun Shi
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast, QLD 4222, Australia
| | - Santosh Rudrawar
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia; School of Pharmacy and Pharmacology, Griffith University, Gold Coast, QLD 4222, Australia; School of Chemistry, The University of Sydney, NSW 2006, Australia.
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52
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Shevchuk M, Wang Q, Pajkert R, Xu J, Mei H, Röschenthaler G, Han J. Recent Advances in Synthesis of Difluoromethylene Phosphonates for Biological Applications. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202001464] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Michael Shevchuk
- Department of Life Sciences and Chemistry Jacobs University Bremen gGmbH Campus Ring 1 28759 Bremen Germany
| | - Qian Wang
- Jiangsu Co–Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering Nanjing Forestry University Nanjing 210037 People's Republic of China
| | - Romana Pajkert
- Department of Life Sciences and Chemistry Jacobs University Bremen gGmbH Campus Ring 1 28759 Bremen Germany
| | - Jingcheng Xu
- Jiangsu Co–Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering Nanjing Forestry University Nanjing 210037 People's Republic of China
| | - Haibo Mei
- Jiangsu Co–Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering Nanjing Forestry University Nanjing 210037 People's Republic of China
| | - Gerd‐Volker Röschenthaler
- Department of Life Sciences and Chemistry Jacobs University Bremen gGmbH Campus Ring 1 28759 Bremen Germany
| | - Jianlin Han
- Jiangsu Co–Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering Nanjing Forestry University Nanjing 210037 People's Republic of China
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Park J, Pandya VR, Ezekiel SJ, Berghuis AM. Phosphonate and Bisphosphonate Inhibitors of Farnesyl Pyrophosphate Synthases: A Structure-Guided Perspective. Front Chem 2021; 8:612728. [PMID: 33490038 PMCID: PMC7815940 DOI: 10.3389/fchem.2020.612728] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022] Open
Abstract
Phosphonates and bisphosphonates have proven their pharmacological utility as inhibitors of enzymes that metabolize phosphate and pyrophosphate substrates. The blockbuster class of drugs nitrogen-containing bisphosphonates represent one of the best-known examples. Widely used to treat bone-resorption disorders, these drugs work by inhibiting the enzyme farnesyl pyrophosphate synthase. Playing a key role in the isoprenoid biosynthetic pathway, this enzyme is also a potential anticancer target. Here, we provide a comprehensive overview of the research efforts to identify new inhibitors of farnesyl pyrophosphate synthase for various therapeutic applications. While the majority of these efforts have been directed against the human enzyme, some have been targeted on its homologs from other organisms, such as protozoan parasites and insects. Our particular focus is on the structures of the target enzymes and how the structural information has guided the drug discovery efforts.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Vishal R Pandya
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Sean J Ezekiel
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
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54
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Zong G, Jork N, Hostachy S, Fiedler D, Jessen HJ, Shears SB, Wang H. New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1. FASEB J 2021; 35:e21275. [PMID: 33475202 DOI: 10.1096/fj.202001489r] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/30/2020] [Accepted: 11/30/2020] [Indexed: 11/11/2022]
Abstract
Nudix hydrolases attract considerable attention for their wide range of specialized activities in all domains of life. One particular group of Nudix phosphohydrolases (DIPPs), through their metabolism of diphosphoinositol polyphosphates (PP-InsPs), regulates the actions of these polyphosphates upon bioenergetic homeostasis. In the current study, we describe, at an atomic level, hitherto unknown properties of human DIPP1.We provide X-ray analysis of the catalytic core of DIPP1 in crystals complexed with either natural PP-InsPs, alternative PP-InsP stereoisomers, or non-hydrolysable methylene bisphosphonate analogs ("PCP-InsPs"). The conclusions that we draw from these data are interrogated by studying the impact upon catalytic activity upon mutagenesis of certain key residues. We present a picture of a V-shaped catalytic furrow with overhanging ridges constructed from flexible positively charged side chains; within this cavity, the labile phosphoanhydride bond is appropriately positioned at the catalytic site by an extensive series of interlocking polar contacts which we analogize as "suspension cables." We demonstrate functionality for a triglycine peptide within a β-strand which represents a non-canonical addition to the standard Nudix catalytic core structure. We describe pre-reaction enzyme/substrate states which we posit to reflect a role for electrostatic steering in substrate capture. Finally, through time-resolved analysis, we uncover a chronological sequence of DIPP1/product post-reaction states, one of which may rationalize a role for InsP6 as an inhibitor of catalytic activity.
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Affiliation(s)
- Guangning Zong
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Nikolaus Jork
- Institute of Organic Chemistry, CIBSS - Center for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Sarah Hostachy
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, CIBSS - Center for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Stephen B Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Huanchen Wang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
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Dal Corso A, Arosio S, Arrighetti N, Perego P, Belvisi L, Pignataro L, Gennari C. A trifunctional self-immolative spacer enables drug release with two non-sequential enzymatic cleavages. Chem Commun (Camb) 2021; 57:7778-7781. [PMID: 34263896 DOI: 10.1039/d1cc02895b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cyclative cleavage of an amine-carbamate self-immolative spacer to deliver a hydroxyl cargo was inhibited by spacer derivatisation with a phosphate monoester handle. This trifunctional spacer was installed in a model anticancer prodrug that showed fast drug release only when incubated with both a protease and a phosphatase enzyme.
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Affiliation(s)
- Alberto Dal Corso
- Università degli Studi di Milano, Dipartimento di Chimica, via C. Golgi, 19, Milan, I-20133, Italy.
| | - Simone Arosio
- Università degli Studi di Milano, Dipartimento di Chimica, via C. Golgi, 19, Milan, I-20133, Italy.
| | - Noemi Arrighetti
- Fondazione IRCCS Istituto Nazionale dei Tumori, Molecular Pharmacology Unit, Department of Applied Research and Technological Development, via Amadeo 42, Milan, 20133, Italy
| | - Paola Perego
- Fondazione IRCCS Istituto Nazionale dei Tumori, Molecular Pharmacology Unit, Department of Applied Research and Technological Development, via Amadeo 42, Milan, 20133, Italy
| | - Laura Belvisi
- Università degli Studi di Milano, Dipartimento di Chimica, via C. Golgi, 19, Milan, I-20133, Italy.
| | - Luca Pignataro
- Università degli Studi di Milano, Dipartimento di Chimica, via C. Golgi, 19, Milan, I-20133, Italy.
| | - Cesare Gennari
- Università degli Studi di Milano, Dipartimento di Chimica, via C. Golgi, 19, Milan, I-20133, Italy.
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Makukhin N, Ciulli A. Recent advances in synthetic and medicinal chemistry of phosphotyrosine and phosphonate-based phosphotyrosine analogues. RSC Med Chem 2020; 12:8-23. [PMID: 34041480 PMCID: PMC8130623 DOI: 10.1039/d0md00272k] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/30/2020] [Indexed: 11/21/2022] Open
Abstract
Phosphotyrosine-containing compounds attract significant attention due to their potential to modulate signalling pathways by binding to phospho-writers, erasers and readers such as SH2 and PTB domain containing proteins. Phosphotyrosine derivatives provide useful chemical tools to study protein phosphorylation/dephosphorylation, and as such represent attractive starting points for the development of binding ligands and chemical probes to study biology, and for inhibitor and degrader drug design. To overcome enzymatic lability of the phosphate group, physiologically stable phosphonate-based phosphotyrosine analogues find utility in a wide range of applications. This review covers advances over the last decade in the design of phosphotyrosine and its phosphonate-based derivatives, highlights the improved and expanded synthetic toolbox, and illustrates applications in medicinal chemistry.
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Affiliation(s)
- Nikolai Makukhin
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee Dow Street DD1 5EH Dundee UK
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57
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Chasák J, Šlachtová V, Urban M, Brulíková L. Squaric acid analogues in medicinal chemistry. Eur J Med Chem 2020; 209:112872. [PMID: 33035923 DOI: 10.1016/j.ejmech.2020.112872] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/12/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022]
Abstract
In this review, we summarize the published data on squaric acid analogues with a special focus on their use in medicinal chemistry and as potential drugs. Squaric acid is an interesting small molecule with an almost perfectly square shape, and its analogues have a variety of biological activities that are enabled by the presence of significant H-bond donors and acceptors. Unfortunately, most of these compounds also exhibit reactive functionalities, and this deters the majority of medicinal chemists and pharmacologists from trying to use them in drug development. However, this group of compounds is experiencing a renaissance, and large numbers of them are being tested for antiprotozoal, antibacterial, antifungal, and antiviral activities. The most useful of these compounds exhibited IC50 values in the nanomolar range, which makes them promising drug candidates. In addition to these activities, their interactions with living systems were intensively explored, revealing that squaric acid analogues inhibit various enzymes and often serve as receptor antagonists and that the squaric acid moiety may be used as a non-classical isosteric replacement for other functional groups such as carboxylate. In summary, this review is focused on squaric acid and its analogues and their use in medicinal chemistry and should serve as a guide for other researchers in the field to demonstrate the potential of these compounds based on previous research.
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Affiliation(s)
- Jan Chasák
- Department of Organic Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Veronika Šlachtová
- Department of Organic Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Milan Urban
- Medicinal Chemistry, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Hněvotínská 5, 779 00, Olomouc, Czech Republic
| | - Lucie Brulíková
- Department of Organic Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46, Olomouc, Czech Republic.
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58
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Shears SB, Wang H. Metabolism and Functions of Inositol Pyrophosphates: Insights Gained from the Application of Synthetic Analogues. Molecules 2020; 25:E4515. [PMID: 33023101 PMCID: PMC7583957 DOI: 10.3390/molecules25194515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 12/17/2022] Open
Abstract
Inositol pyrophosphates (PP-InsPs) comprise an important group of intracellular, diffusible cellular signals that a wide range of biological processes throughout the yeast, plant, and animal kingdoms. It has been difficult to gain a molecular-level mechanistic understanding of the actions of these molecules, due to their highly phosphorylated nature, their low levels, and their rapid metabolic turnover. More recently, these obstacles to success are being surmounted by the chemical synthesis of a number of insightful PP-InsP analogs. This review will describe these analogs and will indicate the important chemical and biological information gained by using them.
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Affiliation(s)
- Stephen B. Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA;
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59
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Kadri H, Taher TE, Xu Q, Sharif M, Ashby E, Bryan RT, Willcox BE, Mehellou Y. Aryloxy Diester Phosphonamidate Prodrugs of Phosphoantigens (ProPAgens) as Potent Activators of Vγ9/Vδ2 T-Cell Immune Responses. J Med Chem 2020; 63:11258-11270. [PMID: 32930595 PMCID: PMC7549095 DOI: 10.1021/acs.jmedchem.0c01232] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Vγ9/Vδ2 T-cells are activated by pyrophosphate-containing small molecules known as phosphoantigens (PAgs). The presence of the pyrophosphate group in these PAgs has limited their drug-like properties because of its instability and polar nature. In this work, we report a novel and short Grubbs olefin metathesis-mediated synthesis of methylene and difluoromethylene monophosphonate derivatives of the PAg (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBP) as well as their aryloxy diester phosphonamidate prodrugs, termed ProPAgens. These prodrugs showed excellent stability in human serum (t1/2 > 12 h) and potent activation of Vγ9/Vδ2 T-cells (EC50 ranging from 5 fM to 73 nM), which translated into sub-nanomolar γδ T-cell-mediated eradication of bladder cancer cells in vitro. Additionally, a combination of in silico and in vitro enzymatic assays demonstrated the metabolism of these phosphonamidates to release the unmasked PAg monophosphonate species. Collectively, this work establishes HMBP monophosphonate ProPAgens as ideal candidates for further investigation as novel cancer immunotherapeutic agents.
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Affiliation(s)
- Hachemi Kadri
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF10 3NB, U.K
| | - Taher E Taher
- Cancer Immunology and Immunotherapy Centre, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.,Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Qin Xu
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF10 3NB, U.K
| | - Maria Sharif
- Cancer Immunology and Immunotherapy Centre, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.,Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Elizabeth Ashby
- Cancer Immunology and Immunotherapy Centre, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.,Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Richard T Bryan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Benjamin E Willcox
- Cancer Immunology and Immunotherapy Centre, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.,Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Youcef Mehellou
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF10 3NB, U.K
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60
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Bellany F, Tsuchiya Y, Tran TM, Chan AWE, Allan H, Gout I, Tabor AB. Design and synthesis of Coenzyme A analogues as Aurora kinase A inhibitors: An exploration of the roles of the pyrophosphate and pantetheine moieties. Bioorg Med Chem 2020; 28:115740. [PMID: 33007553 DOI: 10.1016/j.bmc.2020.115740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/15/2022]
Abstract
Coenzyme A (CoA) is a highly selective inhibitor of the mitotic regulatory enzyme Aurora A kinase, with a novel mode of action. Herein we report the design and synthesis of analogues of CoA as inhibitors of Aurora A kinase. We have designed and synthesised modified CoA structures as potential inhibitors, combining dicarbonyl mimics of the pyrophosphate group with a conserved adenosine headgroup and different length pantetheine-based tail groups. An analogue with a -SH group at the end of the pantotheinate tail showed the best IC50, probably due to the formation of a covalent bond with Aurora A kinase Cys290.
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Affiliation(s)
- Fiona Bellany
- Department of Chemistry, UCL, Christopher Ingold Building, 20, Gordon Street, London WC1H 0AJ, UK
| | - Yugo Tsuchiya
- Department of Structural and Molecular Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Trang M Tran
- Department of Chemistry, UCL, Christopher Ingold Building, 20, Gordon Street, London WC1H 0AJ, UK
| | - A W Edith Chan
- Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Helen Allan
- Department of Chemistry, UCL, Christopher Ingold Building, 20, Gordon Street, London WC1H 0AJ, UK
| | - Ivan Gout
- Department of Structural and Molecular Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Alethea B Tabor
- Department of Chemistry, UCL, Christopher Ingold Building, 20, Gordon Street, London WC1H 0AJ, UK.
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61
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Design and discovery of boronic acid drugs. Eur J Med Chem 2020; 195:112270. [DOI: 10.1016/j.ejmech.2020.112270] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/22/2020] [Accepted: 03/22/2020] [Indexed: 12/15/2022]
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Hammad SG, El-Gazzar MG, Abutaleb NS, Li D, Ramming I, Shekhar A, Abdel-Halim M, Elrazaz EZ, Seleem MN, Bilitewski U, Abouzid KAM, El-Hossary EM. Synthesis and antimicrobial evaluation of new halogenated 1,3-Thiazolidin-4-ones. Bioorg Chem 2019; 95:103517. [PMID: 31884138 DOI: 10.1016/j.bioorg.2019.103517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/08/2019] [Accepted: 12/16/2019] [Indexed: 12/22/2022]
Abstract
The ongoing prevalence of multidrug-resistant bacterial pathogens requires the development of new effective antibacterial agents. In this study, two series of halogenated 1,3-thiazolidin-4-ones were synthesized and characterized. All the synthesized thiazolidinone derivatives were evaluated for their antimicrobial activity. Biological screening of the tested compounds revealed the antibacterial activity of the chlorinated thiazolidinones 4a, 4b and 4c against Escherichia coli TolC-mutant, with MIC values of 16 µg/mL. A combination of a sub-inhibitory concentration of colistin (0.25 × MIC) with compounds 4a, 4b or 4c showed antibacterial activity against different Gram-negative bacteria (MICs = 4-16 µg/mL). Interestingly, compounds 4a, 4b and 4c were not cytotoxic to murine fibroblasts and Caco-2 cells. The chlorinated thiazolidinone derivative 16d demonstrated a bacteriostatic activity against a panel of pathogenic Gram-positive bacteria, including clinical isolates of methicillin and vancomycin-resistant Staphylococcus aureus, Listeria monocytogenes and multidrug-resistant Staphylococcus epidermidis (MICs = 8 - 64 µg/mL), with no cytotoxicity against both Caco-2 and L929 cells. Compound 16d was superior to vancomycin in disruption of the pre-formed MRSA biofilm. Furthermore, the three fluorinated thiazolidinone derivatives 26c, 30c and 33c showed a hindrance to hemolysin activity, without cytotoxicity against L929 cells.
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Affiliation(s)
- Shaymaa G Hammad
- National Centre for Radiation Research & Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Ahmed El-Zomor St. 3, El-Zohoor Dist., Nasr City, Cairo 11765, Egypt
| | - Marwa G El-Gazzar
- National Centre for Radiation Research & Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Ahmed El-Zomor St. 3, El-Zohoor Dist., Nasr City, Cairo 11765, Egypt.
| | - Nader S Abutaleb
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
| | - Daoyi Li
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
| | - Isabell Ramming
- Helmholtz Center for Infection Research, WG Compound Profiling and Screening (COPS), Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Aditya Shekhar
- Helmholtz Center for Infection Research, WG Compound Profiling and Screening (COPS), Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Eman Z Elrazaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain-Shams University, Abbassia, Cairo 11566, Egypt
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA; Purdue Institute of Inflammation, Immunology, and Infectious Diseases, West Lafayette, IN 47907, USA
| | - Ursula Bilitewski
- Helmholtz Center for Infection Research, WG Compound Profiling and Screening (COPS), Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Khaled A M Abouzid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain-Shams University, Abbassia, Cairo 11566, Egypt; Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City, Menoufia, Egypt.
| | - Ebaa M El-Hossary
- National Centre for Radiation Research & Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Ahmed El-Zomor St. 3, El-Zohoor Dist., Nasr City, Cairo 11765, Egypt
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63
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Synthesis of Enantiomerically Pure N-Boc-Protected 1,2,3-Triaminopropylphosphonates and 1,2-Diamino-3-Hydroxypropylphosphonates. Molecules 2019; 24:molecules24213857. [PMID: 31731561 PMCID: PMC6864986 DOI: 10.3390/molecules24213857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/16/2019] [Accepted: 10/22/2019] [Indexed: 11/21/2022] Open
Abstract
All possible isomers of 1,2,3-tri(N-tert-butoxycarbonylamino)propylphosphonate 6 were synthesized from the respective diethyl [N-(1-phenylethyl)]-1-benzylamino-2,3-epiiminopropylphosphonates 5 via opening the aziridine ring with trimethylsilyl azide (TMSN3) followed by hydrogenolysis in the presence of di-tert-butyl dicarbonate (Boc2O). [N-(1-phenylethyl)]-1-benzylamino-2,3-epiiminopropylphosphonates (1R,2R,1′S)-5a and (1S,2S,1′R)-5c were smoothly transformed into diethyl 3-acetoxy-1-benzylamino-2-[N-(1-phenylethyl)amino]propylphosphonates (1R,2R,1′S)-9a and (1S,2S,1′R)-9c, respectively by the opening of the aziridine ring with acetic acid. Transformations of [N-(1-phenylethyl)]-1-benzylamino-2,3-epiiminopropylphosphonates (1S,2R,1′S)-5b and (1R,2S,1′R)-5d into diethyl 3-acetoxy-1-benzylamino-2-[(1-phenylethyl)amino]propylphosphonates (1S,2R,1′S)-9b and (1R,2S,1′R)-9d were accompanied by the formation of ethyl {1-(N-benzylacetamido)-3-hydroxy-2-[(1-phenylethyl)amino]propyl}phosphonate (1S,2R,1′S)-10b and (1R,2S,1′R)-10d and 3-(N-benzylacetamido)-4-[N-(1-phenylethyl)]amino-1,2-oxaphospholane (3S,4R,1′S)-11b and (3R,4S,1′R)-11d as side products. Diethyl (1R,2R)-, (1S,2S)-, (1S,2R)- and (1R,2S)-3-acetoxy-1,2-di(N-tert-butoxycarbonylamino)propylphosphonates 7a–7d were obtained from the respective 3-acetoxy-1-benzylamino-2-[N-(1-phenylethyl)amino]propylphosphonates 9a–9d by hydrogenolysis in the presence of Boc2O.
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Popović V, Morrison E, Rosanally AZ, Balachandran N, Senson AW, Szabla R, Junop MS, Berti PJ. NeuNAc Oxime: A Slow-Binding and Effectively Irreversible Inhibitor of the Sialic Acid Synthase NeuB. Biochemistry 2019; 58:4236-4245. [PMID: 31549502 DOI: 10.1021/acs.biochem.9b00654] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NeuB is a bacterial sialic acid synthase used by neuroinvasive bacteria to synthesize N-acetylneuraminate (NeuNAc), helping them to evade the host immune system. NeuNAc oxime is a potent slow-binding NeuB inhibitor. It dissociated too slowly to be detected experimentally, with initial estimates of its residence time in the active site being >47 days. This is longer than the lifetime of a typical bacterial cell, meaning that inhibition is effectively irreversible. Inhibition data fitted well to a model that included a pre-equilibration step with a Ki of 36 μM, followed by effectively irreversible conversion to an E*·I complex, with a k2 of 5.6 × 10-5 s-1. Thus, the inhibitor can subvert ligand release and achieve extraordinary residence times in spite of a relatively modest initial dissociation constant. The crystal structure showed the oxime functional group occupying the phosphate-binding site normally occupied by the substrate PEP and the tetrahedral intermediate. There was an ≈10% residual rate at high inhibitor concentrations regardless of how long NeuB and NeuNAc oxime were preincubated together. However, complete inhibition was achieved by incubating NeuNAc oxime with the actively catalyzing enzyme. This requirement for the enzyme to be actively turning over for the inhibitor to bind to the second subunit demonstrated an important role for intersubunit communication in the inhibitory mechanism.
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Affiliation(s)
| | | | | | | | | | - Robert Szabla
- Department of Biochemistry, Molecular Biology Lab , Western University , London , ON N6A 5C1 , Canada
| | - Murray S Junop
- Department of Biochemistry, Molecular Biology Lab , Western University , London , ON N6A 5C1 , Canada
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65
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Clausse V, Tao D, Debnath S, Fang Y, Tagad HD, Wang Y, Sun H, LeClair CA, Mazur SJ, Lane K, Shi ZD, Vasalatiy O, Eells R, Baker LK, Henderson MJ, Webb MR, Shen M, Hall MD, Appella E, Appella DH, Coussens NP. Physiologically relevant orthogonal assays for the discovery of small-molecule modulators of WIP1 phosphatase in high-throughput screens. J Biol Chem 2019; 294:17654-17668. [PMID: 31481464 PMCID: PMC6873202 DOI: 10.1074/jbc.ra119.010201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/30/2019] [Indexed: 01/07/2023] Open
Abstract
WT P53-Induced Phosphatase 1 (WIP1) is a member of the magnesium-dependent serine/threonine protein phosphatase (PPM) family and is induced by P53 in response to DNA damage. In several human cancers, the WIP1 protein is overexpressed, which is generally associated with a worse prognosis. Although WIP1 is an attractive therapeutic target, no potent, selective, and bioactive small-molecule modulator with favorable pharmacokinetics has been reported. Phosphatase enzymes are among the most challenging targets for small molecules because of the difficulty of achieving both modulator selectivity and bioavailability. Another major obstacle has been the availability of robust and physiologically relevant phosphatase assays that are suitable for high-throughput screening. Here, we describe orthogonal biochemical WIP1 activity assays that utilize phosphopeptides from native WIP1 substrates. We optimized an MS assay to quantify the enzymatically dephosphorylated peptide reaction product in a 384-well format. Additionally, a red-shifted fluorescence assay was optimized in a 1,536-well format to enable real-time WIP1 activity measurements through the detection of the orthogonal reaction product, Pi. We validated these two optimized assays by quantitative high-throughput screening against the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection and used secondary assays to confirm and evaluate inhibitors identified in the primary screen. Five inhibitors were further tested with an orthogonal WIP1 activity assay and surface plasmon resonance binding studies. Our results validate the application of miniaturized physiologically relevant and orthogonal WIP1 activity assays to discover small-molecule modulators from high-throughput screens.
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Affiliation(s)
- Victor Clausse
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Subrata Debnath
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Harichandra D Tagad
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Hongmao Sun
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Sharlyn J Mazur
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Kelly Lane
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Zhen-Dan Shi
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Olga Vasalatiy
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Rebecca Eells
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Lynn K Baker
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Martin R Webb
- Francis Crick Institute, 1 Midland Road, London NW1 AT, United Kingdom
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Ettore Appella
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Nathan P Coussens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
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66
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Riley AM, Wang H, Shears SB, Potter BVL. Synthesis of an α-phosphono-α,α-difluoroacetamide analogue of the diphosphoinositol pentakisphosphate 5-InsP 7. MEDCHEMCOMM 2019; 10:1165-1172. [PMID: 31391889 PMCID: PMC6657673 DOI: 10.1039/c9md00163h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/08/2019] [Indexed: 12/16/2022]
Abstract
Diphosphoinositol phosphates (PP-InsPs) are an evolutionarily ancient group of signalling molecules that are essential to cellular and organismal homeostasis. As the detailed mechanisms of PP-InsP signalling begin to emerge, synthetic analogues of PP-InsPs containing stabilised mimics of the labile diphosphate group can provide valuable investigational tools. We synthesised 5-PCF2Am-InsP5 (1), a novel fluorinated phosphonate analogue of 5-PP-InsP5, and obtained an X-ray crystal structure of 1 in complex with diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2). 5-PCF2Am-InsP5 binds to the kinase domain of PPIP5K2 in a similar orientation to that of the natural substrate 5-PP-InsP5 and the PCF2Am structure can mimic many aspects of the diphosphate group in 5-PP-InsP5. We propose that 1, the structural and electronic properties of which are in some ways complementary to those of existing phosphonoacetate and methylenebisphosphonate analogues of 5-PP-InsP5, may be a useful addition to the expanding array of chemical tools for the investigation of signalling by PP-InsPs. The PCF2Am group may also deserve attention for wider application as a diphosphate mimic.
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Affiliation(s)
- Andrew M Riley
- Medicinal Chemistry and Drug Discovery , Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , UK . ; ; Tel: +44 (0)1865 271945
| | - Huanchen Wang
- Inositol Signaling Group , Laboratory of Signal Transduction , National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle Park , North Carolina , USA
| | - Stephen B Shears
- Inositol Signaling Group , Laboratory of Signal Transduction , National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle Park , North Carolina , USA
| | - Barry V L Potter
- Medicinal Chemistry and Drug Discovery , Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , UK . ; ; Tel: +44 (0)1865 271945
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67
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Leaver DJ, Cleary B, Nguyen N, Priebbenow DL, Lagiakos HR, Sanchez J, Xue L, Huang F, Sun Y, Mujumdar P, Mudududdla R, Varghese S, Teguh S, Charman SA, White KL, Katneni K, Cuellar M, Strasser JM, Dahlin JL, Walters MA, Street IP, Monahan BJ, Jarman KE, Sabroux HJ, Falk H, Chung MC, Hermans SJ, Parker MW, Thomas T, Baell JB. Discovery of Benzoylsulfonohydrazides as Potent Inhibitors of the Histone Acetyltransferase KAT6A. J Med Chem 2019; 62:7146-7159. [DOI: 10.1021/acs.jmedchem.9b00665] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | | | | | - H. Rachel Lagiakos
- Cancer Therapeutics CRC, 343 Royal Parade, Parkville, Victoria 3052, Australia
| | - Julie Sanchez
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Lian Xue
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People’s Republic of China
| | - Fei Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People’s Republic of China
| | | | | | | | | | | | | | | | | | - Matthew Cuellar
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55455, United States
| | - Jessica M. Strasser
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55455, United States
| | - Jayme L. Dahlin
- Department of Pathology, Brigham and Women’s Hospital, Boston, 75 Francis Street, Boston, Massachusetts 02115, United States
| | - Michael A. Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55455, United States
| | - Ian P. Street
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Cancer Therapeutics CRC, 343 Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Brendon J. Monahan
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Cancer Therapeutics CRC, 343 Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Kate E. Jarman
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Helene Jousset Sabroux
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Hendrik Falk
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Cancer Therapeutics CRC, 343 Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Matthew C. Chung
- ACRF Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Stefan J. Hermans
- ACRF Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Michael W. Parker
- ACRF Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Tim Thomas
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Jonathan B. Baell
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People’s Republic of China
- ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria 3052, Australia
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68
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Al Otaibi A, Deane FM, Russell CC, Hizartzidis L, McCluskey SN, Sakoff JA, McCluskey A. A methanol and protic ionic liquid Ugi multicomponent reaction path to cytotoxic α-phenylacetamido amides. RSC Adv 2019; 9:7652-7663. [PMID: 35521167 PMCID: PMC9061180 DOI: 10.1039/c9ra00118b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 02/04/2019] [Indexed: 12/03/2022] Open
Abstract
The Ugi four component reaction of an aldehyde, amine, isocyanide and an ethanoic acid was effected smoothly in protic ionic liquids ethylammonium nitrate (EAN) and propylammonium nitrate (PAN) to afford analogues of α-phenylacetamido amides in good to excellent isolated yields. The corresponding reactions in [BMIM][PF6] and the protic ionic liquid ethanolammonium nitrate (ETAN) failed. Microwave irradiation in EAN facilitated rapid access to three focused libraries, based on the parent isocyanide: cyclohexyl isocyanide, benzyl isocyanide and ethyl isocyanoacetate. Analysis of the structure activity relationship data suggested the presence of a bulky moiety originating from the isocyanide (cyclohexyl and benzyl) enhanced cytotoxicity. Removal of the acetylenic H-atom from the ethanoic acid moiety was detrimental to cytotoxicity. The most active analogues produced, N-(2-cyclohexylamino)-1-(4-methoxyphenyl)-2-oxoethyl-N-(3,5-dimethoxyphenyl)propiolamide, returned average GI50 values of ≤1 μM across the cancer cell lines evaluated. Combined, these data suggest that analogues of this nature are interesting potential anti-cancer development leads. The Ugi reaction (aldehyde, amine, isocyanide and an ethanoic acid) in the protic ionic liquids ethylammonium nitrate (EAN) and propylammonium nitrate (PAN) gave excellent yields of α-phenylacetamido amides.![]()
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Affiliation(s)
- Ahmed Al Otaibi
- Chemistry, School of Environmental & Life Sciences
- The University of Newcastle
- Australia
| | - Fiona M. Deane
- Chemistry, School of Environmental & Life Sciences
- The University of Newcastle
- Australia
| | - Cecilia C. Russell
- Chemistry, School of Environmental & Life Sciences
- The University of Newcastle
- Australia
| | - Lacey Hizartzidis
- Chemistry, School of Environmental & Life Sciences
- The University of Newcastle
- Australia
| | - Siobhann N. McCluskey
- Chemistry, School of Environmental & Life Sciences
- The University of Newcastle
- Australia
| | | | - Adam McCluskey
- Chemistry, School of Environmental & Life Sciences
- The University of Newcastle
- Australia
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69
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Kershaw NM, Byrne DP, Parsons H, Berry NG, Fernig DG, Eyers PA, Cosstick R. Structure-based design of nucleoside-derived analogues as sulfotransferase inhibitors. RSC Adv 2019; 9:32165-32173. [PMID: 35530783 PMCID: PMC9072872 DOI: 10.1039/c9ra07567d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 10/03/2019] [Indexed: 12/12/2022] Open
Abstract
Regulated sulfation of biomolecules by sulfotransferases (STs) plays a role in many biological processes with implications for a number of disease areas. A structure-based approach and molecular docking were used to design a library of ST inhibitors.
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Affiliation(s)
- Neil M. Kershaw
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - Dominic P. Byrne
- Department of Biochemistry
- Institute of Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
- UK
| | - Hollie Parsons
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - Neil G. Berry
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - David G. Fernig
- Department of Biochemistry
- Institute of Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
- UK
| | - Patrick A. Eyers
- Department of Biochemistry
- Institute of Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
- UK
| | - Richard Cosstick
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
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70
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Dürr E, Doherty W, Lee SY, El‐Sagheer AH, Shivalingam A, McHugh PJ, Brown T, McGouran JF. Squaramide-Based 5'-Phosphate Replacements Bind to the DNA Repair Exonuclease SNM1A. ChemistrySelect 2018; 3:12824-12829. [PMID: 31414040 PMCID: PMC6685075 DOI: 10.1002/slct.201803375] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/19/2018] [Indexed: 12/26/2022]
Abstract
Phosphate groups are often crucial to biological activity and interactions of oligonucleotides, but confer poor membrane permeability. In addition, the group's lability to enzymatic hydrolysis is an obstacle to its use in therapeutics and in biological tools. We present the synthesis of N-oxyamide and squaramide modifications at the 5'-end of oligonucleotides as phosphate replacements and their biological evaluation using the 5'-exonuclease SNM1A. The squaryl diamide modification showed minimal recognition as a 5'-phosphate mimic; however, modest inhibition of SNM1A, postulated to occur through metal coordination at the active site, was observed. Their facile incorporation after solid-phase synthesis and recognition by the exonuclease makes squaryl diamides attractive neutral 5'-phosphate replacements for oligonucleotides. This work is the first example of squaryl diamide modifications at the 5'-terminal position of oligonucleotides and of the potential use of modified oligonucleotides to bind to the metal center of SNM1A.
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Affiliation(s)
- Eva‐Maria Dürr
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College Dublin152-160 Pearse St.Dublin 2Ireland
| | - William Doherty
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College Dublin152-160 Pearse St.Dublin 2Ireland
| | - Sook Y. Lee
- Department of OncologyWeatherall Institute of Molecular MedicineUniversity of Oxford, John Radcliffe HospitalOxford OX3 9DSUK
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
| | - Afaf H. El‐Sagheer
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
- Chemistry Branch, Department of Science and MathematicsFaculty of Petroleum and Mining Engineering, Suez UniversitySuez43721Egypt
| | - Arun Shivalingam
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
| | - Peter J. McHugh
- Department of OncologyWeatherall Institute of Molecular MedicineUniversity of Oxford, John Radcliffe HospitalOxford OX3 9DSUK
| | - Tom Brown
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxford OX1 3TAUK
| | - Joanna F. McGouran
- School of ChemistryTrinity Biomedical Sciences InstituteTrinity College Dublin152-160 Pearse St.Dublin 2Ireland
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71
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Heron PW, Abellán-Flos M, Salmon L, Sygusch J. Bisphosphonate Inhibitors of Mammalian Glycolytic Aldolase. J Med Chem 2018; 61:10558-10572. [PMID: 30418024 DOI: 10.1021/acs.jmedchem.8b01000] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The glycolytic enzyme aldolase is an emerging drug target in diseases such as cancer and protozoan infections which are dependent on a hyperglycolytic phenotype to synthesize adenosine 5'-triphosphate and metabolic precursors for biomass production. To date, structural information for the enzyme in complex with phosphate-derived inhibitors has been lacking. Thus, we determined the crystal structure of mammalian aldolase in complex with naphthalene 2,6-bisphosphate (1) that served as a template for the design of bisphosphonate-based inhibitors, namely, 2-phosphate-naphthalene 6-bisphosphonate (2), 2-naphthol 6-bisphosphonate (3), and 1-phosphate-benzene 4-bisphosphonate (4). All inhibitors targeted the active site, and the most promising lead, 2, exhibited slow-binding inhibition with an overall inhibition constant of ∼38 nM. Compound 2 inhibited proliferation of HeLa cancer cells, whereas HEK293 cells expressing a normal phenotype were not inhibited. The crystal structures delineated the essential features of high-affinity phosphate-derived inhibitors and provide a template for the development of inhibitors with prophylaxis potential.
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Affiliation(s)
- Paul W Heron
- Département de Biochimie et Médecine Moléculaire , Université de Montréal , CP 6128, Succursale Centre-Ville, Montréal , Québec H3C 3J7 , Canada
| | - Marta Abellán-Flos
- Equipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux D'Orsay (ICMMO) , Univ Paris-Saclay, Univ Paris-Sud, CNRS UMR8182, LabEx LERMIT , rue du doyen Georges Poitou , F-91405 Orsay , France
| | - Laurent Salmon
- Equipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux D'Orsay (ICMMO) , Univ Paris-Saclay, Univ Paris-Sud, CNRS UMR8182, LabEx LERMIT , rue du doyen Georges Poitou , F-91405 Orsay , France
| | - Jurgen Sygusch
- Département de Biochimie et Médecine Moléculaire , Université de Montréal , CP 6128, Succursale Centre-Ville, Montréal , Québec H3C 3J7 , Canada
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72
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Pandith A, Koo J, Seo YJ. Daphnetin: A novel blue-green photonic switch for disodium phosphates that allows monitoring of polymerase chain reactions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 204:620-628. [PMID: 29980064 DOI: 10.1016/j.saa.2018.06.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/15/2018] [Accepted: 06/23/2018] [Indexed: 06/08/2023]
Abstract
This paper describes the very simple and robust ratiometric photonic switching properties of daphnetin (DP) toward HPO42- ions selectively in complex biological fluids, without any interference from other relevant anions under physiological conditions. The sensing ability of DP toward HPO42- ions was first demonstrated using UV-Vis and fluorescence spectroscopy, dynamic light scattering (DLS), and one- and two-dimensional NMR spectroscopy. DP can detect HPO42- ions at concentrations up to the sub-micromolar/nanomolar level very effectively, with a ratiometric response resulting from intramolecular charge transfer aided by aggregated-induced emission. The interactions between DP and HPO42- ions resulted in new bands appearing in the UV-Vis (at 385 nm) and emission (at 535 nm) spectra. The noncovalently held HPO42- ions induced pronounced specific aggregation of DP molecules, resulting in the new excimer band at 535 nm while retaining the monomer band centered at 445 nm. In contrast, reciprocal absorptivity changes were observed at 320 and 385 nm, with exponential decrements and increments, respectively. This probe could effectively monitor the consumption of dNTPs during various cycles of the polymerase chain reaction performed with relatively short oligonucleotides as well as genomic DNA from Agrobacterium tumefaciens (AcH5α strain).
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Affiliation(s)
- Anup Pandith
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea
| | - Jachoon Koo
- Division of Science Education and Institute of Fusion Science, Chonbuk National University, Jeonju 54398, Republic of Korea
| | - Young Jun Seo
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea.
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73
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Tu J, Song LT, Zhai HL, Wang J, Zhang XY. Selective mechanisms and molecular design of 2,4 Diarylaminopyrimidines as ALK inhibitors. Int J Biol Macromol 2018; 118:1149-1156. [PMID: 30001602 DOI: 10.1016/j.ijbiomac.2018.06.192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/30/2018] [Accepted: 06/30/2018] [Indexed: 12/30/2022]
Abstract
As an attractive therapeutic target for non-small-cell lung cancer (NSCLC), anaplastic lymphoma kinase (ALK) has got increased attention, and the selectivity of ALK inhibitors is an enormous challenge. Recently, 2,4-Diarylaminopyrimidines with high inhibitory activity over InsR/IGF1R were reported as ALK inhibitors, which harboring phosphine oxide moiety. In this work, it is the first time to reveal that the incorporation of dimethylphosphine oxide moiety and the smaller active pocket of ALK is key factor in the selectivity of inhibitor 11q toward ALK over IGF1R/InsR. The results of molecular simulation indicate that the subtle change in the binding pocket of ALK is mainly associated with the flexibility of P-loop and the own residues K1150 and D1270. The replacement of the dimethylphosphine oxide and methylpiperazine of inhibitor 11q would alter the major inhibitory effects of binding and activation. The results further combined 3D-QSAR can not only profile the binding mechanism between the 2,4-Diarylaminopyrimidines inhibitors and ALK, but also supply the useful information for the rational design of a more potential small molecule inhibitor bound to ALK receptor.
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Affiliation(s)
- Jing Tu
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Li Ting Song
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China.
| | - Juan Wang
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Xiao Yun Zhang
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
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74
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Gama SR, Balachandran N, Berti PJ. Campylobacter jejuni KDO8P Synthase, Its Inhibition by KDO8P Oxime, and Control of the Residence Time of Slow-Binding Inhibition. Biochemistry 2018; 57:5327-5338. [DOI: 10.1021/acs.biochem.8b00748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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75
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Ruddraraju KV, Zhang ZY. Covalent inhibition of protein tyrosine phosphatases. MOLECULAR BIOSYSTEMS 2018; 13:1257-1279. [PMID: 28534914 DOI: 10.1039/c7mb00151g] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein tyrosine phosphatases (PTPs) are a large family of 107 signaling enzymes that catalyze the hydrolytic removal of phosphate groups from tyrosine residues in a target protein. The phosphorylation status of tyrosine residues on proteins serve as a ubiquitous mechanism for cellular signal transduction. Aberrant function of PTPs can lead to many human diseases, such as diabetes, obesity, cancer, and autoimmune diseases. As the number of disease relevant PTPs increases, there is urgency in developing highly potent inhibitors that are selective towards specific PTPs. Most current efforts have been devoted to the development of active site-directed and reversible inhibitors for PTPs. This review summarizes recent progress made in the field of covalent inhibitors to target PTPs. Here, we discuss the in vivo and in vitro inactivation of various PTPs by small molecule-containing electrophiles, such as Michael acceptors, α-halo ketones, epoxides, and isothiocyanates, etc. as well as oxidizing agents. We also suggest potential strategies to transform these electrophiles into isozyme selective covalent PTP inhibitors.
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Affiliation(s)
- Kasi Viswanatharaju Ruddraraju
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA.
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76
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Zhang Y, Jumppanen M, Maksimainen MM, Auno S, Awol Z, Ghemtio L, Venkannagari H, Lehtiö L, Yli-Kauhaluoma J, Xhaard H, Boije Af Gennäs G. Adenosine analogs bearing phosphate isosteres as human MDO1 ligands. Bioorg Med Chem 2018; 26:1588-1597. [PMID: 29501416 DOI: 10.1016/j.bmc.2018.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 02/01/2018] [Accepted: 02/05/2018] [Indexed: 12/19/2022]
Abstract
The human O-acetyl-ADP-ribose deacetylase MDO1 is a mono-ADP-ribosylhydrolase involved in the reversal of post-translational modifications. Until now MDO1 has been poorly characterized, partly since no ligand is known besides adenosine nucleotides. Here, we synthesized thirteen compounds retaining the adenosine moiety and bearing bioisosteric replacements of the phosphate at the ribose 5'-oxygen. These compounds are composed of either a squaryldiamide or an amide group as the bioisosteric replacement and/or as a linker. To these groups a variety of substituents were attached such as phenyl, benzyl, pyridyl, carboxyl, hydroxy and tetrazolyl. Biochemical evaluation showed that two compounds, one from both series, inhibited ADP-ribosyl hydrolysis mediated by MDO1 in high concentrations.
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Affiliation(s)
- Yuezhou Zhang
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, Finland
| | - Mikael Jumppanen
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, Finland
| | - Mirko M Maksimainen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, FI-90014 University of Oulu, Finland
| | - Samuli Auno
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, Finland
| | - Zulfa Awol
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, Finland
| | - Léo Ghemtio
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, FI-00014 University of Helsinki, Finland
| | - Harikanth Venkannagari
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, FI-90014 University of Oulu, Finland
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, FI-90014 University of Oulu, Finland
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, Finland
| | - Henri Xhaard
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, Finland
| | - Gustav Boije Af Gennäs
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, FI-00014 University of Helsinki, Finland.
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77
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Meanwell NA. Fluorine and Fluorinated Motifs in the Design and Application of Bioisosteres for Drug Design. J Med Chem 2018; 61:5822-5880. [PMID: 29400967 DOI: 10.1021/acs.jmedchem.7b01788] [Citation(s) in RCA: 1365] [Impact Index Per Article: 227.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The electronic properties and relatively small size of fluorine endow it with considerable versatility as a bioisostere and it has found application as a substitute for lone pairs of electrons, the hydrogen atom, and the methyl group while also acting as a functional mimetic of the carbonyl, carbinol, and nitrile moieties. In this context, fluorine substitution can influence the potency, conformation, metabolism, membrane permeability, and P-gp recognition of a molecule and temper inhibition of the hERG channel by basic amines. However, as a consequence of the unique properties of fluorine, it features prominently in the design of higher order structural metaphors that are more esoteric in their conception and which reflect a more sophisticated molecular construction that broadens biological mimesis. In this Perspective, applications of fluorine in the construction of bioisosteric elements designed to enhance the in vitro and in vivo properties of a molecule are summarized.
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Affiliation(s)
- Nicholas A Meanwell
- Discovery Chemistry and Molecular Technologies Bristol-Myers Squibb Research and Development P.O. Box 4000, Princeton , New Jersey 08543-4000 , United States
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78
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Ding F, Guy AT, Greimel P, Hirabayashi Y, Kamiguchi H, Ito Y. Squaryl group modified phosphoglycolipid analogs as potential modulators of GPR55. Chem Commun (Camb) 2018; 54:8470-8473. [DOI: 10.1039/c8cc04467h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We report the facile synthesis of a series of LPGlc analogs, their GPR dependent biological activity and a systematic analysis of the structure–activity relationship in regards to GPR55 modulation.
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Affiliation(s)
- Feiqing Ding
- Synthetic Cellular Chemistry Laboratory
- RIKEN
- Wako
- Japan
| | | | | | | | | | - Yukishige Ito
- Synthetic Cellular Chemistry Laboratory
- RIKEN
- Wako
- Japan
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79
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Marques I, Costa PMR, Q. Miranda M, Busschaert N, Howe ENW, Clarke HJ, Haynes CJE, Kirby IL, Rodilla AM, Pérez-Tomás R, Gale PA, Félix V. Full elucidation of the transmembrane anion transport mechanism of squaramides using in silico investigations. Phys Chem Chem Phys 2018; 20:20796-20811. [DOI: 10.1039/c8cp02576b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The anion carrier mechanism promoted by squaramide-based molecules has been elucidated by molecular dynamics and chloride efflux studies.
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Affiliation(s)
- Igor Marques
- Department of Chemistry
- CICECO – Aveiro Institute of Materials
- University of Aveiro
- Aveiro
- Portugal
| | - Pedro M. R. Costa
- Department of Chemistry
- CICECO – Aveiro Institute of Materials
- University of Aveiro
- Aveiro
- Portugal
| | - Margarida Q. Miranda
- Department of Chemistry
- CICECO – Aveiro Institute of Materials
- University of Aveiro
- Aveiro
- Portugal
| | | | - Ethan N. W. Howe
- Chemistry
- University of Southampton
- Southampton
- UK
- School of Chemistry
| | | | | | | | - Ananda M. Rodilla
- University of Barcelona
- Faculty of Medicine
- Dept. Pathology and Experimental Therapeutics
- CCBRG
- Barcelona
| | - Ricardo Pérez-Tomás
- University of Barcelona
- Faculty of Medicine
- Dept. Pathology and Experimental Therapeutics
- CCBRG
- Barcelona
| | - Philip A. Gale
- Chemistry
- University of Southampton
- Southampton
- UK
- School of Chemistry
| | - Vítor Félix
- Department of Chemistry
- CICECO – Aveiro Institute of Materials
- University of Aveiro
- Aveiro
- Portugal
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80
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Saha A, Panda S, Pradhan N, Kalita K, Trivedi V, Manna D. Azidophosphonate Chemistry as a Route for a Novel Class of Vesicle-Forming Phosphonolipids. Chemistry 2017; 24:1121-1127. [DOI: 10.1002/chem.201704000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Abhishek Saha
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati- 781039, Assam India
| | - Subhankar Panda
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati- 781039, Assam India
| | - Nirmalya Pradhan
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati- 781039, Assam India
| | - Kangkan Kalita
- Department of Bioscience and Bioengineering; Indian Institute of Technology Guwahati; Guwahati- 781039, Assam India
| | - Vishal Trivedi
- Department of Bioscience and Bioengineering; Indian Institute of Technology Guwahati; Guwahati- 781039, Assam India
| | - Debasis Manna
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati- 781039, Assam India
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81
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Meanwell NA. Drug-target interactions that involve the replacement or displacement of magnesium ions. Bioorg Med Chem Lett 2017; 27:5355-5372. [DOI: 10.1016/j.bmcl.2017.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 01/11/2023]
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82
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Crespi S, Protti S, Ravelli D, Merli D, Fagnoni M. Sugar-Assisted Photogeneration of Didehydrotoluenes from Chlorobenzylphosphonic Acids. J Org Chem 2017; 82:12162-12172. [PMID: 29019237 DOI: 10.1021/acs.joc.7b01963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Irradiation of the three isomeric chlorobenzylphophonic acids in aqueous buffer led to a pH-dependent photochemistry. Under acidic conditions (pH = 2.5), photocleavage of the Ar-Cl bond occurred and a phenyl cation chemistry resulted. Under basic conditions (pH = 11), a photoinduced release of the chloride anion followed by the detachment of the metaphosphate anion gave α,n-didehydrotoluene diradicals (α,n-DHTs), potential DNA cleaving intermediates. At a physiological pH (pH = 7.2), both a cationic and a diradical reactivity took place depending on the phosphonic acid used. It is noteworthy that the complexation exerted by a monosaccharide (glucose or methylglucopyranoside) present in solution induced an exclusive formation of α,n-DHTs. The mechanistic scenario of the different photoreactivities occurring when changing the pH of the solution and the role of the various intermediates (phenyl cations, diradicals, etc.) in the process was studied by computational analysis.
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Affiliation(s)
- Stefano Crespi
- PhotoGreen Lab, Department of Chemistry, University of Pavia , Viale Taramelli 12, 27100 Pavia, Italy
| | - Stefano Protti
- PhotoGreen Lab, Department of Chemistry, University of Pavia , Viale Taramelli 12, 27100 Pavia, Italy
| | - Davide Ravelli
- PhotoGreen Lab, Department of Chemistry, University of Pavia , Viale Taramelli 12, 27100 Pavia, Italy
| | - Daniele Merli
- PhotoGreen Lab, Department of Chemistry, University of Pavia , Viale Taramelli 12, 27100 Pavia, Italy
| | - Maurizio Fagnoni
- PhotoGreen Lab, Department of Chemistry, University of Pavia , Viale Taramelli 12, 27100 Pavia, Italy
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83
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Edwards RL, Brothers RC, Wang X, Maron MI, Ziniel PD, Tsang PS, Kraft TE, Hruz PW, Williamson KC, Dowd CS, John ARO. MEPicides: potent antimalarial prodrugs targeting isoprenoid biosynthesis. Sci Rep 2017; 7:8400. [PMID: 28827774 PMCID: PMC5567135 DOI: 10.1038/s41598-017-07159-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 06/21/2017] [Indexed: 01/29/2023] Open
Abstract
The emergence of Plasmodium falciparum resistant to frontline therapeutics has prompted efforts to identify and validate agents with novel mechanisms of action. MEPicides represent a new class of antimalarials that inhibit enzymes of the methylerythritol phosphate (MEP) pathway of isoprenoid biosynthesis, including the clinically validated target, deoxyxylulose phosphate reductoisomerase (Dxr). Here we describe RCB-185, a lipophilic prodrug with nanomolar activity against asexual parasites. Growth of P. falciparum treated with RCB-185 was rescued by isoprenoid precursor supplementation, and treatment substantially reduced metabolite levels downstream of the Dxr enzyme. In addition, parasites that produced higher levels of the Dxr substrate were resistant to RCB-185. Notably, environmental isolates resistant to current therapies remained sensitive to RCB-185, the compound effectively treated sexually-committed parasites, and was both safe and efficacious in malaria-infected mice. Collectively, our data demonstrate that RCB-185 potently and selectively inhibits Dxr in P. falciparum, and represents a promising lead compound for further drug development.
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Affiliation(s)
- Rachel L Edwards
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert C Brothers
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Xu Wang
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Maxim I Maron
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
- Albert Einstein College of Medicine, Bronx, New York, USA
| | - Peter D Ziniel
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Patricia S Tsang
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Thomas E Kraft
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Roche Pharma Research and Early Development, Roche Innovation Center, Munich, Nonnenwald, Penzberg, Germany
| | - Paul W Hruz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kim C Williamson
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Cynthia S Dowd
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Audrey R Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
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84
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Pliotas C, Grayer SC, Ekkerman S, Chan AKN, Healy J, Marius P, Bartlett W, Khan A, Cortopassi WA, Chandler SA, Rasmussen T, Benesch JLP, Paton RS, Claridge TDW, Miller S, Booth IR, Naismith JH, Conway SJ. Adenosine Monophosphate Binding Stabilizes the KTN Domain of the Shewanella denitrificans Kef Potassium Efflux System. Biochemistry 2017; 56:4219-4234. [PMID: 28656748 PMCID: PMC5645763 DOI: 10.1021/acs.biochem.7b00300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Ligand binding is
one of the most fundamental properties of proteins.
Ligand functions fall into three basic types: substrates, regulatory
molecules, and cofactors essential to protein stability, reactivity,
or enzyme–substrate complex formation. The regulation of potassium
ion movement in bacteria is predominantly under the control of regulatory
ligands that gate the relevant channels and transporters, which possess
subunits or domains that contain Rossmann folds (RFs). Here we demonstrate
that adenosine monophosphate (AMP) is bound to both RFs of the dimeric
bacterial Kef potassium efflux system (Kef), where it plays a structural
role. We conclude that AMP binds with high affinity, ensuring that
the site is fully occupied at all times in the cell. Loss of the ability
to bind AMP, we demonstrate, causes protein, and likely dimer, instability
and consequent loss of function. Kef system function is regulated
via the reversible binding of comparatively low-affinity glutathione-based
ligands at the interface between the dimer subunits. We propose this
interfacial binding site is itself stabilized, at least in part, by
AMP binding.
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Affiliation(s)
- Christos Pliotas
- Biomedical Sciences Research Complex, University of St Andrews , North Haugh, St Andrews KY16 9ST, U.K
| | - Samuel C Grayer
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Silvia Ekkerman
- Medical Sciences and Nutrition, School of Medicine , Foresterhill, Aberdeen AB25 2ZD, U.K
| | - Anthony K N Chan
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Jess Healy
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Phedra Marius
- Biomedical Sciences Research Complex, University of St Andrews , North Haugh, St Andrews KY16 9ST, U.K
| | - Wendy Bartlett
- Medical Sciences and Nutrition, School of Medicine , Foresterhill, Aberdeen AB25 2ZD, U.K
| | - Amjad Khan
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Wilian A Cortopassi
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Shane A Chandler
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
| | - Tim Rasmussen
- Medical Sciences and Nutrition, School of Medicine , Foresterhill, Aberdeen AB25 2ZD, U.K
| | - Justin L P Benesch
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
| | - Robert S Paton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Timothy D W Claridge
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Samantha Miller
- Medical Sciences and Nutrition, School of Medicine , Foresterhill, Aberdeen AB25 2ZD, U.K
| | - Ian R Booth
- Medical Sciences and Nutrition, School of Medicine , Foresterhill, Aberdeen AB25 2ZD, U.K
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St Andrews , North Haugh, St Andrews KY16 9ST, U.K.,Biotherapy Centre, Sichuan University , Chengdu, China.,RCaH, Rutherford Appleton Laboratory , Harwell Oxford, Didcot OX11 0FA, U.K.,Division of Structural Biology, University of Oxford , Henry Wellcome Building for Genomic Medicine, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7BN, U.K
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K.,Freiburg Institute for Advanced Studies-FRIAS, Albert-Ludwigs-Universität Freiburg , Albertstrasse 19, 79104 Freiburg, Germany
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85
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Wang CS, Dixneuf PH, Soulé JF. Ruthenium-Catalyzed C−H Bond Alkylation of Arylphosphine Oxides with Alkenes: A Straightforward Access to Bifunctional Phosphorous Ligands with a Pendent Carboxylate. ChemCatChem 2017. [DOI: 10.1002/cctc.201700557] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Chang-Sheng Wang
- Institut des Sciences Chimiques de Rennes; UMR 6226 CNRS-Université de Rennes, “Organométalliques: Matériaux et Catalyse”, Campus de Beaulieu; 35042 Rennes France
| | - Pierre H. Dixneuf
- Institut des Sciences Chimiques de Rennes; UMR 6226 CNRS-Université de Rennes, “Organométalliques: Matériaux et Catalyse”, Campus de Beaulieu; 35042 Rennes France
| | - Jean-François Soulé
- Institut des Sciences Chimiques de Rennes; UMR 6226 CNRS-Université de Rennes, “Organométalliques: Matériaux et Catalyse”, Campus de Beaulieu; 35042 Rennes France
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86
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Zhang Y, Borrel A, Ghemtio L, Regad L, Boije af Gennäs G, Camproux AC, Yli-Kauhaluoma J, Xhaard H. Structural Isosteres of Phosphate Groups in the Protein Data Bank. J Chem Inf Model 2017; 57:499-516. [DOI: 10.1021/acs.jcim.6b00519] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Alexandre Borrel
- Laboratoire
Molécules Thérapeutiques in silico (MTi), UMRS-973, Université Paris Diderot, Sorbonne Paris Cité, INSERM, F-75013 Paris, France
| | | | - Leslie Regad
- Laboratoire
Molécules Thérapeutiques in silico (MTi), UMRS-973, Université Paris Diderot, Sorbonne Paris Cité, INSERM, F-75013 Paris, France
| | | | - Anne-Claude Camproux
- Laboratoire
Molécules Thérapeutiques in silico (MTi), UMRS-973, Université Paris Diderot, Sorbonne Paris Cité, INSERM, F-75013 Paris, France
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87
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Targeting Class I Histone Deacetylases in a "Complex" Environment. Trends Pharmacol Sci 2017; 38:363-377. [PMID: 28139258 DOI: 10.1016/j.tips.2016.12.006] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 01/22/2023]
Abstract
Histone deacetylase (HDAC) inhibitors are proven anticancer therapeutics and have potential in the treatment of many other diseases including HIV infection, Alzheimer's disease, and Friedreich's ataxia. A problem with the currently available HDAC inhibitors is that they have limited specificity and target multiple deacetylases. Designing isoform-selective inhibitors has proven challenging due to similarities in the structure and chemistry of HDAC active sites. However, the fact that HDACs 1, 2, and 3 are recruited to several large multi-subunit complexes, each with particular biological functions, raises the possibility of specifically inhibiting individual complexes. This may be assisted by recent structural and functional information about the assembly of these complexes. Here, we review the available structural information and discuss potential targeting strategies.
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88
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Balachandran N, To F, Berti PJ. Linear Free Energy Relationship Analysis of Transition State Mimicry by 3-Deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) Oxime, a DAHP Synthase Inhibitor and Phosphate Mimic. Biochemistry 2017; 56:592-601. [PMID: 28045507 DOI: 10.1021/acs.biochem.6b01211] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Naresh Balachandran
- Department of Chemistry & Chemical Biology and ‡Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Frederick To
- Department of Chemistry & Chemical Biology and ‡Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Paul J. Berti
- Department of Chemistry & Chemical Biology and ‡Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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89
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Xiong Y, Lu J, Hunter J, Li L, Scott D, Choi HG, Lim SM, Manandhar A, Gondi S, Sim T, Westover KD, Gray NS. Covalent Guanosine Mimetic Inhibitors of G12C KRAS. ACS Med Chem Lett 2017; 8:61-66. [PMID: 28105276 DOI: 10.1021/acsmedchemlett.6b00373] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/30/2016] [Indexed: 12/21/2022] Open
Abstract
Ras proteins are members of a large family of GTPase enzymes that are commonly mutated in cancer where they act as dominant oncogenes. We previously developed an irreversible guanosine-derived inhibitor, SML-8-73-1, of mutant G12C RAS that forms a covalent bond with cysteine 12. Here we report exploration of the structure-activity relationships (SAR) of hydrolytically stable analogues of SML-8-73-1 as covalent G12C KRAS inhibitors. We report the discovery of difluoromethylene bisphosphonate analogues such as compound 11, which, despite exhibiting reduced efficiency as covalent G12C KRAS inhibitors, remove the liability of the hydrolytic instability of the diphosphate moiety present in SML-8-73-1 and provide the foundation for development of prodrugs to facilitate cellular uptake. The SAR and crystallographic results reaffirm the exquisite molecular recognition that exists in the diphosphate region of RAS for guanosine nucleotides which must be considered in the design of nucleotide-competitive inhibitors.
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Affiliation(s)
- Yuan Xiong
- Department
of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02115, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jia Lu
- Departments
of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - John Hunter
- Departments
of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Lianbo Li
- Departments
of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - David Scott
- Department
of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02115, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Hwan Geun Choi
- New
Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Sang Min Lim
- Center
for Neuro-Medicine, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Anuj Manandhar
- Departments
of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Sudershan Gondi
- Departments
of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Taebo Sim
- Chemical
Kinomics Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- KU-KIST
Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Kenneth D. Westover
- Departments
of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Nathanael S. Gray
- Department
of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02115, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
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90
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Da Costa D, Roland A, Dousson CB. Novel methods for the synthesis of 1,5,2-diazaphosphinines as potential inhibitors of HCV polymerase. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2016.11.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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91
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Nordeman P, Chow SY, Odell AF, Antoni G, Odell LR. Palladium-mediated11C-carbonylations using aryl halides and cyanamide. Org Biomol Chem 2017; 15:4875-4881. [DOI: 10.1039/c7ob01064h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A rapid, efficient and high-yielding synthesis of11C-cyanobenzamides, including novel analogs of various drug molecules, is described.
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Affiliation(s)
- P. Nordeman
- Preclinical PET Platform Chemistry
- Department of Medicinal Chemistry
- Uppsala University
- Sweden
| | - S. Y. Chow
- Division of Organic Pharmaceutical Chemistry
- Department of Medicinal Chemistry
- Uppsala University
- Uppsala
- Sweden
| | - A. F. Odell
- School of Medicine
- St James’ University Hospital
- University of Leeds
- Leeds
- UK
| | - G. Antoni
- Preclinical PET Platform Chemistry
- Department of Medicinal Chemistry
- Uppsala University
- Sweden
| | - L. R. Odell
- Division of Organic Pharmaceutical Chemistry
- Department of Medicinal Chemistry
- Uppsala University
- Uppsala
- Sweden
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92
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Abstract
To help define the molecular basis of cellular signalling cascades, and their biological functions, there is considerable value in utilizing a high-quality chemical 'probe' that has a well-defined interaction with a specific cellular protein. Such reagents include inhibitors of protein kinases and small molecule kinases, as well as mimics or antagonists of intracellular signals. The purpose of this review is to consider recent progress and promising future directions for the development of novel molecules that can interrogate and manipulate the cellular actions of inositol pyrophosphates (PP-IPs)--a specialized, 'energetic' group of cell-signalling molecules in which multiple phosphate and diphosphate groups are crammed around a cyclohexane polyol scaffold.
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93
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Marinozzi M, Pertusati F, Serpi M. λ5-Phosphorus-Containing α-Diazo Compounds: A Valuable Tool for Accessing Phosphorus-Functionalized Molecules. Chem Rev 2016; 116:13991-14055. [DOI: 10.1021/acs.chemrev.6b00373] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maura Marinozzi
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Fabrizio Pertusati
- School
of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, United Kingdom
| | - Michaela Serpi
- School
of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, United Kingdom
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94
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Sanllehí P, Abad JL, Casas J, Bujons J, Delgado A. Bacterial versus human sphingosine-1-phosphate lyase (S1PL) in the design of potential S1PL inhibitors. Bioorg Med Chem 2016; 24:4381-4389. [DOI: 10.1016/j.bmc.2016.07.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/13/2016] [Accepted: 07/16/2016] [Indexed: 12/28/2022]
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95
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Hager A, Wu M, Wang H, Brown NW, Shears SB, Veiga N, Fiedler D. Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues. Chemistry 2016; 22:12406-14. [PMID: 27460418 PMCID: PMC5076471 DOI: 10.1002/chem.201601754] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Indexed: 12/21/2022]
Abstract
The inositol pyrophosphate messengers (PP-InsPs) are emerging as an important class of cellular regulators. These molecules have been linked to numerous biological processes, including insulin secretion and cancer cell migration, but how they trigger such a wide range of cellular responses has remained unanswered in many cases. Here, we show that the PP-InsPs exhibit complex speciation behaviour and propose that a unique conformational switching mechanism could contribute to their multifunctional effects. We synthesised non-hydrolysable bisphosphonate analogues and crystallised the analogues in complex with mammalian PPIP5K2 kinase. Subsequently, the bisphosphonate analogues were used to investigate the protonation sequence, metal-coordination properties, and conformation in solution. Remarkably, the presence of potassium and magnesium ions enabled the analogues to adopt two different conformations near physiological pH. Understanding how the intrinsic chemical properties of the PP-InsPs can contribute to their complex signalling outputs will be essential to elucidate their regulatory functions.
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Affiliation(s)
- Anastasia Hager
- Department of Chemistry, Princeton University, Washington Rd., Princeton, New Jersey, 08544, USA
| | - Mingxuan Wu
- Department of Chemistry, Princeton University, Washington Rd., Princeton, New Jersey, 08544, USA
| | - Huanchen Wang
- Inositol Signaling Group, National Institutes of Health, Research Triangle Park, North Carolina, 27709, USA
| | - Nathaniel W Brown
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle Strasse 10, 13125, Berlin, Germany
- Department of Chemistry, Princeton University, Washington Rd., Princeton, New Jersey, 08544, USA
| | - Stephen B Shears
- Inositol Signaling Group, National Institutes of Health, Research Triangle Park, North Carolina, 27709, USA
| | - Nicolás Veiga
- Cátedra de Química Inorgánica, Departamento Estrella Campos, Facultad de Química, Universidad de la República, CC 1157, Montevideo, Uruguay.
| | - Dorothea Fiedler
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle Strasse 10, 13125, Berlin, Germany.
- Department of Chemistry, Princeton University, Washington Rd., Princeton, New Jersey, 08544, USA.
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96
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Zlatev I, Foster DJ, Liu J, Charisse K, Brigham B, Parmar RG, Jadhav V, Maier MA, Rajeev KG, Egli M, Manoharan M. 5'-C-Malonyl RNA: Small Interfering RNAs Modified with 5'-Monophosphate Bioisostere Demonstrate Gene Silencing Activity. ACS Chem Biol 2016; 11:953-60. [PMID: 26675211 DOI: 10.1021/acschembio.5b00654] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
5'-Phosphorylation is a critical step in the cascade of events that leads to loading of small interfering RNAs (siRNAs) into the RNA-induced silencing complex (RISC) to elicit gene silencing. 5'-Phosphorylation of exogenous siRNAs is generally accomplished by a cytosolic Clp1 kinase, and in most cases, the presence of a 5'-monophosphate on synthetic siRNAs is not a prerequisite for activity. Chemically introduced, metabolically stable 5'-phosphate mimics can lead to higher metabolic stability, increased RISC loading, and higher gene silencing activities of chemically modified siRNAs. In this study, we report the synthesis of 5'-C-malonyl RNA, a 5'-monophosphate bioisostere. A 5'-C-malonyl-modified nucleotide was incorporated at the 5'-terminus of chemically modified RNA oligonucleotides using solid-phase synthesis. In vitro silencing activity, in vitro metabolic stability, and in vitro RISC loading of 5'-C-malonyl siRNA was compared to corresponding 5'-phosphorylated and 5'-nonphosphorylated siRNAs. The 5'-C-malonyl siRNAs showed sustained or improved in vitro gene silencing and high levels of Ago2 loading and conferred dramatically improved metabolic stability to the antisense strand of the siRNA duplexes. In silico modeling studies indicate a favorable fit of the 5'-C-malonyl group within the 5'-phosphate binding pocket of human Ago2MID domain.
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Affiliation(s)
- Ivan Zlatev
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Donald J. Foster
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Jingxuan Liu
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Benjamin Brigham
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Rubina G. Parmar
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Vasant Jadhav
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin A. Maier
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
| | | | - Martin Egli
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300
Third Street, Cambridge, Massachusetts 02142, United States
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97
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Yates LM, Fiedler D. A Stable Pyrophosphoserine Analog for Incorporation into Peptides and Proteins. ACS Chem Biol 2016; 11:1066-73. [PMID: 26760216 DOI: 10.1021/acschembio.5b00972] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein pyrophosphorylation is a covalent modification of proteins, mediated by the inositol pyrophosphate messengers. Although the inositol pyrophosphates have been linked to a range of cellular processes, the role of protein pyrophosphorylation remains minimally characterized in vivo. The inherent instability of the phosphoanhydride bond has hampered the development of useful bioanalytical techniques to interrogate this novel signaling mechanism. Here, we describe the preparation of a pyrophosphoserine analog containing a stable methylene-bisphosphonate group that is compatible with solid-phase peptide synthesis. The resulting peptides demonstrate enhanced stability in Eukaryotic cell lysates and mammalian plasma and display resistance toward chemical degradation, when compared to the corresponding pyrophosphopeptides. In addition, the peptides containing the stable pyrophosphoserine analog are highly compatible with common ligation methods, such as native chemical ligation, maleimide conjugation, and glutaraldehyde ligation. The bisphosphonate-containing peptides will, therefore, be well-suited for future pyrophosphoserine antibody generation and affinity capture of pyrophosphoprotein binding partners and provide a key entry point to study the regulatory role of protein pyrophosphorylation.
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Affiliation(s)
- Lisa M. Yates
- Department
of Chemistry, Princeton University, Washington Rd, Princeton, New Jersey 08544, United States
| | - Dorothea Fiedler
- Department
of Chemistry, Princeton University, Washington Rd, Princeton, New Jersey 08544, United States
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
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98
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Abstract
Synthetic compounds open up new avenues to interrogate and manipulate intracellular Ca2+ signalling pathways. They may ultimately lead to drug-like analogues to intervene in disease. Recent advances in chemical biology tools available to probe Ca2+ signalling are described, with a particular focus on those synthetic analogues from our group that have enhanced biological understanding or represent a step towards more drug-like molecules. Adenophostin (AdA) is the most potent known agonist at the inositol 1,4,5-trisphosphate receptor (IP3R) and synthetic analogues provide a binding model for receptor activation and channel opening. 2-O-Modified inositol 1,4,5-trisphosphate (IP3) derivatives that are partial agonists at the IP3R reveal key conformational changes of the receptor upon ligand binding. Biphenyl polyphosphates illustrate that simple non-inositol surrogates can be engineered to give prototype IP3R agonists or antagonists and act as templates for protein co-crystallization. Cyclic adenosine 5'-diphosphoribose (cADPR) can be selectively modified using total synthesis, generating chemically and biologically stable tools to investigate Ca2+ release via the ryanodine receptor (RyR) and to interfere with cADPR synthesis and degradation. The first neutral analogues with a synthetic pyrophosphate bioisostere surprisingly retain the ability to release Ca2+, suggesting a new route to membrane-permeant tools. Adenosine 5'-diphosphoribose (ADPR) activates the Ca2+-, Na+- and K+-permeable transient receptor potential melastatin 2 (TRPM2) cation channel. Synthetic ADPR analogues provide the first structure-activity relationship (SAR) for this emerging messenger and the first functional antagonists. An analogue based on the nicotinic acid motif of nicotinic acid adenine dinucleotide phosphate (NAADP) antagonizes NAADP-mediated Ca2+ release in vitro and is effective in vivo against induced heart arrhythmia and autoimmune disease, illustrating the therapeutic potential of targeted small molecules.
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99
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R. Shah N, Vidilaseris K, Xhaard H, Goldman A. Integral membrane pyrophosphatases: a novel drug target for human pathogens? AIMS BIOPHYSICS 2016. [DOI: 10.3934/biophy.2016.1.171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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100
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Jiang J, Kanabar V, Padilla B, Man F, Pitchford SC, Page CP, Wagner GK. Uncharged nucleoside inhibitors of β-1,4-galactosyltransferase with activity in cells. Chem Commun (Camb) 2016; 52:3955-8. [DOI: 10.1039/c5cc09289b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
5-Substituted uridine derivatives are uncharged galactosyltransferase inhibitors that reduce PSGL-1 expression in human monocytes.
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Affiliation(s)
- Jingqian Jiang
- Department of Chemistry
- King's College London
- Faculty of Natural & Mathematical Sciences
- London
- UK
| | - Varsha Kanabar
- Sackler Institute of Pulmonary Pharmacology & Institute of Pharmaceutical Science
- King's College London
- Faculty of Life Sciences & Medicine
- London
- UK
| | - Beatriz Padilla
- Sackler Institute of Pulmonary Pharmacology & Institute of Pharmaceutical Science
- King's College London
- Faculty of Life Sciences & Medicine
- London
- UK
| | - Francis Man
- Sackler Institute of Pulmonary Pharmacology & Institute of Pharmaceutical Science
- King's College London
- Faculty of Life Sciences & Medicine
- London
- UK
| | - Simon C. Pitchford
- Sackler Institute of Pulmonary Pharmacology & Institute of Pharmaceutical Science
- King's College London
- Faculty of Life Sciences & Medicine
- London
- UK
| | - Clive P. Page
- Sackler Institute of Pulmonary Pharmacology & Institute of Pharmaceutical Science
- King's College London
- Faculty of Life Sciences & Medicine
- London
- UK
| | - Gerd K. Wagner
- Department of Chemistry
- King's College London
- Faculty of Natural & Mathematical Sciences
- London
- UK
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