1
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Liu H, Shi H, Han P, Meng Z, Liu T, Han LL. The annulation of N-hydroxyoximes and 1,3-diyne to synthesize alkynylated isoquinolines regioselectively catalyzed by ruthenium: a theoretical study. Org Biomol Chem 2022; 20:7294-7301. [DOI: 10.1039/d2ob01215d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanisms of the regioselective annulation of N-hydroxyoximes and 1,3-diyne to synthesize alkynylated isoquinolines by using catalyst [RuCl2(p-cymene)]2 have been theoretically investigated with the aid of density functional theory (DFT)...
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2
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Gao Y, van Haren MJ, Buijs N, Innocenti P, Zhang Y, Sartini D, Campagna R, Emanuelli M, Parsons RB, Jespers W, Gutiérrez-de-Terán H, van Westen GJP, Martin NI. Potent Inhibition of Nicotinamide N-Methyltransferase by Alkene-Linked Bisubstrate Mimics Bearing Electron Deficient Aromatics. J Med Chem 2021; 64:12938-12963. [PMID: 34424711 PMCID: PMC8436214 DOI: 10.1021/acs.jmedchem.1c01094] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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Nicotinamide N-methyltransferase (NNMT) methylates
nicotinamide (vitamin B3) to generate 1-methylnicotinamide (MNA).
NNMT overexpression has been linked to a variety of diseases, most
prominently human cancers, indicating its potential as a therapeutic
target. The development of small-molecule NNMT inhibitors has gained
interest in recent years, with the most potent inhibitors sharing
structural features based on elements of the nicotinamide substrate
and the S-adenosyl-l-methionine (SAM) cofactor.
We here report the development of new bisubstrate inhibitors that
include electron-deficient aromatic groups to mimic the nicotinamide
moiety. In addition, a trans-alkene linker was found
to be optimal for connecting the substrate and cofactor mimics in
these inhibitors. The most potent NNMT inhibitor identified exhibits
an IC50 value of 3.7 nM, placing it among the most active
NNMT inhibitors reported to date. Complementary analytical techniques,
modeling studies, and cell-based assays provide insights into the
binding mode, affinity, and selectivity of these inhibitors.
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Affiliation(s)
- Yongzhi Gao
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Matthijs J van Haren
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ned Buijs
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Paolo Innocenti
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Yurui Zhang
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Davide Sartini
- Department of Clinical Sciences, Universitá Politecnica delle Marche, Via Ranieri 65, 60131 Ancona, Italy
| | - Roberto Campagna
- Department of Clinical Sciences, Universitá Politecnica delle Marche, Via Ranieri 65, 60131 Ancona, Italy
| | - Monica Emanuelli
- Department of Clinical Sciences, Universitá Politecnica delle Marche, Via Ranieri 65, 60131 Ancona, Italy
| | - Richard B Parsons
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, United Kingdom
| | - Willem Jespers
- Drug Discovery and Safety, Leiden Academic Center for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | | | - Gerard J P van Westen
- Drug Discovery and Safety, Leiden Academic Center for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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3
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Knox HL, Chen PYT, Blaszczyk AJ, Mukherjee A, Grove TL, Schwalm EL, Wang B, Drennan CL, Booker SJ. Structural basis for non-radical catalysis by TsrM, a radical SAM methylase. Nat Chem Biol 2021; 17:485-491. [PMID: 33462497 PMCID: PMC7990684 DOI: 10.1038/s41589-020-00717-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022]
Abstract
TsrM methylates C2 of the indole ring of L-tryptophan (Trp) during the biosynthesis of the quinaldic acid moiety of thiostrepton. It is annotated as a cobalamin-dependent radical S-adenosylmethionine (SAM) methylase; however, TsrM does not reductively cleave SAM to the universal 5ʹ-deoxyadenosyl 5ʹ-radical intermediate, a hallmark of radical-SAM (RS) enzymes. Herein, we report structures of TsrM from Kitasatospora setae, the first of a cobalamin-dependent radical SAM methylase. Unexpectedly, the structures show an essential arginine residue that resides in the proximal coordination sphere of the cobalamin cofactor and a [4Fe–4S] cluster that is ligated by a glutamyl residue and three cysteines in a canonical CxxxCxxC RS motif. Structures in the presence of substrates suggest a substrate-assisted mechanism of catalysis, wherein the carboxylate group of SAM serves as a general base to deprotonate N1 of the tryptophan substrate, facilitating formation of a C2 carbanion. The first crystal structures of a cobalamin-dependent radical SAM methylase reveal an unexpected mode of methylation.
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Affiliation(s)
- Hayley L Knox
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Percival Yang-Ting Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Anthony J Blaszczyk
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.,Catalent Pharma Solutions, Gaithersburg, MD, USA
| | - Arnab Mukherjee
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Erica L Schwalm
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.,Merck & Co., Inc., Rahway, NJ, USA
| | - Bo Wang
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Squire J Booker
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. .,Howard Hughes Medical Institute, Pennsylvania State University, University Park, PA, USA.
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4
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Mordhorst S, Andexer JN. Round, round we go - strategies for enzymatic cofactor regeneration. Nat Prod Rep 2020; 37:1316-1333. [PMID: 32582886 DOI: 10.1039/d0np00004c] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to the beginning of 2020Enzymes depending on cofactors are essential in many biosynthetic pathways of natural products. They are often involved in key steps: catalytic conversions that are difficult to achieve purely with synthetic organic chemistry. Hence, cofactor-dependent enzymes have great potential for biocatalysis, on the condition that a corresponding cofactor regeneration system is available. For some cofactors, these regeneration systems require multiple steps; such complex enzyme cascades/multi-enzyme systems are (still) challenging for in vitro biocatalysis. Further, artificial cofactor analogues have been synthesised that are more stable, show an altered reaction range, or act as inhibitors. The development of bio-orthogonal systems that can be used for the production of modified natural products in vivo is an ongoing challenge. In light of the recent progress in this field, this review aims to provide an overview of general strategies involving enzyme cofactors, cofactor analogues, and regeneration systems; highlighting the current possibilities for application of enzymes using some of the most common cofactors.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
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5
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Fu S, Dong H, Deng X, Zhuo R, Zhong Z. Injectable hyaluronic acid/poly(ethylene glycol) hydrogels crosslinked via strain-promoted azide-alkyne cycloaddition click reaction. Carbohydr Polym 2017; 169:332-340. [PMID: 28504153 DOI: 10.1016/j.carbpol.2017.04.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/10/2017] [Accepted: 04/13/2017] [Indexed: 01/06/2023]
Abstract
This paper reports injectable hyaluronic acid (HA)-based hydrogels crosslinked with azide-modified poly(ethylene glycol) (PEG) via the strain-promoted azide-alkyne cycloaddition (SPAAC) between cyclooctyne and azide groups. Cyclooctyne-modified HA (Cyclooctyne-HA) is prepared by the reaction of HA with 2-(aminoethoxy)cyclooctyne. To crosslink the modified HA, quadruply azide-terminated poly(ethylene glycol) (Azide-PEG) is designed and prepared. The mixture of Cyclooctyne-HA and Azide-PEG gelates in a few minutes to form a strong HA-PEG hydrogel. The hydrogel has fast gelation time, good strength, and slow degradation rate, because of the high reactivity of SPAAC, high crosslinking density originated from the quadruply-substituted Azide-PEG, and the good stability of the crosslinking amide bonds. In vitro cell culturing within the hydrogel demonstrated an excellent cell-compatibility. The bioorthogonality of SPAAC makes the hydrogel injectable. With good mechanical properties and biocompatibility, the hydrogel would be useful in a wide range of applications such as injection filling materials for plastic surgery.
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Affiliation(s)
- Shuangli Fu
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Hui Dong
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Xueyi Deng
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Renxi Zhuo
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Zhenlin Zhong
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, PR China.
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6
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Sadler JC, Chung CWH, Mosley JE, Burley GA, Humphreys LD. Structural and Functional Basis of C-Methylation of Coumarin Scaffolds by NovO. ACS Chem Biol 2017; 12:374-379. [PMID: 28068060 DOI: 10.1021/acschembio.6b01053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
C-methylation of aromatic small molecules by C-methyltransferases (C-MTs) is an important biological transformation that involves C-C bond formation using S-adenosyl-l-methionine (SAM) as the methyl donor. Here, two advances in the mechanistic understanding of C-methylation of the 8-position of coumarin substrates catalyzed by the C-MT NovO from Streptomyces spheroides are described. First, a crystal structure of NovO reveals the Arg116-Asn117 and His120-Arg121 motifs are essential for coumarin substrate binding. Second, the active-site His120 is responsible for deprotonation of the phenolic 7-hydroxyl group on the coumarin substrate, activating the rate-determining methyl transfer step from SAM. This work expands our mechanistic knowledge of C-MTs, which could be used in the downstream development of engineered biocatalysts for small molecule C-alkylations.
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Affiliation(s)
- Joanna C. Sadler
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Chun-wa H. Chung
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | - Julie E. Mosley
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | - Glenn A. Burley
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Luke D. Humphreys
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
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7
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Brockway AJ, Cosner CC, Volkov OA, Phillips MA, De Brabander JK. Improved Synthesis of MDL 73811 - a Potent AdoMetDC Inhibitor and Anti-Trypanosomal Compound. SYNTHESIS-STUTTGART 2016; 48:2065-2068. [PMID: 27482123 DOI: 10.1055/s-0035-1561608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
An improved synthesis of MDL 73811 - a potent AdoMetDC (S-adenosylmethionine decarboxylease) inhibitor and anti-trypanosomal compound with in vivo activity has been completed in four steps from commercially available 2',3'-O-isopropylideneadenosine. Utilization of Mitsunobu chemistry was crucial for the reliable and scalable introduction of the 5'-methylamine moiety, which was problematic using traditional activation/displacement chemistry as previously reported. All reactions in this synthesis were run on gram-scale resulting in a five-fold increase in yield over the original synthesis.
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Affiliation(s)
- Anthony J Brockway
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Casey C Cosner
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Oleg A Volkov
- Department of Pharmacology, The University of Texas Southwestern Medical Center at Dallas,6001 Forest Park Road, Dallas, Texas 75390-9041, United States
| | - Margaret A Phillips
- Department of Pharmacology, The University of Texas Southwestern Medical Center at Dallas,6001 Forest Park Road, Dallas, Texas 75390-9041, United States
| | - Jef K De Brabander
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
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8
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Dong M, Horitani M, Dzikovski B, Pandelia ME, Krebs C, Freed JH, Hoffman BM, Lin H. Organometallic Complex Formed by an Unconventional Radical S-Adenosylmethionine Enzyme. J Am Chem Soc 2016; 138:9755-8. [PMID: 27465315 DOI: 10.1021/jacs.6b04155] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pyrococcus horikoshii Dph2 (PhDph2) is an unusual radical S-adenosylmethionine (SAM) enzyme involved in the first step of diphthamide biosynthesis. It catalyzes the reaction by cleaving SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. To probe the reaction mechanism, we synthesized a SAM analogue (SAMCA), in which the ACP group of SAM is replaced with a 3-carboxyallyl group. SAMCA is cleaved by PhDph2, yielding a paramagnetic (S = 1/2) species, which is assigned to a complex formed between the reaction product, α-sulfinyl-3-butenoic acid, and the [4Fe-4S] cluster. Electron-nuclear double resonance (ENDOR) measurements with (13)C and (2)H isotopically labeled SAMCA support a π-complex between the C═C double bond of α-sulfinyl-3-butenoic acid and the unique iron of the [4Fe-4S] cluster. This is the first example of a radical SAM-related [4Fe-4S](+) cluster forming an organometallic complex with an alkene, shedding additional light on the mechanism of PhDph2 and expanding our current notions for the reactivity of [4Fe-4S] clusters in radical SAM enzymes.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Masaki Horitani
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University , Waltham, Massachusetts 02453, United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.,Howard Hughes Medical Institute, Cornell University , Ithaca, New York 14853, United States
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9
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Debets MF, Prins JS, Merkx D, van Berkel SS, van Delft FL, van Hest JCM, Rutjes FPJT. Synthesis of DIBAC analogues with excellent SPAAC rate constants. Org Biomol Chem 2015; 12:5031-7. [PMID: 24899166 DOI: 10.1039/c4ob00694a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In search for increased reactivity in strain-promoted azide alkyne cycloadditions (SPAAC), the synthesis of new and more reactive cyclooctynes is of pivotal importance. To identify cyclooctynes with enhanced reactivity, without loss of stability, the synthesis and kinetic analysis of new dibenzoazacyclooctyne (DIBAC) analogues were conducted. Starting from iodobenzyl alcohol analogues and ortho-ethynylaniline various substituted dihydrodibenzo[b,f]azocines were produced. Subsequent bromination and elimination proved to be difficult depending on the aromatic substitution pattern, yielding chloro-, bromo-, and methoxy-substituted DIBACs in moderate yield. In the elimination reaction towards nitro- and Br,Cl-DIBAC, the corresponding cyclooctene was obtained instead of the cyclooctyne. Additionally, a dimethoxy-substituted DIBAC analogue was prepared following an alternative route involving light-induced deprotection of a cyclopropenone derivative. In total, four DIBAC analogues were successfully prepared showing excellent rate constants in the SPAAC reaction ranging from 0.45 to 0.9 M(-1) s(-1), which makes them comparable to the fastest cyclooctynes currently known.
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Affiliation(s)
- Marjoke F Debets
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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10
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Kung PP, Huang B, Zehnder L, Tatlock J, Bingham P, Krivacic C, Gajiwala K, Diehl W, Yu X, Maegley KA. SAH derived potent and selective EZH2 inhibitors. Bioorg Med Chem Lett 2015; 25:1532-7. [PMID: 25746813 DOI: 10.1016/j.bmcl.2015.02.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/04/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
Abstract
A series of novel enhancer of zeste homolog 2 (EZH2) inhibitors was designed based on the chemical structure of the histone methyltransferase (HMT) inhibitor SAH (S-adenosyl-l-homocysteine). These nucleoside-based EZH2 inhibitors blocked the methylation of nucleosomes at H3K27 in biochemical assays employing both WT PRC2 complex as well as a Y641N mutant PRC2 complex. The most potent compound, 27, displayed IC50's against both complexes of 270 nM and 70 nM, respectively. To our knowledge, compound 27 is the most potent SAH-derived inhibitor of the EZH2 PRC2 complex yet identified. This compound also displayed improved potency, lipophilic efficiency (LipE), and selectivity profile against other lysine methyltransferases compared with SAH.
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Affiliation(s)
- Pei-Pei Kung
- Oncology Chemistry, Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Dr., San Diego, CA 92121, USA
| | - Buwen Huang
- Oncology Chemistry, Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Dr., San Diego, CA 92121, USA
| | - Luke Zehnder
- Oncology Chemistry, Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Dr., San Diego, CA 92121, USA
| | - John Tatlock
- Oncology Chemistry, Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Dr., San Diego, CA 92121, USA
| | - Patrick Bingham
- Oncology Research Unit, Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Dr., San Diego, CA 92121, USA
| | - Cody Krivacic
- Oncology Research Unit, Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Dr., San Diego, CA 92121, USA
| | - Ketan Gajiwala
- Oncology Chemistry, Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Dr., San Diego, CA 92121, USA
| | - Wade Diehl
- Oncology Chemistry, Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Dr., San Diego, CA 92121, USA
| | - Xiu Yu
- Oncology Chemistry, Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Dr., San Diego, CA 92121, USA
| | - Karen A Maegley
- Oncology Research Unit, Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Dr., San Diego, CA 92121, USA
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11
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Xie Y, Zhou R, Lian F, Liu Y, Chen L, Shi Z, Zhang N, Zheng M, Shen B, Jiang H, Liang Z, Luo C. Virtual screening and biological evaluation of novel small molecular inhibitors against protein arginine methyltransferase 1 (PRMT1). Org Biomol Chem 2014; 12:9665-73. [PMID: 25348815 DOI: 10.1039/c4ob01591f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Protein arginine methylation is a common post-translational modification which is crucial for a variety of biological processes. Dysregulation of protein arginine methyltransferases (PRMTs) activity has been implicated in cancer and other serious diseases. Thus, small molecule inhibitors against PRMT have great potential for therapeutic development. Herein, through the combination of virtual screening and bioassays, six small molecular compounds were identified as PRMT1 inhibitors. Amongst them, the binding affinity of compounds DCLX069 and DCLX078 with PRMT1 was further validated by T1ρ and saturation transfer difference (STD) NMR experiments. Most important of all, both compounds effectively blocked cell proliferation in breast cancer, liver cancer and acute myeloid leukemia cell lines. The binding mode analysis from molecular docking simulations theoretically indicated that both inhibitors occupied the SAM binding pocket to exert the inhibitory effect. Taken together, our compounds enriched the structural scaffolds as PRMT1 inhibitors and afforded clues for further optimization.
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Affiliation(s)
- Yiqian Xie
- Center for Systems Biology, Soochow University, Jiangsu 215006, China.
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12
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Schmidt T, Schwede T, Meuwly M. Computational Analysis of Methyl Transfer Reactions in Dengue Virus Methyltransferase. J Phys Chem B 2014; 118:5882-90. [DOI: 10.1021/jp5028564] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tobias Schmidt
- SIB
Swiss Institute of Bioinformatics, Basel, Switzerland Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Torsten Schwede
- SIB
Swiss Institute of Bioinformatics, Basel, Switzerland Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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13
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Sergeev ME, Morgia F, Javed MR, Doi M, Keng PY. Enzymatic radiofluorination: Fluorinase accepts methylaza-analog of SAM as substrate for FDA synthesis. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.07.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Joce C, White R, Stockley PG, Warriner S, Turnbull WB, Nelson A. Design, synthesis and in vitro evaluation of novel bivalent S-adenosylmethionine analogues. Bioorg Med Chem Lett 2012; 22:278-84. [PMID: 22137339 PMCID: PMC3267017 DOI: 10.1016/j.bmcl.2011.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/03/2011] [Accepted: 11/06/2011] [Indexed: 11/24/2022]
Abstract
In optimal cases, bivalent ligands can bind with exceptionally high affinity to their protein targets. However, designing optimised linkers, that orient the two binding groups perfectly, is challenging, and yet crucial in both fragment-based ligand design and in the discovery of bisubstrate enzyme inhibitors. To further our understanding of linker design, a series of novel bivalent S-adenosylmethionine (SAM) analogues were designed with the aim of interacting with the MetJ dimer in a bivalent sense (1:1 ligand/MetJ dimer). A range of ligands was synthesised and analyzed for ability to promote binding of the Escherichia coli methionine repressor, MetJ, to its operator DNA. Binding of bivalent SAM analogues to the MetJ homodimer in the presence of operator DNA was evaluated by fluorescence anisotropy and the effect of linker length and structure was investigated. The most effective bivalent ligand identified had a flexible linker, and promoted the DNA-protein interaction at 21-times lower concentration than the corresponding monovalent control compound.
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Affiliation(s)
- Catherine Joce
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Rebecca White
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Peter G. Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Stuart Warriner
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - W. Bruce Turnbull
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Adam Nelson
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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15
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Mori S, Iwase K, Iwanami N, Tanaka Y, Kagechika H, Hirano T. Development of novel bisubstrate-type inhibitors of histone methyltransferase SET7/9. Bioorg Med Chem 2010; 18:8158-66. [PMID: 21036620 DOI: 10.1016/j.bmc.2010.10.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 10/06/2010] [Accepted: 10/07/2010] [Indexed: 10/18/2022]
Abstract
Histone modification, for example, by histone deacetylase (HDAC) and histone lysine methyltransferase (HMT), plays an important role in regulating gene expression. To obtain novel inhibitors as tools for investigating the physiological function of members of the HMT family, we designed and synthesized novel inhibitors, which are amine analogues of adenosylmethionine (AdoMet; the cofactor utilized in the methylation reaction) bearing various alkylamino groups coupled via an ethylene linker. The inhibitory activities of these compounds towards SET7/9, an HMT, were evaluated. It was found that introduction of an alkylamino group increased the inhibitory activity.
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Affiliation(s)
- Shuichi Mori
- Tokyo Medical and Dental University, Chiyoda-ku, Japan
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Dowden J, Hong W, Parry RV, Pike RA, Ward SG. Toward the development of potent and selective bisubstrate inhibitors of protein arginine methyltransferases. Bioorg Med Chem Lett 2010; 20:2103-5. [PMID: 20219369 DOI: 10.1016/j.bmcl.2010.02.069] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 02/16/2010] [Accepted: 02/16/2010] [Indexed: 01/28/2023]
Abstract
Prototype inhibitors of protein arginine methyltransferases (PRMTs) have been constructed by attaching guanidine functionality via a variable linker to non-reactive amine analogues of the cellular co-factor (S)-adenosyl methionine (AdoMet). Potent inhibition of PRMT1 (IC(50) of approximately 3-6 microM) combined with weak inhibition of the lysine methyltransferase SET7 (approximately 50% of activity at 100 microM) was observed for two such compounds.
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Affiliation(s)
- James Dowden
- School of Chemistry, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.
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Stacklies W, Xia F, Gräter F. Dynamic allostery in the methionine repressor revealed by force distribution analysis. PLoS Comput Biol 2009; 5:e1000574. [PMID: 19936294 PMCID: PMC2775130 DOI: 10.1371/journal.pcbi.1000574] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 10/21/2009] [Indexed: 11/27/2022] Open
Abstract
Many fundamental cellular processes such as gene expression are tightly regulated by protein allostery. Allosteric signal propagation from the regulatory to the active site requires long-range communication, the molecular mechanism of which remains a matter of debate. A classical example for long-range allostery is the activation of the methionine repressor MetJ, a transcription factor. Binding of its co-repressor SAM increases its affinity for DNA several-fold, but has no visible conformational effect on its DNA binding interface. Our molecular dynamics simulations indicate correlated domain motions within MetJ, and quenching of these dynamics upon SAM binding entropically favors DNA binding. From monitoring conformational fluctuations alone, it is not obvious how the presence of SAM is communicated through the largely rigid core of MetJ and how SAM thereby is able to regulate MetJ dynamics. We here directly monitored the propagation of internal forces through the MetJ structure, instead of relying on conformational changes as conventionally done. Our force distribution analysis successfully revealed the molecular network for strain propagation, which connects collective domain motions through the protein core. Parts of the network are directly affected by SAM binding, giving rise to the observed quenching of fluctuations. Our results are in good agreement with experimental data. The force distribution analysis suggests itself as a valuable tool to gain insight into the molecular function of a whole class of allosteric proteins.
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Affiliation(s)
- Wolfram Stacklies
- CAS-MPG Partner Institute for Computational Biology, Key laboratory of Computational Biology, Chinese Academy of Sciences, Shanghai, China
- Bioquant BQ0031, Heidelberg University, Heidelberg, Germany
| | - Fei Xia
- CAS-MPG Partner Institute for Computational Biology, Key laboratory of Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Frauke Gräter
- CAS-MPG Partner Institute for Computational Biology, Key laboratory of Computational Biology, Chinese Academy of Sciences, Shanghai, China
- Max-Planck-Institute for Metals Research, Stuttgart, Germany
- Bioquant BQ0031, Heidelberg University, Heidelberg, Germany
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