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Hamilton DJ, Ábrányi-Balogh P, Keeley A, Petri L, Hrast M, Imre T, Wijtmans M, Gobec S, de Esch IJP, Keserű GM. Bromo-Cyclobutenaminones as New Covalent UDP- N-Acetylglucosamine Enolpyruvyl Transferase (MurA) Inhibitors. Pharmaceuticals (Basel) 2020; 13:ph13110362. [PMID: 33153141 PMCID: PMC7692735 DOI: 10.3390/ph13110362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/08/2023] Open
Abstract
Drug discovery programs against the antibacterial target UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) have already resulted in covalent inhibitors having small three- and five-membered heterocyclic rings. In the current study, the reactivity of four-membered rings was carefully modulated to obtain a novel family of covalent MurA inhibitors. Screening a small library of cyclobutenone derivatives led to the identification of bromo-cyclobutenaminones as new electrophilic warheads. The electrophilic reactivity and cysteine specificity have been determined in a glutathione (GSH) and an oligopeptide assay, respectively. Investigating the structure-activity relationship for MurA suggests a crucial role for the bromine atom in the ligand. In addition, MS/MS experiments have proven the covalent labelling of MurA at Cys115 and the observed loss of the bromine atom suggests a net nucleophilic substitution as the covalent reaction. This new set of compounds might be considered as a viable chemical starting point for the discovery of new MurA inhibitors.
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Affiliation(s)
- David J. Hamilton
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands; (D.J.H.); (M.W.); (I.J.P.d.E.)
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary; (P.Á.-B.); (A.K.); (L.P.)
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary; (P.Á.-B.); (A.K.); (L.P.)
| | - Aaron Keeley
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary; (P.Á.-B.); (A.K.); (L.P.)
| | - László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary; (P.Á.-B.); (A.K.); (L.P.)
| | - Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia; (M.H.); (S.G.)
| | - Tímea Imre
- MS Metabolomics Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary;
| | - Maikel Wijtmans
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands; (D.J.H.); (M.W.); (I.J.P.d.E.)
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia; (M.H.); (S.G.)
| | - Iwan J. P. de Esch
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands; (D.J.H.); (M.W.); (I.J.P.d.E.)
| | - György Miklós Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary; (P.Á.-B.); (A.K.); (L.P.)
- Correspondence: ; Tel.: +36-1-382-6821
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2
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Chen GS, Yan XX, Chen SJ, Mao XY, Li ZD, Liu YL. Diastereoselective Synthesis of 1,3-Diyne-Tethered Trifluoromethylcyclopropanes through a Sulfur Ylide Mediated Cyclopropanation/DBU-Mediated Epimerization Sequence. J Org Chem 2020; 85:6252-6260. [PMID: 32298579 DOI: 10.1021/acs.joc.0c00162] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A one-pot synthesis of 1,3-diyne-tethered trifluoromethylcyclopropanes starting from 2-CF3-3,5-diyne-1-enes and sulfur ylides via a sulfur ylide mediated cyclopropanation and a DBU-mediated epimerization sequence is described in this work. This process is highly diastereoselective with broad substrate scope. Moreover, a series of synthetic transformations based on the diyne moieties were conducted smoothly, affording cyclopropanes featuring trifluoromethyl-substituted all-carbon quaternary centers.
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Affiliation(s)
- Guo-Shu Chen
- School of Chemistry and Chemical Engineering, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, P.R. China
| | - Xiao-Xue Yan
- School of Chemistry and Chemical Engineering, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, P.R. China
| | - Shu-Jie Chen
- School of Chemistry and Chemical Engineering, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, P.R. China.,Key Laboratory of Functional Molecular Engineering of Guangdong Province, South China University of Technology, Guangzhou 510640, P.R. China
| | - Xiang-Yu Mao
- School of Chemistry and Chemical Engineering, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, P.R. China
| | - Zhao-Dong Li
- Department of Applied Chemistry, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Yun-Lin Liu
- School of Chemistry and Chemical Engineering, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, P.R. China
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3
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Zhu H, Liu S, He C, Zhang J, Wang L. Synthesis of Trifluoromethyl‐Substituted Cyclopropanes via Inorganic Base‐Mediated Cycloaddition Reactions. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900550] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Huijuan Zhu
- Department of Traditional Chinese MedicineJilin Agricultural University Changchun 130118 P. R. China
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Science and Peking Union Medical College Beijing 100193 P. R. China
| | - Shuangshuang Liu
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Science and Peking Union Medical College Beijing 100193 P. R. China
| | - Chunnian He
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Science and Peking Union Medical College Beijing 100193 P. R. China
| | - Jing Zhang
- Department of Traditional Chinese MedicineJilin Agricultural University Changchun 130118 P. R. China
| | - Lei Wang
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Science and Peking Union Medical College Beijing 100193 P. R. China
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4
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Cao ZY, Wang W, Liao K, Wang X, Zhou J, Ma J. Catalytic enantioselective synthesis of cyclopropanes featuring vicinal all-carbon quaternary stereocenters with a CH2F group; study of the influence of C–F⋯H–N interactions on reactivity. Org Chem Front 2018. [DOI: 10.1039/c8qo00842f] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A highly diastereo- and enantioselective synthesis of cyclopropanes with adjacent all-carbon quaternary stereocenters featuring a CH2F group is reported.
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Affiliation(s)
- Zhong-Yan Cao
- Shanghai Key Laboratory of Green Chemistry and Chemical Process
- East China Normal University
- Shanghai 200062
- P. R. China
| | - Wenmin Wang
- Institute of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- P R China
| | - Kui Liao
- Shanghai Key Laboratory of Green Chemistry and Chemical Process
- East China Normal University
- Shanghai 200062
- P. R. China
| | - Xiaoming Wang
- State Key Laboratory of Organometallic Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- P R China
| | - Jian Zhou
- Shanghai Key Laboratory of Green Chemistry and Chemical Process
- East China Normal University
- Shanghai 200062
- P. R. China
- State Key Laboratory of Organometallic Chemistry
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- P R China
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5
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Affiliation(s)
- Yaya Duan
- Key
Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jin-Hong Lin
- Key
Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Ji-Chang Xiao
- Key
Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yu-Cheng Gu
- Syngenta, Jealott’s
Hill International Research Centre, Bracknell, Berkshire RG42 6EY, U.K
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Synthesis of imidazo[1,2-a]pyridin-chromones by a MW assisted Groebke–Blackburn–Bienaymé process. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2014.11.047] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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7
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Suresh D, Dhakshinamoorthy A, Kanagaraj K, Pitchumani K. Synthesis of 2-substituted 3-ethyl-3H-imidazo[4,5-b]pyridines catalyzed by Al3+-exchanged K10 clay as solid acids. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.09.086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Barnes-Seeman D, Jain M, Bell L, Ferreira S, Cohen S, Chen XH, Amin J, Snodgrass B, Hatsis P. Metabolically Stable tert-Butyl Replacement. ACS Med Chem Lett 2013; 4:514-6. [PMID: 24900702 DOI: 10.1021/ml400045j] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/22/2013] [Indexed: 12/13/2022] Open
Abstract
Susceptibility to metabolism is a common issue with the tert-butyl group on compounds of medicinal interest. We demonstrate an approach of removing all the fully sp(3) C-Hs from a tert-butyl group: replacing some C-Hs with C-Fs and increasing the s-character of the remaining C-Hs. This approach gave a trifluoromethylcyclopropyl group, which increased metabolic stability. Trifluoromethylcyclopropyl-containing analogues had consistently higher metabolic stability in vitro and in vivo compared to their tert-butyl-containing counterparts.
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Affiliation(s)
- David Barnes-Seeman
- Department of Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 100 Technology
Square, Cambridge, Massachusetts 02139, United States
| | - Monish Jain
- Department of Metabolism and Pharmacokinetics, Novartis Institutes for Biomedical Research, 250 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Leslie Bell
- Department of Metabolism and Pharmacokinetics, Novartis Institutes for Biomedical Research, 250 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Suzie Ferreira
- Department of Metabolism and Pharmacokinetics, Novartis Institutes for Biomedical Research, 250 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Scott Cohen
- Department of Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 100 Technology
Square, Cambridge, Massachusetts 02139, United States
| | - Xiao-Hui Chen
- Department of Metabolism and Pharmacokinetics, Novartis Institutes for Biomedical Research, 250 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Jakal Amin
- Department of Metabolism and Pharmacokinetics, Novartis Institutes for Biomedical Research, 250 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Brad Snodgrass
- Department of Metabolism and Pharmacokinetics, Novartis Institutes for Biomedical Research, 250 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Panos Hatsis
- Department of Metabolism and Pharmacokinetics, Novartis Institutes for Biomedical Research, 250 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
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CARLEVARO CMANUEL, MARTINS-DA-SILVA JOÃOHERMÍNIO, SAVINO WILSON, CAFFARENA ERNESTORAÚL. PLAUSIBLE BINDING MODE OF THE ACTIVE α4β1 ANTAGONIST, MK-0617, DETERMINED BY DOCKING AND FREE ENERGY CALCULATIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633612501088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the last years, the development of small molecule antagonists of VLA-4 for the treatment of diseases, where cell trafficking and activation are important, has increased considerably. Among them, the MK-0617 ligand has proven to be a highly potent and orally active α4β1 antagonist. However, the binding mode of this ligand in the integrin binding site remains unknown. Herein we report a thermodynamic analysis of the interaction between MK-0617 (and one of its isomers) and the VLA-4 protein using molecular docking and the free energy perturbation calculations, based on a comparative model of the α4β1 receptor. Initial complex coordinates were taken from molecular docking assays and submitted to alchemical transformations. Free energy of binding ΔΔG values, derived from experimental IC50 values, were taken as a parameter for determining the most likely binding mode. In addition, molecular dynamics simulations of these ligands within the α4β1 binding site were carried out to elucidate the binding energy profile and identify the most significant residues. Our results indicate that MK-0617 fits within the binding site in a stretched conformation, pointing the carboxylate group towards the MIDAS ion. We observe that, despite the fact that the main contribution to the energetic binding process is due to the electrostatic ion contribution, the nonpolar contribution is not negligible. Additionally, a network of hydrogen bonds participate in stabilizing the ligand-receptor interaction.
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Affiliation(s)
- C. MANUEL CARLEVARO
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), 59 No 789, La Plata, Buenos Aires 1900, Argentina
| | - JOÃO HERMÍNIO MARTINS-DA-SILVA
- Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Ave. Brasil 4365 Manguinhos, 21040-900, Rio de Janeiro, Brazil
| | - WILSON SAVINO
- Laboratório de Pesquisas sobre o Timo, Fundação Oswaldo Cruz, Ave. Brasil 4365 Manguinhos, 21040-900, Rio de Janeiro, Brazil
| | - ERNESTO RAÚL CAFFARENA
- Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Ave. Brasil 4365 Manguinhos, 21040-900, Rio de Janeiro, Brazil
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Li X, Zhan P, Liu H, Li D, Wang L, Chen X, Liu H, Pannecouque C, Balzarini J, Clercq ED, Liu X. Arylazolyl(azinyl)thioacetanilides. Part 10: Design, synthesis and biological evaluation of novel substituted imidazopyridinylthioacetanilides as potent HIV-1 inhibitors. Bioorg Med Chem 2012; 20:5527-36. [DOI: 10.1016/j.bmc.2012.07.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/15/2012] [Accepted: 07/16/2012] [Indexed: 01/29/2023]
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11
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Grygorenko OO, Artamonov OS, Komarov IV, Mykhailiuk PK. Trifluoromethyl-substituted cyclopropanes. Tetrahedron 2011. [DOI: 10.1016/j.tet.2010.11.068] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Zhao YL, Yang SC, Di CH, Han XD, Liu Q. Highly efficient synthesis of 3-amino-/alkylthio-cyclobut-2-en-1-ones based on the cyclization of acyl ketene dithioacetals. Chem Commun (Camb) 2010; 46:7614-6. [DOI: 10.1039/c0cc02470h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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