1
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Felsztyna I, Villarreal MA, García DA, Miguel V. Insect RDL Receptor Models for Virtual Screening: Impact of the Template Conformational State in Pentameric Ligand-Gated Ion Channels. ACS OMEGA 2022; 7:1988-2001. [PMID: 35071887 PMCID: PMC8771969 DOI: 10.1021/acsomega.1c05465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
The RDL receptor is one of the most relevant protein targets for insecticide molecules. It belongs to the pentameric ligand-gated ion channel (pLGIC) family. Given that the experimental structures of pLGICs are difficult to obtain, homology modeling has been extensively used for these proteins, particularly for the RDL receptor. However, no detailed assessments of the usefulness of homology models for virtual screening (VS) have been carried out for pLGICs. The aim of this study was to evaluate which are the determinant factors for a good VS performance using RDL homology models, specially analyzing the impact of the template conformational state. Fifteen RDL homology models were obtained based on different pLGIC templates representing the closed, open, and desensitized states. A retrospective VS process was performed on each model, and their performance in the prioritization of active ligands was assessed. In addition, the three best-performing models among each of the conformations were subjected to molecular dynamics simulations (MDS) in complex with a representative active ligand. The models showed variations in their VS performance parameters that were related to the structural properties of the binding site. VS performance tended to improve in more constricted binding cavities. The best performance was obtained with a model based on a template in the closed conformation. MDS confirmed that the closed model was the one that best represented the interactions with an active ligand. These results imply that different templates should be evaluated and the structural variations between their channel conformational states should be specially examined, providing guidelines for the application of homology modeling for VS in other proteins of the pLGIC family.
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Affiliation(s)
- Iván Felsztyna
- Facultad
de Ciencias Exactas, Físicas y Naturales, Departamento de Química.
Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Instituto
de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Marcos A. Villarreal
- Facultad
de Ciencias Químicas, Departamento de Química Teórica
y Computacional, Universidad Nacional de
Córdoba, Córdoba 5016, Argentina
- Instituto
de Investigaciones en Físico-Química de Córdoba
(INFIQC), CONICET-Universidad Nacional de
Córdoba, Córdoba 5016, Argentina
| | - Daniel A. García
- Facultad
de Ciencias Exactas, Físicas y Naturales, Departamento de Química.
Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Instituto
de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Virginia Miguel
- Facultad
de Ciencias Exactas, Físicas y Naturales, Departamento de Química.
Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Instituto
de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba 5016, Argentina
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2
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Trofymchuk S, Bugera M, Klipkov AA, Ahunovych V, Razhyk B, Semenov S, Boretskyi A, Tarasenko K, Mykhailiuk PK. Scalable Approach to Fluorinated Heterocycles with Sulfur Tetrafluoride (SF 4). J Org Chem 2021; 86:12181-12198. [PMID: 34424702 DOI: 10.1021/acs.joc.1c01518] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A general approach to fluorinated (hetero)aromatic derivatives is elaborated. The key reaction is a deoxofluorination of substituted acetophenones with sulfur tetrafluoride (SF4). In contrast to previous deoxofluorination methods, this transformation is fast, scalable (up to 70 g), and high-yielding. More than 100 novel or previously hardly accessible fluorinated heterocycles, interesting for medicinal chemistry and agrochemistry, were synthesized.
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Affiliation(s)
- Serhii Trofymchuk
- Enamine Ltd., Chervonotkatska 78, 02094 Kyiv, Ukraine.,Institute of Organic Chemistry, NAS of Ukraine, Murmanska 5, 02094 Kyiv, Ukraine
| | - Maksym Bugera
- Enamine Ltd., Chervonotkatska 78, 02094 Kyiv, Ukraine.,V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Murmanska 1, 02094 Kyiv, Ukraine
| | - Anton A Klipkov
- Enamine Ltd., Chervonotkatska 78, 02094 Kyiv, Ukraine.,V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Murmanska 1, 02094 Kyiv, Ukraine
| | - Volodymyr Ahunovych
- Enamine Ltd., Chervonotkatska 78, 02094 Kyiv, Ukraine.,V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Murmanska 1, 02094 Kyiv, Ukraine
| | - Bohdan Razhyk
- Enamine Ltd., Chervonotkatska 78, 02094 Kyiv, Ukraine
| | | | | | - Karen Tarasenko
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Murmanska 1, 02094 Kyiv, Ukraine.,Chemspace LLC, 85 Chervonotkatska Street, Suite 1, 02094 Kyiv, Ukraine
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3
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Affiliation(s)
- Jie Li
- ShanghaiTech University, Shanghai 201210, China
| | - Yu Xue
- Department
of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Zhoulong Fan
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- State
key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyong Ding
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ao Zhang
- ShanghaiTech University, Shanghai 201210, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- State
key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Chang J, Xu C, Gao J, Gao F, Zhu D, Wang M. Me3SiCF2Br-Self-Assisted Domino Reaction: Catalytic Synthesis of α,α-Difluorocyclopentanones from Methylvinylketones. Org Lett 2017; 19:1850-1853. [DOI: 10.1021/acs.orglett.7b00611] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jian Chang
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Cong Xu
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Jie Gao
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Fengyun Gao
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Dongsheng Zhu
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Mang Wang
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
- State
Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, P. R. China
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5
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Fuchibe K, Aono T, Hu J, Ichikawa J. Copper(I)-Catalyzed [4 + 1] Cycloaddition of Silyl Dienol Ethers with Sodium Bromodifluoroacetate: Access to β,β-Difluorocyclopentanone Derivatives. Org Lett 2016; 18:4502-5. [DOI: 10.1021/acs.orglett.6b02085] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kohei Fuchibe
- Division of Chemistry, Faculty
of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Tatsuya Aono
- Division of Chemistry, Faculty
of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Ji Hu
- Division of Chemistry, Faculty
of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Junji Ichikawa
- Division of Chemistry, Faculty
of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
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6
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Song X, Tian S, Zhao Z, Zhu D, Wang M. Controlled Ring-Opening of Siloxydifluorocyclopropanes for Carbocyclization: Synthesis of Difluorocyclopentenones. Org Lett 2016; 18:3414-7. [DOI: 10.1021/acs.orglett.6b01567] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaoning Song
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Shuangquan Tian
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Ziming Zhao
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Dongsheng Zhu
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Mang Wang
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
- State
Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
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7
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Chen SQ, Zhang XH. The Synthesis of Fipronil Derivatives via Pd-Catalyzed Direct Alkynylation of Phenylpyrazole with Terminal Alkynes in Green Solvents. J Heterocycl Chem 2016. [DOI: 10.1002/jhet.2628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Su-Qin Chen
- College of Chemistry and Materials Science; Wenzhou University; Wenzhou 325035 China
| | - Xiao-Hong Zhang
- College of Chemistry and Materials Science; Wenzhou University; Wenzhou 325035 China
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8
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Aono T, Sasagawa H, Fuchibe K, Ichikawa J. Regioselective Synthesis of α,α-Difluorocyclopentanone Derivatives: Domino Nickel-Catalyzed Difluorocyclopropanation/Ring-Expansion Sequence of Silyl Dienol Ethers. Org Lett 2015; 17:5736-9. [DOI: 10.1021/acs.orglett.5b02726] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tatsuya Aono
- Division
of Chemistry, Faculty
of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Hisashi Sasagawa
- Division
of Chemistry, Faculty
of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Kohei Fuchibe
- Division
of Chemistry, Faculty
of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Junji Ichikawa
- Division
of Chemistry, Faculty
of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
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9
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Linclau B, Leung L, Nonnenmacher J, Tizzard G. Synthesis and crystallographic analysis of meso-2,3-difluoro-1,4-butanediol and meso-1,4-dibenzyloxy-2,3-difluorobutane. Beilstein J Org Chem 2010; 6:62. [PMID: 20625521 PMCID: PMC2900908 DOI: 10.3762/bjoc.6.62] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 05/17/2010] [Indexed: 01/07/2023] Open
Abstract
A large-scale synthesis of meso-2,3-difluoro-1,4-butanediol in 5 steps from (Z)-but-2-enediol is described. Crystallographic analysis of the diol and the corresponding benzyl ether reveals an anti conformation of the vicinal difluoride moiety. Monosilylation of the diol is high-yielding but all attempts to achieve chain extension through addition of alkyl Grignard and acetylide nucleophiles failed.
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Affiliation(s)
- Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Leo Leung
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Jean Nonnenmacher
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Graham Tizzard
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
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