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Deng J, Gu J, Lv K, Du X, Ye X, He C, Li H, Yao Q. A Non-Bonding Interaction-Based Fluorescent Probe for Detection of Halogenated Carbonyl Compounds. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 312:124018. [PMID: 38387410 DOI: 10.1016/j.saa.2024.124018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024]
Abstract
The fluorescent detection of neutral and volatile carbonyl halogenated compounds had not been studied before. We describe here a simple and sensitive turn-on rhodamin fluorescent probe for the selective detection of fluorinated/brominated/chlorinated/iodinated carbonyl compounds. A wide range of linear or cyclic volatile organic halides was detected with a limit of detection as low as 45.6 nM within 1 min. Mechanistic experiments and DFT calculations indicate the reversible formation of a 1:1 complex of sensor and analyst through non-bonding interaction.
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Affiliation(s)
- Jinfei Deng
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Department of Pharmacy, Zunyi Medical University, 6 Xuefu Road West, Zunyi, 563000, China
| | - Jianyu Gu
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Department of Pharmacy, Zunyi Medical University, 6 Xuefu Road West, Zunyi, 563000, China
| | - Kaizhuo Lv
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Department of Pharmacy, Zunyi Medical University, 6 Xuefu Road West, Zunyi, 563000, China
| | - Xiaowei Du
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Department of Pharmacy, Zunyi Medical University, 6 Xuefu Road West, Zunyi, 563000, China
| | - Xiushen Ye
- Qinghai Provincial Key Laboratory of Resources and Chemistry of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai, 810008, China
| | - Chunyang He
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Department of Pharmacy, Zunyi Medical University, 6 Xuefu Road West, Zunyi, 563000, China
| | - Hongyu Li
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Department of Pharmacy, Zunyi Medical University, 6 Xuefu Road West, Zunyi, 563000, China
| | - Qiuli Yao
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Department of Pharmacy, Zunyi Medical University, 6 Xuefu Road West, Zunyi, 563000, China; Qinghai Provincial Key Laboratory of Resources and Chemistry of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai, 810008, China.
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19F NMR Chemical Shifts Are Sensitive to Remote Functional Group Variations. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Lu Y, Sun M, Xi N. Effects of fluorine bonding and nonbonding interactions on 19F chemical shifts. RSC Adv 2022; 12:32082-32096. [PMID: 36415555 PMCID: PMC9644289 DOI: 10.1039/d2ra06660b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 11/03/2023] Open
Abstract
19F-NMR signals are sensitive to local electrostatic fields and are useful in probing protein structures and dynamics. Here, we used chemically identical ortho-F nuclei in N-phenyl γ-lactams to investigate the relationship between 19F NMR chemical shifts and local environments. By varying the structures at the C5- and C7-substituents, we demonstrated that 19F shifts and Hammett coefficients in Hammett plots follow typical relationships in bonding interactions, while manifesting reverse correlations in nonbonding contacts. Quantum mechanics calculations revealed that one of the ortho-F nuclei engages in n → π* orbital delocalization between F lone pair electrons (n) and a C[double bond, length as m-dash]O/Ar[double bond, length as m-dash]N antibonding orbital (π*), and the other ortho-F nucleus exhibits n ↔ σ orbital polarization between the n electrons and the C-H σ bonding orbital. As 19F NMR spectroscopy find increasing use in molecular sensors and biological sciences, our findings are valuable for designing sensitive probes, elucidating molecular structures, and quantifying analytes.
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Affiliation(s)
- Yang Lu
- Institute of Drug Discovery Technology, Ningbo University Ningbo Zhejiang 315211 P. R. China
| | - Mingming Sun
- Department of Chemistry, Nanchang University 999 Xuefu Avenue Nanchang 330031 P. R. China
| | - Ning Xi
- Institute of Drug Discovery Technology, Ningbo University Ningbo Zhejiang 315211 P. R. China
- School of Medicine, Ningbo University Ningbo Zhejiang 315211 P. R. China
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Harry SA, Kazim M, Nguyen PM, Zhu A, Xiang MR, Catazaro J, Siegler M, Lectka T. The Close Interaction of a C-F Bond with an Amide Carbonyl: Crystallographic and Spectroscopic Characterization. Angew Chem Int Ed Engl 2022; 61:e202207966. [PMID: 35716396 PMCID: PMC9544880 DOI: 10.1002/anie.202207966] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 11/26/2022]
Abstract
The putative interaction of a C-F bond with an amide carbonyl has been an intriguing topic of interest in this century for reasons spanning basic physical organic chemistry to biochemistry. However, to date, there exist no examples of a close, well-defined interaction in which its unique aspects can be identified and exploited. Herein, we finally present an engineered system possessing an exceptionally tight C-F-amide interaction, allowing us to obtain spectroscopic, crystallographic, and kinetic details of a distinctive, biochemically relevant chemical system for the first time. In turn, we also explore Lewis acid coordination, C-F bond promotion of amide isomerization, enantiomerization, and ion protonation processes.
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Affiliation(s)
- Stefan Andrew Harry
- Department of ChemistryJohns Hopkins University3400 N. Charles St.BaltimoreMD 21218USA
| | - Muhammad Kazim
- Department of ChemistryJohns Hopkins University3400 N. Charles St.BaltimoreMD 21218USA
| | - Phuong Minh Nguyen
- Department of ChemistryJohns Hopkins University3400 N. Charles St.BaltimoreMD 21218USA
| | | | - Michael Richard Xiang
- Department of ChemistryJohns Hopkins University3400 N. Charles St.BaltimoreMD 21218USA
| | - Jonathan Catazaro
- Department of ChemistryJohns Hopkins University3400 N. Charles St.BaltimoreMD 21218USA
| | - Maxime Siegler
- Department of ChemistryJohns Hopkins University3400 N. Charles St.BaltimoreMD 21218USA
| | - Thomas Lectka
- Department of ChemistryJohns Hopkins University3400 N. Charles St.BaltimoreMD 21218USA
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Harry SA, Kazim M, Nguyen PM, Zhu A, Xiang MR, Catazaro J, Siegler M, Lectka T. The Close Interaction of a C‐F Bond with an Amide Carbonyl: Crystallographic and Spectroscopic Characterization. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stefan Andrew Harry
- Johns Hopkins University Chemistry 3400 n Charles 21212 Baltimore UNITED STATES
| | | | | | - Andrea Zhu
- Johns Hopkins University chemistry UNITED STATES
| | | | | | | | - Thomas Lectka
- Johns Hopkins University Chemistry 3400 N. Charles Street 21218-2685 Baltimore UNITED STATES
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Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease. Nat Commun 2022; 13:2268. [PMID: 35477935 PMCID: PMC9046211 DOI: 10.1038/s41467-022-29915-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/07/2022] [Indexed: 11/08/2022] Open
Abstract
Emerging SARS-CoV-2 variants continue to threaten the effectiveness of COVID-19 vaccines, and small-molecule antivirals can provide an important therapeutic treatment option. The viral main protease (Mpro) is critical for virus replication and thus is considered an attractive drug target. We performed the design and characterization of three covalent hybrid inhibitors BBH-1, BBH-2 and NBH-2 created by splicing components of hepatitis C protease inhibitors boceprevir and narlaprevir, and known SARS-CoV-1 protease inhibitors. A joint X-ray/neutron structure of the Mpro/BBH-1 complex demonstrates that a Cys145 thiolate reaction with the inhibitor’s keto-warhead creates a negatively charged oxyanion. Protonation states of the ionizable residues in the Mpro active site adapt to the inhibitor, which appears to be an intrinsic property of Mpro. Structural comparisons of the hybrid inhibitors with PF-07321332 reveal unconventional F···O interactions of PF-07321332 with Mpro which may explain its more favorable enthalpy of binding. BBH-1, BBH-2 and NBH-2 exhibit comparable antiviral properties in vitro relative to PF-07321332, making them good candidates for further design of improved antivirals. Three covalent hybrid inhibitors of SARS-CoV-2 main protease (Mpro) have been designed and compared to Pfizer’s nirmatrelvir (PF-07321332), providing atomic and thermodynamic details of their binding to the enzyme, and antiviral potency.
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Guo Q, Liao TH, Ye WJ, Liao WK, Zhou ZX, Ji C. SYNTHESIS, CRYSTAL STRUCTURE, AND DFT STUDY OF N-(2-FLUORO-4-(4,4,5,5- TETRAMETHYL-1,3,2-DIOXIN-2-YL)PHENYL)- 3-METHYL-BUTANAMIDE. J STRUCT CHEM+ 2022. [DOI: 10.1134/s0022476622010115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sun M, Chen W, Zhang T, Liu Z, Wei J, Xi N. 19F NMR spectroscopy as a tool to detect rotations in fluorine substituted phenyl compounds. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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