1
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Leite JP, Costa-Rodrigues D, Gales L. Inhibitors of Transthyretin Amyloidosis: How to Rank Drug Candidates Using X-ray Crystallography Data. Molecules 2024; 29:895. [PMID: 38398647 PMCID: PMC10893244 DOI: 10.3390/molecules29040895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Amyloidosis is a group of protein misfolding diseases, which include spongiform encephalopathies, Alzheimer's disease and transthyretin (TTR) amyloidosis; all of them are characterized by extracellular deposits of an insoluble fibrillar protein. TTR amyloidosis is a highly debilitating and life-threatening disease. Patients carry less stable TTR homotetramers that are prone to dissociation into non-native monomers, which in turn rapidly self-assemble into oligomers and, ultimately, amyloid fibrils. Liver transplantation to induce the production of wild-type TTR was the only therapeutic strategy until recently. A promising approach to ameliorate transthyretin (TTR) amyloidosis is based on the so-called TTR kinetic stabilizers. More than 1000 TTR stabilizers have already been tested by many research groups, but the diversity of experimental techniques and conditions used hampers an objective prioritization of the compounds. One of the most reliable and unambiguous techniques applied to determine the structures of the TTR/drug complexes is X-ray diffraction. Most of the potential inhibitors bind in the TTR channel and the crystal structures reveal the atomic details of the interaction between the protein and the compound. Here we suggest that the stabilization effect is associated with a compaction of the quaternary structure of the protein and propose a scoring function to rank drugs based on X-ray crystallography data.
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Affiliation(s)
- José P. Leite
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Diogo Costa-Rodrigues
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Luís Gales
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
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2
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Lee SB, Yu J, Kim H, Kim KW, Jeong JW, Kim YL, Park SJ, Koo TS, Lee C, Hong KB, Choi S. Novel Strategy To Inhibit Transthyretin Amyloidosis via the Synergetic Effect of Chemoselective Acylation and Noncovalent Inhibitor Release. J Med Chem 2023; 66:2893-2903. [PMID: 36749109 DOI: 10.1021/acs.jmedchem.2c01926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Strategies for developing targeted covalent inhibitors (TCIs), which have the advantages of a prolonged duration of action and selectivity toward a drug target, have attracted great interest in drug discovery. Herein, we report chemoselective covalent inhibitors that specifically target lysine ε-amine groups that conjugate with an endogenous protein to prevent disease-causing protein misfolding and aggregation. These TCIs are unique because the benzoyl group is preferentially conjugated to Lys15 at the top of the T4 binding site within transthyretin (TTR) while simultaneously releasing a potent noncovalent TTR kinetic stabilizer. The potency of these covalent inhibitors is superior to tafamidis, the only FDA-approved drug for the treatment of hereditary TTR amyloidosis. In addition to investigations into the covalent modification of TTR via reverse-phase high-performance liquid chromatography, direct methods are performed to confirm and visualize the presumed covalent interaction via mass spectrometry and X-ray crystallography.
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Affiliation(s)
- Seok Beom Lee
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Jaeni Yu
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Hyunwoo Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kun Woo Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Jong Woo Jeong
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Yun Lan Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, Republic of Korea
| | - Tae-Sung Koo
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Changwook Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ki Bum Hong
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, Republic of Korea
| | - Sungwook Choi
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
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3
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Shen D, Jin W, Zhao Q, Wang M, Zhang B, Feng H, Wan W, Bai Y, Lyu H, Sun J, Zhang L, Liu Y. Covalent Solvatochromic Proteome Stress Sensor Based on the Schiff Base Reaction. Anal Chem 2022; 94:14143-14150. [PMID: 36194526 DOI: 10.1021/acs.analchem.2c01281] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Covalent-type probes or sensors have been seldom reported for aggregated proteins. Herein, we reported a series of covalent solvatochromic probes to selectively modify and detect aggregated proteomes through the Schiff base reaction. Such covalent modification was discovered by serendipity using the P1 probe with an aldehyde functional group, exhibiting enhanced fluorescence intensity and unusually large blue shift upon protein aggregation. Supported by the biochemical and mass spectrometry results, we identified that this probe can modify the lysine residue of aggregated proteins selectively over folded ones via the Schiff base reaction. The generality of designing such a covalent-type probe was demonstrated in multiple probe scaffolds using different model proteins. Finally, we exploited the distinct solvatochromism of P1 after Schiff base linkage with aggregated proteins to visualize the distinct morphology of aggregated proteomes, as well as to quantify the polarity heterogeneity inside it. This work may intrigue the exploration of other chemical reaction types to covalently functionalize aggregated proteins that were difficult to analyze.
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Affiliation(s)
- Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Beirong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Feng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Jialu Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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4
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Sun F, Liu J, Huang Y, Zhu X, Liu Y, Zhang L, Yan J. A quinoline derived D-A-D type fluorescent probe for sensing tetrameric transthyretin. Bioorg Med Chem Lett 2021; 52:128408. [PMID: 34626785 DOI: 10.1016/j.bmcl.2021.128408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/20/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
Nowadays, with an upward trend in the prevalence of intracerebral amyloidosis, it is of great significance to use fluorescent probes for early diagnosis in vitro. In this study, a quinoline-derived D-A-D type chemosensor was rationally designed and synthesized as a probe for the sensitive detection of tetrameric transthyretin (WT-TTR).
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Affiliation(s)
- Fantao Sun
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jinsheng Liu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
| | - Xinyin Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
| | - Lei Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jinwu Yan
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
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5
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The discovery and development of transthyretin amyloidogenesis inhibitors: what are the lessons? Future Med Chem 2021; 13:2083-2105. [PMID: 34633220 DOI: 10.4155/fmc-2021-0248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Transthyretin (TTR) is associated with several human amyloid diseases. Various kinetic stabilizers have been developed to inhibit the dissociation of TTR tetramer and the formation of amyloid fibrils. Most of them are bisaryl derivatives, natural flavonoids, crown ethers and carborans. In this review article, we focus on TTR tetramer stabilizers, genetic therapeutic approaches and fibril remodelers. The binding modes of typical bisaryl derivatives, natural flavonoids, crown ethers and carborans are discussed. Based on knowledge of the binding of thyroxine to TTR tetramer, many stabilizers have been screened to dock into the thyroxine binding sites, leading to TTR tetramer stabilization. Particularly, those stabilizers with unique binding profiles have shown great potential in developing the therapeutic management of TTR amyloidogenesis.
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6
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A proteome-wide atlas of lysine-reactive chemistry. Nat Chem 2021; 13:1081-1092. [PMID: 34504315 DOI: 10.1038/s41557-021-00765-4] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/05/2021] [Indexed: 01/24/2023]
Abstract
Recent advances in chemical proteomics have begun to characterize the reactivity and ligandability of lysines on a global scale. Yet, only a limited diversity of aminophilic electrophiles have been evaluated for interactions with the lysine proteome. Here, we report an in-depth profiling of >30 uncharted aminophilic chemotypes that greatly expands the content of ligandable lysines in human proteins. Aminophilic electrophiles showed disparate proteomic reactivities that range from selective interactions with a handful of lysines to, for a set of dicarboxaldehyde fragments, remarkably broad engagement of the covalent small-molecule-lysine interactions captured by the entire library. We used these latter 'scout' electrophiles to efficiently map ligandable lysines in primary human immune cells under stimulatory conditions. Finally, we show that aminophilic compounds perturb diverse biochemical functions through site-selective modification of lysines in proteins, including protein-RNA interactions implicated in innate immune responses. These findings support the broad potential of covalent chemistry for targeting functional lysines in the human proteome.
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7
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Liu J, Xiong Y, Huang Y, Zhu X, Liu Y, Zhang L, Yan J. A quinoline–benzothiazole hybrid as the first near-infrared fluorescent probe for transthyretin. NEW J CHEM 2021. [DOI: 10.1039/d1nj02472h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A quinoline-benzothiazole hybrid was rationally developed as the first NIR fluorescent probe for detecting transthyretin.
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Affiliation(s)
- Jinsheng Liu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yinghong Xiong
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xinyin Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Lei Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jinwu Yan
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
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8
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Chen L, Tan Y, Xu H, Wang K, Chen ZH, Zheng N, Li YQ, Lin LR. Enhanced E/ Z-photoisomerization and luminescence of stilbene derivative co-coordinated in di-β-diketonate lanthanide complexes. Dalton Trans 2020; 49:16745-16761. [PMID: 33146650 DOI: 10.1039/d0dt03383a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new tetradentate chelating ligand appending a stilbene derivative, E-N',N'-bis(pyridin-2-ylmethyl)-4-styrylbenzohydrazide (HL) was synthesized, together with two β-diketonates (4,4,4-trifluoro-1-phenylbutane-1,3-dionate, tfd), with or without the trifluoroacetate anion present as a ligand for coordination with lanthanide(iii) ions to form [Ln(tfd)2(HL)(CF3CO2)] (LnC49H36F9N4O7, Ln = La (1), Nd (2), Eu (3), Gd (4)) and [Yb(tfd)2(L)] (YbC47H35F6N4O5 (5), L = deprotonated HL). All five complexes were structurally characterized, and five crystals were obtained and analyzed by single-crystal X-ray diffraction. The quantum yield of trans-to-cis photoisomerization of the stilbene group in gadolinium complex 4 was enhanced about five-fold compared with that of HL itself. Other complexes showed slightly enhanced or depressed photoisomerization. The total luminescence quantum yield/sensitization efficiency of europium complex 3 in the solid state and acetonitrile solution were 22.1%/96.7% and 19.3%/97.9%, respectively. The transfer of ligand energy to the Eu3+ ion was highly efficient. This enhanced photoisomerization and luminescence of the stilbene group within complexes was found to be related to the energy level of lanthanide ions and whether a ligand-to-metal center or ligand-to-ligand charge transfer process was present. The interpretation of experimental results is rationally supported by time-dependent density-functional theory calculations. In complex 4, except for the intramolecular absorption transition of HL ligand itself (IL, πHL-π*HL), the presence of the ligand-to-ligand charge transfer transition from tfd to HL (LLCT, πtfd-π*HL) and the triplet state energy of HL being unable to transfer to the higher 6P7/2 excited energy level of the Gd3+ ion would facilitate HL photoisomerization. For complex 3, this was due to reversed ligand-to-ligand charge transfer transition from HL to tfd (LLCT, πHL-π*tfd) and its energy transfer to the metal center. Although the observed radiative lifetimes of NIR luminescent complexes 2 and 5 were around 10 μs, these systems contained only two diketone ligands, indicating that HL still had a certain promoting effect compared with tris(diketonate) lanthanide complexes. These results offer an important route for the design of new lanthanide-based molecular switching materials.
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Affiliation(s)
- Lu Chen
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China.
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9
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Xie J, Wu T, Wang X, Yu C, Huang W, Wu D. Azo-Label Heterometal-Organic Rhomboids Exhibiting Photoswitchable NIR Luminescence in Crystalline State. Inorg Chem 2020; 59:15460-15466. [PMID: 32990428 DOI: 10.1021/acs.inorgchem.0c02488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photochromism is an important strategy for realizing reversible light-controllable fluorescence switching. In spite of several reports on fluorescence switching via a photochromic process, the success of photochromic multimetallic complexes reversibly showing fluorescence switching in the solid or crystalline state has been limited for their application importance. Here, we report a photoswitchable near-infrared (NIR) fluorescence based on photochromism in the azo-label 3d/4f heterometal-organic rhomboids, azo-Zn2Ln2 (Ln = Eu (1), Yb (2), and Er (3)), in the crystalline state. An individual metallorhomboid contains up to four azobenzene fragments, which is prepared via the three-component assembly of a trans-azobenzene-grafted multifunctional ligand, and 3d and 4f metal ions. The photoisomerization quantum yields of azo-Zn2Ln2 complexes can be retained or even higher when compared to the free ligand due to the modification of electronic structure. The impressive crystalline-state NIR luminescence is observed for the complexes of azo-Zn2Yb2 (2) and azo-Zn2Er2 (3) at room temperature. Intriguingly, the switchable NIR luminescence can be effectively regulated by photochromism in the crystalline state. These features endow the self-assembly of the 3d/4f metallorhomboid with synergetic multifunctional behavior between photochromism and NIR luminescence.
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Affiliation(s)
- Jing Xie
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, Advanced Catalysis & Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, Jiangsu 213164, P. R. China
| | - Ting Wu
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, Advanced Catalysis & Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, Jiangsu 213164, P. R. China
| | - Xiaoling Wang
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, Advanced Catalysis & Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, Jiangsu 213164, P. R. China
| | - Chengfeng Yu
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, Advanced Catalysis & Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, Jiangsu 213164, P. R. China
| | - Wei Huang
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, Advanced Catalysis & Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, Jiangsu 213164, P. R. China
| | - Dayu Wu
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, Advanced Catalysis & Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, Jiangsu 213164, P. R. China
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10
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Abstract
Covalent inhibitors are widely used in drug discovery and chemical biology. Although covalent inhibitors are frequently designed to react with noncatalytic cysteines, many ligand binding sites lack an accessible cysteine. Here, we review recent advances in the chemical biology of lysine-targeted covalent inhibitors and chemoproteomic probes. By analyzing crystal structures of proteins bound to common metabolites and enzyme cofactors, we identify a large set of mostly unexplored lysines that are potentially targetable with covalent inhibitors. In addition, we describe mass spectrometry-based approaches for determining proteome-wide lysine ligandability and lysine-reactive chemoproteomic probes for assessing drug-target engagement. Finally, we discuss the design of amine-reactive inhibitors that form reversible covalent bonds with their protein targets.
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Affiliation(s)
- Adolfo Cuesta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA; ,
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA; ,
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11
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Solovyeva EV, Smirnov AN, Odintsova OV, Starova GL, Denisova AS. Vibrational spectroscopy and X-ray study of three stilbene dyes combined with DFT calculations. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.07.088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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12
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Huang R, Li Z, Sheng Y, Yu J, Wu Y, Zhan Y, Chen H, Jiang B. N-Methyl-N-phenylvinylsulfonamides for Cysteine-Selective Conjugation. Org Lett 2018; 20:6526-6529. [DOI: 10.1021/acs.orglett.8b02849] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Rong Huang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Zhihong Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Yao Sheng
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Jianghui Yu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Yue Wu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Yuexiong Zhan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Hongli Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China
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13
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N
-Phenyl-N
-aceto-vinylsulfonamides as Efficient and Chemoselective Handles for N-Terminal Modification of Peptides and Proteins. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701715] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Hanaki M, Murakami K, Katayama S, Akagi KI, Irie K. Mechanistic analyses of the suppression of amyloid β42 aggregation by apomorphine. Bioorg Med Chem 2018; 26:1538-1546. [PMID: 29429575 DOI: 10.1016/j.bmc.2018.01.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 01/05/2023]
Abstract
(R)-Apomorphine (1) has the potential to reduce the accumulation of amyloid β-protein (Aβ42), a causative agent of Alzheimer's disease (AD). Although the inhibition of Aβ42 aggregation by 1 is ascribable to the antioxidative effect of its phenol moiety, its inhibitory mechanism at the molecular level remains to be fully elucidated. LC-MS and UV analyses revealed that 1 is autoxidized during incubation to produce an unstable o-quinone form (2), which formed a Michael adduct with Lys 16 and 28 of Aβ42. A further autoxidized form of 1 (3) with o-quinone and phenanthrene moieties suppressed Aβ42 aggregation comparable to 1, whereas treating 1 with a reductant, tris(2-carboxyethyl)phosphine diminished its inhibitory activity. 1H-15N SOFAST-HMQC NMR studies suggested that 1 interacts with Arg5, His13,14, Gln15, and Lys16 of the Aβ42 monomer. These regions form intermolecular β-sheets in Aβ42 aggregates. Since 3 did not perturb the chemical shift of monomeric Aβ42, we performed aggregation experiments using 1,1,1,3,3,3-hexafluoro-2-propanol-treated Aβ42 to investigate whether 3 associates with Aβ42 oligomers. Compounds 1 and 3 delayed the onset of the oligomer-driven nucleation phase. Despite their cytotoxicity, they did not exacerbate Aβ42-mediated neurotoxicity in SH-SY5Y neuroblastoma cells. These results demonstrate that extension of the conjugated system in 1 by autoxidation can promote its planarity, which is required for intercalation into the β-sheet of Aβ42 nuclei, thereby suppressing further aggregation.
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Affiliation(s)
- Mizuho Hanaki
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Sumie Katayama
- National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
| | - Ken-Ichi Akagi
- National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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15
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Pan S, Jang SY, Liew SS, Fu J, Wang D, Lee JS, Yao SQ. A Vinyl Sulfone-Based Fluorogenic Probe Capable of Selective Labeling of PHGDH in Live Mammalian Cells. Angew Chem Int Ed Engl 2017; 57:579-583. [PMID: 29193627 DOI: 10.1002/anie.201710856] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Indexed: 11/05/2022]
Abstract
Chemical probes are powerful tools for interrogating small molecule-target interactions. With additional fluorescence Turn-ON functionality, such probes might enable direct measurements of target engagement in live mammalian cells. DNS-pE (and its terminal alkyne-containing version DNS-pE2) is the first small molecule that can selectively label endogenous 3-phosphoglycerate dehydrogenase (PHGDH) from various mammalian cells. Endowed with an electrophilic vinyl sulfone moiety that possesses fluorescence-quenching properties, DNS-pE/DNS-pE2 became highly fluorescent only upon irreversible covalent modification of PHGDH. With an inhibitory property (in vitro Ki =7.4 μm) comparable to that of known PHGDH inhibitors, our probes thus offer a promising approach to simultaneously image endogenous PHGDH activities and study its target engagement in live-cell settings.
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Affiliation(s)
- Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Se-Young Jang
- Molecular Recognition Research Center, Bio-Med Program of KIST-School UST, Korea Institute of Science & Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, 136791, Korea
| | - Si Si Liew
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Jiaqi Fu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Danyang Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Bio-Med Program of KIST-School UST, Korea Institute of Science & Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, 136791, Korea
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
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16
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Pan S, Jang SY, Liew SS, Fu J, Wang D, Lee JS, Yao SQ. A Vinyl Sulfone-Based Fluorogenic Probe Capable of Selective Labeling of PHGDH in Live Mammalian Cells. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710856] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sijun Pan
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Se-Young Jang
- Molecular Recognition Research Center; Bio-Med Program of KIST-School UST; Korea Institute of Science & Technology; Hwarangno 14-gil 5 Seongbuk-gu Seoul 136-791 136791 Korea
| | - Si Si Liew
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Jiaqi Fu
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Danyang Wang
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Jun-Seok Lee
- Molecular Recognition Research Center; Bio-Med Program of KIST-School UST; Korea Institute of Science & Technology; Hwarangno 14-gil 5 Seongbuk-gu Seoul 136-791 136791 Korea
| | - Shao Q. Yao
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
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17
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Sun X, Dyson HJ, Wright PE. Fluorotryptophan Incorporation Modulates the Structure and Stability of Transthyretin in a Site-Specific Manner. Biochemistry 2017; 56:5570-5581. [PMID: 28920433 DOI: 10.1021/acs.biochem.7b00815] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Abnormal deposition of aggregated wild-type (WT) human transthyretin (TTR) and its pathogenic variants is responsible for cardiomyopathy and neuropathy related to TTR amyloidosis. The tryptophan (Trp) fluorescence measurements typically used to study structural changes of TTR do not yield site-specific information on the two Trp residues per TTR protomer. To obtain such information, tryptophan labeled with fluorine at the 5 and 6 positions (5FW and 6FW) was incorporated into TTR. Fluorescence of 5FW and 6FW-labeled WT-TTR (WT-5FW and WT-6FW) and a single-Trp mutant W41Y showed that the photophysics of incorporated fluoro-Trp is consistent with site-specific solvation of the indole ring of W41 and W79. 19F-NMR showed that solvent accessibility depends on both the location of the Trp and the position of the fluorine substituent in the indole ring. Unexpectedly, differences were observed in the rates of aggregation, with WT-6FW aggregating more rapidly than WT-5FW or WT-TTR. Real-time 19F-NMR urea unfolding experiments revealed that WT-5FW is kinetically more stable than WT-6FW, consistent with the aggregation assay. In addition, structural perturbations of residues distant from either Trp site are more extensive in WT-6FW. Notably, residues in the dimer interfaces are perturbed by 6FW at residue 79; pathogenic mutations in these regions are associated with reduced tetramer stability and amyloidogenesis. The differences in behavior that arise from the replacement of a fluorine at the 5-position of a tryptophan with one at the adjacent 6-position emphasize the delicate balance of stability in the TTR tetramer.
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Affiliation(s)
- Xun Sun
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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18
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Smith TP, Windsor IW, Forest KT, Raines RT. Stilbene Boronic Acids Form a Covalent Bond with Human Transthyretin and Inhibit Its Aggregation. J Med Chem 2017; 60:7820-7834. [PMID: 28920684 DOI: 10.1021/acs.jmedchem.7b00952] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Transthyretin (TTR) is a homotetrameric protein. Its dissociation into monomers leads to the formation of fibrils that underlie human amyloidogenic diseases. The binding of small molecules to the thyroxin-binding sites in TTR stabilizes the homotetramer and attenuates TTR amyloidosis. Herein, we report on boronic acid-substituted stilbenes that limit TTR amyloidosis in vitro. Assays of affinity for TTR and inhibition of its tendency to form fibrils were coupled with X-ray crystallographic analysis of nine TTR·ligand complexes. The ensuing structure-function data led to a symmetrical diboronic acid that forms a boronic ester reversibly with serine 117. This diboronic acid inhibits fibril formation by both wild-type TTR and a common disease-related variant, V30M TTR, as effectively as does tafamidis, a small-molecule drug used to treat TTR-related amyloidosis in the clinic. These findings establish a new modality for covalent inhibition of fibril formation and illuminate a path for future optimization.
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Affiliation(s)
- Thomas P Smith
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Ian W Windsor
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Katrina T Forest
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Ronald T Raines
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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19
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Li Z, Huang R, Xu H, Chen J, Zhan Y, Zhou X, Chen H, Jiang B. Divinylsulfonamides as Specific Linkers for Stapling Disulfide Bonds in Peptides. Org Lett 2017; 19:4972-4975. [PMID: 28880566 DOI: 10.1021/acs.orglett.7b02464] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A new class of N-phenyl-divinylsulfonamides which can be easily prepared have been successfully developed and utilized as efficient linkers in the field of disulfide bond modification. Functional divinylsulfonamides provide opportunities for the specific introduction of various functionalities, including affinity probes, fluorescent tags, and drugs, into peptides.
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Affiliation(s)
- Zhihong Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University , Shanghai 201210, 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
| | - Rong Huang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University , Shanghai 201210, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University , Shanghai 201210, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Jiakang Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University , Shanghai 201210, China
| | - Yuexiong Zhan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University , Shanghai 201210, China
| | - Xianhao Zhou
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University , Shanghai 201210, China
| | - Hongli Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University , Shanghai 201210, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University , Shanghai 201210, China
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20
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Laha JK, Sharma S, Kirar S, Banerjee UC. Design, Sustainable Synthesis, and Programmed Reactions of Templated N-Heteroaryl-Fused Vinyl Sultams. J Org Chem 2017; 82:9350-9359. [PMID: 28825838 DOI: 10.1021/acs.joc.7b01340] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A de novo design and synthesis of N-heteroaryl-fused vinyl sultams as templates for programming chemical reactions on vinyl sultam periphery or (hetero)aryl ring is described. The key features include rational designing and sustainable synthesis of the template, customized reactions of vinyl sultams at C═C bond or involving N-S bond cleavage, and reactions on the periphery of the heteroaryl ring for late-stage diversification. The simple, easy access to the template coupled with opportunities for the synthesis of diversely functionalized heterocyles from a single template constitutes a rare study in contemporary organic synthesis.
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Affiliation(s)
- Joydev K Laha
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research , S. A. S. Nagar, Punjab 160062, India
| | - Shubhra Sharma
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research , S. A. S. Nagar, Punjab 160062, India
| | - Seema Kirar
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research , S. A. S. Nagar, Punjab 160062, India
| | - Uttam C Banerjee
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research , S. A. S. Nagar, Punjab 160062, India
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21
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Chen H, Huang R, Li Z, Zhu W, Chen J, Zhan Y, Jiang B. Selective lysine modification of native peptides via aza-Michael addition. Org Biomol Chem 2017; 15:7339-7345. [DOI: 10.1039/c7ob01866e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-Phenylvinylsulfonamides were developed as applicable reagents for site-selective lysine functionalization in native peptides with a free N-terminus.
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Affiliation(s)
- Hongli Chen
- The institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- P.R. China
| | - Rong Huang
- The institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- P.R. China
| | - Zhihong Li
- The institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- P.R. China
| | - Wei Zhu
- The institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- P.R. China
| | - Jiakang Chen
- The institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- P.R. China
| | - Yuexiong Zhan
- The institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- P.R. China
| | - Biao Jiang
- The institute for Advanced Immunochemical Studies
- ShanghaiTech University
- Shanghai
- P.R. China
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22
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Systemic optimization and structural evaluation of quinoline derivatives as transthyretin amyloidogenesis inhibitors. Eur J Med Chem 2016; 123:777-787. [PMID: 27541261 DOI: 10.1016/j.ejmech.2016.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/02/2016] [Accepted: 08/04/2016] [Indexed: 12/12/2022]
Abstract
Wild type transthyretin (TTR) and mutant TTR misfold and misassemble into a variety of extracellular insoluble amyloid fibril and/or amorphous aggregate, which are associated with a variety of human amyloid diseases. To develop potent TTR amyloidogenesis inhibitors, we have designed and synthesized a focused library of quinoline derivatives by Pd-catalyzed coupling reaction and by the Horner-Wadsworth-Emmons reaction. The resulting 2-alkynylquinoline derivatives, (E)-2-alkenylquinoline derivatives, and (E)-3-alkenylquinoline derivatives were evaluated to inhibit TTR amyloidogenesis by utilizing the acid-mediated TTR fibril formation. Among these quinoline derivatives, compound 14c exhibited the most potent anti-TTR fibril formation activity in the screening studies, with IC50 values of 1.49 μM against WT-TTR and 1.63 μM against more amyloidogenic V30 M TTR mutant. That is comparable to that of approved therapeutic drug, tafamidis, to ameliorate transthyretin-related amyloidosis. Furthermore, rationalization of the increased efficacy of compound 14c bearing a hydrophobic substituent, such as chloride, was carried out by utilizing in silico docking study that could focus on the region of the thyroid hormone thyroxine (T4) binding sites. Additionally, the most potent compound 14c exhibited good pharmacokinetics properties. Taken together, the novel quinoline derivatives could potentially be explored as potential drug candidates to treat the human TTR amyloidosis.
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23
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Rastede EE, Tanha M, Yaron D, Watkins SC, Waggoner AS, Armitage BA. Spectral fine tuning of cyanine dyes: electron donor-acceptor substituted analogues of thiazole orange. Photochem Photobiol Sci 2015; 14:1703-12. [PMID: 26171668 PMCID: PMC4557812 DOI: 10.1039/c5pp00117j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 07/02/2015] [Indexed: 12/21/2022]
Abstract
The introduction of electron donor and acceptor groups at strategic locations on a fluorogenic cyanine dye allows fine-tuning of the absorption and emission spectra while preserving the ability of the dye to bind to biomolecular hosts such as double-stranded DNA and a single-chain antibody fragment originally selected for binding to the parent unsubstituted dye, thiazole orange (TO). The observed spectral shifts are consistent with calculated HOMO-LUMO energy gaps and reflect electron density localization on the quinoline half of TO in the LUMO. A dye bearing donating methoxy and withdrawing trifluoromethyl groups on the benzothiazole and quinoline rings, respectively, shifts the absorption spectrum to sufficiently longer wavelengths to allow excitation at green wavelengths as opposed to the parent dye, which is optimally excited in the blue.
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Affiliation(s)
- Elizabeth E Rastede
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
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24
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Latent analysis of unmodified biomolecules and their complexes in solution with attomole detection sensitivity. Nat Chem 2015; 7:802-9. [DOI: 10.1038/nchem.2344] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 08/06/2015] [Indexed: 12/30/2022]
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25
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Liu Y, Zhang X, Chen W, Tan YL, Kelly JW. Fluorescence Turn-On Folding Sensor To Monitor Proteome Stress in Live Cells. J Am Chem Soc 2015; 137:11303-11. [PMID: 26305239 PMCID: PMC4755273 DOI: 10.1021/jacs.5b04366] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Proteome misfolding and/or aggregation, caused by a thermal perturbation or a related stress, transiently challenges the cellular protein homeostasis (proteostasis) network capacity of cells by consuming chaperone/chaperonin pathway and degradation pathway capacity. Developing protein client-based probes to quantify the cellular proteostasis network capacity in real time is highly desirable. Herein we introduce a small-molecule-regulated fluorescent protein folding sensor based on a thermo-labile mutant of the de novo designed retroaldolase (RA) enzyme. Since RA enzyme activity is not present in any cell, the protein folding sensor is bioorthogonal. The fluorogenic small molecule was designed to become fluorescent when it binds to and covalently reacts with folded and functional RA. Thus, in the first experimental paradigm, cellular proteostasis network capacity and its dynamics are reflected by RA-small molecule conjugate fluorescence, which correlates with the amount of folded and functional RA present, provided that pharmacologic chaperoning is minimized. In the second experimental scenario, the RA-fluorogenic probe conjugate is pre-formed in a cell by simply adding the fluorogenic probe to the cell culture media. Unreacted probe is then washed away before a proteome misfolding stress is applied in a pulse-chase-type experiment. Insufficient proteostasis network capacity is reflected by aggregate formation of the fluorescent RA-fluorogenic probe conjugate. Removal of the stress results in apparent RA-fluorogenic probe conjugate re-folding, mediated in part by the heat-shock response transcriptional program augmenting cytosolic proteostasis network capacity, and in part by time-dependent RA-fluorogenic probe conjugate degradation by cellular proteolysis.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Xin Zhang
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Wentao Chen
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Yun Lei Tan
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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26
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Baranczak A, Liu Y, Connelly S, Du WGH, Greiner ER, Genereux JC, Wiseman RL, Eisele YS, Bradbury NC, Dong J, Noodleman L, Sharpless KB, Wilson IA, Encalada SE, Kelly JW. A fluorogenic aryl fluorosulfate for intraorganellar transthyretin imaging in living cells and in Caenorhabditis elegans. J Am Chem Soc 2015; 137:7404-14. [PMID: 26051248 PMCID: PMC4472559 DOI: 10.1021/jacs.5b03042] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fluorogenic probes, due to their often greater spatial and temporal sensitivity in comparison to permanently fluorescent small molecules, represent powerful tools to study protein localization and function in the context of living systems. Herein, we report fluorogenic probe 4, a 1,3,4-oxadiazole designed to bind selectively to transthyretin (TTR). Probe 4 comprises a fluorosulfate group not previously used in an environment-sensitive fluorophore. The fluorosulfate functional group does not react covalently with TTR on the time scale required for cellular imaging, but does red shift the emission maximum of probe 4 in comparison to its nonfluorosulfated analogue. We demonstrate that probe 4 is dark in aqueous buffers, whereas the TTR·4 complex exhibits a fluorescence emission maximum at 481 nm. The addition of probe 4 to living HEK293T cells allows efficient binding to and imaging of exogenous TTR within intracellular organelles, including the mitochondria and the endoplasmic reticulum. Furthermore, live Caenorhabditis elegans expressing human TTR transgenically and treated with probe 4 display TTR·4 fluorescence in macrophage-like coelomocytes. An analogue of fluorosulfate probe 4 does react selectively with TTR without labeling the remainder of the cellular proteome. Studies on this analogue suggest that certain aryl fluorosulfates, due to their cell and organelle permeability and activatable reactivity, could be considered for the development of protein-selective covalent probes.
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Affiliation(s)
- Aleksandra Baranczak
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Yu Liu
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Stephen Connelly
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Erin R. Greiner
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Joseph C. Genereux
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - R. Luke Wiseman
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Yvonne S. Eisele
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Nadine C. Bradbury
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Jiajia Dong
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - K. Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Sandra E. Encalada
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Dorris Neuroscience Center, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, USA
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27
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Jedinák L, Kryštof V, Cankař P. The Synthesis and Biological Evaluation ofN-Substituted 1H-Benzimidazol-2-yl-1H-pyrazole-3,5-diamines. J Heterocycl Chem 2015. [DOI: 10.1002/jhet.2315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lukáš Jedinák
- Department of Organic Chemistry, Faculty of Science; Palacky University; 17. Listopadu 1192/12 771 46 Olomouc Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators; Institute of Experimental Botany AS CR and Palacky University; Slechtitelu 11 783 71 Olomouc Czech Republic
| | - Petr Cankař
- Department of Organic Chemistry, Faculty of Science; Palacky University; 17. Listopadu 1192/12 771 46 Olomouc Czech Republic
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28
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Liu Y, Zhang X, Tan YL, Bhabha G, Ekiert DC, Kipnis Y, Bjelic S, Baker D, Kelly JW. De novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters. J Am Chem Soc 2014; 136:13102-5. [PMID: 25209927 PMCID: PMC4183642 DOI: 10.1021/ja5056356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Enzyme-based tags attached to a protein-of-interest (POI) that react with a small molecule, rendering the conjugate fluorescent, are very useful for studying the POI in living cells. These tags are typically based on endogenous enzymes, so protein engineering is required to ensure that the small-molecule probe does not react with the endogenous enzyme in the cell of interest. Here we demonstrate that de novo-designed enzymes can be used as tags to attach to POIs. The inherent bioorthogonality of the de novo-designed enzyme-small-molecule probe reaction circumvents the need for protein engineering, since these enzyme activities are not present in living organisms. Herein, we transform a family of de novo-designed retroaldolases into variable-molecular-weight tags exhibiting fluorescence imaging, reporter, and electrophoresis applications that are regulated by tailored, reactive small-molecule fluorophores.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, Department of Molecular and Experimental Medicine, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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29
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Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts. Proc Natl Acad Sci U S A 2014; 111:4449-54. [PMID: 24591605 DOI: 10.1073/pnas.1323268111] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although much is known about protein folding in buffers, it remains unclear how the cellular protein homeostasis network functions as a system to partition client proteins between folded and functional, soluble and misfolded, and aggregated conformations. Herein, we develop small molecule folding probes that specifically react with the folded and functional fraction of the protein of interest, enabling fluorescence-based quantification of this fraction in cell lysate at a time point of interest. Importantly, these probes minimally perturb a protein's folding equilibria within cells during and after cell lysis, because sufficient cellular chaperone/chaperonin holdase activity is created by rapid ATP depletion during cell lysis. The folding probe strategy and the faithful quantification of a particular protein's functional fraction are exemplified with retroaldolase, a de novo designed enzyme, and transthyretin, a nonenzyme protein. Our findings challenge the often invoked assumption that the soluble fraction of a client protein is fully folded in the cell. Moreover, our results reveal that the partitioning of destabilized retroaldolase and transthyretin mutants between the aforementioned conformational states is strongly influenced by cytosolic proteostasis network perturbations. Overall, our results suggest that applying a chemical folding probe strategy to other client proteins offers opportunities to reveal how the proteostasis network functions as a system to regulate the folding and function of individual client proteins in vivo.
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