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Wang YC, Bai SC, Ye WL, Jiang J, Li G. Recent Progress in Site-Selective Modification of Peptides and Proteins Using Macrocycles. Bioconjug Chem 2024; 35:277-285. [PMID: 38417023 DOI: 10.1021/acs.bioconjchem.3c00534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Peptides and proteins undergo crucial modifications to alter their physicochemical properties to expand their applications in diverse fields. Various techniques, such as unnatural amino acid incorporation, enzyme catalysis, and chemoselective methods, have been employed for site-selective peptide and protein modification. While traditional methods remain valuable, advancement in host-guest chemistry introduces innovative and promising approaches for the selective modification of peptides and proteins. Macrocycles exhibit robust binding affinities, particularly with natural amino acids, which facilitates their use in selectively binding to specific sequences. This distinctive property endows macrocycles with the potential for modification of target peptides and proteins. This review provides a comprehensive overview of strategies utilizing macrocycles for the selective modification of peptides and proteins. These strategies unlock new possibilities for constructing antibody-drug conjugates and stabilizing volatile medications.
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Affiliation(s)
- Ye-Cheng Wang
- Fuzhou Institute of Oceanography, College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian 350108, China
- College of Chemical Engineering, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Si-Cong Bai
- School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Wei-Lin Ye
- Fuzhou Institute of Oceanography, College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian 350108, China
- College of Chemical Engineering, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Jing Jiang
- Fuzhou Institute of Oceanography, College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian 350108, China
| | - Gao Li
- Fuzhou Institute of Oceanography, College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian 350108, China
- Fujian-Taiwan-Hongkong-Macao Science and Technology Co-operation Base of Intelligent Pharmaceutics, Minjiang University, Fuzhou, Fujian 350108, China
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2
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Maus H, Müller P, Meta M, Hoba SN, Hammerschmidt SJ, Zimmermann RA, Zimmer C, Fuchs N, Schirmeister T, Barthels F. Next Generation of Fluorometric Protease Assays: 7-Nitrobenz-2-oxa-1,3-diazol-4-yl-amides (NBD-Amides) as Class-Spanning Protease Substrates. Chemistry 2023; 29:e202301855. [PMID: 37313627 DOI: 10.1002/chem.202301855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/15/2023]
Abstract
Fluorometric assays are one of the most frequently used methods in medicinal chemistry. Over the last 50 years, the reporter molecules for the detection of protease activity have evolved from first-generation colorimetric p-nitroanilides, through FRET substrates, and 7-amino-4-methyl coumarin (AMC)-based substrates. The aim of further substrate development is to increase sensitivity and reduce vulnerability to assay interferences. Herein, we describe a new generation of substrates for protease assays based on 7-nitrobenz-2-oxa-1,3-diazol-4-yl-amides (NBD-amides). In this study, we synthesized and tested substrates for 10 different proteases from the serine-, cysteine-, and metalloprotease classes. Enzyme- and substrate-specific parameters as well as the inhibitory activity of literature-known inhibitors confirmed their suitability for application in fluorometric assays. Hence, we were able to present NBD-based alternatives for common protease substrates. In conclusion, these NBD substrates are not only less susceptible to common assay interference, but they are also able to replace FRET-based substrates with the requirement of a prime site amino acid residue.
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Affiliation(s)
- Hannah Maus
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Patrick Müller
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Mergim Meta
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Sabrina N Hoba
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Stefan J Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Natalie Fuchs
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128, Mainz, Germany
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3
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Thimaradka V, Utsunomiya H, Tamura T, Hamachi I. Endogenous Cell-Surface Receptor Modification by Metal Chelation-Assisted Pyridinium Oxime Catalyst. Org Lett 2023; 25:2118-2122. [PMID: 36947590 DOI: 10.1021/acs.orglett.3c00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Organocatalyst-mediated acyl transfer reactions hold promise for selective protein labeling in biological milieu. However, they often suffer from off-target reactions and high background signals because of the requirement of high concentrations of substrates. Here, we report a new catalytic protein acylation strategy promoted by the His-tag/NiNTA interaction. The recognition-assisted activation mechanism allows efficient protein labeling even with >10-fold lower substrate concentrations than conventional reactions, thereby enabling highly selective and efficient cell-surface receptor modification in live cells.
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Affiliation(s)
- Vikram Thimaradka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hayata Utsunomiya
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Sanbancho, Chiyodaku, Tokyo 102-0075, Japan
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4
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Xie Y, Du S, Liu Z, Liu M, Xu Z, Wang X, Kee JX, Yi F, Sun H, Yao SQ. Chemical Biology Tools for Protein Lysine Acylation. Angew Chem Int Ed Engl 2022; 61:e202200303. [PMID: 35302274 DOI: 10.1002/anie.202200303] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Indexed: 01/10/2023]
Abstract
Lysine acylation plays pivotal roles in cell physiology, including DNA transcription and repair, signal transduction, immune defense, metabolism, and many other key cellular processes. Molecular mechanisms of dysregulated lysine acylation are closely involved in the pathophysiological progress of many human diseases, most notably cancers. In recent years, chemical biology tools have become instrumental in studying the function of post-translational modifications (PTMs), identifying new "writers", "erasers" and "readers", and in targeted therapies. Here, we describe key developments in chemical biology approaches that have advanced the study of lysine acylation and its regulatory proteins (2016-2021). We further discuss the discovery of ligands (inhibitors and PROTACs) that are capable of targeting regulators of lysine acylation. Next, we discuss some current challenges of these chemical biology probes and suggest how chemists and biologists can utilize chemical probes with more discriminating capacity. Finally, we suggest some critical considerations in future studies of PTMs from our perspective.
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Affiliation(s)
- Yusheng Xie
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Shubo Du
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Zhiyang Liu
- Department of Chemistry, COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Min Liu
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Zhiqiang Xu
- Department of Chemistry, COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Xiaojie Wang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Jia Xuan Kee
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Fan Yi
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Hongyan Sun
- Department of Chemistry, COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
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Zhong W, Hooley RJ. Combining Excellent Selectivity with Broad Target Scope: Biosensing with Arrayed Deep Cavitand Hosts. Acc Chem Res 2022; 55:1035-1046. [PMID: 35302733 DOI: 10.1021/acs.accounts.2c00026] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Simple macrocyclic water-soluble hosts such as cucurbiturils, cyclophanes, and calixarenes have long been used for biosensing via indicator displacement assays. Using multiple hosts and dyes in an arrayed format allows pattern recognition-based "chemical nose" sensing, which confers exquisite selectivity, even rivaling the abilities of biological recognition tools such as antibodies. However, a challenge in indicator displacement-based biosensing with macrocyclic hosts is that selectivity and scope are often inversely correlated: strong selectivity for a specific target can limit wide application, and broad scope sensing can suffer from a lack of selectivity between similar targets. This problem can be addressed by using water-soluble, self-folding deep cavitands as hosts. These flexible bowl-shaped receptors can be easily functionalized with different motifs at the upper and lower rim, and the large cavities can bind many different fluorescent dyes, causing either fluorescence enhancement or quenching upon binding.Cavity-based affinity is strongest for NMe3+ groups such as trimethyl-lysine, and we have exploited this for the site-selective recognition of post-translational lysine methylations in oligopeptides. The host recognizes the NMe3+ group, and by applying differently functionalized hosts in an arrayed format, discrimination between identical modifications at different positions on the oligopeptide is possible. Multiple recognition elements can be exploited for selectivity, including a defined, yet "breathable" cavity, and variable upper rim functions oriented toward the target.While the performance of the host/guest sensing system is impressive for lysine methylations, the most important advance is the use of multiple different sensing mechanisms that can target a broad range of different biorelevant species. The amphiphilic deep cavitands can both bind fluorescent dyes and interact with charged biomolecules. These non-cavity-based interactions, when paired with additives such as heavy metal ions, modulate fluorescence response in an indirect manner, and these different mechanisms allow selective recognition of serine phosphorylation, lysine acetylation, and arginine citrullination. Other targets include heavy metals, drugs of abuse, and protein isoforms. Furthermore, the hosts can be applied in supramolecular tandem assays of enzyme function: the broad scope allows analysis of such different enzymes as chromatin writers/erasers, kinases, and phosphatases, all from a single host scaffold. Finally, the indirect sensing concept allows application in sensing different oligonucleotide secondary structures, including G-quadruplexes, hairpins, triplexes, and i-motifs. Discrimination between DNA strands with highly similar structures such as G-quadruplex strands with bulges and vacancies can be achieved. Instead of relying on a single highly specific fluorescent probe, the synthetic hosts tune the fluorophore-DNA interaction, introducing multiple recognition equilibria that modulate the fluorescence signal. By applying machine learning algorithms, a classification model can be established that can accurately predict the folding state of unknown sequences. Overall, the unique recognition profile of self-folded deep cavitands provides a powerful, yet simple sensing platform, one that can be easily tuned for a wide scope of biorelevant targets, in complex biological media, without sacrificing selectivity in the recognition.
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6
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Xie Y, Du S, Liu Z, Liu M, Xu Z, Wang X, Kee JX, Yi F, Sun H, Yao SQ. Chemical Biology Tools for Protein Lysine Acylation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Yusheng Xie
- Shandong University School of Basic Medical Science 250012 Jinan CHINA
| | - Shubo Du
- National University of Singapore Department of Chemistry SINGAPORE
| | - Zhiyang Liu
- City University of Hong Kong chemistry HONG KONG
| | - Min Liu
- Shandong University School of Basic Medical Sciences CHINA
| | - Zhiqiang Xu
- City University of Hong Kong Department of Chemistry HONG KONG
| | - Xiaojie Wang
- Shandong University School of Basic Medical Sciences CHINA
| | - Jia Xuan Kee
- National University of Singapore Chemistry SINGAPORE
| | - Fan Yi
- Shandong University School of basic medical sciences CHINA
| | - Hongyan Sun
- City University of Hong Kong department of chemistry HONG KONG
| | - Shao Q. Yao
- National University of Singapore Department of Chemistry 3 Science Dr. 117543 Singapore SINGAPORE
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7
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Zhang Z, Nakata E, Dinh H, Saimura M, Rajendran A, Matsuda K, Morii T. Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation. Chemistry 2021; 27:18118-18128. [PMID: 34747070 DOI: 10.1002/chem.202103304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Indexed: 11/09/2022]
Abstract
Recognition-driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site-specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition-driven modification of DNA as they consist of both a sequence-specific DNA-binding domain (DBD) and a self-ligating protein-tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence-specific reaction. However, combining an MA consisting of a reactive protein-tag and its substrate, for example, SNAP-tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP-tag have been designed to realize sequence-selective rapid crosslinking reactions of MAs with SNAP-tag. The reactions of substrates with SNAP-tag were verified by kinetic analyses to enable the sequence-selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP-tag against CLIP-tag to achieve orthogonal DNA-protein crosslinking by six unique MAs.
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Affiliation(s)
- Zhengxiao Zhang
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Masayuki Saimura
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | | | - Kazunari Matsuda
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
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8
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Jiang C, Huang H, Kang X, Yang L, Xi Z, Sun H, Pluth MD, Yi L. NBD-based synthetic probes for sensing small molecules and proteins: design, sensing mechanisms and biological applications. Chem Soc Rev 2021; 50:7436-7495. [PMID: 34075930 PMCID: PMC8763210 DOI: 10.1039/d0cs01096k] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Compounds with a nitrobenzoxadiazole (NBD) skeleton exhibit prominent useful properties including environmental sensitivity, high reactivity toward amines and biothiols (including H2S) accompanied by distinct colorimetric and fluorescent changes, fluorescence-quenching ability, and small size, all of which facilitate biomolecular sensing and self-assembly. Amines are important biological nucleophiles, and the unique activity of NBD ethers with amines has allowed for site-specific protein labelling and for the detection of enzyme activities. Both H2S and biothiols are involved in a wide range of physiological processes in mammals, and misregulation of these small molecules is associated with numerous diseases including cancers. In this review, we focus on NBD-based synthetic probes as advanced chemical tools for biomolecular sensing. Specifically, we discuss the sensing mechanisms and selectivity of the probes, the design strategies for multi-reactable multi-quenching probes, and the associated biological applications of these important constructs. We also highlight self-assembled NBD-based probes and outline future directions for NBD-based chemosensors. We hope that this comprehensive review will facilitate the development of future probes for investigating and understanding different biological processes and aid the development of potential theranostic agents.
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Affiliation(s)
- Chenyang Jiang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Haojie Huang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Xueying Kang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Liu Yang
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China.
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China.
| | - Hongyan Sun
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China. and Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
| | - Michael D Pluth
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
| | - Long Yi
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
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9
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Li G, Hu J, Chen H, Chen YX, Li YM. Cucurbit[8]uril facilitated Michael addition for regioselective cysteine modification. Chem Commun (Camb) 2021; 57:6086-6089. [PMID: 34037637 DOI: 10.1039/d1cc01404h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Utilizing the interactions between tryptophan, methyl viologen and cucurbit[8]uril, we found that the distance between the targeted peptides/protein and the reactive peptide was shortened, which facilitated the Michael addition reaction between cysteine and dehydroalanine. The highest acceleration was observed on cysteines with suitable pKa and spatial location to tryptophan, suggesting that our system can be used for regioselective cysteine modification.
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Affiliation(s)
- Gao Li
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian 350108, China.
| | - Jun Hu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China.
| | - Huai Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China.
| | - Yong-Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China.
| | - Yan-Mei Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China. and Beijing Institute for Brain Disorders, Beijing 100069, China and Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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10
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11
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Xie Y, Yang L, Chen Q, Zhang J, Feng L, Chen JL, Hao Q, Zhang L, Sun H. Single-step fluorescent probes to detect decrotonylation activity of HDACs through intramolecular reactions. Eur J Med Chem 2020; 212:113120. [PMID: 33422982 DOI: 10.1016/j.ejmech.2020.113120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 02/07/2023]
Abstract
Lysine crotonylation plays vital roles in gene transcription and cellular metabolism. Nevertheless, methods for dissecting the molecular mechanisms of decrotonyaltion remains limited. So far, there is no single-step fluorescent method developed for enzymatic decrotonylation activity detection. The major difficulty is that the aliphatic crotonylated lysine doesn't allow π-conjugation to a fluorophore and decrotonylation can not modulate the electronic state directly. Herein, we have designed and synthesized two activity-based single-step fluorogenic probes KTcr-I and KTcr-II for detecting enzymatic decrotonylation activity. These two probes can be recognized by histone deacetylases and undergo intramolecular nucleophilic exchange reaction to generate fluorescence signal. Notably, peptide sequence-dependent effect was observed. KTcr-I can be recognized by Sirt2 more effectively, while KTcr-II with LGKcr peptide sequence preferentially reacted with HDAC3. Compared to other methods of studying enzymatic decrotonylation activity, our single-step fluorescent method has a number of advantages, such as facileness, high sensitivity, cheap facility and little material consumed. We envision that the probes developed in this study will provide useful tools to screen inhibitors which suppress the decrotonylation activity of HDACs. Such probes will be useful for further delineating the roles of decrotonylation enzyme and aid in biomarker identification and drug discovery.
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Affiliation(s)
- Yusheng Xie
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Liu Yang
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Qingxin Chen
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Jie Zhang
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Ling Feng
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Jian Lin Chen
- School of Science and Technology, The Open University of Hong Kong, Hong Kong Special Administrative Region
| | - Quan Hao
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Liang Zhang
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China; Department of Biomedical Science, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Hongyan Sun
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
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12
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Beyer JN, Raniszewski NR, Burslem GM. Advances and Opportunities in Epigenetic Chemical Biology. Chembiochem 2020; 22:17-42. [PMID: 32786101 DOI: 10.1002/cbic.202000459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The study of epigenetics has greatly benefited from the development and application of various chemical biology approaches. In this review, we highlight the key targets for modulation and recent methods developed to enact such modulation. We discuss various chemical biology techniques to study DNA methylation and the post-translational modification of histones as well as their effect on gene expression. Additionally, we address the wealth of protein synthesis approaches to yield histones and nucleosomes bearing epigenetic modifications. Throughout, we highlight targets that present opportunities for the chemical biology community, as well as exciting new approaches that will provide additional insight into the roles of epigenetic marks.
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Affiliation(s)
- Jenna N Beyer
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - Nicole R Raniszewski
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA.,Department of Cancer Biology and Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
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13
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Gorbunov A, Iskandarova A, Puchnin K, Nenajdenko V, Kovalev V, Vatsouro I. A route to virtually unlimited functionalization of water-soluble p-sulfonatocalix[4]arenes. Chem Commun (Camb) 2020; 56:4122-4125. [PMID: 32166302 DOI: 10.1039/d0cc01196g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The functionality of p-sulfonatocalix[4]arenes can be easily extended using the propargylation/CuAAC reaction sequence, which allows the introduction of up to four substituted triazole units to the narrow rims of the macrocycles while maintaining their cone shapes and water solubility and, thus, biomedical applicability.
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Affiliation(s)
- Alexander Gorbunov
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Anna Iskandarova
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Kirill Puchnin
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Valentine Nenajdenko
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Vladimir Kovalev
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Ivan Vatsouro
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
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14
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Yamaguchi T. [Development of a Novel Affinity Labeling Method for Target Identification of Bioactive Small Molecules]. YAKUGAKU ZASSHI 2020; 139:1513-1521. [PMID: 31787638 DOI: 10.1248/yakushi.19-00171] [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: 11/22/2022]
Abstract
Target identification (target-ID) is an important step in elucidating the mechanisms of action of bioactive small molecules. In the past few decades, a number of target-ID methods have been developed. Among these, affinity labeling has been reliably used for specific modifications, as well as for the identification of weakly interacting protein targets, membrane-associated protein targets, and target-interacting proteins under native cellular conditions, which are generally difficult to achieve by conventional pull-down methods. In general, affinity labeling utilizes chemical probes composed of a bioactive small molecule, a reactive group, and a detection unit. However, the design and synthesis of highly functionalized chemical probes is often time-consuming. To address this issue, we have recently developed some simple affinity labeling methods using small fluorogenic tags, such as 4-alkoxy-7-nitro-2,1,3-benzoxadiazole (O-NBD), 2,3-dichloromaleimide (diCMI), and 4-azidophthalimide (AzPI), and successfully achieved the specific fluorescent labeling of target proteins, even in living cells. These methods should be useful for target-ID in phenotypic drug discovery.
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Affiliation(s)
- Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University
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15
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Gill AD, Hickey BL, Wang S, Xue M, Zhong W, Hooley RJ. Sensing of citrulline modifications in histone peptides by deep cavitand hosts. Chem Commun (Camb) 2019; 55:13259-13262. [PMID: 31621759 PMCID: PMC6872487 DOI: 10.1039/c9cc07002h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Arrayed cavitand:fluorophore sensor complexes can selectively sense small citrulline modifications at arginine residues on post-translationally modified peptides. The sensor can differentiate between different numbers of citrulline modifications, and a simple two-fluorophore, 6-component array can effect cross-reactive discrimination between single modifications in aqueous solution.
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Affiliation(s)
- Adam D Gill
- Department of Biochemistry and Molecular Biology, University of California-Riverside, Riverside, CA 92521, USA.
| | - Briana L Hickey
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA
| | - Siwen Wang
- Environmental Toxicology Program, University of California-Riverside, Riverside, CA 92521, USA
| | - Min Xue
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA and Environmental Toxicology Program, University of California-Riverside, Riverside, CA 92521, USA
| | - Wenwan Zhong
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA and Environmental Toxicology Program, University of California-Riverside, Riverside, CA 92521, USA
| | - Richard J Hooley
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA and Department of Biochemistry and Molecular Biology, University of California-Riverside, Riverside, CA 92521, USA.
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16
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Beatty MA, Selinger AJ, Li Y, Hof F. Parallel Synthesis and Screening of Supramolecular Chemosensors That Achieve Fluorescent Turn-on Detection of Drugs in Saliva. J Am Chem Soc 2019; 141:16763-16771. [DOI: 10.1021/jacs.9b07073] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Meagan A. Beatty
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3 V6, Canada
| | - Allison J. Selinger
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3 V6, Canada
| | - YuQi Li
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3 V6, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3 V6, Canada
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17
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Zhao H, Peng K, Lv F, Liu L, Wang S. Boronic Acid-Functionalized Conjugated Polymer for Controllable Cell Membrane Imaging. ACS APPLIED BIO MATERIALS 2019; 2:1787-1791. [DOI: 10.1021/acsabm.9b00212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Hao Zhao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Ke Peng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Libing Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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18
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Okada K, Yamaguchi T, Dodo K, Sodeoka M, Obika S. Detection of esterase activity by chromogenic and fluorogenic probe based on an O-nitrobenzoxadiazole (O-NBD) unit. Bioorg Med Chem 2019; 27:1444-1448. [DOI: 10.1016/j.bmc.2019.02.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/13/2019] [Accepted: 02/16/2019] [Indexed: 10/27/2022]
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19
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Zhang Y, Liang Y, Huang F, Zhang Y, Li X, Xia J. Site-Selective Lysine Reactions Guided by Protein-Peptide Interaction. Biochemistry 2019; 58:1010-1018. [PMID: 30624906 DOI: 10.1021/acs.biochem.8b01223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Site-selective lysine post-translational modifications such as acetylation, methylation, hydroxylation, and isopeptide formation mediate the precise control of important signaling events in cells with unmistakable accuracy. This unparalleled site selectivity (modification of a single lysine in a particular protein in the proteome) is still a challenge for non-enzymatic protein reactions; the difficulty lies in the differentiation of the lysine ε-amino group from other reactive groups and in the precise pinpointing of one particular lysine ε-amino group out of many other lysine ε-amino groups and the N-terminal amine of the protein that have similar chemical reactivity. Here, we have explored proximal lysine conjugation reactions through peptide-guided fluorodinitrobenzene, isothiocyanate, and phenyl ester reactions and have validated the site-specific targeting of the ε-amino group of one single lysine in natural proteins that contain multiple lysine residues. This precise site selectivity is a result of the proximity-induced reactivity guided by a specific protein-peptide interaction: the binding interaction preorganizes an amine-reactive group in the peptide and one of the lysine side chain ε-amino groups of the protein into close proximity, thereby confining the reactivity to a selected area of the target protein. The binding-guide lysine reactions were first examined on an SH3 domain and then tested on several ubiquitin-like proteins such as SUMO, Atg8 protein family, plant ATG8, and mammalian LC3 proteins that contain at least seven lysine residues on the surface. Exquisite site selectivity was confirmed in all of the proteins tested. A set of amine reactions were tested for their feasibility in the site-selective lysine reaction. Selected amine-reactive groups were optimized, and the reaction sites on the LC3 protein were confirmed by mass spectrometry.
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Affiliation(s)
- Yu Zhang
- Department of Chemistry , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China
| | - Yujie Liang
- Department of Chemistry , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China
| | - Feng Huang
- Department of Chemistry , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China
| | - Yue Zhang
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , Hong Kong SAR
| | - Xuechen Li
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , Hong Kong SAR
| | - Jiang Xia
- Department of Chemistry , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China
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20
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Fang X, Zheng Y, Duan Y, Liu Y, Zhong W. Recent Advances in Design of Fluorescence-Based Assays for High-Throughput Screening. Anal Chem 2019; 91:482-504. [PMID: 30481456 PMCID: PMC7262998 DOI: 10.1021/acs.analchem.8b05303] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiaoni Fang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yongzan Zheng
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yaokai Duan
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yang Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California, Riverside, California 92521, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
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21
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Gruber T. Synthetic Receptors for the Recognition and Discrimination of Post-Translationally Methylated Lysines. Chembiochem 2018; 19:2324-2340. [DOI: 10.1002/cbic.201800398] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Tobias Gruber
- School of Pharmacy; University of Lincoln; Joseph Banks Laboratories; Green Lane Lincoln LN6 7DL UK
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22
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Beatty MA, Busmann JA, Fagen NG, Garnett GAE, Hof F. A clip-like host that undergoes self-assembly and competitive guest-induced disassembly in water. Supramol Chem 2018. [DOI: 10.1080/10610278.2018.1494275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Meagan A. Beatty
- Department of Chemistry, University of Victoria, Victoria, Canada
| | - Jil A. Busmann
- Department of Chemistry, University of Victoria, Victoria, Canada
| | - Noah G. Fagen
- Department of Chemistry, University of Victoria, Victoria, Canada
| | | | - Fraser Hof
- Department of Chemistry, University of Victoria, Victoria, Canada
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23
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Guagnini F, Antonik PM, Rennie ML, O'Byrne P, Khan AR, Pinalli R, Dalcanale E, Crowley PB. Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803232] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Francesca Guagnini
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Paweł M. Antonik
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Peter O'Byrne
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Roberta Pinalli
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Enrico Dalcanale
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
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24
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Guagnini F, Antonik PM, Rennie ML, O'Byrne P, Khan AR, Pinalli R, Dalcanale E, Crowley PB. Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. Angew Chem Int Ed Engl 2018; 57:7126-7130. [DOI: 10.1002/anie.201803232] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Francesca Guagnini
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Paweł M. Antonik
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Peter O'Byrne
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Roberta Pinalli
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Enrico Dalcanale
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
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25
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Lee J, Perez L, Liu Y, Wang H, Hooley RJ, Zhong W. Separation of Methylated Histone Peptides via Host-Assisted Capillary Electrophoresis. Anal Chem 2018; 90:1881-1888. [PMID: 29286640 DOI: 10.1021/acs.analchem.7b03969] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Lysine methylation in protein is one important epigenetic mechanism that regulates diverse biological processes but is challenging to study due to the large variability in methylation levels and sites. Here, we show that supramolecular hosts such as calixarenes and cucurbiturils can be applied in the background electrolyte (BGE) of capillary electrophoresis (CE) for highly effective separation of post-translationally methylated histone peptides. The molecular recognition event causes a shift in the electrophoretic mobility of the peptide, allowing affinity measurement for binding between the synthetic receptor and various methylated lysine species. Successful separation of the H3 peptides carrying different methylation levels at the K9 position can be achieved using CX4 and CX6 as the BGE additives in CE, enabling monitoring of the activity of the histone lysine demethylase JMJD2E. This reveals the power of combining high resolution CE with synthetic hosts for study of protein methylation, and the method should be capable of analyzing complex biological samples for better understanding of the functions of histone methylation.
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Affiliation(s)
| | | | | | - Hua Wang
- Instrument Analysis Center, Yancheng Teachers University , Yancheng, Jiangsu 224007, China
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26
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27
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He M, Han Z, Qiao J, Ngo L, Xiong MP, Zheng YG. A bioorthogonal turn-on fluorescent strategy for the detection of lysine acetyltransferase activity. Chem Commun (Camb) 2018; 54:5594-5597. [DOI: 10.1039/c8cc02987c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bioorthogonal labelling was applied to design “turn-on” fluorescent probes for sensitive and selective detection of histone acetyltransferase enzymatic activity in a simple mix-and-read manner.
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Affiliation(s)
- Maomao He
- Department of Pharmaceutical and Biomedical Sciences
- College of Pharmacy
- University of Georgia
- Athens
- USA
| | - Zhen Han
- Department of Pharmaceutical and Biomedical Sciences
- College of Pharmacy
- University of Georgia
- Athens
- USA
| | - Jing Qiao
- Department of Pharmaceutical and Biomedical Sciences
- College of Pharmacy
- University of Georgia
- Athens
- USA
| | - Liza Ngo
- Department of Pharmaceutical and Biomedical Sciences
- College of Pharmacy
- University of Georgia
- Athens
- USA
| | - May P. Xiong
- Department of Pharmaceutical and Biomedical Sciences
- College of Pharmacy
- University of Georgia
- Athens
- USA
| | - Y. George Zheng
- Department of Pharmaceutical and Biomedical Sciences
- College of Pharmacy
- University of Georgia
- Athens
- USA
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28
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Castañeda CA, Wolfson NA, Leng KR, Kuo YM, Andrews AJ, Fierke CA. HDAC8 substrate selectivity is determined by long- and short-range interactions leading to enhanced reactivity for full-length histone substrates compared with peptides. J Biol Chem 2017; 292:21568-21577. [PMID: 29109148 PMCID: PMC5766737 DOI: 10.1074/jbc.m117.811026] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/05/2017] [Indexed: 01/03/2023] Open
Abstract
Histone deacetylases (HDACs) catalyze deacetylation of acetyl-lysine residues within proteins. To date, HDAC substrate specificity and selectivity have been largely estimated using peptide substrates. However, it is unclear whether peptide substrates accurately reflect the substrate selectivity of HDAC8 toward full-length proteins. Here, we compare HDAC8 substrate selectivity in the context of peptides, full-length proteins, and protein-nucleic acid complexes. We demonstrate that HDAC8 catalyzes deacetylation of tetrameric histone (H3/H4) substrates with catalytic efficiencies that are 40-300-fold higher than those for corresponding peptide substrates. Thus, we conclude that additional contacts with protein substrates enhance catalytic efficiency. However, the catalytic efficiency decreases for larger multiprotein complexes. These differences in HDAC8 substrate selectivity for peptides and full-length proteins suggest that HDAC8 substrate preference is based on a combination of short- and long-range interactions. In summary, this work presents detailed kinetics for HDAC8-catalyzed deacetylation of singly-acetylated, full-length protein substrates, revealing that HDAC8 substrate selectivity is determined by multiple factors. These insights provide a foundation for understanding recognition of full-length proteins by HDACs.
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Affiliation(s)
| | | | - Katherine R Leng
- Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Yin-Ming Kuo
- the Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | | | - Carol A Fierke
- From the Program in Chemical Biology and
- the Departments of Biological Chemistry and
- Chemistry, University of Michigan, Ann Arbor, Michigan 48109 and
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29
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Amaike K, Tamura T, Hamachi I. Recognition-driven chemical labeling of endogenous proteins in multi-molecular crowding in live cells. Chem Commun (Camb) 2017; 53:11972-11983. [PMID: 29026906 DOI: 10.1039/c7cc07177a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Endogenous protein labeling is one of the most invaluable methods for studying the bona fide functions of proteins in live cells. However, multi-molecular crowding conditions, such as those that occur in live cells, hamper the highly selective chemical labeling of a protein of interest (POI). We herein describe how the efficient coupling of molecular recognition with a chemical reaction is crucial for selective protein labeling. Recognition-driven protein labeling is carried out by a synthetic labeling reagent containing a protein (recognition) ligand, a reporter tag, and a reactive moiety. The molecular recognition of a POI can be used to greatly enhance the reaction kinetics and protein selectivity, even under live cell conditions. In this review, we also briefly discuss how such selective chemical labeling of an endogenous protein can have a variety of applications at the interface of chemistry and biology.
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Affiliation(s)
- Kazuma Amaike
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Tomonori Tamura
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Itaru Hamachi
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan. and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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30
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Liu Y, Perez L, Gill AD, Mettry M, Li L, Wang Y, Hooley RJ, Zhong W. Site-Selective Sensing of Histone Methylation Enzyme Activity via an Arrayed Supramolecular Tandem Assay. J Am Chem Soc 2017; 139:10964-10967. [PMID: 28777546 DOI: 10.1021/jacs.7b05002] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Arrayed deep cavitands can be coupled to a fluorescence-based supramolecular tandem assay that allows site-selective in situ monitoring of post-translational modifications catalyzed by the lysine methyltransferase PRDM9 or the lysine demethylase JMJD2E. An arrayed sensor system containing only three cavitand components can detect the specific substrates of enzyme modification, in the presence of other histone peptides in the enzyme assay, enabling investigation of cross-reactivity over multiple methylation sites and interference from nonsubstrate peptides.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Lizeth Perez
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Adam D Gill
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Magi Mettry
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Lin Li
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Yinsheng Wang
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Richard J Hooley
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
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31
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Gober IN, Waters ML. Optimization of a synthetic receptor for dimethyllysine using a biphenyl-2,6-dicarboxylic acid scaffold: insights into selective recognition of hydrophilic guests in water. Org Biomol Chem 2017; 15:7789-7795. [DOI: 10.1039/c7ob01921a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Introduction of an endo-carboxylate in a building block for dynamic combinatorial chemistry resulted in amplification of a new host with a Kd of 200 nM for dimethyllysine, a biologically important post-translational modification.
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Affiliation(s)
- Isaiah N. Gober
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
| | - Marcey L. Waters
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
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32
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Xie Y, Ge J, Lei H, Peng B, Zhang H, Wang D, Pan S, Chen G, Chen L, Wang Y, Hao Q, Yao SQ, Sun H. Fluorescent Probes for Single-Step Detection and Proteomic Profiling of Histone Deacetylases. J Am Chem Soc 2016; 138:15596-15604. [DOI: 10.1021/jacs.6b07334] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yusheng Xie
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Jingyan Ge
- College
of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People’s Republic of China
| | - Haipeng Lei
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Bo Peng
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Huatang Zhang
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Danyang Wang
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Sijun Pan
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Ganchao Chen
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
| | - Lanfang Chen
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Yi Wang
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Quan Hao
- Department
of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong, People’s Republic of China
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore, Singapore 119077
| | - Hongyan Sun
- Department
of Biology and Chemistry, City University of Hong Kong, 83 Tat
Chee Avenue, Kowloon, Hong Kong, People’s Republic of China
- Key
Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, People’s Republic of China
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