1
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Das BK, Chowdhury A, Chatterjee S, Tripathi NM, Pati B, Dutta S, Bandyopadhyay A. Harnessing a bis-electrophilic boronic acid lynchpin for azaborolo thiazolidine (ABT) grafting in cyclic peptides. Chem Sci 2024:d4sc04348k. [PMID: 39144456 PMCID: PMC11320178 DOI: 10.1039/d4sc04348k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 07/24/2024] [Indexed: 08/16/2024] Open
Abstract
Chemical modifications of native peptides have significantly advanced modern drug discovery in recent decades. On this front, the installation of multitasking molecular grafts onto macrocyclic peptides offers numerous opportunities in biomedical applications. Here, we showcase a new class of borono-cyclic peptides featuring an azaborolo thiazolidine (ABT) graft, which can be readily assembled utilizing a bis-electrophilic boronic acid lynchpin while harnessing the inherent reactivity difference (>103 M-1 s-1) between the N-terminal cysteine and backbone cysteine for rapid and highly regioselective macrocyclization (∼1 h) under physiological conditions. The ABT-crosslinked peptides are fairly stable in endogenous environments, but can provide the linear diazaborine peptides via treatment with α-nucleophiles. This efficient peptide crosslinking protocol was further extended for regioselective bicyclizations and engineering of α-helical structures. Finally, ABT-grafted peptides were exploited in biorthogonal conjugation, leading to highly effective intracellular delivery of an apoptotic peptide (KLA) in cancer cells. The mechanism of action by which ABT-grafted KLA peptide induces apoptosis was also explored.
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Affiliation(s)
- Basab Kanti Das
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India
| | - Arnab Chowdhury
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India
| | - Saurav Chatterjee
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India
| | - Nitesh Mani Tripathi
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India
| | - Bibekananda Pati
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India
| | - Soumit Dutta
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India
| | - Anupam Bandyopadhyay
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India
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2
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Dash R, Holsinger KA, Chordia MD, Gh. MS, Pires MM. Bioluminescence-Based Determination of Cytosolic Accumulation of Antibiotics in Escherichia coli. ACS Infect Dis 2024; 10:1602-1611. [PMID: 38592927 PMCID: PMC11091882 DOI: 10.1021/acsinfecdis.3c00684] [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: 12/11/2023] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Antibiotic resistance is an alarming public health concern that affects millions of individuals across the globe each year. A major challenge in the development of effective antibiotics lies in their limited ability to permeate cells, noting that numerous susceptible antibiotic targets reside within the bacterial cytosol. Consequently, improving the cellular permeability is often a key consideration during antibiotic development, underscoring the need for reliable methods to assess the permeability of molecules across cellular membranes. Currently, methods used to measure permeability often fail to discriminate between the arrival within the cytoplasm and the overall association of molecules with the cell. Additionally, these techniques typically possess throughput limitations. In this work, we describe a luciferase-based assay designed for assessing the permeability of molecules in the cytosolic compartment of Gram-negative bacteria. Our findings demonstrate a robust system that can elucidate the kinetics of intracellular antibiotic accumulation in live bacterial cells in real time.
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Affiliation(s)
- Rachita Dash
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Kadie A. Holsinger
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Mahendra D. Chordia
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Mohammad Sharifian Gh.
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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3
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Guo M, Lei Y, Zhao K, Guo L, Dang B. A single backbone amide modification method to achieve single site-specific chemical protein conjugation. Methods Enzymol 2024; 698:57-88. [PMID: 38886040 DOI: 10.1016/bs.mie.2024.04.010] [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] [Indexed: 06/20/2024]
Abstract
Efficient and precise chemical protein modification methods are highly sought after in biotechnology. However, chemically distinguishing a single site within a large protein is challenging. This study introduces a Copper Assisted Sequence-specific Conjugation Tag (CAST) method, enabling rapid (second order rate 8.1 M-1s-1) and site-specific chemical modification of the protein backbone with pinpoint accuracy. The versatility of this method is demonstrated through the preparation of antibody-drug conjugates, showcasing high plasma stability and potent efficacy in both in vitro and in vivo settings. Thus, CAST emerges as an efficient and quantitative approach for attaching payloads to large, native proteins.
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Affiliation(s)
- Mengzhun Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, P.R. China; Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P.R. China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, P.R. China
| | - Yingjie Lei
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, P.R. China; Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P.R. China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, P.R. China
| | - Kai Zhao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, P.R. China; Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P.R. China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, P.R. China
| | - Liang Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, P.R. China; Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P.R. China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, P.R. China
| | - Bobo Dang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, P.R. China; Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P.R. China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, P.R. China.
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4
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Dash R, Holsinger KA, Chordia MD, Sharifian Gh M, Pires MM. Bioluminescence-Based Determination of Cytosolic Accumulation of Antibiotics in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570448. [PMID: 38106213 PMCID: PMC10723488 DOI: 10.1101/2023.12.06.570448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Antibiotic resistance is an alarming public health concern that affects millions of individuals across the globe each year. A major challenge in the development of effective antibiotics lies in their limited ability to permeate into cells, noting that numerous susceptible antibiotic targets reside within the bacterial cytosol. Consequently, improving cellular permeability is often a key consideration during antibiotic development, underscoring the need for reliable methods to assess the permeability of molecules across cellular membranes. Currently, methods used to measure permeability often fail to discriminate between arrival within the cytoplasm and the overall association of molecules with the cell. Additionally, these techniques typically possess throughput limitations. In this work, we describe a luciferase-based assay designed for assessing the permeability of molecules into the cytosolic compartment of Gram-negative bacteria. Our findings demonstrate a robust system that can elucidate the kinetics of intracellular antibiotics accumulation in live bacterial cells in real time.
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5
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Guo M, Zhao K, Guo L, Zhou R, He Q, Lu K, Li T, Liu D, Chen J, Tang J, Fu X, Zhou J, Zheng B, Mann SI, Zhang Y, Huang J, Yang B, Zhou T, Lei Y, Dang B. Copper assisted sequence-specific chemical protein conjugation at a single backbone amide. Nat Commun 2023; 14:8063. [PMID: 38052794 DOI: 10.1038/s41467-023-43753-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Direct, site-specific methods of protein functionalization are highly desirable for biotechnology. However, such methods are challenging due to the difficulty of chemically differentiating a single site within a large protein. Herein, we propose "metal binding targeting" strategy and develop a Copper Assisted Sequence-specific conjugation Tag (CAST) method to achieve rapid (second order rate 8.1 M-1 s-1), site-specific protein backbone chemical modification with pinpoint accuracy. We demonstrate the versatility of CAST conjugation by preparing various on-demand modified recombinant proteins, including a homogeneous antibody-drug conjugate with high plasma stability and potent efficacy in vitro and in vivo. Thus, CAST provides an efficient and quantitative method to site-specifically attach payloads on large, native proteins.
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Affiliation(s)
- Mengzhun Guo
- Fudan University, Shanghai, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Kai Zhao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Liang Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Rui Zhou
- Department of Nuclear Medicine and Positron Emission Tomography Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Qiuju He
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Kuan Lu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Tian Li
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Dandan Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jinfeng Chen
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jing Tang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Xin Fu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jinyun Zhou
- Department of Nuclear Medicine and Positron Emission Tomography Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Bei Zheng
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Samuel I Mann
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA, 94158, USA
| | - Yongdeng Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jing Huang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ting Zhou
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Yingjie Lei
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Bobo Dang
- Fudan University, Shanghai, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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6
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Spears RJ, Chudasama V. Recent advances in N- and C-terminus cysteine protein bioconjugation. Curr Opin Chem Biol 2023; 75:102306. [PMID: 37236135 DOI: 10.1016/j.cbpa.2023.102306] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/12/2023] [Accepted: 03/20/2023] [Indexed: 05/28/2023]
Abstract
Advances in the site-specific chemical modification of proteins, also referred to as protein bioconjugation, have proved instrumental in revolutionary approaches to designing new protein-based therapeutics. Of the sites available for protein modification, cysteine residues or the termini of proteins have proved especially popular owing to their favorable properties for site-specific modification. Strategies that, therefore, specifically target cysteine at the termini offer a combination of these favorable properties of cysteine and termini bioconjugation. In this review, we discuss these strategies with a particular focus on those reported recently and provide our opinion on the future direction of the field.
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Affiliation(s)
- Richard J Spears
- Department of Chemistry, University College London, 20 Gordon Street, London, UK
| | - Vijay Chudasama
- Department of Chemistry, University College London, 20 Gordon Street, London, UK.
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7
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Proj M, Strašek N, Pajk S, Knez D, Sosič I. Tunable Heteroaromatic Nitriles for Selective Bioorthogonal Click Reaction with Cysteine. Bioconjug Chem 2023. [PMID: 37354098 PMCID: PMC10360065 DOI: 10.1021/acs.bioconjchem.3c00163] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2023]
Abstract
The binucleophilic properties of 1,2-aminothiol and its rare occurrence in nature make it a useful reporter for tracking molecules in living systems. The 1,2-aminothiol moiety is present in cysteine, which is a substrate for a biocompatible click reaction with heteroaromatic nitriles. Despite the wide range of applications for this reaction, the scope of nitrile substrates has been explored only to a limited extent. In this study, we expand the chemical space of heteroaromatic nitriles for bioconjugation under physiologically relevant conditions. We systematically assembled a library of 116 2-cyanobenzimidazoles, 1-methyl-2-cyanobenzimidazoles, 2-cyanobenzothiazoles, and 2-cyanobenzoxazoles containing electron-donating and electron-withdrawing substituents at all positions of the benzene ring. The compounds were evaluated for their stability, reactivity, and selectivity toward the N-terminal cysteine of model oligopeptides. In comparison to the benchmark 6-hydroxy-2-cyanobenzothiazole or 6-amino-2-cyanobenzothiazole, we provide highly selective and moderately reactive nitriles as well as highly reactive yet less selective analogs with a variety of enabling attachment chemistries to aid future applications in bioconjugation, chemical biology, and nanomaterial science.
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Affiliation(s)
- Matic Proj
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Nika Strašek
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Stane Pajk
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Damijan Knez
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
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8
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Tao W, He W, Feng X, Liu G, Shi Q, Tan J, Hu J, Yang S, Liu G, Yang R. Cationic Single-Unit Monomer Insertion (cSUMI): From Discrete Oligomers to the α-/ω-End and In-Chain Sequence-Regulated Polymers. J Am Chem Soc 2023; 145:3636-3646. [PMID: 36724078 DOI: 10.1021/jacs.2c12873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Single-unit monomer insertion (SUMI) has become an important strategy for the synthesis of sequence-controlled vinyl polymers due to its strong versatility and high efficiency. However, all reported SUMI processes are based on a free-radical mechanism, resulting in a limited number of monomer types being applicable to SUMI or a limited number of sequences of structural units that SUMI can synthesize. Herein, we developed a novel SUMI based on a cationic mechanism (cSUMI), which operates through a degenerative (similar to radical SUMI) but cationic chain transfer process. By optimizing the chain transfer agent (CTA) and monomer pairs, a high-efficiency cSUMI was achieved for vinyl ether and styrene monomers. Based on this reaction, a range of discrete oligomers containing vinyl ether and styrene moieties, and even α-/ω-end and in-chain sequence-regulated polymers were synthesized, most of which cannot be achieved by radical SUMI. In addition, we explored the application of these sequence-regulated polymers in the preparation of miktoarm star polymers, delivery of photosensitizers, and solubilization of fluorescence probes. The development of SUMI with a new mechanism will certainly broaden the scope of structures and sequences in precise vinyl-based polymers.
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Affiliation(s)
- Wei Tao
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China.,Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wei He
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Xuepu Feng
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Guoqin Liu
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qiangqiang Shi
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jiajia Tan
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jinming Hu
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Sheng Yang
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Guhuan Liu
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China.,Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ronghua Yang
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
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9
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Jensen KJ, Thygesen MB, Sørensen KK, Wu S, Treiberg T, Schoffelen S. Selective Acylation of Proteins at Gly and Lys in His Tags. Chembiochem 2022; 23:e202200359. [PMID: 35984670 DOI: 10.1002/cbic.202200359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/19/2022] [Indexed: 01/25/2023]
Abstract
The chemical modification of proteins is of great importance in chemical biology, biotechnology, and for the production of modified biopharmaceuticals, as it enables introduction of fluorophores, biotin, half-life extending moieties, and more. We have developed two methods that use poly-His sequences to direct the highly selective acylation of proteins, either at the N-terminus or at a specific Lys residue. For the former, we used an N-terminal Gly-His6 segment (Gly-His tag) that directed acylation of the N-terminal Nα -amine with 4-methoxyphenyl esters, resulting in stable conjugates. Next, we developed the peptide sequences Hisn -Lys-Hism (Lys-His tags) that direct the acylation of the designated Lys Nϵ -amine under mild conditions and with high selectivity over native Lys residues. Both the Gly-His and Lys-His tags maintain the capacity for immobilized metal ion affinity chromatography. We have demonstrated the robustness of these methods by attaching different moieties such as azides, fluorophores, and biotin to different proteins, including antibodies.
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Affiliation(s)
- Knud J Jensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Mikkel B Thygesen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Kasper K Sørensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Shunliang Wu
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Tuule Treiberg
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Sanne Schoffelen
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
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10
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Zhu Y, Zhang X, You Q, Jiang Z. Recent applications of CBT-Cys click reaction in biological systems. Bioorg Med Chem 2022; 68:116881. [PMID: 35716587 DOI: 10.1016/j.bmc.2022.116881] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/02/2022]
Abstract
Click chemistry is a hot topic in many research fields. A biocompatible reaction from fireflies has attracted increasing attention since 2009. Herein, we focus on the firefly-sourced click reaction between cysteine (Cys) and 2-cyanobenzothiazole (2-CBT). This reaction has many excellent properties, such as rapidity, simplicity and high selectivity, which make it successfully applied in protein labeling, molecular imaging, drug discovery and other fields. Meanwhile, its unique ability to form nanoparticles expands its applications in biological systems. We review its principle, development, and latest applications in the past 5 years and hope this review provides more profound and comprehensive insights to its further application.
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Affiliation(s)
- Yuechao Zhu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xian Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Zhengyu Jiang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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11
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Melsen PRA, Yoshisada R, Jongkees SAK. Opportunities for Expanding Encoded Chemical Diversification and Improving Hit Enrichment in mRNA-Displayed Peptide Libraries. Chembiochem 2022; 23:e202100685. [PMID: 35100479 PMCID: PMC9306583 DOI: 10.1002/cbic.202100685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Indexed: 11/07/2022]
Abstract
DNA-encoded small-molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide-tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the 'drug-likeness' of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA-encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA-encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA-displayed peptide library to allow a more diversity-oriented approach to library modification. Finally, we outline alternate approaches for enriching target-binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA-display based approach could be used to discover new 'drug-like' modified small peptides.
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Affiliation(s)
- Paddy R. A. Melsen
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Ryoji Yoshisada
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Seino A. K. Jongkees
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
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12
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Lin J, Gao D, Wang S, Lv G, Wang X, Lu C, Peng Y, Qiu L. Stimuli-Responsive Macrocyclization Scaffold Allows In Situ Self-Assembly of Radioactive Tracers for Positron Emission Tomography Imaging of Enzyme Activity. J Am Chem Soc 2022; 144:7667-7675. [PMID: 35452229 DOI: 10.1021/jacs.1c12935] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Target-enabled bioorthogonal reaction and self-assembly of a small-molecule probe into supramolecules have shown promise for molecular imaging. In this paper, we report a new stimuli-responsive bioorthogonal reaction scaffold (SF) for controlling in situ self-assembly by engineering the condensation reaction between 2-cyanobenzothiazole and cysteine. For probes with the SF scaffold, intramolecular cyclization took place soon after activation, which could efficiently outcompete free cysteine even at a low concentration and result in efficient aggregation in the target. Through integration with different enzyme-responsive substrates and an ammoniomethyl-trifluoroborate moiety (AmBF3), two radioactive positron emission tomography (PET) tracers, [18F]SF-DEVD and [18F]SF-Glu, were designed, which showed high stability under physiological conditions and could produce clear PET signal in tumors to detect enzyme activity (e.g., caspase-3, γ-glutamyltranspeptidase) timely and accurately. Our results demonstrated that the scaffold SF could serve as a general molecular scaffold in the development of smart PET tracers for noninvasive imaging of enzyme activity, which could contribute to tumor detection and treatment efficacy evaluation.
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Affiliation(s)
- Jianguo Lin
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.,Department of Radiopharmaceuticals, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Dingyao Gao
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Shijie Wang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Gaochao Lv
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Xiuting Wang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Chunmei Lu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Ying Peng
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Ling Qiu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.,Department of Radiopharmaceuticals, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
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13
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Kofoed C, Wu S, Sørensen KK, Treiberg T, Arnsdorf J, Bjørn SP, Jensen TL, Voldborg BG, Thygesen MB, Jensen KJ, Schoffelen S. Highly Selective Lysine Acylation in Proteins Using a Lys-His Tag Sequence. Chemistry 2022; 28:e202200147. [PMID: 35099088 DOI: 10.1002/chem.202200147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Indexed: 11/07/2022]
Abstract
Chemical modification of proteins has numerous applications, but it has been challenging to achieve the required high degree of selectivity on lysine amino groups. Recently, we described the highly selective acylation of proteins with an N-terminal Gly-His6 segment. This tag promoted acylation of the N-terminal Nα -amine resulting in stable conjugates. Herein, we report the peptide sequences Hisn -Lys-Hism , which we term Lys-His tags. In combination with simple acylating agents, they facilitate the acylation of the designated Lys Nϵ -amine under mild conditions and with high selectivity over native Lys residues. We show that the Lys-His tags, which are 7 to 10 amino acids in length and still act as conventional His tags, can be inserted in proteins at the C-terminus or in loops, thus providing high flexibility regarding the site of modification. Finally, the selective and efficient acylation of the therapeutic antibody Rituximab, pure or mixed with other proteins, demonstrates the scope of the Lys-His tag acylation method.
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Affiliation(s)
- Christian Kofoed
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Present address: Frick Chemistry Laboratories, Princeton University, 08544, New Jersey, USA
| | - Shunliang Wu
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Kasper K Sørensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Tuule Treiberg
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Johnny Arnsdorf
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Sara P Bjørn
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Tanja L Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Bjørn G Voldborg
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Mikkel B Thygesen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Knud J Jensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Sanne Schoffelen
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
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14
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Vummidi BR, Farrera-Soler L, Daguer JP, Dockerill M, Barluenga S, Winssinger N. A mating mechanism to generate diversity for the Darwinian selection of DNA-encoded synthetic molecules. Nat Chem 2022; 14:141-152. [PMID: 34873299 DOI: 10.1038/s41557-021-00829-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/30/2021] [Indexed: 12/18/2022]
Abstract
DNA-encoded library technologies enable the screening of synthetic molecules but have thus far not tapped into the power of Darwinian selection with iterative cycles of selection, amplification and diversification. Here we report a simple strategy to rapidly assemble libraries of conformationally constrained peptides that are paired in a combinatorial fashion (suprabodies). We demonstrate that the pairing can be shuffled after each amplification cycle in a process similar to DNA shuffling or mating to regenerate diversity. Using simulations, we show the benefits of this recombination in yielding a more accurate correlation of selection fitness with affinity after multiple rounds of selection, particularly if the starting library is heterogeneous in the concentration of its members. The method was validated with selections against streptavidin and applied to the discovery of PD-L1 binders. We further demonstrate that the binding of self-assembled suprabodies can be recapitulated by smaller (∼7 kDa) synthetic products that maintain the conformational constraint of the peptides.
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Affiliation(s)
- Balayeshwanth R Vummidi
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Lluc Farrera-Soler
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Jean-Pierre Daguer
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sofia Barluenga
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland.
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15
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Wu Y, Li C, Fan S, Zhao Y, Wu C. Fast and Selective Reaction of 2-Benzylacrylaldehyde with 1,2-Aminothiol for Stable N-Terminal Cysteine Modification and Peptide Cyclization. Bioconjug Chem 2021; 32:2065-2072. [PMID: 34405993 DOI: 10.1021/acs.bioconjchem.1c00378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-terminal cysteine (Cys)-specific reactions have been exploited for protein and peptide modifications. However, existing reactions for N-terminal Cys suffer from low reaction rate, unavoidable side reactions, or poor stability for reagents or products. Herein we report a fast, efficient, and selective conjugation between 2-benzylacrylaldehyde (BAA) and 1,2-aminothiol, which involves multistep reactions including aldimine condensation, Michael addition, and reduction of imine by NaBH3CN. This conjugation proceeds with a rate constant of ∼2700 M-1 s-1 under neutral condition at room temperature to produce a pair of seven-membered ring diastereoisomers, which are stable under neutral and acidic conditions. This method enables the selective modifications of the N-terminal Cys residue without interference from the internal Cys and lysine residues, providing a useful alternative to existing approaches for site-specific peptide or protein modifications and synthesis of cyclic peptides.
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Affiliation(s)
- Yaqi Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P.R. China
| | - Cong Li
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P.R. China
| | - Shihui Fan
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P.R. China
| | - Yibing Zhao
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P.R. China
| | - Chuanliu Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P.R. China
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16
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Yang X, Miao H, Xiao R, Wang L, Zhao Y, Wu Q, Ji Y, Du J, Qin H, Xuan W. Diverse protein manipulations with genetically encoded glutamic acid benzyl ester. Chem Sci 2021; 12:9778-9785. [PMID: 34349951 PMCID: PMC8299518 DOI: 10.1039/d1sc01882e] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/16/2021] [Indexed: 01/01/2023] Open
Abstract
Site-specific modification of proteins has significantly advanced the use of proteins in biological research and therapeutics development. Among various strategies aimed at this end, genetic code expansion (GCE) allows structurally and functionally distinct non-canonical amino acids (ncAAs) to be incorporated into specific sites of a protein. Herein, we genetically encode an esterified glutamic acid analogue (BnE) into proteins, and demonstrate that BnE can be applied in different types of site-specific protein modifications, including N-terminal pyroglutamation, caging Glu in the active site of a toxic protein, and endowing proteins with metal chelator hydroxamic acid and versatile reactive handle acyl hydrazide. Importantly, novel epigenetic mark Gln methylation is generated on histones via the derived acyl hydrazide handle. This work provides useful and unique tools to modify proteins at specific Glu or Gln residues, and complements the toolbox of GCE.
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Affiliation(s)
- Xiaochen Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Hui Miao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Ruotong Xiao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Luyao Wang
- School of Pharmaceutical Sciences, Tsinghua University 30 Shuangqing Rd. Beijing China
| | - Yan Zhao
- School of Pharmaceutical Sciences, Tsinghua University 30 Shuangqing Rd. Beijing China
| | - Qifan Wu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Yanli Ji
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Juanjuan Du
- School of Pharmaceutical Sciences, Tsinghua University 30 Shuangqing Rd. Beijing China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS) Dalian, 116023 China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
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17
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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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18
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Tuang S, Dieppa-Matos D, Zhang C, Shugrue CR, Dai P, Loas A, Pentelute BL. A reactive peptide interface for site-selective cysteine bioconjugation. Chem Commun (Camb) 2021; 57:3227-3230. [PMID: 33645592 PMCID: PMC8048384 DOI: 10.1039/d1cc00095k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report aqueous, site-selective modification of proteins using a reactive peptide interface comprising a nine-residue sequence. This interface is the fastest (second-order rate constant of 152 M-1 s-1) catalyst-free, cysteine-based method for modifying proteins available to date, and enables near-quantitative labeling of antibodies in cell lysate.
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Affiliation(s)
- Suan Tuang
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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19
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Guo AD, Wei D, Nie HJ, Hu H, Peng C, Li ST, Yan KN, Zhou BS, Feng L, Fang C, Tan M, Huang R, Chen XH. Light-induced primary amines and o-nitrobenzyl alcohols cyclization as a versatile photoclick reaction for modular conjugation. Nat Commun 2020; 11:5472. [PMID: 33122644 PMCID: PMC7596520 DOI: 10.1038/s41467-020-19274-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 09/30/2020] [Indexed: 12/31/2022] Open
Abstract
The advent of click chemistry has had a profound impact on many fields and fueled a need for reliable reactions to expand the click chemistry toolkit. However, developing new systems to fulfill the click chemistry criteria remains highly desirable yet challenging. Here, we report the development of light-induced primary amines and o-nitrobenzyl alcohols cyclization (PANAC) as a photoclick reaction via primary amines as direct click handle, to rapid and modular functionalization of diverse small molecules and native biomolecules. With intrinsic advantages of temporal control, good biocompatibility, reliable chemoselectivity, excellent efficiency, readily accessible reactants, operational simplicity and mild conditions, the PANAC photoclick is robust for direct diversification of pharmaceuticals and biorelevant molecules, lysine-specific modifications of unprotected peptides and native proteins in vitro, temporal profiling of endogenous kinases and organelle-targeted labeling in living systems. This strategy provides a versatile platform for organic synthesis, bioconjugation, medicinal chemistry, chemical biology and materials science.
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Affiliation(s)
- An-Di Guo
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Dan Wei
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Hui-Jun Nie
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chengyuan Peng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shao-Tong Li
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Ke-Nian Yan
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Bin-Shan Zhou
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lei Feng
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Chao Fang
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Ruimin Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiao-Hua Chen
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
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20
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Cui L, Vivona S, Smith BR, Kothapalli SR, Liu J, Ma X, Chen Z, Taylor M, Kierstead PH, Fréchet JM, Gambhir SS, Rao J. Reduction Triggered In Situ Polymerization in Living Mice. J Am Chem Soc 2020; 142:15575-15584. [PMID: 32804495 PMCID: PMC8171073 DOI: 10.1021/jacs.0c07594] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
"Smart" biomaterials that are responsive to physiological or biochemical stimuli have found many biomedical applications for tissue engineering, therapeutics, and molecular imaging. In this work, we describe in situ polymerization of activatable biorthogonal small molecules in response to a reducing environment change in vivo. We designed a carbohydrate linker- and cyanobenzothiazole-cysteine condensation reaction-based small molecule scaffold that can undergo rapid condensation reaction upon physiochemical changes (such as a reducing environment) to form polymers (pseudopolysaccharide). The fluorescent and photoacoustic properties of a fluorophore-tagged condensation scaffold before and after the transformation have been examined with a dual-modality optical imaging method. These results confirmed the in situ polymerization of this probe after both local and systemic administration in living mice.
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Affiliation(s)
- Lina Cui
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA
- Molecular Imaging Program at Stanford, Bio-X Program, Department of Radiology, School of medicine, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, CA, USA
| | - Sandro Vivona
- Department of Molecular and Cellular Physiology, Stanford University, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
| | - Bryan Ronain Smith
- Molecular Imaging Program at Stanford, Bio-X Program, Department of Radiology, School of medicine, Stanford University, Stanford, CA, USA
| | - Sri R. Kothapalli
- Molecular Imaging Program at Stanford, Bio-X Program, Department of Radiology, School of medicine, Stanford University, Stanford, CA, USA
| | - Jun Liu
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Xiaowei Ma
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Zixin Chen
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA
- Department of Chemistry, Stanford University, CA, USA
| | - Madelynn Taylor
- Molecular Imaging Program at Stanford, Bio-X Program, Department of Radiology, School of medicine, Stanford University, Stanford, CA, USA
| | | | | | - Sanjiv S. Gambhir
- Molecular Imaging Program at Stanford, Bio-X Program, Department of Radiology, School of medicine, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, CA, USA
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Jianghong Rao
- Molecular Imaging Program at Stanford, Bio-X Program, Department of Radiology, School of medicine, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, CA, USA
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21
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Qing Y, Liu MD, Hartmann D, Zhou L, Ramsay WJ, Bayley H. Single-Molecule Observation of Intermediates in Bioorthogonal 2-Cyanobenzothiazole Chemistry. Angew Chem Int Ed Engl 2020; 59:15711-15716. [PMID: 32589803 PMCID: PMC7496719 DOI: 10.1002/anie.202005729] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Indexed: 11/17/2022]
Abstract
We report a single-molecule mechanistic investigation into 2-cyanobenzothiazole (CBT) chemistry within a protein nanoreactor. When simple thiols reacted reversibly with CBT, the thioimidate monoadduct was approximately 80-fold longer-lived than the tetrahedral bisadduct, with important implications for the design of molecular walkers. Irreversible condensation between CBT derivatives and N-terminal cysteine residues has been established as a biocompatible reaction for site-selective biomolecular labeling and imaging. During the reaction between CBT and aminothiols, we resolved two transient intermediates, the thioimidate and the cyclic precursor of the thiazoline product, and determined the rate constants associated with the stepwise condensation, thereby providing critical information for a variety of applications, including the covalent inhibition of protein targets and dynamic combinatorial chemistry.
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Affiliation(s)
- Yujia Qing
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
| | - Mira D. Liu
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
- W. M. Keck Science DepartmentClaremont McKenna CollegeClaremontCA91711USA
- Present address: Department of ChemistryUniversity of CaliforniaBerkeleyCA94720-1460USA
| | - Denis Hartmann
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
| | - Linna Zhou
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
| | | | - Hagan Bayley
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
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22
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Qing Y, Liu MD, Hartmann D, Zhou L, Ramsay WJ, Bayley H. Single‐Molecule Observation of Intermediates in Bioorthogonal 2‐Cyanobenzothiazole Chemistry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yujia Qing
- Department of Chemistry University of Oxford Oxford OX1 3TA UK
| | - Mira D. Liu
- Department of Chemistry University of Oxford Oxford OX1 3TA UK
- W. M. Keck Science Department Claremont McKenna College Claremont CA 91711 USA
- Present address: Department of Chemistry University of California Berkeley CA 94720-1460 USA
| | - Denis Hartmann
- Department of Chemistry University of Oxford Oxford OX1 3TA UK
| | - Linna Zhou
- Department of Chemistry University of Oxford Oxford OX1 3TA UK
| | | | - Hagan Bayley
- Department of Chemistry University of Oxford Oxford OX1 3TA UK
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23
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Schleyer KA, Datko BD, Burnside B, Cui C, Ma X, Grey JK, Cui L. Responsive Fluorophore Aggregation Provides Spectral Contrast for Fluorescence Lifetime Imaging. Chembiochem 2020; 21:2196-2204. [PMID: 32180309 PMCID: PMC8247454 DOI: 10.1002/cbic.202000056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/03/2020] [Indexed: 11/06/2022]
Abstract
Fluorophores experience altered emission lifetimes when incorporated into and liberated from macromolecules or molecular aggregates; this trend suggests the potential for a fluorescent, responsive probe capable of undergoing self-assembly and aggregation and consequently altering the lifetime of its fluorescent moiety to provide contrast between the active and inactive probes. We developed a cyanobenzothioazole-fluorescein conjugate (1), and spectroscopically examined the lifetime changes caused by its reduction-induced aggregation in vitro. A decrease in lifetime was observed for compound 1 in a buffered system activated by the biological reducing agent glutathione, thus suggesting a possible approach for designing responsive self-aggregating lifetime imaging probes.
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Affiliation(s)
- Kelton A Schleyer
- Department of Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, 300 Terrace St. NE, Albuquerque, NM 87131, USA
- Department of Medicinal Chemistry, College of Pharmacy, UF Health Science Center, UF Health Cancer Center University of Florida, 1345 Center Dr., Gainesville, FL 32610, USA
| | - Benjamin D Datko
- Department of Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, 300 Terrace St. NE, Albuquerque, NM 87131, USA
- Center for High Technology Materials, University of New Mexico, MSC04 2710, 1313 Goddard St. SE, Albuquerque, NM 87106, USA
| | - Brandon Burnside
- Department of Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, 300 Terrace St. NE, Albuquerque, NM 87131, USA
- Center for High Technology Materials, University of New Mexico, MSC04 2710, 1313 Goddard St. SE, Albuquerque, NM 87106, USA
| | - Chao Cui
- Department of Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, 300 Terrace St. NE, Albuquerque, NM 87131, USA
- Department of Medicinal Chemistry, College of Pharmacy, UF Health Science Center, UF Health Cancer Center University of Florida, 1345 Center Dr., Gainesville, FL 32610, USA
| | - Xiaowei Ma
- Department of Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, 300 Terrace St. NE, Albuquerque, NM 87131, USA
- Department of Medicinal Chemistry, College of Pharmacy, UF Health Science Center, UF Health Cancer Center University of Florida, 1345 Center Dr., Gainesville, FL 32610, USA
| | - John K Grey
- Department of Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, 300 Terrace St. NE, Albuquerque, NM 87131, USA
- Center for High Technology Materials, University of New Mexico, MSC04 2710, 1313 Goddard St. SE, Albuquerque, NM 87106, USA
| | - Lina Cui
- Department of Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, 300 Terrace St. NE, Albuquerque, NM 87131, USA
- Department of Medicinal Chemistry, College of Pharmacy, UF Health Science Center, UF Health Cancer Center University of Florida, 1345 Center Dr., Gainesville, FL 32610, USA
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24
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Li K, Wang W, Gao J. Fast and Stable N‐Terminal Cysteine Modification through Thiazolidino Boronate Mediated Acyl Transfer. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000837] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kaicheng Li
- Department of Chemistry Boston College Merkert Chemistry Center 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Wenjian Wang
- Department of Chemistry Boston College Merkert Chemistry Center 2609 Beacon Street Chestnut Hill MA 02467 USA
| | - Jianmin Gao
- Department of Chemistry Boston College Merkert Chemistry Center 2609 Beacon Street Chestnut Hill MA 02467 USA
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25
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Li K, Wang W, Gao J. Fast and Stable N-Terminal Cysteine Modification through Thiazolidino Boronate Mediated Acyl Transfer. Angew Chem Int Ed Engl 2020; 59:14246-14250. [PMID: 32437040 DOI: 10.1002/anie.202000837] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/02/2020] [Indexed: 01/07/2023]
Abstract
We report a novel conjugation of N-terminal cysteines (NCys) that proceeds with fast kinetics and exquisite selectivity, thereby enabling facile modification of NCys-bearing proteins in complex biological milieu. This new NCys conjugation proceeds via a thiazolidine boronate (TzB) intermediate that results from fast (k2 : ≈5000 m-1 s-1 ) and reversible conjugation of NCys with 2-formylphenylboronic acid (FPBA). We designed a FPBA derivative that upon TzB formation elicits intramolecular acyl transfer to give N-acyl thiazolidines. In contrast to the quick hydrolysis of TzB, the N-acylated thiazolidines exhibit robust stability under physiologic conditions. The utility of the TzB-mediated NCys conjugation is demonstrated by rapid and non-disruptive labeling of two enzymes. Furthermore, applying this chemistry to bacteriophage allows facile chemical modification of phage libraries, which greatly expands the chemical space amenable to phage display.
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Affiliation(s)
- Kaicheng Li
- Department of Chemistry, Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Wenjian Wang
- Department of Chemistry, Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Jianmin Gao
- Department of Chemistry, Boston College, Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
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26
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Chen Z, Chen M, Cheng Y, Kowada T, Xie J, Zheng X, Rao J. Exploring the Condensation Reaction between Aromatic Nitriles and Amino Thiols To Optimize In Situ Nanoparticle Formation for the Imaging of Proteases and Glycosidases in Cells. Angew Chem Int Ed Engl 2020; 59:3272-3279. [PMID: 31828913 DOI: 10.1002/anie.201913314] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Indexed: 12/31/2022]
Abstract
The condensation reaction between 6-hydroxy-2-cyanobenzothiazole (CBT) and cysteine has been shown for various applications such as site-specific protein labelling and in vivo cancer imaging. This report further expands the substrate scope of this reaction by varying the substituents on aromatic nitriles and amino thiols and testing their reactivity and ability to form nanoparticles for cell imaging. The structure-activity relationship study leads to the identification of the minimum structural requirement for the macrocyclization and assembly process in forming nanoparticles. One of the scaffolds made of 2-pyrimidinecarbonitrile and cysteine joined by a benzyl linker was applied to design fluorescent probes for imaging caspase-3/7 and β-galactosidase activity in live cells. These results demonstrate the generality of this system for imaging hydrolytic enzymes.
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Affiliation(s)
- Zixin Chen
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Min Chen
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yunfeng Cheng
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Toshiyuki Kowada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Jinghang Xie
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Xianchuang Zheng
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jianghong Rao
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, 94305, USA
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27
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Chen Z, Chen M, Cheng Y, Kowada T, Xie J, Zheng X, Rao J. Exploring the Condensation Reaction between Aromatic Nitriles and Amino Thiols To Optimize In Situ Nanoparticle Formation for the Imaging of Proteases and Glycosidases in Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913314] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zixin Chen
- Departments of Radiology and Chemistry Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA 94305 USA
| | - Min Chen
- Departments of Radiology and Chemistry Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA 94305 USA
| | - Yunfeng Cheng
- Departments of Radiology and Chemistry Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA 94305 USA
| | - Toshiyuki Kowada
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University 2-1-1 Katahira, Aoba-ku Sendai Miyagi 980-8577 Japan
| | - Jinghang Xie
- Departments of Radiology and Chemistry Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA 94305 USA
| | - Xianchuang Zheng
- Departments of Radiology and Chemistry Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA 94305 USA
| | - Jianghong Rao
- Departments of Radiology and Chemistry Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA 94305 USA
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28
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Abstract
Bioorthogonal chemistry has offered an invaluable reactivity-based tool to chemical biology owing to its exquisite specificity in tagging a diverse set of biomolecules in their native environment. Despite tremendous progress in the field over the past decade, designing a suitable bioorthogonal chemical probe to investigate a given biological system remains a challenge. In this Perspective, we put forward a series of fitness factors that can be used to assess the performance of bioorthogonal chemical probes. The consideration of these criteria should encourage continuous innovation in bioorthogonal probe development as well as enhance the quality of biological data.
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Affiliation(s)
- Yulin Tian
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
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29
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Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling. iScience 2019; 22:256-268. [PMID: 31786521 PMCID: PMC6906691 DOI: 10.1016/j.isci.2019.11.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/26/2019] [Accepted: 11/12/2019] [Indexed: 11/16/2022] Open
Abstract
Electron microscopy (EM) is a technology that enables visualization of single proteins at a nanometer resolution. However, current protein analysis by EM mainly relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised by large size of antibody, precluding precise detection of protein location in biological samples. Here, we develop a specific chemical labeling method for EM detection of proteins at single-molecular level. Rational design of α-helical peptide tag and probe structure provided a complementary reaction pair that enabled specific cysteine conjugation of the tag. The developed chemical labeling with gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency and detectability of high-density clusters of tag-fused G protein-coupled receptors in freeze-fracture replicas compared with immunogold labeling. Furthermore, in ultrathin sections, the spatial resolution of the chemical labeling was significantly higher than that of antibody-mediated labeling. These results demonstrate substantial advantages of the chemical labeling approach for single protein visualization by EM.
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Affiliation(s)
- Shigekazu Tabata
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan; Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Marijo Jevtic
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Nobutaka Kurashige
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Hirokazu Fuchida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Munetsugu Kido
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Kazushi Tani
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Naoki Zenmyo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Shohei Uchinomiya
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Harumi Harada
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Makoto Itakura
- Department of Biochemistry, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
| | - Ryuichi Shigemoto
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria.
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan.
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30
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Zhao E, St-Jean F, Robinson SJ, Sirois LE, Pellett J, Al-Sayah MA. Identification of an acetonitrile addition impurity formed during peptide disulfide bond reduction using dithiothreitol and Tris(2-carboxyethyl)phosphine. J Pharm Biomed Anal 2019; 174:518-524. [DOI: 10.1016/j.jpba.2019.06.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/14/2019] [Accepted: 06/14/2019] [Indexed: 02/06/2023]
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31
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Li H, Zhang X, Wu HY, Sun L, Ma Y, Xu J, Lin Q, Zeng D. 64Cu-Labeled Ubiquitin for PET Imaging of CXCR4 Expression in Mouse Breast Tumor. ACS OMEGA 2019; 4:12432-12437. [PMID: 31460362 PMCID: PMC6682141 DOI: 10.1021/acsomega.9b00678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/28/2019] [Indexed: 05/10/2023]
Abstract
Ubiquitin has been recently identified as a chemokine receptor 4 (CXCR4) natural ligand, offering great potential for positron emission computed tomography (PET) imaging of CXCR4 expression. This study reports the preparation and evaluation of (64Cu)-radiolabeled ubiquitin for CXCR4 imaging. The ubiquitin was first fused with a C-terminal GGCGG sequence, and the resulting recombinant ubiquitin derivative UbCG4 was then functionalized with the trans-cyclooctene (TCO) moiety via thiol-maleimide click reaction, followed by 64Cu-radiolabeling through the TCO/Tz (tetrazine)-based Diels-Alder click reaction. In the prepared in vitro studies, the prepared (64Cu)-UbCG4 showed significantly higher specific uptakes in the 4T1 breast cancer cells compared with the uptakes in the CXCR4-knockdown 4T1 cells. In the in vivo evaluation in the 4T1-xenograft mouse model, (64Cu)-UbCG4 demonstrated a similar tumor uptake but much lower backgrounds compared with 64Cu-labeled AMD3465. These results suggested that (64Cu)-UbCG4 could serve as a potent PET tracer for the noninvasive imaging of CXCR4 expression in tumors.
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Affiliation(s)
- Huiqiang Li
- PET-CT
Center, Department of Nuclear Medicine, Henan Provincial People’s Hospital, Weiwu Road, No. 7, Jinshui District, Zhengzhou, Henan CN 450003, China
- Molecular
Imaging Laboratory, Department of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15219, United States
| | - Xiaohui Zhang
- Molecular
Imaging Laboratory, Department of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15219, United States
| | - Hsuan Yi Wu
- Department
of Chemistry, State University of New York
at Buffalo, 679 Natural
Sciences Complex, Buffalo, New York 14260, United
States
| | - Lingyi Sun
- Molecular
Imaging Laboratory, Department of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15219, United States
- Department
of Diagnostic Radiology, Oregon Health &
Science University, 3181
S.W. Sam Jackson Park Rd., CRR210B, Portland, Oregon 97239, United States
| | - Yongyong Ma
- Molecular
Imaging Laboratory, Department of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15219, United States
- Department
of Diagnostic Radiology, Oregon Health &
Science University, 3181
S.W. Sam Jackson Park Rd., CRR210B, Portland, Oregon 97239, United States
| | - Junling Xu
- PET-CT
Center, Department of Nuclear Medicine, Henan Provincial People’s Hospital, Weiwu Road, No. 7, Jinshui District, Zhengzhou, Henan CN 450003, China
| | - Qing Lin
- Department
of Chemistry, State University of New York
at Buffalo, 679 Natural
Sciences Complex, Buffalo, New York 14260, United
States
| | - Dexing Zeng
- Molecular
Imaging Laboratory, Department of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15219, United States
- Department
of Diagnostic Radiology, Oregon Health &
Science University, 3181
S.W. Sam Jackson Park Rd., CRR210B, Portland, Oregon 97239, United States
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32
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Dong P, Wang X, Zheng J, Zhang X, Li Y, Wu H, Li L. Recent Advances in Targeting Nuclear Molecular Imaging Driven by Tetrazine Bioorthogonal Chemistry. Curr Med Chem 2019; 27:3924-3943. [PMID: 31267851 DOI: 10.2174/1386207322666190702105829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/18/2019] [Accepted: 05/03/2019] [Indexed: 02/05/2023]
Abstract
Molecular imaging techniques apply sophisticated technologies to monitor, directly or indirectly, the spatiotemporal distribution of molecular or cellular processes for biomedical, diagnostic, or therapeutic purposes. For example, Single-Photon Emission Computed Tomography (SPECT) and Positron Emission Tomography (PET) imaging, the most representative modalities of molecular imaging, enable earlier and more accurate diagnosis of cancer and cardiovascular diseases. New possibilities for noninvasive molecular imaging in vivo have emerged with advances in bioorthogonal chemistry. For example, tetrazine-related Inverse Electron Demand Diels-Alder (IEDDA) reactions can rapidly generate short-lived radioisotope probes in vivo that provide strong contrast for SPECT and PET. Here, we review pretargeting strategies for molecular imaging and novel radiotracers synthesized via tetrazine bioorthogonal chemistry. We systematically describe advances in direct radiolabeling and pretargeting approaches in SPECT and PET using metal and nonmetal radioisotopes based on tetrazine bioorthogonal reactions, and we discuss prospects for the future of such contrast agents.
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Affiliation(s)
- Ping Dong
- Department of Nuclear Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xueyi Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Junwei Zheng
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiaoyang Zhang
- Department of Nuclear Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yiwen Li
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Haoxing Wu
- Huaxi MR Research Center, Department of Radiology, West China Hospital and West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Li
- Department of Nuclear Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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33
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Zenmyo N, Tokumaru H, Uchinomiya S, Fuchida H, Tabata S, Hamachi I, Shigemoto R, Ojida A. Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Naoki Zenmyo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroki Tokumaru
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Shohei Uchinomiya
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Hirokazu Fuchida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigekazu Tabata
- Institute of Science and Technology Austria, A-3400 Klosterneuburg, Austria
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Ryuichi Shigemoto
- Institute of Science and Technology Austria, A-3400 Klosterneuburg, Austria
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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34
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35
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Evans ED, Pentelute BL. Studies on a landscape of perfluoroaromatic-reactive peptides. Org Biomol Chem 2019; 17:1862-1868. [PMID: 30065992 DOI: 10.1039/c8ob01678j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated 26 midsized peptides (∼30 amino acids in length) selected using mRNA display to perform a nucleophilic aromatic substitution reaction (SNAr). Analysis suggested a diverse set of reactive sequences with significant differences in primary sequence, secondary structure and even predicted tertiary structural features. Several of the sequences displayed rapid kinetics allowing for near complete labeling in under one hour. Rosetta ab initio structure prediction of these sequences suggested a landscape of structural features, ranging from beta-sheet-based sequences to those possessing more alpha-helical-like character. Circular dichroism spectroscopy confirmed elements of the structure predictions for the majority of peptides. This analysis additionally uncovered that several peptides underwent secondary structure alterations upon reaction. These results suggest a broad sequence and structural landscape of SNAr active peptides along with a potentially important feature of these biopolymers.
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Affiliation(s)
- Ethan D Evans
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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36
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Evans ED, Gates ZP, Sun ZYJ, Mijalis AJ, Pentelute BL. Conformational Stabilization and Rapid Labeling of a 29-Residue Peptide by a Small Molecule Reaction Partner. Biochemistry 2019; 58:1343-1353. [DOI: 10.1021/acs.biochem.8b00940] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ethan D. Evans
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Zachary P. Gates
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Zhen-Yu J. Sun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Alexander J. Mijalis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bradley L. Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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37
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Mao W, Shi W, Li J, Su D, Wang X, Zhang L, Pan L, Wu X, Wu H. Organocatalytic and Scalable Syntheses of Unsymmetrical 1,2,4,5-Tetrazines by Thiol-Containing Promotors. Angew Chem Int Ed Engl 2018; 58:1106-1109. [PMID: 30488591 DOI: 10.1002/anie.201812550] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/27/2018] [Indexed: 02/05/2023]
Abstract
Despite the growing application of tetrazine bioorthogonal chemistry, it is still challenging to access tetrazines conveniently from easily available materials. Described here is the de novo formation of tetrazine from nitriles and hydrazine hydrate using a broad array of thiol-containing catalysts, including peptides. Using this facile methodology, the syntheses of 14 unsymmetric tetrazines, containing a range of reactive functional groups, on the gram scale were achieved with satisfactory yields. Using tetrazine methylphosphonate as a building block, a highly efficient Horner-Wadsworth-Emmons reaction was developed for further derivatization under mild reaction conditions. Tetrazine probes with diverse functions can be scalably produced in yields of 87-93 %. This methodology may facilitate the widespread application of tetrazine bioorthogonal chemistry.
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Affiliation(s)
- Wuyu Mao
- Huaxi MR Research Center, Department of Radiology, West China Hospital and West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Wei Shi
- Huaxi MR Research Center, Department of Radiology, West China Hospital and West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Jie Li
- Huaxi MR Research Center, Department of Radiology, West China Hospital and West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Dunyan Su
- Huaxi MR Research Center, Department of Radiology, West China Hospital and West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Xiaomeng Wang
- Huaxi MR Research Center, Department of Radiology, West China Hospital and West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Lyuye Zhang
- Huaxi MR Research Center, Department of Radiology, West China Hospital and West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Lili Pan
- Department of Nuclear Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaoai Wu
- Department of Nuclear Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Haoxing Wu
- Huaxi MR Research Center, Department of Radiology, West China Hospital and West China School of Medicine, Sichuan University, Chengdu, 610041, China
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38
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Mao W, Shi W, Li J, Su D, Wang X, Zhang L, Pan L, Wu X, Wu H. Organocatalytic and Scalable Syntheses of Unsymmetrical 1,2,4,5‐Tetrazines by Thiol‐Containing Promotors. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201812550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wuyu Mao
- Huaxi MR Research CenterDepartment of RadiologyWest China Hospital and West China School of MedicineSichuan University Chengdu 610041 China
| | - Wei Shi
- Huaxi MR Research CenterDepartment of RadiologyWest China Hospital and West China School of MedicineSichuan University Chengdu 610041 China
| | - Jie Li
- Huaxi MR Research CenterDepartment of RadiologyWest China Hospital and West China School of MedicineSichuan University Chengdu 610041 China
| | - Dunyan Su
- Huaxi MR Research CenterDepartment of RadiologyWest China Hospital and West China School of MedicineSichuan University Chengdu 610041 China
| | - Xiaomeng Wang
- Huaxi MR Research CenterDepartment of RadiologyWest China Hospital and West China School of MedicineSichuan University Chengdu 610041 China
| | - Lyuye Zhang
- Huaxi MR Research CenterDepartment of RadiologyWest China Hospital and West China School of MedicineSichuan University Chengdu 610041 China
| | - Lili Pan
- Department of Nuclear MedicineWest China HospitalSichuan University Chengdu 610041 China
| | - Xiaoai Wu
- Department of Nuclear MedicineWest China HospitalSichuan University Chengdu 610041 China
| | - Haoxing Wu
- Huaxi MR Research CenterDepartment of RadiologyWest China Hospital and West China School of MedicineSichuan University Chengdu 610041 China
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39
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Akgun B, Hall DG. Boronic Acids as Bioorthogonal Probes for Site‐Selective Labeling of Proteins. Angew Chem Int Ed Engl 2018; 57:13028-13044. [DOI: 10.1002/anie.201712611] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/23/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry—CCIS 4–010University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Dennis G. Hall
- Department of Chemistry—CCIS 4–010University of Alberta Edmonton Alberta T6G 2G2 Canada
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40
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Godinat A, Bazhin AA, Goun EA. Bioorthogonal chemistry in bioluminescence imaging. Drug Discov Today 2018; 23:1584-1590. [DOI: 10.1016/j.drudis.2018.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/23/2018] [Accepted: 05/14/2018] [Indexed: 01/08/2023]
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41
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Akgun B, Hall DG. Boronsäuren als bioorthogonale Sonden für zentrenselektives Protein‐Labeling. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712611] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry – CCIS 4-010University of Alberta Edmonton Alberta T6G 2G2 Kanada
| | - Dennis G. Hall
- Department of Chemistry – CCIS 4-010University of Alberta Edmonton Alberta T6G 2G2 Kanada
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42
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Keyser SGL, Utz A, Bertozzi CR. Computation-Guided Rational Design of a Peptide Motif That Reacts with Cyanobenzothiazoles via Internal Cysteine-Lysine Relay. J Org Chem 2018; 83:7467-7479. [PMID: 29771122 DOI: 10.1021/acs.joc.8b00625] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Site-selective protein modification based on covalent reactions of peptide tags and small molecules is a key capability for basic research as well as for the development of new therapeutic bioconjugates. Here, we describe the computation-guided rational design of a cysteine- and lysine-containing 11-residue peptide sequence that reacts with 2-cyanobenzothiazole (CBT) derivatives. Our data show that the cysteine residue reversibly reacts with the nitrile group on the CBT moiety to form an intermediate thioimidate, which undergoes irreversible SN transfer to the lysine residue, yielding an amidine-linked product. The concepts outlined herein lay a foundation for future development of peptide tags in the context of site-selective modification of lysine residues within engineered microenvironments.
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Affiliation(s)
- Samantha G L Keyser
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
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43
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Zhang C, Dai P, Vinogradov AA, Gates ZP, Pentelute BL. Site-Selective Cysteine-Cyclooctyne Conjugation. Angew Chem Int Ed Engl 2018; 57:6459-6463. [PMID: 29575377 DOI: 10.1002/anie.201800860] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/07/2018] [Indexed: 11/06/2022]
Abstract
We report a site-selective cysteine-cyclooctyne conjugation reaction between a seven-residue peptide tag (DBCO-tag, Leu-Cys-Tyr-Pro-Trp-Val-Tyr) at the N or C terminus of a peptide or protein and various aza-dibenzocyclooctyne (DBCO) reagents. Compared to a cysteine peptide control, the DBCO-tag increases the rate of the thiol-yne reaction 220-fold, thereby enabling selective conjugation of DBCO-tag to DBCO-linked fluorescent probes, affinity tags, and cytotoxic drug molecules. Fusion of DBCO-tag with the protein of interest enables regioselective cysteine modification on proteins that contain multiple endogenous cysteines; these examples include green fluorescent protein and the antibody trastuzumab. This study demonstrates that short peptide tags can aid in accelerating bond-forming reactions that are often slow to non-existent in water.
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Affiliation(s)
- Chi Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Peng Dai
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Alexander A Vinogradov
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Zachary P Gates
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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44
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Zhang C, Dai P, Vinogradov AA, Gates ZP, Pentelute BL. Site‐Selective Cysteine–Cyclooctyne Conjugation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Chi Zhang
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Peng Dai
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Alexander A. Vinogradov
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Zachary P. Gates
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Bradley L. Pentelute
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
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45
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Evans ED, Pentelute BL. Discovery of a 29-Amino-Acid Reactive Abiotic Peptide for Selective Cysteine Arylation. ACS Chem Biol 2018; 13:527-532. [PMID: 29283243 DOI: 10.1021/acschembio.7b00520] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The regio- and chemoselective modification of proteins or peptides with chemical reagents is often challenging. One approach to overcome this problem involves identifying abiotic polypeptide sequences that react with specific small molecules. Toward this goal, we profiled ∼5 × 1013 randomized 30-mer peptides using mRNA display and high-throughput sequencing in search of polypeptides that can undergo cysteine arylation with a water-soluble perfluoroarene. Within this vast chemical space, we discovered a cysteine-containing sequence with a second-order rate constant of 0.29 M-1 s-1 for arylation. An N- and C-terminal truncation reduced the reaction rate, as did the addition of denaturants. When the reactive peptide was covalently fused to the enzyme Sortase A, we observed regiospecific arylation at a single cysteine site, leaving the enzyme's active site cysteine unchanged. Taken together, these results demonstrate that long polypeptides of defined sequence, when matched with the appropriate reactive group, can be used for selective arylation of cysteine in water.
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Affiliation(s)
- Ethan D. Evans
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bradley L. Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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46
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Affiliation(s)
- Lindsey C. Szymczak
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Hsin-Yu Kuo
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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47
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Wang Y, An R, Luo Z, Ye D. Firefly Luciferin-Inspired Biocompatible Chemistry for Protein Labeling and In Vivo Imaging. Chemistry 2017; 24:5707-5722. [PMID: 29068109 DOI: 10.1002/chem.201704349] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Indexed: 12/27/2022]
Abstract
Biocompatible reactions have emerged as versatile tools to build various molecular imaging probes that hold great promise for the detection of biological processes in vitro and/or in vivo. In this Minireview, we describe the recent advances in the development of a firefly luciferin-inspired biocompatible reaction between cyanobenzothiazole (CBT) and cysteine (Cys), and highlight its versatility to label proteins and build multimodality molecular imaging probes. The review starts from the general introduction of biocompatible reactions, which is followed by briefly describing the development of the firefly luciferin-inspired biocompatible chemistry. We then discuss its applications for the specific protein labeling and for the development of multimodality imaging probes (fluorescence, bioluminescence, MRI, PET, photoacoustic, etc.) that enable high sensitivity and spatial resolution imaging of redox environment, furin and caspase-3/7 activity in living cells and mice. Finally, we offer the conclusions and our perspective on the various and potential applications of this reaction. We hope that this review will contribute to the research of biocompatible reactions for their versatile applications in protein labeling and molecular imaging.
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Affiliation(s)
- Yuqi Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Ruibing An
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Zhiliang Luo
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Deju Ye
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
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48
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Sharma DK, Adams ST, Liebmann KL, Miller SC. Rapid Access to a Broad Range of 6'-Substituted Firefly Luciferin Analogues Reveals Surprising Emitters and Inhibitors. Org Lett 2017; 19:5836-5839. [PMID: 29039673 PMCID: PMC5836729 DOI: 10.1021/acs.orglett.7b02806] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Light-emitting firefly luciferin analogues contain electron-donating groups in the 6'-position, but the scope of known 6'-substitution remains narrow. A two-step route to a broad range of 6'-substituted luciferin analogues was developed to fill this void and enable more extensive study of the 6'-functionality. This chemistry allowed direct access to "caged" amide and bright azetidine analogues, but also revealed thioether inhibitors and unexpectedly luminogenic aryl amine derivatives.
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Affiliation(s)
- Deepak K. Sharma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605
| | - Spencer T. Adams
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605
| | - Kate L. Liebmann
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605
| | - Stephen C. Miller
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605
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49
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Ramil CP, Dong M, An P, Lewandowski TM, Yu Z, Miller LJ, Lin Q. Spirohexene-Tetrazine Ligation Enables Bioorthogonal Labeling of Class B G Protein-Coupled Receptors in Live Cells. J Am Chem Soc 2017; 139:13376-13386. [PMID: 28876923 DOI: 10.1021/jacs.7b05674] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A new bioorthogonal reactant pair, spiro[2.3]hex-1-ene (Sph) and 3,6-di(2-pyridyl)-s-tetrazine (DpTz), for the strain-promoted inverse electron-demand Diels-Alder cycloaddition, that is, tetrazine ligation, is reported. As compared to the previously reported strained alkenes such as trans-cyclooctene (TCO) and 1,3-disubstituted cyclopropene, Sph exhibits balanced reactivity and stability in tetrazine ligation with the protein substrates. A lysine derivative of Sph, SphK, was site-selectively incorporated into the extracellular loop regions (ECLs) of GCGR and GLP-1R, two members of class B G protein-coupled receptors (GPCRs) in mammalian cells with the incorporation efficiency dependent on the location. Subsequent bioorthogonal reactions with the fluorophore-conjugated DpTz reagents afforded the fluorescently labeled GCGR and GLP-1R ECL mutants with labeling yield as high as 68%. A multitude of functional assays were performed with these GPCR mutants, including ligand binding, ligand-induced receptor internalization, and ligand-stimulated intracellular cAMP accumulation. Several positions in the ECL3s of GCGR and GLP-1R were identified that tolerate SphK mutagenesis and subsequent bioorthogonal labeling. The generation of functional, fluorescently labeled ECL3 mutants of GCGR and GLP-1R should allow biophysical studies of conformation dynamics of this important class of GPCRs in their native environment in live cells.
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Affiliation(s)
- Carlo P Ramil
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Maoqing Dong
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Scottsdale, Arizona 85259, United States
| | - Peng An
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Tracey M Lewandowski
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Zhipeng Yu
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Laurence J Miller
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Scottsdale, Arizona 85259, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
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50
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Dai P, Williams JK, Zhang C, Welborn M, Shepherd JJ, Zhu T, Van Voorhis T, Hong M, Pentelute BL. A structural and mechanistic study of π-clamp-mediated cysteine perfluoroarylation. Sci Rep 2017; 7:7954. [PMID: 28801573 PMCID: PMC5554146 DOI: 10.1038/s41598-017-08402-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/07/2017] [Indexed: 01/27/2023] Open
Abstract
Natural enzymes use local environments to tune the reactivity of amino acid side chains. In searching for small peptides with similar properties, we discovered a four-residue π-clamp motif (Phe-Cys-Pro-Phe) for regio- and chemoselective arylation of cysteine in ribosomally produced proteins. Here we report mutational, computational, and structural findings directed toward elucidating the molecular factors that drive π-clamp-mediated arylation. We show the significance of a trans conformation prolyl amide bond for the π-clamp reactivity. The π-clamp cysteine arylation reaction enthalpy of activation (ΔH‡) is significantly lower than a non-π-clamp cysteine. Solid-state NMR chemical shifts indicate the prolyl amide bond in the π-clamp motif adopts a 1:1 ratio of the cis and trans conformation, while in the reaction product Pro3 was exclusively in trans. In two structural models of the perfluoroarylated product, distinct interactions at 4.7 Å between Phe1 side chain and perfluoroaryl electrophile moiety are observed. Further, solution 19F NMR and isothermal titration calorimetry measurements suggest interactions between hydrophobic side chains in a π-clamp mutant and the perfluoroaryl probe. These studies led us to design a π-clamp mutant with an 85-fold rate enhancement. These findings will guide us toward the discovery of small reactive peptides to facilitate abiotic chemistry in water.
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Affiliation(s)
- Peng Dai
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Jonathan K Williams
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Chi Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Matthew Welborn
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - James J Shepherd
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Tianyu Zhu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States.
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