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Abstract
The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M Snodgrass
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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52
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Zhang P, Wang X, Wang X, Huang C, James TD, Sun X, Qian X. Chemoselective Fluorogenic Bioconjugation of Vicinal Dithiol-Containing Proteins for Live Cellular Imaging via Small Molecular Conjugate Acceptors. Anal Chem 2023; 95:11953-11959. [PMID: 37490273 DOI: 10.1021/acs.analchem.3c01518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
To develop small molecular fluorogenic tools for the chemoselective labeling of vicinal dithiol-containing proteins (VDPs) in live cells is important for studying intracellular redox homeostasis. With this research, we developed small molecule-based fluorescent probes, achieving selective labeling of VDPs through thiol-thiol substitutions on bisvinylogous thioester conjugated acceptors (IDAs). Initially, IDAs demonstrated its ability to bridge vicinal cysteine-sulfhydryls on a peptide as a mimic. Then, the peptide complex could be decoupled to recover the original peptide-SH in the presence of dithiothreitol. Furthermore, fluorometric signal amplification of the fluorescent probes occurred with high sensitivity, low limit of detection, and selectivity toward vicinal dithiols on reduced bovine serum albumin, as an example of real world VDPs. More importantly, the probes were utilized successfully for labeling of endogenous VDPs at different redox states in live cells. Thus, the bisvinylogous thioester-based receptor as a functional probe represents a new platform for uncovering the function of VDPs in live cells.
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Affiliation(s)
- Peng Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, No. 28, West Xianning Road, Xi'an 710049, People's Republic of China
| | - Xuechuan Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science & Technology, Xi'an 710021, People's Republic of China
| | - Xiao Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science & Technology, Xi'an 710021, People's Republic of China
| | - Chusen Huang
- The Education Ministry Key Laboratory of Resource Chemistry, Shanghai Normal University, No. 100 Guilin Road, Shanghai 200234, People's Republic of China
| | - Tony D James
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Xiaolong Sun
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, No. 28, West Xianning Road, Xi'an 710049, People's Republic of China
| | - Xuhong Qian
- State Key Laboratory of Bioreactor Engineering; Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, No. 130 Meilong Road, Shanghai 200237, People's Republic of China
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53
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Zhang GR, Tan W, Wang XQ. Chemical Tailoring of Aptamer Glues with Significantly Enhanced Recognition Ability for Targeted Membrane Protein Degradation. ACS NANO 2023; 17:15146-15154. [PMID: 37494291 DOI: 10.1021/acsnano.3c04457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Cell membrane proteins play a crucial role in the development of early cancer diagnosis strategies and precision medicine techniques. However, the application of aptamers in cell membrane protein-based biomedical research is limited by their inherent drawbacks, such as sensitivity to the recognition environment and susceptibility to enzymatic degradation, which leads to the loss of recognition ability. To address these challenges, this study presents a subzero-temperature-enabled molecule stacking strategy for the on-demand tailoring of aptamer glues for the precision recognition and efficient degradation of membrane protein. Mechanistic studies revealed that nucleic acid molecule stacking occurred during the freezing and melting processes, facilitating a rapid click reaction by bringing two reactive groups together. In vitro investigations demonstrated that the strategy confers aptamer glues with significantly enhanced specific recognition ability and binding affinity, allowing the distinction of a targeted cell line from a nontargeted cell line. Moreover, the engineered aptamer glue exhibited impressive targeted cell membrane protein degradation ability; around 74% of the c-Met protein was degraded in 24 h. These findings hold great potential for advancing cancer diagnosis and targeted therapy through the development of more stable and reliable aptamer probes.
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Affiliation(s)
- Guo-Rong Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Qiang Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou 311121, China
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54
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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: 0] [Impact Index Per Article: 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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55
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Li C, Tian Y, Liu C, Dou Z, Diao J. Effects of Heat Treatment on the Structural and Functional Properties of Phaseolus vulgaris L. Protein. Foods 2023; 12:2869. [PMID: 37569138 PMCID: PMC10417349 DOI: 10.3390/foods12152869] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
The paper presents the effect of heat treatment at 80 °C at different times (3, 5, 7, and 9 min) on the structural and functional properties of Phaseolus vulgaris L. protein (PVP, bean protein powder). Surface and structure properties of PVP after heat treatment were analyzed using a Fourier transform infrared spectrometer (FTIR), a fluorescence spectrophotometer, a visible light spectrophotometer, a laser particle size analyzer, and other equipment. The secondary structure and surface hydrophobicity (H0) of PVP changed significantly after heat treatment: the β-sheet content decreased from 25.32 ± 0.09% to 24.66 ± 0.09%, the random coil content increased from 23.91 ± 0.11% to 25.68 ± 0.08%, and the H0 rose by 28.96-64.99%. In addition, the functional properties of PVP after heat treatment were analyzed. After heat treatment, the emulsifying activity index (EAI) of PVP increased from 78.52 ± 2.01 m2/g to 98.21 ± 1.33 m2/g, the foaming ability (FA) improved from 87.31 ± 2.56% to 95.82 ± 2.96%, and the foam stability (FS) rose from 53.23 ± 1.72% to 58.71 ± 2.18%. Finally, the degree of hydrolysis (DH) of PVP after gastrointestinal simulated digestion in vitro was detected by the Ortho-Phthal (OPA) method. Heat treatment enhanced the DH of PVP from 62.34 ± 0.31% to 73.64 ± 0.53%. It was confirmed that heat treatment changed the structural properties of PVP and improved its foamability, emulsification, and digestibility. It provides ideas for improving PVP's potential and producing new foods with rich nutrition, multiple functions, and easy absorption.
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Affiliation(s)
- Chaoyang Li
- National Coarse Cereal Engineering Technology Research Center, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (C.L.); (Z.D.)
| | - Yachao Tian
- School of Food Science and Engineering, Qilu University of Technology, Jinan 250353, China;
| | - Caihua Liu
- College of Food Science, Northeast Agricultural University, Harbin 150030, China;
| | - Zhongyou Dou
- National Coarse Cereal Engineering Technology Research Center, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (C.L.); (Z.D.)
| | - Jingjing Diao
- National Coarse Cereal Engineering Technology Research Center, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (C.L.); (Z.D.)
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56
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Lee JC, Cuthbertson JD, Mitchell NJ. Chemoselective Late-Stage Functionalization of Peptides via Photocatalytic C2-Alkylation of Tryptophan. Org Lett 2023; 25:5459-5464. [PMID: 37462428 PMCID: PMC10391624 DOI: 10.1021/acs.orglett.3c01795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Across eukaryotic proteomes, tryptophan is the least abundant of the 20 canonical amino acids, which makes it an ideal chemical handle for the late-stage functionalization of peptide and protein scaffolds with minimal production of undesired isoforms. Herein, we report the photocatalytic C2-alkylation of tryptophan using bromodifluoroacetate/acetamide-derived radical precursors. This rapid visible-light-mediated reaction is additive-free, operationally simple, and tolerates diverse functionality. We demonstrate the late-stage modification of a variety of complex peptides, including examples of biological significance.
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Affiliation(s)
- Joanna C Lee
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
- School of Chemistry, GlaxoSmithKline Carbon Neutral Laboratories for Sustainable Chemistry, University of Nottingham, Jubilee Campus, Nottingham NG7 2TU, United Kingdom
| | - James D Cuthbertson
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
- School of Chemistry, GlaxoSmithKline Carbon Neutral Laboratories for Sustainable Chemistry, University of Nottingham, Jubilee Campus, Nottingham NG7 2TU, United Kingdom
| | - Nicholas J Mitchell
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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57
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Zhang S, De Leon Rodriguez LM, Li FF, Brimble MA. Recent developments in the cleavage, functionalization, and conjugation of proteins and peptides at tyrosine residues. Chem Sci 2023; 14:7782-7817. [PMID: 37502317 PMCID: PMC10370606 DOI: 10.1039/d3sc02543h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Peptide and protein selective modification at tyrosine residues has become an exploding field of research as tyrosine constitutes a robust alternative to lysine and cysteine-targeted traditional peptide/protein modification protocols. This review offers a comprehensive summary of the latest advances in tyrosine-selective cleavage, functionalization, and conjugation of peptides and proteins from the past three years. This updated overview complements the extensive body of work on site-selective modification of peptides and proteins, which holds significant relevance across various disciplines, including chemical, biological, medical, and material sciences.
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Affiliation(s)
- Shengping Zhang
- Center for Translational Medicine, Shenzhen Bay Laboratory New Zealand
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
| | | | - Freda F Li
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
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58
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Grain B, Desmet R, Snella B, Melnyk O, Agouridas V. Incorporation of a Highly Reactive Oxalyl Thioester-Based Interacting Handle into Proteins. Org Lett 2023; 25:5117-5122. [PMID: 37384828 PMCID: PMC10353032 DOI: 10.1021/acs.orglett.3c01846] [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: 06/06/2023] [Indexed: 07/01/2023]
Abstract
Providing biomolecules with extended physicochemical, biochemical, or biological properties is a contemporary challenge motivated by impactful benefits in life or materials sciences. In this study, we show that a latent and highly reactive oxalyl thioester precursor can be efficiently introduced as a pending functionality into a fully synthetic protein domain following a protection/late-stage deprotection strategy and can serve as an on-demand reactive handle. The approach is illustrated with the production of a 10 kDa ubiquitin Lys48 conjugate.
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Affiliation(s)
- Benjamin Grain
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Rémi Desmet
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Benoît Snella
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Vangelis Agouridas
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -
UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
- Centrale
Lille, F-59000 Lille, France
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59
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Singha Roy SJ, Loynd C, Jewel D, Canarelli SE, Ficaretta ED, Pham QA, Weerapana E, Chatterjee A. Photoredox-Catalyzed Labeling of Hydroxyindoles with Chemoselectivity (PhotoCLIC) for Site-Specific Protein Bioconjugation. Angew Chem Int Ed Engl 2023; 62:e202300961. [PMID: 37219923 PMCID: PMC10330600 DOI: 10.1002/anie.202300961] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Indexed: 05/24/2023]
Abstract
We have developed a novel visible-light-catalyzed bioconjugation reaction, PhotoCLIC, that enables chemoselective attachment of diverse aromatic amine reagents onto a site-specifically installed 5-hydroxytryptophan residue (5HTP) on full-length proteins of varied complexity. The reaction uses catalytic amounts of methylene blue and blue/red light-emitting diodes (455/650 nm) for rapid site-specific protein bioconjugation. Characterization of the PhotoCLIC product reveals a unique structure formed likely through a singlet oxygen-dependent modification of 5HTP. PhotoCLIC has a wide substrate scope and its compatibility with strain-promoted azide-alkyne click reaction, enables site-specific dual-labeling of a target protein.
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Affiliation(s)
| | - Conor Loynd
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Sarah E Canarelli
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Elise D Ficaretta
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Quan A Pham
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467, USA
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60
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Liao Y, Wang M, Jiang X. Sulfur-containing peptides: Synthesis and application in the discovery of potential drug candidates. Curr Opin Chem Biol 2023; 75:102336. [PMID: 37269675 DOI: 10.1016/j.cbpa.2023.102336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/29/2023] [Accepted: 05/05/2023] [Indexed: 06/05/2023]
Abstract
Peptides act as biological mediators and play a key role of various physiological activities. Sulfur-containing peptides are widely used in natural products and drug molecules due to their unique biological activity and chemical reactivity of sulfur. Disulfides, thioethers, and thioamides are the most common motifs of sulfur-containing peptides, and they have been extensively studied and developed for synthetic methodology as well as pharmaceutical applications. This review focuses on the illustration of these three motifs in natural products and drugs, as well as the recent advancements in the synthesis of the corresponding core scaffolds.
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Affiliation(s)
- Yanyan Liao
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Ming Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
| | - Xuefeng Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China; State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Elemento-Organic Chemistry, Nankai University, China.
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61
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Prasad PK, Eizenshtadt N, Goliand I, Fellus-Alyagor L, Oren R, Golani O, Motiei L, Margulies D. Chemically programmable bacterial probes for the recognition of cell surface proteins. Mater Today Bio 2023; 20:100669. [PMID: 37334185 PMCID: PMC10275978 DOI: 10.1016/j.mtbio.2023.100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/01/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
Common methods to label cell surface proteins (CSPs) involve the use of fluorescently modified antibodies (Abs) or small-molecule-based ligands. However, optimizing the labeling efficiency of such systems, for example, by modifying them with additional fluorophores or recognition elements, is challenging. Herein we show that effective labeling of CSPs overexpressed in cancer cells and tissues can be obtained with fluorescent probes based on chemically modified bacteria. The bacterial probes (B-probes) are generated by non-covalently linking a bacterial membrane protein to DNA duplexes appended with fluorophores and small-molecule binders of CSPs overexpressed in cancer cells. We show that B-probes are exceptionally simple to prepare and modify because they are generated from self-assembled and easily synthesized components, such as self-replicating bacterial scaffolds and DNA constructs that can be readily appended, at well-defined positions, with various types of dyes and CSP binders. This structural programmability enabled us to create B-probes that can label different types of cancer cells with distinct colors, as well as generate very bright B-probes in which the multiple dyes are spatially separated along the DNA scaffold to avoid self-quenching. This enhancement in the emission signal enabled us to label the cancer cells with greater sensitivity and follow the internalization of the B-probes into these cells. The potential to apply the design principles underlying B-probes in therapy or inhibitor screening is also discussed here.
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Affiliation(s)
- Pragati K. Prasad
- Department of Chemical and Structural Biology, Weizmann Institute of Science Rehovot, 7610001, Israel
| | - Noa Eizenshtadt
- Department of Chemical and Structural Biology, Weizmann Institute of Science Rehovot, 7610001, Israel
| | - Inna Goliand
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Liat Fellus-Alyagor
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Roni Oren
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ofra Golani
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Leila Motiei
- Department of Chemical and Structural Biology, Weizmann Institute of Science Rehovot, 7610001, Israel
| | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science Rehovot, 7610001, Israel
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62
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Debon A, Siirola E, Snajdrova R. Enzymatic Bioconjugation: A Perspective from the Pharmaceutical Industry. JACS AU 2023; 3:1267-1283. [PMID: 37234110 PMCID: PMC10207132 DOI: 10.1021/jacsau.2c00617] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 05/27/2023]
Abstract
Enzymes have firmly established themselves as bespoke catalysts for small molecule transformations in the pharmaceutical industry, from early research and development stages to large-scale production. In principle, their exquisite selectivity and rate acceleration can also be leveraged for modifying macromolecules to form bioconjugates. However, available catalysts face stiff competition from other bioorthogonal chemistries. In this Perspective, we seek to illuminate applications of enzymatic bioconjugation in the face of an expanding palette of new drug modalities. With these applications, we wish to highlight some examples of current successes and pitfalls of using enzymes for bioconjugation along the pipeline and try to illustrate opportunities for further development.
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Affiliation(s)
- Aaron Debon
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
| | - Elina Siirola
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
| | - Radka Snajdrova
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
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63
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Nisavic M, Wørmer GJ, Nielsen CS, Jeppesen SM, Palmfeldt J, Poulsen TB. oxSTEF Reagents Are Tunable and Versatile Electrophiles for Selective Disulfide-Rebridging of Native Proteins. Bioconjug Chem 2023. [PMID: 37201197 DOI: 10.1021/acs.bioconjchem.3c00005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Site-selective disulfide rebridging has emerged as a powerful strategy to modulate the structural and functional properties of proteins. Here, we introduce a novel class of electrophilic reagents, designated oxSTEF, that demonstrate excellent efficiency in disulfide rebridging via double thiol exchange. The oxSTEF reagents are prepared using an efficient synthetic sequence which may be diverted to obtain a range of derivatives allowing for tuning of reactivity or steric bulk. We demonstrate highly selective rebridging of cyclic peptides and native proteins, such as human growth hormone, and the absence of cross-reactivity with other nucleophilic amino acid residues. The oxSTEF conjugates undergo glutathione-mediated disintegration under tumor-relevant glutathione concentrations, which highlights their potential for use in targeted drug delivery. Finally, the α-dicarbonyl motif of the oxSTEF reagents enables "second phase" oxime ligation, which furthermore increases the thiol stability of the conjugates significantly.
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Affiliation(s)
- Marija Nisavic
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
- Department of Clinical Medicine─Research Unit for Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 82, DK-8200 Aarhus N, Denmark
| | - Gustav J Wørmer
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Cecilie S Nielsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Sofie M Jeppesen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Johan Palmfeldt
- Department of Clinical Medicine─Research Unit for Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 82, DK-8200 Aarhus N, Denmark
| | - Thomas B Poulsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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64
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Qian L, Lin X, Gao X, Khan RU, Liao JY, Du S, Ge J, Zeng S, Yao SQ. The Dawn of a New Era: Targeting the "Undruggables" with Antibody-Based Therapeutics. Chem Rev 2023. [PMID: 37186942 DOI: 10.1021/acs.chemrev.2c00915] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The high selectivity and affinity of antibodies toward their antigens have made them a highly valuable tool in disease therapy, diagnosis, and basic research. A plethora of chemical and genetic approaches have been devised to make antibodies accessible to more "undruggable" targets and equipped with new functions of illustrating or regulating biological processes more precisely. In this Review, in addition to introducing how naked antibodies and various antibody conjugates (such as antibody-drug conjugates, antibody-oligonucleotide conjugates, antibody-enzyme conjugates, etc.) work in therapeutic applications, special attention has been paid to how chemistry tools have helped to optimize the therapeutic outcome (i.e., with enhanced efficacy and reduced side effects) or facilitate the multifunctionalization of antibodies, with a focus on emerging fields such as targeted protein degradation, real-time live-cell imaging, catalytic labeling or decaging with spatiotemporal control as well as the engagement of antibodies inside cells. With advances in modern chemistry and biotechnology, well-designed antibodies and their derivatives via size miniaturization or multifunctionalization together with efficient delivery systems have emerged, which have gradually improved our understanding of important biological processes and paved the way to pursue novel targets for potential treatments of various diseases.
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Affiliation(s)
- Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xuefen Lin
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xue Gao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Rizwan Ullah Khan
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jia-Yu Liao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shubo Du
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544
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65
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Soro DM, Roque JB, Rackl JW, Park B, Payer S, Shi Y, Ruble JC, Kaledin AL, Baik MH, Musaev DG, Sarpong R. Photo- and Metal-Mediated Deconstructive Approaches to Cyclic Aliphatic Amine Diversification. J Am Chem Soc 2023; 145:11245-11257. [PMID: 37171220 DOI: 10.1021/jacs.3c01318] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Described herein are studies toward the core modification of cyclic aliphatic amines using either a riboflavin/photo-irradiation approach or Cu(I) and Ag(I) to mediate the process. Structural remodeling of cyclic amines is explored through oxidative C-N and C-C bond cleavage using peroxydisulfate (persulfate) as an oxidant. Ring-opening reactions to access linear aldehydes or carboxylic acids with flavin-derived photocatalysis or Cu salts, respectively, are demonstrated. A complementary ring-opening process mediated by Ag(I) facilitates decarboxylative Csp3-Csp2 coupling in Minisci-type reactions through a key alkyl radical intermediate. Heterocycle interconversion is demonstrated through the transformation of N-acyl cyclic amines to oxazines using Cu(II) oxidation of the alkyl radical. These transformations are investigated by computation to inform the proposed mechanistic pathways. Computational studies indicate that persulfate mediates oxidation of cyclic amines with concomitant reduction of riboflavin. Persulfate is subsequently reduced by formal hydride transfer from the reduced riboflavin catalyst. Oxidation of the cyclic aliphatic amines with a Cu(I) salt is proposed to be initiated by homolysis of the peroxy bond of persulfate followed by α-HAT from the cyclic amine and radical recombination to form an α-sulfate adduct, which is hydrolyzed to the hemiaminal. Investigation of the pathway to form oxazines indicates a kinetic preference for cyclization over more typical elimination pathways to form olefins through Cu(II) oxidation of alkyl radicals.
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Affiliation(s)
- David M Soro
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jose B Roque
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jonas W Rackl
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Bohyun Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Stefan Payer
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Yuan Shi
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - J Craig Ruble
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Alexey L Kaledin
- Cherry L. Emerson Center for Scientific Computation, and Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Mu-Hyun Baik
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Djamaladdin G Musaev
- Cherry L. Emerson Center for Scientific Computation, and Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Richmond Sarpong
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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66
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Niu W, Guo J. Co-translational Installation of Posttranslational Modifications by Non-canonical Amino Acid Mutagenesis. Chembiochem 2023; 24:e202300039. [PMID: 36853967 PMCID: PMC10202221 DOI: 10.1002/cbic.202300039] [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: 01/18/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/02/2023]
Abstract
Protein posttranslational modifications (PTMs) play critical roles in regulating cellular activities. Here we provide a survey of genetic code expansion (GCE) methods that were applied in the co-translational installation and studies of PTMs through noncanonical amino acid (ncAA) mutagenesis. We begin by reviewing types of PTM that have been installed by GCE with a focus on modifications of tyrosine, serine, threonine, lysine, and arginine residues. We also discuss examples of applying these methods in biological studies. Finally, we end the piece with a short discussion on the challenges and the opportunities of the field.
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Affiliation(s)
- Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, N-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
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67
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Ruskowitz ER, Munoz-Robles BG, Strange AC, Butcher CH, Kurniawan S, Filteau JR, DeForest CA. Spatiotemporal functional assembly of split protein pairs through a light-activated SpyLigation. Nat Chem 2023; 15:694-704. [PMID: 37069270 PMCID: PMC10164143 DOI: 10.1038/s41557-023-01152-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/26/2023] [Indexed: 04/19/2023]
Abstract
Proteins provide essential functional regulation of many bioprocesses across all scales of life; however, new techniques to specifically modulate protein activity within living systems and in engineered biomaterials are needed to better interrogate fundamental cell signalling and guide advanced decisions of biological fate. Here we establish a generalizable strategy to rapidly and irreversibly activate protein function with full spatiotemporal control. Through the development of a genetically encoded and light-activated SpyLigation (LASL), bioactive proteins can be stably reassembled from non-functional split fragment pairs following brief exposure (typically minutes) to cytocompatible light. Employing readily accessible photolithographic processing techniques to specify when, where and how much photoligation occurs, we demonstrate precise protein activation of UnaG, NanoLuc and Cre recombinase using LASL in solution, biomaterials and living mammalian cells, as well as optical control over protein subcellular localization. Looking forward, we expect that these photoclick-based optogenetic approaches will find tremendous utility in probing and directing complex cellular fates in both time and three-dimensional space.
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Affiliation(s)
- Emily R Ruskowitz
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | | | - Alder C Strange
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Carson H Butcher
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Sebastian Kurniawan
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Jeremy R Filteau
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Cole A DeForest
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Department of Chemistry, University of Washington, Seattle, WA, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
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68
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Ebrahimi SB, Samanta D. Engineering protein-based therapeutics through structural and chemical design. Nat Commun 2023; 14:2411. [PMID: 37105998 PMCID: PMC10132957 DOI: 10.1038/s41467-023-38039-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Protein-based therapeutics have led to new paradigms in disease treatment. Projected to be half of the top ten selling drugs in 2023, proteins have emerged as rivaling and, in some cases, superior alternatives to historically used small molecule-based medicines. This review chronicles both well-established and emerging design strategies that have enabled this paradigm shift by transforming protein-based structures that are often prone to denaturation, degradation, and aggregation in vitro and in vivo into highly effective therapeutics. In particular, we discuss strategies for creating structures with increased affinity and targetability, enhanced in vivo stability and pharmacokinetics, improved cell permeability, and reduced amounts of undesired immunogenicity.
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Affiliation(s)
- Sasha B Ebrahimi
- Drug Product Development-Steriles, GlaxoSmithKline, Collegeville, PA, 19426, USA.
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA.
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69
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Chen X, Josephson B, Davis BG. Carbon-Centered Radicals in Protein Manipulation. ACS CENTRAL SCIENCE 2023; 9:614-638. [PMID: 37122447 PMCID: PMC10141601 DOI: 10.1021/acscentsci.3c00051] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 05/03/2023]
Abstract
Methods to directly post-translationally modify proteins are perhaps the most straightforward and operationally simple ways to create and study protein post-translational modifications (PTMs). However, precisely altering or constructing the C-C scaffolds pervasive throughout biology is difficult with common two-electron chemical approaches. Recently, there has been a surge of new methods that have utilized single electron/radical chemistry applied to site-specifically "edit" proteins that have started to create this potential-one that in principle could be near free-ranging. This review provides an overview of current methods that install such "edits", including those that generate function and/or PTMs, through radical C-C bond formation (as well as C-X bond formation via C• where illustrative). These exploit selectivity for either native residues, or preinstalled noncanonical protein side-chains with superior radical generating or accepting abilities. Particular focus will be on the radical generation approach (on-protein or off-protein, use of light and photocatalysts), judging the compatibility of conditions with proteins and cells, and novel chemical biology applications afforded by these methods. While there are still many technical hurdles, radical C-C bond formation on proteins is a promising and rapidly growing area in chemical biology with long-term potential for biological editing.
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Affiliation(s)
- Xuanxiao Chen
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
- The
Rosalind Franklin Institute, Oxfordshire, OX11 OFA, U.K.
| | - Brian Josephson
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
| | - Benjamin G. Davis
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
- The
Rosalind Franklin Institute, Oxfordshire, OX11 OFA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford, OX1 3QT, U.K.
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70
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Li H, Pan Y, Li C, Yang Z, Rao J, Chen B. Lysozyme-phenolics bioconjugates with antioxidant and antibacterial bifunctionalities: Structural basis underlying the dual-function. Food Chem 2023; 406:135070. [PMID: 36462353 DOI: 10.1016/j.foodchem.2022.135070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/26/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
This work aims at adopting an Electron Paramagnetic Resonance (EPR) spectroscopic technique to help understanding protein-phenolic conjugation and final functionalities relationship as well as the underlying structural basis of antioxidant and antibacterial dual functionalities. Specifically, lysozyme (Lys) was conjugated with two natural phenolic acids, i.e. rosmarinic acid (RA) and gentisic acid (GA, our previous work) with obviously different molecular features. Lys-RA displayed 8.6- and 4.0-times enhanced antioxidant stoichiometry compared to the native Lys and ones with GA, respectively, due to the stronger antioxidant activity of RA. However, RA conjugation mitigated both enzymatic and antibacterial activities of Lys-RA conjugates. Such inhibition effect is attributed to the greater structural and surface property changes of Lys upon conjugating with RA. Furthermore, the polyphenol conjugation related structural basis of disturbance, reactivity and selectivity were explored via site-directed spin labeling (SDSL)-EPR. A dynamic picture of reactivity and selectivity of phenolics conjugation on Lys was proposed.
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Affiliation(s)
- Hui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Yanxiong Pan
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, United States
| | - Chun Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, United States.
| | - Jiajia Rao
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Bingcan Chen
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States.
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71
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Thoreau F, Rochet LNC, Baker JR, Chudasama V. Enabling the formation of native mAb, Fab' and Fc-conjugates using a bis-disulfide bridging reagent to achieve tunable payload-to-antibody ratios (PARs). Chem Sci 2023; 14:3752-3762. [PMID: 37035695 PMCID: PMC10074397 DOI: 10.1039/d2sc06318b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Either as full IgGs or as fragments (Fabs, Fc, etc.), antibodies have received tremendous attention in the development of new therapeutics such as antibody-drug conjugates (ADCs). The production of ADCs involves the grafting of active payloads onto an antibody, which is generally enabled by the site-selective modification of native or engineered antibodies via chemical or enzymatic methods. Whatever method is employed, controlling the payload-antibody ratio (PAR) is a challenge in terms of multiple aspects including: (i) obtaining homogeneous protein conjugates; (ii) obtaining unusual PARs (PAR is rarely other than 2, 4 or 8); (iii) using a single method to access a range of different PARs; (iv) applicability to various antibody formats; and (v) flexibility for the production of heterofunctional antibody-conjugates (e.g. attachment of multiple types of payloads). In this article, we report a single pyridazinedione-based trifunctional dual bridging linker that enables, in a two-step procedure (re-bridging/click), the generation of either mAb-, Fab'-, or Fc-conjugates from native mAb, (Fab')2 or Fc formats, respectively. Fc and (Fab')2 formats were generated via enzymatic digestion of native mAbs. Whilst the same reduction and re-bridging protocols were applied to all three of the protein formats, the subsequent click reaction(s) employed to graft payload(s) drove the generation of a range of PARs, including heterofunctional PARs. As such, exploiting click reactivity and/or orthogonality afforded mAb-conjugates with PARs of 6, 4, 2 or 4 + 2, and Fab'- and Fc-conjugates with a PAR of 3, 2, 1 or 2 + 1 on-demand. We believe that the homogeneity, novelty and variety in accessible PARs, as well as the applicability to various antibody-conjugate formats enabled by our non-recombinant method could be a suitable tool for antibody-drug conjugates optimisation (optimal PAR value, optimal payloads combination) and boost the development of new antibody therapeutics (Fab'- and Fc-conjugates).
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Affiliation(s)
- Fabien Thoreau
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Léa N C Rochet
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - James R Baker
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Vijay Chudasama
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
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72
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Thoreau F, Szijj PA, Greene MK, Rochet LNC, Thanasi IA, Blayney JK, Maruani A, Baker JR, Scott CJ, Chudasama V. Modular Chemical Construction of IgG-like Mono- and Bispecific Synthetic Antibodies (SynAbs). ACS CENTRAL SCIENCE 2023; 9:476-487. [PMID: 36968530 PMCID: PMC10037451 DOI: 10.1021/acscentsci.2c01437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Indexed: 06/18/2023]
Abstract
In recent years there has been rising interest in the field of protein-protein conjugation, especially related to bispecific antibodies (bsAbs) and their therapeutic applications. These constructs contain two paratopes capable of binding two distinct epitopes on target molecules and are thus able to perform complex biological functions (mechanisms of action) not available to monospecific mAbs. Traditionally these bsAbs have been constructed through protein engineering, but recently chemical methods for their construction have started to (re)emerge. While these have been shown to offer increased modularity, speed, and for some methods even the inherent capacity for further functionalization (e.g., with small molecule cargo), most of these approaches lacked the ability to include a fragment crystallizable (Fc) modality. The Fc component of IgG antibodies offers effector function and increased half-life. Here we report a first-in-class disulfide rebridging and click-chemistry-based method for the generation of Fc-containing, IgG-like mono- and bispecific antibodies. These are in the FcZ-(FabX)-FabY format, i.e., two distinct Fabs and an Fc, potentially all from different antibodies, attached in a homogeneous and covalent manner. We have dubbed these molecules synthetic antibodies (SynAbs). We have constructed a T cell-engager (TCE) SynAb, FcCD20-(FabHER2)-FabCD3, and have confirmed that it exhibits the expected biological functions, including the ability to kill HER2+ target cells in a coculture assay with T cells.
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Affiliation(s)
- Fabien Thoreau
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Peter A. Szijj
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Michelle K. Greene
- Patrick
G Johnston Centre for Cancer Research, School of Medicine, Dentistry
and Biomedical Sciences, Queen’s
University Belfast, Belfast BT9 7AEU.K.
| | - Léa N. C. Rochet
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Ioanna A. Thanasi
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Jaine K. Blayney
- Patrick
G Johnston Centre for Cancer Research, School of Medicine, Dentistry
and Biomedical Sciences, Queen’s
University Belfast, Belfast BT9 7AEU.K.
| | - Antoine Maruani
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - James R. Baker
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Christopher J. Scott
- Patrick
G Johnston Centre for Cancer Research, School of Medicine, Dentistry
and Biomedical Sciences, Queen’s
University Belfast, Belfast BT9 7AEU.K.
| | - Vijay Chudasama
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
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73
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Somsen BA, Schellekens RJC, Verhoef CJA, Arkin MR, Ottmann C, Cossar PJ, Brunsveld L. Reversible Dual-Covalent Molecular Locking of the 14-3-3/ERRγ Protein-Protein Interaction as a Molecular Glue Drug Discovery Approach. J Am Chem Soc 2023; 145:6741-6752. [PMID: 36926879 PMCID: PMC10064330 DOI: 10.1021/jacs.2c12781] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Molecules that stabilize protein-protein interactions (PPIs) are invaluable as tool compounds for biophysics and (structural) biology, and as starting points for molecular glue drug discovery. However, identifying initial starting points for PPI stabilizing matter is highly challenging, and chemical optimization is labor-intensive. Inspired by chemical crosslinking and reversible covalent fragment-based drug discovery, we developed an approach that we term "molecular locks" to rapidly access molecular glue-like tool compounds. These dual-covalent small molecules reversibly react with a nucleophilic amino acid on each of the partner proteins to dynamically crosslink the protein complex. The PPI between the hub protein 14-3-3 and estrogen-related receptor γ (ERRγ) was used as a pharmacologically relevant case study. Based on a focused library of dual-reactive small molecules, a molecular glue tool compound was rapidly developed. Biochemical assays and X-ray crystallographic studies validated the ternary covalent complex formation and overall PPI stabilization via dynamic covalent crosslinking. The molecular lock approach is highly selective for the specific 14-3-3/ERRγ complex, over other 14-3-3 complexes. This selectivity is driven by the interplay of molecular reactivity and molecular recognition of the composite PPI binding interface. The long lifetime of the dual-covalent locks enabled the selective stabilization of the 14-3-3/ERRγ complex even in the presence of several other competing 14-3-3 clients with higher intrinsic binding affinities. The molecular lock approach enables systematic, selective, and potent stabilization of protein complexes to support molecular glue drug discovery.
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Affiliation(s)
- Bente A Somsen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Rick J C Schellekens
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Carlo J A Verhoef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California, San Francisco, California 94143, United States
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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74
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Xia Y, Li F, Zhang X, Balamkundu S, Tang F, Hu S, Lescar J, Tam JP, Liu CF. A Cascade Enzymatic Reaction Scheme for Irreversible Transpeptidative Protein Ligation. J Am Chem Soc 2023; 145:6838-6844. [PMID: 36924109 DOI: 10.1021/jacs.2c13628] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Enzymatic peptide ligation holds great promise in the study of protein functions and development of protein therapeutics. Owing to their high catalytic efficiency and a minimal tripeptide recognition motif, peptidyl asparaginyl ligases (PALs) are particularly useful tools for bioconjugation. However, as an inherent limitation of transpeptidases, PAL-mediated ligation is reversible, requiring a large excess of one of the ligation partners to shift the reaction equilibrium in the forward direction. Herein, we report a method to make PAL-mediated intermolecular ligation irreversible by coupling it to glutaminyl cyclase (QC)-catalyzed pyroglutamyl formation. In this method, the acyl donor substrate of PALs is designed to have glutamine at the P1' position of the Asn-P1'-P2' tripeptide PAL recognition motif. Upon ligation with an acyl acceptor substrate, the acyl donor substrate releases a leaving group in which the exposed N-terminal glutamine is cyclized by QC, quenching the Gln Nα-amine in a lactam. Using this method, PAL-mediated ligation can achieve near-quantitative yields even at an equal molar ratio between the two ligation partners. We have demonstrated this method for a wide range of applications, including protein-to-protein ligations. We anticipate that this cascade enzymatic reaction scheme will make PAL enzymes well suited for numerous new uses in biotechnology.
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Affiliation(s)
- Yiyin Xia
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Fupeng Li
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | | | - Fan Tang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Side Hu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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75
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Griffiths RC, Smith FR, Li D, Wyatt J, Rogers DM, Long JE, Cusin LML, Tighe PJ, Layfield R, Hirst JD, Müller MM, Mitchell NJ. Cysteine-Selective Modification of Peptides and Proteins via Desulfurative C-C Bond Formation. Chemistry 2023; 29:e202202503. [PMID: 36534955 PMCID: PMC10946470 DOI: 10.1002/chem.202202503] [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: 08/11/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
The site-selective modification of peptides and proteins facilitates the preparation of targeted therapeutic agents and tools to interrogate biochemical pathways. Among the numerous bioconjugation techniques developed to install groups of interest, those that generate C(sp3 )-C(sp3 ) bonds are significantly underrepresented despite affording proteolytically stable, biogenic linkages. Herein, a visible-light-mediated reaction is described that enables the site-selective modification of peptides and proteins via desulfurative C(sp3 )-C(sp3 ) bond formation. The reaction is rapid and high yielding in peptide systems, with comparable translation to proteins. Using this chemistry, a range of moieties is installed into model systems and an effective PTM-mimic is successfully integrated into a recombinantly expressed histone.
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Affiliation(s)
- Rhys C. Griffiths
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Frances R. Smith
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Diyuan Li
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Jasmine Wyatt
- Department of ChemistryKing's College LondonLondonSE1 1DB
| | - David M. Rogers
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Jed E. Long
- School of Life SciencesUniversity of Nottingham Medical SchoolNottinghamNG7 2UHUK
| | - Lola M. L. Cusin
- School of Life SciencesUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Patrick J. Tighe
- School of Life SciencesUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Robert Layfield
- School of Life SciencesUniversity of Nottingham Medical SchoolNottinghamNG7 2UHUK
| | - Jonathan D. Hirst
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
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76
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O WY, Cui JF, Yu Q, Kung KKY, Chung SF, Leung YC, Wong MK. Isoindolium-Based Allenes: Reactivity Studies and Applications in Fluorescence Temperature Sensing and Cysteine Bioconjugation. Angew Chem Int Ed Engl 2023; 62:e202218038. [PMID: 36670048 DOI: 10.1002/anie.202218038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023]
Abstract
The reaction of a series of electron-deficient isoindolium-based allenes with sulfhydryl compounds has been studied, leading to the formation of isoindolium-based vinyl sulfides. The vinyl sulfides generated could be readily converted into the corresponding indanones and amines upon heating at 30-70 °C with good yields up to 61 %. The thermal cleavage reaction of vinyl sulfides was further studied for developing temperature-sensitive systems. Notably, a novel FRET-based fluorescent temperature sensor was designed and synthesized for temperature sensing at 50 °C, giving a 6.5-fold blue fluorescence enhancement. Moreover, chemoselective bioconjugation of cysteine-containing peptides with the isoindolium-based allenes for the construction of multifunctional peptide bioconjugates was investigated. Thermal cleavage of isoindoliums on the modified peptides at 35-70 °C gave indanone bioconjugates with up to >99 % conversion. These results indicated the biocompatibility of this novel temperature-sensitive reaction.
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Affiliation(s)
- Wa-Yi O
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China.,The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Jian-Fang Cui
- Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, 518055, China
| | - Qiong Yu
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Karen Ka-Yan Kung
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China.,The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Sai-Fung Chung
- Henry Cheng Research Laboratory for Drug Development, Lo Ka Chung Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - Yun-Chung Leung
- Henry Cheng Research Laboratory for Drug Development, Lo Ka Chung Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - Man-Kin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China.,The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
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77
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Kuschert S, Stroet M, Chin YKY, Conibear AC, Jia X, Lee T, Bartling CRO, Strømgaard K, Güntert P, Rosengren KJ, Mark AE, Mobli M. Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2023; 4:57-72. [PMID: 37904802 PMCID: PMC10583272 DOI: 10.5194/mr-4-57-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/07/2023] [Indexed: 11/01/2023]
Abstract
Peptides and proteins containing non-canonical amino acids (ncAAs) are a large and important class of biopolymers. They include non-ribosomally synthesised peptides, post-translationally modified proteins, expressed or synthesised proteins containing unnatural amino acids, and peptides and proteins that are chemically modified. Here, we describe a general procedure for generating atomic descriptions required to incorporate ncAAs within popular NMR structure determination software such as CYANA, CNS, Xplor-NIH and ARIA. This procedure is made publicly available via the existing Automated Topology Builder (ATB) server (https://atb.uq.edu.au, last access: 17 February 2023) with all submitted ncAAs stored in a dedicated database. The described procedure also includes a general method for linking of side chains of amino acids from CYANA templates. To ensure compatibility with other systems, atom names comply with IUPAC guidelines. In addition to describing the workflow, 3D models of complex natural products generated by CYANA are presented, including vancomycin. In order to demonstrate the manner in which the templates for ncAAs generated by the ATB can be used in practice, we use a combination of CYANA and CNS to solve the structure of a synthetic peptide designed to disrupt Alzheimer-related protein-protein interactions. Automating the generation of structural templates for ncAAs will extend the utility of NMR spectroscopy to studies of more complex biomolecules, with applications in the rapidly growing fields of synthetic biology and chemical biology. The procedures we outline can also be used to standardise the creation of structural templates for any amino acid and thus have the potential to impact structural biology more generally.
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Affiliation(s)
- Sarah Kuschert
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Martin Stroet
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yanni Ka-Yan Chin
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Anne Claire Conibear
- Institute of Applied Synthetic Chemistry, Technische Universität Wien, Getreidemarkt 9/163, Wien 1060, Vienna, Austria
| | - Xinying Jia
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Lee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zurich, Switzerland
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, Hachiōji, Tokyo 192-0397, Japan
| | - Karl Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alan Edward Mark
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
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78
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Chauhan P, V. R, Kumar M, Molla R, V. B. U, Rai V. Dis integrate (DIN) Theory Enabling Precision Engineering of Proteins. ACS CENTRAL SCIENCE 2023; 9:137-150. [PMID: 36844488 PMCID: PMC9951294 DOI: 10.1021/acscentsci.2c01455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Indexed: 06/18/2023]
Abstract
The chemical toolbox for the selective modification of proteins has witnessed immense interest in the past few years. The rapid growth of biologics and the need for precision therapeutics have fuelled this growth further. However, the broad spectrum of selectivity parameters creates a roadblock to the field's growth. Additionally, bond formation and dissociation are significantly redefined during the translation from small molecules to proteins. Understanding these principles and developing theories to deconvolute the multidimensional attributes could accelerate the area. This outlook presents a disintegrate (DIN) theory for systematically disintegrating the selectivity challenges through reversible chemical reactions. An irreversible step concludes the reaction sequence to render an integrated solution for precise protein bioconjugation. In this perspective, we highlight the key advancements, unsolved challenges, and potential opportunities.
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79
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Jin GQ, Wang JX, Lu J, Zhang H, Yao Y, Ning Y, Lu H, Gao S, Zhang JL. Two birds one stone: β-fluoropyrrolyl-cysteine S NAr chemistry enabling functional porphyrin bioconjugation. Chem Sci 2023; 14:2070-2081. [PMID: 36845938 PMCID: PMC9944650 DOI: 10.1039/d2sc06209g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Bioconjugation, a synthetic tool that endows small molecules with biocompatibility and target specificity through covalent attachment of a biomolecule, holds promise for next-generation diagnosis or therapy. Besides the establishment of chemical bonding, such chemical modification concurrently allows alteration of the physicochemical properties of small molecules, but this has been paid less attention in designing novel bioconjugates. Here, we report a "two birds one stone" methodology for irreversible porphyrin bioconjugation based on β-fluoropyrrolyl-cysteine SNAr chemistry, in which the β-fluorine of porphyrin is selectively replaced by a cysteine in either peptides or proteins to generate novel β-peptidyl/proteic porphyrins. Notably, due to the distinct electronic nature between fluorine and sulfur, such replacement makes the Q band red-shift to the near-infrared region (NIR, >700 nm). This facilitates intersystem crossing (ISC) to enhance the triplet population and thus singlet oxygen production. This new methodology features water tolerance, a fast reaction time (15 min), good chemo-selectivity, and broad substrate scope, including various peptides and proteins under mild conditions. To demonstrate its potential, we applied porphyrin β-bioconjugates in several scenarios, including (1) cytosolic delivery of functional proteins, (2) metabolic glycan labeling, (3) caspase-3 detection, and (4) tumor-targeting phototheranostics.
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Affiliation(s)
- Guo-Qing Jin
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Jing-Xiang Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Jianhua Lu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Hang Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Yuhang Yao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Yingying Ning
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Hua Lu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Song Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China .,Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China.,Spin-X Institute, School of Chemistry and Chemical Engineering, State Key Laboratory of Luminescent Materials and Devices, Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, South China University of Technology Guangzhou 510641 China
| | - Jun-Long Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China .,Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
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80
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Wang Y, Zhang J, Han B, Tan L, Cai W, Li Y, Su Y, Yu Y, Wang X, Duan X, Wang H, Shi X, Wang J, Yang X, Liu T. Noncanonical amino acids as doubly bio-orthogonal handles for one-pot preparation of protein multiconjugates. Nat Commun 2023; 14:974. [PMID: 36810592 PMCID: PMC9944564 DOI: 10.1038/s41467-023-36658-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Genetic encoding of noncanonical amino acid (ncAA) for site-specific protein modification has been widely applied for many biological and therapeutic applications. To efficiently prepare homogeneous protein multiconjugates, we design two encodable noncanonical amino acids (ncAAs), 4-(6-(3-azidopropyl)-s-tetrazin-3-yl) phenylalanine (pTAF) and 3-(6-(3-azidopropyl)-s-tetrazin-3-yl) phenylalanine (mTAF), containing mutually orthogonal and bioorthogonal azide and tetrazine reaction handles. Recombinant proteins and antibody fragments containing the TAFs can easily be functionalized in one-pot reactions with combinations of commercially available fluorophores, radioisotopes, PEGs, and drugs in a plug-and-play manner to afford protein dual conjugates to assess combinations of tumor diagnosis, image-guided surgery, and targeted therapy in mouse models. Furthermore, we demonstrate that simultaneously incorporating mTAF and a ketone-containing ncAA into one protein via two non-sense codons allows preparation of a site-specific protein triconjugate. Our results demonstrate that TAFs are doubly bio-orthogonal handles for efficient and scalable preparation of homogeneous protein multiconjugates.
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Affiliation(s)
- Yong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, 100191, Beijing, China
| | - Jingming Zhang
- Department of Nuclear Medicine, Peking University First Hospital, 100034, Beijing, China
| | - Boyang Han
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, 100191, Beijing, China
| | - Linzhi Tan
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, 100191, Beijing, China
| | - Wenkang Cai
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, 100191, Beijing, China
| | - Yuxuan Li
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, 100191, Beijing, China
| | - Yeyu Su
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, 100191, Beijing, China
| | - Yutong Yu
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, 100191, Beijing, China
| | - Xin Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, 100191, Beijing, China
| | - Xiaojiang Duan
- Department of Nuclear Medicine, Peking University First Hospital, 100034, Beijing, China
| | - Haoyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, 100191, Beijing, China
| | - Xiaomeng Shi
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, 100191, Beijing, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, 100191, Beijing, China
| | - Xing Yang
- Department of Nuclear Medicine, Peking University First Hospital, 100034, Beijing, China. .,Institute of Medical Technology, Peking University Health Science Center, 100191, Beijing, China.
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, 100191, Beijing, China.
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81
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Hashad RA, Jap E, Casey JL, Candace Ho YT, Wright A, Thalmann C, Sleeman M, Lupton DW, Hagemeyer CE, Cryle MJ, Robert R, Alt K. Chemoselective Methionine Labelling of Recombinant Trastuzumab Shows High In Vitro and In Vivo Tumour Targeting. Chemistry 2023; 29:e202202491. [PMID: 36451579 PMCID: PMC10946977 DOI: 10.1002/chem.202202491] [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: 08/10/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
A highly effective 2-step system for site-specific antibody modification and conjugation of the monoclonal antibody Herceptin (commercially available under Trastuzumab) in a cysteine-independent manner was used to generate labelled antibodies for in vivo imaging. The first step contains redox-activated chemical tagging (ReACT) of thioethers via engineered methionine residues to introduce specific alkyne moieties, thereby offering a novel easy way to fundamentally change the process of antibody bioconjugation. The second step involves modification of the introduced alkyne via azide-alkyne cycloaddition 'click' conjugation. The versatility of this 2-step approach is demonstrated here by the selective incorporation of a fluorescent dye but can also be applied to a wide variety of different conjugation partners depending on the desired application in a facile manner. Methionine-modified antibodies were characterised in vitro, and the diagnostic potential of the most promising variant was further analysed in an in vivo xenograft animal model using a fluorescence imaging modality. This study demonstrates how methionine-mediated antibody conjugation offers an orthogonal and versatile route to the generation of tailored antibody conjugates with in vivo applicability.
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Affiliation(s)
- Rania A. Hashad
- Australian Centre for Blood DiseasesCentral Clinical SchoolMonash UniversityMelbourneVictoria3004Australia
- Department of Pharmaceutics and Industrial PharmacyFaculty of PharmacyAin Shams University1181CairoEgypt
| | - Edwina Jap
- Australian Centre for Blood DiseasesCentral Clinical SchoolMonash UniversityMelbourneVictoria3004Australia
| | - Joanne L. Casey
- Department of PhysiologyBiomedicine Discovery InstituteMonash UniversityClaytonVictoria3800Australia
| | - Y. T. Candace Ho
- Department of Biochemistry and Molecular BiologyBiomedicine Discovery InstituteMonash UniversityClaytonVictoria 3800 (Australia)EMBL AustraliaMonash UniversityClaytonVictoria3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceMonash UniversityClayton3800VictoriaAustralia
| | - Alexander Wright
- School of ChemistryMonash UniversityClayton3800VictoriaAustralia
| | - Claudia Thalmann
- Department of PhysiologyBiomedicine Discovery InstituteMonash UniversityClaytonVictoria3800Australia
| | - Mark Sleeman
- Department of PhysiologyBiomedicine Discovery InstituteMonash UniversityClaytonVictoria3800Australia
| | - David W. Lupton
- School of ChemistryMonash UniversityClayton3800VictoriaAustralia
| | - Christoph E. Hagemeyer
- Australian Centre for Blood DiseasesCentral Clinical SchoolMonash UniversityMelbourneVictoria3004Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular BiologyBiomedicine Discovery InstituteMonash UniversityClaytonVictoria 3800 (Australia)EMBL AustraliaMonash UniversityClaytonVictoria3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceMonash UniversityClayton3800VictoriaAustralia
| | - Remy Robert
- Department of PhysiologyBiomedicine Discovery InstituteMonash UniversityClaytonVictoria3800Australia
| | - Karen Alt
- Australian Centre for Blood DiseasesCentral Clinical SchoolMonash UniversityMelbourneVictoria3004Australia
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82
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Kaplaneris N, Puet A, Kallert F, Pöhlmann J, Ackermann L. Late-stage C-H Functionalization of Tryptophan-Containing Peptides with Thianthrenium Salts: Conjugation and Ligation. Angew Chem Int Ed Engl 2023; 62:e202216661. [PMID: 36581584 DOI: 10.1002/anie.202216661] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
Bioorthogonal late-stage diversification of structurally complex peptides bears enormous potential for drug discovery and molecular imaging, among other applications. Herein, we report on a palladium-catalyzed C-H arylation of tryptophan-containing peptides with readily accessible and modular arylthianthrenium salts. Under exceedingly mild reaction conditions, the late-stage diversification of structurally complex peptides was accomplished. The tunability and ease of preparation of arylthianthrenium salts allowed the expedient stitching of tryptophan-containing peptides with drug, natural product, and peptidic scaffolds by forging sterically congested biaryl linkages. The robustness of the palladium catalysis regime was reflected by the full tolerance of a plethora of sensitive and coordinating functional groups. Hence, our manifold enabled efficient access to highly decorated, labelled, conjugated, and ligated linear and cyclic peptides.
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Affiliation(s)
- Nikolaos Kaplaneris
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammanstrasse 2, 37077, Göttingen, Germany
| | - Alejandro Puet
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammanstrasse 2, 37077, Göttingen, Germany
| | - Felix Kallert
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammanstrasse 2, 37077, Göttingen, Germany
| | - Julia Pöhlmann
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammanstrasse 2, 37077, Göttingen, Germany
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammanstrasse 2, 37077, Göttingen, Germany.,Wöhler Research Institute for Sustainable Chemistry, Georg-August-Universität Göttingen, Tammanstrasse 2, 37077, Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Potsdamer Strasse 58, 10785, Berlin, Germany
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83
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Fitzpatrick NA, Musacchio PZ. Shining light on diselenide bonds. Nat Chem 2023; 15:163-164. [PMID: 36747033 DOI: 10.1038/s41557-023-01134-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Nicholas A Fitzpatrick
- Department of Chemistry & Biochemistry, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Patricia Z Musacchio
- Department of Chemistry & Biochemistry, Worcester Polytechnic Institute, Worcester, MA, USA.
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84
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Fischer NH, Oliveira MT, Diness F. Chemical modification of proteins - challenges and trends at the start of the 2020s. Biomater Sci 2023; 11:719-748. [PMID: 36519403 DOI: 10.1039/d2bm01237e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosomally expressed proteins perform multiple, versatile, and specialized tasks throughout Nature. In modern times, chemically modified proteins, including improved hormones, enzymes, and antibody-drug-conjugates have become available and have found advanced industrial and pharmaceutical applications. Chemical modification of proteins is used to introduce new functionalities, improve stability or drugability. Undertaking chemical reactions with proteins without compromising their native function is still a core challenge as proteins are large conformation dependent multifunctional molecules. Methods for functionalization ideally should be chemo-selective, site-selective, and undertaken under biocompatible conditions in aqueous buffer to prevent denaturation of the protein. Here the present challenges in the field are discussed and methods for modification of the 20 encoded amino acids as well as the N-/C-termini and protein backbone are presented. For each amino acid, common and traditional modification methods are presented first, followed by more recent ones.
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Affiliation(s)
- Niklas Henrik Fischer
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Maria Teresa Oliveira
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Frederik Diness
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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85
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Rodríguez Á, Maneiro M, Lence E, Otero JM, van Raaij MJ, Thompson P, Hawkins AR, González-Bello C. Quinate-based ligands for irreversible inactivation of the bacterial virulence factor DHQ1 enzyme-A molecular insight. Front Mol Biosci 2023; 10:1111598. [PMID: 36762206 PMCID: PMC9902378 DOI: 10.3389/fmolb.2023.1111598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
Irreversible inhibition of the enzyme type I dehydroquinase (DHQ1), a promising target for anti-virulence drug development, has been explored by enhancing the electrophilicity of specific positions of the ligand towards covalent lysine modification. For ligand design, we made use of the advantages offered by the intrinsic acid-base properties of the amino substituents introduced in the quinate scaffold, namely compounds 6-7 (R configuration at C3), to generate a potential leaving group, as well as the recognition pattern of the enzyme. The reactivity of the C2-C3 bond (Re face) in the scaffold was also explored using compound 8. The results of the present study show that replacement of the C3 hydroxy group of (-)-quinic acid by a hydroxyamino substituent (compound 6) provides a time-dependent irreversible inhibitor, while compound 7, in which the latter functionality was substituted by an amino group, and the introduction of an oxirane ring at C2-C3 bond, compound 8, do not allow covalent modification of the enzyme. These outcomes were supported by resolution of the crystal structures of DHQ1 from Staphylococcus aureus (Sa-DHQ1) and Salmonella typhi (St-DHQ1) chemically modified by 6 at a resolution of 1.65 and 1.90 Å, respectively, and of St-DHQ1 in the complex with 8 (1.55 Å). The combination of these structural studies with extensive molecular dynamics simulation studies allowed us to understand the molecular basis of the type of inhibition observed. This study is a good example of the importance of achieving the correct geometry between the reactive center of the ligand (electrophile) and the enzyme nucleophile (lysine residue) to allow selective covalent modification. The outcomes obtained with the hydroxyamino derivative 6 also open up new possibilities in the design of irreversible inhibitors based on the use of amino substituents.
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Affiliation(s)
- Ángela Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María Maneiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - José M. Otero
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Mark J. van Raaij
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
| | - Paul Thompson
- Newcastle University Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alastair R. Hawkins
- Newcastle University Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain,*Correspondence: Concepción González-Bello,
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86
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Karipal Padinjare Veedu D, Connal LA, Malins LR. Tunable Electrochemical Peptide Modifications: Unlocking New Levels of Orthogonality for Side-Chain Functionalization. Angew Chem Int Ed Engl 2023; 62:e202215470. [PMID: 36336657 PMCID: PMC10107541 DOI: 10.1002/anie.202215470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Electrochemical transformations provide enticing opportunities for programmable, residue-specific peptide modifications. Herein, we harness the potential of amidic side-chains as underutilized handles for late-stage modification through the development of an electroauxiliary-assisted oxidation of glutamine residues within unprotected peptides. Glutamine building blocks bearing electroactive side-chain N,S-acetals are incorporated into peptides using standard Fmoc-SPPS. Anodic oxidation of the electroauxiliary in the presence of diverse alcohol nucleophiles enables the installation of high-value N,O-acetal functionalities. Proof-of-principle for an electrochemical peptide stapling protocol, as well as the functionalization of dynorphin B, an endogenous opioid peptide, demonstrates the applicability of the method to intricate peptide systems. Finally, the site-selective and tunable electrochemical modification of a peptide bearing two discretely oxidizable sites is achieved.
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Affiliation(s)
- Dhanya Karipal Padinjare Veedu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
| | - Luke A Connal
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Lara R Malins
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
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87
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Tantipanjaporn A, Wong MK. Development and Recent Advances in Lysine and N-Terminal Bioconjugation for Peptides and Proteins. Molecules 2023; 28:molecules28031083. [PMID: 36770752 PMCID: PMC9953373 DOI: 10.3390/molecules28031083] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
The demand for creation of protein diversity and regulation of protein function through native protein modification and post-translational modification has ignited the development of selective chemical modification methods for peptides and proteins. Chemical bioconjugation offers selective functionalization providing bioconjugates with desired properties and functions for diverse applications in chemical biology, medicine, and biomaterials. The amino group existing at the lysine residue and N-terminus of peptides and proteins has been extensively studied in bioconjugation because of its good nucleophilicity and high surface exposure. Herein, we review the development of chemical methods for modification of the amino groups on lysine residue and N-terminus featuring excellent selectivity, mild reaction conditions, short reaction time, high conversion, biocompatibility, and preservation of protein integrity. This review is organized based on the chemoselectivity and site-selectivity of the chemical bioconjugation reagents to the amino acid residues aiming to provide guidance for the selection of appropriate bioconjugation methods.
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88
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Wan C, Hou Z, Yang D, Zhou Z, Xu H, Wang Y, Dai C, Liang M, Meng J, Chen J, Yin F, Wang R, Li Z. The thiol-sulfoxonium ylide photo-click reaction for bioconjugation. Chem Sci 2023; 14:604-612. [PMID: 36741507 PMCID: PMC9847666 DOI: 10.1039/d2sc05650j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/01/2022] [Indexed: 12/04/2022] Open
Abstract
Visible-light-mediated methods were heavily studied as a useful tool for cysteine-selective bio-conjugation; however, many current methods suffer from bio-incompatible reaction conditions and slow kinetics. To address these challenges, herein, we report a transition metal-free thiol-sulfoxonium ylide photo-click reaction that enables bioconjugation under bio-compatible conditions. The reaction is highly cysteine-selective and generally finished within minutes with naturally occurring riboflavin derivatives as organic photocatalysts. The catalysts and substrates are readily accessible and bench stable and have satisfactory water solubility. As a proof-of-concept study, the reaction was smoothly applied in chemo-proteomic analysis, which provides efficient tools to explore the druggable content of the human proteome.
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Affiliation(s)
- Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhen518055P. R. China
| | - Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhen518055P. R. China
| | - Dongyan Yang
- College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and EngineeringGuangzhou510225P. R. China
| | - Ziyuan Zhou
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhen518116P. R. China
| | - Hongkun Xu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhen518055P. R. China
| | - Yuena Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhen518055P. R. China
| | - Chuan Dai
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhen518055P. R. China
| | - Mingchan Liang
- Pingshan Translational Medicine Center, Shenzhen Bay LaboratoryShenzhen518118P. R. China
| | - Jun Meng
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhen518116P. R. China
| | - Jiean Chen
- Pingshan Translational Medicine Center, Shenzhen Bay LaboratoryShenzhen518118P. R. China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay LaboratoryShenzhen518118P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay LaboratoryShenzhen518118P. R. China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhen518055P. R. China,Pingshan Translational Medicine Center, Shenzhen Bay LaboratoryShenzhen518118P. R. China
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89
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Wu CS, Cheng L. Recent Advances towards the Reversible Chemical Modification of Proteins. Chembiochem 2023; 24:e202200468. [PMID: 36201252 DOI: 10.1002/cbic.202200468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/05/2022] [Indexed: 01/20/2023]
Abstract
Proteins are intriguing biomacromolecules for all living systems, not only as essential building blocks of organisms, but also as participants in almost every aspect of cellular activity such as metabolism and gene transcription/expression. Developing chemical biology tools that are capable of labeling/modifying proteins is a powerful method for decoding their detailed structures and functions. However, most current approaches heavily rely on the installation of permanent tags or genetic engineering of unnatural amino acids. There has been slow development in reversible chemical labeling using small organic probes and bioorthogonal transformations to construct site-selectively modified proteins and conditionally restore their activities or structures. This review summarizes recent advances in the field of chemical regulation of proteins with reversible transformations towards distinct motifs, including amino acid residues, amide backbones and native post-translational lysine. Finally, current challenges and future perspectives are discussed.
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Affiliation(s)
- Chuan-Shuo Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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90
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Electron transfer in protein modifications: from detection to imaging. Sci China Chem 2023. [DOI: 10.1007/s11426-022-1417-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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91
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Sun H, Huang Y, Tsai YH. Genetically Encoded 1,2-Aminothiol for Site-Specific Modification of a Cellular Membrane Protein via TAMM Condensation. Methods Mol Biol 2023; 2676:191-199. [PMID: 37277634 DOI: 10.1007/978-1-0716-3251-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Site-specific modification of proteins has wide applications in probing and perturbing biological systems. A popular means to achieve such a modification on a target protein is through a reaction between bioorthogonal functionalities. Indeed, various bioorthogonal reactions have been developed, including a recently reported reaction between 1,2-aminothiol and ((alkylthio)(aryl)methylene)malononitrile (TAMM). Here, we describe the procedure that combines genetic code expansion and TAMM condensation for site-specific modification of cellular membrane proteins. The 1,2-aminothiol functionality is introduced through a genetically incorporated noncanonical amino acid to a model membrane protein on mammalian cells. Treatment of the cells with a fluorophore-TAMM conjugate leads to fluorescent labeling of the target protein. This method can be applied to modify different membrane proteins on live mammalian cells.
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Affiliation(s)
- Han Sun
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yang Huang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yu-Hsuan Tsai
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China.
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92
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Thioester-mediated biocatalytic amide bond synthesis with in situ thiol recycling. Nat Catal 2022. [DOI: 10.1038/s41929-022-00889-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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93
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Liu H, Li G, Peng Z, Zhang S, Zhou X, Liu Q, Wang J, Liu Y, Jia T. Tagging Peptides with a Redox Responsive Fluorescent Probe Enabled by Photoredox Difunctionalization of Phenylacetylenes with Sulfinates and Disulfides. JACS AU 2022; 2:2821-2829. [PMID: 36590269 PMCID: PMC9795567 DOI: 10.1021/jacsau.2c00577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/07/2022] [Indexed: 05/09/2023]
Abstract
Herein, we describe a photoredox three-component atom-transfer radical addition (ATRA) reaction of aryl alkynes directly with dialkyl disulfides and alkylsulfinates, circumventing the utilization of chemically unstable and synthetically challenging S-alkyl alkylthiosulfonates as viable addition partners. A vast array of (E)-β-alkylsulfonylvinyl alkylsulfides was prepared with great regio- and stereoselectivity. Moreover, this powerful tactic could be employed to tag cysteine residues of complex polypeptides in solution or on resin merging with solid phase peptide synthesis (SPPS) techniques. A sulfonyl-derived redox responsive fluorescent probe could be conveniently introduced on the peptide, which displays green fluorescence in cells while showing blue fluorescence in medium. The photophysical investigations reveal that the red shift of the emission fluorescence is attested to reduction of carbonyl group to the corresponding hydroxyl moiety. Interestingly, the fluorescence change of tagged peptide could be reverted in cells by treatment of H2O2, arising from the reoxidation of hydroxyl group back to ketone by the elevated level of reactive oxygen species (ROS).
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Affiliation(s)
- Hong Liu
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
| | - Guolin Li
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
- Department
of Pharmaceutical Engineering, College of Chemical Engineering, Northwest University, Taibai North Road 229, Xi’an, Shanxi 710069, P. R. China
| | - Zhiyuan Peng
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
| | - Shishuo Zhang
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
| | - Xin Zhou
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
- Department
of Pharmaceutical Engineering, College of Chemical Engineering, Northwest University, Taibai North Road 229, Xi’an, Shanxi 710069, P. R. China
| | - Qingchao Liu
- Department
of Pharmaceutical Engineering, College of Chemical Engineering, Northwest University, Taibai North Road 229, Xi’an, Shanxi 710069, P. R. China
| | - Junfeng Wang
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong
Key Laboratory of Marine Materia Medica/Innovation Academy of South
China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xinggang Road, Guangzhou 510301, P. R. China
| | - Yonghong Liu
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong
Key Laboratory of Marine Materia Medica/Innovation Academy of South
China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xinggang Road, Guangzhou 510301, P. R. China
- E-mail:
| | - Tiezheng Jia
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
- State
Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94
Weijin Road, Tianjin 300071, P. R. China
- E-mail:
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94
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Berkeley RF, Debelouchina GT. Chemical tools for study and modulation of biomolecular phase transitions. Chem Sci 2022; 13:14226-14245. [PMID: 36545140 PMCID: PMC9749140 DOI: 10.1039/d2sc04907d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022] Open
Abstract
Biomolecular phase transitions play an important role in organizing cellular processes in space and time. Methods and tools for studying these transitions, and the intrinsically disordered proteins (IDPs) that often drive them, are typically less developed than tools for studying their folded protein counterparts. In this perspective, we assess the current landscape of chemical tools for studying IDPs, with a specific focus on protein liquid-liquid phase separation (LLPS). We highlight methodologies that enable imaging and spectroscopic studies of these systems, including site-specific labeling with small molecules and the diverse range of capabilities offered by inteins and protein semisynthesis. We discuss strategies for introducing post-translational modifications that are central to IDP and LLPS function and regulation. We also investigate the nascent field of noncovalent small-molecule modulators of LLPS. We hope that this review of the state-of-the-art in chemical tools for interrogating IDPs and LLPS, along with an associated perspective on areas of unmet need, can serve as a valuable and timely resource for these rapidly expanding fields of study.
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Affiliation(s)
- Raymond F. Berkeley
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
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95
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Gonzalez-Valero A, Reeves AG, Page ACS, Moon PJ, Miller E, Coulonval K, Crossley SWM, Xie X, He D, Musacchio PZ, Christian AH, McKenna JM, Lewis RA, Fang E, Dovala D, Lu Y, McGregor LM, Schirle M, Tallarico JA, Roger PP, Toste FD, Chang CJ. An Activity-Based Oxaziridine Platform for Identifying and Developing Covalent Ligands for Functional Allosteric Methionine Sites: Redox-Dependent Inhibition of Cyclin-Dependent Kinase 4. J Am Chem Soc 2022; 144:22890-22901. [PMID: 36484997 PMCID: PMC10124963 DOI: 10.1021/jacs.2c04039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Activity-based protein profiling (ABPP) is a versatile strategy for identifying and characterizing functional protein sites and compounds for therapeutic development. However, the vast majority of ABPP methods for covalent drug discovery target highly nucleophilic amino acids such as cysteine or lysine. Here, we report a methionine-directed ABPP platform using Redox-Activated Chemical Tagging (ReACT), which leverages a biomimetic oxidative ligation strategy for selective methionine modification. Application of ReACT to oncoprotein cyclin-dependent kinase 4 (CDK4) as a representative high-value drug target identified three new ligandable methionine sites. We then synthesized a methionine-targeting covalent ligand library bearing a diverse array of heterocyclic, heteroatom, and stereochemically rich substituents. ABPP screening of this focused library identified 1oxF11 as a covalent modifier of CDK4 at an allosteric M169 site. This compound inhibited kinase activity in a dose-dependent manner on purified protein and in breast cancer cells. Further investigation of 1oxF11 found prominent cation-π and H-bonding interactions stabilizing the binding of this fragment at the M169 site. Quantitative mass-spectrometry studies validated 1oxF11 ligation of CDK4 in breast cancer cell lysates. Further biochemical analyses revealed cross-talk between M169 oxidation and T172 phosphorylation, where M169 oxidation prevented phosphorylation of the activating T172 site on CDK4 and blocked cell cycle progression. By identifying a new mechanism for allosteric methionine redox regulation on CDK4 and developing a unique modality for its therapeutic intervention, this work showcases a generalizable platform that provides a starting point for engaging in broader chemoproteomics and protein ligand discovery efforts to find and target previously undruggable methionine sites.
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Affiliation(s)
- Angel Gonzalez-Valero
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Audrey G. Reeves
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Annika C. S. Page
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Patrick J. Moon
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Edward Miller
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Katia Coulonval
- Faculté de Médecine, Institute of Interdisciplinary Research, Université Libre de Bruxelles, Campus Erasme, Brussels 1070, Belgium
| | - Steven W. M. Crossley
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Xiao Xie
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Dan He
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Patricia Z. Musacchio
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Alec H. Christian
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jeffrey M. McKenna
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Richard A. Lewis
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Eric Fang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Dustin Dovala
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Yipin Lu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Lynn M. McGregor
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - John A. Tallarico
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Pierre P. Roger
- Faculté de Médecine, Institute of Interdisciplinary Research, Université Libre de Bruxelles, Campus Erasme, Brussels 1070, Belgium
| | - F. Dean Toste
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
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96
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Dowman LJ, Kulkarni SS, Alegre-Requena JV, Giltrap AM, Norman AR, Sharma A, Gallegos LC, Mackay AS, Welegedara AP, Watson EE, van Raad D, Niederacher G, Huhmann S, Proschogo N, Patel K, Larance M, Becker CFW, Mackay JP, Lakhwani G, Huber T, Paton RS, Payne RJ. Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine. Nat Commun 2022; 13:6885. [PMID: 36371402 PMCID: PMC9653470 DOI: 10.1038/s41467-022-34530-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
The importance of modified peptides and proteins for applications in drug discovery, and for illuminating biological processes at the molecular level, is fueling a demand for efficient methods that facilitate the precise modification of these biomolecules. Herein, we describe the development of a photocatalytic method for the rapid and efficient dimerization and site-specific functionalization of peptide and protein diselenides. This methodology, dubbed the photocatalytic diselenide contraction, involves irradiation at 450 nm in the presence of an iridium photocatalyst and a phosphine and results in rapid and clean conversion of diselenides to reductively stable selenoethers. A mechanism for this photocatalytic transformation is proposed, which is supported by photoluminescence spectroscopy and density functional theory calculations. The utility of the photocatalytic diselenide contraction transformation is highlighted through the dimerization of selenopeptides, and by the generation of two families of protein conjugates via the site-selective modification of calmodulin containing the 21st amino acid selenocysteine, and the C-terminal modification of a ubiquitin diselenide.
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Affiliation(s)
- Luke J. Dowman
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Sameer S. Kulkarni
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Juan V. Alegre-Requena
- grid.47894.360000 0004 1936 8083Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872 USA
| | - Andrew M. Giltrap
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Alexander R. Norman
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Ashish Sharma
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence in Exciton Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Liliana C. Gallegos
- grid.47894.360000 0004 1936 8083Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872 USA
| | - Angus S. Mackay
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Adarshi P. Welegedara
- grid.1001.00000 0001 2180 7477Research School of Chemistry, Australian National University, Canberra, ACT 2601 Australia
| | - Emma E. Watson
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Damian van Raad
- grid.1001.00000 0001 2180 7477Research School of Chemistry, Australian National University, Canberra, ACT 2601 Australia
| | - Gerhard Niederacher
- grid.10420.370000 0001 2286 1424Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Susanne Huhmann
- grid.10420.370000 0001 2286 1424Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Nicholas Proschogo
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia
| | - Karishma Patel
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Mark Larance
- grid.1013.30000 0004 1936 834XCharles Perkins Centre and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Christian F. W. Becker
- grid.10420.370000 0001 2286 1424Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Joel P. Mackay
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Girish Lakhwani
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence in Exciton Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Thomas Huber
- grid.1001.00000 0001 2180 7477Research School of Chemistry, Australian National University, Canberra, ACT 2601 Australia
| | - Robert S. Paton
- grid.47894.360000 0004 1936 8083Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872 USA
| | - Richard J. Payne
- grid.1013.30000 0004 1936 834XSchool of Chemistry, The University of Sydney, Sydney, NSW 2006 Australia ,grid.1013.30000 0004 1936 834XAustralian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006 Australia
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97
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Declas N, Maynard JRJ, Menin L, Gasilova N, Götze S, Sprague JL, Stallforth P, Matile S, Waser J. Tyrosine bioconjugation with hypervalent iodine. Chem Sci 2022; 13:12808-12817. [PMID: 36519034 PMCID: PMC9645396 DOI: 10.1039/d2sc04558c] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/03/2022] [Indexed: 01/24/2023] Open
Abstract
Hypervalent iodine reagents have recently emerged as powerful tools for late-stage peptide and protein functionalization. Herein we report a tyrosine bioconjugation methodology for the introduction of hypervalent iodine onto biomolecules under physiological conditions. Tyrosine residues were engaged in a selective addition onto the alkynyl bond of ethynylbenziodoxolones (EBX), resulting in stable vinylbenziodoxolones (VBX) bioconjugates. The methodology was successfully applied to peptides and proteins and tolerated all other nucleophilic residues, with the exception of cysteine. The generated VBX were further functionalized by palladium-catalyzed cross-coupling and azide-alkyne cycloaddition reactions. The method could be successfully used to modify bioactive natural products and native streptavidin to enable thiol-mediated cellular uptake.
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Affiliation(s)
- Nina Declas
- Laboratory of Catalysis and Organic Synthesis, Institut des Sciences et Ingénierie Chimique, Ecole Polytechnique Fédérale de LausanneCH-1015LausanneSwitzerland
| | - John R. J. Maynard
- Department of Organic Chemistry, University of Geneva1211 GenevaSwitzerland
| | - Laure Menin
- Institut des Sciences et Ingénierie Chimique, Ecole Polytechnique Fédérale de Lausanne, EPFL1015 LausanneSwitzerland
| | - Natalia Gasilova
- Institut des Sciences et Ingénierie Chimique, Ecole Polytechnique Fédérale de Lausanne, EPFL1015 LausanneSwitzerland
| | - Sebastian Götze
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI)07745 JenaGermany
| | - Jakob L. Sprague
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI)07745 JenaGermany
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI)07745 JenaGermany
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva1211 GenevaSwitzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis, Institut des Sciences et Ingénierie Chimique, Ecole Polytechnique Fédérale de LausanneCH-1015LausanneSwitzerland
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98
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Lipka BM, Betti VM, Honeycutt DS, Zelmanovich DL, Adamczyk M, Wu R, Blume HS, Mendina CA, Goldberg JM, Wang F. Rapid Electrophilic Cysteine Arylation with Pyridinium Salts. Bioconjug Chem 2022; 33:2189-2196. [DOI: 10.1021/acs.bioconjchem.2c00419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bradley M. Lipka
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island02881, United States
| | - Vincent M. Betti
- Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, New York13346, United States
| | - Daniel S. Honeycutt
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island02881, United States
| | - Daniel L. Zelmanovich
- Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, New York13346, United States
| | - Max Adamczyk
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island02881, United States
| | - Ruojun Wu
- Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, New York13346, United States
| | - Harrison S. Blume
- Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, New York13346, United States
| | - Caitlin A. Mendina
- Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, New York13346, United States
| | - Jacob M. Goldberg
- Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, New York13346, United States
| | - Fang Wang
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island02881, United States
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99
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Gueta O, Amiram M. Expanding the chemical repertoire of protein-based polymers for drug-delivery applications. Adv Drug Deliv Rev 2022; 190:114460. [PMID: 36030987 DOI: 10.1016/j.addr.2022.114460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 01/24/2023]
Abstract
Expanding the chemical repertoire of natural and artificial protein-based polymers (PBPs) can enable the production of sequence-defined, yet chemically diverse, biopolymers with customized or new properties that cannot be accessed in PBPs composed of only natural amino acids. Various approaches can enable the expansion of the chemical repertoire of PBPs, including chemical and enzymatic treatments or the incorporation of unnatural amino acids. These techniques are employed to install a wide variety of chemical groups-such as bio-orthogonally reactive, cross-linkable, post-translation modifications, and environmentally responsive groups-which, in turn, can facilitate the design of customized PBP-based drug-delivery systems with modified, fine-tuned, or entirely new properties and functions. Here, we detail the existing and emerging technologies for expanding the chemical repertoire of PBPs and review several chemical groups that either demonstrate or are anticipated to show potential in the design of PBP-based drug delivery systems. Finally, we provide our perspective on the remaining challenges and future directions in this field.
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Affiliation(s)
- Osher Gueta
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel
| | - Miriam Amiram
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
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100
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Meziadi A, Zuberi N, de Haan HW, Gauthier MA. Overcoming PEG─Protein Mutual Repulsion to Improve the Efficiency of PEGylation. Biomacromolecules 2022; 23:4948-4956. [DOI: 10.1021/acs.biomac.2c01192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ahlem Meziadi
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes J3X 1S2, Quebec, Canada
| | - Navid Zuberi
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes J3X 1S2, Quebec, Canada
| | - Hendrick W. de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa L1H 7K4, Ontario, Canada
| | - Marc A. Gauthier
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes J3X 1S2, Quebec, Canada
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