1
|
Esteve F, Schmitt JL, Kolodych S, Koniev O, Lehn JM. Selective Protein (Post-)modifications through Dynamic Covalent Chemistry: Self-activated S NAr Reactions. J Am Chem Soc 2025; 147:2049-2060. [PMID: 39746158 DOI: 10.1021/jacs.4c15421] [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: 01/04/2025]
Abstract
SNAr reactions were remarkably accelerated using a pretargeting and activating unit based on dynamic covalent chemistry (DCvC). A Cys attack at the C-F bond on the aromatic ring of salicylaldehyde derivatives was only observed upon iminium formation with a neighboring Lys residue of model small peptides. Such self-activation was ascribed to the stronger electron-withdrawing capability of the iminium bond with respect to that of the parent aldehyde that stabilized the transition state of the reaction, together with the higher preorganization of the reactive groups in the cationic aldiminium species. This approach was further applied for the functionalization of two antibodies. In both cases, the presence of the aldehyde group in close proximity to the reactive C-F bond resulted in a noteworthy increase in bioconjugation yields, with excellent chemo-selectivity. Whereas the modification of an IgG1 antibody led to stochastic product distributions, microenvironment selectivity was noted when employing IgG4, in line with the lower number of Lys residues in the hinge region of the latter. Additionally, the postfunctionalization of the modified antibodies was attained through the dynamic covalent exchange of the tethered iminium derivative with hydrazides, representing an unprecedented "tag and modify" selective bioconjugation strategy based on DCvC.
Collapse
Affiliation(s)
- Ferran Esteve
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, Strasbourg 67000, France
| | - Jean-Louis Schmitt
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, Strasbourg 67000, France
| | | | | | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, Strasbourg 67000, France
| |
Collapse
|
2
|
Abbas SJ, Yesmin S, Vittala SK, Sepay N, Xia F, Ali SI, Chang WC, Hung YC, Ma WL. Target Bioconjugation of Protein Through Chemical, Molecular Dynamics, and Artificial Intelligence Approaches. Metabolites 2024; 14:668. [PMID: 39728449 DOI: 10.3390/metabo14120668] [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: 10/02/2024] [Revised: 11/18/2024] [Accepted: 11/22/2024] [Indexed: 12/28/2024] Open
Abstract
Covalent modification of proteins at specific, predetermined sites is essential for advancing biological and biopharmaceutical applications. Site-selective labeling techniques for protein modification allow us to effectively track biological function, intracellular dynamics, and localization. Despite numerous reports on modifying target proteins with functional chemical probes, unique organic reactions that achieve site-selective integration without compromising native functional properties remain a significant challenge. In this review, we delve into site-selective protein modification using synthetic probes, highlighting both chemical and computational methodologies for chemo- and regioselective modifications of naturally occurring amino acids, as well as proximity-driven protein-selective chemical modifications. We also underline recent traceless affinity labeling strategies that involve exchange/cleavage reactions and catalyst tethering modifications. The rapid development of computational infrastructure and methods has made the bioconjugation of proteins more accessible, enabling precise predictions of structural changes due to protein modifications. Hence, we discuss bioconjugational computational approaches, including molecular dynamics and artificial intelligence, underscoring their potential applications in enhancing our understanding of cellular biology and addressing current challenges in the field.
Collapse
Affiliation(s)
- Sk Jahir Abbas
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
- Department of Obstetrics and Gynecology, Asia University Hospital, Taichung 41354, Taiwan
| | - Sabina Yesmin
- Institute of Chemistry, Academia Sinica, Taipei 115201, Taiwan
- Department of Physics, National Dong Hwa University, Hualien 97401, Taiwan
| | - Sandeepa K Vittala
- Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands
| | - Nayim Sepay
- Department of Chemistry, Lady Brabourne College, Kolkata 700017, India
| | - Fangfang Xia
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Centre, Houston, TX 77030, USA
| | - Sk Imran Ali
- Department of Chemistry, University of Kalyani, Kalyani 741235, India
| | - Wei-Chun Chang
- Ph.D. Program for Health Science and Industry, China Medical University, Taichung 40402, Taiwan
- Department of Medical Research, Department of Obstetrics and Gynecology, China Medical University Hospital, Taichung 40402, Taiwan
| | - Yao-Ching Hung
- Department of Obstetrics and Gynecology, Asia University Hospital, Taichung 41354, Taiwan
| | - Wen-Lung Ma
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
- Department of Medical Research, Department of Obstetrics and Gynecology, China Medical University Hospital, Taichung 40402, Taiwan
| |
Collapse
|
3
|
Wang W, Zhang L, Liu Y, Liu X, Liu X. Oriental covalent immobilization of N-glycan binding protein via N-terminal selective modification. Anal Chim Acta 2024; 1330:343311. [PMID: 39489947 DOI: 10.1016/j.aca.2024.343311] [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: 04/16/2024] [Revised: 09/17/2024] [Accepted: 10/06/2024] [Indexed: 11/05/2024]
Abstract
Lectin affinity chromatography is one of powerful tools for the study of protein glycosylation. Different lectin proteins can recognize different structures of monosaccharides or oligosaccharide units, allowing for the selective separation of glycopeptides or glycoproteins containing different polysaccharide structures. However, the N-glycans were only partially captured by most of common lectins, reducing the coverage rate of identifying N-glycoconjugates. Recently, it has been reported that the engineering variant of glycan binding protein Fbs1 has a high affinity for innermost Man3GlcNAc2 structure and is able to bind diverse types of N-glycans, which can be suitable for the analysis of protein N-glycosylation. However, efficient immobilization of protein to separation matrix is particularly challenging as it requires the functionality and integrity of the protein to be preserved. Herein, we describe a simple and robust strategy for oriental covalent immobilization of proteins on magnetic nanoparticles by N-terminal selective labeling techniques. We inserted the enterokinase cleavage site to produce the specific N- terminal glycine of protein. Under physiological conditions, the protein was immobilized on the surface of the MNPs by this glycine tag, and the enrichment process could be completed within 30 min. A whole enrichment and purification of glycan and glycopeptides were completed and analyzed by MALDI TOF-MS. The functional materials achieved stable enrichment of glycan structure in different enzyme digestion systems or complex samples, showing excellent anti-interference and applicability.
Collapse
Affiliation(s)
- Wenhui Wang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Liang Zhang
- Hubei Superior Discipline Group of Exercise and Brain Science from Hubei Provincial, Wuhan Sports University, Wuhan, 430079, China
| | - Yuanyuan Liu
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xiang Liu
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China; Department of Laboratory Medicine, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430016, China
| | - Xin Liu
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| |
Collapse
|
4
|
Cai Y. Conjugation of primary amine groups in targeted proteomics. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39229771 DOI: 10.1002/mas.21906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/21/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024]
Abstract
Primary amines, in the form of unmodified N-terminus of peptide/protein and unmodified lysine residue, are perhaps the most important functional groups that can serve as the starting points in proteomic analysis, especially via mass spectrometry-based approaches. A variety of multifunctional probes that conjugate primary amine groups through covalent bonds have been developed and employed to facilitate protein/protein complex characterization, including identification, quantification, structure and localization elucidation, protein-protein interaction investigation, and so forth. As an integral part of more accurate peptide quantification in targeted proteomics, isobaric stable isotope-coded primary amine labeling approaches eventually facilitated protein/peptide characterization at the single-cell level, paving the way for single-cell proteomics. The development and advances in the field can be reviewed in terms of key components of a multifunctional probe: functional groups and chemistry for primary amine conjugation; hetero-bifunctional moiety for separation/enrichment of conjugated protein/protein complex; and functionalized linker/spacer. Perspectives are primarily focused on optimizing primary amine conjugation under physiological conditions to improve characterization of native proteins, especially those associated with the surface of living cells/microorganisms.
Collapse
Affiliation(s)
- Yang Cai
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, USA
| |
Collapse
|
5
|
Sen S, Ali R, Onkar A, Verma S, Ahmad QT, Bhadauriya P, Sinha P, Nair NN, Ganesh S, Verma S. Synthesis of a highly thermostable insulin by phenylalanine conjugation at B29 Lysine. Commun Chem 2024; 7:161. [PMID: 39043846 PMCID: PMC11266353 DOI: 10.1038/s42004-024-01241-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 07/10/2024] [Indexed: 07/25/2024] Open
Abstract
Globally, millions of diabetic patients require daily life-saving insulin injections. Insulin heat-lability and fibrillation pose significant challenges, especially in parts of the world without ready access to uninterrupted refrigeration. Here, we have synthesized four human insulin analogs by conjugating ε-amine of B29 lysine of insulin with acetic acid, phenylacetic acid, alanine, and phenylalanine residues. Of these, phenylalanine-conjugated insulin, termed FHI, was the most stable under high temperature (65 °C), elevated salt stress (25 mM NaCl), and varying pH levels (ranging from highly acidic pH 1.6 to physiological pH 7.4). It resists fibrillation for a significantly longer duration with sustained biological activity in in vitro, ex vivo, and in vivo and displays prolonged stability over its native counterpart. We further unravel the critical interactions, such as additional aromatic π-π interactions and hydrogen bonding in FHI, that are notably absent in native insulin. These interactions confer enhanced structural stability of FHI and offer a promising solution to the challenges associated with insulin heat sensitivity.
Collapse
Affiliation(s)
- Shantanu Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Rafat Ali
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Akanksha Onkar
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Shivani Verma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Quazi Taushif Ahmad
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Pratibha Bhadauriya
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Pradip Sinha
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Subramaniam Ganesh
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
- Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology, Kanpur, 208016, UP, India
- Gangwal School of Medical Sciences and Technology, Indian Institute of Technology, Kanpur, 208016, UP, India
| | - Sandeep Verma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India.
- Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology, Kanpur, 208016, UP, India.
- Gangwal School of Medical Sciences and Technology, Indian Institute of Technology, Kanpur, 208016, UP, India.
| |
Collapse
|
6
|
Esteve F, Rieu T, Lehn JM. Key structural features to favour imines over hydrates in water: pyridoxal phosphate as a muse. Chem Sci 2024; 15:10408-10415. [PMID: 38994419 PMCID: PMC11234862 DOI: 10.1039/d4sc02206h] [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: 04/03/2024] [Accepted: 06/10/2024] [Indexed: 07/13/2024] Open
Abstract
Imination reactions in water represent a challenge not only because of the high propensity of imines to be hydrolysed but also as a result of the competing hydrate formation through H2O addition to the aldehyde. In the present work we report a successful approach that allows for favouring imitation reactions while silencing hydrate formation. Such remarkable reactivity and selectivity can be attained by fine-tuning the electronic and steric structural features of the ortho-substituents of the carbonyl groups. It resulted from studying the structure-reactivity relationships in a series of condensation reactions between different amines and aldehydes, comparing the results to the ones obtained in the presence of the biologically-relevant pyridoxal phosphate (PLP). The key role of negatively-charged and sterically-crowding units (i.e., sulfonate groups) in disfavouring hydrate formation was corroborated by DFT and steric-hindrance calculations. Furthermore, the best-performing aldehyde leads to higher imine yields, selectivity and stability than those of PLP itself, allowing for the inhibition of a PLP-dependent enzyme (transaminase) through dynamic aldimine exchange. These results will increase the applicability of imine-based dynamic covalent chemistry (DCvC) under physiological conditions and will pave the way for the design of new carbonyl derivatives that might be used in the dynamic modification of biomolecules.
Collapse
Affiliation(s)
- Ferran Esteve
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg 8 allée Gaspard Monge Strasbourg 67000 France
| | - Tanguy Rieu
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg 8 allée Gaspard Monge Strasbourg 67000 France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg 8 allée Gaspard Monge Strasbourg 67000 France
| |
Collapse
|
7
|
Liu H, Deol H, Raeisbahrami A, Askari H, Wight CD, Lynch VM, Anslyn EV. A Method for Rigorously Selective Capture and Simultaneous Fluorescent Labeling of N-Terminal Glycine Peptides. J Am Chem Soc 2024; 146:13727-13732. [PMID: 38728661 PMCID: PMC11776846 DOI: 10.1021/jacs.4c04141] [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] [Indexed: 05/12/2024]
Abstract
Although chemical methods for the selective derivatization of amino acid (AA) side chains in peptides and proteins are available, selective N-terminal labeling is challenging, especially for glycine, which has no side chain at the α-carbon position. We report here a double activation at glycine's α-methylene group that allows this AA to be differentiated from the other 19 AAs. A condensation reaction of dibenzoylmethane with glycine results in the formation of an imine, and subsequent tautomerization is followed by intramolecular cyclization, leading to the formation of a fluorescent pyrrole ring. Additionally, the approach exhibits compatibility with AAs possessing reactive side chains. Further, the method allows for selective pull-down assays of N-terminal glycine peptides from mixtures without prior knowledge of the N-terminal peptide distribution.
Collapse
Affiliation(s)
- Hongxu Liu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Harnimarta Deol
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ava Raeisbahrami
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Hadis Askari
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Christopher D Wight
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Vincent M Lynch
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
8
|
Hampton JT, Liu WR. Diversification of Phage-Displayed Peptide Libraries with Noncanonical Amino Acid Mutagenesis and Chemical Modification. Chem Rev 2024; 124:6051-6077. [PMID: 38686960 PMCID: PMC11082904 DOI: 10.1021/acs.chemrev.4c00004] [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: 01/02/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Sitting on the interface between biologics and small molecules, peptides represent an emerging class of therapeutics. Numerous techniques have been developed in the past 30 years to take advantage of biological methods to generate and screen peptide libraries for the identification of therapeutic compounds, with phage display being one of the most accessible techniques. Although traditional phage display can generate billions of peptides simultaneously, it is limited to expression of canonical amino acids. Recently, several groups have successfully undergone efforts to apply genetic code expansion to introduce noncanonical amino acids (ncAAs) with novel reactivities and chemistries into phage-displayed peptide libraries. In addition to biological methods, several different chemical approaches have also been used to install noncanonical motifs into phage libraries. This review focuses on these recent advances that have taken advantage of both biological and chemical means for diversification of phage libraries with ncAAs.
Collapse
Affiliation(s)
- J. Trae Hampton
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe Ray Liu
- Texas
A&M Drug Discovery Center and Department of Chemistry, College
of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States
- Institute
of Biosciences and Technology and Department of Translational Medical
Sciences, College of Medicine, Texas A&M
University, Houston, Texas 77030, United States
- Department
of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas 77843, United States
- Department
of Cell Biology and Genetics, College of Medicine, Texas A&M University, College
Station, Texas 77843, United States
- Department
of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
9
|
Zhang M, Zhou N, Zhao L, Zhao L. Black rice anthocyanins nanoparticles based on bovine serum albumin and hyaluronic acid: Preparation, characterization, absorption and intestinal barrier function protection in Caco-2 monolayers. Int J Biol Macromol 2024; 267:131325. [PMID: 38604425 DOI: 10.1016/j.ijbiomac.2024.131325] [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: 11/30/2023] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 04/13/2024]
Abstract
Black rice anthocyanins (BRA) nanoparticles (NPs) were prepared using hyaluronic acid (HA), oxidized hyaluronic acid (OHA) and bovine serum albumin (BSA) to enhance the absorption and bioactivity of anthocyanins (ACNs). Results showed that HA/OHA-BSA-BRA NPs had a spherical morphology and excellent dispensability, with hydrated radius ~ 500 nm, zeta potential ~ - 30 mV, and encapsulation efficiency ~21 %. Moreover, using in vitro gastrointestinal release assay, we demonstrated that both BRA-loaded NPs exhibited effective controlled release properties of ACNs, significantly enhancing the accessibility of ACNs to the intestine. Cellular experiments showed that both two NPs had good biocompatibility and increased uptake of BRA. Furthermore, in comparison to the free BRA group, both BRA NPs groups significantly decreased the TEER value and increased the expression of tight junction proteins (Claudin 1, Occludin and ZO-1) in Caco-2 cell monolayers with LPS-induced damage. Therefore, our study demonstrated that HA/OHA-BSA-BRA NPs are promising carriers of ACNs and can effectively prevent the LPS-induced intestinal barrier injury in vitro.
Collapse
Affiliation(s)
- Mingxin Zhang
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China; Key Laboratory of Green Manufacturing and Biosynthesis of Food Bioactive Substances, China General Chamber of Commerce, 100048, China
| | - Na Zhou
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China; Key Laboratory of Green Manufacturing and Biosynthesis of Food Bioactive Substances, China General Chamber of Commerce, 100048, China
| | - Lei Zhao
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China; Key Laboratory of Green Manufacturing and Biosynthesis of Food Bioactive Substances, China General Chamber of Commerce, 100048, China.
| | - Liang Zhao
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing 100048, China; Key Laboratory of Green Manufacturing and Biosynthesis of Food Bioactive Substances, China General Chamber of Commerce, 100048, China.
| |
Collapse
|
10
|
Machida H, Kanemoto K. N-Terminal-Specific Dual Modification of Peptides through Copper-Catalyzed [3+2] Cycloaddition. Angew Chem Int Ed Engl 2024; 63:e202320012. [PMID: 38282290 DOI: 10.1002/anie.202320012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 01/30/2024]
Abstract
Site-specific introduction of multiple components into peptides is greatly needed for the preparation of densely functionalized and structurally uniform peptides. In this regard, N-terminal-specific peptide modification is attractive, but it can be difficult due to the presence of highly nucleophilic lysine ϵ-amine. In this work, we developed a method for the N-terminal-specific dual modification of peptides through a three-component [3+2] cycloaddition with aldehydes and maleimides under mild copper catalysis. This approach enables exclusive functionalization at the glycine N-terminus of iminopeptides, regardless of the presence of lysine ϵ-amine, thus affording the cycloadducts in excellent yields. Tolerating a broad range of functional groups and molecules, the present method provides the opportunity to rapidly construct doubly functionalized peptides using readily accessible aldehyde and maleimide modules.
Collapse
Affiliation(s)
- Haruka Machida
- Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Kazuya Kanemoto
- Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga Bunkyo-ku, Tokyo, 112-8551, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| |
Collapse
|
11
|
Koutsopetras I, Vaur V, Benazza R, Diemer H, Sornay C, Ersoy Y, Rochet L, Longo C, Hernandez-Alba O, Erb S, Detappe A, Skerra A, Wagner A, Cianferani S, Chaubet G. Site-Selective Protein Conjugation by a Multicomponent Ugi Reaction. Chemistry 2024; 30:e202303242. [PMID: 38050774 DOI: 10.1002/chem.202303242] [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: 10/03/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
The chemical bioconjugation of proteins has seen tremendous applications in the past decades, with the booming of antibody-drug conjugates and their use in oncology. While genetic engineering has permitted to produce bespoke proteins featuring key (un-)natural amino acid residues poised for site-selective modifications, the conjugation of native proteins is riddled with selectivity issues. Chemoselective strategies are plentiful and enable the precise modification of virtually any residue with a reactive side-chain; site-selective methods are less common and usually most effective on small and medium-sized proteins. In this context, we studied the application of the Ugi multicomponent reaction for the site-selective conjugation of amine and carboxylate groups on proteins, and antibodies in particular. Through an in-depth mechanistic methodology work supported by peptide mapping studies, we managed to develop a set of conditions allowing the highly selective modification of antibodies bearing N-terminal glutamate and aspartate residues. We demonstrated that this strategy did not alter their affinity toward their target antigen and produced an antibody-drug conjugate with subnanomolar potency. Excitingly, we showed that the high site selectivity of our strategy was maintained on other protein formats, especially on anticalins, for which directed mutagenesis helped to highlight the key importance of a single lysine residue.
Collapse
Affiliation(s)
- Ilias Koutsopetras
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Rania Benazza
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | - Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Yağmur Ersoy
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany
| | - Léa Rochet
- Department of Chemistry, University College London, London, UK
| | - Carmen Longo
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | | | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087, Strasbourg, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| |
Collapse
|
12
|
De Jesus IS, Vélez JAC, Pissinati EF, Correia JTM, Rivera DG, Paixao MW. Recent Advances in Photoinduced Modification of Amino Acids, Peptides, and Proteins. CHEM REC 2024; 24:e202300322. [PMID: 38279622 DOI: 10.1002/tcr.202300322] [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: 10/09/2023] [Revised: 12/01/2023] [Indexed: 01/28/2024]
Abstract
The chemical modification of biopolymers like peptides and proteins is a key technology to access vaccines and pharmaceuticals. Similarly, the tunable derivatization of individual amino acids is important as they are key building blocks of biomolecules, bioactive natural products, synthetic polymers, and innovative materials. The high diversity of functional groups present in amino acid-based molecules represents a significant challenge for their selective derivatization Recently, visible light-mediated transformations have emerged as a powerful strategy for achieving chemoselective biomolecule modification. This technique offers numerous advantages over other methods, including a higher selectivity, mild reaction conditions and high functional-group tolerance. This review provides an overview of the most recent methods covering the photoinduced modification for single amino acids and site-selective functionalization in peptides and proteins under mild and even biocompatible conditions. Future challenges and perspectives are discussed beyond the diverse types of photocatalytic transformations that are currently available.
Collapse
Affiliation(s)
- Iva S De Jesus
- Laboratory for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos - UFSCar, São Carlos, São Paulo, 13565-905, Brazil
| | - Jeimy A C Vélez
- Laboratory for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos - UFSCar, São Carlos, São Paulo, 13565-905, Brazil
| | - Emanuele F Pissinati
- Laboratory for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos - UFSCar, São Carlos, São Paulo, 13565-905, Brazil
| | - Jose Tiago M Correia
- Laboratory for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos - UFSCar, São Carlos, São Paulo, 13565-905, Brazil
| | - Daniel G Rivera
- Laboratory of Synthetic and Biomolecular Chemistry, Faculty of Chemistry, University of Havana Zapata & G, Havana, 10400, Cuba
| | - Márcio W Paixao
- Laboratory for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos - UFSCar, São Carlos, São Paulo, 13565-905, Brazil
| |
Collapse
|
13
|
Schlotter T, Kloter T, Hengsteler J, Yang K, Zhan L, Ragavan S, Hu H, Zhang X, Duru J, Vörös J, Zambelli T, Nakatsuka N. Aptamer-Functionalized Interface Nanopores Enable Amino Acid-Specific Peptide Detection. ACS NANO 2024; 18:6286-6297. [PMID: 38355286 PMCID: PMC10906075 DOI: 10.1021/acsnano.3c10679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
Single-molecule proteomics based on nanopore technology has made significant advances in recent years. However, to achieve nanopore sensing with single amino acid resolution, several bottlenecks must be tackled: controlling nanopore sizes with nanoscale precision and slowing molecular translocation events. Herein, we address these challenges by integrating amino acid-specific DNA aptamers into interface nanopores with dynamically tunable pore sizes. A phenylalanine aptamer was used as a proof-of-concept: aptamer recognition of phenylalanine moieties led to the retention of specific peptides, slowing translocation speeds. Importantly, while phenylalanine aptamers were isolated against the free amino acid, the aptamers were determined to recognize the combination of the benzyl or phenyl and the carbonyl group in the peptide backbone, enabling binding to specific phenylalanine-containing peptides. We decoupled specific binding between aptamers and phenylalanine-containing peptides from nonspecific interactions (e.g., electrostatics and hydrophobic interactions) using optical waveguide lightmode spectroscopy. Aptamer-modified interface nanopores differentiated peptides containing phenylalanine vs. control peptides with structurally similar amino acids (i.e., tyrosine and tryptophan). When the duration of aptamer-target interactions inside the nanopore were prolonged by lowering the applied voltage, discrete ionic current levels with repetitive motifs were observed. Such reoccurring signatures in the measured signal suggest that the proposed method has the possibility to resolve amino acid-specific aptamer recognition, a step toward single-molecule proteomics.
Collapse
Affiliation(s)
- Tilman Schlotter
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Tom Kloter
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Julian Hengsteler
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Kyungae Yang
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Lijian Zhan
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Sujeni Ragavan
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Haiying Hu
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Xinyu Zhang
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Jens Duru
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - János Vörös
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Tomaso Zambelli
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Nako Nakatsuka
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| |
Collapse
|
14
|
Chauhan P, V R, Kumar M, Molla R, Mishra SD, Basa S, Rai V. Chemical technology principles for selective bioconjugation of proteins and antibodies. Chem Soc Rev 2024; 53:380-449. [PMID: 38095227 DOI: 10.1039/d3cs00715d] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Proteins are multifunctional large organic compounds that constitute an essential component of a living system. Hence, control over their bioconjugation impacts science at the chemistry-biology-medicine interface. A chemical toolbox for their precision engineering can boost healthcare and open a gateway for directed or precision therapeutics. Such a chemical toolbox remained elusive for a long time due to the complexity presented by the large pool of functional groups. The precise single-site modification of a protein requires a method to address a combination of selectivity attributes. This review focuses on guiding principles that can segregate them to simplify the task for a chemical method. Such a disintegration systematically employs a multi-step chemical transformation to deconvolute the selectivity challenges. It constitutes a disintegrate (DIN) theory that offers additional control parameters for tuning precision in protein bioconjugation. This review outlines the selectivity hurdles faced by chemical methods. It elaborates on the developments in the perspective of DIN theory to demonstrate simultaneous regulation of reactivity, chemoselectivity, site-selectivity, modularity, residue specificity, and protein specificity. It discusses the progress of such methods to construct protein and antibody conjugates for biologics, including antibody-fluorophore and antibody-drug conjugates (AFCs and ADCs). It also briefs how this knowledge can assist in developing small molecule-based covalent inhibitors. In the process, it highlights an opportunity for hypothesis-driven routes to accelerate discoveries of selective methods and establish new targetome in the precision engineering of proteins and antibodies.
Collapse
Affiliation(s)
- Preeti Chauhan
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Ragendu V
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Rajib Molla
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Surya Dev Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Sneha Basa
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| |
Collapse
|
15
|
Zhang Y, Hung-Chieh Chou D. From Natural Insulin to Designed Analogs: A Chemical Biology Exploration. Chembiochem 2023; 24:e202300470. [PMID: 37800626 DOI: 10.1002/cbic.202300470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/25/2023] [Indexed: 10/07/2023]
Abstract
Since its discovery in 1921, insulin has been at the forefront of scientific breakthroughs. From its amino acid sequencing to the revelation of its three-dimensional structure, the progress in insulin research has spurred significant therapeutic breakthroughs. In recent years, protein engineering has introduced innovative chemical and enzymatic methods for insulin modification, fostering the development of therapeutics with tailored pharmacological profiles. Alongside these advances, the quest for self-regulated, glucose-responsive insulin remains a holy grail in the field. In this article, we highlight the pivotal role of chemical biology in driving these innovations and discuss how it continues to shape the future trajectory of insulin research.
Collapse
Affiliation(s)
- Yanxian Zhang
- Division of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University, 1701 Page Mill Road, Palo Alto, CA 94304, USA
| | - Danny Hung-Chieh Chou
- Division of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University, 1701 Page Mill Road, Palo Alto, CA 94304, USA
| |
Collapse
|
16
|
Zielke FM, Rutjes FPJT. Recent Advances in Bioorthogonal Ligation and Bioconjugation. Top Curr Chem (Cham) 2023; 381:35. [PMID: 37991570 PMCID: PMC10665463 DOI: 10.1007/s41061-023-00445-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
The desire to create biomolecules modified with functionalities that go beyond nature's toolbox has resulted in the development of biocompatible and selective methodologies and reagents, each with different scope and limitations. In this overview, we highlight recent advances in the field of bioconjugation from 2016 to 2023. First, (metal-mediated) protein functionalization by exploiting the specific reactivity of amino acids will be discussed, followed by novel bioorthogonal reagents for bioconjugation of modified biomolecules.
Collapse
Affiliation(s)
- Florian M Zielke
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| |
Collapse
|
17
|
Esteve F, Rahmatova F, Lehn JM. Supramolecular multivalency effects enhance imine formation in aqueous medium allowing for dynamic modification of enzymatic activity. Chem Sci 2023; 14:10249-10257. [PMID: 37772124 PMCID: PMC10530293 DOI: 10.1039/d3sc04128j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023] Open
Abstract
Imine formation under physiological conditions represents a challenging reaction due to the strong propensity of aldimines to be hydrolyzed. Herein we disclose the remarkable effect of supramolecular multivalency on increasing imine stability. A family of reactive aldehydes was synthesized bearing supramolecularly-active sites within their structure. The imine formation activity for such aldehydes was evaluated and compared with model aldehydes. The reaction of the best-performing species - containing two carboxylate groups-with a set of amines showed a significant decrease in imine yields as the degree of supramolecular multivalency between sidechains decreased. The reversible conjugation of amino acid derivatives and small peptides was also assayed, with excellent selectivities for the imine formation at the Nα position even in substrates containing competing sites. Preliminary results on protein bioconjugation revealed that a model enzyme could be dynamically inhibited upon reaction with the aldehyde, with its native activity being recovered by displacing the imine bonds with a suitable chemical effector (i.e., acylhydrazide).
Collapse
Affiliation(s)
- Ferran Esteve
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg 8 allée Gaspard Monge 67000 Strasbourg France
| | - Fidan Rahmatova
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg 8 allée Gaspard Monge 67000 Strasbourg France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg 8 allée Gaspard Monge 67000 Strasbourg France
| |
Collapse
|
18
|
Hossain MS, Shovon MTI, Hasan MR, Hakim FT, Hasan MM, Esha SA, Tasnim S, Nazir MS, Akhter F, Ali MA, Halim MA. Therapeutic Potential of Antiviral Peptides against the NS2B/NS3 Protease of Zika Virus. ACS OMEGA 2023; 8:35207-35218. [PMID: 37779969 PMCID: PMC10536883 DOI: 10.1021/acsomega.3c04903] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023]
Abstract
The NS2B/NS3 protease is highly conserved among various proteases of the Zika virus, making it an important therapeutic target for developing broad-spectrum antiviral drugs. The NS2B/NS3 protease is a crucial enzyme in the replication cycle of Zika virus and plays a significant role in viral maturation and assembly. Inhibiting the activity of this protease can potentially prevent viral replication, making it an attractive target for developing therapies against Zika virus infection. This work screens 429 antiviral peptides in comparison with substrate peptide against the NS2B/NS3 of Zika virus using molecular docking and molecular dynamics (MD) simulation. Based on the docking screening, MD simulation conducted for the best four peptides including AVP0239, AVP0642, AVP0660, and AVP2044, could be effective against NS2B/NS3. These results were compared with the control substrate peptide. Further analysis indicates that AVP0642 and AVP2044 are the most promising candidates. The interaction analysis showed that the catalytic site residues including His51, Asp75, Ser135 and other non-catalytic residues such as Asp129, Asp83, and Asp79 contribute substantial interactions. Hydrogen bonds (41%) and hydrophobic interactions (33%) are observed as the prominent non-covalent interaction prompting the peptide-protein complex formation. Furthermore, the structure-activity relationship (SAR) illustrates that positively charged (Lys, Arg) residues in the peptides dominate the interactions. This study provides the basis for developing novel peptide-based protease inhibitors for Zika virus.
Collapse
Affiliation(s)
- Md. Shahadat Hossain
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Md. Tanjil Islam Shovon
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Md. Rafid Hasan
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Fuad Taufiqul Hakim
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Mohammad Mehedi Hasan
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Sadia Afrose Esha
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Sabiha Tasnim
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Md. Shahoriar Nazir
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Fahmida Akhter
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department
of Chemistry and Biochemistry, Kennesaw
State University, Kennesaw, Georgia 30144, United States
| | - Mohammad A. Halim
- Department
of Chemistry and Biochemistry, Kennesaw
State University, Kennesaw, Georgia 30144, United States
| |
Collapse
|
19
|
Kurbanov M, Kirsch ZJ, Krishna J, Dutta R, Vachet RW, Thayumanavan S. Multisite Labeling of Proteins Using the Ligand-Directed Reactivity of Triggerable Michael Acceptors. Bioconjug Chem 2023; 34:1130-1138. [PMID: 37220065 PMCID: PMC10363337 DOI: 10.1021/acs.bioconjchem.3c00155] [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] [Indexed: 05/25/2023]
Abstract
Targeted modification of endogenous proteins without genetic manipulation of protein expression machinery has a range of applications from chemical biology to drug discovery. Despite being demonstrated to be effective in various applications, target-specific protein labeling using ligand-directed strategies is limited by stringent amino acid selectivity. Here, we present highly reactive ligand-directed triggerable Michael acceptors (LD-TMAcs) that feature rapid protein labeling. Unlike previous approaches, the unique reactivity of LD-TMAcs enables multiple modifications on a single target protein, effectively mapping the ligand binding site. This capability is attributed to the tunable reactivity of TMAcs that enable the labeling of several amino acid functionalities via a binding-induced increase in local concentration while remaining fully dormant in the absence of protein binding. We demonstrate the target selectivity of these molecules in cell lysates using carbonic anhydrase as the model protein. Furthermore, we demonstrate the utility of this method by selectively labeling membrane-bound carbonic anhydrase XII in live cells. We envision that the unique features of LD-TMAcs will find use in target identification, investigation of binding/allosteric sites, and studying membrane proteins.
Collapse
Affiliation(s)
- Myrat Kurbanov
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Zachary J Kirsch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Jithu Krishna
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Ranit Dutta
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - S Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| |
Collapse
|
20
|
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: 1.0] [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.
Collapse
|
21
|
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: 19] [Impact Index Per Article: 9.5] [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.
Collapse
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
| |
Collapse
|
22
|
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: 7] [Impact Index Per Article: 3.5] [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.
Collapse
|
23
|
Barber LJ, Yates NDJ, Fascione MA, Parkin A, Hemsworth GR, Genever PG, Spicer CD. Selectivity and stability of N-terminal targeting protein modification chemistries. RSC Chem Biol 2023; 4:56-64. [PMID: 36685256 PMCID: PMC9811658 DOI: 10.1039/d2cb00203e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
Protein N-termini provide uniquely reactive motifs for single site protein modification. Though a number of reactions have been developed to target this site, the selectivity, generality, and stability of the conjugates formed has not been studied. We have therefore undertaken a comprehensive comparative study of the most promising methods for N-terminal protein modification, and find that there is no 'one size fits all' approach, necessitating reagent screening for a particular protein or application. Moreover, we observed limited stability in all cases, leading to a need for continued innovation and development in the bioconjugation field.
Collapse
Affiliation(s)
- Lydia J Barber
- Department of Chemistry, University of York Heslington YO10 5DD UK
- York Biomedical Research Institute, University of York Heslington YO10 5DD UK
- Department of Biology, University of York Heslington YO10 5DD UK
| | - Nicholas D J Yates
- Department of Chemistry, University of York Heslington YO10 5DD UK
- York Biomedical Research Institute, University of York Heslington YO10 5DD UK
| | - Martin A Fascione
- Department of Chemistry, University of York Heslington YO10 5DD UK
- York Biomedical Research Institute, University of York Heslington YO10 5DD UK
| | - Alison Parkin
- Department of Chemistry, University of York Heslington YO10 5DD UK
| | - Glyn R Hemsworth
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds Leeds LS2 9JT UK
| | - Paul G Genever
- York Biomedical Research Institute, University of York Heslington YO10 5DD UK
- Department of Biology, University of York Heslington YO10 5DD UK
| | - Christopher D Spicer
- Department of Chemistry, University of York Heslington YO10 5DD UK
- York Biomedical Research Institute, University of York Heslington YO10 5DD UK
- Department of Biology, University of York Heslington YO10 5DD UK
| |
Collapse
|
24
|
Ahmad A, Akram W, Wang R, Shahzadi I, Umer M, Yasin NA, Wu T. Pathogenicity factors of Phytophthora melonis revealed by comparative proteomics. JOURNAL OF PLANT INTERACTIONS 2022; 17:183-197. [DOI: 10.1080/17429145.2021.2014581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/01/2021] [Indexed: 06/16/2023]
Affiliation(s)
- Aqeel Ahmad
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences (IFA, GDAAS) / Vegetable Research Institute, Guangdong Academy of Agriculture Sciences / Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, People’s Republic of China
| | - Waheed Akram
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Rui Wang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences (IFA, GDAAS) / Vegetable Research Institute, Guangdong Academy of Agriculture Sciences / Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, People’s Republic of China
| | - Iqra Shahzadi
- Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, Hubei Engineering Center of Natural Polymers-based Medical Materials, School of Resource and Environmental Science, Wuhan University, Wuhan, People’s Republic of China
| | - Muhammad Umer
- Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, People’s Republic of China
- Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
| | | | - Tingquan Wu
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences (IFA, GDAAS) / Vegetable Research Institute, Guangdong Academy of Agriculture Sciences / Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, People’s Republic of China
| |
Collapse
|
25
|
Thakur K, T K S, Singh SK, V R, Rawale DG, Adusumalli SR, Kalra N, Shukla S, Mishra RK, Rai V. Human Behavior-Inspired Linchpin-Directed Catalysis for Traceless Precision Labeling of Lysine in Native Proteins. Bioconjug Chem 2022; 33:2370-2380. [PMID: 36383773 DOI: 10.1021/acs.bioconjchem.2c00454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The complex social ecosystem regulates the spectrum of human behavior. However, it becomes relatively easier to understand if we disintegrate the contributing factors, such as locality and interacting partners. Interestingly, it draws remarkable similarity with the behavior of a residue placed in a social setup of functional groups in a protein. Can it inspire principles for creating a unique environment for the precision engineering of proteins? We demonstrate that localization-regulated interacting partner(s) could render precise and traceless single-site modification of structurally diverse native proteins. The method targets a combination of high-frequency Lys residues through an array of reversible and irreversible reactions. However, excellent simultaneous control over chemoselectivity, site selectivity, and modularity ensures that the user-friendly protocol renders acyl group installation, including post-translational modifications (PTMs), on a single Lys. Besides, it offers a chemically orthogonal handle for the installation of probes. Also, a purification protocol integration delivers analytically pure single-site tagged protein bioconjugates. The precise labeling of a surface Lys residue ensures that the structure and enzymatic activities remain conserved post-bioconjugation. For example, the precise modification of insulin does not affect its uptake and downstream signaling pathway. Further, the method enables the synthesis of homogeneous antibody-fluorophore and antibody-drug conjugates (AFC and ADC; K183 and K249 labeling). The trastuzumab-rhodamine B conjugate displays excellent serum stability along with antigen-specific cellular imaging. Further, the trastuzumab-emtansine conjugate offers highly specific antiproliferative activity toward HER-2 positive SKBR-3 breast cancer cells. This work validates that disintegrate theory can create a comprehensive platform to enrich the chemical toolbox to meet the technological demands at the chemistry, biology, and medicine interface.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Neetu Kalra
- School of Bioengineering, VIT Bhopal, Bhopal 466114, Madhya Pradesh, India
| | | | | | | |
Collapse
|
26
|
Reddy NC, Molla R, Joshi PN, T. K. S, Basu I, Kawadkar J, Kalra N, Mishra RK, Chakrabarty S, Shukla S, Rai V. Traceless cysteine-linchpin enables precision engineering of lysine in native proteins. Nat Commun 2022; 13:6038. [PMID: 36229616 PMCID: PMC9561114 DOI: 10.1038/s41467-022-33772-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
The maintenance of machinery requires its operational understanding and a toolbox for repair. The methods for the precision engineering of native proteins meet a similar requirement in biosystems. Its success hinges on the principles regulating chemical reactions with a protein. Here, we report a technology that delivers high-level control over reactivity, chemoselectivity, site-selectivity, modularity, dual-probe installation, and protein-selectivity. It utilizes cysteine-based chemoselective Linchpin-Directed site-selective Modification of lysine residue in a protein (LDMC-K). The efficiency of the end-user-friendly protocol is evident in quantitative conversions within an hour. A chemically orthogonal C-S bond-formation and bond-dissociation are essential among multiple regulatory attributes. The method offers protein selectivity by targeting a single lysine residue of a single protein in a complex biomolecular mixture. The protocol renders analytically pure single-site probe-engineered protein bioconjugate. Also, it provides access to homogeneous antibody conjugates (AFC and ADC). The LDMC-K-ADC exhibits highly selective anti-proliferative activity towards breast cancer cells.
Collapse
Affiliation(s)
- Neelesh C. Reddy
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Rajib Molla
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Pralhad Namdev Joshi
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Sajeev T. K.
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Ipsita Basu
- grid.452759.80000 0001 2188 427XDepartment of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700 106 W.B. India
| | - Jyotsna Kawadkar
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | | | - Ram Kumar Mishra
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Suman Chakrabarty
- grid.452759.80000 0001 2188 427XDepartment of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700 106 W.B. India
| | - Sanjeev Shukla
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Vishal Rai
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| |
Collapse
|
27
|
Kjærsgaard NL, Nielsen TB, Gothelf KV. Chemical Conjugation to Less Targeted Proteinogenic Amino Acids. Chembiochem 2022; 23:e202200245. [PMID: 35781760 PMCID: PMC9796363 DOI: 10.1002/cbic.202200245] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/01/2022] [Indexed: 01/01/2023]
Abstract
Protein bioconjugates are in high demand for applications in biomedicine, diagnostics, chemical biology and bionanotechnology. Proteins are large and sensitive molecules containing multiple different functional groups and in particular nucleophilic groups. In bioconjugation reactions it can therefore be challenging to obtain a homogeneous product in high yield. Numerous strategies for protein conjugation have been developed, of which a vast majority target lysine, cysteine and to a lesser extend tyrosine. Likewise, several methods that involve recombinantly engineered protein tags have been reported. In recent years a number of methods have emerged for chemical bioconjugation to other amino acids and in this review, we present the progress in this area.
Collapse
Affiliation(s)
- Nanna L. Kjærsgaard
- Center for Multifunctional Biomolecular Drug Design Interdisciplinary Nanoscience CenterAarhus UniversityGustav Wieds Vej 148000Aarhus CDenmark
- Department of ChemistryAarhus UniversityLangelandsgade 1408000Aarhus CDenmark
| | | | - Kurt V. Gothelf
- Center for Multifunctional Biomolecular Drug Design Interdisciplinary Nanoscience CenterAarhus UniversityGustav Wieds Vej 148000Aarhus CDenmark
- Department of ChemistryAarhus UniversityLangelandsgade 1408000Aarhus CDenmark
| |
Collapse
|
28
|
Hanaya K, Yamoto K, Taguchi K, Matsumoto K, Higashibayashi S, Sugai T. Single‐Step N‐Terminal Modification of Proteins via a Bio‐Inspired Copper(II)‐Mediated Aldol Reaction. Chemistry 2022; 28:e202201677. [DOI: 10.1002/chem.202201677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Kengo Hanaya
- Faculty of Pharmacy Keio University 1-5-30 Shibakoen, Minato-ku Tokyo Japan
| | - Kaho Yamoto
- Faculty of Pharmacy Keio University 1-5-30 Shibakoen, Minato-ku Tokyo Japan
| | - Kazuaki Taguchi
- Faculty of Pharmacy Keio University 1-5-30 Shibakoen, Minato-ku Tokyo Japan
| | - Kazuaki Matsumoto
- Faculty of Pharmacy Keio University 1-5-30 Shibakoen, Minato-ku Tokyo Japan
| | | | - Takeshi Sugai
- Faculty of Pharmacy Keio University 1-5-30 Shibakoen, Minato-ku Tokyo Japan
| |
Collapse
|
29
|
Sun H, Xi M, Jin Q, Zhu Z, Zhang Y, Jia G, Zhu G, Sun M, Zhang H, Ren X, Zhang Y, Xu Z, Huang H, Shen J, Li B, Ge G, Chen K, Zhu W. Chemo- and Site-Selective Lysine Modification of Peptides and Proteins under Native Conditions Using the Water-Soluble Zolinium. J Med Chem 2022; 65:11840-11853. [DOI: 10.1021/acs.jmedchem.2c00937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haiguo Sun
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Mengyu Xi
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Qiang Jin
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yani Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Guihua Jia
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Guanghao Zhu
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Mengru Sun
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Hongwei Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Xuelian Ren
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yong Zhang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - He Huang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jingshan Shen
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Bo Li
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, No. 38 Xue Yuan Road, Haidian District, Beijing 100191, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Kaixian Chen
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| |
Collapse
|
30
|
Abstract
A platform to enable precise modifications of insulin could improve drug functionality.
Collapse
Affiliation(s)
- Nai-Pin Lin
- Stanford University, School of Medicine, Palo Alto, CA, USA
| | | |
Collapse
|
31
|
Wang B, Li X, Wang Y, Mao X, Wang X. Post-translational site-specific protein azidolation with an azido pyridoxal derivative. Chem Commun (Camb) 2022; 58:7408-7411. [PMID: 35695118 DOI: 10.1039/d2cc03051a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An azido pyridoxal derivative (PLAA) was developed as a protein azidolation reagent, with selectivity towards N-terminal glycine. Successful PLAA modification was achieved with small peptides, natural proteins and lab-expressed proteins under mild conditions, offering a unique method for post-synthesis site-specific azidolation of a peptide or protein.
Collapse
Affiliation(s)
- Baochuan Wang
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Xun Li
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Yiwan Wang
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Xianxian Mao
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China. .,School of Pharmacy, Jiangsu Health Vocational College, Nanjing 211800, China
| | - Xiaojian Wang
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China.
| |
Collapse
|
32
|
Sahu T, Chilamari M, Rai V. Protein inspired chemically orthogonal imines for linchpin directed precise and modular labeling of lysine in proteins. Chem Commun (Camb) 2022; 58:1768-1771. [PMID: 35037678 DOI: 10.1039/d1cc05559c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a chemoselective, site-selective, and modular technology for precision engineering of high-frequency lysine residues in native proteins. It enables a unique, unexplored reactivity landscape on the protein surface to facilitate their single-site modification. Further, the method presents bond-architecture flexibility and enables orthogonal tagging with probes of interest.
Collapse
Affiliation(s)
- Tularam Sahu
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal 462066, MP, India.
| | - Maheshwerreddy Chilamari
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal 462066, MP, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal 462066, MP, India.
| |
Collapse
|
33
|
Wang S, Zhou Q, Zhang X, Wang P. Site‐Selective Itaconation of Complex Peptides by Photoredox Catalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University No. 800, Dongchuan Rd Shanghai 200240 China
| | - QingQing Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University No. 800, Dongchuan Rd Shanghai 200240 China
| | - Xiaheng Zhang
- School of Chemistry and Materials Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences 1 Sub-lane Xiangshan Hangzhou 310024 China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University No. 800, Dongchuan Rd Shanghai 200240 China
| |
Collapse
|
34
|
Wang S, Zhou Q, Zhang X, Wang P. Site-Selective Itaconation of Complex Peptides by Photoredox Catalysis. Angew Chem Int Ed Engl 2022; 61:e202111388. [PMID: 34845804 DOI: 10.1002/anie.202111388] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Indexed: 12/20/2022]
Abstract
Site-selective peptide functionalization provides a straightforward and cost-effective access to diversify peptides for biological studies. Among many existing non-invasive peptide conjugations methodologies, photoredox catalysis has emerged as one of the powerful approaches for site-specific manipulation on native peptides. Herein, we report a highly N-termini-specific method to rapidly access itaconated peptides and their derivatives through a combination of transamination and photoredox conditions. This strategy exploits the facile reactivity of peptidyl-dihydropyridine in the complex peptide settings, complementing existing approaches for bioconjugations with excellent selectivity under mild conditions. Distinct from conventional methods, this method utilizes the highly reactive carbamoyl radical derived from a peptidyl-dihydropyridine. In addition, this itaconated peptide can be further functionalized as a Michael acceptor to access the corresponding peptide-protein conjugate.
Collapse
Affiliation(s)
- Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, No. 800, Dongchuan Rd, Shanghai, 200240, China
| | - QingQing Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, No. 800, Dongchuan Rd, Shanghai, 200240, China
| | - Xiaheng Zhang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, No. 800, Dongchuan Rd, Shanghai, 200240, China
| |
Collapse
|
35
|
Schwaab G, Pérez de Tudela R, Mani D, Pal N, Roy TK, Gabas F, Conte R, Durán Caballero L, Ceotto M, Marx D, Havenith M. Zwitter Ionization of Glycine at Outer Space Conditions due to Microhydration by Six Water Molecules. PHYSICAL REVIEW LETTERS 2022; 128:033001. [PMID: 35119904 DOI: 10.1103/physrevlett.128.033001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 08/09/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
We investigate glycine microsolvation with water molecules, mimicking astrophysical conditions, in our laboratory by embedding these clusters in helium nanodroplets at 0.37 K. We recorded mass selective infrared spectra in the frequency range 1500-1800 cm^{-1} where two bands centered at 1630 and 1724 cm^{-1} were observed. By comparison with the extensive accompanying calculations, the band at 1630 cm^{-1} was assigned to the COO^{-} asymmetric stretching mode of the zwitter ion and the band at 1724 cm^{-1} was assigned to redshifted C=O stretch within neutral clusters. We show that zwitter ion formation of amino acids readily occurs with only few water molecules available even under extreme conditions.
Collapse
Affiliation(s)
- Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | | | - Devendra Mani
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
| | - Nitish Pal
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Tarun Kumar Roy
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, 20133 Milano, Italy
| | | | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44780 Bochum, Germany
| |
Collapse
|
36
|
Sahu T, Kumar M, T. K. S, Joshi M, Mishra RK, Rai V. Residue-specific N-terminal glycine to aldehyde transformation renders analytically pure single-site labeled proteins. Chem Commun (Camb) 2022; 58:12451-12454. [DOI: 10.1039/d2cc04196k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we demonstrate the residue-specific transformation of N-Gly into N-Gly-glyoxamide. The aldehyde introduction opens the residue-specific synthetic flexibility for the N-Gly proteome.
Collapse
Affiliation(s)
- Tularam Sahu
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP 462 066, India
| | - Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP 462 066, India
| | - Sajeev T. K.
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, MP 462 066, India
| | - Manas Joshi
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP 462 066, India
| | - Ram Kumar Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, MP 462 066, India
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP 462 066, India
| |
Collapse
|
37
|
Jiang H, Chen W, Wang J, Zhang R. Selective N-terminal modification of peptides and proteins: Recent progresses and applications. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
38
|
Sornay C, Vaur V, Wagner A, Chaubet G. An overview of chemo- and site-selectivity aspects in the chemical conjugation of proteins. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211563. [PMID: 35116160 PMCID: PMC8790347 DOI: 10.1098/rsos.211563] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/20/2021] [Indexed: 05/03/2023]
Abstract
The bioconjugation of proteins-that is, the creation of a covalent link between a protein and any other molecule-has been studied for decades, partly because of the numerous applications of protein conjugates, but also due to the technical challenge it represents. Indeed, proteins possess inner physico-chemical properties-they are sensitive and polynucleophilic macromolecules-that make them complex substrates in conjugation reactions. This complexity arises from the mild conditions imposed by their sensitivity but also from selectivity issues, viz the precise control of the conjugation site on the protein. After decades of research, strategies and reagents have been developed to address two aspects of this selectivity: chemoselectivity-harnessing the reacting chemical functionality-and site-selectivity-controlling the reacting amino acid residue-most notably thanks to the participation of synthetic chemistry in this effort. This review offers an overview of these chemical bioconjugation strategies, insisting on those employing native proteins as substrates, and shows that the field is active and exciting, especially for synthetic chemists seeking new challenges.
Collapse
Affiliation(s)
- Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| |
Collapse
|
39
|
Reddi RN, Rogel A, Resnick E, Gabizon R, Prasad PK, Gurwicz N, Barr H, Shulman Z, London N. Site-Specific Labeling of Endogenous Proteins Using CoLDR Chemistry. J Am Chem Soc 2021; 143:20095-20108. [PMID: 34817989 PMCID: PMC8662641 DOI: 10.1021/jacs.1c06167] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Chemical modifications
of native proteins can affect their stability,
activity, interactions, localization, and more. However, there are
few nongenetic methods for the installation of chemical modifications
at a specific protein site in cells. Here we report a covalent ligand
directed release (CoLDR) site-specific labeling strategy, which enables
the installation of a variety of functional tags on a target protein
while releasing the directing ligand. Using this approach, we were
able to label various proteins such as BTK, K-RasG12C,
and SARS-CoV-2 PLpro with different tags. For BTK we have
shown selective labeling in cells of both alkyne and fluorophores
tags. Protein labeling by traditional affinity methods often inhibits
protein activity since the directing ligand permanently occupies the
target binding pocket. We have shown that using CoLDR chemistry, modification
of BTK by these probes in cells preserves its activity. We demonstrated
several applications for this approach including determining the half-life
of BTK in its native environment with minimal perturbation, as well
as quantification of BTK degradation by a noncovalent proteolysis
targeting chimera (PROTAC) by in-gel fluorescence. Using an environment-sensitive
“turn-on” fluorescent probe, we were able to monitor
ligand binding to the active site of BTK. Finally, we have demonstrated
efficient CoLDR-based BTK PROTACs (DC50 < 100 nM), which
installed a CRBN binder onto BTK. This approach joins very few available
labeling strategies that maintain the target protein activity and
thus makes an important addition to the toolbox of chemical biology.
Collapse
Affiliation(s)
- Rambabu N Reddi
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Efrat Resnick
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Pragati Kishore Prasad
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Neta Gurwicz
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Barr
- Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ziv Shulman
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| |
Collapse
|
40
|
Cong M, Tavakolpour S, Berland L, Glöckner H, Andreiuk B, Rakhshandehroo T, Uslu S, Mishra S, Clark L, Rashidian M. Direct N- or C-Terminal Protein Labeling Via a Sortase-Mediated Swapping Approach. Bioconjug Chem 2021; 32:2397-2406. [PMID: 34748323 PMCID: PMC9595177 DOI: 10.1021/acs.bioconjchem.1c00442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Site-specific protein labeling is important in biomedical research and biotechnology. While many methods allow site-specific protein modification, a straightforward approach for efficient N-terminal protein labeling is not available. We introduce a novel sortase-mediated swapping approach for a one-step site-specific N-terminal labeling with a near-quantitative yield. We show that this method allows rapid and efficient cleavage and simultaneous labeling of the N or C termini of fusion proteins. The method does not require any prior modification beyond the genetic incorporation of the sortase recognition motif. This new approach provides flexibility for protein engineering and site-specific protein modifications.
Collapse
Affiliation(s)
- Min Cong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Soheil Tavakolpour
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Lea Berland
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Université Côte d'Azur, CNRS, INSERM, IRCAN, 06100 Nice, France
| | - Hannah Glöckner
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Bohdan Andreiuk
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Taha Rakhshandehroo
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Safak Uslu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Medical Scientist Training Program, Hacettepe University Faculty of Medicine, Ankara, 06230, Turkey
| | - Shruti Mishra
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Louise Clark
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Mohammad Rashidian
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, United States
| |
Collapse
|
41
|
Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
Collapse
Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
42
|
Kumar M, Reddy NC, Rai V. Chemical technologies for precise protein bioconjugation interfacing biology and medicine. Chem Commun (Camb) 2021; 57:7083-7095. [PMID: 34180471 DOI: 10.1039/d1cc02268g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins provide an excellent means to monitor and regulate biological processes. Hence, a precise chemical toolbox for their modification becomes indispensable. In this perspective, this feature article outlines our efforts to establish the core principles of chemoselectivity, site-selectivity, site-specificity, site-modularity, residue-modularity, and protein-specificity. With the knowledge to systematically regulate these parameters, the field has access to technological platforms that can address multiple challenges at the interface of chemistry, biology, and medicine.
Collapse
Affiliation(s)
- Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| | - Neelesh C Reddy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| |
Collapse
|
43
|
El-Shaffey HM, Gross EJ, Hall YD, Ohata J. An Ionic Liquid Medium Enables Development of a Phosphine-Mediated Amine-Azide Bioconjugation Method. J Am Chem Soc 2021; 143:12974-12979. [PMID: 34387473 DOI: 10.1021/jacs.1c06092] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
While a diverse set of design strategies have produced various chemical tools for biomolecule labeling in aqueous media, the development of nonaqueous, biomolecule-compatible media for bioconjugation has significantly lagged behind. In this report, we demonstrate that an aprotic ionic liquid serves as a novel reaction solvent for protein bioconjugation without noticeable loss of the biomolecule functions. The ionic liquid bioconjugation approach led to discovery of a novel triphenylphosphine-mediated amine-azide coupling reaction that forges a stable tetrazene linkage on unprotected peptides and proteins. This strategy of using untraditional media would provide untapped opportunities for expanding the scope of chemical approaches for bioconjugation.
Collapse
Affiliation(s)
- Hisham M El-Shaffey
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Elizabeth J Gross
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yvonne D Hall
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jun Ohata
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| |
Collapse
|
44
|
Kordasht HK, Hasanzadeh M, Seidi F, Alizadeh PM. Poly (amino acids) towards sensing: Recent progress and challenges. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
45
|
Adakkattil R, Thakur K, Rai V. Reactivity and Selectivity Principles in Native Protein Bioconjugation. CHEM REC 2021; 21:1941-1956. [PMID: 34184826 DOI: 10.1002/tcr.202100108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/10/2021] [Indexed: 12/24/2022]
Abstract
Are chemical methods capable of precisely engineering the native proteins? Is it possible to develop platforms that can empower the regulation of chemoselectivity, site-selectivity, modularity, protein-specificity, and site-specificity? This account delineates our research journey in the last ten years on the developments revolving around these questions. It will range from the realization of chemoselective and site-selective labeling of reactivity hotspots to modular linchpin directed modification (LDM®) platform and site-specific Gly-tag® technology. Also, we outline a few biotechnology tools, including Maspecter®, that accelerated the detailed analysis of the bioconjugates and rendered a powerful toolbox for homogeneous antibody-drug conjugates (ADCs).
Collapse
Affiliation(s)
- Ramesh Adakkattil
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, 462 066, Bhopal, Madhya Pradesh, India
| | - Kalyani Thakur
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, 462 066, Bhopal, Madhya Pradesh, India
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, 462 066, Bhopal, Madhya Pradesh, India
| |
Collapse
|
46
|
Asiimwe N, Al Mazid MF, Murale DP, Kim YK, Lee J. Recent advances in protein modifications techniques for the targeting
N‐terminal
cysteine. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nicholas Asiimwe
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST) Seoul Korea
- Bio‐Med Program, KIST‐School UST Seoul Korea
| | | | | | - Yun Kyung Kim
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST) Seoul Korea
- Bio‐Med Program, KIST‐School UST Seoul Korea
| | - Jun‐Seok Lee
- Department of Pharmacology Korea University College of Medicine Seoul Korea
| |
Collapse
|
47
|
Sumam de Oliveira D, Kronenberger T, Palmisano G, Wrenger C, de Souza EE. Targeting SUMOylation in Plasmodium as a Potential Target for Malaria Therapy. Front Cell Infect Microbiol 2021; 11:685866. [PMID: 34178724 PMCID: PMC8224225 DOI: 10.3389/fcimb.2021.685866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Malaria is a parasitic disease that represents a public health problem worldwide. Protozoans of the Plasmodium genus are responsible for causing malaria in humans. Plasmodium species have a complex life cycle that requires post-translational modifications (PTMs) to control cellular activities temporally and spatially and regulate the levels of critical proteins and cellular mechanisms for maintaining an efficient infection and immune evasion. SUMOylation is a PTM formed by the covalent linkage of a small ubiquitin-like modifier protein to the lysine residues on the protein substrate. This PTM is reversible and is triggered by the sequential action of three enzymes: E1-activating, E2-conjugating, and E3 ligase. On the other end, ubiquitin-like-protein-specific proteases in yeast and sentrin-specific proteases in mammals are responsible for processing SUMO peptides and for deconjugating SUMOylated moieties. Further studies are necessary to comprehend the molecular mechanisms and cellular functions of SUMO in Plasmodium. The emergence of drug-resistant malaria parasites prompts the discovery of new targets and antimalarial drugs with novel mechanisms of action. In this scenario, the conserved biological processes regulated by SUMOylation in the malaria parasites such as gene expression regulation, oxidative stress response, ubiquitylation, and proteasome pathways, suggest PfSUMO as a new potential drug target. This mini-review focuses on the current understanding of the mechanism of action of the PfSUMO during the coordinated multi-step life cycle of Plasmodium and discusses them as attractive new target proteins for the development of parasite-specific inhibitors and therapeutic intervention toward malaria disease.
Collapse
Affiliation(s)
- Daffiny Sumam de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen, Germany
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Edmarcia Elisa de Souza
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| |
Collapse
|
48
|
De Rosa L, Di Stasi R, Romanelli A, D’Andrea LD. Exploiting Protein N-Terminus for Site-Specific Bioconjugation. Molecules 2021; 26:3521. [PMID: 34207845 PMCID: PMC8228110 DOI: 10.3390/molecules26123521] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 11/29/2022] Open
Abstract
Although a plethora of chemistries have been developed to selectively decorate protein molecules, novel strategies continue to be reported with the final aim of improving selectivity and mildness of the reaction conditions, preserve protein integrity, and fulfill all the increasing requirements of the modern applications of protein conjugates. The targeting of the protein N-terminal alpha-amine group appears a convenient solution to the issue, emerging as a useful and unique reactive site universally present in each protein molecule. Herein, we provide an updated overview of the methodologies developed until today to afford the selective modification of proteins through the targeting of the N-terminal alpha-amine. Chemical and enzymatic strategies enabling the selective labeling of the protein N-terminal alpha-amine group are described.
Collapse
Affiliation(s)
- Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy; (L.D.R.); (R.D.S.)
| | - Rossella Di Stasi
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy; (L.D.R.); (R.D.S.)
| | - Alessandra Romanelli
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy;
| | - Luca Domenico D’Andrea
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR Via M. Bianco 9, 20131 Milano, Italy
| |
Collapse
|
49
|
Yu W, Gillespie KP, Chhay B, Svensson AS, Nygren PÅ, Blair IA, Yu F, Tsourkas A. Efficient Labeling of Native Human IgG by Proximity-Based Sortase-Mediated Isopeptide Ligation. Bioconjug Chem 2021; 32:1058-1066. [PMID: 34029057 DOI: 10.1021/acs.bioconjchem.1c00099] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Antibody-drug conjugates (ADCs) have demonstrated great therapeutic potential due to their ability to target the delivery of potent cytotoxins. However, the heterogeneous nature of conventional drug conjugation strategies can affect the safety, efficacy, and stability of ADCs. Site-specific conjugations can resolve these issues, but often require genetic modification of Immunoglobulin G (IgG), which can impact yield or cost of production, or require undesirable chemical linkages. Here, we describe a near-traceless conjugation method that enables the efficient modification of native IgG, without the need for genetic engineering or glycan modification. This method utilizes engineered variants of sortase A to catalyze noncanonical isopeptide ligation. Sortase A was fused to an antibody-binding domain to improve ligation efficiency. Antibody labeling is limited to five lysine residues on the heavy chain and one on the light chain of human IgG1. The ADCs exhibit conserved antigen and Fc-receptor interactions, as well as potent cytolytic activity.
Collapse
Affiliation(s)
- Wendy Yu
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kevin P Gillespie
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Bonirath Chhay
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Anne-Sophie Svensson
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH-Royal Institute of Technology, Stockholm, Sweden and Sonia SE-100-44 Sweden
| | - Per-Åke Nygren
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH-Royal Institute of Technology, Stockholm, Sweden and Sonia SE-100-44 Sweden
| | - Ian A Blair
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Feifan Yu
- AlphaThera, LLC, Philadelphia, Pennsylvania 19146, United States
| | - Andrew Tsourkas
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
50
|
Modification of N-terminal α-amine of proteins via biomimetic ortho-quinone-mediated oxidation. Nat Commun 2021; 12:2257. [PMID: 33859198 PMCID: PMC8050078 DOI: 10.1038/s41467-021-22654-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/09/2021] [Indexed: 11/22/2022] Open
Abstract
Naturally abundant quinones are important molecules, which play essential roles in various biological processes due to their reduction potential. In contrast to their universality, the investigation of reactions between quinones and proteins remains sparse. Herein, we report the development of a convenient strategy to protein modification via a biomimetic quinone-mediated oxidation at the N-terminus. By exploiting unique reactivity of an ortho-quinone reagent, the α-amine of protein N-terminus is oxidized to generate aldo or keto handle for orthogonal conjugation. The applications have been demonstrated using a range of proteins, including myoglobin, ubiquitin and small ubiquitin-related modifier 2 (SUMO2). The effect of this method is further highlighted via the preparation of a series of 17 macrophage inflammatory protein 1β (MIP-1β) analogs, followed by preliminary anti-HIV activity and cell viability assays, respectively. This method offers an efficient and complementary approach to existing strategies for N-terminal modification of proteins. Methods for selective modification of the N-terminus of proteins are of high interest, but mostly require specific amino acid residues. Here, the authors report a selective and fast method for N-terminal modification of proteins based on quinone-mediated oxidation of the alpha-amine to aldehyde or ketone, and apply it to diverse proteins.
Collapse
|