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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.
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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
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2
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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: 0] [Impact Index Per Article: 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.
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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.
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3
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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: 1.5] [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.
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Affiliation(s)
| | | | | | | | | | | | - Neetu Kalra
- School of Bioengineering, VIT Bhopal, Bhopal 466114, Madhya Pradesh, India
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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: 1.0] [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.
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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.
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5
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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: 3.0] [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.
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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.
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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: 13] [Impact Index Per Article: 4.3] [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.
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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.
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7
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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: 2.3] [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).
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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
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Rawale DG, Thakur K, Sreekumar P, T K S, A R, Adusumalli SR, Mishra RK, Rai V. Linchpins empower promiscuous electrophiles to enable site-selective modification of histidine and aspartic acid in proteins. Chem Sci 2021; 12:6732-6736. [PMID: 34040749 PMCID: PMC8133000 DOI: 10.1039/d1sc00335f] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/03/2021] [Indexed: 11/29/2022] Open
Abstract
The conservation of chemoselectivity becomes invalid for multiple electrophilic warheads during protein bioconjugation. Consequently, it leads to unpredictable heterogeneous labeling of proteins. Here, we report that a linchpin can create a unique chemical space to enable site-selectivity for histidine and aspartic acid modifications overcoming the pre-requisite of chemoselectivity.
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Affiliation(s)
- Dattatraya Gautam Rawale
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Kalyani Thakur
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Pranav Sreekumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Sajeev T K
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Ramesh A
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Srinivasa Rao Adusumalli
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Ram Kumar Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri Bhopal 462 066 India
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