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Liu J, Yang B, Wang L. Residue selective crosslinking of proteins through photoactivatable or proximity-enabled reactivity. Curr Opin Chem Biol 2023; 74:102285. [PMID: 36913752 PMCID: PMC10225350 DOI: 10.1016/j.cbpa.2023.102285] [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: 12/27/2022] [Revised: 02/08/2023] [Accepted: 02/12/2023] [Indexed: 03/13/2023]
Abstract
Photo- and chemical crosslinking of proteins have offered various avenues for studying protein structure and protein interactions with biomolecules. Conventional photoactivatable groups generally lack reaction selectivity toward amino acid residues. New photoactivatable groups reacting with selected residues have emerged recently, increasing crosslinking efficiency and facilitating crosslink identification. Traditional chemical crosslinking usually employs highly reactive functional groups, while recent advance has developed latent reactive groups with reactivity triggered by proximity, which reduce spurious crosslinks and improve biocompatibility. The employment of these residue selective chemical functional groups, activated by light or proximity, in small molecule crosslinkers and in genetically encoded unnatural amino acids is summarized. Together with new software development in identifying protein crosslinks, residue selective crosslinking has enhanced the research of elusive protein-protein interactions in vitro, in cell lysate, and in live cells. Residue selective crosslinking is expected to expand to other methods for the investigation of various protein-biomolecule interactions.
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Affiliation(s)
- Jun Liu
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Bing Yang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA.
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Li Y, Zhou H, Liu H, Gan Y, Zheng Y, Sheng J, Wang R. Development of Nitroso-Based Probes for Labeling and Regulation of RAS Proteins in Cancer Cells via Sequential Ene-Ligation and Oxime Condensation. J Org Chem 2023; 88:1762-1771. [PMID: 36691112 DOI: 10.1021/acs.joc.2c02922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Prenyl functionalities have been widely discovered in natural products, nucleic acids, and proteins with significant biological roles in both healthy and diseased cells. In this work, we develop a series of new nitroso-based probes for the labeling, enrichment, and regulation of prenylated RAS protein, which is highly associated with ∼20% of human cancers and used to be regarded as an "undruggable" target via a sequential ene-ligation and oxime condensation (SELOC) process. We found that these nitroso species can rapidly react with prenyl-containing molecules through ene-ligation and install a molecular tag for functional applications under physiological conditions. We first investigated this ligation process on two peptide models and demonstrated its labeling efficiency on various proteins such as myoglobin, lysozyme, RNase A, BSA, and HSP40. We further coupled this reactive platform with proteolysis-targeting chimera technology targeting to increase its efficiency and accuracy, as well as to expand its application range. Using the prenylated RAS protein as the model, we demonstrated that RAS could be efficiently decorated with our nitroso probes, which further condensate with oxime and rapidly react with a pomalidomide-containing hydroxylamine probe for protein degradation. As a result, the RAS protein in both HeLa and A549 cell lines has been determined to be efficiently degraded both in vitro and in vivo. This is the first case targeting post-translational modification other than ligand-protein interaction to degrade and regulate RAS proteins. We envision that our SELOC strategy will have great potential in studying the fundamental structures and functions of prenylated biomolecules and developing new drugs based on these unique cellular pathways.
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Affiliation(s)
- Yuanyuan Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Hongling Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Huili Liu
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Youfang Gan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yaying Zheng
- Department of Chemistry, and The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Jia Sheng
- Department of Chemistry, and The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong 518063, China
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Gan Y, Li Y, Zhou H, Wang R. Deciphering Regulatory Proteins of Prenylated Protein via the FRET Technique Using Nitroso-Based Ene-Ligation and Sequential Azidation and Click Reaction. Org Lett 2022; 24:6625-6630. [PMID: 36054498 DOI: 10.1021/acs.orglett.2c02662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report here the selective incorporations of nitroso species into a wide range of proteins targeting lysine residue(s). The corresponding azo functionalities were formed in a highly selective manner with excellent yields, displaying rather good stability under physiological conditions. Furthermore, the azodation proceeded smoothly in high yields on targeted peptides. Fluorescent and/or dual fluorescent labeling of varied proteins following this protocol have been determined efficiently and selectively. With this established protocol, we aim to determine its usage in the evaluation of the interaction of prenylated proteins with their interacted enzyme(s) via FRET assays. Delightedly, chemically modified proteins with a 1-pyrenyl fluorophore through 254 nm UV irradiation and the sequential azodation and click reaction of protein prenyl functionality, which enable the incorporation of naphthene, indeed increase the fluorescence energy transferred since we observed significantly enhanced absorption located at 218 nm in lysed HEK293T cells and a clearly strengthened greenish fluorescence in living HEK293T cells.
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Affiliation(s)
- Youfang Gan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yuanyuan Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Hongling Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong 518057, China
| | - Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong 518057, China
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Zhang H, Wu J, Zhou J, Liu W, Liang L, Xia S, Yan J, Sun X. Photolysis study of two indene-fused coumarin-based photoremovable protecting groups for potential biological applications. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114200] [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]
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Xue Y, Liu D, Wang X, Xiang Y, Du S, Ye K, Bao C, Zhu L. A photopatterned SERS substrate with a sandwich structure for multiplex detection. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Bhatt M, Shende P. Surface patterning techniques for proteins on nano- and micro-systems: a modulated aspect in hierarchical structures. J Mater Chem B 2022; 10:1176-1195. [PMID: 35119060 DOI: 10.1039/d1tb02455h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The surface patterning of protein using fabrication or the external functionalization of structures demonstrates various applications in the biomedical field for bioengineering, biosensing and antifouling. This review article offers an outline of the existing advances in protein patterning technology with a special emphasis on the current physical and physicochemical methods, including stencil patterning, trap- and droplet-based microfluidics, and chemical modification of surfaces via photolithography, microcontact printing and scanning probe nanolithography. Different approaches are applied for the biological studies of recent trends for single-protein patterning technology, such as robotic printing, stencil printing and colloidal lithography, wherein the concepts of physical confinement, electrostatic and capillary forces, as well as dielectrophoretics, are summarised to understand the design approaches. Photochemical alterations with diazirine, nitrobenzyl and aryl azide functional groups for the implication of modified substrates, such as self-assembled monolayers functionalized with amino silanes, organosilanes and alkanethiols on gold surfaces, as well as topographical effects of patterning techniques for protein functionalization and orientation, are discussed. Analytical methods for the evaluation of protein functionality are also mentioned. Regarding their selectivity, protein pattering methods will be readily used to fabricate modified surfaces and target-specific delivery systems for the transportation of macromolecules such as streptavidin, and albumin. Future applications of patterning techniques include high-throughput screening, the evaluation of intracellular interactions, accurate screening and personalized treatments.
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Affiliation(s)
- Maitri Bhatt
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India.
| | - Pravin Shende
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India.
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Xue Y, Ye K, Wang X, Xiang Y, Pang S, Bao C, Zhu L. Precise macroscopic supramolecular assembly of photopatterned hydrogels. Chem Commun (Camb) 2021; 57:8786-8789. [PMID: 34382046 DOI: 10.1039/d1cc03428f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Here we demonstrate that a precise macroscopic supramolecular assembly (MSA) can be achieved using a surface photopatterning strategy. The electrostatic interaction of the photopatterned polyelectrolytes drives hydrogel cuboids to form a stable MSA on a millimeter scale and the spatial controllability of light enables the hydrogels to be assembled into complex supramolecular architectures.
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Affiliation(s)
- Yuan Xue
- Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science and Technology, 130# Meilong Road, Shanghai 200237, China.
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Zhou Y, Yang H, Wang C, Xue Y, Wang X, Bao C, Zhu L. In situ formation of a biomimetic lipid membrane triggered by an aggregation-enhanced photoligation chemistry. Chem Sci 2021; 12:3627-3632. [PMID: 34163636 PMCID: PMC8179432 DOI: 10.1039/d0sc06049f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
Nature or synthetic systems that can self-assemble into biomimetic membranes and form compartments in aqueous solution have received extensive attention. However, these systems often have the problems of requiring complex processes or lacking of control in simulating lipid synthesis and membrane formation of cells. This paper demonstrates a conceptually new strategy that uses a photoligation chemistry to convert nonmembrane molecules to yield liposomes. Lysosphingomyelin (Lyso) and 2-nitrobenzyl alcohol derivatives (NBs) are used as precursors and the amphiphilic character of Lyso promotes the formation of mixed aggregates with NBs, bringing the lipid precursors into close proximity. Light irradiation triggers the conversion of NBs into reactive aldehyde intermediates, and the preassembly facilitates the efficient and specific ligation between aldehyde and Lyso amine over other biomolecules, thereby accelerating the synthesis of phospholipids and forming membrane compartments similar to natural lipids. The light-controllable transformation represents the use of an external energy stimulus to form a biomimetic phospholipid membrane, which has a wide range of applications in medicinal chemistry, synthetic biological and abiogenesis.
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Affiliation(s)
- Yaowu Zhou
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
| | - Huiting Yang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
| | - Chenxi Wang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
| | - Yuan Xue
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
| | - Xuebin Wang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
| | - Chunyan Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology 130# Meilong Road Shanghai 200237 China
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology 130# Meilong Road Shanghai 200237 China
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130# Meilong Road Shanghai 200237 China
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