1
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Yu J, Ge W, Wang K, Hao W, Yang S, Xu Y, Feng T, Han P, Sun X. Crosslinking ability of hydrolyzed distarch phosphate and its stabilizing effect on rehydrated sea cucumber. Food Chem 2024; 456:139866. [PMID: 38852446 DOI: 10.1016/j.foodchem.2024.139866] [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: 03/13/2024] [Revised: 05/07/2024] [Accepted: 05/26/2024] [Indexed: 06/11/2024]
Abstract
Effective crosslinking among food constituents has the potential to enhance their overall quality. Distarch phosphate (DSP), a common food additive employed as a thickening agent, bears a pre-crosslinked oligosaccharide (PCO) moiety within its molecular structure. Once this moiety is released, its double reducing end has the potential to undergo crosslinking with amino-rich macromolecules through Maillard reaction. In this study, hydrolyzed distarch phosphate (HDSP) was synthesized, and spectroscopic analysis verified the presence of PCO within HDSP. Preliminary validation experiment showed that HDSP could crosslink chitosan to form a hydrogel and significant browning was also observed during the process. Furthermore, rehydrated sea cucumber (RSC) crosslinked with HDSP exhibited a more intact appearance, higher mechanical strength, better color profile, and increased water-holding capacity. This series of results have confirmed that HDSP is capable to crosslink amino-rich macromolecules and form more stable three-dimensional network.
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Affiliation(s)
- Jiaqi Yu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China.
| | - Wenhao Ge
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Kaifeng Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Wenhui Hao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Shangju Yang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Ying Xu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China.
| | - Tingyu Feng
- Qingdao Institute of Marine Bioresources for Nutrition & Health Innovation, Ocean University of China, Qingdao 266109, China
| | - Peng Han
- Dalian Municipal central hospital, Dalian 116021, China
| | - Xun Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao 266100, China.
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2
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Cao L, Wang L. Biospecific Chemistry for Covalent Linking of Biomacromolecules. Chem Rev 2024; 124:8516-8549. [PMID: 38913432 PMCID: PMC11240265 DOI: 10.1021/acs.chemrev.4c00066] [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: 06/26/2024]
Abstract
Interactions among biomacromolecules, predominantly noncovalent, underpin biological processes. However, recent advancements in biospecific chemistry have enabled the creation of specific covalent bonds between biomolecules, both in vitro and in vivo. This Review traces the evolution of biospecific chemistry in proteins, emphasizing the role of genetically encoded latent bioreactive amino acids. These amino acids react selectively with adjacent natural groups through proximity-enabled bioreactivity, enabling targeted covalent linkages. We explore various latent bioreactive amino acids designed to target different protein residues, ribonucleic acids, and carbohydrates. We then discuss how these novel covalent linkages can drive challenging protein properties and capture transient protein-protein and protein-RNA interactions in vivo. Additionally, we examine the application of covalent peptides as potential therapeutic agents and site-specific conjugates for native antibodies, highlighting their capacity to form stable linkages with target molecules. A significant focus is placed on proximity-enabled reactive therapeutics (PERx), a pioneering technology in covalent protein therapeutics. We detail its wide-ranging applications in immunotherapy, viral neutralization, and targeted radionuclide therapy. Finally, we present a perspective on the existing challenges within biospecific chemistry and discuss the potential avenues for future exploration and advancement in this rapidly evolving field.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
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3
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Liu DD, Ding W, Cheng JT, Wei Q, Lin Y, Zhu TY, Tian J, Sun K, Zhang L, Lu P, Yang F, Liu C, Tang S, Yang B. Characterize direct protein interactions with enrichable, cleavable and latent bioreactive unnatural amino acids. Nat Commun 2024; 15:5221. [PMID: 38890329 PMCID: PMC11189575 DOI: 10.1038/s41467-024-49517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Latent bioreactive unnatural amino acids (Uaas) have been widely used in the development of covalent drugs and identification of protein interactors, such as proteins, DNA, RNA and carbohydrates. However, it is challenging to perform high-throughput identification of Uaa cross-linking products due to the complexities of protein samples and the data analysis processes. Enrichable Uaas can effectively reduce the complexities of protein samples and simplify data analysis, but few cross-linked peptides were identified from mammalian cell samples with these Uaas. Here we develop an enrichable and multiple amino acids reactive Uaa, eFSY, and demonstrate that eFSY is MS cleavable when eFSY-Lys and eFSY-His are the cross-linking products. An identification software, AixUaa is developed to decipher eFSY mass cleavable data. We systematically identify direct interactomes of Thioredoxin 1 (Trx1) and Selenoprotein M (SELM) with eFSY and AixUaa.
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Affiliation(s)
- Dan-Dan Liu
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Wenlong Ding
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jin-Tao Cheng
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Qiushi Wei
- School of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Yinuo Lin
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China
| | - Tian-Yi Zhu
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jing Tian
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China
| | - Ke Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, China
| | - Long Zhang
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Peilong Lu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310030, China
| | - Fan Yang
- Department of Biophysics, Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Chao Liu
- School of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing, 100191, China.
| | - Shibing Tang
- State Key Laboratory of Respiratory Disease, Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, China.
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, 510530, China.
| | - Bing Yang
- Life Sciences Institute, Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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4
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Cao L, Yu B, Li S, Zhang P, Li Q, Wang L. Genetically Enabling Phosphorus Fluoride Exchange Click Chemistry in Proteins. Chem 2024; 10:1868-1884. [PMID: 38975291 PMCID: PMC11225796 DOI: 10.1016/j.chempr.2024.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Phosphorus Fluoride Exchange (PFEx), recently debuted in small molecules, represents the forefront of click chemistry. To explore PFEx's potential in biological settings, we developed amino acids PFY and PFK featuring phosphoramidofluoridates and incorporated them into proteins through genetic code expansion. PFY/PFK selectively reacted with nearby His, Tyr, Lys, or Cys in proteins, both in vitro and in living cells, demonstrating that proximity enabled PFEx reactivity without external reagents. The reaction with His showed unique pH-dependent properties and created thermally sensitive linkages. Additionally, Na2SiO3 enhanced PFEx reactions with Tyr and Cys. PFEx, by generating defined covalent P-N/O linkages, extends the utility of phosphorus linkages in proteins, aligning with nature's use of phosphate connectors in other biomolecules. More versatile and durable than SuFEx, PFEx in proteins expands the latent bioreactive arsenal for covalent protein engineering and will facilitate the broad application of this potent click chemistry in biological and biomedical fields.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- These authors contributed equally
| | - Bingchen Yu
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- These authors contributed equally
| | - Shanshan Li
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Pan Zhang
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Qingke Li
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen 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 Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Lead contact
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5
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Zhang J, Wang X, Huang Q, Ye J, Wang J. Genetically Encoded Epoxide Warhead for Precise and Versatile Covalent Targeting of Proteins. J Am Chem Soc 2024; 146:16173-16183. [PMID: 38819260 PMCID: PMC11177858 DOI: 10.1021/jacs.4c03974] [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: 03/20/2024] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 06/01/2024]
Abstract
Genetically encoding a proximal reactive warhead into the protein binder/drug has emerged as an efficient strategy for covalently binding to protein targets, enabling broad applications. To expand the reactivity scope for targeting the diverse natural residues under physiological conditions, the development of a genetically encoded reactive warhead with excellent stability and broad reactivity is highly desired. Herein, we reported the genetic encoding of epoxide-containing tyrosine (EPOY) for developing covalent protein drugs. Our study demonstrates that EPOY, when incorporated into a nanobody (KN035), can cross-link with different side chains (mutations) at the same position of PD-L1 protein. Significantly, a single genetically encoded reactive warhead that is capable of covalent and site-specific targeting to 10 different nucleophilic residues was achieved for the first time. This would largely expand the scope of covalent warhead and inspire the development of covalent warheads for both small-molecule drugs and protein drugs. Furthermore, we incorporate the EPOY into a designed ankyrin repeat protein (DarpinK13) to create the covalent binders of KRAS. This covalent KRAS binder holds the potential to achieve pan-covalent targeting of KRAS based on the structural similarity among all oncogenic KRAS mutants while avoiding off-target binding to NRAS/HRAS through a covalent interaction with KRAS-specific residues (H95 and E107). We envision that covalently targeting to H95 will be a promising strategy for the development of covalent pan-KRAS inhibitors in the future.
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Affiliation(s)
| | | | | | - Jinsong Ye
- Department of Chemistry,
Research Center for Chemical Biology and Omics Analysis, College of
Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jie Wang
- Department of Chemistry,
Research Center for Chemical Biology and Omics Analysis, College of
Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
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6
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [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: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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7
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Cui XY, Li Z, Kong Z, Liu Y, Meng H, Wen Z, Wang C, Chen J, Xu M, Li Y, Gao J, Zhu W, Hao Z, Huo L, Liu S, Yang Z, Liu Z. Covalent targeted radioligands potentiate radionuclide therapy. Nature 2024; 630:206-213. [PMID: 38778111 DOI: 10.1038/s41586-024-07461-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Targeted radionuclide therapy, in which radiopharmaceuticals deliver potent radionuclides to tumours for localized irradiation, has addressed unmet clinical needs and improved outcomes for patients with cancer1-4. A therapeutic radiopharmaceutical must achieve both sustainable tumour targeting and fast clearance from healthy tissue, which remains a major challenge5,6. A targeted ligation strategy that selectively fixes the radiopharmaceutical to the target protein in the tumour would be an ideal solution. Here we installed a sulfur (VI) fluoride exchange (SuFEx) chemistry-based linker on radiopharmaceuticals to prevent excessively fast tumour clearance. When the engineered radiopharmaceutical binds to the tumour-specific protein, the system undergoes a binding-to-ligation transition and readily conjugates to the tyrosine residues through the 'click' SuFEx reaction. The application of this strategy to a fibroblast activation protein (FAP) inhibitor (FAPI) triggered more than 80% covalent binding to the protein and almost no dissociation for six days. In mice, SuFEx-engineered FAPI showed 257% greater tumour uptake than did the original FAPI, and increased tumour retention by 13-fold. The uptake in healthy tissues was rapidly cleared. In a pilot imaging study, this strategy identified more tumour lesions in patients with cancer than did other methods. SuFEx-engineered FAPI also successfully achieved targeted β- and α-radionuclide therapy, causing nearly complete tumour regression in mice. Another SuFEx-engineered radioligand that targets prostate-specific membrane antigen (PSMA) also showed enhanced therapeutic efficacy. Considering the broad scope of proteins that can potentially be ligated to SuFEx warheads, it might be possible to adapt this strategy to other cancer targets.
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Affiliation(s)
- Xi-Yang Cui
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Zhu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Peking University Cancer Hospital and Institute, Beijing, P. R. China
| | - Ziren Kong
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Yu Liu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Hao Meng
- Changping Laboratory, Beijing, P. R. China
| | - Zihao Wen
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Changlun Wang
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Junyi Chen
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Mengxin Xu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Yiyan Li
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Jingyue Gao
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Wenjia Zhu
- Department of Nuclear Medicine, Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine and State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Zhixin Hao
- Department of Nuclear Medicine, Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine and State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Li Huo
- Department of Nuclear Medicine, Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine and State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Shaoyan Liu
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Zhi Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Peking University Cancer Hospital and Institute, Beijing, P. R. China
| | - Zhibo Liu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Peking University Cancer Hospital and Institute, Beijing, P. R. China.
- Peking University-Tsinghua University Center for Life Sciences, Peking University, Beijing, P. R. China.
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8
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Jame-Chenarboo Z, Gray TE, Macauley MS. Advances in understanding and exploiting Siglec-glycan interactions. Curr Opin Chem Biol 2024; 80:102454. [PMID: 38631213 DOI: 10.1016/j.cbpa.2024.102454] [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: 02/05/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024]
Abstract
Sialic-acid-binding immunoglobulin-type lectins (Siglecs) are a family of cell-surface immunomodulatory receptors that recognize sialic-acid-containing glycans. The majority of Siglecs have an inhibitory motif in their intercellular domain and can regulate the cellular activation of immune cells. Importantly, the immunomodulatory role of Siglecs is regulated by engagement with distinct sialoglycan ligands. However, there are still many unanswered questions about the precise ligand(s) recognized by individual Siglec family members. New tools and approaches to study Siglec-ligand interactions are rapidly filling this knowledge gap. This review provides an overview of recent advances in discovering Siglec ligands as well as the development of approaches to modulate the function of Siglecs. In both aspects, chemical biology approaches are emphasized with a discussion on how these are complementing biochemical and genetic strategies.
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Affiliation(s)
| | - Taylor E Gray
- Department of Chemistry, University of Alberta, Canada
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Canada; Department of Medical Microbiology and Immunology, University of Alberta, Canada.
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9
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Huang W, Laughlin ST. Cell-selective bioorthogonal labeling. Cell Chem Biol 2024; 31:409-427. [PMID: 37837964 DOI: 10.1016/j.chembiol.2023.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/25/2023] [Accepted: 09/19/2023] [Indexed: 10/16/2023]
Abstract
In classic bioorthogonal labeling experiments, the cell's biosynthetic machinery incorporates bioorthogonal tags, creating tagged biomolecules that are subsequently reacted with a corresponding bioorthogonal partner. This two-step approach labels biomolecules throughout the organism indiscriminate of cell type, which can produce background in applications focused on specific cell populations. In this review, we cover advances in bioorthogonal chemistry that enable targeting of bioorthogonal labeling to a desired cell type. Such cell-selective bioorthogonal labeling is achieved in one of three ways. The first approach restricts labeling to specific cells by cell-selective expression of engineered enzymes that enable the bioorthogonal tag's incorporation. The second approach preferentially localizes the bioorthogonal reagents to the desired cell types to restrict their uptake to the desired cells. Finally, the third approach cages the reactivity of the bioorthogonal reagents, allowing activation of the reaction in specific cells by uncaging the reagents selectively in those cell populations.
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Affiliation(s)
- Wei Huang
- Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA
| | - Scott T Laughlin
- Department of Chemistry and Institute for Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794, USA.
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10
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Giltrap A, Yuan Y, Davis BG. Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology. Chem Rev 2024; 124:889-928. [PMID: 38231473 PMCID: PMC10870719 DOI: 10.1021/acs.chemrev.3c00579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/18/2024]
Abstract
With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.
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Affiliation(s)
- Andrew
M. Giltrap
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Yizhi Yuan
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Benjamin G. Davis
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
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11
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Borrel G, Fadhlaoui K, Ben Hania W, Gaci N, Pehau-Arnaudet G, Chaudhary PP, Vandekerckove P, Ballet N, Alric M, O’Toole PW, Fardeau ML, Ollivier B, Brugère JF. Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov. Microorganisms 2023; 11:2794. [PMID: 38004804 PMCID: PMC10673518 DOI: 10.3390/microorganisms11112794] [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: 10/28/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The methanogenic strain Mx-05T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05T were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05T required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05T grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L-1 NaCl (optimum 0.12 mol.L-1 NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05T as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05T (JCM 31474T).
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Affiliation(s)
- Guillaume Borrel
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell, 75015 Paris, France
| | - Khaled Fadhlaoui
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
- Université Clermont Auvergne, INRA, MEDIS, 63000 Clermont-Ferrand, France
- Université Clermont Auvergne, CNRS, UMR 6023 CNRS-UCA, Laboratoire Microorganismes: Génome et Environnement LMGE, 63000 Clermont-Ferrand, France
| | - Wajdi Ben Hania
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | - Nadia Gaci
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | - Gérard Pehau-Arnaudet
- Institut Pasteur, Université Paris Cité, Ultrastructural Bioimaging, 75015 Paris, France
| | - Prem Prashant Chaudhary
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Nathalie Ballet
- Lesaffre International, Lesaffre Group, 59700 Marcq-en-Barœul, France
| | - Monique Alric
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | | | - Marie-Laure Fardeau
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
| | - Bernard Ollivier
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
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12
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Homer JA, Xu L, Kayambu N, Zheng Q, Choi EJ, Kim BM, Sharpless KB, Zuilhof H, Dong J, Moses JE. Sulfur fluoride exchange. NATURE REVIEWS. METHODS PRIMERS 2023; 3:58. [PMID: 38873592 PMCID: PMC11171465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Sulfur Fluoride Exchange (SuFEx) is a click reaction par excellence that has revolutionized multiple research fields. In this Primer, we delve into the essential elements of SuFEx operation, catalysis, and SuFExable connective hubs. We also explore the cutting-edge applications of SuFEx in drug development, polymer science, and biochemistry. Additionally, we examine the potential limitations and promising prospects for this versatile click reaction.
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Affiliation(s)
- Joshua A. Homer
- Cancer Center, Cold Spring Harbor Laboratory, 1 Bungtown Road, NY 11724, USA
| | - Long Xu
- Institute of Translational Medicine, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Namitharan Kayambu
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Qinheng Zheng
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Current affiliation: Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Eun Joung Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - Byeong Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - K. Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- School of Pharmaceutical Science & Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jiajia Dong
- Institute of Translational Medicine, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
| | - John E. Moses
- Cancer Center, Cold Spring Harbor Laboratory, 1 Bungtown Road, NY 11724, USA
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13
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Yu B, Cao L, Li S, Klauser PC, Wang L. The proximity-enabled sulfur fluoride exchange reaction in the protein context. Chem Sci 2023; 14:7913-7921. [PMID: 37502323 PMCID: PMC10370592 DOI: 10.1039/d3sc01921g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/20/2023] [Indexed: 07/29/2023] Open
Abstract
The proximity-enabled sulfur(vi) fluoride exchange (SuFEx) reaction generates specific covalent linkages between proteins in cells and in vivo, which opens innovative avenues for studying elusive protein-protein interactions and developing potent covalent protein drugs. To exploit the power and expand the applications of covalent proteins, covalent linkage formation between proteins is the critical step, for which fundamental kinetic and essential properties remain unexplored. Herein, we systematically studied SuFEx kinetics in different proteins and conditions. In contrast to in small molecules, SuFEx in interacting proteins conformed with a two-step mechanism involving noncovalent binding, followed by covalent bond formation, exhibiting nonlinear rate dependence on protein concentration. The protein SuFEx rate consistently changed with protein binding affinity as well as chemical reactivity of the functional group and was impacted by target residue identity and solution pH. In addition, kinetic analyses of nanobody SR4 binding with SARS-CoV-2 spike protein revealed that viral target mutations did not abolish covalent binding but decreased the SuFEx rate with affinity decrease. Moreover, off-target cross-linking of a SuFEx-capable nanobody in human serum was not detected, and the SuFEx-generated protein linkage was stable at cellular acidic pHs, suggesting SuFEx suitability for in vivo usage. These results advanced our understanding of SuFEx reactivity and kinetics in proteins, which is invaluable for ongoing exploration of SuFEx-enabled covalent proteins for basic biological research and creative biotherapeutics.
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Affiliation(s)
- Bingchen Yu
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| | - Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| | - Shanshan Li
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| | - Paul C Klauser
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
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14
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Abstract
A SuFEx linkage reaction between sulfonimidoyl fluoride and allyltrimethylsilane was achieved for the construction of N-modified allylsulfoximines in minutes with BF3 as a nonmetal difunctional activator enabling the activation of both S-F and C-Si bonds to forge the S-Callyl (sp3) bond swiftly. Mechanistic studies and DFT calculations indicated that the linkage was initiated with the activation of sulfonimidoyl fluoride and then followed with the transfer of the fluoride anion to the TMS group.
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Affiliation(s)
- Daming Zeng
- State Key Laboratory of Molecular and Process Engineering, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, P. R. China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Suqin Zhao
- State Key Laboratory of Molecular and Process Engineering, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, P. R. China
| | - Wei-Ping Deng
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xuefeng Jiang
- State Key Laboratory of Molecular and Process Engineering, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, P. R. China
- State Key Laboratory of Elemento-organic Chemistry, Nankai University, Tianjin 300071, P. R. China
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15
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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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16
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Liu Z, Chen X, Yang S, Tian R, Wang F. Integrated mass spectrometry strategy for functional protein complex discovery and structural characterization. Curr Opin Chem Biol 2023; 74:102305. [PMID: 37071953 DOI: 10.1016/j.cbpa.2023.102305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 04/20/2023]
Abstract
The discovery of functional protein complex and the interrogation of the complex structure-function relationship (SFR) play crucial roles in the understanding and intervention of biological processes. Affinity purification-mass spectrometry (AP-MS) has been proved as a powerful tool in the discovery of protein complexes. However, validation of these novel protein complexes as well as elucidation of their molecular interaction mechanisms are still challenging. Recently, native top-down MS (nTDMS) is rapidly developed for the structural analysis of protein complexes. In this review, we discuss the integration of AP-MS and nTDMS in the discovery and structural characterization of functional protein complexes. Further, we think the emerging artificial intelligence (AI)-based protein structure prediction is highly complementary to nTDMS and can promote each other. We expect the hybridization of integrated structural MS with AI prediction to be a powerful workflow in the discovery and SFR investigation of functional protein complexes.
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Affiliation(s)
- Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shirui Yang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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17
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Update of the Pyrrolysyl-tRNA Synthetase/tRNA Pyl Pair and Derivatives for Genetic Code Expansion. J Bacteriol 2023; 205:e0038522. [PMID: 36695595 PMCID: PMC9945579 DOI: 10.1128/jb.00385-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The cotranslational incorporation of pyrrolysine (Pyl), the 22nd proteinogenic amino acid, into proteins in response to the UAG stop codon represents an outstanding example of natural genetic code expansion. Genetic encoding of Pyl is conducted by the pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA, tRNAPyl. Owing to the high tolerance of PylRS toward diverse amino acid substrates and great orthogonality in various model organisms, the PylRS/tRNAPyl-derived pairs are ideal for genetic code expansion to insert noncanonical amino acids (ncAAs) into proteins of interest. Since the discovery of cellular components involved in the biosynthesis and genetic encoding of Pyl, synthetic biologists have been enthusiastic about engineering PylRS/tRNAPyl-derived pairs to rewrite the genetic code of living cells. Recently, considerable progress has been made in understanding the molecular phylogeny, biochemical properties, and structural features of the PylRS/tRNAPyl pair, guiding its further engineering and optimization. In this review, we cover the basic and updated knowledge of the PylRS/tRNAPyl pair's unique characteristics that make it an outstanding tool for reprogramming the genetic code. In addition, we summarize the recent efforts to create efficient and (mutually) orthogonal PylRS/tRNAPyl-derived pairs for incorporation of diverse ncAAs by genome mining, rational design, and advanced directed evolution methods.
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18
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Wang D, Zhang J, huang Z, Yang Y, Fu T, Yang Y, Lyu Y, Jiang J, Qiu L, Cao Z, Zhang X, You Q, Lin Y, Zhao Z, Tan W. Robust Covalent Aptamer Strategy Enables Sensitive Detection and Enhanced Inhibition of SARS-CoV-2 Proteins. ACS CENTRAL SCIENCE 2023; 9:72-83. [PMID: 36712483 PMCID: PMC9881204 DOI: 10.1021/acscentsci.2c01263] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Indexed: 06/18/2023]
Abstract
Aptamer-based detection and therapy have made substantial progress with cost control and easy modification. However, the conformation lability of an aptamer typically causes the dissociation of aptamer-target complexes during harsh washes and other environmental stresses, resulting in only moderate detection sensitivity and a decreasing therapeutic effect. Herein, we report a robust covalent aptamer strategy to sensitively detect nucleocapsid protein and potently neutralize spike protein receptor binding domain (RBD), two of the most important proteins of SARS-CoV-2, after testing different cross-link electrophilic groups via integrating the specificity and efficiency. Covalent aptamers can specifically convert aptamer-protein complexes from the dynamic equilibrium state to stable and irreversible covalent complexes even in harsh environments. Covalent aptamer-based ELISA detection of nucleocapsid protein can surpass the gold standard, antibody-based sandwich ELISA. Further, covalent aptamer performs enhanced functional inhibition to RBD protein even in a blood vessel-mimicking flowing circulation system. The robust covalent aptamer-based strategy is expected to inspire more applications in accurate molecular modification, disease biomarker discovery, and other theranostic fields.
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Affiliation(s)
- Dan Wang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- LIMES
Chemical Biology Unit, Universität
Bonn, 53121 Bonn, Germany
| | - Jing Zhang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Zhiyong huang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yuhang Yang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Ting Fu
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yu Yang
- Institute
of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University
School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yifan Lyu
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Jianhui Jiang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Liping Qiu
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Zehui Cao
- Institute
of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University
School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaobing Zhang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Qimin You
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Ustar
Biotechnologies (Hangzhou) Ltd., Hangzhou, Zhejiang 310053, China
| | - Yuankui Lin
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Ustar
Biotechnologies (Hangzhou) Ltd., Hangzhou, Zhejiang 310053, China
| | - Zilong Zhao
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute
of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University
School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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19
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A (cross)link in the chains. Nat Chem 2023; 15:5-6. [PMID: 36609645 DOI: 10.1038/s41557-022-01116-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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