1
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Petrova VV, Solovev YV, Porozov YB, Polynski MV. Will We Witness Enzymatic or Pd-(Oligo)Peptide Catalysis in Suzuki Cross-Coupling Reactions? J Org Chem 2024; 89:8478-8485. [PMID: 38861408 DOI: 10.1021/acs.joc.4c00409] [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: 06/13/2024]
Abstract
Despite the development of numerous advanced ligands for Pd-catalyzed Suzuki cross-coupling reaction, the potential of (oligo)peptides serving as ligands remains unexplored. This study demonstrates via density functional theory (DFT) modeling that (oligo)peptide ligands can drive superior activity compared to classic phosphines in these reactions. The utilization of natural amino acids such as Met, SeMet, and His leads to strong binding of the Pd center, thereby ensuring substantial stability of the system. The increasing sustainability and economic viability of (oligo)peptide synthesis open new prospects for applying Pd-(oligo)peptide systems as greener catalysts. The feasibility of de novo engineering an artificial Pd-based enzyme for Suzuki cross-coupling is discussed, laying the groundwork for future innovations in catalytic systems.
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Affiliation(s)
- Vlada V Petrova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Quantum Chemistry Department, Institute of Chemistry, St. Petersburg State University, Universitetsky Prospect 26, Saint Petersburg 198504, Russia
| | - Yaroslav V Solovev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Yuri B Porozov
- St. Petersburg School of Physics, Mathematics, and Computer Science, HSE University, Kantemirovskaya Street 3-1A, Saint Petersburg 194100, Russia
- Advitam Laboratory, Vodovodska 158, Belgrade 11147, Serbia
| | - Mikhail V Polynski
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
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2
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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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3
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Zheng Y, Zhu X, Jiang M, Cao F, You Q, Chen X. Development and Applications of D-Amino Acid Derivatives-based Metabolic Labeling of Bacterial Peptidoglycan. Angew Chem Int Ed Engl 2024; 63:e202319400. [PMID: 38284300 DOI: 10.1002/anie.202319400] [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: 12/18/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
Peptidoglycan, an essential component within the cell walls of virtually all bacteria, is composed of glycan strands linked by stem peptides that contain D-amino acids. The peptidoglycan biosynthesis machinery exhibits high tolerance to various D-amino acid derivatives. D-amino acid derivatives with different functionalities can thus be specifically incorporated into and label the peptidoglycan of bacteria, but not the host mammalian cells. This metabolic labeling strategy is highly selective, highly biocompatible, and broadly applicable, which has been utilized in various fields. This review introduces the metabolic labeling strategies of peptidoglycan by using D-amino acid derivatives, including one-step and two-step strategies. In addition, we emphasize the various applications of D-amino acid derivative-based metabolic labeling, including bacterial peptidoglycan visualization (existence, biosynthesis, and dynamics, etc.), bacterial visualization (including bacterial imaging and visualization of growth and division, metabolic activity, antibiotic susceptibility, etc.), pathogenic bacteria-targeted diagnostics and treatment (positron emission tomography (PET) imaging, photodynamic therapy, photothermal therapy, gas therapy, immunotherapy, etc.), and live bacteria-based therapy. Finally, a summary of this metabolic labeling and an outlook is provided.
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Affiliation(s)
- Yongfang Zheng
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Xinyu Zhu
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Mingyi Jiang
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Fangfang Cao
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Qing You
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
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4
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Petrovskii SK, Grachova EV, Monakhov KY. Bioorthogonal chemistry of polyoxometalates - challenges and prospects. Chem Sci 2024; 15:4202-4221. [PMID: 38516091 PMCID: PMC10952089 DOI: 10.1039/d3sc06284h] [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: 11/28/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Abstract
Bioorthogonal chemistry has enabled scientists to carry out controlled chemical processes in high yields in vivo while minimizing hazardous effects. Its extension to the field of polyoxometalates (POMs) could open up new possibilities and new applications in molecular electronics, sensing and catalysis, including inside living cells. However, this comes with many challenges that need to be addressed to effectively implement and exploit bioorthogonal reactions in the chemistry of POMs. In particular, how to protect POMs from the biological environment but make their reactivity selective towards specific bioorthogonal tags (and thereby reduce their toxicity), as well as which bioorthogonal chemistry protocols are suitable for POMs and how reactions can be carried out are questions that we are exploring herein. This perspective conceptualizes and discusses advances in the supramolecular chemistry of POMs, their click chemistry, and POM-based surface engineering to develop innovative bioorthogonal approaches tailored to POMs and to improve POM biological tolerance.
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Affiliation(s)
| | - Elena V Grachova
- Institute of Chemistry, St Petersburg University Universitetskii pr. 26 St. Petersburg 198504 Russia
| | - Kirill Yu Monakhov
- Leibniz Institute of Surface Engineering (IOM) Permoserstr. 15 Leipzig 04318 Germany
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5
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Meeus EJ, Álvarez M, Koelman E, Pérez PJ, Reek JNH, de Bruin B. Copper-Catalyzed Sulfimidation in Aqueous Media: a Fast, Chemoselective and Biomolecule-Compatible Reaction. Chemistry 2024; 30:e202303939. [PMID: 38116945 DOI: 10.1002/chem.202303939] [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: 11/27/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/21/2023]
Abstract
Performing transition metal-catalyzed reactions in cells and living systems has equipped scientists with a toolbox to study biological processes and release drugs on demand. Thus far, an impressive scope of reactions has been performed in these settings, but many are yet to be introduced. Nitrene transfer presents a rather unexplored new-to-nature reaction. The reaction products are frequently encountered motifs in pharmaceuticals, presenting opportunities for the controlled, intracellular synthesis of drugs. Hence, we explored the transition metal-catalyzed sulfimidation reaction in water for future in vivo application. Two Cu(I) complexes containing trispyrazolylborate ligands (Tpx ) were selected, and the catalytic system was evaluated with the aid of three fitness factors. The excellent nitrene transfer reactivity and high chemoselectivity of the catalysts, coupled with good biomolecule compatibility, successfully enabled the sulfimidation of thioethers in aqueous media. We envision that this copper-catalyzed sulfimidation reaction could be an interesting starting point to unlock the potential of nitrene transfer catalysis in vivo.
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Affiliation(s)
- Eva J Meeus
- Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - María Álvarez
- CIQSO-Centro de Investigación en Química Sostenible and Departamento de Química, Universidad de Huelva, Campus de El Carmen, 21007, Huelva, Spain
| | - Emma Koelman
- Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Pedro J Pérez
- CIQSO-Centro de Investigación en Química Sostenible and Departamento de Química, Universidad de Huelva, Campus de El Carmen, 21007, Huelva, Spain
| | - Joost N H Reek
- Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Bas de Bruin
- Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
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6
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Andrikopoulos N, Tang H, Wang Y, Liang X, Li Y, Davis TP, Ke PC. Exploring Peptido-Nanocomposites in the Context of Amyloid Diseases. Angew Chem Int Ed Engl 2024; 63:e202309958. [PMID: 37943171 DOI: 10.1002/anie.202309958] [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: 07/12/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/10/2023]
Abstract
Therapeutic peptides are a major class of pharmaceutical drugs owing to their target-binding specificity as well as their versatility in inhibiting aberrant protein-protein interactions associated with human pathologies. Within the realm of amyloid diseases, the use of peptides and peptidomimetics tailor-designed to overcome amyloidogenesis has been an active research endeavor since the late 90s. In more recent years, incorporating nanoparticles for enhancing the biocirculation and delivery of peptide drugs has emerged as a frontier in nanomedicine, and nanoparticles have further demonstrated a potency against amyloid aggregation and cellular inflammation to rival strategies employing small molecules, peptides, and antibodies. Despite these efforts, however, a fundamental understanding of the chemistry, characteristics and function of peptido-nanocomposites is lacking, and a systematic analysis of such strategy for combating a range of amyloid pathogeneses is missing. Here we review the history, principles and evolving chemistry of constructing peptido-nanocomposites from bottom up and discuss their future application against amyloid diseases that debilitate a significant portion of the global population.
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Affiliation(s)
- Nicholas Andrikopoulos
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Huayuan Tang
- College of Mechanics and Materials, Hohai University, Nanjing, 211100, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Yue Wang
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 510006, China
| | - Xiufang Liang
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou 510006, China
| | - Yuhuan Li
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Thomas P Davis
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Pu Chun Ke
- Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
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7
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Schauenburg D, Weil T. Chemical Reactions in Living Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303396. [PMID: 37679060 PMCID: PMC10885656 DOI: 10.1002/advs.202303396] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/18/2023] [Indexed: 09/09/2023]
Abstract
The term "in vivo ("in the living") chemistry" refers to chemical reactions that take place in a complex living system such as cells, tissue, body liquids, or even in an entire organism. In contrast, reactions that occur generally outside living organisms in an artificial environment (e.g., in a test tube) are referred to as in vitro. Over the past decades, significant contributions have been made in this rapidly growing field of in vivo chemistry, but it is still not fully understood, which transformations proceed efficiently without the formation of by-products or how product formation in such complex environments can be characterized. Potential applications can be imagined that synthesize drug molecules directly within the cell or confer new cellular functions through controlled chemical transformations that will improve the understanding of living systems and develop new therapeutic strategies. The guiding principles of this contribution are twofold: 1) Which chemical reactions can be translated from the laboratory to the living system? 2) Which characterization methods are suitable for studying reactions and structure formation in complex living environments?
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Affiliation(s)
| | - Tanja Weil
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
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8
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Stone DJ, Macias-Contreras M, Crist SM, Bucag CFT, Seo G, Zhu L. SNAP-tagging live cells via chelation-assisted copper-catalyzed azide-alkyne cycloaddition. Org Biomol Chem 2023; 21:7419-7436. [PMID: 37665276 DOI: 10.1039/d3ob01003a] [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: 09/05/2023]
Abstract
SNAP-tag is a single-turnover enzyme that has become a powerful tool, hence a popular choice, of targeted cellular protein labeling. Three SNAP-tag substrates that carry the copper-chelating 2-picolyl azide moiety are prepared, one of which has an unconventional 5-pyridylmethyl-substituted guanine structure, rather than the usual benzylguanine that is optimized to be accepted by SNAP-tag. All three substrates are effective in transferring a 2-picolyl azide moiety to SNAP-tag in live cells under conventional labeling conditions (30-minute incubation of cells with labeling reagents at 37 °C under 5% CO2). Live cells that are decorated with chelating azido groups on the extracellular side of membranes undergo copper-catalyzed azide-alkyne cycloaddition (CuAAC) with an ethynyl-functionalized fluorophore to accomplish membrane protein labeling by a fluorescent dye. The chelation-assisted CuAAC labeling step is rapid (<1 minute) with a relatively low dose of the copper catalyst (20 μM), and consequently exerts no ill effect on the labeled cells. A SNAP-tag substrate that carries a non-chelating azide moiety, on the other hand, fails to produce satisfactory labeling under the same constraints. The rapid, live cell-compatible SNAP-tag/chelation-assisted CuAAC two-step method expands the utility of SNAP-tag in protein labeling applications.
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Affiliation(s)
- Daniel J Stone
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
| | - Miguel Macias-Contreras
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
| | - Shaun M Crist
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
| | - Christelle F T Bucag
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
| | - Gwimoon Seo
- Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL 32306-4380, USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
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9
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Pan S, Ding A, Li Y, Sun Y, Zhan Y, Ye Z, Song N, Peng B, Li L, Huang W, Shao H. Small-molecule probes from bench to bedside: advancing molecular analysis of drug-target interactions toward precision medicine. Chem Soc Rev 2023; 52:5706-5743. [PMID: 37525607 DOI: 10.1039/d3cs00056g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Over the past decade, remarkable advances have been witnessed in the development of small-molecule probes. These molecular tools have been widely applied for interrogating proteins, pathways and drug-target interactions in preclinical research. While novel structures and designs are commonly explored in probe development, the clinical translation of small-molecule probes remains limited, primarily due to safety and regulatory considerations. Recent synergistic developments - interfacing novel chemical probes with complementary analytical technologies - have introduced and expedited diverse biomedical opportunities to molecularly characterize targeted drug interactions directly in the human body or through accessible clinical specimens (e.g., blood and ascites fluid). These integrated developments thus offer unprecedented opportunities for drug development, disease diagnostics and treatment monitoring. In this review, we discuss recent advances in the structure and design of small-molecule probes with novel functionalities and the integrated development with imaging, proteomics and other emerging technologies. We further highlight recent applications of integrated small-molecule technologies for the molecular analysis of drug-target interactions, including translational applications and emerging opportunities for whole-body imaging, tissue-based measurement and blood-based analysis.
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Affiliation(s)
- Sijun Pan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Aixiang Ding
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yisi Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yaxin Sun
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yueqin Zhan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Zhenkun Ye
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Ning Song
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Wei Huang
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore 117599, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore 117583, Singapore
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10
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Abstract
The impact of click chemistry was recently recognized with the 2022 Nobel Prize in Chemistry. The breadth of areas where click chemistry has accelerated discovery is prodigal. In one of the most written about subjects in chemistry over recent years, this short perspective zones in on a small fragment of what we, the authors, consider are some of the most critical developments in synthetic chemistry, which have expanded access to the click chemistry toolbox. In addition, we touch upon areas within medicinal chemistry and novel approaches to drug discovery enabled by click chemistry, where we believe there is untapped potential for biological function to be found and exploited.
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Affiliation(s)
- Adam D Moorhouse
- Cancer Centre, Cold Spring Harbor Laboratory, 1 Bungtown Road, New York, NY 11724, USA
| | - Joshua A Homer
- Cancer Centre, Cold Spring Harbor Laboratory, 1 Bungtown Road, New York, NY 11724, USA
| | - John E Moses
- Cancer Centre, Cold Spring Harbor Laboratory, 1 Bungtown Road, New York, NY 11724, USA
- Lead Contact
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11
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Oerlemans RAJF, Shao J, Huisman SGAM, Li Y, Abdelmohsen LKEA, van Hest JCM. Compartmentalized Intracellular Click Chemistry with Biodegradable Polymersomes. Macromol Rapid Commun 2023; 44:e2200904. [PMID: 36607841 DOI: 10.1002/marc.202200904] [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: 11/18/2022] [Revised: 12/17/2022] [Indexed: 01/07/2023]
Abstract
Polymersome nanoreactors that can be employed as artificial organelles have gained much interest over the past decades. Such systems often include biological catalysts (i.e., enzymes) so that they can undertake chemical reactions in cellulo. Examples of nanoreactor artificial organelles that acquire metal catalysts in their structure are limited, and their application in living cells remains fairly restricted. In part, this shortfall is due to difficulties associated with constructing systems that maintain their stability in vitro, let alone the toxicity they impose on cells. This study demonstrates a biodegradable and biocompatible polymersome nanoreactor platform, which can be applied as an artificial organelle in living cells. The ability of the artificial organelles to covalently and non-covalently incorporate tris(triazolylmethyl)amine-Cu(I) complexes in their membrane is shown. Such artificial organelles are capable of effectively catalyzing a copper-catalyzed azide-alkyne cycloaddition intracellularly, without compromising the cells' integrity. The platform represents a step forward in the application of polymersome-based nanoreactors as artificial organelles.
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Affiliation(s)
- Roy A J F Oerlemans
- Department of Bio-medical engineering and Chemical engineering & Chemistry, Eindhoven University of Technology: Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jingxin Shao
- Department of Bio-medical engineering and Chemical engineering & Chemistry, Eindhoven University of Technology: Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Sander G A M Huisman
- Department of Bio-medical engineering and Chemical engineering & Chemistry, Eindhoven University of Technology: Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Yudong Li
- Department of Bio-medical engineering and Chemical engineering & Chemistry, Eindhoven University of Technology: Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Loai K E A Abdelmohsen
- Department of Bio-medical engineering and Chemical engineering & Chemistry, Eindhoven University of Technology: Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jan C M van Hest
- Department of Bio-medical engineering and Chemical engineering & Chemistry, Eindhoven University of Technology: Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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12
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Mitry MMA, Greco F, Osborn HMI. In Vivo Applications of Bioorthogonal Reactions: Chemistry and Targeting Mechanisms. Chemistry 2023; 29:e202203942. [PMID: 36656616 DOI: 10.1002/chem.202203942] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
Bioorthogonal chemistry involves selective biocompatible reactions between functional groups that are not normally present in biology. It has been used to probe biomolecules in living systems, and has advanced biomedical strategies such as diagnostics and therapeutics. In this review, the challenges and opportunities encountered when translating in vitro bioorthogonal approaches to in vivo settings are presented, with a focus on methods to deliver the bioorthogonal reaction components. These methods include metabolic bioengineering, active targeting, passive targeting, and simultaneously used strategies. The suitability of bioorthogonal ligation reactions and bond cleavage reactions for in vivo applications is critically appraised, and practical considerations such as the optimum scheduling regimen in pretargeting approaches are discussed. Finally, we present our own perspectives for this area and identify what, in our view, are the key challenges that must be overcome to maximise the impact of these approaches.
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Affiliation(s)
- Madonna M A Mitry
- Reading School of Pharmacy, University of Reading Whiteknights, Reading, RG6 6AD, UK.,Department of Pharmaceutical Chemistry Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt
| | - Francesca Greco
- Reading School of Pharmacy, University of Reading Whiteknights, Reading, RG6 6AD, UK
| | - Helen M I Osborn
- Reading School of Pharmacy, University of Reading Whiteknights, Reading, RG6 6AD, UK
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13
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Bioorthogonal chemistry based on-demand drug delivery system in cancer therapy. Front Chem Sci Eng 2023. [DOI: 10.1007/s11705-022-2227-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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14
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Wu P. The Nobel Prize in Chemistry 2022: Fulfilling Demanding Applications with Simple Reactions. ACS Chem Biol 2022; 17:2959-2961. [PMID: 36279258 DOI: 10.1021/acschembio.2c00788] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The Nobel Prize in Chemistry 2022 was awarded jointly to Carolyn R. Bertozzi, Morten Meldal, and K. Barry Sharpless "for the development of click chemistry and bioorthogonal chemistry". Such rapid, selective, and nontoxic covalent reactions that link two components together under benign conditions have led to a paradigm shift in basic research and practical applications.
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Affiliation(s)
- Peng Wu
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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15
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Seoane A, Mascareñas JL. Exporting Homogeneous Transition Metal Catalysts to Biological Habitats. European J Org Chem 2022; 2022:e202200118. [PMID: 36248016 PMCID: PMC9542366 DOI: 10.1002/ejoc.202200118] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Indexed: 01/23/2023]
Abstract
The possibility of performing designed transition-metal catalyzed reactions in biological and living contexts can open unprecedented opportunities to interrogate and interfere with biology. However, the task is far from obvious, in part because of the presumed incompatibly between organometallic chemistry and complex aqueous environments. Nonetheless, in the past decade there has been a steady progress in this research area, and several transition-metal (TM)-catalyzed bioorthogonal and biocompatible reactions have been developed. These reactions encompass a wide range of mechanistic profiles, which are very different from those used by natural metalloenzymes. Herein we present a summary of the latest progress in the field of TM-catalyzed bioorthogonal reactions, with a special focus on those triggered by activation of multiple carbon-carbon bonds.
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Affiliation(s)
- Andrés Seoane
- Centro Singular de Investigación Química Biolóxica e Materiais Moleculares (CIQUS)Departamento de Química Orgánica.Universidade de Santiago de Compostela15782Santiago de CompostelaA CoruñaSpain
| | - José Luis Mascareñas
- Centro Singular de Investigación Química Biolóxica e Materiais Moleculares (CIQUS)Departamento de Química Orgánica.Universidade de Santiago de Compostela15782Santiago de CompostelaA CoruñaSpain
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16
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Liu Y, Lai KL, Vong K. Transition Metal Scaffolds Used To Bring New‐to‐Nature Reactions into Biological Systems. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yifei Liu
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Ka Lun Lai
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
| | - Kenward Vong
- Department of Chemistry The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon Hong Kong China
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17
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Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins. Bioorg Med Chem 2022; 62:116721. [PMID: 35358862 DOI: 10.1016/j.bmc.2022.116721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022]
Abstract
Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.
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18
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Synthesis and Fluorescent Properties of Aminopyridines and the Application in "Click and Probing". Molecules 2022; 27:molecules27051596. [PMID: 35268697 PMCID: PMC8912075 DOI: 10.3390/molecules27051596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 11/17/2022] Open
Abstract
Unsubstituted pyridin-2-amine has a high quantum yield and is a potential scaffold for a fluorescent probe. However, the facile access to conjugated highly substituted aminopyridines and the study of their fluorescent properties is scarce. In this paper, synthesis and fluorescent properties of multisubstituted aminopyridines were studied based on a recently developed Rh-catalyzed coupling of vinyl azide with isonitrile to form a vinyl carbodiimide intermediate, following tandem cyclization with an alkyne. An aminopyridine substituted with an azide group as a potential probe was further designed, synthesized, and evaluated. The “clicking-and-probing” experiment of it on BSA protein showed the potential of aminopyridine as a scaffold of a biological probe.
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19
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Partipilo G, Graham AJ, Belardi B, Keitz BK. Extracellular Electron Transfer Enables Cellular Control of Cu(I)-Catalyzed Alkyne-Azide Cycloaddition. ACS CENTRAL SCIENCE 2022; 8:246-257. [PMID: 35233456 PMCID: PMC8875427 DOI: 10.1021/acscentsci.1c01208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Indexed: 05/03/2023]
Abstract
Extracellular electron transfer (EET) is an anaerobic respiration process that couples carbon oxidation to the reduction of metal species. In the presence of a suitable metal catalyst, EET allows for cellular metabolism to control a variety of synthetic transformations. Here, we report the use of EET from the electroactive bacterium Shewanella oneidensis for metabolic and genetic control over Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC). CuAAC conversion under anaerobic and aerobic conditions was dependent on live, actively respiring S. oneidensis cells. The reaction progress and kinetics were manipulated by tailoring the central carbon metabolism. Similarly, EET-CuAAC activity was dependent on specific EET pathways that could be regulated via inducible expression of EET-relevant proteins: MtrC, MtrA, and CymA. EET-driven CuAAC exhibited modularity and robustness in the ligand and substrate scope. Furthermore, the living nature of this system could be exploited to perform multiple reaction cycles without regeneration, something inaccessible to traditional chemical reductants. Finally, S. oneidensis enabled bioorthogonal CuAAC membrane labeling on live mammalian cells without affecting cell viability, suggesting that S. oneidensis can act as a dynamically tunable biocatalyst in complex environments. In summary, our results demonstrate how EET can expand the reaction scope available to living systems by enabling cellular control of CuAAC.
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Affiliation(s)
- Gina Partipilo
- McKetta
Department of Chemical Engineering, University
of Texas at Austin, Austin, Texas 78712, United States
- Center
for Dynamics and Control of Materials, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Austin J. Graham
- McKetta
Department of Chemical Engineering, University
of Texas at Austin, Austin, Texas 78712, United States
- Center
for Dynamics and Control of Materials, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Brian Belardi
- McKetta
Department of Chemical Engineering, University
of Texas at Austin, Austin, Texas 78712, United States
| | - Benjamin K. Keitz
- McKetta
Department of Chemical Engineering, University
of Texas at Austin, Austin, Texas 78712, United States
- Center
for Dynamics and Control of Materials, University
of Texas at Austin, Austin, Texas 78712, United States
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20
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Banahene N, Kavunja HW, Swarts BM. Chemical Reporters for Bacterial Glycans: Development and Applications. Chem Rev 2022; 122:3336-3413. [PMID: 34905344 PMCID: PMC8958928 DOI: 10.1021/acs.chemrev.1c00729] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacteria possess an extraordinary repertoire of cell envelope glycans that have critical physiological functions. Pathogenic bacteria have glycans that are essential for growth and virulence but are absent from humans, making them high-priority targets for antibiotic, vaccine, and diagnostic development. The advent of metabolic labeling with bioorthogonal chemical reporters and small-molecule fluorescent reporters has enabled the investigation and targeting of specific bacterial glycans in their native environments. These tools have opened the door to imaging glycan dynamics, assaying and inhibiting glycan biosynthesis, profiling glycoproteins and glycan-binding proteins, and targeting pathogens with diagnostic and therapeutic payload. These capabilities have been wielded in diverse commensal and pathogenic Gram-positive, Gram-negative, and mycobacterial species─including within live host organisms. Here, we review the development and applications of chemical reporters for bacterial glycans, including peptidoglycan, lipopolysaccharide, glycoproteins, teichoic acids, and capsular polysaccharides, as well as mycobacterial glycans, including trehalose glycolipids and arabinan-containing glycoconjugates. We cover in detail how bacteria-targeting chemical reporters are designed, synthesized, and evaluated, how they operate from a mechanistic standpoint, and how this information informs their judicious and innovative application. We also provide a perspective on the current state and future directions of the field, underscoring the need for interdisciplinary teams to create novel tools and extend existing tools to support fundamental and translational research on bacterial glycans.
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21
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Hoffmann P, Lherbet C, Fabing I, Barthélémy MC, Borjon-Piron Y, Laurent C, Vigroux A. A mesoporous metal–organic framework used to sustainably release copper( ii) into reducing aqueous media to promote the CuAAC click reaction. RSC Adv 2022; 12:26825-26833. [PMID: 36320833 PMCID: PMC9494208 DOI: 10.1039/d2ra04298c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022] Open
Abstract
The mesoporous metal–organic framework Cr-MIL-101-NH2 (MOF1) has been used to encapsulate, by a simple impregnation method, large amounts of copper sulfate. The resulting loaded material, Cu@MOF1, was successfully employed to slowly release copper(ii) into an appropriate reaction medium in which the reducing agent sodium ascorbate reduces copper(ii) to copper(i), thus allowing the well-known copper(i)-catalyzed alkyne–azide cycloaddition (CuAAC) “click” reaction to proceed in the absence of potentially high local copper(i) concentrations. The use of a MOF-based controlled copper release system such as Cu@MOF1 may be relevant for copper(i)-catalyzed reactions having substrates that could be degraded by potentially high local concentrations of copper(i). The copper chelating ligand TBTA (tris(benzyltriazolylmethyl)amine), a very useful ligand for click chemistry, has been successfully attached to the pores of MOF1. The resulting TBTA-functionalized MOF (MOF3) was compared with its non-functionalized version (MOF1). At copper loadings of ca. 3 mmol g−1, the results revealed that the performances of the two materials are strikingly similar. Upon immersion in methanol/water (95/5) containing sodium ascorbate, both materials slowly released copper encapsulated in their pores and could be recovered and reused efficiently for up to five reaction cycles without reloading with metal ion, while allowing the CuAAC reaction to proceed with excellent conversion rates and yields. Cr-MIL-101-NH2 (MOF1) has been used to encapsulate large amounts of copper sulfate and the resulting loaded material, Cu@MOF1, was successfully used to promote the CuAAC click reaction.![]()
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Affiliation(s)
- Pascal Hoffmann
- LSPCMIB, Université Toulouse 3 Paul Sabatier, UMR CNRS UPS 5068, 118 Route de Narbonne, 31062 Toulouse, France
| | - Christian Lherbet
- LSPCMIB, Université Toulouse 3 Paul Sabatier, UMR CNRS UPS 5068, 118 Route de Narbonne, 31062 Toulouse, France
| | - Isabelle Fabing
- Institut de Chimie de Toulouse, Université Toulouse 3 Paul Sabatier, ICT-FR CNRS 2599, 118 Route de Narbonne, 31062 Toulouse, France
| | - Marie-Claire Barthélémy
- CIRIMAT, Université Toulouse 3 Paul Sabatier, UMR CNRS UPS INP 5085, 118 Route de Narbonne, 31062 Toulouse, France
| | - Yann Borjon-Piron
- CIRIMAT, Université Toulouse 3 Paul Sabatier, UMR CNRS UPS INP 5085, 118 Route de Narbonne, 31062 Toulouse, France
| | - Christophe Laurent
- CIRIMAT, Université Toulouse 3 Paul Sabatier, UMR CNRS UPS INP 5085, 118 Route de Narbonne, 31062 Toulouse, France
| | - Alain Vigroux
- LSPCMIB, Université Toulouse 3 Paul Sabatier, UMR CNRS UPS 5068, 118 Route de Narbonne, 31062 Toulouse, France
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22
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Xiong H, Liu L, Wang Y, Jiang H, Wang X. Engineered Aptamer-Organic Amphiphile Self-Assemblies for Biomedical Applications: Progress and Challenges. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104341. [PMID: 34622570 DOI: 10.1002/smll.202104341] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/21/2021] [Indexed: 06/13/2023]
Abstract
Currently, nucleic acid aptamers are exploited as robust targeting ligands in the biomedical field, due to their specific molecular recognition, little immunogenicity, low cost, ect. Thanks to the facile chemical modification and high hydrophilicity, aptamers can be site-specifically linked with hydrophobic moieties to prepare aptamer-organic amphiphiles (AOAs), which spontaneously assemble into aptamer-organic amphiphile self-assemblies (AOASs). These polyvalent self-assemblies feature with enhanced target-binding ability, increased resistance to nuclease, and efficient cargo-loading, making them powerful platforms for bioapplications, including targeted drug delivery, cell-based cancer therapy, biosensing, and bioimaging. Besides, the morphology of AOASs can be elaborately manipulated for smarter biomedical functions, by regulating the hydrophilicity/hydrophobicity ratio of AOAs. Benefiting from the boom in DNA synthesis technology and nanotechnology, various types of AOASs, including aptamer-polymer amphiphile self-assemblies, aptamer-lipid amphiphile self-assemblies, aptamer-cell self-assemblies, ect, have been constructed with great biomedical potential. Particularly, stimuli-responsive AOASs with transformable structure can realize site-specific drug release, enhanced tumor penetration, and specific target molecule detection. Herein, the general synthesis methods of oligonucleotide-organic amphiphiles are firstly summarized. Then recent progress in different types of AOASs for bioapplications and strategies for morphology control are systematically reviewed. The present challenges and future perspectives of this field are also discussed.
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Affiliation(s)
- Hongjie Xiong
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Liu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yihan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Hui Jiang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xuemei Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
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23
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Xiong TM, Garcia ES, Chen J, Zhu L, Alzona AJ, Zimmerman SC. Enzyme-like catalysis by single chain nanoparticles that use transition metal cofactors. Chem Commun (Camb) 2021; 58:985-988. [PMID: 34935784 DOI: 10.1039/d1cc05578j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report a modular approach in which a noncovalently cross-linked single chain nanoparticle (SCNP) selectively binds catalyst "cofactors" and substrates to increase both the catalytic activity of a Cu-catalyzed alkyne-azide cycloaddition reaction and the Ru-catalyzed cleavage of allylcarbamate groups compared to the free catalysts.
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Affiliation(s)
- Thao M Xiong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Edzna S Garcia
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Junfeng Chen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Lingyang Zhu
- NMR Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana 61801, USA
| | - Ariale J Alzona
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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24
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Abstract
Bioorthogonal chemistry is a set of methods using the chemistry of non-native functional groups to explore and understand biology in living organisms. In this review, we summarize the most common reactions used in bioorthogonal methods, their relative advantages and disadvantages, and their frequency of occurrence in the published literature. We also briefly discuss some of the less common but potentially useful methods. We then analyze the bioorthogonal-related publications in the CAS Content Collection to determine how often different types of biomolecules such as proteins, carbohydrates, glycans, and lipids have been studied using bioorthogonal chemistry. The most prevalent biological and chemical methods for attaching bioorthogonal functional groups to these biomolecules are elaborated. We also analyze the publication volume related to different types of bioorthogonal applications in the CAS Content Collection. The use of bioorthogonal chemistry for imaging, identifying, and characterizing biomolecules and for delivering drugs to treat disease is discussed at length. Bioorthogonal chemistry for the surface attachment of proteins and in the use of modified carbohydrates is briefly noted. Finally, we summarize the state of the art in bioorthogonal chemistry and its current limitations and promise for its future productive use in chemistry and biology.
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Affiliation(s)
- Robert E Bird
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Steven A Lemmel
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Xiang Yu
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Qiongqiong Angela Zhou
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
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25
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Li Z, Chen Q, Wang J, Pan X, Lu W. Research Progress and Application of Bioorthogonal Reactions in Biomolecular Analysis and Disease Diagnosis. Top Curr Chem (Cham) 2021; 379:39. [PMID: 34590223 DOI: 10.1007/s41061-021-00352-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022]
Abstract
Bioorthogonal reactions are rapid, specific and high yield reactions that can be performed in in vivo microenvironments or simulated microenvironments. At present, the main biorthogonal reactions include Staudinger ligation, copper-catalyzed azide alkyne cycloaddition, strain-promoted [3 + 2] reaction, tetrazine ligation, metal-catalyzed coupling reaction and photo-induced biorthogonal reactions. To date, many reviews have reported that bioorthogonal reactions have been used widely as a powerful tool in the field of life sciences, such as in target recognition, drug discovery, drug activation, omics research, visualization of life processes or exogenous bacterial infection processes, signal transduction pathway research, chemical reaction dynamics analysis, disease diagnosis and treatment. In contrast, to date, few studies have investigated the application of bioorthogonal reactions in the analysis of biomacromolecules in vivo. Therefore, the application of bioorthogonal reactions in the analysis of proteins, nucleic acids, metabolites, enzyme activities and other endogenous molecules, and the determination of disease-related targets is reviewed. In addition, this review discusses the future development opportunities and challenges of biorthogonal reactions. This review presents an overview of recent advances for application in biomolecular analysis and disease diagnosis, with a focus on proteins, metabolites and RNA detection.
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Affiliation(s)
- Zilong Li
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qinhua Chen
- Department of Pharmacy, Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Jin Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xiaoyan Pan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Wen Lu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China.
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26
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Hui E, Sumey JL, Caliari SR. Click-functionalized hydrogel design for mechanobiology investigations. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2021; 6:670-707. [PMID: 36338897 PMCID: PMC9631920 DOI: 10.1039/d1me00049g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The advancement of click-functionalized hydrogels in recent years has coincided with rapid growth in the fields of mechanobiology, tissue engineering, and regenerative medicine. Click chemistries represent a group of reactions that possess high reactivity and specificity, are cytocompatible, and generally proceed under physiologic conditions. Most notably, the high level of tunability afforded by these reactions enables the design of user-controlled and tissue-mimicking hydrogels in which the influence of important physical and biochemical cues on normal and aberrant cellular behaviors can be independently assessed. Several critical tissue properties, including stiffness, viscoelasticity, and biomolecule presentation, are known to regulate cell mechanobiology in the context of development, wound repair, and disease. However, many questions still remain about how the individual and combined effects of these instructive properties regulate the cellular and molecular mechanisms governing physiologic and pathologic processes. In this review, we discuss several click chemistries that have been adopted to design dynamic and instructive hydrogels for mechanobiology investigations. We also chart a path forward for how click hydrogels can help reveal important insights about complex tissue microenvironments.
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Affiliation(s)
- Erica Hui
- Department of Chemical Engineering, University of Virginia, 102 Engineer's Way, Charlottesville, Virginia 22904, USA
| | - Jenna L Sumey
- Department of Chemical Engineering, University of Virginia, 102 Engineer's Way, Charlottesville, Virginia 22904, USA
| | - Steven R Caliari
- Department of Chemical Engineering, University of Virginia, 102 Engineer's Way, Charlottesville, Virginia 22904, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22904, USA
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27
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Wang W, Zhang X, Huang R, Hirschbiegel CM, Wang H, Ding Y, Rotello VM. In situ activation of therapeutics through bioorthogonal catalysis. Adv Drug Deliv Rev 2021; 176:113893. [PMID: 34333074 PMCID: PMC8440397 DOI: 10.1016/j.addr.2021.113893] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/01/2021] [Accepted: 07/20/2021] [Indexed: 12/29/2022]
Abstract
Bioorthogonal chemistry refers to any chemical reactions that can occur inside of living systems without interfering with native biochemical processes, which has become a promising strategy for modulating biological processes. The development of synthetic metal-based catalysts to perform bioorthogonal reactions has significantly expanded the toolkit of bioorthogonal chemistry for medicinal chemistry and synthetic biology. A wide range of homogeneous and heterogeneous transition metal catalysts (TMCs) have been reported, mediating different transformations such as cycloaddition reactions, as well as bond forming and cleaving reactions. However, the direct application of 'naked' TMCs in complex biological media poses numerous challenges, including poor water solubility, toxicity and catalyst deactivation. Incorporating TMCs into nanomaterials to create bioorthogonal nanocatalysts can solubilize and stabilize catalyst molecules, with the decoration of the nanocatalysts used to provide spatiotemporal control of catalysis. This review presents an overview of the advances in the creation of bioorthogonal nanocatalysts, highlighting different choice of nano-scaffolds, and the therapeutic and diagnostic applications.
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Affiliation(s)
- Wenjie Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Xianzhi Zhang
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, MA 01003, USA
| | - Rui Huang
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, MA 01003, USA
| | | | - Huaisong Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Ya Ding
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China.
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, MA 01003, USA.
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28
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Li S, Li G, Gao B, Pujari SP, Chen X, Kim H, Zhou F, Klivansky LM, Liu Y, Driss H, Liang DD, Lu J, Wu P, Zuilhof H, Moses J, Sharpless KB. SuFExable polymers with helical structures derived from thionyl tetrafluoride. Nat Chem 2021; 13:858-867. [PMID: 34400816 DOI: 10.1038/s41557-021-00726-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 05/05/2021] [Indexed: 11/09/2022]
Abstract
Sulfur(VI) fluoride exchange (SuFEx) is a category of click chemistry that enables covalent linking of modular units through sulfur(VI) connective hubs. The efficiency of SuFEx and the stability of the resulting bonds have led to polymer chemistry applications. Now, we report the SuFEx click chemistry synthesis of several structurally diverse SOF4-derived copolymers based on the polymerization of bis(iminosulfur oxydifluorides) and bis(aryl silyl ethers). This polymer class presents two key characteristics. First, the [-N=S(=O)F-O-] polymer backbone linkages are themselves SuFExable and undergo precise SuFEx-based post-modification with phenols or amines to yield branched functional polymers. Second, studies of individual polymer chains of several of these new materials indicate helical polymer structures. The robust nature of SuFEx click chemistry offers the potential for post-polymerization modification, enabling the synthesis of materials with control over composition and conformation.
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Affiliation(s)
- Suhua Li
- School of Chemistry, Sun Yat-Sen University, Guangzhou, People's Republic of China. .,Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Gencheng Li
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Bing Gao
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sidharam P Pujari
- Laboratory of Organic Chemistry, Wageningen University, Wageningen, Netherlands
| | - Xiaoyan Chen
- School of Chemistry, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Hyunseok Kim
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Feng Zhou
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, China
| | - Liana M Klivansky
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yi Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hafedh Driss
- Department of Chemical and Materials Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Dong-Dong Liang
- Laboratory of Organic Chemistry, Wageningen University, Wageningen, Netherlands
| | - Jianmei Lu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, China
| | - Peng Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, Wageningen, Netherlands. .,Department of Chemical and Materials Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia. .,School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin, People's Republic of China.
| | - John Moses
- Cold Spring Harbor Laboratory, New York, NY, USA.
| | - K Barry Sharpless
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
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Banahene N, Swarts BM. Metabolic Labeling of Live Mycobacteria with Trehalose-Based Probes. Methods Mol Biol 2021; 2314:385-398. [PMID: 34235664 DOI: 10.1007/978-1-0716-1460-0_18] [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] [Indexed: 03/02/2023]
Abstract
The mycobacterial cell envelope includes a unique outer membrane, also known as the mycomembrane, which is the major defense barrier that confers intrinsic drug tolerance to Mycobacterium tuberculosis (Mtb) and related bacteria. The mycomembrane is typified by long-chain mycolic acids that are esterified to various acceptors, including: (1) trehalose, forming trehalose mono- and di-mycolate; (2) arabinogalactan, forming arabinogalactan-linked mycolates; and (3) in some species, protein serine residues, forming O-mycoloylated proteins. Synthetic trehalose and trehalose monomycolate analogs have been shown to specifically and metabolically incorporate into mycomembrane components, facilitating their analysis in native contexts and opening new avenues for the specific detection and therapeutic targeting of mycobacterial pathogens in complex settings. This chapter highlights trehalose-based probes that have been developed to date, briefly discusses their applications, and describes protocols for their use in mycobacteria research.
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Affiliation(s)
- Nicholas Banahene
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA
| | - Benjamin M Swarts
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI, USA.
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30
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Chiu WT, Wakabayashi K, Umise A, Tahara M, Inamura T, Hosoda H. Enhancement of mechanical properties and shape memory effect of Ti-Cr-based alloys via Au and Cu modifications. J Mech Behav Biomed Mater 2021; 123:104707. [PMID: 34352487 DOI: 10.1016/j.jmbbm.2021.104707] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/10/2021] [Accepted: 07/07/2021] [Indexed: 01/19/2023]
Abstract
The requirements for biomedical materials have been raised greatly due to the rapidly aging global population. Shape memory alloys (SMAs) are indeed promising materials for biomedical applications due to their controllable shape deformation via the manipulation of temperature and/or stress. This study investigated the enhancement of the fundamental mechanical properties and the shape memory effect (SME) in the Ti-Cr-based alloys via the modification of Au and Cu. The quaternary Ti-Cr-Au-Cu alloys were successfully manufactured by physical metallurgy methods and their phase constitutions, mechanical properties, SME, and superelastic (SE) behaviors have been investigated in this study. Cold-workability, which was enhanced by the introduction of the Au element, was elaborated by the phase constitutions of the alloys. The β-parent phase was stabilized to around body temperature by the introduction of the β-stabilizers of Cr, Au, and Cu, and the functionalities of the specimens were revealed at the operating temperature. Perfect SME at the shape recovery rate of 100% was practiced by the substitution of Au by Cu and the mechanical properties, such as strength and ductility, were also enhanced. Functional mappings of the fundamental mechanical properties, which could be a helpful tool for the investigations of the quaternary Ti-Cr-Au-Cu alloys, were constructed in this work.
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Affiliation(s)
- Wan-Ting Chiu
- Institute of Innovative Research (IIR), Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.
| | - Kaoru Wakabayashi
- Institute of Innovative Research (IIR), Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Akira Umise
- Institute of Innovative Research (IIR), Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaki Tahara
- Institute of Innovative Research (IIR), Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Tomonari Inamura
- Institute of Innovative Research (IIR), Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Hideki Hosoda
- Institute of Innovative Research (IIR), Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
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31
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Handula M, Chen KT, Seimbille Y. IEDDA: An Attractive Bioorthogonal Reaction for Biomedical Applications. Molecules 2021; 26:molecules26154640. [PMID: 34361793 PMCID: PMC8347371 DOI: 10.3390/molecules26154640] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/26/2022] Open
Abstract
The pretargeting strategy has recently emerged in order to overcome the limitations of direct targeting, mainly in the field of radioimmunotherapy (RIT). This strategy is directly dependent on chemical reactions, namely bioorthogonal reactions, which have been developed for their ability to occur under physiological conditions. The Staudinger ligation, the copper catalyzed azide-alkyne cycloaddition (CuAAC) and the strain-promoted [3 + 2] azide–alkyne cycloaddition (SPAAC) were the first bioorthogonal reactions introduced in the literature. However, due to their incomplete biocompatibility and slow kinetics, the inverse-electron demand Diels-Alder (IEDDA) reaction was advanced in 2008 by Blackman et al. as an optimal bioorthogonal reaction. The IEDDA is the fastest bioorthogonal reaction known so far. Its biocompatibility and ideal kinetics are very appealing for pretargeting applications. The use of a trans-cyclooctene (TCO) and a tetrazine (Tz) in the reaction encouraged researchers to study them deeply. It was found that both reagents are sensitive to acidic or basic conditions. Furthermore, TCO is photosensitive and can be isomerized to its cis-conformation via a radical catalyzed reaction. Unfortunately, the cis-conformer is significantly less reactive toward tetrazine than the trans-conformation. Therefore, extensive research has been carried out to optimize both click reagents and to employ the IEDDA bioorthogonal reaction in biomedical applications.
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Affiliation(s)
- Maryana Handula
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands;
| | - Kuo-Ting Chen
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 974301, Taiwan;
| | - Yann Seimbille
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands;
- Life Sciences Division, TRIUMF, 4004 Wesbrook Mall, Vancouver, BC V6T 2A3, Canada
- Correspondence: ; Tel.: +31-10-703-8961
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32
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Cheng B, Tang Q, Zhang C, Chen X. Glycan Labeling and Analysis in Cells and In Vivo. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:363-387. [PMID: 34314224 DOI: 10.1146/annurev-anchem-091620-091314] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As one of the major types of biomacromolecules in the cell, glycans play essential functional roles in various biological processes. Compared with proteins and nucleic acids, the analysis of glycans in situ has been more challenging. Herein we review recent advances in the development of methods and strategies for labeling, imaging, and profiling of glycans in cells and in vivo. Cellular glycans can be labeled by affinity-based probes, including lectin and antibody conjugates, direct chemical modification, metabolic glycan labeling, and chemoenzymatic labeling. These methods have been applied to label glycans with fluorophores, which enables the visualization and tracking of glycans in cells, tissues, and living organisms. Alternatively, labeling glycans with affinity tags has enabled the enrichment of glycoproteins for glycoproteomic profiling. Built on the glycan labeling methods, strategies enabling cell-selective and tissue-specific glycan labeling and protein-specific glycan imaging have been developed. With these methods and strategies, researchers are now better poised than ever to dissect the biological function of glycans in physiological or pathological contexts.
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Affiliation(s)
- Bo Cheng
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Qi Tang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Che Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
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33
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Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Christophe Biot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Cedric Lion
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
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34
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Agrahari AK, Bose P, Jaiswal MK, Rajkhowa S, Singh AS, Hotha S, Mishra N, Tiwari VK. Cu(I)-Catalyzed Click Chemistry in Glycoscience and Their Diverse Applications. Chem Rev 2021; 121:7638-7956. [PMID: 34165284 DOI: 10.1021/acs.chemrev.0c00920] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Copper(I)-catalyzed 1,3-dipolar cycloaddition between organic azides and terminal alkynes, commonly known as CuAAC or click chemistry, has been identified as one of the most successful, versatile, reliable, and modular strategies for the rapid and regioselective construction of 1,4-disubstituted 1,2,3-triazoles as diversely functionalized molecules. Carbohydrates, an integral part of living cells, have several fascinating features, including their structural diversity, biocompatibility, bioavailability, hydrophilicity, and superior ADME properties with minimal toxicity, which support increased demand to explore them as versatile scaffolds for easy access to diverse glycohybrids and well-defined glycoconjugates for complete chemical, biochemical, and pharmacological investigations. This review highlights the successful development of CuAAC or click chemistry in emerging areas of glycoscience, including the synthesis of triazole appended carbohydrate-containing molecular architectures (mainly glycohybrids, glycoconjugates, glycopolymers, glycopeptides, glycoproteins, glycolipids, glycoclusters, and glycodendrimers through regioselective triazole forming modular and bio-orthogonal coupling protocols). It discusses the widespread applications of these glycoproducts as enzyme inhibitors in drug discovery and development, sensing, gelation, chelation, glycosylation, and catalysis. This review also covers the impact of click chemistry and provides future perspectives on its role in various emerging disciplines of science and technology.
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Affiliation(s)
- Anand K Agrahari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Priyanka Bose
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Manoj K Jaiswal
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Sanchayita Rajkhowa
- Department of Chemistry, Jorhat Institute of Science and Technology (JIST), Jorhat, Assam 785010, India
| | - Anoop S Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Srinivas Hotha
- Department of Chemistry, Indian Institute of Science and Engineering Research (IISER), Pune, Maharashtra 411021, India
| | - Nidhi Mishra
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Vinod K Tiwari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
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Oerlemans RAJF, Timmermans SBPE, van Hest JCM. Artificial Organelles: Towards Adding or Restoring Intracellular Activity. Chembiochem 2021; 22:2051-2078. [PMID: 33450141 PMCID: PMC8252369 DOI: 10.1002/cbic.202000850] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/15/2021] [Indexed: 12/15/2022]
Abstract
Compartmentalization is one of the main characteristics that define living systems. Creating a physically separated microenvironment allows nature a better control over biological processes, as is clearly specified by the role of organelles in living cells. Inspired by this phenomenon, researchers have developed a range of different approaches to create artificial organelles: compartments with catalytic activity that add new function to living cells. In this review we will discuss three complementary lines of investigation. First, orthogonal chemistry approaches are discussed, which are based on the incorporation of catalytically active transition metal-containing nanoparticles in living cells. The second approach involves the use of premade hybrid nanoreactors, which show transient function when taken up by living cells. The third approach utilizes mostly genetic engineering methods to create bio-based structures that can be ultimately integrated with the cell's genome to make them constitutively active. The current state of the art and the scope and limitations of the field will be highlighted with selected examples from the three approaches.
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Affiliation(s)
- Roy A. J. F. Oerlemans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Suzanne B. P. E. Timmermans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Jan C. M. van Hest
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
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36
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Rigolot V, Biot C, Lion C. To View Your Biomolecule, Click inside the Cell. Angew Chem Int Ed Engl 2021; 60:23084-23105. [PMID: 34097349 DOI: 10.1002/anie.202101502] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
Abstract
The surging development of bioorthogonal chemistry has profoundly transformed chemical biology over the last two decades. Involving chemical partners that specifically react together in highly complex biological fluids, this branch of chemistry now allows researchers to probe biomolecules in their natural habitat through metabolic labelling technologies. Chemical reporter strategies include metabolic glycan labelling, site-specific incorporation of unnatural amino acids in proteins, and post-synthetic labelling of nucleic acids. While a majority of literature reports mark cell-surface exposed targets, implementing bioorthogonal ligations in the interior of cells constitutes a more challenging task. Owing to limiting factors such as membrane permeability of reagents, fluorescence background due to hydrophobic interactions and off-target covalent binding, and suboptimal balance between reactivity and stability of the designed molecular reporters and probes, these strategies need mindful planning to achieve success. In this review, we discuss the hurdles encountered when targeting biomolecules localized in cell organelles and give an easily accessible summary of the strategies at hand for imaging intracellular targets.
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Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Christophe Biot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Cedric Lion
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
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37
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Nguyen DP, Nguyen HTH, Do LH. Tools and Methods for Investigating Synthetic Metal-Catalyzed Reactions in Living Cells. ACS Catal 2021; 11:5148-5165. [PMID: 34824879 PMCID: PMC8612649 DOI: 10.1021/acscatal.1c00438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although abiotic catalysts are capable of promoting numerous new-to-nature reactions, only a small subset has so far been successfully integrated into living systems. Research in intracellular catalysis requires an interdisciplinary approach that takes advantage of both chemical and biological tools as well as state-of-the-art instrumentations. In this perspective, we will focus on the techniques that have made studying metal-catalyzed reactions in cells possible using representative examples from the literature. Although the lack of quantitative data in vitro and in vivo has somewhat limited progress in the catalyst development process, recent advances in characterization methods should help overcome some of these deficiencies. Given its tremendous potential, we believe that intracellular catalysis will play a more prominent role in the development of future biotechnologies and therapeutics.
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Affiliation(s)
- Dat P. Nguyen
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
| | - Huong T. H. Nguyen
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
| | - Loi H. Do
- Department of Chemistry, University of Houston, 4800 Calhoun Rd, Houston, Texas 77004, United States
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38
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Petit E, Bosch L, Costa AM, Rodríguez-Izquierdo I, Sepúlveda-Crespo D, Muñoz-Fernández MA, Vilarrasa J. BMS Derivatives C7-Linked to β-Cyclodextrin and Hyperbranched Polyglycerol Retain Activity against R5-HIV-1 NLAD8 Isolates and Can Be Deemed Potential Microbicides. ChemMedChem 2021; 16:2217-2222. [PMID: 33843142 DOI: 10.1002/cmdc.202100080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/02/2021] [Indexed: 12/30/2022]
Abstract
Amides from indole-3-glyoxylic acid and 4-benzoyl-2-methylpiperazine, which are related to entry inhibitors developed by Bristol-Myers Squibb (BMS), have been synthesized with aliphatic chains located at the C7 position of the indole ring. These spacers contain an azido group suitable for the well-known Cu(I)-catalyzed (3+2)-cycloaddition or an activated triple bond for the nucleophilic addition of thiols under physiological conditions. Reaction with polyols (β-cyclodextrin and hyperbranched polyglycerol) decorated with complementary click partners has afforded polyol-BMS-like conjugates that are not cytotoxic (TZM.bl cells) and retain the activity against R5-HIV-1NLAD8 isolates. Thus, potential vaginal microbicides based on entry inhibitors, which can be called of 4th generation, are reported here for the first time.
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Affiliation(s)
- Elena Petit
- Organic Chemistry Section, Facultat de Química, Universitat de Barcelona, Diagonal 645, 08028, Barcelona, Catalonia, Spain
| | - Lluís Bosch
- Organic Chemistry Section, Facultat de Química, Universitat de Barcelona, Diagonal 645, 08028, Barcelona, Catalonia, Spain
| | - Anna M Costa
- Organic Chemistry Section, Facultat de Química, Universitat de Barcelona, Diagonal 645, 08028, Barcelona, Catalonia, Spain
| | - Ignacio Rodríguez-Izquierdo
- Laboratorio de Inmunobiología Molecular, Hospital General Universitario Gregorio Marañón (HGUGM), Dr. Esquerdo 46, 28007, Madrid, Spain
| | - Daniel Sepúlveda-Crespo
- Laboratorio de Inmunobiología Molecular, Hospital General Universitario Gregorio Marañón (HGUGM), Dr. Esquerdo 46, 28007, Madrid, Spain
| | - M Angeles Muñoz-Fernández
- Laboratorio de Inmunobiología Molecular, Hospital General Universitario Gregorio Marañón (HGUGM), Dr. Esquerdo 46, 28007, Madrid, Spain
| | - Jaume Vilarrasa
- Organic Chemistry Section, Facultat de Química, Universitat de Barcelona, Diagonal 645, 08028, Barcelona, Catalonia, Spain
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Gao Z, Li Y, Liu Z, Zhang Y, Chen F, An P, Lu W, Hu J, You C, Xu J, Zhang X, Sun B. Small-Molecule-Selective Organosilica Nanoreactors for Copper-Catalyzed Azide-Alkyne Cycloaddition Reactions in Cellular and Living Systems. NANO LETTERS 2021; 21:3401-3409. [PMID: 33843242 DOI: 10.1021/acs.nanolett.0c04930] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We reported the synthesis of a tris(triazolylmethyl)amine (TTA)-bridged organosilane, functioning as Cu(I)-stabilizing ligands, and the installation of this building block into the backbone of mesoporous organosilica nanoparticles (TTASi) by a sol-gel way. Upon coordinating with Cu(I), the mesoporous CuI-TTASi, with a restricted metal active center inside the pore, functions as a molecular-sieve-typed nanoreactor to efficiently perform Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reactions on small-molecule substrates but fails to work on macromolecules larger than the pore diameter. As a proof of concept, we witnessed the advantages of selective nanoreactors in screening protein substrates for small molecules. Also, the robust CuI-TTASi could be implanted into the body of animal models including zebrafish and mice as biorthogonal catalysts without apparent toxicity, extending its utilization in vivo ranging from fluorescent labeling to in situ drug synthesis.
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Affiliation(s)
- Zhiguo Gao
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Yaojia Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Zhikun Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Yu Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Fanghui Chen
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Peijing An
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Wenjun Lu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Jinzhong Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Chaoqun You
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Jun Xu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Baiwang Sun
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
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40
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Scinto SL, Bilodeau DA, Hincapie R, Lee W, Nguyen SS, Xu M, am Ende CW, Finn MG, Lang K, Lin Q, Pezacki JP, Prescher JA, Robillard MS, Fox JM. Bioorthogonal chemistry. NATURE REVIEWS. METHODS PRIMERS 2021; 1:30. [PMID: 34585143 PMCID: PMC8469592 DOI: 10.1038/s43586-021-00028-z] [Citation(s) in RCA: 158] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/05/2021] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistry represents a class of high-yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions towards endogenous functional groups. Rooted in the principles of physical organic chemistry, bioorthogonal reactions are intrinsically selective transformations not commonly found in biology. Key reactions include native chemical ligation and the Staudinger ligation, copper-catalysed azide-alkyne cycloaddition, strain-promoted [3 + 2] reactions, tetrazine ligation, metal-catalysed coupling reactions, oxime and hydrazone ligations as well as photoinducible bioorthogonal reactions. Bioorthogonal chemistry has significant overlap with the broader field of 'click chemistry' - high-yielding reactions that are wide in scope and simple to perform, as recently exemplified by sulfuryl fluoride exchange chemistry. The underlying mechanisms of these transformations and their optimal conditions are described in this Primer, followed by discussion of how bioorthogonal chemistry has become essential to the fields of biomedical imaging, medicinal chemistry, protein synthesis, polymer science, materials science and surface science. The applications of bioorthogonal chemistry are diverse and include genetic code expansion and metabolic engineering, drug target identification, antibody-drug conjugation and drug delivery. This Primer describes standards for reproducibility and data deposition, outlines how current limitations are driving new research directions and discusses new opportunities for applying bioorthogonal chemistry to emerging problems in biology and biomedicine.
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Affiliation(s)
- Samuel L. Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Robert Hincapie
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Wankyu Lee
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Sean S. Nguyen
- Department of Chemistry, University of California, Irvine, CA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Minghao Xu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | | | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kathrin Lang
- Department of Chemistry, Technical University of Munich, Garching, Germany
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | | | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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41
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Suazo KF, Park KY, Distefano MD. A Not-So-Ancient Grease History: Click Chemistry and Protein Lipid Modifications. Chem Rev 2021; 121:7178-7248. [PMID: 33821625 DOI: 10.1021/acs.chemrev.0c01108] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein lipid modification involves the attachment of hydrophobic groups to proteins via ester, thioester, amide, or thioether linkages. In this review, the specific click chemical reactions that have been employed to study protein lipid modification and their use for specific labeling applications are first described. This is followed by an introduction to the different types of protein lipid modifications that occur in biology. Next, the roles of click chemistry in elucidating specific biological features including the identification of lipid-modified proteins, studies of their regulation, and their role in diseases are presented. A description of the use of protein-lipid modifying enzymes for specific labeling applications including protein immobilization, fluorescent labeling, nanostructure assembly, and the construction of protein-drug conjugates is presented next. Concluding remarks and future directions are presented in the final section.
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Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Keun-Young Park
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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42
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Pedowitz NJ, Pratt MR. Design and Synthesis of Metabolic Chemical Reporters for the Visualization and Identification of Glycoproteins. RSC Chem Biol 2021; 2:306-321. [PMID: 34337414 PMCID: PMC8323544 DOI: 10.1039/d1cb00010a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Glycosylation events play an invaluable role in regulating cellular processes including enzymatic activity, immune recognition, protein stability, and cell-cell interactions. However, researchers have yet to realize the full range of glycan mediated biological functions due to a lack of appropriate chemical tools. Fortunately, the past 25 years has seen the emergence of modified sugar analogs, termed metabolic chemical reporters (MCRs), which are metabolized by endogenous enzymes to label complex glycan structures. Here, we review the major reporters for each class of glycosylation and highlight recent applications that have made a tremendous impact on the field of glycobiology.
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Affiliation(s)
- Nichole J Pedowitz
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, United States
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, United States
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States
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43
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Idiago-López J, Moreno-Antolín E, de la Fuente JM, Fratila RM. Nanoparticles and bioorthogonal chemistry joining forces for improved biomedical applications. NANOSCALE ADVANCES 2021; 3:1261-1292. [PMID: 36132873 PMCID: PMC9419263 DOI: 10.1039/d0na00873g] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/21/2021] [Indexed: 05/08/2023]
Abstract
Bioorthogonal chemistry comprises chemical reactions that can take place inside complex biological environments, providing outstanding tools for the investigation and elucidation of biological processes. Its use in combination with nanotechnology can lead to further developments in diverse areas of biomedicine, such as molecular bioimaging, targeted delivery, in situ drug activation, study of cell-nanomaterial interactions, biosensing, etc. Here, we summarise the recent efforts to bring together the unique properties of nanoparticles and the remarkable features of bioorthogonal reactions to create a toolbox of new or improved biomedical applications. We show how, by joining forces, bioorthogonal chemistry and nanotechnology can overcome some of the key current limitations in the field of nanomedicine, providing better, faster and more sensitive nanoparticle-based bioimaging and biosensing techniques, as well as therapeutic nanoplatforms with superior efficacy.
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Affiliation(s)
- Javier Idiago-López
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza Zaragoza 50009 Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Spain
| | - Eduardo Moreno-Antolín
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza Zaragoza 50009 Spain
| | - Jesús M de la Fuente
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza Zaragoza 50009 Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Spain
| | - Raluca M Fratila
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza Zaragoza 50009 Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Spain
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44
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Saini P, Sonika, Singh G, Kaur G, Singh J, Singh H. Robust and Versatile Cu(I) metal frameworks as potential catalysts for azide-alkyne cycloaddition reactions: Review. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111432] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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45
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Luo M, Wu X, Li Y, Guo F. Synthesis of Four Pentacyclic Triterpene-Sialylglycopeptide Conjugates and Their Affinity Assays with Hemagglutinin. Molecules 2021; 26:895. [PMID: 33567740 PMCID: PMC7915185 DOI: 10.3390/molecules26040895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 01/30/2021] [Accepted: 02/03/2021] [Indexed: 11/16/2022] Open
Abstract
Influenza outbreaks pose a serious threat to human health. Hemagglutinin (HA) is an important target for influenza virus entry inhibitors. In this study, we synthesized four pentacyclic triterpene conjugates with a sialylglycopeptide scaffold through the Cu(I)-catalyzed alkyne-azide cycloaddition reaction (CuAAC) and prepared affinity assays of these conjugates with two HAs, namely H1N1 (A/WSN/1933) and H5N1 (A/Hong Kong/483/97), respectively. With a dissociation constant (KD) of 6.89 μM, SCT-Asn-betulinic acid exhibited the strongest affinity with the H1N1 protein. Furthermore, with a KD value of 9.10 μM, SCT-Asn-oleanolic acid exhibited the strongest affinity with the H5N1 protein. The conjugates considerably enhanced antiviral activity, which indicates that pentacyclic triterpenes can be used as a ligand to improve the anti-influenza ability of the sialylglycopeptide molecule by acting on the HA protein.
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Affiliation(s)
| | | | - Yiming Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (M.L.); (X.W.)
| | - Fujiang Guo
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (M.L.); (X.W.)
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46
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Ahmad A, Shah SNA, Arshad M, Bélanger‐Gariepy F, Tiekink ER, Rehman Z. A copper diimine‐based honeycomb‐like porous network as an efficient reduction catalyst. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Abrar Ahmad
- Department of Chemistry Quaid‐i‐Azam University Islamabad 45320 Pakistan
| | - Syed Niaz Ali Shah
- Department of Chemistry Quaid‐i‐Azam University Islamabad 45320 Pakistan
| | - Mehwish Arshad
- Department of Chemistry Quaid‐i‐Azam University Islamabad 45320 Pakistan
| | | | - Edward R.T. Tiekink
- Research Centre for Crystalline Materials, School of Science and Technology Sunway University Subang Jay 47500 Malaysia
| | - Zia Rehman
- Department of Chemistry Quaid‐i‐Azam University Islamabad 45320 Pakistan
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47
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Verhelst SHL, Bonger KM, Willems LI. Bioorthogonal Reactions in Activity-Based Protein Profiling. Molecules 2020; 25:E5994. [PMID: 33352858 PMCID: PMC7765892 DOI: 10.3390/molecules25245994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/27/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase our understanding of physiological and pathological processes, to identify novel drug targets, to evaluate selectivity of drugs, and to image probe targets in cells. Bioorthogonal chemistry has substantially contributed to the field of ABPP, as it allows the introduction of tags, which may be bulky or have unfavorable physicochemical properties, at a late stage in the experiment. In this review, we give an overview of the bioorthogonal reactions that have been implemented in ABPP, provide examples of applications of bioorthogonal chemistry in ABPP, and share some thoughts on future directions.
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Affiliation(s)
- Steven H. L. Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Herestr. 49, Box 802, 3000 Leuven, Belgium
- AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Kimberly M. Bonger
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Lianne I. Willems
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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48
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Vatansever EC, Kang J, Tuley A, Ward ES, Liu WR. An optimal "Click" formulation strategy for antibody-drug conjugate synthesis. Bioorg Med Chem 2020; 28:115808. [PMID: 33071032 PMCID: PMC7736079 DOI: 10.1016/j.bmc.2020.115808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 11/19/2022]
Abstract
As a versatile reaction for bioconjugation, Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC) has enormous potential in the synthesis of antibody-drug conjugates (ADCs). In order to optimize CuAAC-based ADC synthesis, we characterized kinetically different formulation processes by mimicking ADC synthesis using small molecules and subsequently revealed unique kinetic behaviors of different combinations of alkyne and azide conditions. Our results indicate that under ADC synthesis conditions, for an alkyne-containing drug, its concentration has minimal impact on the reaction rate when an antibody has a non-metal-chelating azide but is proportional to concentration when an antibody contains a metal-chelating azide; however, for an alkyne-containing antibody, the ADC synthesis rate is proportional to the concentration of a drug with a non-metal-chelating azide but displays almost no dependence on drug concentration with a metal-chelating azide. Based on our results, we designed and tested an optimal "click" formulation strategy that allowed rapid and cost-effective synthesis of a new ADC.
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Affiliation(s)
- Erol C Vatansever
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | - Jeffrey Kang
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Alfred Tuley
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | - E Sally Ward
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA; Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA; Centre for Cancer Immunology, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton SO16 4YD, UK.
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, United States; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA.
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49
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Ravetz B, Tay NES, Joe CL, Sezen-Edmonds M, Schmidt MA, Tan Y, Janey JM, Eastgate MD, Rovis T. Development of a Platform for Near-Infrared Photoredox Catalysis. ACS CENTRAL SCIENCE 2020; 6:2053-2059. [PMID: 33274281 PMCID: PMC7706074 DOI: 10.1021/acscentsci.0c00948] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 05/05/2023]
Abstract
Over the past decade, chemists have embraced visible-light photoredox catalysis due to its remarkable ability to activate small molecules. Broadly, these methods employ metal complexes or organic dyes to convert visible light into chemical energy. Unfortunately, the excitation of widely utilized Ru and Ir chromophores is energetically wasteful as ∼25% of light energy is lost thermally before being quenched productively. Hence, photoredox methodologies require high-energy, intense light to accommodate said catalytic inefficiency. Herein, we report photocatalysts which cleanly convert near-infrared (NIR) and deep red (DR) light into chemical energy with minimal energetic waste. We leverage the strong spin-orbit coupling (SOC) of Os(II) photosensitizers to directly access the excited triplet state (T1) with NIR or DR irradiation from the ground state singlet (S0). Through strategic catalyst design, we access a wide range of photoredox, photopolymerization, and metallaphotoredox reactions which usually require 15-50% higher excitation energy. Finally, we demonstrate superior light penetration and scalability of NIR photoredox catalysis through a mole-scale arene trifluoromethylation in a batch reactor.
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Affiliation(s)
- Benjamin
D. Ravetz
- Department
of Chemistry, Columbia University, New York, New York 10027, United States
| | - Nicholas E. S. Tay
- Department
of Chemistry, Columbia University, New York, New York 10027, United States
| | - Candice L. Joe
- Chemical
Process Development, Bristol Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
- E-mail:
| | - Melda Sezen-Edmonds
- Chemical
Process Development, Bristol Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michael A. Schmidt
- Chemical
Process Development, Bristol Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Yichen Tan
- Chemical
Process Development, Bristol Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Jacob M. Janey
- Chemical
Process Development, Bristol Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Martin D. Eastgate
- Chemical
Process Development, Bristol Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Tomislav Rovis
- Department
of Chemistry, Columbia University, New York, New York 10027, United States
- E-mail:
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50
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Roy S, Cha JN, Goodwin AP. Nongenetic Bioconjugation Strategies for Modifying Cell Membranes and Membrane Proteins: A Review. Bioconjug Chem 2020; 31:2465-2475. [PMID: 33146010 DOI: 10.1021/acs.bioconjchem.0c00529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The cell membrane possesses an extensive library of proteins, carbohydrates, and lipids that control a significant portion of inter- and intracellular functions, including signaling, proliferation, migration, and adhesion, among others. Augmenting the cell surface composition would open possibilities for advances in therapy, tissue engineering, and probing fundamental cell processes. While genetic engineering has proven effective for many in vitro applications, these techniques result in irreversible changes to cells and are difficult to apply in vivo. Another approach is to instead attach exogenous functional groups to the cell membrane without changing the genetic nature of the cell. This review focuses on more recent approaches of nongenetic methods of cell surface modification through metabolic pathways, anchorage by hydrophobic interactions, and chemical conjugation. Benefits and drawbacks of each approach are considered, followed by a discussion of potential applications for nongenetic cell surface modification and an outlook on the future of the field.
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