1
|
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: 19] [Impact Index Per Article: 19.0] [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.
Collapse
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
| |
Collapse
|
2
|
Zhang Y, Wang Y, Uslu S, Venkatachalapathy S, Rashidian M, Schaefer JV, Plückthun A, Distefano MD. Enzymatic Construction of DARPin-Based Targeted Delivery Systems Using Protein Farnesyltransferase and a Capture and Release Strategy. Int J Mol Sci 2022; 23:11537. [PMID: 36232839 PMCID: PMC9569580 DOI: 10.3390/ijms231911537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Protein-based conjugates have been extensively utilized in various biotechnological and therapeutic applications. In order to prepare homogeneous conjugates, site-specific modification methods and efficient purification strategies are both critical factors to be considered. The development of general and facile conjugation and purification strategies is therefore highly desirable. Here, we apply a capture and release strategy to create protein conjugates based on Designed Ankyrin Repeat Proteins (DARPins), which are engineered antigen-binding proteins with prominent affinity and selectivity. In this case, DARPins that target the epithelial cell adhesion molecule (EpCAM), a diagnostic cell surface marker for many types of cancer, were employed. The DARPins were first genetically modified with a C-terminal CVIA sequence to install an enzyme recognition site and then labeled with an aldehyde functional group employing protein farnesyltransferase. Using a capture and release strategy, conjugation of the labeled DARPins to a TAMRA fluorophore was achieved with either purified proteins or directly from crude E. coli lysate and used in subsequent flow cytometry and confocal imaging analysis. DARPin-MMAE conjugates were also prepared yielding a construct manifesting an IC50 of 1.3 nM for cell killing of EpCAM positive MCF-7 cells. The method described here is broadly applicable to enable the streamlined one-step preparation of protein-based conjugates.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yiao Wang
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Safak Uslu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Mohammad Rashidian
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jonas V. Schaefer
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
3
|
Hering A, Braga Emidio N, Muttenthaler M. Expanding the versatility and scope of the oxime ligation: rapid bioconjugation to disulfide-rich peptides. Chem Commun (Camb) 2022; 58:9100-9103. [PMID: 35880482 PMCID: PMC9367247 DOI: 10.1039/d2cc03752a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022]
Abstract
The oxime ligation is a valuable bioorthogonal conjugation reaction but with limited compatibility with disulfide-rich peptides/proteins and time-sensitive applications. Here we overcome these limitations by introducing a strategy that supports regiospecific control, oxidative folding, production of stable aminooxy-precursors for on-demand modification, and complete ligation within 5 min.
Collapse
Affiliation(s)
- Anke Hering
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia.
| | - Nayara Braga Emidio
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia.
| | - Markus Muttenthaler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia.
- Institute of Biological Chemistry, University of Vienna, Währingerstraße 38, Vienna, 1090, Austria.
| |
Collapse
|
4
|
Meijlink MA, Chua YC, Chan STS, Anderson RJ, Rosenberg MW, Cozijnsen A, Mollard V, McFadden GI, Draper SL, Holz LE, Hermans IF, Heath WR, Painter GF, Compton BJ. 6″-Modifed α-GalCer-peptide conjugate vaccine candidates protect against liver-stage malaria. RSC Chem Biol 2022; 3:551-560. [PMID: 35656478 PMCID: PMC9092427 DOI: 10.1039/d1cb00251a] [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: 12/24/2021] [Accepted: 03/02/2022] [Indexed: 11/21/2022] Open
Abstract
Self-adjuvanting vaccines consisting of peptide epitopes conjugated to immune adjuvants are a powerful way of generating antigen-specific immune responses. We previously showed that a Plasmodium-derived peptide conjugated to a rearranged form of α-galactosylceramide (α-GalCer) could stimulate liver-resident memory T (TRM) cells that were effective killers of liver-stage Plasmodium berghei ANKA (Pba)-infected cells. To investigate if similar or even superior TRM responses can be induced by modifying the α-GalCer adjuvant, we created new conjugate vaccine cadidates by attaching an immunogenic Plasmodium-derived peptide antigen to 6″-substituted α-GalCer analogues. Vaccine synthesis involved developing an efficient route to α-galactosylphytosphingosine (α-GalPhs), from which the prototypical iNKT cell agonist, α-GalCer, and its 6″-deoxy-6″-thio and -amino analogues were derived. Attaching a cathepsin B-cleavable linker to the 6″-modified α-GalCer created pro-adjuvants bearing a pendant ketone group available for peptide conjugation. Optimized reaction conditions were developed that allow for the efficient conjugation of peptide antigens to the pro-adjuvants via oxime ligation to create new glycolipid-peptide (GLP) conjugate vaccines. A single dose of the vaccine candidates induced acute NKT and Plasmodium-specific CD8+ T cell responses that generated potent hepatic TRM responses in mice. Our findings demonstrate that attaching antigenic peptides to 6″-modifed α-GalCer generates powerful self-adjuvanting conjugate vaccine candidates that could potentially control hepatotropic infections such as liver-stage malaria. Candidate vaccines comprised of peptide antigen conjugated to 6″-modified α-GalCer analogues generate potent hepatic TRM responses in mice with a single dose inducing protective immunity against malaria in a Plasmodium sporozoite challenge model.![]()
Collapse
Affiliation(s)
- Michael A. Meijlink
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Yu Cheng Chua
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Susanna T. S. Chan
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Regan J. Anderson
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Matthew W. Rosenberg
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Anton Cozijnsen
- School of BioSciences, University of Melbourntie, Parkville, VIC, Australia
| | - Vanessa Mollard
- School of BioSciences, University of Melbourntie, Parkville, VIC, Australia
| | | | - Sarah L. Draper
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Lauren E. Holz
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Ian F. Hermans
- Malaghan Institute of Medical Research, Wellington, New Zealand
- Avalia Immunotherapies Limited, Lower Hutt, New Zealand
| | - William R. Heath
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Gavin F. Painter
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
- Avalia Immunotherapies Limited, Lower Hutt, New Zealand
| | - Benjamin J. Compton
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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 PMCID: PMC8820976 DOI: 10.1021/acs.chemrev.0c01108] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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.
Collapse
Affiliation(s)
- Kiall F. Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Keun-Young Park
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| |
Collapse
|
7
|
An LY, Dai Z, Di B, Xu LL. Advances in Cryochemistry: Mechanisms, Reactions and Applications. Molecules 2021; 26:750. [PMID: 33535547 PMCID: PMC7867104 DOI: 10.3390/molecules26030750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 01/23/2023] Open
Abstract
It is counterintuitive that chemical reactions can be accelerated by freezing, but this amazing phenomenon was discovered as early as the 1960s. In frozen systems, the increase in reaction rate is caused by various mechanisms and the freeze concentration effect is the main reason for the observed acceleration. Some accelerated reactions have great application value in the chemistry synthesis and environmental fields; at the same time, certain reactions accelerated at low temperature during the storage of food, medicine, and biological products should cause concern. The study of reactions accelerated by freezing will overturn common sense and provide a new strategy for researchers in the chemistry field. In this review, we mainly introduce various mechanisms for accelerating reactions induced by freezing and summarize a variety of accelerated cryochemical reactions and their applications.
Collapse
Affiliation(s)
- Lu-Yan An
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (L.-Y.A.); (Z.D.)
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Zhen Dai
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (L.-Y.A.); (Z.D.)
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Bin Di
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (L.-Y.A.); (Z.D.)
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Li Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; (L.-Y.A.); (Z.D.)
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
8
|
Jang K, Horne WS, Asher SA. Human Serum Phenylpyruvate Quantification Using Responsive 2D Photonic Crystal Hydrogels via Chemoselective Oxime Ligation: Progress toward Developing Phenylalanine-Sensing Elements. ACS APPLIED MATERIALS & INTERFACES 2020; 12:39612-39619. [PMID: 32805910 DOI: 10.1021/acsami.0c08787] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
There is a need to develop at-home phenylalanine (Phe) test kits, analogous to home glucose meters, for phenylketonuria patients who must measure their blood Phe levels frequently to adjust their diet. Unfortunately, such test kits are not available yet because of the lack of simple and inexpensive Phe-sensing elements. With the goal of developing a Phe-sensing element, we fabricated two-dimensional photonic crystal (2DPC) hydrogels that quantify human serum phenylpyruvate (PhPY), which is the product of the reaction between Phe and the enzyme phenylalanine dehydrogenase. The PhPY-sensing hydrogels have oxyamine recognition groups that link PhPY to the hydrogel polymer network via chemoselective oxime ligation. This structural modification induces the hydrogel to swell, which then increases interparticle spacings within the embedded 2DPC. The PhPY-induced particle spacing changes are measured from light diffraction and used to quantify the PhPY concentrations. The estimated limit of detection of PhPY in human serum for a detection time of 30 min is 19 μM, which is comparable to the minimum blood Phe concentrations of healthy people. Besides the potential application for developing Phe-sensing elements, this new hydrogel sensing approach via chemoselective oxime ligation is generalizable to the development of other chemical sensors working in complex biological environments.
Collapse
Affiliation(s)
- Kyeongwoo Jang
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Sanford A Asher
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
9
|
Zhou Y, Piergentili I, Hong J, van der Helm MP, Macchione M, Li Y, Eelkema R, Luo S. Indoline Catalyzed Acylhydrazone/Oxime Condensation under Neutral Aqueous Conditions. Org Lett 2020; 22:6035-6040. [PMID: 32790427 DOI: 10.1021/acs.orglett.0c02128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Acylhydrazones formation has been widely applied in materials science and biolabeling. However, their sluggish condensation rate under neutral conditions limits its application. Herein, indolines with electron-donating groups are reported as a new catalyst scaffold, which can catalyze acylhydrazone, hydrazone, and oxime formation via an iminium ion intermediate. This new type of catalyst showed up to 15-fold rate enhancement over the traditional aniline-catalyzed reaction at neutral conditions. The identified indoline catalyst was successfully applied in hydrogel formation.
Collapse
Affiliation(s)
- Yuntao Zhou
- Center of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Irene Piergentili
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Jennifer Hong
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Michelle P van der Helm
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Mariano Macchione
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Yao Li
- Center of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Rienk Eelkema
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Sanzhong Luo
- Center of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| |
Collapse
|
10
|
Vargas EL, Velázquez JA, Rodrigo E, Reinecke H, Rodríguez-Hernández J, Fernández-Mayoralas A, Gallardo A, Cid MB. p Ka Modulation of Pyrrolidine-Based Catalytic Polymers Used for the Preparation of Glycosyl Hydrazides at Physiological pH and Temperature. ACS APPLIED BIO MATERIALS 2020; 3:1955-1967. [PMID: 35025318 DOI: 10.1021/acsabm.9b01123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Inspired by the ability of enzymes to use the surrounding hydrophobic and/or polarizable groups to modulate the pKa of a given amino acid, we designed a series of soluble polymers able to decrease the basicity of pyrrolidine (from 11.2 to 8.6 pKa units), which clearly increases its aminocatalytic activity at physiological pH in C═N bond formation reactions via ion iminium activation. Other parameters such as charge density, hydrophobic/hydrophilic balance, and aggregation state have been studied as important factors in the catalytic activity of the polymers for a given substrate. To demonstrate the utility of our approach, an optimal pyrrolidine-based catalytic polymer has been used for the formation of C-N bonds between hydrazides and free sugars as the model system for the preparation of glycoconjugates.
Collapse
Affiliation(s)
- Emily L Vargas
- Department of Organic Chemistry, Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid, Spain
| | - J Antonio Velázquez
- Department of Organic Chemistry, Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid, Spain
| | - Eduardo Rodrigo
- Department of Organic Chemistry, Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid, Spain
| | - Helmut Reinecke
- Instituto de Ciencia y Tecnologı́a de Polı́meros (ICTP-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Juan Rodríguez-Hernández
- Instituto de Ciencia y Tecnologı́a de Polı́meros (ICTP-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Alberto Gallardo
- Instituto de Ciencia y Tecnologı́a de Polı́meros (ICTP-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - María Belén Cid
- Department of Organic Chemistry, Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
11
|
Sugiura T, Kanada T, Mori D, Sakai H, Shibata A, Kitamura Y, Ikeda M. Chemical stimulus-responsive supramolecular hydrogel formation and shrinkage of a hydrazone-containing short peptide derivative. SOFT MATTER 2020; 16:899-906. [PMID: 31829395 DOI: 10.1039/c9sm01969c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Artificial supramolecular nanostructures showing transient properties have attracted significant attention in recent years. New discoveries in this area may provide insights into a better understanding of the sophisticated organization of complex biomolecular systems. Nevertheless, research concerning such materials is still limited. Better knowledge of the chemical reactivity and corresponding molecular transformations of self-assembling molecules, which guide their assembly/disassembly, may provide an opportunity to construct transient supramolecular nanostructures capable of showing chemical stimulus responsiveness. Herein, we report a short peptide derivative containing a hydrazone bond, which shows transient hydrogel formation (no only sol-to-gel but also gel-to-shrunken gel phase transition) accompanied by continuous transformation and growth of supramolecular nanostructures triggered by hydrazone-oxime exchange reaction in response to hydroxylamine. Such controlled shrinkage behavior of supramolecular hydrogels in response to specific chemical stimuli has rarely been explored compared with conventional polymer hydrogel systems.
Collapse
Affiliation(s)
- Takumi Sugiura
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Takurou Kanada
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Daisuke Mori
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Hiroyuki Sakai
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Aya Shibata
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Yoshiaki Kitamura
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Masato Ikeda
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan. and United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan and Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), 1-1 Yanagido, Gifu 501-1193, Japan and Institute of Nano-Life-Systems, Institute of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| |
Collapse
|
12
|
Cistrone PA, Dirksen A, Ingale S, Dawson PE. Scandium(III) Triflate as a Lewis Acid Catalyst of Oxime Ligation. Aust J Chem 2020. [DOI: 10.1071/ch20042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Imine-forming reactions are widely applicable in bioconjugation owing to their high chemoselectivity. The ligation of a ketone or aldehyde with an aminooxy functional group to form a physiologically stable oxime bond is often used to link complex and precious biomolecules. Although the reaction proceeds modestly in acidic solution, the abundance of protonated carbonyl species at pH 7 limits its utility in many biological applications. The use of nucleophilic aryl amines, such as aniline or a phenylenediamine, allows a high population of protonated Schiff base to undergo transimination to the oxime product. Although this method affords significant enhancements at low pH, reactions can still be sluggish at neutral pH, especially with ketones such as acetophenone that are commonly used in bioconjugation. Here, we employ scandium(iii) trifluromethanesulfonate (triflate) (Sc(OTf)3), a uniquely water-stable Lewis acid, as a co-catalyst with ortho-phenylenediamine in the oxime ligation to yield up to an order of magnitude rate enhancement over the catalysts when applied individually.
Collapse
|
13
|
Duflocq S, Zhou J, Huguenot F, Vidal M, Liu WQ. One-pot oxime ligation from peptides bearing thiazolidine and aminooxyacetyl groups. RSC Adv 2020; 10:17681-17685. [PMID: 35515616 PMCID: PMC9053634 DOI: 10.1039/d0ra03235b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 11/25/2022] Open
Abstract
One-pot oxime ligation under mild conditions using Pd(ii) as a shared catalyst from an aldehyde precursor (Thz) and a protected aminooxyacetyl group (Proc-Aoa) is reported. Two complementary metal-free protocols using unmasked Aoa-peptide are also described. Acetoxime-peptide can proceed to the desired oxime through an additional transoximation step. Pd(ii), acidic hydrolysis and iodine lead to one-pot oxime ligation from peptides bearing thiazolidine and aminooxyacetyl groups.![]()
Collapse
Affiliation(s)
| | - Jingjing Zhou
- Université de Paris
- CiTCoM
- 8038 CNRS
- U 1268 INSERM
- F-75006 Paris
| | | | - Michel Vidal
- Université de Paris
- CiTCoM
- 8038 CNRS
- U 1268 INSERM
- F-75006 Paris
| | - Wang-Qing Liu
- Université de Paris
- CiTCoM
- 8038 CNRS
- U 1268 INSERM
- F-75006 Paris
| |
Collapse
|
14
|
He M, Lehn JM. Time-Dependent Switching of Constitutional Dynamic Libraries and Networks from Kinetic to Thermodynamic Distributions. J Am Chem Soc 2019; 141:18560-18569. [DOI: 10.1021/jacs.9b09395] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Meixia He
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
| |
Collapse
|
15
|
Guthrie QAE, Young HA, Proulx C. Ketoxime peptide ligations: oxidative couplings of alkoxyamines to N-aryl peptides. Chem Sci 2019; 10:9506-9512. [PMID: 32110307 PMCID: PMC7017874 DOI: 10.1039/c9sc04028e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 08/22/2019] [Indexed: 01/01/2023] Open
Abstract
Chemoselective ligation methods that preserve or introduce side chain diversity are critical for chemical synthesis of peptides and proteins. Starting from ketone substrates instead of aldehydes in oxime ligation reactions would allow substitution at the site of ligation; however, synthetic challenges to readily access ketone derivatives from common amino acid building blocks have precluded the widespread use of ketoxime peptide ligation reactions thus far. Moreover, ketones are typically much slower to react in condensation reactions compared to aldehydes. Here, one-pot catalyst-free oxidative couplings of α-substituted N-aryl peptides with alkoxyamines provide access to oxime linkages with diverse side chains. Electron-rich N-(p-Me2N-phenyl)-amino acids possessing substituents at the α-carbon were found to be uniquely capable of undergoing site-selective α-C-H oxidations in situ under an O2 atmosphere at neutral pH. Comparative studies with N-arylglycinyl peptides revealed that substitution at the α-carbon caused notable changes in reactivity, with greater sensitivity to solvent and buffer salt composition.
Collapse
Affiliation(s)
- Quibria A E Guthrie
- Department of Chemistry , North Carolina State University , Raleigh , NC 27695-8204 , USA .
| | - Hailey A Young
- Department of Chemistry , North Carolina State University , Raleigh , NC 27695-8204 , USA .
| | - Caroline Proulx
- Department of Chemistry , North Carolina State University , Raleigh , NC 27695-8204 , USA .
| |
Collapse
|
16
|
Roloff A, Nirmalananthan-Budau N, Rühle B, Borcherding H, Thiele T, Schedler U, Resch-Genger U. Quantification of Aldehydes on Polymeric Microbead Surfaces via Catch and Release of Reporter Chromophores. Anal Chem 2019; 91:8827-8834. [PMID: 31188569 DOI: 10.1021/acs.analchem.8b05515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Aldehyde moieties on 2D-supports or micro- and nanoparticles can function as anchor groups for the attachment of biomolecules or as reversible binding sites for proteins on cell surfaces. The use of aldehyde-based materials in bioanalytical and medical settings calls for reliable methods to detect and quantify this functionality. We report here on a versatile concept to quantify the accessible aldehyde moieties on particle surfaces through the specific binding and subsequent release of small reporter molecules such as fluorescent dyes and nonfluorescent chromophores utilizing acylhydrazone formation as a reversible covalent labeling strategy. This is representatively demonstrated for a set of polymer microparticles with different aldehyde labeling densities. Excess reporter molecules can be easily removed by washing, eliminating inaccuracies caused by unspecific adsorption to hydrophobic surfaces. Cleavage of hydrazones at acidic pH assisted by a carbonyl trap releases the fluorescent reporters rapidly and quasi-quantitatively and allows for their fluorometric detection at low concentration. Importantly, this strategy separates the signal-generating molecules from the bead surface. This circumvents common issues associated with light scattering and signal distortions that are caused by binding-induced changes in reporter fluorescence as well as quenching dye-dye interactions on crowded particle surfaces. In addition, we demonstrate that the release of a nonfluorescent chromophore via disulfide cleavage and subsequent quantification by absorption spectroscopy gives comparable results, verifying that both assays are capable of rapid and sensitive quantification of aldehydes on microbead surfaces. These strategies enable a quantitative comparison of bead batches with different functionalization densities, and a qualitative prediction of their coupling efficiencies in bioconjugations, as demonstrated in reductive amination reactions with Streptavidin.
Collapse
Affiliation(s)
- Alexander Roloff
- Federal Institute for Materials Research and Testing (BAM) , Richard-Willstätter-Straße 11 , D-12489 Berlin , Germany
| | - Nithiya Nirmalananthan-Budau
- Federal Institute for Materials Research and Testing (BAM) , Richard-Willstätter-Straße 11 , D-12489 Berlin , Germany.,Institut für Chemie und Biochemie , Freie Universität Berlin , Takustrasse 3 , D-14195 Berlin , Germany
| | - Bastian Rühle
- Federal Institute for Materials Research and Testing (BAM) , Richard-Willstätter-Straße 11 , D-12489 Berlin , Germany
| | | | - Thomas Thiele
- PolyAn GmbH , Rudolf-Baschant-Straße 2 , D-13086 Berlin , Germany
| | - Uwe Schedler
- PolyAn GmbH , Rudolf-Baschant-Straße 2 , D-13086 Berlin , Germany
| | - Ute Resch-Genger
- Federal Institute for Materials Research and Testing (BAM) , Richard-Willstätter-Straße 11 , D-12489 Berlin , Germany
| |
Collapse
|
17
|
Blomkvist B, Dinér P. Mild and Rapid Aniline/HBF
4
•DEE‐Catalysed Formation of Sulfinyl Imines. ChemistrySelect 2019. [DOI: 10.1002/slct.201901218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Björn Blomkvist
- Division of Organic ChemistryDepartment of ChemistrySchool of Engineering Sciences in Chemistry, Biology and Health, KTH – Royal Institute of Technology Teknikringen 30 10044 Stockholm Sweden
| | - Peter Dinér
- Division of Organic ChemistryDepartment of ChemistrySchool of Engineering Sciences in Chemistry, Biology and Health, KTH – Royal Institute of Technology Teknikringen 30 10044 Stockholm Sweden
| |
Collapse
|
18
|
Xu Y, Wang Y, Liu P, Chu GC, Xu H, Li YM, Wang J, Shi J. Catalyst free hydrazone ligation for protein labeling and modification using electron-deficient benzaldehyde reagents. Org Biomol Chem 2019; 16:7036-7040. [PMID: 30238118 DOI: 10.1039/c8ob01810c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Bioorthogonal reactions have emerged as valuable tools for site-specific protein labeling and modification in vitro and in vivo. Hydrazone and oxime ligation has recently attracted considerable attention for wide applications in the conjugation of biomolecules. However, this kind of reaction has suffered from slow kinetics under physiological conditions and toxicity or complications of the reaction system due to catalysts. In this work we have developed an electron-deficient benzaldehyde reagent, which can be easily equipped with various types of bio-functional molecules for catalyst-free hydrazone ligation. The reagent can be equipped with not only small molecules such as fluorescence dyes or drugs, but also macromolecules like PEG. These can be precisely ligated to the C-terminus of proteins by an efficient hydrazone reaction at neutral pH and room temperature. The new reagent based catalyst-free hydrazone ligation provides a practical approach for the site specific modification of proteins.
Collapse
Affiliation(s)
- Yang Xu
- School of Biological and Medical Engineering, Hefei University of Technology, Hefei 230009, P. R. China.
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Men G, Lehn JM. Multiple adaptation of constitutional dynamic networks and information storage in constitutional distributions of acylhydrazones. Chem Sci 2019; 10:90-98. [PMID: 30713621 PMCID: PMC6333171 DOI: 10.1039/c8sc03858a] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/25/2018] [Indexed: 01/07/2023] Open
Abstract
We report a study of the behavior of four dynamic covalent libraries (DCLs) based on acylhydrazones aAbB and of the corresponding square constitutional dynamic networks (CDNs) NA-ND under the effect of three agents, namely, metal cations, base + metal cations and light irradiation; in particular, the successful switching of the CDN NB between two orthogonal distributions results, respectively, from metallo-selection and photo-selection. The four DCLs undergo triple adaptation when subjected to the three agents with the generation of specific CDN distributions characteristic of each of the four DCLs. The ternary outputs displayed by the DCLs present three states (-1, 0 and 1) related to three different constitutional distributions expressed in response to the triple inputs applied. This latter process amounts to the storage of molecular information in dynamic distributions rather than in selective interactions between complementary entities undergoing molecular recognition.
Collapse
Affiliation(s)
- Guangwen Men
- Laboratoire de Chimie Supramoléculaire , Institut de Science et d'Ingénierie Supramoléculaires , Université de Strasbourg , 8 allée Gaspard Monge , 67000 Strasbourg , France . ; ; Tel: +33 3 68 85 51 44
- State Key Laboratory of Supramolecular Structure and Materials , Jilin University , 2699 Qianjin Avenue , Changchun , 130012 , P. R. China
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire , Institut de Science et d'Ingénierie Supramoléculaires , Université de Strasbourg , 8 allée Gaspard Monge , 67000 Strasbourg , France . ; ; Tel: +33 3 68 85 51 44
| |
Collapse
|
20
|
Grünewald J, Brock A, Geierstanger BH. Site-Specific Antibody Labeling Using Phosphopantetheinyl Transferase-Catalyzed Ligation. Methods Mol Biol 2019; 2012:237-278. [PMID: 31161512 DOI: 10.1007/978-1-4939-9546-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
4'-Phosphopantetheinyl transferases (PPTases) have been employed by researchers as versatile biocatalysts for the site-specific modification of numerous protein targets with structurally diverse molecules. Here we describe the use of these enzymes for the production of homogeneous antibody-drug conjugates (ADCs), which have garnered much attention as innovative anticancer drugs. The exceptionally broad substrate tolerance of PPTases allows for one-step and two-step conjugation strategies for site-specific ADC synthesis. While one-step conjugation involves direct coupling of a drug molecule to an antibody, two-step conjugation provides increased flexibility and efficiency of the conjugation process by first attaching a bioorthogonal chemical handle that is then used for drug molecule attachment in a second step. The aim of this chapter is to outline detailed protocols for both labeling procedures, as well as to provide guidance on enzyme and substrate preparation.
Collapse
Affiliation(s)
- Jan Grünewald
- Biotherapeutics, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA.
| | - Ansgar Brock
- Biotherapeutics, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | | |
Collapse
|
21
|
Wang S, Nawale GN, Oommen OP, Hilborn J, Varghese OP. Influence of ions to modulate hydrazone and oxime reaction kinetics to obtain dynamically cross-linked hyaluronic acid hydrogels. Polym Chem 2019. [DOI: 10.1039/c9py00862d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simple monovalent and divalent salts are presented as a novel catalyst for performing hydrazone and oxime coupling chemistry at physiological pH with excellent yields.
Collapse
Affiliation(s)
- Shujiang Wang
- Maisonneuve-Rosemont Hospital Research Centre & Dept. of Ophthalmology
- University of Montreal
- Montreal
- Canada
- Translational Chemical Biology Laboratory
| | - Ganesh N. Nawale
- Translational Chemical Biology Laboratory
- Department of Chemistry
- Ångström Laboratory
- Uppsala University
- Uppsala
| | - Oommen P. Oommen
- Bioengineering and Nanomedicine Lab
- Faculty of Medicine and Health Technologies and BioMediTech Institute
- Tampere University
- Tampere-33720
- Finland
| | - Jöns Hilborn
- Translational Chemical Biology Laboratory
- Department of Chemistry
- Ångström Laboratory
- Uppsala University
- Uppsala
| | - Oommen P. Varghese
- Translational Chemical Biology Laboratory
- Department of Chemistry
- Ångström Laboratory
- Uppsala University
- Uppsala
| |
Collapse
|
22
|
Karadeniz Ş, Ataol CY, Özen T, Demir R, Öğütçü H, Bati H. Synthesis, characterization and biological activities of Ni(II), Cu(II) and UO2(VI) complexes of N'-((2Z,3E)-3-(hydroxyimino)butan-2-ylidene)-2-phenylacetohydrazide. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.07.060] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
23
|
Zhang Y, Park KY, Suazo KF, Distefano MD. Recent progress in enzymatic protein labelling techniques and their applications. Chem Soc Rev 2018; 47:9106-9136. [PMID: 30259933 PMCID: PMC6289631 DOI: 10.1039/c8cs00537k] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein-based conjugates are valuable constructs for a variety of applications. Conjugation of proteins to fluorophores is commonly used to study their cellular localization and the protein-protein interactions. Modification of therapeutic proteins with either polymers or cytotoxic moieties greatly enhances their pharmacokinetics or potency. To label a protein of interest, conventional direct chemical reaction with the side-chains of native amino acids often yields heterogeneously modified products. This renders their characterization complicated, requires difficult separation steps and may impact protein function. Although modification can also be achieved via the insertion of unnatural amino acids bearing bioorthogonal functional groups, these methods can have lower protein expression yields, limiting large scale production. As a site-specific modification method, enzymatic protein labelling is highly efficient and robust under mild reaction conditions. Significant progress has been made over the last five years in modifying proteins using enzymatic methods for numerous applications, including the creation of clinically relevant conjugates with polymers, cytotoxins or imaging agents, fluorescent or affinity probes to study complex protein interaction networks, and protein-linked materials for biosensing. This review summarizes developments in enzymatic protein labelling over the last five years for a panel of ten enzymes, including sortase A, subtiligase, microbial transglutaminase, farnesyltransferase, N-myristoyltransferase, phosphopantetheinyl transferases, tubulin tyrosin ligase, lipoic acid ligase, biotin ligase and formylglycine generating enzyme.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | | | | | | |
Collapse
|
24
|
Kaur K, Qian Y, Gandour RD, Matson JB. Hydrolytic Decomposition of S-Aroylthiooximes: Effect of pH and N-Arylidene Substitution on Reaction Rate. J Org Chem 2018; 83:13363-13369. [PMID: 30347157 DOI: 10.1021/acs.joc.8b02151] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydrolytic decomposition of four peptides containing S-aroylthiooximes (SATOs) with variable N-arylidene substituents was investigated in 10 aqueous buffer solutions at pH values ranging from 6.0 to 10.9. UV-vis spectroscopy was employed to study the reaction kinetics, which revealed V-shaped pH-rate profiles for all peptides with a minimum near pH 8, suggesting a change from an acid-catalyzed to a base-activated reaction. Hammett plots showed positive ρ values above pH 8 and negative ρ values below pH 8, providing further evidence for a mechanism change. Based on these data, along with mass spectral evidence, we propose specific acid catalysis under mildly acidic and neutral conditions and multiple base-promoted decomposition reactions under mildly basic conditions.
Collapse
|
25
|
Liu X, Sun J, Gao W. Site-selective protein modification with polymers for advanced biomedical applications. Biomaterials 2018; 178:413-434. [DOI: 10.1016/j.biomaterials.2018.04.050] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/21/2018] [Accepted: 04/24/2018] [Indexed: 12/12/2022]
|
26
|
Houdier S, Lévêque J, Sabatier T, Jacob V, Jaffrezo JL. Aniline-based catalysts as promising tools to improve analysis of carbonyl compounds through derivatization techniques: preliminary results using dansylacetamidooxyamine derivatization and LC-fluorescence. Anal Bioanal Chem 2018; 410:7031-7042. [PMID: 30094788 DOI: 10.1007/s00216-018-1304-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/20/2018] [Accepted: 08/02/2018] [Indexed: 11/24/2022]
Affiliation(s)
- Stéphan Houdier
- CNRS, IRD, Grenoble INP, IGE, Univ. Grenoble Alpes, 38000, Grenoble, France.
| | - Justine Lévêque
- CNRS, IRD, Grenoble INP, IGE, Univ. Grenoble Alpes, 38000, Grenoble, France
| | - Tiphaine Sabatier
- CNRS, IRD, Grenoble INP, IGE, Univ. Grenoble Alpes, 38000, Grenoble, France
- CNRM, UMR3589, METEO-FRANCE & CNRS, 42 Avenue G. Coriolis, 31057, Toulouse Cedex 01, France
| | - Véronique Jacob
- CNRS, IRD, Grenoble INP, IGE, Univ. Grenoble Alpes, 38000, Grenoble, France
| | - Jean-Luc Jaffrezo
- CNRS, IRD, Grenoble INP, IGE, Univ. Grenoble Alpes, 38000, Grenoble, France
| |
Collapse
|
27
|
Trausel F, Fan B, van Rossum SAP, van Esch JH, Eelkema R. Aniline Catalysed Hydrazone Formation Reactions Show a Large Variation in Reaction Rates and Catalytic Effects. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Fanny Trausel
- Department of Chemical Engineering; Delft University of Technology; van der Maasweg 9 2629 HZ Delft, the Netherlands
| | - Bowen Fan
- Department of Chemical Engineering; Delft University of Technology; van der Maasweg 9 2629 HZ Delft, the Netherlands
| | - Susan A. P. van Rossum
- Department of Chemical Engineering; Delft University of Technology; van der Maasweg 9 2629 HZ Delft, the Netherlands
| | - Jan H. van Esch
- Department of Chemical Engineering; Delft University of Technology; van der Maasweg 9 2629 HZ Delft, the Netherlands
| | - Rienk Eelkema
- Department of Chemical Engineering; Delft University of Technology; van der Maasweg 9 2629 HZ Delft, the Netherlands
| |
Collapse
|
28
|
Larsen D, Kietrys AM, Clark SA, Park HS, Ekebergh A, Kool ET. Exceptionally rapid oxime and hydrazone formation promoted by catalytic amine buffers with low toxicity. Chem Sci 2018; 9:5252-5259. [PMID: 29997880 PMCID: PMC6001384 DOI: 10.1039/c8sc01082j] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/18/2018] [Indexed: 12/30/2022] Open
Abstract
Hydrazone and oxime bond formation between α-nucleophiles (e.g. hydrazines, alkoxy-amines) and carbonyl compounds (aldehydes and ketones) is convenient and is widely applied in multiple fields of research. While the reactants are simple, a substantial drawback is the relatively slow reaction at neutral pH. Here we describe a novel molecular strategy for accelerating these reactions, using bifunctional buffer compounds that not only control pH but also catalyze the reaction. The buffers can be employed at pH 5-9 (5-50 mM) and accelerate reactions by several orders of magnitude, yielding second-order rate constants of >10 M-1 s-1. Effective bifunctional amines include 2-(aminomethyl)imidazoles and N,N-dimethylethylenediamine. Unlike previous diaminobenzene catalysts, the new buffer amines are found to have low toxicity to human cells, and can be used to promote reactions in cellular applications.
Collapse
Affiliation(s)
- Dennis Larsen
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Anna M Kietrys
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Spencer A Clark
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Hyun Shin Park
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Andreas Ekebergh
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Eric T Kool
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| |
Collapse
|
29
|
Abstract
Mild conditions for oxime ligations via in situ generation of α-imino amide intermediates are reported. The evaluation of a variety of N-terminal N-phenylglycine residues revealed that a metal-free, chemoselective oxidation was possible using oxygen as the only oxidant in buffer at pH 7.0. Moreover, selective unmasking of an inert residue by addition of potassium ferricyanide is demonstrated. These simple and mild conditions, which can be fine-tuned by the electronic properties of the N-phenylglycine residue, offer unique advantages over conventional approaches for oxime ligations.
Collapse
Affiliation(s)
- Quibria A E Guthrie
- Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695-8204 , United States
| | - Caroline Proulx
- Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695-8204 , United States
| |
Collapse
|
30
|
Hewitt SH, Wilson AJ. Generation of Dynamic Combinatorial Libraries Using Hydrazone-Functionalized Surface Mimetics. European J Org Chem 2018; 2018:1872-1879. [PMID: 29780280 PMCID: PMC5947633 DOI: 10.1002/ejoc.201800022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Indexed: 01/01/2023]
Abstract
Dynamic combinatorial chemistry (DCC) represents an approach, whereby traditional supramolecular scaffolds used for protein surface recognition might be exploited to achieve selective high affinity target recognition. Synthesis, in situ screening and amplification under selection pressure allows the generation of ligands, which bear different moieties capable of making multivalent non‐covalent interactions with target proteins. Generic tetracarboxyphenyl porphyrin scaffolds bearing four hydrazide moieties have been used to form dynamic combinatorial libraries (DCLs) using aniline‐catalyzed reversible hydrazone exchange reactions, in 10 % DMSO, 5 mm NH4OAc, at pH 6.75. High resolution mass spectrometry (HRMS) was used to monitor library composition and establish conditions under which equilibria were established.
Collapse
Affiliation(s)
- Sarah H Hewitt
- School of Chemistry University of Leeds Woodhouse Lane 9JT Leeds LS2 UK.,Astbury Centre for Structural Molecular Biology University of Leeds Woodhouse Lane 9JT Leeds LS2 UK
| | - Andrew J Wilson
- School of Chemistry University of Leeds Woodhouse Lane 9JT Leeds LS2 UK.,Astbury Centre for Structural Molecular Biology University of Leeds Woodhouse Lane 9JT Leeds LS2 UK
| |
Collapse
|
31
|
Lv J, Zhang Q, Cai M, Han Y, Luo S. Aromatic Aminocatalysis. Chem Asian J 2018; 13:740-753. [PMID: 29493891 DOI: 10.1002/asia.201701773] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/01/2018] [Indexed: 11/08/2022]
Abstract
Aromatic aminocatalysis refers to transformations that employ aromatic amines, such as anilines or aminopyridines, as catalysts. Owing to the conjugation of the amine moiety with the aromatic ring, aromatic amines demonstrate distinctive features in aminocatalysis compared with their aliphatic counterparts. For example, aromatic aminocatalysis typically proceeds with slower turnover, but is more active and conformationally rigid as a result of the stabilized aromatic imine or iminium species. In fact, the advent of aromatic aminocatalysis can be traced back to before the renaissance of organocatalysis in the early 2000s. So far, aromatic aminocatalysis has been widely applied in bioconjugation reactions through transamination; in asymmetric organocatalysis through imine/enamine tautomerization; and in cooperative catalysis with transition metals through C-H/C-C activation and functionalization. This Focus Review summarizes the advent of and major advances in the use of aromatic aminocatalysis in bioconjugation reactions and organic synthesis.
Collapse
Affiliation(s)
- Jian Lv
- Key Laboratory for Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qi Zhang
- Key Laboratory for Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Mao Cai
- Key Laboratory for Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yanfang Han
- Key Laboratory for Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Sanzhong Luo
- Key Laboratory for Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| |
Collapse
|
32
|
Østergaard M, Christensen NJ, Hjuler CT, Jensen KJ, Thygesen MB. Glycoconjugate Oxime Formation Catalyzed at Neutral pH: Mechanistic Insights and Applications of 1,4-Diaminobenzene as a Superior Catalyst for Complex Carbohydrates. Bioconjug Chem 2018; 29:1219-1230. [PMID: 29437382 DOI: 10.1021/acs.bioconjchem.8b00019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction of unprotected carbohydrates with aminooxy reagents to provide oximes is a key method for the construction of glycoconjugates. Aniline and derivatives serve as organocatalysts for the formation of oximes from simple aldehydes, and we have previously reported that aniline also catalyzes the formation of oximes from the more complex aldehydes, carbohydrates. Here, we present a comprehensive study of the effect of aniline analogues on the formation of carbohydrate oximes and related glycoconjugates depending on organocatalyst structure, pH, nucleophile, and carbohydrate, covering more than 150 different reaction conditions. The observed superiority of the 1,4-diaminobenzene (PDA) catalyst at neutral pH is rationalized by NMR analyses and DFT studies of reaction intermediates. Carbohydrate oxime formation at pH 7 is demonstrated by the formation of a bioactive glycoconjugate from a labile, decorated octasaccharide originating from exopolysaccharides of the soil bacterium Mesorhizobium loti. This study of glycoconjugate formation includes the first direct comparison of aniline-catalyzed reaction rates and equilibrium constants for different classes of nucleophiles, including primary oxyamines, secondary N-alkyl oxyamines, as well as aryl and arylsulfonyl hydrazides. We identified 1,4-diaminobenzene as a superior catalyst for the construction of oxime-linked glycoconjugates under mild conditions.
Collapse
Affiliation(s)
- Mads Østergaard
- Department of Chemistry, Faculty of Science , University of Copenhagen , Thorvaldsensvej 40 , DK-1871 Frederiksberg C , Denmark
| | - Niels Johan Christensen
- Department of Chemistry, Faculty of Science , University of Copenhagen , Thorvaldsensvej 40 , DK-1871 Frederiksberg C , Denmark
| | - Christian T Hjuler
- Department of Chemistry, Faculty of Science , University of Copenhagen , Thorvaldsensvej 40 , DK-1871 Frederiksberg C , Denmark
| | - Knud J Jensen
- Department of Chemistry, Faculty of Science , University of Copenhagen , Thorvaldsensvej 40 , DK-1871 Frederiksberg C , Denmark
| | - Mikkel B Thygesen
- Department of Chemistry, Faculty of Science , University of Copenhagen , Thorvaldsensvej 40 , DK-1871 Frederiksberg C , Denmark
| |
Collapse
|
33
|
Saline Accelerates Oxime Reaction with Aldehyde and Keto Substrates at Physiological pH. Sci Rep 2018; 8:2193. [PMID: 29391582 PMCID: PMC5794741 DOI: 10.1038/s41598-018-20735-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/23/2018] [Indexed: 12/29/2022] Open
Abstract
We have discovered a simple and versatile reaction condition for oxime mediated bioconjugation reaction that could be adapted for both aldehyde and keto substrates. We found that saline accelerated the oxime kinetics in a concentration-dependent manner under physiological conditions. The reaction mechanism is validated by computational studies, and the versatility of the reaction is demonstrated by cell-surface labeling experiments. Saline offers an efficient and non-toxic catalytic option for performing the bioorthogonal-coupling reaction of biomolecules at the physiological pH. This saline mediated bioconjugation reaction represents the most biofriendly, mild and versatile approach for conjugating sensitive biomolecules and does not require any extensive purification step.
Collapse
|
34
|
Braun AC, Gutmann M, Lühmann T, Meinel L. Bioorthogonal strategies for site-directed decoration of biomaterials with therapeutic proteins. J Control Release 2018; 273:68-85. [PMID: 29360478 DOI: 10.1016/j.jconrel.2018.01.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 01/04/2023]
Abstract
Emerging strategies targeting site-specific protein modifications allow for unprecedented selectivity, fast kinetics and mild reaction conditions with high yield. These advances open exciting novel possibilities for the effective bioorthogonal decoration of biomaterials with therapeutic proteins. Site-specificity is particularly important to the therapeutics' end and translated by targeting specific functional groups or introducing new functional groups into the therapeutic at predefined positions. Biomimetic strategies are designed for modification of therapeutics emulating enzymatic strategies found in Nature. These strategies are suitable for a diverse range of applications - not only for protein-polymer conjugation, particle decoration and surface immobilization, but also for the decoration of complex biomaterials and the synthesis of bioresponsive drug delivery systems. This article reviews latest chemical and enzymatic strategies for the biorthogonal decoration of biomaterials with therapeutic proteins and inter-positioned linker structures. Finally, the numerous reports at the interface of biomaterials, linkers, and therapeutic protein decoration are integrated into practical advice for design considerations intended to support the selection of productive ligation strategies.
Collapse
Affiliation(s)
- Alexandra C Braun
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, DE-97074 Würzburg, Germany
| | - Marcus Gutmann
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, DE-97074 Würzburg, Germany
| | - Tessa Lühmann
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, DE-97074 Würzburg, Germany
| | - Lorenz Meinel
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, DE-97074 Würzburg, Germany.
| |
Collapse
|
35
|
Nisal R, P. Jose G, Shanbhag C, Kalia J. Rapid and reversible hydrazone bioconjugation in cells without the use of extraneous catalysts. Org Biomol Chem 2018; 16:4304-4310. [DOI: 10.1039/c8ob00946e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Rapid, catalyst-free and reversible bioconjugation in mammalian cells.
Collapse
Affiliation(s)
- Rahul Nisal
- Indian Institute of Science Education and Research (IISER) Pune
- Pune-411008
- India
| | - Gregor P. Jose
- Indian Institute of Science Education and Research (IISER) Pune
- Pune-411008
- India
| | - Chitra Shanbhag
- Indian Institute of Science Education and Research (IISER) Pune
- Pune-411008
- India
| | - Jeet Kalia
- Indian Institute of Science Education and Research (IISER) Pune
- Pune-411008
- India
| |
Collapse
|
36
|
Liew SK, Holownia A, Diaz DB, Cistrone PA, Dawson PE, Yudin AK. Borylated oximes: versatile building blocks for organic synthesis. Chem Commun (Camb) 2017; 53:11237-11240. [PMID: 28959806 PMCID: PMC6097236 DOI: 10.1039/c7cc06579e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we demonstrate the synthesis and functionalization of α-boryl aldoximes from α-boryl aldehydes, with no sign of C-to-N boryl migration. Selective modification of the oxime functionality enables access to a wide range of borylated compounds, such as borylated heterocycles and N-acetoxyamides. By reducing the α-boryl aldoximes, MIDA deprotection yields the corresponding β-boryl hydroxylamines. As part of this study, we also demonstrate the utility of the boryl aldoxime motif in peptide conjugation.
Collapse
Affiliation(s)
- Sean K Liew
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| | | | | | | | | | | |
Collapse
|
37
|
Akgun B, Li C, Hao Y, Lambkin G, Derda R, Hall DG. Synergic “Click” Boronate/Thiosemicarbazone System for Fast and Irreversible Bioorthogonal Conjugation in Live Cells. J Am Chem Soc 2017; 139:14285-14291. [DOI: 10.1021/jacs.7b08693] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Caishun Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yubin Hao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Gareth Lambkin
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Dennis G. Hall
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| |
Collapse
|
38
|
Abstract
The formation of oximes and hydrazones is employed in numerous scientific fields as a simple and versatile conjugation strategy. This imine-forming reaction is applied in fields as diverse as polymer chemistry, biomaterials and hydrogels, dynamic combinatorial chemistry, organic synthesis, and chemical biology. Here we outline chemical developments in this field, with special focus on the past ∼10 years of developments. Recent strategies for installing reactive carbonyl groups and α-nucleophiles into biomolecules are described. The basic chemical properties of reactants and products in this reaction are then reviewed, with an eye to understanding the reaction's mechanism and how reactant structure controls rates and equilibria in the process. Recent work that has uncovered structural features and new mechanisms for speeding the reaction, sometimes by orders of magnitude, is discussed. We describe recent studies that have identified especially fast reacting aldehyde/ketone substrates and structural effects that lead to rapid-reacting α-nucleophiles as well. Among the most effective new strategies has been the development of substituents near the reactive aldehyde group that either transfer protons at the transition state or trap the initially formed tetrahedral intermediates. In addition, the recent development of efficient nucleophilic catalysts for the reaction is outlined, improving greatly upon aniline, the classical catalyst for imine formation. A number of uses of such second- and third-generation catalysts in bioconjugation and in cellular applications are highlighted. While formation of hydrazone and oxime has been traditionally regarded as being limited by slow rates, developments in the past 5 years have resulted in completely overturning this limitation; indeed, the reaction is now one of the fastest and most versatile reactions available for conjugations of biomolecules and biomaterials.
Collapse
Affiliation(s)
- Dominik K Kölmel
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| |
Collapse
|
39
|
Pifferi C, Daskhan GC, Fiore M, Shiao TC, Roy R, Renaudet O. Aminooxylated Carbohydrates: Synthesis and Applications. Chem Rev 2017; 117:9839-9873. [PMID: 28682060 DOI: 10.1021/acs.chemrev.6b00733] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Among other classes of biomolecules, carbohydrates and glycoconjugates are widely involved in numerous biological functions. In addition to addressing the related synthetic challenges, glycochemists have invested intense efforts in providing access to structures that can be used to study, activate, or inhibit these biological processes. Over the past few decades, aminooxylated carbohydrates have been found to be key building blocks for achieving these goals. This review provides the first in-depth overview covering several aspects related to the syntheses and applications of aminooxylated carbohydrates. After a brief introduction to oxime bonds and their relative stabilities compared to related C═N functions, synthetic aspects of oxime ligation and methodologies for introducing the aminooxy functionality onto both glycofuranosyls and glycopyranosyls are described. The subsequent section focuses on biological applications involving aminooxylated carbohydrates as components for the construcion of diverse architectures. Mimetics of natural structures represent useful tools for better understanding the features that drive carbohydrate-receptor interaction, their biological output and they also represent interesting structures with improved stability and tunable properties. In the next section, multivalent structures such as glycoclusters and glycodendrimers obtained through oxime ligation are described in terms of synthetic design and their biological applications such as immunomodulators. The second-to-last section discusses miscellaneous applications of oxime-based glycoconjugates, such as enantioselective catalysis and glycosylated oligonucleotides, and conclusions and perspectives are provided in the last section.
Collapse
Affiliation(s)
- Carlo Pifferi
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Gour Chand Daskhan
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Michele Fiore
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Tze Chieh Shiao
- Pharmaqam, Department of Chemistry, Université du Québec à Montreal , P.O. Box 8888, Succursale Centre-ville, Montréal, Québec H3C 3P8, Canada
| | - René Roy
- Pharmaqam, Department of Chemistry, Université du Québec à Montreal , P.O. Box 8888, Succursale Centre-ville, Montréal, Québec H3C 3P8, Canada
| | - Olivier Renaudet
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France.,Institut Universitaire de France , 103 Boulevard Saint-Michel, 75005 Paris, France
| |
Collapse
|
40
|
Fisher SA, Baker AEG, Shoichet MS. Designing Peptide and Protein Modified Hydrogels: Selecting the Optimal Conjugation Strategy. J Am Chem Soc 2017; 139:7416-7427. [PMID: 28481537 DOI: 10.1021/jacs.7b00513] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hydrogels are used in a wide variety of biomedical applications including tissue engineering, biomolecule delivery, cell delivery, and cell culture. These hydrogels are often designed with a specific biological function in mind, requiring the chemical incorporation of bioactive factors to either mimic extracellular matrix or to deliver a payload to diseased tissue. Appropriate synthetic techniques to ligate bioactive factors, such as peptides and proteins, onto hydrogels are critical in designing materials with biological function. Here, we outline strategies for peptide and protein immobilization. We specifically focus on click chemistry, enzymatic ligation, and affinity binding for transient immobilization. Protein modification strategies have shifted toward site-specific modification using unnatural amino acids and engineered site-selective amino acid sequences to preserve both activity and structure. The selection of appropriate protein immobilization strategies is vital to engineering functional hydrogels. We provide insight into chemistry that balances the need for facile reactions while maintaining protein bioactivity or desired release.
Collapse
Affiliation(s)
- Stephanie A Fisher
- The Donnelly Centre for Cellular and Biomolecular Research, ‡Department of Chemical Engineering and Applied Chemistry, §Institute of Biomaterials and Biomedical Engineering, and ∥Department of Chemistry, University of Toronto , 160 College Street, Room 514, Toronto, Ontario M5S 3E1, Canada
| | - Alexander E G Baker
- The Donnelly Centre for Cellular and Biomolecular Research, ‡Department of Chemical Engineering and Applied Chemistry, §Institute of Biomaterials and Biomedical Engineering, and ∥Department of Chemistry, University of Toronto , 160 College Street, Room 514, Toronto, Ontario M5S 3E1, Canada
| | - Molly S Shoichet
- The Donnelly Centre for Cellular and Biomolecular Research, ‡Department of Chemical Engineering and Applied Chemistry, §Institute of Biomaterials and Biomedical Engineering, and ∥Department of Chemistry, University of Toronto , 160 College Street, Room 514, Toronto, Ontario M5S 3E1, Canada
| |
Collapse
|
41
|
Patil M. A revised mechanism for the α-ketoacid hydroxylamine amide forming ligations. Org Biomol Chem 2017; 15:416-425. [DOI: 10.1039/c6ob02057g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The α-ketoacid-hydroxylamine amide-forming (KAHA) ligation reactions were investigated using computational methods to provide improved insights on the mechanism of these reactions.
Collapse
Affiliation(s)
- Mahendra Patil
- UM-DAE Centre for Excellence in Basic Sciences
- Health Centre
- University of Mumbai
- Mumbai 400098
- India
| |
Collapse
|
42
|
Maxson T, Tietz JI, Hudson GA, Guo XR, Tai HC, Mitchell DA. Targeting Reactive Carbonyls for Identifying Natural Products and Their Biosynthetic Origins. J Am Chem Soc 2016; 138:15157-15166. [PMID: 27797509 DOI: 10.1021/jacs.6b06848] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Natural products (NPs) serve important roles as drug candidates and as tools for chemical biology. However, traditional NP discovery, largely based on bioassay-guided approaches, is biased toward abundant compounds and rediscovery rates are high. Orthogonal methods to facilitate discovery of new NPs are thus needed, and herein we describe an isotope tag-based expansion of reactivity-based NP screening to address these shortcomings. Reactivity-based screening is a directed discovery approach in which a specific reactive handle on the NP is targeted by a chemoselective probe to enable its detection by mass spectrometry. In this study, we have developed an aminooxy-containing probe to guide the discovery of aldehyde- and ketone-containing NPs. To facilitate the detection of labeling events, the probe was dibrominated, imparting a unique isotopic signature to distinguish labeled metabolites from spectral noise. As a proof of concept, the probe was then utilized to screen a collection of bacterial extracts, leading to the identification of a new analogue of antipain, deimino-antipain. The bacterial producer of deimino-antipain was sequenced and the responsible biosynthetic gene cluster was identified by bioinformatic analysis and heterologous expression. These data reveal the previously undetermined genetic basis for a well-known family of aldehyde-containing, peptidic protease inhibitors, including antipain, chymostatin, leupeptin, elastatinal, and microbial alkaline protease inhibitor, which have been widely used for over 40 years.
Collapse
Affiliation(s)
- Tucker Maxson
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jonathan I Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Xiao Rui Guo
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Hua-Chia Tai
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| |
Collapse
|
43
|
Baudendistel OR, Wieland DE, Schmidt MS, Wittmann V. Real-Time NMR Studies of Oxyamine Ligations of Reducing Carbohydrates under Equilibrium Conditions. Chemistry 2016; 22:17359-17365. [DOI: 10.1002/chem.201603369] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Oliver R. Baudendistel
- Department of Chemistry; Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; 78457 Konstanz Germany
| | - Daniel E. Wieland
- Department of Chemistry; Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; 78457 Konstanz Germany
| | - Magnus S. Schmidt
- Department of Chemistry; Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; 78457 Konstanz Germany
| | - Valentin Wittmann
- Department of Chemistry; Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; 78457 Konstanz Germany
| |
Collapse
|
44
|
Morales S, Aceña JL, García Ruano JL, Cid MB. Sustainable Synthesis of Oximes, Hydrazones, and Thiosemicarbazones under Mild Organocatalyzed Reaction Conditions. J Org Chem 2016; 81:10016-10022. [PMID: 27668816 DOI: 10.1021/acs.joc.6b01912] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Pyrrolidine catalyzes very efficiently, presumably via iminium activation, the formation of acyloximes, acylhydrazones, and thiosemicarbazones derived from aromatic and aliphatic aldehydes using equimolar amounts of reagents and green solvents. Experimental simplicity and excellent yields after a simple filtration are the main advantages of the method, being an alternative to those currently available especially for the acyl derivatives, which do not work under uncatalyzed conditions. Its application to the synthesis of acyloximes by direct condensation between aldehydes and acylhydroxylamines is unprecedented.
Collapse
Affiliation(s)
- Sara Morales
- Department of Organic Chemistry, Universidad Autónoma de Madrid , Cantoblanco, 28049 Madrid, Spain
| | - José Luis Aceña
- Department of Organic Chemistry, Universidad Autónoma de Madrid , Cantoblanco, 28049 Madrid, Spain
| | - José Luis García Ruano
- Department of Organic Chemistry, Universidad Autónoma de Madrid , Cantoblanco, 28049 Madrid, Spain
| | - M Belén Cid
- Department of Organic Chemistry, Universidad Autónoma de Madrid , Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
45
|
Trindade AF, Bode JW. Irreversible Conjugation of Aldehydes in Water To Form Stable 1,2,4-Oxadiazinan-5-ones. Org Lett 2016; 18:4210-3. [PMID: 27541010 DOI: 10.1021/acs.orglett.6b01889] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A new, irreversible aldehyde conjugation reaction in aqueous media was developed. α-Aminooxy acetohydrazides undergo irreversible condensation reactions with aliphatic, aromatic, or unsaturated aldehydes and isatins in a mixture of acetonitrile and acetate buffer at pH 4 to yield 1,2,4-oxadiazinan-5-one heterocycles in excellent isolated yields (40-99%). This class of heterocycles proved to be hydrolytically stable throughout a wide range of temperatures and pH (4.5-7).
Collapse
Affiliation(s)
- Alexandre F Trindade
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich , 8093 Zürich, Switzerland.,Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa , Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich , 8093 Zürich, Switzerland
| |
Collapse
|
46
|
Herbst E, Shabat D. FRET-based cyanine probes for monitoring ligation reactions and their applications to mechanistic studies and catalyst screening. Org Biomol Chem 2016; 14:3715-28. [PMID: 26909686 DOI: 10.1039/c5ob02127h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There is an ever-increasing need to design better methods to selectively connect two molecules under mild aqueous conditions on a small scale. The process of finding such methods significantly relies on the employment of an appropriate assay. We report here a modular FRET-based assay to monitor such reactions and illustrate how the assay is used to monitor two particular reactions: native chemical ligation (NCL) and oxime ligation. For both reactions we show that by employing appropriately designed probes FRET measurements could be used to monitor the reaction's progress. We additionally demonstrate the usefulness of the developed probe system to study the mechanisms of the ligation reactions, for example, in monitoring the formation of a trimeric intermediate in the NCL reaction. Finally, we demonstrate that FRET measurements conducted in our system allow the quantification of the reaction yield and we show the application of our FRET-based assay to catalyst screening for the oxime ligation.
Collapse
Affiliation(s)
- E Herbst
- School of Chemistry, Department of Organic Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv, 69978 Israel
| | - D Shabat
- School of Chemistry, Department of Organic Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv, 69978 Israel
| |
Collapse
|
47
|
Lascano S, Zhang KD, Wehlauch R, Gademann K, Sakai N, Matile S. The third orthogonal dynamic covalent bond. Chem Sci 2016; 7:4720-4724. [PMID: 30155121 PMCID: PMC6014071 DOI: 10.1039/c6sc01133k] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 04/09/2016] [Indexed: 01/30/2023] Open
Abstract
Orthogonal dynamic covalent bonds are of interest for the construction of functional systems. The orthogonality of disulfide and hydrazone exchange under basic and acidic conditions, respectively, is well established. However, the integration of boronate esters as the third bond has failed so far because they exchanged too easily, especially under hydrazone exchange conditions. In this report, a collection of bioinspired catechols derived from adhesive natural products from cyanobacteria is screened with phenylboronic acids with proximal alcohols (benzoboroxoles), amines and fluorines to identify the least labile boronate esters. Moreover, Kool's 2-aminophenol catalysts are introduced to selectively accelerate hydrazone exchange without disturbing sufficiently inert boronate esters. Based on these results, we identified three different conditions to selectively exchange disulfides, hydrazones and boronate esters, that is to demonstrate the existence of three orthogonal dynamic covalent bonds. Moreover, their compatibility with functional systems is confirmed by successful hydrazone exchange in multicomponent surface architectures in the presence of intact boronate esters and disulfides.
Collapse
Affiliation(s)
- Santiago Lascano
- National Centre of Competence in Research (NCCR) , Molecular Systems Engineering (MSE) , Switzerland . http://www.nccr-mse.ch
- Department of Organic Chemistry , University of Geneva , Geneva , Switzerland . ; http://www.unige.ch/sciences/chiorg/matile/ ; ; Tel: +41 22 379 6523
| | - Kang-Da Zhang
- National Centre of Competence in Research (NCCR) , Molecular Systems Engineering (MSE) , Switzerland . http://www.nccr-mse.ch
- Department of Organic Chemistry , University of Geneva , Geneva , Switzerland . ; http://www.unige.ch/sciences/chiorg/matile/ ; ; Tel: +41 22 379 6523
| | - Robin Wehlauch
- National Centre of Competence in Research (NCCR) , Molecular Systems Engineering (MSE) , Switzerland . http://www.nccr-mse.ch
- Department of Chemistry , University of Zurich , Zurich , Switzerland
| | - Karl Gademann
- National Centre of Competence in Research (NCCR) , Molecular Systems Engineering (MSE) , Switzerland . http://www.nccr-mse.ch
- Department of Chemistry , University of Zurich , Zurich , Switzerland
| | - Naomi Sakai
- National Centre of Competence in Research (NCCR) , Molecular Systems Engineering (MSE) , Switzerland . http://www.nccr-mse.ch
- Department of Organic Chemistry , University of Geneva , Geneva , Switzerland . ; http://www.unige.ch/sciences/chiorg/matile/ ; ; Tel: +41 22 379 6523
| | - Stefan Matile
- National Centre of Competence in Research (NCCR) , Molecular Systems Engineering (MSE) , Switzerland . http://www.nccr-mse.ch
- Department of Organic Chemistry , University of Geneva , Geneva , Switzerland . ; http://www.unige.ch/sciences/chiorg/matile/ ; ; Tel: +41 22 379 6523
| |
Collapse
|
48
|
Beezer DB, Harth E. Post-polymerization modification of branched polyglycidol withN-Hydroxy phthalimide to give ratio-controlled amino-oxy functionalized species. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/pola.28168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dain B. Beezer
- Department of Chemistry; Vanderbilt University, 7665 Stevenson Center; Nashville Tennessee 37235
| | - Eva Harth
- Department of Chemistry; Vanderbilt University, 7665 Stevenson Center; Nashville Tennessee 37235
| |
Collapse
|
49
|
Abstract
Hydrazone chemistry is widely utilized in biomedical field as a means of bioconjugation protocol, especially in drug delivery field due to pH labile nature of this linkage. In the light of kinetics studies, the generally accepted mechanism for the hydrolysis of hydrazones involves two main steps, namely, nucleophilic addition of water molecule to the hydrazone molecule to form carbinolamine intermediate and subsequent decomposition of this intermediate into the hydrazine and aldehyde/ketone moieties. Hydrolysis of hydrazones is catalyzed in the acidic environments and is thought to proceed through several proton transfer steps. To the best of our knowledge, in the literature no detailed theoretical study has been reported related to the mechanism of hydrolysis. In this study, we evaluated the proposed mechanism with DFT calculations with M06-2X functional at the 6-311+g(d,p) level including conductor-like polarizable continuum model solvation model. We also analyzed possible proton transfer pathways and assessed energetics of each step.
Collapse
Affiliation(s)
- Ibrahim Yildiz
- Applied Mathematics & Sciences, Khalifa University , PO Box 127788, Abu Dhabi, UAE
| |
Collapse
|
50
|
Agten SM, Dawson PE, Hackeng TM. Oxime conjugation in protein chemistry: from carbonyl incorporation to nucleophilic catalysis. J Pept Sci 2016; 22:271-9. [PMID: 27006095 DOI: 10.1002/psc.2874] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 02/17/2016] [Accepted: 02/17/2016] [Indexed: 12/30/2022]
Abstract
Use of oxime forming reactions has become a widely applied strategy for peptide and protein bioconjugation. The efficiency of the reaction and robust stability of the oxime product has led to the development of a growing list of methods to introduce the required ketone or aldehyde functionality site specifically into proteins. Early methods focused on site-specific oxidation of an N-terminal serine or threonine and more recently transamination methods have been developed to convert a broader set of N-terminal amino acids into a ketone or aldehyde. More recently, site-specific modification of protein has been attained through engineering enzymes involved in posttranslational modifications in order to accommodate aldehyde-containing substrates. Similarly, a growing list of unnatural amino acids can be introduced through development of selective amino-acyl tRNA synthetase/tRNA pairs combined with codon reassignment. In the case of glycoproteins, glycans can be selectively modified chemically or enzymatically to introduce aldehyde functional groups. Finally, the total chemical synthesis of proteins complements these biological and chemoenzymatic approaches. Once introduced, the oxime ligation of these aldehyde and ketone groups can be catalyzed by aniline or a variety of aniline derivatives to tune the activity, pH preference, stability and solubility of the catalyst. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Stijn M Agten
- Department of Biochemistry, Maastricht University, Maastricht, Netherlands
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Tilman M Hackeng
- Department of Biochemistry, Maastricht University, Maastricht, Netherlands
| |
Collapse
|