1
|
Cao L, Wang L. Biospecific Chemistry for Covalent Linking of Biomacromolecules. Chem Rev 2024. [PMID: 38913432 DOI: 10.1021/acs.chemrev.4c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Interactions among biomacromolecules, predominantly noncovalent, underpin biological processes. However, recent advancements in biospecific chemistry have enabled the creation of specific covalent bonds between biomolecules, both in vitro and in vivo. This Review traces the evolution of biospecific chemistry in proteins, emphasizing the role of genetically encoded latent bioreactive amino acids. These amino acids react selectively with adjacent natural groups through proximity-enabled bioreactivity, enabling targeted covalent linkages. We explore various latent bioreactive amino acids designed to target different protein residues, ribonucleic acids, and carbohydrates. We then discuss how these novel covalent linkages can drive challenging protein properties and capture transient protein-protein and protein-RNA interactions in vivo. Additionally, we examine the application of covalent peptides as potential therapeutic agents and site-specific conjugates for native antibodies, highlighting their capacity to form stable linkages with target molecules. A significant focus is placed on proximity-enabled reactive therapeutics (PERx), a pioneering technology in covalent protein therapeutics. We detail its wide-ranging applications in immunotherapy, viral neutralization, and targeted radionuclide therapy. Finally, we present a perspective on the existing challenges within biospecific chemistry and discuss the potential avenues for future exploration and advancement in this rapidly evolving field.
Collapse
Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
| |
Collapse
|
2
|
Guo QR, Cao YJ. Applications of genetic code expansion technology in eukaryotes. Protein Cell 2024; 15:331-363. [PMID: 37847216 PMCID: PMC11074999 DOI: 10.1093/procel/pwad051] [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: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
Unnatural amino acids (UAAs) have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins. In eukaryotes, genetic code expansion (GCE) enables the incorporation of UAAs and facilitates posttranscriptional modification (PTM), which is not feasible in prokaryotic systems. GCE is also a powerful tool for cell or animal imaging, the monitoring of protein interactions in target cells, drug development, and switch regulation. Therefore, there is keen interest in utilizing GCE in eukaryotic systems. This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.
Collapse
Affiliation(s)
- Qiao-ru Guo
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yu J Cao
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| |
Collapse
|
3
|
Fröhlich M, Söllner J, Derler I. Insights into the dynamics of the Ca2+ release-activated Ca2+ channel pore-forming complex Orai1. Biochem Soc Trans 2024; 52:747-760. [PMID: 38526208 DOI: 10.1042/bst20230815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024]
Abstract
An important calcium (Ca2+) entry pathway into the cell is the Ca2+ release-activated Ca2+ (CRAC) channel, which controls a series of downstream signaling events such as gene transcription, secretion and proliferation. It is composed of a Ca2+ sensor in the endoplasmic reticulum (ER), the stromal interaction molecule (STIM), and the Ca2+ ion channel Orai in the plasma membrane (PM). Their activation is initiated by receptor-ligand binding at the PM, which triggers a signaling cascade within the cell that ultimately causes store depletion. The decrease in ER-luminal Ca2+ is sensed by STIM1, which undergoes structural rearrangements that lead to coupling with Orai1 and its activation. In this review, we highlight the current understanding of the Orai1 pore opening mechanism. In this context, we also point out the questions that remain unanswered and how these can be addressed by the currently emerging genetic code expansion (GCE) technology. GCE enables the incorporation of non-canonical amino acids with novel properties, such as light-sensitivity, and has the potential to provide novel insights into the structure/function relationship of CRAC channels at a single amino acid level in the living cell.
Collapse
Affiliation(s)
- Maximilian Fröhlich
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Julia Söllner
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| |
Collapse
|
4
|
Cheng L, Wang Y, Guo Y, Zhang SS, Xiao H. Advancing protein therapeutics through proximity-induced chemistry. Cell Chem Biol 2024; 31:428-445. [PMID: 37802076 PMCID: PMC10960704 DOI: 10.1016/j.chembiol.2023.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/21/2023] [Accepted: 09/15/2023] [Indexed: 10/08/2023]
Abstract
Recent years have seen a remarkable growth in the field of protein-based medical treatments. Nevertheless, concerns have arisen regarding the cytotoxicity limitations, low affinity, potential immunogenicity, low stability, and challenges to modify these proteins. To overcome these obstacles, proximity-induced chemistry has emerged as a next-generation strategy for advancing protein therapeutics. This method allows site-specific modification of proteins with therapeutic agents, improving their effectiveness without extensive engineering. In addition, this innovative approach enables spatial control of the reaction based on proximity, facilitating the formation of irreversible covalent bonds between therapeutic proteins and their targets. This capability becomes particularly valuable in addressing challenges such as the low affinity frequently encountered between therapeutic proteins and their targets, as well as the limited availability of small molecules for specific protein targets. As a result, proximity-induced chemistry is reshaping the field of protein drug preparation and propelling the revolution in novel protein therapeutics.
Collapse
Affiliation(s)
- Linqi Cheng
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Yixian Wang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Yiming Guo
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Sophie S Zhang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Han Xiao
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA; Department of Biosciences, Rice University, 6100 Main Street, Houston, TX 77005, USA; Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX 77005, USA.
| |
Collapse
|
5
|
Bacsa B, Hopl V, Derler I. Synthetic Biology Meets Ca 2+ Release-Activated Ca 2+ Channel-Dependent Immunomodulation. Cells 2024; 13:468. [PMID: 38534312 DOI: 10.3390/cells13060468] [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: 02/05/2024] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
Many essential biological processes are triggered by the proximity of molecules. Meanwhile, diverse approaches in synthetic biology, such as new biological parts or engineered cells, have opened up avenues to precisely control the proximity of molecules and eventually downstream signaling processes. This also applies to a main Ca2+ entry pathway into the cell, the so-called Ca2+ release-activated Ca2+ (CRAC) channel. CRAC channels are among other channels are essential in the immune response and are activated by receptor-ligand binding at the cell membrane. The latter initiates a signaling cascade within the cell, which finally triggers the coupling of the two key molecular components of the CRAC channel, namely the stromal interaction molecule, STIM, in the ER membrane and the plasma membrane Ca2+ ion channel, Orai. Ca2+ entry, established via STIM/Orai coupling, is essential for various immune cell functions, including cytokine release, proliferation, and cytotoxicity. In this review, we summarize the tools of synthetic biology that have been used so far to achieve precise control over the CRAC channel pathway and thus over downstream signaling events related to the immune response.
Collapse
Affiliation(s)
- Bernadett Bacsa
- Division of Medical Physics und Biophysics, Medical University of Graz, A-8010 Graz, Austria
| | - Valentina Hopl
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| |
Collapse
|
6
|
Singh D, Ghorpade M, Regar R, Collot M, Soppina V, Kanvah S. Fluorescent styrenes for mitochondrial imaging and viscosity sensing. Photochem Photobiol 2024. [PMID: 38385897 DOI: 10.1111/php.13910] [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: 09/13/2023] [Revised: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
Fluorophores bearing cationic pendants, such as the pyridinium group, tend to preferentially accumulate in mitochondria, whereas those with pentafluorophenyl groups display a distinct affinity for the endoplasmic reticulum. In this study, we designed fluorophores incorporating pyridinium and pentafluorophenyl pendants and examined their impact on sub-cellular localization. Remarkably, the fluorophores exhibited a notable propensity for the mitochondrial membrane. Furthermore, these fluorophores revealed dual functionality by facilitating the detection of viscosity changes within the sub-cellular environment and serving as heavy-atom-free photosensitizers. With easy chemical tunability, wash-free imaging, and a favorable signal-to-noise ratio, these fluorophores are valuable tools for imaging mitochondria and investigating their cellular processes.
Collapse
Affiliation(s)
- Deepmala Singh
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Mohini Ghorpade
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Ramprasad Regar
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Mayeul Collot
- Laboratoire de Bioimagerie et Pathologies UMR 7021, CNRS/Université de Strasbourg, Strasbourg, France
| | - Virupakshi Soppina
- Department of Biological Engineering, Indian Institute of Technology, Gandhinagar, India
| | - Sriram Kanvah
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| |
Collapse
|
7
|
Volarić J, van der Heide NJ, Mutter NL, Samplonius DF, Helfrich W, Maglia G, Szymanski W, Feringa BL. Visible Light Control over the Cytolytic Activity of a Toxic Pore-Forming Protein. ACS Chem Biol 2024; 19:451-461. [PMID: 38318850 PMCID: PMC10877574 DOI: 10.1021/acschembio.3c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Enabling control over the bioactivity of proteins with light, along with the principles of photopharmacology, has the potential to generate safe and targeted medical treatments. Installing light sensitivity in a protein can be achieved through its covalent modification with a molecular photoswitch. The general challenge in this approach is the need for the use of low energy visible light for the regulation of bioactivity. In this study, we report visible light control over the cytolytic activity of a protein. A water-soluble visible-light-operated tetra-ortho-fluoro-azobenzene photoswitch was synthesized by utilizing the nucleophilic aromatic substitution reaction for installing a solubilizing sulfonate group onto the electron-poor photoswitch structure. The azobenzene was attached to two cysteine mutants of the pore-forming protein fragaceatoxin C (FraC), and their respective activities were evaluated on red blood cells. For both mutants, the green-light-irradiated sample, containing predominantly the cis-azobenzene isomer, was more active compared to the blue-light-irradiated sample. Ultimately, the same modulation of the cytolytic activity pattern was observed toward a hypopharyngeal squamous cell carcinoma. These results constitute the first case of using low energy visible light to control the biological activity of a toxic protein.
Collapse
Affiliation(s)
- Jana Volarić
- Stratingh
Institute for Organic Chemistry, University
of Groningen, 9747 AG Groningen, The Netherlands
| | - Nieck J. van der Heide
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Natalie L. Mutter
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Douwe F. Samplonius
- Department
of Surgery, Translational Surgical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Wijnand Helfrich
- Department
of Surgery, Translational Surgical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Wiktor Szymanski
- Stratingh
Institute for Organic Chemistry, University
of Groningen, 9747 AG Groningen, The Netherlands
- Department
of Radiology, Medical Imaging Center, University
of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Ben L. Feringa
- Stratingh
Institute for Organic Chemistry, University
of Groningen, 9747 AG Groningen, The Netherlands
| |
Collapse
|
8
|
Kapun M, Pérez-Areales FJ, Ashman N, Rowling PJE, Schober T, Fowler E, Itzhaki LS, Spring DR. Red-light modulated ortho-chloro azobenzene photoswitch for peptide stapling via aromatic substitution. RSC Chem Biol 2024; 5:49-54. [PMID: 38179193 PMCID: PMC10763561 DOI: 10.1039/d3cb00176h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/05/2023] [Indexed: 01/06/2024] Open
Abstract
The application of peptide stapling using photoswitchable linkers has gained notable interest for potential therapeutic applications. However, many existing methodologies of photoswitching still rely on the use of tissue-damaging and weakly skin-penetrating UV light. Herein, we describe the development of a tetra-ortho-chloro azobenzene linker that was successfully used for cysteine-selective peptide stapling via SNAr. This linker facilitates precise photocontrol of peptide structure via trans to cis isomerisation under red light irradiation. As a proof-of-concept, we applied the developed peptide stapling platform to a modified PMI peptide, targeting the inhibition of MDM2/p53 protein-protein interaction (PPI). Biophysical characterisation of the photoswitchable peptide by competitive fluorescence polarisation showed a significant difference in affinity between the trans and cis isomer for the p53-interacting domain of the human MDM2. Remarkably, the cis isomer displayed a >240-fold higher potency. To the best of our knowledge, this is the highest reported difference in binding affinity between isoforms of a photoswitchable therapeutic peptide. Overall, our findings demonstrate the potential of this novel photoswitchable peptide stapling system for tuneable, selective modulation of PPIs via visible-light isomerisation with deeply-tissue penetrating red light.
Collapse
Affiliation(s)
- Mia Kapun
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | | | - Nicola Ashman
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Pamela J E Rowling
- Department of Pharmacology, University of Cambridge Tennis Court Road CB2 1PD Cambridge UK
| | - Tim Schober
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Elaine Fowler
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge Tennis Court Road CB2 1PD Cambridge UK
| | - David R Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| |
Collapse
|
9
|
Strugach D, Hadar D, Amiram M. Robust Photocontrol of Elastin-like Polypeptide Phase Transition with a Genetically Encoded Arylazopyrazole. ACS Synth Biol 2023; 12:2802-2811. [PMID: 37714526 PMCID: PMC10594652 DOI: 10.1021/acssynbio.3c00146] [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: 03/09/2023] [Indexed: 09/17/2023]
Abstract
The rational design of light-responsive proteins and protein-based polymers requires both a photoswitch with suitable light-responsive properties and the ability to incorporate it at (multiple) defined positions in the protein chain. This Letter describes the evolution of high-performance aminoacyl-tRNA synthetases for recognizing a photoswitchable arylazopyrazole-bearing unnatural amino acid (AAP-uAA), which we then incorporated at multiple sites within elastin-like polypeptides (ELPs). The incorporation of AAP-uAA into ELPs yielded proteins capable of an isothermal, reversible, and robust light-mediated soluble-to-insoluble phase transition, which occurred faster (after only 1 min of light irradiation) and demonstrated a larger transition temperature difference (up to a 45 °C difference in the ELP transition temperature upon a cis to trans AAP isomerization) than similar azobenzene-containing ELPs. The evolved translation machinery can be used for the multisite incorporation of AAP at the polypeptide level; moreover, it constitutes a general methodology for designing light-responsive proteins and protein-based polymers with robust light-responsive behavior, made possible by the superior photoswitchable properties of AAP.
Collapse
Affiliation(s)
- Daniela
S. Strugach
- The Avram and Stella Goldstein Goren
Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 8410501, Israel
| | - Dagan Hadar
- The Avram and Stella Goldstein Goren
Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 8410501, Israel
| | - Miriam Amiram
- The Avram and Stella Goldstein Goren
Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 8410501, Israel
| |
Collapse
|
10
|
Janosko C, Shade O, Courtney TM, Horst TJ, Liu M, Khare SD, Deiters A. Genetic Encoding of Arylazopyrazole Phenylalanine for Optical Control of Translation. ACS OMEGA 2023; 8:26590-26596. [PMID: 37521667 PMCID: PMC10373180 DOI: 10.1021/acsomega.3c03512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
An arylazopyrazole was explored for its use as an enhanced photoswitchable amino acid in genetic code expansion. This new unnatural amino acid was successfully incorporated into proteins in both bacterial and mammalian cells. While photocontrol of translation required pulsed irradiations, complete selectivity for the trans-configuration by the pyrrolysyl tRNA synthetase was observed, demonstrating expression of a gene of interest selectively controlled via light exposure.
Collapse
Affiliation(s)
- Chasity
P. Janosko
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Olivia Shade
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Taylor M. Courtney
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Trevor J. Horst
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Melinda Liu
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Sagar D. Khare
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway, New Jersey 08854, United States
| | - Alexander Deiters
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
11
|
Cataldi E, Raschig M, Gutmann M, Geppert PT, Ruopp M, Schock M, Gerwe H, Bertermann R, Meinel L, Finze M, Nowak-Król A, Decker M, Lühmann T. Amber Light Control of Peptide Secondary Structure by a Perfluoroaromatic Azobenzene Photoswitch. Chembiochem 2023; 24:e202200570. [PMID: 36567253 DOI: 10.1002/cbic.202200570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 12/27/2022]
Abstract
The incorporation of photoswitches into the molecular structure of peptides and proteins enables their dynamic photocontrol in complex biological systems. Here, a perfluorinated azobenzene derivative triggered by amber light was site-specifically conjugated to cysteines in a helical peptide by perfluoroarylation chemistry. In response to the photoisomerization (trans→cis) of the conjugated azobenzene with amber light, the secondary structure of the peptide was modulated from a disorganized into an amphiphilic helical structure.
Collapse
Affiliation(s)
- Eleonora Cataldi
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Martina Raschig
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Marcus Gutmann
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Patrick T Geppert
- Universität Würzburg, Institute of Inorganic Chemistry and Institute for Sustainable Chemistry and Catalysis with Boron, Am Hubland, 97074, Würzburg, Germany
| | - Matthias Ruopp
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Marvin Schock
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Hubert Gerwe
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Rüdiger Bertermann
- Universität Würzburg, Institute of Inorganic Chemistry and Institute for Sustainable Chemistry and Catalysis with Boron, Am Hubland, 97074, Würzburg, Germany
| | - Lorenz Meinel
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany.,Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), 97080, Würzburg, Germany
| | - Maik Finze
- Universität Würzburg, Institute of Inorganic Chemistry and Institute for Sustainable Chemistry and Catalysis with Boron, Am Hubland, 97074, Würzburg, Germany
| | - Agnieszka Nowak-Król
- Universität Würzburg, Institute of Inorganic Chemistry and Institute for Sustainable Chemistry and Catalysis with Boron, Am Hubland, 97074, Würzburg, Germany
| | - Michael Decker
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| | - Tessa Lühmann
- Universität Würzburg, Institute for Pharmacy and Food Chemistry, Am Hubland, 97074, Würzburg, Germany
| |
Collapse
|
12
|
Crone NSA, van Hilten N, van der Ham A, Risselada HJ, Kros A, Boyle AL. Azobenzene-Based Amino Acids for the Photocontrol of Coiled-Coil Peptides. Bioconjug Chem 2023; 34:345-357. [PMID: 36705971 PMCID: PMC9936496 DOI: 10.1021/acs.bioconjchem.2c00534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Coiled-coil peptides are high-affinity, selective, self-assembling binding motifs, making them attractive components for the preparation of functional biomaterials. Photocontrol of coiled-coil self-assembly allows for the precise localization of their activity. To rationally explore photoactivity in a model coiled coil, three azobenzene-containing amino acids were prepared and substituted into the hydrophobic core of the E3/K3 coiled-coil heterodimer. Two of the non-natural amino acids, APhe1 and APhe2, are based on phenylalanine and differ in the presence of a carboxylic acid group. These have previously been demonstrated to modulate protein activity. When incorporated into peptide K3, coiled-coil binding strength was affected upon isomerization, with the two variants differing in their most folded state. The third azobenzene-containing amino acid, APgly, is based on phenylglycine and was prepared to investigate the effect of amino acid size on photoisomerization. When APgly is incorporated into the coiled coil, a 4.7-fold decrease in folding constant is observed upon trans-to-cis isomerization─the largest difference for all three amino acids. Omitting the methylene group between azobenzene and α-carbon was theorized to both position the diazene of APgly closer to the hydrophobic amino acids and reduce the possible rotations of the amino acid, with molecular dynamics simulations supporting these hypotheses. These results demonstrate the ability of photoswitchable amino acids to control coiled-coil assembly through disruption of the hydrophobic interface, a strategy that should be widely applicable.
Collapse
Affiliation(s)
- Niek S A Crone
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Niek van Hilten
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Alex van der Ham
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Herre Jelger Risselada
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Alexander Kros
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| | - Aimee L Boyle
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CCLeiden, The Netherlands
| |
Collapse
|
13
|
Zheng T, Fu J, Xiong Q, Shen X, Li B, Zhao X, Yu Z. Photo-regulated genetic encoding of dibenzo[ c,g][1,2]diazocine on proteins via configuration switching. Chem Commun (Camb) 2023; 59:1201-1204. [PMID: 36629150 DOI: 10.1039/d2cc06738b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We report two evolved Methanosarcina mazei pyrrolysine tRNA synthetases to genetically incorporate the isomers of dibenzo[c,g][1,2]diazocine-alanine (DBDAA) into proteins either in the dark or under regulation of 405 nm photo-stimulation. The genetic-encoded DBDAA realizes photo-tuning of enzymatic activity via the host-guest recognition of cucurbit[7]uril.
Collapse
Affiliation(s)
- Tingting Zheng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Jielin Fu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Qin Xiong
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Xin Shen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Baolin Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Xiaohu Zhao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, P. R. China.
| |
Collapse
|
14
|
Wang Z, Rabb JD, Lin Q. Orthogonal Crosslinking: A Strategy to Generate Novel Protein Topology and Function. Chemistry 2023; 29:e202202828. [PMID: 36251567 PMCID: PMC9839582 DOI: 10.1002/chem.202202828] [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: 09/10/2022] [Indexed: 11/27/2022]
Abstract
Compared to the disulfide bond, other naturally occurring intramolecular crosslinks have received little attention, presumably due to their rarity in the vast protein space. Here we presented examples of natural non-disulfide crosslinks, which we refer to as orthogonal crosslinks, emphasizing their effect on protein topology and function. We summarize recent efforts on expanding orthogonal crosslinks by using either the enzymes that catalyze protein circularization or the genetic code expansion strategy to add electrophilic amino acids site-specifically in proteins. The advantages and disadvantages of each method are discussed, along with their applications to generate novel protein topology and function. In particular, we highlight our recent work on spontaneous orthogonal crosslinking, in which a carbamate-based crosslink was generated in situ, and its applications in designing orthogonally crosslinked domain antibodies with their topology-mimicking bacterial adhesins.
Collapse
Affiliation(s)
- Zheng Wang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| | - Johnathan D Rabb
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| |
Collapse
|
15
|
Genetically encoded chemical crosslinking of carbohydrate. Nat Chem 2023; 15:33-42. [PMID: 36216893 PMCID: PMC9840686 DOI: 10.1038/s41557-022-01059-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/02/2022] [Indexed: 01/17/2023]
Abstract
Protein-carbohydrate interactions play important roles in various biological processes, such as organism development, cancer metastasis, pathogen infection and immune response, but they remain challenging to study and exploit due to their low binding affinity and non-covalent nature. Here we site-specifically engineered covalent linkages between proteins and carbohydrates under biocompatible conditions. We show that sulfonyl fluoride reacts with glycans via a proximity-enabled reactivity, and to harness this a bioreactive unnatural amino acid (SFY) that contains sulfonyl fluoride was genetically encoded into proteins. SFY-incorporated Siglec-7 crosslinked with its sialoglycan ligand specifically in vitro and on the surface of cancer cells. Through irreversible cloaking of sialoglycan at the cancer cell surface, SFY-incorporated Siglec-7 enhanced the killing of cancer cells by natural killer cells. Genetically encoding the chemical crosslinking of proteins to carbohydrates (GECX-sugar) offers a solution to address the low affinity and weak strength of protein-sugar interactions.
Collapse
|
16
|
Hiefinger C, Mandl S, Wieland M, Kneuttinger A. Rational design, production and in vitro analysis of photoxenoproteins. Methods Enzymol 2023; 682:247-288. [PMID: 36948704 DOI: 10.1016/bs.mie.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In synthetic biology, the artificial control of proteins by light is of growing interest since it enables the spatio-temporal regulation of downstream molecular processes. This precise photocontrol can be established by the site-directed incorporation of photo-sensitive non-canonical amino acids (ncAAs) into proteins, which generates so-called photoxenoproteins. Photoxenoproteins can be engineered using ncAAs that facilitate the irreversible activation or reversible regulation of their activity upon irradiation. In this chapter, we provide a general outline of the engineering process based on the current methodological state-of-the-art to obtain artificial photocontrol in proteins using the ncAAs o-nitrobenzyl-O-tyrosine as example for photocaged ncAAs (irreversible), and phenylalanine-4'-azobenzene as example for photoswitchable ncAAs (reversible). We thereby focus on the initial design as well as the production and characterization of photoxenoproteins in vitro. Finally, we outline the analysis of photocontrol under steady-state and non-steady-state conditions using the allosteric enzyme complexes imidazole glycerol phosphate synthase and tryptophan synthase as examples.
Collapse
Affiliation(s)
- Caroline Hiefinger
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Sabrina Mandl
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Wieland
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Andrea Kneuttinger
- Institute of Biophysics and Physical Biochemistry & Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany.
| |
Collapse
|
17
|
Volarić J, Buter J, Schulte AM, van den Berg KO, Santamaría-Aranda E, Szymanski W, Feringa BL. Design and Synthesis of Visible-Light-Responsive Azobenzene Building Blocks for Chemical Biology. J Org Chem 2022; 87:14319-14333. [PMID: 36285612 PMCID: PMC9639001 DOI: 10.1021/acs.joc.2c01777] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Tetra-ortho-fluoro-azobenzenes are a class of photoswitches useful for the construction of visible-light-controlled molecular systems. They can be used to achieve spatio-temporal control over the properties of a chosen bioactive molecule. However, the introduction of different substituents to the tetra-fluoro-azobenzene core can significantly affect the photochemical properties of the switch and compromise biocompatibility. Herein, we explored the effect of useful substituents, such as functionalization points, attachment handles, and water-solubilizing groups, on the photochemical properties of this photochromic system. In general, all the tested fluorinated azobenzenes exhibited favorable photochemical properties, such as high photostationary state distribution and long half-lives, both in organic solvents and in water. One of the azobenzene building blocks was functionalized with a trehalose group to enable the uptake of the photoswitch into mycobacteria. Following metabolic uptake and incorporation of the trehalose-based azobenzene in the mycobacterial cell wall, we demonstrated photoswitching of the azobenzene in the isolated total lipid extract.
Collapse
Affiliation(s)
- Jana Volarić
- Stratingh
Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Jeffrey Buter
- Stratingh
Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Albert M. Schulte
- Stratingh
Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | | | - Eduardo Santamaría-Aranda
- Stratingh
Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands,Departamento
de Química, Universidad de la Rioja, Centro de investigación en Síntesis Química, Madre de Dios 53, 26006 Logroño, Spain
| | - Wiktor Szymanski
- Stratingh
Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands,Department
of Radiology, Medical Imaging, Center, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands,
| | - Ben L. Feringa
- Stratingh
Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands,
| |
Collapse
|
18
|
Gueta O, Amiram M. Expanding the chemical repertoire of protein-based polymers for drug-delivery applications. Adv Drug Deliv Rev 2022; 190:114460. [PMID: 36030987 DOI: 10.1016/j.addr.2022.114460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 01/24/2023]
Abstract
Expanding the chemical repertoire of natural and artificial protein-based polymers (PBPs) can enable the production of sequence-defined, yet chemically diverse, biopolymers with customized or new properties that cannot be accessed in PBPs composed of only natural amino acids. Various approaches can enable the expansion of the chemical repertoire of PBPs, including chemical and enzymatic treatments or the incorporation of unnatural amino acids. These techniques are employed to install a wide variety of chemical groups-such as bio-orthogonally reactive, cross-linkable, post-translation modifications, and environmentally responsive groups-which, in turn, can facilitate the design of customized PBP-based drug-delivery systems with modified, fine-tuned, or entirely new properties and functions. Here, we detail the existing and emerging technologies for expanding the chemical repertoire of PBPs and review several chemical groups that either demonstrate or are anticipated to show potential in the design of PBP-based drug delivery systems. Finally, we provide our perspective on the remaining challenges and future directions in this field.
Collapse
Affiliation(s)
- Osher Gueta
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel
| | - Miriam Amiram
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
| |
Collapse
|
19
|
Engineering of enzymes using non-natural amino acids. Biosci Rep 2022; 42:231590. [PMID: 35856922 PMCID: PMC9366748 DOI: 10.1042/bsr20220168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
In enzyme engineering, the main targets for enhancing properties are enzyme activity, stereoselective specificity, stability, substrate range, and the development of unique functions. With the advent of genetic code extension technology, non-natural amino acids (nnAAs) are able to be incorporated into proteins in a site-specific or residue-specific manner, which breaks the limit of 20 natural amino acids for protein engineering. Benefitting from this approach, numerous enzymes have been engineered with nnAAs for improved properties or extended functionality. In this review, we focus on applications and strategies for using nnAAs in enzyme engineering. Notably, approaches to computational modelling of enzymes with nnAAs are also addressed. Finally, we discuss the bottlenecks that currently need to be addressed in order to realise the broader prospects of this genetic code extension technique.
Collapse
|
20
|
Klauser PC, Berdan VY, Cao L, Wang L. Encoding latent SuFEx reactive meta-fluorosulfate tyrosine to expand covalent bonding of proteins. Chem Commun (Camb) 2022; 58:6861-6864. [PMID: 35621237 PMCID: PMC9816398 DOI: 10.1039/d2cc01902g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The introduction of new covalent bonds into proteins is affording novel avenues for protein research and applications, yet it remains difficult to generate covalent linkages at all possible sites and across diverse protein classes. Herein, we genetically encoded meta-fluorosulfate-L-tyrosine (mFSY) to selectively react with lysine, tyrosine, and histidine via proximity-enabled SuFEx reaction. mFSY was able to target residues that were elusive for previous unnatural amino acids, and permitted engineering of various proteins including affibody, nanobody, and Fab into covalent binders that irreversibly cross-linked EGFR and HER2. mFSY is thus valuable for developing covalent proteins for biological research, synthetic biology, and biotherapeutics.
Collapse
Affiliation(s)
- Paul C. Klauser
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| | - Viktoriya Y. Berdan
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| | - Li Cao
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| |
Collapse
|
21
|
Xu Y, Rahim A, Lin Q. Spontaneous Orthogonal Protein Crosslinking via a Genetically Encoded 2-Carboxy-4-Aryl-1,2,3-Triazole. Angew Chem Int Ed Engl 2022; 61:e202202657. [PMID: 35290708 PMCID: PMC9117480 DOI: 10.1002/anie.202202657] [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: 02/17/2022] [Indexed: 11/08/2022]
Abstract
Here we report the design of N2 -carboxy-4-aryl-1,2,3-triazole-lysines (CATKs) and their site-specific incorporation into proteins via genetic code expansion. When introduced into the protein dimer interface, CATKs permitted spontaneous, proximity-driven, site-selective crosslinking to generate covalent protein dimers in living cells, with phenyl-bearing CATK-1 exhibiting high reactivity toward the proximal Lys and Tyr. Furthermore, when introduced into the N-terminal β-strand of either a single-chain VHH antibody or a supercharged monobody, CATK-1 enabled site-specific, inter-strand, orthogonal crosslinking with a proximal Tyr located on the opposing β-strand. Compared with a non-crosslinked monobody, the orthogonally crosslinked monobody displayed improved cellular uptake and enhanced proteolytic stability against an endosomal enzyme. The robust crosslinking reactivity of CATKs should facilitate the design of novel protein topologies with improved physicochemical properties.
Collapse
Affiliation(s)
- Yali Xu
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| | - Abdur Rahim
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| |
Collapse
|
22
|
Qiao Z, Fu W, Huang Q, Li Z, Zhao C, Shao X. Optical Regulation of GABA Receptor by Visible Light via Azobenzene-Phenylpyrazole. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5541-5550. [PMID: 35475355 DOI: 10.1021/acs.jafc.2c01463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Photopharmacology provides superior temporal and spatial resolution for the study of biological functions of γ-aminobutyric acid receptors (GABARs), and photopharmacology based on GABARs has significantly advanced the research of neurons and cells. Herein, we reported the azobenzene-phenylpyrazole (ABPs) for controlling the function of GABARs by light. The insecticidal activity of ABPs against Aedes albopictus larvae was different before and after light illumination. ABP3 (1 μM) could induce depolarization of dorsal unpaired median neurons and enable the real-time photoregulation of mosquito larval behavior. An electrophysiological experiment indicated that ABP3 had different inhibitory effects on GABARs before and after illumination. ABPs realized optical control of GABARs utilizing visible light, providing valuable supplements to the existing GABAR photocontrol tools.
Collapse
Affiliation(s)
- Zhi Qiao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wen Fu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Qiutang Huang
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chunqing Zhao
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xusheng Shao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| |
Collapse
|
23
|
Zubi YS, Seki K, Li Y, Hunt AC, Liu B, Roux B, Jewett MC, Lewis JC. Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches. Nat Commun 2022; 13:1864. [PMID: 35387988 PMCID: PMC8987029 DOI: 10.1038/s41467-022-29239-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
Dynamic control over protein function is a central challenge in synthetic biology. To address this challenge, we describe the development of an integrated computational and experimental workflow to incorporate a metal-responsive chemical switch into proteins. Pairs of bipyridinylalanine (BpyAla) residues are genetically encoded into two structurally distinct enzymes, a serine protease and firefly luciferase, so that metal coordination biases the conformations of these enzymes, leading to reversible control of activity. Computational analysis and molecular dynamics simulations are used to rationally guide BpyAla placement, significantly reducing experimental workload, and cell-free protein synthesis coupled with high-throughput experimentation enable rapid prototyping of variants. Ultimately, this strategy yields enzymes with a robust 20-fold dynamic range in response to divalent metal salts over 24 on/off switches, demonstrating the potential of this approach. We envision that this strategy of genetically encoding chemical switches into enzymes will complement other protein engineering and synthetic biology efforts, enabling new opportunities for applications where precise regulation of protein function is critical.
Collapse
Affiliation(s)
- Yasmine S Zubi
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Kosuke Seki
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Ying Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Andrew C Hunt
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Bingqing Liu
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA.
| |
Collapse
|
24
|
Kneuttinger AC. A guide to designing photocontrol in proteins: methods, strategies and applications. Biol Chem 2022; 403:573-613. [PMID: 35355495 DOI: 10.1515/hsz-2021-0417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Light is essential for various biochemical processes in all domains of life. In its presence certain proteins inside a cell are excited, which either stimulates or inhibits subsequent cellular processes. The artificial photocontrol of specifically proteins is of growing interest for the investigation of scientific questions on the organismal, cellular and molecular level as well as for the development of medicinal drugs or biocatalytic tools. For the targeted design of photocontrol in proteins, three major methods have been developed over the last decades, which employ either chemical engineering of small-molecule photosensitive effectors (photopharmacology), incorporation of photoactive non-canonical amino acids by genetic code expansion (photoxenoprotein engineering), or fusion with photoreactive biological modules (hybrid protein optogenetics). This review compares the different methods as well as their strategies and current applications for the light-regulation of proteins and provides background information useful for the implementation of each technique.
Collapse
Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| |
Collapse
|
25
|
Xu Y, Rahim A, Lin Q. Spontaneous Orthogonal Protein Crosslinking via a Genetically Encoded 2‐Carboxy‐4‐Aryl‐1,2,3‐Triazole. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yali Xu
- Department of Chemistry State University of New York at Buffalo Buffalo NY 14260-3000 USA
| | - Abdur Rahim
- Department of Chemistry State University of New York at Buffalo Buffalo NY 14260-3000 USA
| | - Qing Lin
- Department of Chemistry State University of New York at Buffalo Buffalo NY 14260-3000 USA
| |
Collapse
|
26
|
Xiong Q, Zheng T, Shen X, Li B, Fu J, Zhao X, Wang C, Yu Z. Expanding the functionality of proteins with genetically encoded dibenzo[ b, f][1,4,5]thiadiazepine: a photo-transducer for photo-click decoration. Chem Sci 2022; 13:3571-3581. [PMID: 35432856 PMCID: PMC8943893 DOI: 10.1039/d1sc05710c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/28/2022] [Indexed: 12/15/2022] Open
Abstract
Genetic incorporation of novel noncanonical amino acids (ncAAs) that are specialized for the photo-click reaction allows the precisely orthogonal and site-specific functionalization of proteins in living cells under photo-control. However, the development of a r̲ing-strain i̲n situ l̲oadable d̲ipolarophile (RILD) as a genetically encodable reporter for photo-click bioconjugation with spatiotemporal controllability is quite rare. Herein, we report the design and synthesis of a photo-switchable d̲ib̲enzo[b,f][1,4,5]t̲hiad̲iazepine-based a̲lanine (DBTDA) ncAA, together with the directed evolution of a pyrrolysyl-tRNA synthetase/tRNACUA pair (PylRS/tRNACUA), to encode the DBTDA into recombinant proteins as a RILD in living E. coli cells. The fast-responsive photo-isomerization of the DBTDA residue can be utilized as a converter of photon energy into ring-strain energy to oscillate the conformational changes of the parent proteins. Due to the photo-activation of RILD, the photo-switching of the DBTDA residue on sfGFP and OmpC is capable of promoting the photo-click ligation with diarylsydnone (DASyd) derived probes with high efficiency and selectivity. We demonstrate that the genetic code expansion (GCE) with DBTDA benefits the studies on the distribution of decorated OmpC-DBTD on specific E. coli cells under a spatiotemporal resolved photo-stimulation. The GCE for encoding DBTDA enables further functional diversity of artificial proteins in living systems.
Collapse
Affiliation(s)
- Qin Xiong
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Tingting Zheng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Xin Shen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Baolin Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Jielin Fu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Xiaohu Zhao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Chunxia Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University 29 Wangjiang Road Chengdu 610064 P. R. China
| |
Collapse
|
27
|
Leistner AL, Pianowski Z. Smart photochromic materials triggered with visible light. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Anna-Lena Leistner
- KIT: Karlsruher Institut fur Technologie Institute of Organic Chemistry Fritz-Haber-Weg 6 76131 Karlsruhe GERMANY
| | - Zbigniew Pianowski
- Karlsruher Institut fur Technologie Fakultat fur Chemie und Biowissenschaften Institute of Organic Chemistry Fritz-Haber-Weg 6 76131 Karlsruhe GERMANY
| |
Collapse
|
28
|
Cao L, Wang L. New covalent bonding ability for proteins. Protein Sci 2022; 31:312-322. [PMID: 34761448 PMCID: PMC8819847 DOI: 10.1002/pro.4228] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 02/03/2023]
Abstract
To expand protein's covalent bonding ability, latent bioreactive unnatural amino acids have been designed and genetically encoded into proteins, which react with specific natural amino acid residues through proximity-enabled bioreactivity. The resultant new covalent bonds can be selectively created within and between proteins in vitro, in cells, and in vivo. Offering diverse properties previously unattainable, these covalent linkages have been harnessed to enhance protein properties, to modulate protein function, to probe ligand-receptor binding, to identify elusive protein interactions, and to develop covalent protein drugs. Selective introduction of covalent bonds into proteins is affording novel avenues for biological studies, synthetic biology, and biotherapeutics.
Collapse
Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry and the Cardiovascular Research InstituteUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research InstituteUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| |
Collapse
|
29
|
Orellana-Maldonado I, Aspée A, Barrias P, Santana PA, Tirapegui C. Photoswitching studies of new photochromic ionic liquids studied in real time by in situ irradiation. NEW J CHEM 2022. [DOI: 10.1039/d2nj01194h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In situ irradiation allowed us to study in detail the photostationary state of new photoswitchable bicationic azobenzenes.
Collapse
Affiliation(s)
| | - Alexis Aspée
- Departamento de Ciencias Del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Pablo Barrias
- Departamento de Ciencias Del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Paula A. Santana
- Grupo de Química y Bioquímica Aplicada a la Biotecnología, Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Chile
| | - Cristian Tirapegui
- Grupo de Química y Bioquímica Aplicada a la Biotecnología, Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Chile
| |
Collapse
|
30
|
Tomar R, Suwasia S, Choudhury AR, Venkataramani S, Babu SA. Azobenzene-based unnatural amino acid scaffolds via a Pd( ii)-catalyzed C(sp 3)–H arylation strategy. Chem Commun (Camb) 2022; 58:12967-12970. [DOI: 10.1039/d2cc04870a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Azobenzene-based unnatural amino acid motifs were constructed via the Pd(ii)-catalyzed diastereoselective β-C(sp3)–H arylation and Mills azo coupling tactics.
Collapse
Affiliation(s)
- Radha Tomar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| | - Sonam Suwasia
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| | - Sugumar Venkataramani
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| | - Srinivasarao Arulananda Babu
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| |
Collapse
|
31
|
Wang H, Bisoyi H, Zhang X, Hassan F, Li Q. Visible Light-Driven Molecular Switches and Motors: Recent Developments and Applications. Chemistry 2021; 28:e202103906. [PMID: 34964995 DOI: 10.1002/chem.202103906] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Indexed: 11/09/2022]
Abstract
Inspired by human vision, a diverse range of light-driven molecular switches and motors has been developed for fundamental understanding and application in material science and biology. Recently, the design and synthesis of visible light-driven molecular switches and motors have been actively pursued. This emerging trend is partly motivated to avoid the harmful effects of ultraviolet light, which was necessary to drive the classical molecular switches and motors at least in one direction, impeding their employment in biomedical and photopharmacology applications. Moreover, visible light-driven molecular switches and motors are demonstrated to enable benign optical materials for advanced photonic devices. Therefore, during the past several years, visible light-driven molecular switches based on azobenzene derivatives, diarylethenes, 1,2-dicyanodithienylethenes, hemithioindigo derivatives, iminothioindoxyls, donor-acceptor Stenhouse adducts, and overcrowded alkene based molecular motors have been judiciously designed, synthesized, and used in the development of functional materials and systems for a wide range of applications. In this Review, we present the recent developments toward the design of visible light-driven molecular switches and motors, with their applications in the fabrication of functional materials and systems in material science, bioscience, pharmacology, etc . The visible light-driven molecular switches and motors realized so far undoubtedly widen the scope of these interesting compounds for technological and biological applications. We hope this Review article could provide additional impetus and inspire further research interests for future exploration of visible light-driven advanced materials, systems, and devices.
Collapse
Affiliation(s)
- Hao Wang
- Kent State University, Advanced Materials and Liquid Crystal Institute, UNITED STATES
| | - Hari Bisoyi
- Kent State University, Advanced Materials and Liquid Crystal Institute, UNITED STATES
| | - Xinfang Zhang
- Kent State University, Advanced Materials and Liquid Crystal Institue, UNITED STATES
| | - Fathy Hassan
- Kent State University, Advanced Materials and Liquid Crystal Institute, UNITED STATES
| | - Quan Li
- Kent State University, Liquid Crystal Institute and Chemical Physics Interdiscinplary Program, 3273 Crown Pointe Drive, 44224, Stow, UNITED STATES
| |
Collapse
|
32
|
Genetically encoding latent bioreactive amino acids and the development of covalent protein drugs. Curr Opin Chem Biol 2021; 66:102106. [PMID: 34968810 DOI: 10.1016/j.cbpa.2021.102106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/07/2021] [Accepted: 11/25/2021] [Indexed: 12/11/2022]
Abstract
As natural proteins generally do not bind targets in a covalent mode, the therapeutic potential of covalent protein drugs remains largely unexplored. Recently, latent bioreactive amino acids have been incorporated into proteins through genetic code expansion, which selectively react with nearby natural residues via proximity-enabled reactivity, generating diverse covalent linkages for proteins in vitro and in cells. These new covalent linkages provide novel avenues for protein research and engineering. In addition, a general platform technology, proximity-enabled reactive therapeutics (PERx), has been established for the development of covalent protein drugs. The first covalent protein drug demonstrates advantageous features in cancer immunotherapy in mice. Selective introduction of covalent bonds into proteins will advance biological studies, synthetic biology, and biotherapeutics with the power of biocompatible covalent chemistries.
Collapse
|
33
|
Peverini L, Dunning K, Peralta FA, Grutter T. Photo-isomerizable tweezers to probe ionotropic receptor mechanisms. Curr Opin Pharmacol 2021; 62:109-116. [PMID: 34965483 DOI: 10.1016/j.coph.2021.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/05/2021] [Accepted: 11/18/2021] [Indexed: 12/15/2022]
Abstract
Ligand-gated ion channels (LGIC, also referred to as ionotropic receptors) are important transmembrane proteins that open to allow ions to flow across the membrane and locally modify the membrane potential in response to the binding of a ligand. For more than a decade, a tremendous effort has been carried out in the determination of many LGIC structures in high resolution, leading to an unprecedented molecular description of channel gating. However, it is sometimes difficult to classify experimentally derived structures to their corresponding functional states, and alternative methods may help resolve or refine this issue. In this review, we focus on the application of photo-isomerizable tweezers (PIT) as a powerful strategy to interrogate molecular mechanisms of LGIC while assessing their functionality by electrophysiology.
Collapse
Affiliation(s)
- Laurie Peverini
- Unité Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, 75015, Paris, France
| | - Kate Dunning
- CNM Team, Université de Strasbourg, Centre National de La Recherche Scientifique, CAMB UMR 7199, Faculté de Pharmacie, 67401, Illkirch, France
| | - Francisco Andres Peralta
- CNM Team, Université de Strasbourg, Centre National de La Recherche Scientifique, CAMB UMR 7199, Faculté de Pharmacie, 67401, Illkirch, France; University of Strasbourg Institute for Advanced Studies (USIAS), 67000, Strasbourg, France
| | - Thomas Grutter
- CNM Team, Université de Strasbourg, Centre National de La Recherche Scientifique, CAMB UMR 7199, Faculté de Pharmacie, 67401, Illkirch, France; University of Strasbourg Institute for Advanced Studies (USIAS), 67000, Strasbourg, France.
| |
Collapse
|
34
|
Bozovic O, Jankovic B, Hamm P. Using azobenzene photocontrol to set proteins in motion. Nat Rev Chem 2021; 6:112-124. [PMID: 37117294 DOI: 10.1038/s41570-021-00338-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 02/06/2023]
Abstract
Controlling the activity of proteins with azobenzene photoswitches is a potent tool for manipulating their biological function. With the help of light, it is possible to change binding affinities, control allostery or manipulate complex biological processes, for example. Additionally, owing to their intrinsically fast photoisomerization, azobenzene photoswitches can serve as triggers that initiate out-of-equilibrium processes. Such switching of the activity initiates a cascade of conformational events that can be accessed with time-resolved methods. In this Review, we show how the potency of azobenzene photoswitching can be combined with transient spectroscopic techniques to disclose the order of events and experimentally observe biomolecular interactions in real time. This strategy will further our understanding of how a protein can accommodate, adapt and readjust its structure to answer an incoming signal, revealing more of the dynamical character of proteins.
Collapse
|
35
|
Tian H, Yang J, Guo AD, Ran Y, Yang YZ, Yang B, Huang R, Liu H, Chen XH. Genetically Encoded Benzoyllysines Serve as Versatile Probes for Interrogating Histone Benzoylation and Interactions in Living Cells. ACS Chem Biol 2021; 16:2560-2569. [PMID: 34618427 DOI: 10.1021/acschembio.1c00614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Histone posttranslational modifications (PTMs) are vital epigenetic regulators in many fundamental cell signaling pathways and diverse biological processes. Histone lysine benzoylation is a recently identified epigenetic mark associated with active transcription; however, it remains to be explored. Herein, we first report the genetic encoding of benzoyllysine and fluorinated benzoyllysines into full-length histone proteins in a site-specific manner in live cells, based on our rationally designed synthetase and fine-integrated fluorine element into benzoyllysines. The incorporated unnatural amino acids integrating unique features were demonstrated as versatile probes for investigating histone benzoylation under biological environments, conferring multiplex signals such as 19F NMR spectra with chemical clarity and fluorescence signals for benzoylation. Moreover, the site specifically incorporated lysine benzoylation within native full-length histone proteins revealed distinct dynamics of debenzoylation in the presence of debenzoylase sirtuin 2 (SIRT2). Our developed strategy for genetic encoding of benzoyllysines offers a general and novel approach to gain insights into interactions of site-specific histone benzoylation modifications with interactomes and molecular mechanisms in physiological settings, which could not be accessible with fragment histone peptides. This versatile chemical tool enables a direct and new avenue to explore benzoylation, interactions, and histone epigenetics, which will provide broad utilities in chemical biology, protein science, and basic biology research.
Collapse
Affiliation(s)
- Hongtao Tian
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiale Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - An-Di Guo
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Ran
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Zhi Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
| | - Bing Yang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ruimin Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiming Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiao-Hua Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| |
Collapse
|
36
|
Volarić J, Szymanski W, Simeth NA, Feringa BL. Molecular photoswitches in aqueous environments. Chem Soc Rev 2021; 50:12377-12449. [PMID: 34590636 PMCID: PMC8591629 DOI: 10.1039/d0cs00547a] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Indexed: 12/17/2022]
Abstract
Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.
Collapse
Affiliation(s)
- Jana Volarić
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Department of Radiology, Medical Imaging Center, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Nadja A Simeth
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Institute for Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| |
Collapse
|
37
|
Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
Collapse
Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
38
|
Haim A, Neubacher S, Grossmann TN. Protein Macrocyclization for Tertiary Structure Stabilization. Chembiochem 2021; 22:2672-2679. [PMID: 34060202 PMCID: PMC8453710 DOI: 10.1002/cbic.202100111] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/26/2021] [Indexed: 12/30/2022]
Abstract
Proteins possess unique molecular recognition capabilities and enzymatic activities, features that are usually tied to a particular tertiary structure. To make use of proteins for biotechnological and biomedical purposes, it is often required to enforce their tertiary structure in order to ensure sufficient stability under the conditions inherent to the application of interest. The introduction of intramolecular crosslinks has proven efficient in stabilizing native protein folds. Herein, we give an overview of methods that allow the macrocyclization of expressed proteins, discussing involved reaction mechanisms and structural implications.
Collapse
Affiliation(s)
- Anissa Haim
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
- Incircular B.V.De Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Tom N. Grossmann
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
- Amsterdam Institute of Molecular and Life SciencesVU University AmsterdamAmsterdamThe Netherlands
| |
Collapse
|
39
|
Liu J, Cao L, Klauser PC, Cheng R, Berdan VY, Sun W, Wang N, Ghelichkhani F, Yu B, Rozovsky S, Wang L. A Genetically Encoded Fluorosulfonyloxybenzoyl-l-lysine for Expansive Covalent Bonding of Proteins via SuFEx Chemistry. J Am Chem Soc 2021; 143:10341-10351. [PMID: 34213894 DOI: 10.1021/jacs.1c04259] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genetically introducing novel chemical bonds into proteins provides innovative avenues for biochemical research, protein engineering, and biotherapeutic applications. Recently, latent bioreactive unnatural amino acids (Uaas) have been incorporated into proteins to covalently target natural residues through proximity-enabled reactivity. Aryl fluorosulfate is particularly attractive due to its exceptional biocompatibility and multitargeting capability via sulfur(VI) fluoride exchange (SuFEx) reaction. Thus far, fluorosulfate-l-tyrosine (FSY) is the only aryl fluorosulfate-containing Uaa that has been genetically encoded. FSY has a relatively rigid and short side chain, which restricts the diversity of proteins targetable and the scope of applications. Here we designed and genetically encoded a new latent bioreactive Uaa, fluorosulfonyloxybenzoyl-l-lysine (FSK), in E. coli and mammalian cells. Due to its long and flexible aryl fluorosulfate-containing side chain, FSK was particularly useful in covalently linking protein sites that are unreachable with FSY, both intra- and intermolecularly, in vitro and in live cells. In addition, we created covalent nanobodies that irreversibly bound to epidermal growth factor receptors (EGFR) on cells, with FSK and FSY targeting distinct positions on EGFR to counter potential mutational resistance. Moreover, we established the use of FSK and FSY for genetically encoded chemical cross-linking to capture elusive enzyme-substrate interactions in live cells, allowing us to target residues aside from Cys and to cross-link at the binding periphery. FSK complements FSY to expand target diversity and versatility. Together, they provide a powerful, genetically encoded, latent bioreactive SuFEx system for creating covalent bonds in diverse proteins in vitro and in vivo, which will be widely useful for biological research and applications.
Collapse
Affiliation(s)
- Jun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| | - Li Cao
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| | - Paul C Klauser
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| | - Rujin Cheng
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Viktoriya Y Berdan
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| | - Wei Sun
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| | - Nanxi Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| | - Farid Ghelichkhani
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Bingchen Yu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| |
Collapse
|
40
|
Genetically encoded selective cross-linkers and emerging applications. Biochem Soc Trans 2021; 48:1807-1817. [PMID: 32657352 DOI: 10.1042/bst20200508] [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: 05/06/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 02/08/2023]
Abstract
There has been a large amount of interest in the development of genetically encoded cross-linkers that target functional groups naturally present in cells. Recently, a new class of unnatural amino acids that specifically react with target residues were developed and genetically incorporated. The selective reaction shows higher cross-linking efficiency, lower background and predictable cross-linking sites. It has been applied to enhance protein/peptide stability, pinpoint protein-protein interactions, stabilize protein complexes, engineer covalent protein inhibitors, identify phosphatases in living cells, etc. These new covalent linkages provide excellent new tools for protein engineering and biological studies. Their applications in biotherapy will provide considerable opportunities for innovating and improving biomolecular medicines.
Collapse
|
41
|
Cao W, Qin X, Wang Y, Dai Z, Dai X, Wang H, Xuan W, Zhang Y, Liu Y, Liu T. A General Supramolecular Approach to Regulate Protein Functions by Cucurbit[7]uril and Unnatural Amino Acid Recognition. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Wenbing Cao
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xuewen Qin
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yong Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Zhen Dai
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xianyin Dai
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Haoyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Weimin Xuan
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Yingming Zhang
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Yu Liu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| |
Collapse
|
42
|
Cao W, Qin X, Wang Y, Dai Z, Dai X, Wang H, Xuan W, Zhang Y, Liu Y, Liu T. A General Supramolecular Approach to Regulate Protein Functions by Cucurbit[7]uril and Unnatural Amino Acid Recognition. Angew Chem Int Ed Engl 2021; 60:11196-11200. [PMID: 33580548 DOI: 10.1002/anie.202100916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/10/2021] [Indexed: 01/24/2023]
Abstract
Regulation of specific protein function is of great importance for both research and therapeutic development. Many small or large molecules have been developed to control specific protein function, but there is a lack of a universal approach to regulate the function of any given protein. We report a general host-guest molecular recognition approach involving modification of the protein functional surfaces with genetically encoded unnatural amino acids bearing guest side chains that can be specifically recognized by cucurbit[7]uril. Using two enzymes and a cytokine as models, we showed that the activity of proteins bearing unnatural amino acid could be turned off by host molecule binding, which blocked its functional binding surface. Protein activity can be switched back by treatment with a competitive guest molecule. Our approach provides a general tool for reversibly regulating protein function through molecular recognition and can be expected to be valuable for studying protein functions.
Collapse
Affiliation(s)
- Wenbing Cao
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xuewen Qin
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Yong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Zhen Dai
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xianyin Dai
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Haoyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Weimin Xuan
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Yingming Zhang
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Yu Liu
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| |
Collapse
|
43
|
Covalent peptides and proteins for therapeutics. Bioorg Med Chem 2021; 29:115896. [DOI: 10.1016/j.bmc.2020.115896] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/11/2022]
|
44
|
Cui Z, Johnston WA, Alexandrov K. Cell-Free Approach for Non-canonical Amino Acids Incorporation Into Polypeptides. Front Bioeng Biotechnol 2020; 8:1031. [PMID: 33117774 PMCID: PMC7550873 DOI: 10.3389/fbioe.2020.01031] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
Synthetic biology holds promise to revolutionize the life sciences and biomedicine via expansion of macromolecular diversity outside the natural chemical space. Use of non-canonical amino acids (ncAAs) via codon reassignment has found diverse applications in protein structure and interaction analysis, introduction of post-translational modifications, production of constrained peptides, antibody-drug conjugates, and novel enzymes. However, simultaneously encoding multiple ncAAs in vivo requires complex engineering and is sometimes restricted by the cell's poor uptake of ncAAs. In contrast the open nature of cell-free protein synthesis systems offers much greater freedom for manipulation and repurposing of the biosynthetic machinery by controlling the level and identity of translational components and reagents, and allows simultaneous incorporation of multiple ncAAs with non-canonical side chains and even backbones (N-methyl, D-, β-amino acids, α-hydroxy acids etc.). This review focuses on the two most used Escherichia coli-based cell-free protein synthesis systems; cell extract- and PURE-based systems. The former is a biological mixture with >500 proteins, while the latter consists of 38 individually purified biomolecules. We delineate compositions of these two systems and discuss their respective advantages and applications. Also, we dissect the translational components required for ncAA incorporation and compile lists of ncAAs that can be incorporated into polypeptides via different acylation approaches. We highlight the recent progress in using unnatural nucleobase pairs to increase the repertoire of orthogonal codons, as well as using tRNA-specific ribozymes for in situ acylation. We summarize advances in engineering of translational machinery such as tRNAs, aminoacyl-tRNA synthetases, elongation factors, and ribosomes to achieve efficient incorporation of structurally challenging ncAAs. We note that, many engineered components of biosynthetic machinery are developed for the use in vivo but are equally applicable to the in vitro systems. These are included in the review to provide a comprehensive overview for ncAA incorporation and offer new insights for the future development in cell-free systems. Finally, we highlight the exciting progress in the genomic engineering, resulting in E. coli strains free of amber and some redundant sense codons. These strains can be used for preparation of cell extracts offering multiple reassignment options.
Collapse
Affiliation(s)
- Zhenling Cui
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Wayne A Johnston
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kirill Alexandrov
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| |
Collapse
|
45
|
Lee LCC, Tsang AWY, Liu HW, Lo KKW. Photofunctional Cyclometalated Iridium(III) Polypyridine Complexes Bearing a Perfluorobiphenyl Moiety for Bioconjugation, Bioimaging, and Phototherapeutic Applications. Inorg Chem 2020; 59:14796-14806. [DOI: 10.1021/acs.inorgchem.0c01343] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lawrence Cho-Cheung Lee
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Hong Kong, P. R. China
| | - Ada Wun-Yu Tsang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Hong Kong, P. R. China
| | - Hua-Wei Liu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Hong Kong, P. R. China
| | - Kenneth Kam-Wing Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Hong Kong, P. R. China
- State Key Laboratory of Terahertz and Millimeter Waves, City University of Hong Kong, Tat Chee Avenue, Hong Kong, P. R. China
- Center of Functional Photonics, City University of Hong Kong, Tat Chee Avenue, Hong Kong, P. R. China
| |
Collapse
|
46
|
Abstract
In this issue of Cell Chemical Biology, the Sterner lab reports the application of photoswitchable unnatural amino acids in controlling protein allostery in the enzyme complex imidazole glycerol phosphate synthase (Kneuttinger et al., 2019). Remarkable switching in enzyme activity was achieved upon photoisomerization of an azobenzene amino acid.
Collapse
Affiliation(s)
- Taylor M Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| |
Collapse
|
47
|
Paoletti P, Ellis-Davies GCR, Mourot A. Optical control of neuronal ion channels and receptors. Nat Rev Neurosci 2020; 20:514-532. [PMID: 31289380 DOI: 10.1038/s41583-019-0197-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Light-controllable tools provide powerful means to manipulate and interrogate brain function with relatively low invasiveness and high spatiotemporal precision. Although optogenetic approaches permit neuronal excitation or inhibition at the network level, other technologies, such as optopharmacology (also known as photopharmacology) have emerged that provide molecular-level control by endowing light sensitivity to endogenous biomolecules. In this Review, we discuss the challenges and opportunities of photocontrolling native neuronal signalling pathways, focusing on ion channels and neurotransmitter receptors. We describe existing strategies for rendering receptors and channels light sensitive and provide an overview of the neuroscientific insights gained from such approaches. At the crossroads of chemistry, protein engineering and neuroscience, optopharmacology offers great potential for understanding the molecular basis of brain function and behaviour, with promises for future therapeutics.
Collapse
Affiliation(s)
- Pierre Paoletti
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
| | | | - Alexandre Mourot
- Neuroscience Paris Seine-Institut de Biologie Paris Seine (NPS-IBPS), CNRS, INSERM, Sorbonne Université, Paris, France.
| |
Collapse
|
48
|
Zhou J, Smirnov A, Dietler G, Sekatskii SK. Gap-Plasmon-Enhanced High-Spatial-Resolution Imaging by Photothermal-Induced Resonance in the Visible Range. NANO LETTERS 2019; 19:8278-8286. [PMID: 31650844 DOI: 10.1021/acs.nanolett.9b03844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chemical characterization at the nanoscale is of significant importance for many applications in physics, analytical chemistry, material science, and biology. Despite the intensive studies in the infrared range, high-spatial-resolution and high-sensitivity imaging for compositional identification in the visible range is rarely exploited. In this work, we present a gap-plasmon-enhanced imaging approach based on photothermal-induced resonance (PTIR) for nanoscale chemical identification. With this approach, we experimentally obtained a high spatial resolution of ∼5 nm for rhodamine nanohill characterization and achieved monolayer sensitivity for mapping the single-layer chlorophyll-a islands with the thickness of only 1.9 nm. We also successfully characterized amyloid fibrils stained with methylene blue dye, indicating that this methodology can be also utilized for identification of the radiation-insensitive macromolecules. We believe that our proposed high-performance visible PTIR system can be used to broaden the applications of nanoscale chemical identification ranging from nanomaterial to life science areas.
Collapse
Affiliation(s)
- Jiangtao Zhou
- Laboratory of Physics of Living Matter , IPHYS, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Anton Smirnov
- Laboratory of Physics of Living Matter , IPHYS, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter , IPHYS, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Sergey K Sekatskii
- Laboratory of Physics of Living Matter , IPHYS, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| |
Collapse
|
49
|
Liu J, Li S, Aslam NA, Zheng F, Yang B, Cheng R, Wang N, Rozovsky S, Wang PG, Wang Q, Wang L. Genetically Encoding Photocaged Quinone Methide to Multitarget Protein Residues Covalently in Vivo. J Am Chem Soc 2019; 141:9458-9462. [PMID: 31184146 DOI: 10.1021/jacs.9b01738] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetically introducing covalent bonds into proteins in vivo with residue specificity is affording innovative ways for protein research and engineering, yet latent bioreactive unnatural amino acids (Uaas) genetically encoded to date react with one to few natural residues only, limiting the variety of proteins and the scope of applications amenable to this technology. Here we report the genetic encoding of (2 R)-2-amino-3-fluoro-3-(4-((2-nitrobenzyl)oxy) phenyl) propanoic acid (FnbY) in Escherichia coli and mammalian cells. Upon photoactivation, FnbY generated a reactive quinone methide (QM), which selectively reacted with nine natural amino acid residues placed in proximity in proteins directly in live cells. In addition to Cys, Lys, His, and Tyr, photoactivated FnbY also reacted with Trp, Met, Arg, Asn, and Gln, which are inaccessible with existing latent bioreactive Uaas. FnbY thus dramatically expanded the number of residues for covalent targeting in vivo. QM has longer half-life than the intermediates of conventional photo-cross-linking Uaas, and FnbY exhibited cross-linking efficiency higher than p-azido-phenylalanine. The photoactivatable and multitargeting reactivity of FnbY with selectivity toward nucleophilic residues will be valuable for addressing diverse proteins and broadening the scope of applications through exploiting covalent bonding in vivo for chemical biology, biotherapeutics, and protein engineering.
Collapse
Affiliation(s)
- Jun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States
| | - Shanshan Li
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States.,Department of Chemistry and Center for Therapeutics and Diagnostics , Georgia State University , Atlanta , Georgia 30302 , United States
| | - Nayyar A Aslam
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Hangzhou 310018 , China
| | - Feng Zheng
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Hangzhou 310018 , China
| | - Bing Yang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States
| | - Rujin Cheng
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Nanxi Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Peng G Wang
- Department of Chemistry and Center for Therapeutics and Diagnostics , Georgia State University , Atlanta , Georgia 30302 , United States
| | - Qian Wang
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Hangzhou 310018 , China
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States
| |
Collapse
|
50
|
Mirarefi P, Ted Lee C. Reversible control of enzyme-inhibitor interactions with light illumination using a photoresponsive surfactant. Proteins 2019; 87:715-722. [PMID: 30980557 DOI: 10.1002/prot.25695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 11/07/2022]
Abstract
The effects of a photoresponsive surfactant and light illumination on the complex formed between ribonuclease A (RNase A) and a protein ribonuclease inhibitor (RI) have been investigated to develop a light-based technique to reactivate an enzyme through surfactant-induced dissociation of the enzyme-inhibitor complex. The photoresponsive surfactant undergoes a photoisomerization from the relatively hydrophobic trans isomer under visible light to the relatively hydrophilic cis isomer upon UV illumination, providing a means to reversibly control protein-inhibitor interactions. In the absence of surfactant, RI binds tightly to RNase A through noncovalent interactions, which inhibits the enzyme activity. Upon addition of the surfactant under visible light, RNase A is reactivated, regaining ~75% of the native activity in the absence of RI. In the presence of the surfactant under UV light, however, the enzyme remains inhibited. Fluorescence spectroscopy, dynamic light scattering, and circular dichroism spectroscopy reveal that RI dramatically unfolds upon addition of the trans form of the surfactant, while RNase A does not undergo noticeable structural changes under the same conditions. This indicates that RNase A reactivation occurs through dissociation of the enzyme-inhibitor complex arising from surfactant-induced unfolding of the inhibitor. As a result, photoresponsive surfactant and light illumination can be used as a novel light-based technique to dissociate enzyme-inhibitor complexes and, thus, reactivate an inhibited enzyme.
Collapse
Affiliation(s)
- Panteha Mirarefi
- Department of Chemical Engineering and Materials Science, University of Southern California, California, Los Angeles
| | - C Ted Lee
- Department of Chemical Engineering and Materials Science, University of Southern California, California, Los Angeles
| |
Collapse
|