1
|
Iacobucci I, Monaco V, Hovasse A, Dupouy B, Keumoe R, Cichocki B, Elhabiri M, Meunier B, Strub JM, Monti M, Cianférani S, Blandin SA, Schaeffer-Reiss C, Davioud-Charvet E. Proteomic Profiling of Antimalarial Plasmodione Using 3-Benz(o)ylmenadione Affinity-Based Probes. Chembiochem 2024; 25:e202400187. [PMID: 38639212 DOI: 10.1002/cbic.202400187] [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: 02/29/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/20/2024]
Abstract
Understanding the mechanisms of drug action in malarial parasites is crucial for the development of new drugs to combat infection and to counteract drug resistance. Proteomics is a widely used approach to study host-pathogen systems and to identify drug protein targets. Plasmodione is an antiplasmodial early-lead drug exerting potent activities against young asexual and sexual blood stages in vitro with low toxicity to host cells. To elucidate its molecular mechanisms, an affinity-based protein profiling (AfBPP) approach was applied to yeast and P. falciparum proteomes. New (pro-) AfBPP probes based on the 3-benz(o)yl-6-fluoro-menadione scaffold were synthesized. With optimized conditions of both photoaffinity labeling and click reaction steps, the AfBPP protocol was then applied to a yeast proteome, yielding 11 putative drug-protein targets. Among these, we found four proteins associated with oxidoreductase activities, the hypothesized type of targets for plasmodione and its metabolites, and other proteins associated with the mitochondria. In Plasmodium parasites, the MS analysis revealed 44 potential plasmodione targets that need to be validated in further studies. Finally, the localization of a 3-benzyl-6-fluoromenadione AfBPP probe was studied in the subcellular structures of the parasite at the trophozoite stage.
Collapse
Affiliation(s)
- Ilaria Iacobucci
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia 26, I-80126, Napoli, Italy
| | - Vittoria Monaco
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia 26, I-80126, Napoli, Italy
| | - Agnès Hovasse
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Baptiste Dupouy
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| | - Rodrigue Keumoe
- Institut de Biologie Moléculaire et Cellulaire, INSERM U1257 - CNRS UPR9022 - Université de Strasbourg, 2, Allée Konrad Roentgen, -67084, Strasbourg, France
| | - Bogdan Cichocki
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| | - Mourad Elhabiri
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-Sur-Yvette Cedex, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia 26, I-80126, Napoli, Italy
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Stéphanie A Blandin
- Institut de Biologie Moléculaire et Cellulaire, INSERM U1257 - CNRS UPR9022 - Université de Strasbourg, 2, Allée Konrad Roentgen, -67084, Strasbourg, France
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Elisabeth Davioud-Charvet
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| |
Collapse
|
2
|
Guo J, Qian J, Cai D, Huang J, Yang X, Sun N, Zhang J, Pang T, Zhao W, Wu G, Chen X, Zhong F, Wu Y. Chemogenetic Evolution of Diversified Photoenzymes for Enantioselective [2 + 2] Cycloadditions in Whole Cells. J Am Chem Soc 2024; 146:19030-19041. [PMID: 38976645 DOI: 10.1021/jacs.4c03087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Artificial photoenzymes with novel catalytic modes not found in nature are in high demand; yet, they also present significant challenges in the field of biocatalysis. In this study, a chemogenetic modification strategy is developed to facilitate the rapid diversification of photoenzymes. This strategy integrates site-specific chemical conjugation of various artificial photosensitizers into natural protein cavities and the iterative mutagenesis in cell lysates. Through rounds of directed evolution, prominent visible-light-activatable photoenzyme variants were developed, featuring a thioxanthone chromophore. They successfully enabled the enantioselective [2 + 2] photocycloaddition of 2-carboxamide indoles, a class of UV-sensitive substrates that are traditionally challenging for known photoenzymes. Furthermore, the versatility of this photoenzyme is demonstrated in enantioselective whole-cell photobiocatalysis, enabling the efficient synthesis of enantioenriched cyclobutane-fused indoline tetracycles. These findings significantly expand the photophysical properties of artificial photoenzymes, a critical factor in enhancing their potential for harnessing excited-state reactivity in stereoselective transformations.
Collapse
Affiliation(s)
- Juan Guo
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Junyi Qian
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, China
| | - Daihong Cai
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Jianjian Huang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Xinjie Yang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
- Longgang Institute of Zhejiang Sci-Tech University, Wenzhou 325802, China
| | - Ningning Sun
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Junshuai Zhang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Tengfei Pang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Weining Zhao
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Guojiao Wu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Xi Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, China
| | - Fangrui Zhong
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Yuzhou Wu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| |
Collapse
|
3
|
Ohata J. Friedel-Crafts reactions for biomolecular chemistry. Org Biomol Chem 2024; 22:3544-3558. [PMID: 38624091 DOI: 10.1039/d4ob00406j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Chemical tools and principles have become central to biological and medical research/applications by leveraging a range of classical organic chemistry reactions. Friedel-Crafts alkylation and acylation are arguably some of the most well-known and used synthetic methods for the preparation of small molecules but their use in biological and medical fields is relatively less frequent than the other reactions, possibly owing to the notion of their plausible incompatibility with biological systems. This review demonstrates advances in Friedel-Crafts alkylation and acylation reactions in a variety of biomolecular chemistry fields. With the discoveries and applications of numerous biomolecule-catalyzed or -assisted processes, these reactions have garnered considerable interest in biochemistry, enzymology, and biocatalysis. Despite the challenges of reactivity and selectivity of biomolecular reactions, the alkylation and acylation reactions demonstrated their utility for the construction and functionalization of all the four major biomolecules (i.e., nucleosides, carbohydrates/saccharides, lipids/fatty acids, and amino acids/peptides/proteins), and their diverse applications in biological, medical, and material fields are discussed. As the alkylation and acylation reactions are often fundamental educational components of organic chemistry courses, this review is intended for both experts and nonexperts by discussing their basic reaction patterns (with the depiction of each reaction mechanism in the ESI) and relevant real-world impacts in order to enrich chemical research and education. The significant growth of biomolecular Friedel-Crafts reactions described here is a testament to their broad importance and utility, and further development and investigations of the reactions will surely be the focus in the organic biomolecular chemistry fields.
Collapse
Affiliation(s)
- Jun Ohata
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA.
| |
Collapse
|
4
|
Walrant A, Sachon E. Photoaffinity labeling coupled to MS to identify peptide biological partners: Secondary reactions, for better or for worse? MASS SPECTROMETRY REVIEWS 2024. [PMID: 38576378 DOI: 10.1002/mas.21880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 02/22/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Affinity photolabeling is a smart method to study noncovalent and transient interactions and provide a submolecular picture of the contacts between interacting partners. In this review, we will focus on the identification of peptide partners using photoaffinity labeling coupled to mass spectrometry in different contexts such as in vitro with a purified potential partner, in model systems such as model membranes, and with live cells using both targeted and nontargeted proteomics studies. Different biological partners will be described, among which glycoconjugates, oligonucleotides, peptides, proteins, and lipids, with the photoreactive label inserted either on the peptide of interest or on the potential partner. Particular attention will be paid to the observation and characterization of specific rearrangements following the photolabeling reaction, which can help characterize photoadducts and provide a better understanding of the interacting systems and environment.
Collapse
Affiliation(s)
- Astrid Walrant
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
| | - Emmanuelle Sachon
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
- Sorbonne Université, Mass Spectrometry Sciences Sorbonne Université, MS3U platform, Fédération de Chimie moléculaire de Paris centre, Paris, France
| |
Collapse
|
5
|
Kim D, Kim H, Jeon W, Kim HJ, Choi J, Kim Y, Kwon MS. Ultraviolet Light Debondable Optically Clear Adhesives for Flexible Displays through Efficient Visible-Light Curing. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309891. [PMID: 38146993 DOI: 10.1002/adma.202309891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/19/2023] [Indexed: 12/27/2023]
Abstract
With growing sustainability concerns, the need for products that facilitate easy disassembly and reuse has increased. Adhesives, initially designed for bonding, now face demands for selective removal, enabling rapid assembly-disassembly and efficient maintenance across industries. This need is particularly evident in the display industry, with the rise of foldable devices necessitating specialized adhesives. A novel optically clear adhesive (OCA) is presented for foldable display, featuring a unique UV-stimulated selective removal feature. This approach incorporates benzophenone derivatives into the polymer network, facilitating rapid debonding under UV irradiation. A key feature of this method is the adept use of visible-light-driven radical polymerization for OCA film fabrication. This method shows remarkable compatibility with various monomers and exhibits orthogonal reactivity to benzophenone, rendering it ideal for large-scale production. The resultant OCA not only has high transparency and balanced elasticity, along with excellent resistance to repeated folding, but it also exhibits significantly reduced adhesion when exposed to UV irradiation. By merging this customized formulation with strategically integrated UV-responsive elements, an effective solution is offered that enhances manufacturing efficiency and product reliability in the rapidly evolving field of sustainable electronics and displays. This research additionally contributes to eco-friendly device fabrication, aligning with emerging technology demands.
Collapse
Affiliation(s)
- Daewhan Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hongdeok Kim
- Department of Mechanical Design Engineering, Hanyang University, Seoul, 04763, Republic of Korea
- Department of Mechanical Engineering, BK21 FOUR ERICA-ACE Center, Hanyang University, Ansan, 15588, Republic of Korea
| | - Woojin Jeon
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Joong Kim
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Republic of Korea
| | - Joonmyung Choi
- Department of Mechanical Design Engineering, Hanyang University, Seoul, 04763, Republic of Korea
- Department of Mechanical Engineering, BK21 FOUR ERICA-ACE Center, Hanyang University, Ansan, 15588, Republic of Korea
| | - Youngdo Kim
- Mobile Display Module Development Team, Samsung Display Co., Ltd., Cheonan, 31086, Republic of Korea
| | - Min Sang Kwon
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| |
Collapse
|
6
|
Bo Y, Zhang H, Li Y, Reva Y, Xie L, Guldi DM. Tuning the Absorption, Fluorescence, Intramolecular Charge Transfer, and Intersystem Crossing in Spiro[fluorene]acridinone. Angew Chem Int Ed Engl 2024; 63:e202313936. [PMID: 38314965 DOI: 10.1002/anie.202313936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/07/2024]
Abstract
In this work, we prepared a series of electron donor-acceptor systems based on spiro[fluorene-9,7'-dibenzo[c,h]acridine]-5'-one (SFDBAO). Our SFDBAOs consist of orthogonally positioned fluorenes and aromatic ketones. By fine-tuning the substitution of electron-donating pyrenes, the complex interplay among different excited-state decay channels and the overall impact of solvents on these decay channels were uncovered. Placing pyrene, for example, at the aromatic ketones resulted in a profound solvatochromism in the form of a bright charge-transfer (CT) emission spanning from yellow to red-NIR. In contrast, a dark non-emissive CT was noted upon pyrene substitution at the fluorenes. In apolar solvents, efficient triplet-excited state generation was observed for all SFDBAOs. Either charge transfer was concluded to mediate the intersystem crossing (ISC) in the case of pyrene substitution or the El-Sayed rule was applicable when lacking pyrene substitution as in the case of SFABAO. In polar solvents, charge separation is the sole decay upon pyrene substitution. Moreover, competition between ISC and CT lowered the triplet-excited state generation in SFDBAO.
Collapse
Affiliation(s)
- Yifan Bo
- Department of Chemistry and Pharmacy &, Interdisciplinary Center of Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstrasse 3, 91058, Erlangen, Germany
| | - He Zhang
- Key Laboratory for Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Center for Molecular Systems and Organic Devices (CMSOD), Nanjing University of Posts and Telecommunications, Wenyuan Road 9, Nanjing, 210023, China
- School of Materials Science and Engineering, Anhui University, Jiulong Road 111, Hefei, 230601, China
| | - Yue Li
- Key Laboratory for Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Center for Molecular Systems and Organic Devices (CMSOD), Nanjing University of Posts and Telecommunications, Wenyuan Road 9, Nanjing, 210023, China
| | - Yana Reva
- Department of Chemistry and Pharmacy &, Interdisciplinary Center of Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstrasse 3, 91058, Erlangen, Germany
| | - Linghai Xie
- Key Laboratory for Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Center for Molecular Systems and Organic Devices (CMSOD), Nanjing University of Posts and Telecommunications, Wenyuan Road 9, Nanjing, 210023, China
- School of Flexible Electronics (SoFE), Henan Institute of Flexible Electronics (HIFE), Henan University, Mingli Road 379, Zhengzhou, 450046, China
| | - Dirk M Guldi
- Department of Chemistry and Pharmacy &, Interdisciplinary Center of Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstrasse 3, 91058, Erlangen, Germany
| |
Collapse
|
7
|
Hu Q, Song S, Zeng T, Wang L, Li Z, Wu J, Zhu J. 1,3-Butadiene Dicarbofunctionalization Enabled by the Dual Role of Diaryl Ketone in Photo-HAT/Chromium Catalysis. Org Lett 2024; 26:1550-1555. [PMID: 38364868 DOI: 10.1021/acs.orglett.3c04205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
We report a three-component Nozaki-Hiyama-Kishi type reaction of 1,3-dioxolane, 1,3-butadienes, and aldehydes to access masked aldehyde-incorporated homoallylic alcohols, facilitated by photo-hydrogen atom transfer (HAT)/chromium dual catalysis. The diaryl ketone serves dual roles both in the HAT process and in facilitating the turnover of the chromium catalyst. A range of functional groups are tolerated owing to the mild conditions. Both aromatic and aliphatic aldehydes are suitable substrates for coupling with several 1,3-butadienes and 1,3-dioxolane.
Collapse
Affiliation(s)
- Qiang Hu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Shuo Song
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Tianlong Zeng
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Lele Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Zhongxian Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Jiacheng Wu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Jun Zhu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, China
| |
Collapse
|
8
|
Großkopf J, Plaza M, Kutta RJ, Nuernberger P, Bach T. Creating a Defined Chirality in Amino Acids and Cyclic Dipeptides by Photochemical Deracemization. Angew Chem Int Ed Engl 2023; 62:e202313606. [PMID: 37793026 DOI: 10.1002/anie.202313606] [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: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/06/2023]
Abstract
2,5-Diketopiperazines are cyclic dipeptides displaying a wide range of applications. Their enantioselective preparation has now been found possible from the respective racemates by a photochemical deracemization (53 examples, 74 % to quantitative yield, 71-99 % ee). A chiral benzophenone catalyst in concert with irradiation at λ=366 nm enables to establish the configuration at the stereogenic carbon atom C6 at will. If other stereogenic centers are present in the diketopiperazines they remain unaffected and a stereochemical editing is possible at a single position. Consecutive reactions, including the conversion into N-aryl or N-alkyl amino acids or the reduction to piperazines, occur without compromising the newly created stereogenic center. Transient absorption spectroscopy revealed that the benzophenone catalyst processes one enantiomer of the 2,5-diketopiperazines preferentially and enables a reversible hydrogen atom transfer that is responsible for the deracemization process. The remarkably long lifetime of the protonated ketyl radical implies a yet unprecedented mode of action.
Collapse
Affiliation(s)
- Johannes Großkopf
- Department Chemie and Catalysis Research Center (CRC), School of Natural Sciences, Technische Universität München, D-85747, Garching, Germany
| | - Manuel Plaza
- Department Chemie and Catalysis Research Center (CRC), School of Natural Sciences, Technische Universität München, D-85747, Garching, Germany
| | - Roger Jan Kutta
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Patrick Nuernberger
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Thorsten Bach
- Department Chemie and Catalysis Research Center (CRC), School of Natural Sciences, Technische Universität München, D-85747, Garching, Germany
| |
Collapse
|
9
|
Peng L, Shu Y, Jiang L, Liu W, Zhao G, Zhang R. A New Strategy of Chemical Photo Grafting Metal Organic Framework to Construct NH 2-UiO-66/BiOBr/PVDF Photocatalytic Membrane for Synergistic Separation and Self-Cleaning Dyes. Molecules 2023; 28:7667. [PMID: 38005388 PMCID: PMC10675660 DOI: 10.3390/molecules28227667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Photocatalytic membranes are typical multifunctional membranes that have emerged in recent years. The lack of active functional groups on the surface of membranes made of inert materials such as polyvinylidene fluoride(PVDF) makes it difficult to have a stable binding interaction with photocatalysts directly. Therefore, in this study, we developed a simple method to prepare NH2-UiO-66/BiOBr/PVDF(MUB) membranes for efficient dye treatment by grafting benzophenolic acid-functionalized NH2-UiO-66 onto the surface of membranes with photocatalytic properties under visible light irradiation using benzophenolic acid with photoinitiating ability as an anchor. The structural characteristics, photocatalytic properties, antifouling properties, and reusability of the composite membranes were investigated in subsequent experiments using a series of experiments and characterizations. The results showed that the benzophenone acid grafting method was stable and the nanoparticles were not easily dislodged. The MUB composite membrane achieved a higher dye degradation efficiency (99.2%) than the pristine PVDF membrane at 62.9% within a reaction time of 180 min. In addition, the composite membranes exhibited higher permeate fluxes for both pure and mixed dyes and also demonstrated outstanding water flux recovery (>96%) after the light self-cleaning cycle operation. This combination proved to improve the performance of the membranes instead of reducing them, increasing their durability and reusability, and helping to broaden the application areas of membrane filtration technology.
Collapse
Affiliation(s)
- Lin Peng
- PetroChina Research Institute of Petroleum Exploration & Development, Beijing 100083, China
- Key Laboratory of Oilfield Chemicals, China National Petroleum Corporation (CNPC), Beijing 100083, China
| | - Yong Shu
- PetroChina Research Institute of Petroleum Exploration & Development, Beijing 100083, China
- Key Laboratory of Oilfield Chemicals, China National Petroleum Corporation (CNPC), Beijing 100083, China
| | - Luming Jiang
- PetroChina Research Institute of Petroleum Exploration & Development, Beijing 100083, China
- Key Laboratory of Oilfield Chemicals, China National Petroleum Corporation (CNPC), Beijing 100083, China
| | - Weidong Liu
- PetroChina Research Institute of Petroleum Exploration & Development, Beijing 100083, China
- Key Laboratory of Oilfield Chemicals, China National Petroleum Corporation (CNPC), Beijing 100083, China
| | - Guixiang Zhao
- PetroChina Research Institute of Petroleum Exploration & Development, Beijing 100083, China
- Key Laboratory of Oilfield Chemicals, China National Petroleum Corporation (CNPC), Beijing 100083, China
| | - Rui Zhang
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu 610500, China
| |
Collapse
|
10
|
Campbell AD, Ellis K, Gordon LK, Riley JE, Le V, Hollister KK, Ajagbe SO, Gozem S, Hughley RB, Boswell AM, Adjei-Sah O, Baruah PD, Malone R, Whitt LM, Gilliard RJ, Saint-Louis CJ. Solvatochromic and Aggregation-Induced Emission Active Nitrophenyl-Substituted Pyrrolidinone-Fused-1,2-Azaborine with a Pre-Twisted Molecular Geometry. JOURNAL OF MATERIALS CHEMISTRY. C 2023; 11:13740-13751. [PMID: 38855717 PMCID: PMC11160477 DOI: 10.1039/d3tc03278g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Boron-nitrogen-containing heterocycles with extended conjugated π-systems such as polycyclic aromatic 1,2-azaborines, hold the fascination of organic chemists due to their unique optoelectronic properties. However, the majority of polycyclic aromatic 1,2-azaborines aggregate at high concentrations or in the solid-state, resulting in aggregation-caused quenching (ACQ) of emission. This practical limitation poses significant challenges for polycyclic aromatic 1,2-azaborines' use in many applications. Additionally, only a few solvatochromic polycyclic aromatic 1,2-azaborines have been reported and they all display minimal solvatochromism. Therefore, the scope of available polycyclic 1,2-azaborines needs to be expanded to include those displaying fluorescence at high concentration and in the solid-state as well as those that exhibit significant changes in emission intensity in various solvents due to different polarities. To address the ACQ issue, we evaluate the effect of a pre-twisted molecular geometry on the optoelectronic properties of polycyclic aromatic 1,2-azaborines. Specifically, three phenyl-substituted pyrrolidinone-fused 1,2-azaborines (PFAs) with similar structures and functionalized with diverse electronic moieties (-H, -NO2, -CN, referred to as PFA 1, 2, and 3, respectively) were experimentally and computationally studied. Interestingly, PFA 2 displays two distinct emission properties: 1) solvatochromism, in which its emission and quantum yields are tunable with respect to solvent polarity, and 2) fluorescence that can be completely "turned off" and "turned on" via aggregation-induced emission (AIE). This report provides the first example of a polycyclic aromatic 1,2-azaborine that displays both AIE and solvatochromism properties in a single BN-substituted backbone. According to time-dependent density function theory (TD-DFT) calculations, the fluorescence properties of PFA 2 can be explained by the presence of a low-lying n-π* charge transfer state inaccessible to PFA 1 or PFA 3. These findings will help in the design of future polycyclic aromatic 1,2-azaborines that are solvatochromic and AIE-active as well as in understanding how molecular geometry affects these compounds' optoelectronic properties.
Collapse
Affiliation(s)
- Albert D Campbell
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, 30144, United States
| | - Kaia Ellis
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, 30144, United States
| | - Lyric K Gordon
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, 30144, United States
| | - Janiyah E Riley
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, 30144, United States
| | - VuongVy Le
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, United States
| | - Kimberly K Hollister
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, United States
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, United States
| | - Stephen O Ajagbe
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, United States
| | - Robert B Hughley
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, 30144, United States
| | - Adeline M Boswell
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, 30144, United States
| | - Ophelia Adjei-Sah
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, 30144, United States
| | - Prioska D Baruah
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, 30144, United States
| | - Ra'Nya Malone
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, 30144, United States
| | - Logan M Whitt
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama, 35487, United States
| | - Robert J Gilliard
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, United States
| | - Carl Jacky Saint-Louis
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, 30144, United States
| |
Collapse
|
11
|
Furuhashi T, Sakamoto K, Wada A. Genetic Code Expansion and a Photo-Cross-Linking Reaction Facilitate Ribosome Display Selections for Identifying a Wide Range of Affinity Peptides. Int J Mol Sci 2023; 24:15661. [PMID: 37958644 PMCID: PMC10650079 DOI: 10.3390/ijms242115661] [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: 09/03/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Cell-free molecular display techniques have been utilized to select various affinity peptides from peptide libraries. However, conventional techniques have difficulties associated with the translational termination through in-frame UAG stop codons and the amplification of non-specific peptides, which hinders the desirable selection of low-affinity peptides. To overcome these problems, we established a scheme for ribosome display selection of peptide epitopes bound to monoclonal antibodies and then applied genetic code expansion with synthetic X-tRNAUAG reprogramming of the UAG codons (X = Tyr, Trp, or p-benzoyl-l-phenylalanine (pBzo-Phe)) to the scheme. Based on the assessment of the efficiency of in vitro translation with X-tRNAUAG, we carried out ribosome display selection with genetic code expansion using Trp-tRNAUAG, and we verified that affinity peptides could be identified efficiently regardless of the presence of UAG codons in the peptide coding sequences. Additionally, after evaluating the photo-cross-linking reactions of pBzo-Phe-incorporated peptides, we performed ribosome display selection of low-affinity peptides in combination with genetic code expansion using pBzo-Phe-tRNAUAG and photo-irradiation. The results demonstrated that sub-micromolar low-affinity peptide epitopes could be identified through the formation of photo-induced covalent bonds with monoclonal antibodies. Thus, the developed ribosome display techniques could contribute to the promotion of diverse peptide-based research.
Collapse
Affiliation(s)
- Takuto Furuhashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Laboratory for Advanced Biomolecular Engineering, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
| | - Kensaku Sakamoto
- Laboratory for Nonnatural Amino Acid Technology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan;
- Department of Drug Target Protein Research, School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto 390-8621, Nagano, Japan
| | - Akira Wada
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Laboratory for Advanced Biomolecular Engineering, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Laboratory for Nonnatural Amino Acid Technology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan;
| |
Collapse
|
12
|
Hindricks KDJ, Schaate A, Behrens P. Postsynthetic Photochemical Modification and 2D Structuring of Zr-MOF Thin Films Containing Benzophenone Linker Molecules. Angew Chem Int Ed Engl 2023; 62:e202303753. [PMID: 37154383 DOI: 10.1002/anie.202303753] [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: 03/15/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
Abstract
For the fabrication of next-generation MOF-based devices the availability of highly adaptable materials in suitable shapes is crucial. Here, we present thin films of a metal-organic framework (MOF) containing photoreactive benzophenone units. Crystalline, oriented and porous films of the zirconium-based bzpdc-MOF (bzpdc=benzophenone-4-4'-dicarboxylate) are prepared by direct growth on silicon or glass substrates. Via a subsequent photochemical modification of the Zr-bzpdc-MOF films, various properties can be tuned postsynthetically by covalent attachment of modifying agents. Apart from the modification with small molecules, also grafting-from polymerization reactions are possible. In a further extension, 2D structuring and photo-writing of defined structures is also possible, for example by using a photolithographic approach, paving the way towards micro-patterned MOF surfaces.
Collapse
Affiliation(s)
- Karen D J Hindricks
- Institute of Inorganic Chemistry, Leibniz University Hannover, Callinstr. 9, 30167, Hannover, Germany
- Cluster of Excellence PhoenixD, Leibniz University Hannover, Welfengarten 1A, 30167, Hannover, Germany
| | - Andreas Schaate
- Institute of Inorganic Chemistry, Leibniz University Hannover, Callinstr. 9, 30167, Hannover, Germany
- Cluster of Excellence PhoenixD, Leibniz University Hannover, Welfengarten 1A, 30167, Hannover, Germany
| | - Peter Behrens
- Institute of Inorganic Chemistry, Leibniz University Hannover, Callinstr. 9, 30167, Hannover, Germany
- Cluster of Excellence PhoenixD, Leibniz University Hannover, Welfengarten 1A, 30167, Hannover, Germany
| |
Collapse
|
13
|
Fu J, Li S, Deng L, Zhao X, Yu Z. A genetically encodable and fluorogenic photo-crosslinker via photo-induced defluorination acyl fluoride exchange. Chem Commun (Camb) 2023; 59:11073-11076. [PMID: 37624030 DOI: 10.1039/d3cc02771f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
We report a genetically encodable m-trifluoromethylaniline modified L-lysine (m-TFMAK) which defluorinates upon light activation and covalently conjugates to native residues via acyl fluoride exchange. The encoded m-TFMAK photo-crosslinks with temporal controllability, residue selectivity, and fluorogenic tracking features, making it suitable for identifying protein interactions in living systems.
Collapse
Affiliation(s)
- 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.
| | - Sitong 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.
| | - Lijun Deng
- 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
|
Patel R, Negrón Terón K, Zhou M, Nakayasu E, Drown B, Das C. Genetically Encoded Crosslinking Enables Identification of Multivalent Ubiquitin-Deubiquitylating Enzyme Interactions. Chembiochem 2023; 24:e202300305. [PMID: 37262077 PMCID: PMC11088939 DOI: 10.1002/cbic.202300305] [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: 04/18/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
Ubiquitin (Ub) proteoforms control nearly every aspect of eukaryotic cell biology through their diversity. Inspired by the widely used Ub C-terminal electrophiles (Ub-E), here we report the identification of multivalent binding of Ub with deubiquitylating enzymes (Dubs) using genetic code expansion (GCE) and crosslinking mass spectrometry. While the Ub-Es only gather structural information with the S1 Dub sites, we demonstrate that GCE of Ub with p-benzoyl-L-phenylalanine enables identification of interaction modes beyond the S1 site with a panel of Dubs of both eukaryotic and prokaryotic origin. Collectively, this represents the next generation of Ub-based affinity probes with a unique ability to unravel Ub interaction landscapes beyond what is afforded by cysteine-based chemistries.
Collapse
Affiliation(s)
- Rishi Patel
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Kristos Negrón Terón
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Mowei Zhou
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352, USA
| | - Ernesto Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352, USA
| | - Bryon Drown
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| |
Collapse
|
15
|
Wu Y, Bertran MT, Joshi D, Maslen SL, Hurd C, Walport LJ. Identification of photocrosslinking peptide ligands by mRNA display. Commun Chem 2023; 6:103. [PMID: 37258712 PMCID: PMC10232439 DOI: 10.1038/s42004-023-00898-2] [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: 03/07/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023] Open
Abstract
Photoaffinity labelling is a promising method for studying protein-ligand interactions. However, obtaining a specific, efficient crosslinker can require significant optimisation. We report a modified mRNA display strategy, photocrosslinking-RaPID (XL-RaPID), and exploit its ability to accelerate the discovery of cyclic peptides that photocrosslink to a target of interest. As a proof of concept, we generated a benzophenone-containing library and applied XL-RaPID screening against a model target, the second bromodomain of BRD3. This crosslinking screening gave two optimal candidates that selectively labelled the target protein in cell lysate. Overall, this work introduces direct photocrosslinking screening as a versatile technique for identifying covalent peptide ligands from mRNA display libraries incorporating reactive warheads.
Collapse
Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK
| | - M Teresa Bertran
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Dhira Joshi
- Chemical Biology, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sarah L Maslen
- Proteomics, The Francis Crick Institute, London, NW1 1AT, UK
| | - Catherine Hurd
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Louise J Walport
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK.
| |
Collapse
|
16
|
Shekhar AC, Sun YE, Khoo SK, Lin YC, Malau E, Chang WH, Chen HT. Site-directed biochemical analyses reveal that the switchable C-terminus of Rpc31 contributes to RNA polymerase III transcription initiation. Nucleic Acids Res 2023; 51:4223-4236. [PMID: 36484109 PMCID: PMC10201443 DOI: 10.1093/nar/gkac1163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/14/2022] [Accepted: 11/23/2022] [Indexed: 08/23/2023] Open
Abstract
Rpc31 is a subunit in the TFIIE-related Rpc82/34/31 heterotrimeric subcomplex of Saccharomyces cerevisiae RNA polymerase III (pol III). Structural analyses of pol III have indicated that the N-terminal region of Rpc31 anchors on Rpc82 and further interacts with the polymerase core and stalk subcomplex. However, structural and functional information for the C-terminal region of Rpc31 is sparse. We conducted a mutational analysis on Rpc31, which uncovered a functional peptide adjacent to the highly conserved Asp-Glu-rich acidic C-terminus. This C-terminal peptide region, termed 'pre-acidic', is important for optimal cell growth, tRNA synthesis, and stable association of Rpc31 in the pre-initiation complex (PIC). Our site-directed photo-cross-linking to map protein interactions within the PIC reveal that this pre-acidic region specifically targets Rpc34 during transcription initiation, but also interacts with the DNA entry surface in free pol III. Thus, we have uncovered a switchable Rpc31 C-terminal region that functions in an initiation-specific protein interaction for pol III transcription.
Collapse
Affiliation(s)
| | - Yuan-En Sun
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, R.O.C
| | - Seok-Kooi Khoo
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, R.O.C
| | - Yu-Chun Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, R.O.C
| | | | - Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taiwan, R.O.C
| | - Hung-Ta Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, R.O.C
| |
Collapse
|
17
|
Fu Y, Liu X, Xia Y, Guo X, Guo J, Zhang J, Zhao W, Wu Y, Wang J, Zhong F. Whole-cell-catalyzed hydrogenation/deuteration of aryl halides with a genetically repurposed photodehalogenase. Chem 2023. [DOI: 10.1016/j.chempr.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
|
18
|
Yu D, Basumatary IB, Kumar S, Ye F, Dutta J. Chitosan modified with bio-extract as an antibacterial coating with UV filtering feature. Int J Biol Macromol 2023; 230:123145. [PMID: 36621742 DOI: 10.1016/j.ijbiomac.2023.123145] [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: 11/17/2022] [Revised: 12/19/2022] [Accepted: 01/01/2023] [Indexed: 01/07/2023]
Abstract
Benzophenone-3 grafted chitosan (CS-BP-3) was successfully synthesized and applied as an antibacterial coating for the first time. The grafting mechanism is based on the reaction between ketone and primary amine to form imine derivatives and the chemical structure of grafted chitosan was studied by Fourier transform infrared (FT-IR) spectroscopy. Water solubility of BP-3 is enhanced after covalently grafted on chitosan and consequently renders the chitosan coating with UV blocking property. Results of thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC) further confirmed the thermal stability of BP-3 modified chitosan is enhanced. The CS-BP-3 coating was applied on a variety of substrates of glass, plastics, wood, and metal. The surface features of the coatings such as morphology, water contact angle (WCA), and surface roughness were investigated. The optical and thermal stabilities of the coatings under UV irradiation were studied for 16 h. Antibacterial activity of CS-BP-3 was evaluated against both Gram-negative and Gram-positive bacteria. And the results of bacterial inhibition by CS-BP-3 coating indicate its potential for future application in food packaging.
Collapse
Affiliation(s)
- Dongkun Yu
- Functional Materials Group, Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Hannes Alfvéns väg 12, 114 19 Stockholm, Sweden
| | - Indra Bhusan Basumatary
- Department of Food Engineering and Technology, Central Institute of Technology, Kokrajhar 783370, India
| | - Santosh Kumar
- Department of Food Engineering and Technology, Central Institute of Technology, Kokrajhar 783370, India
| | - Fei Ye
- Functional Materials Group, Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Hannes Alfvéns väg 12, 114 19 Stockholm, Sweden.
| | - Joydeep Dutta
- Functional Materials Group, Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Hannes Alfvéns väg 12, 114 19 Stockholm, Sweden.
| |
Collapse
|
19
|
Peng K, Wang R, Zhou J. One-step fabrication of three-dimensional macropore copolymer-modified polycarbonate array by photo-crosslinking for protein immunoassay. RSC Adv 2023; 13:6936-6946. [PMID: 36865573 PMCID: PMC9973421 DOI: 10.1039/d3ra00696d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
A photocross-linked copolymer was prepared, and could rapidly form a macropore structure in phosphate buffer solution (PBS) without the addition of porogen. The photo-crosslinking process contained the crosslinking of the copolymer itself and that with the polycarbonate substrate. The three-dimensional (3D) surface was achieved through one-step photo-crosslinking of the macropore structure. The macropore structure can be finely regulated by multiple dimensions, including monomer structure of the copolymer, PBS and copolymer concentration. Compared with the two-dimensional (2D) surface, the 3D surface has a controllable structure, a high loading capacity (59 μg cm-2) and immobilization efficiency (92%), and the effect of inhibiting the coffee ring for protein immobilization. Immunoassay results show that a 3D surface immobilized by IgG has high sensitivity (LOD value of 5 ng mL-1) and broader dynamic range (0.005-50 μg mL-1). This simple and structure-controllable method for preparing 3D surfaces modified by macropore polymer has great potential applications in the fields of biochips and biosensing.
Collapse
Affiliation(s)
- Kaimei Peng
- School of Chemistry and Chemical Engineering, Qiannan Normal University for Nationalities Duyun 558000 China.,Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province School of Biomedical Engineering, Sun Yat-sen University Guangzhou 510275 China
| | - Runping Wang
- School of Chemistry and Chemical Engineering, Qiannan Normal University for NationalitiesDuyun 558000China
| | - Jianhua Zhou
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province School of Biomedical Engineering, Sun Yat-sen University Guangzhou 510275 China
| |
Collapse
|
20
|
Kutta RJ, Großkopf J, van Staalduinen N, Seitz A, Pracht P, Breitenlechner S, Bannwarth C, Nuernberger P, Bach T. Multifaceted View on the Mechanism of a Photochemical Deracemization Reaction. J Am Chem Soc 2023; 145:2354-2363. [PMID: 36660908 DOI: 10.1021/jacs.2c11265] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Upon irradiation in the presence of a chiral benzophenone catalyst (5 mol %), a racemic mixture of a given chiral imidazolidine-2,4-dione (hydantoin) can be converted almost quantitatively into the same compound with high enantiomeric excess (80-99% ee). The mechanism of this photochemical deracemization reaction was elucidated by a suite of mechanistic experiments. It was corroborated by nuclear magnetic resonance titration that the catalyst binds the two enantiomers by two-point hydrogen bonding. In one of the diastereomeric complexes, the hydrogen atom at the stereogenic carbon atom is ideally positioned for hydrogen atom transfer (HAT) to the photoexcited benzophenone. Detection of the protonated ketyl radical by transient absorption revealed hydrogen abstraction to occur from only one but not from the other hydantoin enantiomer. Quantum chemical calculations allowed us to visualize the HAT within this complex and, more importantly, showed that the back HAT does not occur to the carbon atom of the hydantoin radical but to its oxygen atom. The achiral enol formed in this process could be directly monitored by its characteristic transient absorption signal at λ ≅ 330 nm. Subsequent tautomerization leads to both hydantoin enantiomers, but only one of them returns to the catalytic cycle, thus leading to an enrichment of the other enantiomer. The data are fully consistent with deuterium labeling experiments and deliver a detailed picture of a synthetically useful photochemical deracemization reaction.
Collapse
Affiliation(s)
- Roger Jan Kutta
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Universitätsstr. 31, RegensburgD-93053, Germany
| | - Johannes Großkopf
- Department Chemie and Catalysis Research Center (CRC), School of Natural Sciences, Technische Universität München, D-85747Garching, Germany
| | - Nils van Staalduinen
- Institut für Physikalische Chemie, RWTH Aachen University, D-52074Aachen, Germany
| | - Antonia Seitz
- Department Chemie and Catalysis Research Center (CRC), School of Natural Sciences, Technische Universität München, D-85747Garching, Germany
| | - Philipp Pracht
- Institut für Physikalische Chemie, RWTH Aachen University, D-52074Aachen, Germany.,Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Stefan Breitenlechner
- Department Chemie and Catalysis Research Center (CRC), School of Natural Sciences, Technische Universität München, D-85747Garching, Germany
| | - Christoph Bannwarth
- Institut für Physikalische Chemie, RWTH Aachen University, D-52074Aachen, Germany
| | - Patrick Nuernberger
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, Universitätsstr. 31, RegensburgD-93053, Germany
| | - Thorsten Bach
- Department Chemie and Catalysis Research Center (CRC), School of Natural Sciences, Technische Universität München, D-85747Garching, Germany
| |
Collapse
|
21
|
Kozoriz K, Shkel O, Hong KT, Kim DH, Kim YK, Lee JS. Multifunctional Photo-Cross-Linking Probes: From Target Protein Searching to Imaging Applications. Acc Chem Res 2023; 56:25-36. [PMID: 36534922 DOI: 10.1021/acs.accounts.2c00505] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Despite advances in genome sequencing technology, the complete molecular interaction networks reflecting the biological functions of gene products have not been fully elucidated due to the lack of robust molecular interactome profiling techniques. Traditionally, molecular interactions have been investigated in vitro by measuring their affinity. However, such a reductionist approach comes with throughput constraints and does not depict an intact living cell environment. Therefore, molecular interactions in live cells must be captured to minimize false-positive results. The photo-cross-linking technique is a promising tool because the production of a temporally controlled reactive functional group can be induced using light exposure. Photoaffinity labeling is used in biochemistry and medicinal chemistry for bioconjugation, including drug and antibody conjugation, target protein identification of bioactive compounds, and fluorescent labeling of target proteins. This Account summarizes recent advances in multifunctional photo-cross-linkers for drug target identification and bioimaging. In addition to our group's contributions, we reviewed the most notable examples from the last few decades to provide a comprehensive overview of how this field is evolving. Based on cross-linking chemistry, photo-cross-linkers are classified as either (i) reactive intermediate-generating or (ii) electrophile-generating. Reactive intermediates generating photoaffinity tags have been extensively modified to target a molecule of interest using aryl azide, benzophenone, diazirine, diazo, and acyl silanes. These species are highly reactive and can form covalent bonds, irrespective of residue. Their short lifetime is ideal for the instant capture and labeling of biomolecules. Recently, photocaged electrophiles have been investigated to take advantage of their residue selectivity and relatively high yield for adduct formation with tetrazole, nitrobenzyl alcohol, o-nitrophenylethylene, pyrone, and pyrimidone. Multifunctional photo-cross-linkers for two parallel practical applications have been developed using both classes of photoactivatable groups. Unbiased target interactome profiling of small-molecule drugs requires a challenging structure-activity relationship study (SAR) step to retain the nature or biological activity of the lead compound, which led to the design of a multifunctional "minimalist tag" comprising a bio-orthogonal handle, a photoaffinity labeling group, and functional groups to load target molecules. In contrast, fluorogenic photo-cross-linking is advantageous for bioimaging because it does not require an additional bio-orthogonal reaction to introduce a fluorophore to the minimalist tag. Our group has made progress on minimalist tags and fluorogenic photo-cross-linkers through fruitful collaborations with other groups. The current range of photoactivation reactions and applications demonstrate that photoaffinity tags can be improved. We expect exciting days in the rational design of new multifunctional photo-cross-linkers, particularly clinically interesting versions used in photodynamic or photothermal therapy.
Collapse
Affiliation(s)
- Kostiantyn Kozoriz
- Department of Pharmacology, Korea University College of Medicine, 73 Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Olha Shkel
- Convergence Research Center for Brain Science, Korea Institute of Science and Technology (KIST) & Bio-Med Program, KIST-School UST, Hwarang-ro 14 gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Kyung Tae Hong
- Convergence Research Center for Brain Science, Korea Institute of Science and Technology (KIST) & Bio-Med Program, KIST-School UST, Hwarang-ro 14 gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Dong Hoon Kim
- Department of Pharmacology, Korea University College of Medicine, 73 Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Yun Kyung Kim
- Convergence Research Center for Brain Science, Korea Institute of Science and Technology (KIST) & Bio-Med Program, KIST-School UST, Hwarang-ro 14 gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Jun-Seok Lee
- Department of Pharmacology, Korea University College of Medicine, 73 Goryeodae-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| |
Collapse
|
22
|
Diecker J, Dörner W, Rüschenbaum J, Mootz HD. Unraveling Structural Information of Multi-Domain Nonribosomal Peptide Synthetases by Using Photo-Cross-Linking Analysis with Genetic Code Expansion. Methods Mol Biol 2023; 2670:165-185. [PMID: 37184704 DOI: 10.1007/978-1-0716-3214-7_8] [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: 05/16/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large, multifunctional enzymes that facilitate the stepwise synthesis of modified peptides, many of which serve as important pharmaceutical products. Typically, NRPSs contain one module for the incorporation of one amino acid into the growing peptide chain. A module consists of the domains required for activation, covalent binding, condensation, termination, and optionally modification of the aminoacyl or peptidyl moiety. We here describe a protocol using genetically encoded photo-cross-linking amino acids to probe the 3D architecture of NRPSs by determining spatial proximity constraints. p-benzoyl-L-phenylalanine (BpF) is incorporated at positions of presumed contact interfaces between domains. The covalent cross-link products are visualized by SDS-PAGE-based methods and precisely mapped by tandem mass spectrometry. Originally intended to study the communication (COM) domains, a special pair of docking domains of unknown structure between two interacting subunits of one NRPS system, this cross-linking approach was also found to be useful to interrogate the spatial proximity of domains that are not connected on the level of the primary structure. The presented photo-cross-linking technique thus provides structural insights complementary to those obtained by protein crystallography and reports on the protein in solution.
Collapse
Affiliation(s)
- Julia Diecker
- University of Münster, Institute of Biochemistry, Münster, Germany
| | - Wolfgang Dörner
- University of Münster, Institute of Biochemistry, Münster, Germany
| | | | - Henning D Mootz
- University of Münster, Institute of Biochemistry, Münster, Germany.
| |
Collapse
|
23
|
Wang J, Xia Y, Guo X. Repurposing Photosensitizer Proteins Through Genetic Code Expansion to Facilitate Photo-Biocatalysis. Methods Mol Biol 2023; 2676:41-54. [PMID: 37277623 DOI: 10.1007/978-1-0716-3251-2_3] [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: 06/07/2023]
Abstract
Artificial photoenzymes with noncanonical photo-redox cofactors have paved the way for enzyme rational design and the creation of new-to-nature biocatalysts. Genetically encoded photo-redox cofactors endow photoenzymes with enhanced or novel activities that catalyze numerous transformations with high efficiency. Herein, we describe a protocol of repurposing photosensitizer proteins (PSP) through genetic code expansion to facilitate multiple photocatalytic conversions including photo-activated dehalogenation of aryl halides, CO2 to CO and CO2 to formic acid reduction. The methods for expression, purification, and characterization of the PSP are detailed. The installation of the catalytic modules and the utilization of PSP-based artificial photoenzymes for photoenzymatic CO2 reduction and dehalogenation are also described.
Collapse
Affiliation(s)
- Jiangyun Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.
| | - Yan Xia
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Xuzhen Guo
- CAS Key Laboratory of Quantitative Engineering Biology, Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| |
Collapse
|
24
|
Hashmi Y, Thongpanchang T. Synthesis and Properties of Bis(naphthofuran)‐Fused [7]Helicene Derivatives. European J Org Chem 2022. [DOI: 10.1002/ejoc.202201373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yuttawat Hashmi
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC) Faculty of Science Mahidol University Rama 6 Road Bangkok 10400 Thailand
| | - Tienthong Thongpanchang
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC) Faculty of Science Mahidol University Rama 6 Road Bangkok 10400 Thailand
| |
Collapse
|
25
|
Haensch VG, Görls H, Hertweck C. A Photochemical Macrocyclization Route to Asymmetric Strained [3.2] Paracyclophanes. Chemistry 2022; 28:e202202577. [PMID: 36094023 PMCID: PMC10092696 DOI: 10.1002/chem.202202577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Indexed: 12/14/2022]
Abstract
The intricate frameworks of paracyclophanes are an important target for synthesis since they are found in various chiral auxiliaries, solar cells, high-performance plastics, pharmaceuticals, and molecular machines. Whereas numerous methods exist for the preparation of symmetric paracyclophanes, protocols for the efficient synthesis of strained asymmetric scaffolds are limited. Here we report a remarkably simple photochemical route to strained [3.2]paracyclophanes starting from readily available educts. By way of NMR and X-ray analyses, we discovered that UV-irradiation of an aromatic carboxylic ester tethered to a toluene moiety leads to the intramolecular formation of a new C-C bond, with loss of an alcohol. A systematic evaluation of the reaction conditions and substituents, as well as radical starter and triplet quenching experiments, point to a reaction mechanism involving an excited triplet state and hydrogen atom transfer. The new method proved to be robust and versatile enabling the synthesis of a range of cyclophanes with different substitutions, including an unusual diastereoisomer with two planar chiral centers, and thus proved to be a valuable addition to the synthetic toolbox.
Collapse
Affiliation(s)
- Veit G Haensch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Helmar Görls
- Institute of Inorganic and Analytical Chemistry (IAAC), Friedrich Schiller University Jena, Humboldtstraße 8, 07743, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, Humboldtstraße 8, 07743, Jena, Germany
| |
Collapse
|
26
|
West AV, Woo CM. Photoaffinity Labeling Chemistries Used to Map Biomolecular Interactions. Isr J Chem 2022. [DOI: 10.1002/ijch.202200081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Alexander V. West
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford St Cambridge MA USA
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford St Cambridge MA USA
| |
Collapse
|
27
|
Abstract
Creating, conserving and modifying the stereochemistry of organic compounds has been the subject of significant research efforts in synthetic chemistry. Most synthetic routes are designed according to the stereoselectivity-determining step. Stereochemical editing is an alternative strategy, wherein the chiral-defining or geometry-defining steps are independent of the construction of the major scaffold or complexity. It enables late-stage alterations of stereochemistry and can generate isomers from a single compound. However, in many instances, stereochemical editing processes are contra-thermodynamic, meaning the transformation is unfavourable. To overcome this barrier, photocatalysis uses photogenerated radical species and introduces thermochemical biases. A range of synthetically valuable contra-thermodynamic stereochemical editing processes have been invented, including deracemization of chiral molecules, positional alkene isomerization and dynamic epimerization of sugars and diols. In this Review, we highlight the fundamental mechanisms of visible-light photocatalysis and the general reactivity modes of the photogenerated radical intermediates towards contra-thermodynamic stereochemical editing processes.
Collapse
|
28
|
Sanjosé-Orduna J, Silva RC, Raymenants F, Reus B, Thaens J, de Oliveira KT, Noël T. Dual role of benzophenone enables a fast and scalable C-4 selective alkylation of pyridines in flow. Chem Sci 2022; 13:12527-12532. [PMID: 36382292 PMCID: PMC9629060 DOI: 10.1039/d2sc04990b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/08/2022] [Indexed: 08/27/2023] Open
Abstract
The efficient C-4 selective modification of pyridines is a major challenge for the synthetic community. Current strategies are plagued with at least one drawback regarding functional group-tolerant electronic activation of the heteroarene, mild generation of the required alkyl radicals, regioselectivity, safety and/or scalability. Herein, we describe a fast, safe and scalable flow process which allows preparation of said C-4 alkylated pyridines. The process involves a photochemical hydrogen atom transfer (HAT) event to generate the carbon-centered radicals needed to alkylate the C-2 blocked pyridine. In a two-step streamlined flow process, this light-mediated alkylation step is combined with a nearly instantaneous inline removal of the blocking group. Notably, cheap benzophenone plays a dual role in the pyridine alkylation mechanism by activating the hydrocarbon feedstock reagents via a HAT mechanism, and by acting as a benign, terminal oxidant. The key role of benzophenone in the operative reaction mechanism has also been revealed through a combination of experimental and computational studies.
Collapse
Affiliation(s)
- Jesús Sanjosé-Orduna
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands https://www.noelresearchgroup.com/
| | - Rodrigo C Silva
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands https://www.noelresearchgroup.com/
- Departamento de Química, Universidade Federal de São Carlos SP 13565-905 Brazil
| | - Fabian Raymenants
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands https://www.noelresearchgroup.com/
| | - Bente Reus
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands https://www.noelresearchgroup.com/
| | - Jannik Thaens
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands https://www.noelresearchgroup.com/
| | | | - Timothy Noël
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands https://www.noelresearchgroup.com/
| |
Collapse
|
29
|
Hahm D, Lim J, Kim H, Shin JW, Hwang S, Rhee S, Chang JH, Yang J, Lim CH, Jo H, Choi B, Cho NS, Park YS, Lee DC, Hwang E, Chung S, Kang CM, Kang MS, Bae WK. Direct patterning of colloidal quantum dots with adaptable dual-ligand surface. NATURE NANOTECHNOLOGY 2022; 17:952-958. [PMID: 35953539 DOI: 10.1038/s41565-022-01182-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Colloidal quantum dots (QDs) stand at the forefront of a variety of photonic applications given their narrow spectral bandwidth and near-unity luminescence efficiency. However, integrating luminescent QD films into photonic devices without compromising their optical or transport characteristics remains challenging. Here we devise a dual-ligand passivation system comprising photocrosslinkable ligands and dispersing ligands to enable QDs to be universally compatible with solution-based patterning techniques. The successful control over the structure of both ligands allows the direct patterning of dual-ligand QDs on various substrates using commercialized photolithography (i-line) or inkjet printing systems at a resolution up to 15,000 pixels per inch without compromising the optical properties of the QDs or the optoelectronic performance of the device. We demonstrate the capabilities of our approach for QD-LED applications. Our approach offers a versatile way of creating various structures of luminescent QDs in a cost-effective and non-destructive manner, and could be implemented in nearly all commercial photonics applications where QDs are used.
Collapse
Affiliation(s)
- Donghyo Hahm
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, Republic of Korea
| | - Jaemin Lim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, Republic of Korea
| | - Hyeokjun Kim
- Department of Chemical and Biomolecular Engineering, Institute of Emergent Materials, Sogang University, Seoul, Republic of Korea
| | - Jin-Wook Shin
- Reality Display Research Section, Electronics and Telecommunications Research Institute (ETRI), Daejeon, Republic of Korea
| | - Seongkwon Hwang
- Soft Hybrid Materials Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Seunghyun Rhee
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, Republic of Korea
- Advanced Materials Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Jun Hyuk Chang
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, Republic of Korea
| | - Jeehye Yang
- Department of Chemical and Biomolecular Engineering, Institute of Emergent Materials, Sogang University, Seoul, Republic of Korea
| | - Chang Hyeok Lim
- Department of Chemical and Biomolecular Engineering, Institute of Emergent Materials, Sogang University, Seoul, Republic of Korea
| | - Hyunwoo Jo
- Department of Chemical and Biomolecular Engineering, Institute of Emergent Materials, Sogang University, Seoul, Republic of Korea
| | - Beomgyu Choi
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, Republic of Korea
| | - Nam Sung Cho
- Reality Display Research Section, Electronics and Telecommunications Research Institute (ETRI), Daejeon, Republic of Korea
| | - Young-Shin Park
- Department of Chemical and Biomolecular Engineering, KAIST Institute for the Nanocentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Doh C Lee
- Department of Chemical and Biomolecular Engineering, KAIST Institute for the Nanocentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Euyheon Hwang
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, Republic of Korea
| | - Seungjun Chung
- Soft Hybrid Materials Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Chan-Mo Kang
- Reality Display Research Section, Electronics and Telecommunications Research Institute (ETRI), Daejeon, Republic of Korea.
| | - Moon Sung Kang
- Department of Chemical and Biomolecular Engineering, Institute of Emergent Materials, Sogang University, Seoul, Republic of Korea.
| | - Wan Ki Bae
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, Republic of Korea.
| |
Collapse
|
30
|
Development of fluorizoline analogues as prohibitin ligands that modulate C-RAF signaling, p21 expression and melanogenesis. Eur J Med Chem 2022; 242:114635. [DOI: 10.1016/j.ejmech.2022.114635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022]
|
31
|
Jeremias N, Peschel MT, Jaschke C, de Vivie-Riedle R, Bach T. Photochemical Ring Contraction of 5,5-Dialkylcyclopent-2-enones and in situ Trapping by Primary Amines. J Org Chem 2022; 88:6294-6303. [PMID: 35786889 DOI: 10.1021/acs.joc.2c01156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
If substituted in the 5,5-position, cyclopent-2-enones undergo a smooth photochemical rearrangement to ketenes. A concomitant cyclopropane formation occurs due to a 1,3-shift of the C5 carbon atom from the carbonyl carbon atom (C1) to carbon atom C3. In this study, the cyclopropyl-substituted ketene intermediates were trapped in situ by primary amines providing an efficient entry into 2,2-disubstituted cyclopropaneacetic amides (24 examples, 49-95% yield). A remarkable feature of the reaction is the fact that the photochemical rearrangement can occur from either the first excited singlet (S1) or the respective triplet state (T1). In line with experimental results (triplet quenching, sensitization), XMS-CASPT2 calculations support the existence of efficient reaction pathways to the intermediate ketene both on the singlet and on the triplet hypersurface.
Collapse
Affiliation(s)
- Noah Jeremias
- School of Natural Sciences, Department of Chemistry and Catalysis Research Center (CRC), Technical University of Munich, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Martin T Peschel
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, 81377 München, Germany
| | - Constantin Jaschke
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, 81377 München, Germany
| | - Regina de Vivie-Riedle
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, 81377 München, Germany
| | - Thorsten Bach
- School of Natural Sciences, Department of Chemistry and Catalysis Research Center (CRC), Technical University of Munich, Lichtenbergstrasse 4, 85747 Garching, Germany
| |
Collapse
|
32
|
Brüninghoff K, Wulff S, Dörner W, Geiss-Friedlander R, Mootz HD. A Photo-Crosslinking Approach to Identify Class II SUMO-1 Binders. Front Chem 2022; 10:900989. [PMID: 35707458 PMCID: PMC9191277 DOI: 10.3389/fchem.2022.900989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
The small ubiquitin-like modifier (SUMO) is involved in various cellular processes and mediates known non-covalent protein-protein interactions by three distinct binding surfaces, whose interactions are termed class I to class III. While interactors for the class I interaction, which involves binding of a SUMO-interacting motif (SIM) to a hydrophobic groove in SUMO-1 and SUMO-2/3, are widely abundant, only a couple of examples have been reported for the other two types of interactions. Class II binding is conveyed by the E67 loop region on SUMO-1. Many previous studies to identify SUMO binders using pull-down or microarray approaches did not strategize on the SUMO binding mode. Identification of SUMO binding partners is further complicated due to the typically transient and low affinity interactions with the modifier. Here we aimed to identify SUMO-1 binders selectively enriched for class II binding. Using a genetically encoded photo-crosslinker approach, we have designed SUMO-1 probes to covalently capture class II SUMO-1 interactors by strategically positioning the photo-crosslinking moiety on the SUMO-1 surface. The probes were validated using known class II and class I binding partners. We utilized the probe with p-benzoyl-phenylalanine (BzF, also termed BpF or Bpa) at the position of Gln69 to identify binding proteins from mammalian cell extracts using mass spectrometry. By comparison with results obtained with a similarly designed SUMO-1 probe to target SIM-mediated binders of the class I type, we identified 192 and 96 proteins specifically enriched by either probe, respectively. The implicated preferential class I or class II binding modes of these proteins will further contribute to unveiling the complex interplay of SUMO-1-mediated interactions.
Collapse
Affiliation(s)
- Kira Brüninghoff
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Stephanie Wulff
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Wolfgang Dörner
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Ruth Geiss-Friedlander
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Henning D. Mootz
- Institute of Biochemistry, University of Münster, Münster, Germany
- *Correspondence: Henning D. Mootz,
| |
Collapse
|
33
|
Golden DL, Suh SE, Stahl SS. Radical C(sp3)–H functionalization and cross-coupling reactions. Nat Rev Chem 2022; 6:405-427. [DOI: 10.1038/s41570-022-00388-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
34
|
Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins. Bioorg Med Chem 2022; 62:116721. [PMID: 35358862 DOI: 10.1016/j.bmc.2022.116721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022]
Abstract
Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.
Collapse
|
35
|
Metz S, Marian CM. Modulation of Intersystem Crossing by Chemical Composition and Solvent Effects: Benzophenone, Anthrone and Fluorenone. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Simon Metz
- Heinrich-Heine-University Düsseldorf Theoretical and Computational Chemistry Universitätsstraße 1 40225 Düsseldorf GERMANY
| | - Christel Maria Marian
- Heinrich-Heine-University Düsseldorf Insitute of Theoretical and Computational Chemistry Universitätsstr. 126.32 40225 Düsseldorf GERMANY
| |
Collapse
|
36
|
Bollu A, Peters A, Rentmeister A. Chemo-Enzymatic Modification of the 5' Cap To Study mRNAs. Acc Chem Res 2022; 55:1249-1261. [PMID: 35420432 DOI: 10.1021/acs.accounts.2c00059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The central dogma of molecular biology hinges on messenger RNA (mRNA), which presents a blueprint of the genetic information encoded in the DNA and serves as a template for translation into proteins. In addition to its fundamental importance in basic research, this class of biomolecules has recently become the first approved Covid vaccine, underscoring its utility in medical applications.Eukaryotic mRNA is heavily processed, including the 5' cap as the primary hallmark. This 5' cap protects mRNA from degradation by exoribonucleases but also interacts specifically with several proteins and enzymes to ensure mRNA turnover and processing, like splicing, export from the nucleus to the cytoplasm, and initiation of translation. The absence of a 5' cap leads to a strong immune response, and the methylation status contributes to distinguishing self from non-self RNA.Non-natural modifications of the 5' cap provide an avenue to label mRNAs and make them accessible to analyses, which is important to study their cellular localization, trafficking, and binding partners. They bear potential to engineer mRNAs, e.g., more stable or immunogenic mRNAs that are still translated, by impacting select interactions in a distinct manner. The modification of the 5' cap itself is powerful as it can be applied to make long mRNAs (∼1000 nt, not directly accessible by solid-phase synthesis) by in vitro transcription.This Account describes our contribution to the field of chemo-enzymatic modification of mRNA at the 5' cap. Our approach relies on RNA methyltransferases (MTases) with promiscuous activity on analogues of their natural cosubstrate S-adenosyl-L-methionine (AdoMet). We will describe how RNA MTases in combination with non-natural cosubstrates provide access to site-specific modification of different positions of the 5' cap, namely, the N2 and N7 position of guanosine and the N6 position of adenosine as the transcription start nucleotide (TSN) and exemplify strategies to make long mRNAs with modified 5' caps.We will compare the chemical and enzymatic synthesis of the AdoMet analogues used for this purpose. We could overcome previous limitations in methionine adenosyltransferase (MAT) substrate scope by engineering variants (termed PC-MATs) with the ability to convert methionine analogues with benzylic and photocaging groups at the sulfonium ion.The final part of this Account will highlight applications of the modified mRNAs. Like in many chemo-enzymatic approaches, a versatile strategy is to install small functional groups enzymatically and use them as handles in subsequent bioorthogonal reactions. We showed fluorescent labeling of mRNAs via different types of click chemistry in vitro and in cells. In a second line of applications, we used the handles to make mRNAs amenable for analyses, most notably next-generation sequencing. In the case of extremely promiscuous enzymes, the direct installation of photo-cross-linking groups was successful also and provided a way to covalently bind protein-interaction partners. Finally, the non-natural modifications of mRNAs can also modulate the properties of mRNAs. Propargylation of Am as the transcription start nucleotide at its N6 position maintained the translation of mRNAs but increased their immunogenicity. The installation of photocaging groups provides a way to revert these effects and control interactions by light.
Collapse
Affiliation(s)
- Amarnath Bollu
- Department of Chemistry and Pharmacy, Institute of Biochemistry Westfälische Wilhelms-Universität Münster, University of Münster, Corrensstrasse 36, 48149 Münster, Germany
| | - Aileen Peters
- Department of Chemistry and Pharmacy, Institute of Biochemistry Westfälische Wilhelms-Universität Münster, University of Münster, Corrensstrasse 36, 48149 Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute of Biochemistry Westfälische Wilhelms-Universität Münster, University of Münster, Corrensstrasse 36, 48149 Münster, Germany
| |
Collapse
|
37
|
Anti-diabetic potential, crystal structure, molecular docking, DFT, and optical-electrochemical studies of new dimethyl and diethyl carbamoyl-N, N′-disubstituted based thioureas. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
38
|
Earley D, Guillou A, Klingler S, Fay R, Gut M, d’Orchymont F, Behmaneshfar S, Reichert L, Holland JP. Charting the Chemical and Mechanistic Scope of Light-Triggered Protein Ligation. JACS AU 2022; 2:646-664. [PMID: 35373206 PMCID: PMC8970001 DOI: 10.1021/jacsau.1c00530] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Indexed: 05/04/2023]
Abstract
The creation of discrete, covalent bonds between a protein and a functional molecule like a drug, fluorophore, or radiolabeled complex is essential for making state-of-the-art tools that find applications in basic science and clinical medicine. Photochemistry offers a unique set of reactive groups that hold potential for the synthesis of protein conjugates. Previous studies have demonstrated that photoactivatable desferrioxamine B (DFO) derivatives featuring a para-substituted aryl azide (ArN3) can be used to produce viable zirconium-89-radiolabeled monoclonal antibodies (89Zr-mAbs) for applications in noninvasive diagnostic positron emission tomography (PET) imaging of cancers. Here, we report on the synthesis, 89Zr-radiochemistry, and light-triggered photoradiosynthesis of 89Zr-labeled human serum albumin (HSA) using a series of 14 different photoactivatable DFO derivatives. The photoactive groups explore a range of substituted, and isomeric ArN3 reagents, as well as derivatives of benzophenone, a para-substituted trifluoromethyl phenyl diazirine, and a tetrazole species. For the compounds studied, efficient photochemical activation occurs inside the UVA-to-visible region of the electromagnetic spectrum (∼365-450 nm) and the photochemical reactions with HSA in water were complete within 15 min under ambient conditions. Under standardized experimental conditions, photoradiosynthesis with compounds 1-14 produced the corresponding 89ZrDFO-PEG3-HSA conjugates with decay-corrected isolated radiochemical yields between 18.1 ± 1.8% and 62.3 ± 3.6%. Extensive density functional theory (DFT) calculations were used to explore the reaction mechanisms and chemoselectivity of the light-induced bimolecular conjugation of compounds 1-14 to protein. The photoactivatable DFO-derivatives operate by at least five distinct mechanisms, each producing a different type of bioconjugate bond. Overall, the experimental and computational work presented here confirms that photochemistry is a viable option for making diverse, functionalized protein conjugates.
Collapse
|
39
|
Tavakoli A, Min JH. Photochemical modifications for DNA/RNA oligonucleotides. RSC Adv 2022; 12:6484-6507. [PMID: 35424630 PMCID: PMC8982246 DOI: 10.1039/d1ra05951c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022] Open
Abstract
Light-triggered chemical reactions can provide excellent tools to investigate the fundamental mechanisms important in biology. Light is easily applicable and orthogonal to most cellular events, and its dose and locality can be controlled in tissues and cells. Light-induced conversion of photochemical groups installed on small molecules, proteins, and oligonucleotides can alter their functional states and thus the ensuing biological events. Recently, photochemical control of DNA/RNA structure and function has garnered attention thanks to the rapidly expanding photochemistry used in diverse biological applications. Photoconvertible groups can be incorporated in the backbone, ribose, and nucleobase of an oligonucleotide to undergo various irreversible and reversible light-induced reactions such as cleavage, crosslinking, isomerization, and intramolecular cyclization reactions. In this review, we gather a list of photoconvertible groups used in oligonucleotides and summarize their reaction characteristics, impacts on DNA/RNA thermal stability and structure, as well as their biological applications.
Collapse
Affiliation(s)
- Amirrasoul Tavakoli
- Department of Chemistry & Biochemistry, Baylor University Waco TX 76706 USA +1-254-710-2095
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University Waco TX 76706 USA +1-254-710-2095
| |
Collapse
|
40
|
Moriyama T, Mizukami D, Yoritate M, Usui K, Takahashi D, Ota E, Sodeoka M, Ueda T, Karasawa S, Hirai G. Effect of Alkynyl Group on Reactivity in Photoaffinity Labeling with 2‐Thienyl‐Substituted α‐Ketoamide. Chemistry 2022; 28:e202103925. [DOI: 10.1002/chem.202103925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 11/07/2022]
Affiliation(s)
- Takahiro Moriyama
- Graduate School of Pharmaceutical Sciences Kyushu University Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Daiki Mizukami
- Graduate School of Pharmaceutical Sciences Kyushu University Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Makoto Yoritate
- Graduate School of Pharmaceutical Sciences Kyushu University Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Kazuteru Usui
- Graduate School of Pharmaceutical Sciences Kyushu University Maidashi Higashi-ku Fukuoka 812-8582 Japan
- Faculty of Pharmaceutical Sciences Showa Pharmaceutical University Higashi-Tamagawagakuen, Machida Tokyo 194-8543 Japan
| | - Daisuke Takahashi
- Graduate School of Pharmaceutical Sciences Kyushu University Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Eisuke Ota
- RIKEN Cluster for Pioneering Research 2-1, Hirosawa Wako Saitama 351-0198 Japan
| | - Mikiko Sodeoka
- RIKEN Cluster for Pioneering Research 2-1, Hirosawa Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa Wako Saitama 351-0198 Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences Kyushu University Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Satoru Karasawa
- Faculty of Pharmaceutical Sciences Showa Pharmaceutical University Higashi-Tamagawagakuen, Machida Tokyo 194-8543 Japan
| | - Go Hirai
- Graduate School of Pharmaceutical Sciences Kyushu University Maidashi Higashi-ku Fukuoka 812-8582 Japan
- RIKEN Cluster for Pioneering Research 2-1, Hirosawa Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa Wako Saitama 351-0198 Japan
| |
Collapse
|
41
|
Abstract
Hydrogels are important structural and operative components of microfluidic systems, finding diverse utility in biological sample preparation and interrogation. One inherent challenge for integrating hydrogels into microfluidic tools is thermodynamic molecular partitioning, which reduces the in-gel concentration of molecular solutes (e.g., biomolecular regents), as compared to the solute concentration in an applied solution. Consequently, biomolecular reagent access to in-gel scaffolded biological samples (e.g., encapsulated cells, microbial cultures, target analytes) is adversely impacted in hydrogels. Further, biomolecular reagents are typically introduced to the hydrogel via diffusion. This passive process requires long incubation periods compared to active biomolecular delivery techniques. Electrotransfer is an active technique used in Western blots and other gel-based immunoassays that overcomes limitations of size exclusion (increasing the total probe mass delivered into gel) and expedites probe delivery, even in millimeter-thick slab gels. While compatible with conventional slab gels, electrotransfer has not been adapted to thin gels (50-250 μm thick), which are of great interest as components of open microfluidic devices (vs enclosed microchannel-based devices). Mechanically delicate, thin gels are often mounted on rigid support substrates (glass, plastic) that are electrically insulating. Consequently, to adapt electrotransfer to thin-gel devices, we replace rigid insulating support substrates with novel, mechanically robust, yet electrically conductive nanoporous membranes. We describe grafting nanoporous membranes to thin-polyacrylamide-gel layers via silanization, characterize the electrical conductivity of silane-treated nanoporous membranes, and report the dependence of in-gel immunoprobe concentration on transfer duration for passive diffusion and active electrotransfer. Alternative microdevice component layers─including the mechanically robust, electrically conductive nanoporous membranes reported here─provide new functionality for integration into an increasing array of open microfluidic systems.
Collapse
Affiliation(s)
- Andoni P Mourdoukoutas
- The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, California 94720, United States
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| |
Collapse
|
42
|
Gu Y, Yin H, Wakeling M, An J, Martin R. Defunctionalization of sp3 C–Heteroatom and sp3 C–C Bonds Enabled by Photoexcited Triplet Ketone Catalysts. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05329] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yiting Gu
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Hongfei Yin
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Matthew Wakeling
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Juzeng An
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Ruben Martin
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain
- ICREA, Passeig Lluïs Companys, 23, 08010, Barcelona, Spain
| |
Collapse
|
43
|
Jaik TG, Ciubini B, Frascella F, Jonas U. Thermal Response and Thermochromism of Methyl Red-Based Copolymer Systems - Coupled Responsiveness in Critical Solution Behaviour and Optical Absorption Properties. Polym Chem 2022. [DOI: 10.1039/d1py01361k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Until now, only limited experimental knowledge and sparse theoretical treatment about the mechanisms of thermochromism of azo dyes in solution has been available. Especially the coupling of thermoresponsiveness of polymers...
Collapse
|
44
|
Michele A, Luft D, Tovar GEM, Southan A. Photo-crosslinking and surface-attachment of polyvinyl alcohol nanocoatings by C,H insertion to customize their swelling behavior and stability in polar media. Polym Chem 2022. [DOI: 10.1039/d2py00443g] [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
Benzophenone-modified polyvinyl alcohol is synthesized, processed to nanocoatings and converted to UV-crosslinked surface-bound polymer networks.
Collapse
Affiliation(s)
- Andre Michele
- Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Nobelstr. 12, 70569 Stuttgart, Germany
| | - Daniel Luft
- Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Nobelstr. 12, 70569 Stuttgart, Germany
| | - Günter E. M. Tovar
- Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Nobelstr. 12, 70569 Stuttgart, Germany
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Nobelstr. 12, 70569 Stuttgart, Germany
| | - Alexander Southan
- Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Nobelstr. 12, 70569 Stuttgart, Germany
| |
Collapse
|
45
|
Großkopf J, Plaza M, Seitz A, Breitenlechner S, Storch G, Bach T. Photochemical Deracemization at sp 3-Hybridized Carbon Centers via a Reversible Hydrogen Atom Transfer. J Am Chem Soc 2021; 143:21241-21245. [PMID: 34902253 DOI: 10.1021/jacs.1c11266] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A photochemical deracemization of 5-substituted 3-phenylimidazolidine-2,4-diones (hydantoins) is reported (27 examples, 69%-quant., 80-99% ee). The reaction is catalyzed by a chiral diarylketone which displays a two-point hydrogen bonding site. Mechanistic evidence (DFT calculations, radical clock experiments, H/D labeling) suggests the reaction to occur by selective hydrogen atom transfer (HAT). Upon hydrogen binding, one substrate enantiomer displays the hydrogen atom at the stereogenic center to the photoexcited catalyst allowing for a HAT from the substrate and eventually for its conversion into the product enantiomer. The product enantiomer is not processed by the catalyst and is thus enriched in the photostationary state.
Collapse
Affiliation(s)
- Johannes Großkopf
- School of Natural Sciences, Department Chemie, and Catalysis Research Center (CRC), Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Manuel Plaza
- School of Natural Sciences, Department Chemie, and Catalysis Research Center (CRC), Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Antonia Seitz
- School of Natural Sciences, Department Chemie, and Catalysis Research Center (CRC), Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Stefan Breitenlechner
- School of Natural Sciences, Department Chemie, and Catalysis Research Center (CRC), Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Golo Storch
- School of Natural Sciences, Department Chemie, and Catalysis Research Center (CRC), Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Thorsten Bach
- School of Natural Sciences, Department Chemie, and Catalysis Research Center (CRC), Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| |
Collapse
|
46
|
Fallon DJ, Lehmann S, Chung CW, Phillipou A, Eberl C, Fantom KGM, Zappacosta F, Patel VK, Bantscheff M, Schofield CJ, Tomkinson NCO, Bush JT. One-Step Synthesis of Photoaffinity Probes for Live-Cell MS-Based Proteomics. Chemistry 2021; 27:17880-17888. [PMID: 34328642 DOI: 10.1002/chem.202102036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 11/06/2022]
Abstract
We present a one-step Ugi reaction protocol for the expedient synthesis of photoaffinity probes for live-cell MS-based proteomics. The reaction couples an amine affinity function with commonly used photoreactive groups, and a variety of handle functionalities. Using this technology, a series of pan-BET (BET: bromodomain and extra-terminal domain) selective bromodomain photoaffinity probes were obtained by parallel synthesis. Studies on the effects of photoreactive group, linker length and irradiation wavelength on photocrosslinking efficiency provide valuable insights into photoaffinity probe design. Optimal probes were progressed to MS-based proteomics to capture the BET family of proteins from live cells and reveal their potential on- and off-target profiles.
Collapse
Affiliation(s)
- David J Fallon
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, Glasgow, G1 1XL, UK
| | - Stephanie Lehmann
- Cellzome GmbH, a GSK company, Meyerhofstraße 1, Heidelberg, 69117, Germany
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Alex Phillipou
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Christian Eberl
- Cellzome GmbH, a GSK company, Meyerhofstraße 1, Heidelberg, 69117, Germany
| | - Ken G M Fantom
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | | | | | - Marcus Bantscheff
- Cellzome GmbH, a GSK company, Meyerhofstraße 1, Heidelberg, 69117, Germany
| | | | - Nicholas C O Tomkinson
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, Glasgow, G1 1XL, UK
| | - Jacob T Bush
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| |
Collapse
|
47
|
Shuster A, Pechalrieu D, Jackson CB, Abegg D, Choe H, Adibekian A. Clinical Antiviral Drug Arbidol Inhibits Infection by SARS-CoV-2 and Variants through Direct Binding to the Spike Protein. ACS Chem Biol 2021; 16:2845-2851. [PMID: 34792325 PMCID: PMC8610013 DOI: 10.1021/acschembio.1c00756] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/09/2021] [Indexed: 12/24/2022]
Abstract
Arbidol (ARB) is a broad-spectrum antiviral drug approved in Russia and China for the treatment of influenza. ARB was tested in patients as a drug candidate for the treatment at the early onset of COVID-19 caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite promising clinical results and multiple ongoing trials, preclinical data are lacking and the molecular mechanism of action of ARB against SARS-CoV-2 remains unknown. Here, we demonstrate that ARB binds to the spike viral fusion glycoprotein of the SARS-CoV-2 Wuhan strain as well as its more virulent variants from the United Kingdom (strain B.1.1.7) and South Africa (strain B.1.351). We pinpoint the ARB binding site on the S protein to the S2 membrane fusion domain and use an infection assay with Moloney murine leukemia virus (MLV) pseudoviruses (PVs) pseudotyped with the S proteins of the Wuhan strain and the new variants to show that this interaction is sufficient for the viral cell entry inhibition by ARB. Finally, our experiments reveal that the ARB interaction leads to a significant destabilization and eventual lysosomal degradation of the S protein in cells. Collectively, our results identify ARB as the first clinically approved small molecule drug binder of the SARS-CoV-2 S protein and place ARB among the more promising drug candidates for COVID-19.
Collapse
Affiliation(s)
- Anton Shuster
- Department of Chemistry, The Scripps
Research Institute, 130 Scripps Way, Jupiter, Florida 33458,
United States
| | - Dany Pechalrieu
- Department of Chemistry, The Scripps
Research Institute, 130 Scripps Way, Jupiter, Florida 33458,
United States
| | - Cody B Jackson
- Department of Immunology and Microbiology,
The Scripps Research Institute, 130 Scripps Way, Jupiter,
Florida 33458, United States
| | - Daniel Abegg
- Department of Chemistry, The Scripps
Research Institute, 130 Scripps Way, Jupiter, Florida 33458,
United States
| | - Hyeryun Choe
- Department of Immunology and Microbiology,
The Scripps Research Institute, 130 Scripps Way, Jupiter,
Florida 33458, United States
| | - Alexander Adibekian
- Department of Chemistry, The Scripps
Research Institute, 130 Scripps Way, Jupiter, Florida 33458,
United States
| |
Collapse
|
48
|
Abstract
Photochemical reactions are increasingly being used for chemical and materials synthesis, for example, in photoredox catalysis, and generally involve photoexcitation of molecular chromophores dissolved in a liquid solvent. The choice of solvent influences the outcomes of the photochemistry because solute-solvent interactions modify the energies of and crossings between electronic states of the chromophores, and they affect the evolving structures of the photoexcited molecules. Ultrafast laser spectroscopy methods with femtosecond to picosecond time resolution can resolve the dynamics of these photoexcited molecules as they undergo structural and electronic changes, relax back to the ground state, dissipate their excess internal energy to the surrounding solvent, or undergo photochemical reactions. In this Account, we illustrate how experimental studies using ultrafast lasers can reveal the influences that different solvents or cosolutes exert on the photoinduced nonadiabatic dynamics of internal conversion and intersystem crossing in nonradiative relaxation pathways. Although the environment surrounding a solute molecule is rapidly changing, with fluctuations in the coordination to neighboring solvent molecules occurring on femtosecond or picosecond time scales, we show that it is possible to photoexcite selectively only those molecular chromophores transiently experiencing specific solute-solvent interactions such as intermolecular hydrogen bonding.The effects of different solvation environments on the photodynamics are illustrated using four selected examples of photochemical processes in which the solvent has a marked effect on the outcomes. We first consider two aromatic carbonyl compounds, benzophenone and acetophenone, which are known to undergo fast intersystem crossing to populate the first excited triplet state on time scales of a few picoseconds. We show that the nonadiabatic excited-state dynamics are modified by transient hydrogen bonding of the carbonyl group to a protic solvent or by coordination to a metal cation cosolute. We then examine how different solvents modify the competition between two alternative relaxation pathways in a photoexcited UVA-sunscreen molecule, diethylamino hydroxybenzoyl hexyl benzoate (DHHB). This relaxation back to the ground electronic state is an essential part of the effective operation of the sunscreen compound, but the dynamics are sensitive to the surrounding environment. Finally, we consider how solvents of different polarity affect the energies and lifetimes of excited states with locally excited or charge-transfer character in heterocyclic organic compounds used as excited-state electron donors for photoredox catalysis. With these and other examples, we seek to develop a molecular level understanding of how the choice of solution environment might be used to control the outcomes of photochemical reactions.
Collapse
Affiliation(s)
- Ravi Kumar Venkatraman
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Andrew J. Orr-Ewing
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| |
Collapse
|
49
|
Zhang QL, Yu QQ, Ma L, Lu X, Fan QT, Duan TS, Zhou Y, Zhang FL. A Metal-Free Visible-Light Photoredox Construction and Direct C-H Functionalization of Pyridines: Green Synthesis of Polysubstituted Picolinaldehydes. J Org Chem 2021; 86:17244-17248. [PMID: 34807586 DOI: 10.1021/acs.joc.1c02312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The development of a novel environmental benign and sustainable synthetic method for highly efficient construction and direct C-H functionalization of N-heterocycles remains a pivotal central research topic for organic and medicinal chemistry. Herein, a novel visible-light-enabled biomimetic aza-6π electrocyclization for efficient assembly of diverse pyridines and further tandem Minisci-type reaction were developed. A broad spectrum of polysubstituted picolinaldehydes were readily constructed with high efficacy and good functional group tolerance under metal- and oxidant-free conditions.
Collapse
Affiliation(s)
- Qun-Liang Zhang
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China.,Shenzhen Research Institute, Wuhan University of Technology, Shenzhen, Guangdong 518057, China
| | - Qin-Qin Yu
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Li Ma
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Xuelian Lu
- Shenzhen Research Institute, Wuhan University of Technology, Shenzhen, Guangdong 518057, China
| | - Qing-Tian Fan
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Tian-Shun Duan
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Yirong Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, China
| | - Fang-Lin Zhang
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China.,Shenzhen Research Institute, Wuhan University of Technology, Shenzhen, Guangdong 518057, China
| |
Collapse
|
50
|
Abstract
Colicins are protein antibiotics deployed by Escherichia coli to eliminate competing strains. Colicins frequently exploit outer membrane (OM) nutrient transporters to penetrate the selectively permeable bacterial cell envelope. Here, by applying live-cell fluorescence imaging, we were able to monitor the entry of the pore-forming toxin colicin B (ColB) into E. coli and localize it within the periplasm. We further demonstrate that single-stranded DNA coupled to ColB can also be transported to the periplasm, emphasizing that the import routes of colicins can be exploited to carry large cargo molecules into bacteria. Moreover, we characterize the molecular mechanism of ColB association with its OM receptor FepA by applying a combination of photoactivated cross-linking, mass spectrometry, and structural modeling. We demonstrate that complex formation is coincident with large-scale conformational changes in the colicin. Thereafter, active transport of ColB through FepA involves the colicin taking the place of the N-terminal half of the plug domain that normally occludes this iron transporter. IMPORTANCE Decades of excessive use of readily available antibiotics has generated a global problem of antibiotic resistance and, hence, an urgent need for novel antibiotic solutions. Bacteriocins are protein-based antibiotics produced by bacteria to eliminate closely related competing bacterial strains. Bacteriocin toxins have evolved to bypass the complex cell envelope in order to kill bacterial cells. Here, we uncover the cellular penetration mechanism of a well-known but poorly understood bacteriocin called colicin B that is active against Escherichia coli. Moreover, we demonstrate that the colicin B-import pathway can be exploited to deliver conjugated DNA cargo into bacterial cells. Our work leads to a better understanding of the way bacteriocins, as potential alternative antibiotics, execute their mode of action as well as highlighting how they might even be exploited in the genomic manipulation of Gram-negative bacteria.
Collapse
|