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Weissenboeck F, Klöcker N, Špaček P, Hüwel S, Rentmeister A. Stabilized 5' Cap Analogue for Optochemical Activation of mRNA Translation. ACS Omega 2024; 9:12810-12816. [PMID: 38524462 PMCID: PMC10955689 DOI: 10.1021/acsomega.3c08505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/02/2024] [Accepted: 01/19/2024] [Indexed: 03/26/2024]
Abstract
The 5' cap is a distinguishing feature of transcripts made by polymerase II and characterized by an N7-methylated guanosine (m7G) linked to the first transcribed nucleotide by a 5'-5' triphosphate bridge. It stabilizes eukaryotic mRNAs and plays a crucial role in translation initiation. Its importance in mRNA processing, translation, and turnover makes the 5' cap a privileged structure for engineering by non-natural modifications. A photocleavable group at the 5' cap of guanosine was recently used to mute translation of exogenous mRNAs. Its removal by light enabled direct control of protein production at the posttranscriptional level. Modifications in the triphosphate bridge impede degradation by specific decapping enzymes and maintain translation. Here, we combined 5' cap modifications at different positions and investigated how they impact 5' cap-dependent processes in distinct manners. We synthesized 5' cap analogues with a photocleavable group at the N2-position of m7G in addition to a medronate in the triphosphate bridge to obtain a photoactivatable 5' cap analogue featuring a methylene group between the β and γ phosphates. The resulting Medronate-FlashCap transiently or permanently impeded distinct crucial interactions of the 5' cap required for translation and degradation. We show that the Medronate-FlashCap is compatible with in vitro transcription to generate muted mRNA and that light can be used to activate translation in cells. After light-induced removal of the photocleavable group, the Medronate-FlashCap remained stable against degradation by the decapping enzyme DcpS. The additional methylene group renders the 5' cap resistant to DcpS, while maintaining the interaction with cap-binding proteins.
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Affiliation(s)
| | - Nils Klöcker
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| | - Petr Špaček
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Münster 48149, Germany
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2
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Bollu A, Schepers H, Klöcker N, Erguven M, Lawrence-Dörner AM, Rentmeister A. Visible Light Activates Coumarin-Caged mRNA for Cytoplasmic Cap Methylation in Cells. Chemistry 2024; 30:e202303174. [PMID: 37883670 DOI: 10.1002/chem.202303174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023]
Abstract
Protein synthesis is important and regulated by various mechanisms in the cell. Translation initiation in eukaryotes starts at the 5' cap and is the most complex of the three phases of mRNA translation. It requires methylation of the N7 position of the terminal guanosine (m7 G). The canonical capping occurs in the nucleus, however, cytoplasmic recapping has been discovered. It functions in switching mRNAs between translating and non-translating states, but the individual steps are difficult to dissect. We targeted cytoplasmic cap methylation as the ultimate step of cytoplasmic recapping. We present an N7G photocaged 5' cap that can be activated for cytoplasmic methylation by visible light. We report chemical and chemo-enzymatic synthesis of this 5' cap with 7-(diethylamino)-4-methyl-coumarin (DEACM) at the N7G and validate that it is not bound by translation initiation factor 4E (eIF4E). We demonstrate incorporation into mRNA, the release of unmethylated cap analog and enzymatic remethylation to functional cap 0 after irradiation at 450 nm. In cells, irradiation triggers translation of mRNAs with the N7G photocaged 5' cap via cytoplasmic cap methylation.
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Affiliation(s)
- Amarnath Bollu
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Helena Schepers
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Mehmet Erguven
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
- Cells in Motion Interfaculty Centre, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
| | - Ann-Marie Lawrence-Dörner
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany
- Cells in Motion Interfaculty Centre, University of Münster, Waldeyerstraße 15, 48149, Münster, Germany
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3
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Wang J, Peled TS, Klajn R. Photocleavable Anionic Glues for Light-Responsive Nanoparticle Aggregates. J Am Chem Soc 2023; 145:4098-4108. [PMID: 36757850 PMCID: PMC9951211 DOI: 10.1021/jacs.2c11973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Indexed: 02/10/2023]
Abstract
Integrating light-sensitive molecules within nanoparticle (NP) assemblies is an attractive approach to fabricate new photoresponsive nanomaterials. Here, we describe the concept of photocleavable anionic glue (PAG): small trianions capable of mediating interactions between (and inducing the aggregation of) cationic NPs by means of electrostatic interactions. Exposure to light converts PAGs into dianionic products incapable of maintaining the NPs in an assembled state, resulting in light-triggered disassembly of NP aggregates. To demonstrate the proof-of-concept, we work with an organic PAG incorporating the UV-cleavable o-nitrobenzyl moiety and an inorganic PAG, the photosensitive trioxalatocobaltate(III) complex, which absorbs light across the entire visible spectrum. Both PAGs were used to prepare either amorphous NP assemblies or regular superlattices with a long-range NP order. These NP aggregates disassembled rapidly upon light exposure for a specific time, which could be tuned by the incident light wavelength or the amount of PAG used. Selective excitation of the inorganic PAG in a system combining the two PAGs results in a photodecomposition product that deactivates the organic PAG, enabling nontrivial disassembly profiles under a single type of external stimulus.
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Affiliation(s)
- Jinhua Wang
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tzuf Shay Peled
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rafal Klajn
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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4
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Li Z, Liu N, Yang W, Tu J, Huang Y, Wang W, Sheng C. Controlling antifungal activity with light: Optical regulation of fungal ergosterol biosynthetic pathway with photo-responsive CYP51 inhibitors. Acta Pharm Sin B 2023. [PMID: 37521860 PMCID: PMC10372832 DOI: 10.1016/j.apsb.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Invasive fungal infections (IFIs) have been associated with high mortality, highlighting the urgent need for developing novel antifungal strategies. Herein the first light-responsive antifungal agents were designed by optical control of fungal ergosterol biosynthesis pathway with photocaged triazole lanosterol 14α-demethylase (CYP51) inhibitors. The photocaged triazoles completely shielded the CYP51 inhibition. The content of ergosterol in fungi before photoactivation and after photoactivation was 4.4% and 83.7%, respectively. Importantly, the shielded antifungal activity (MIC80 ≥ 64 μg/mL) could be efficiently recovered (MIC80 = 0.5-8 μg/mL) by light irradiation. The new chemical tools enable optical control of fungal growth arrest, morphological conversion and biofilm formation. The ability for high-precision antifungal treatment was validated by in vivo models. The light-activated compound A1 was comparable to fluconazole in prolonging survival in Galleria mellonella larvae with a median survival of 14 days and reducing fungal burden in the mouse skin infection model. Overall, this study paves the way for precise regulation of antifungal therapy with improved efficacy and safety.
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5
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Bollu A, Klöcker N, Špaček P, P Weissenboeck F, Hüwel S, Rentmeister A. Light-Activated Translation of Different mRNAs in Cells via Wavelength-Dependent Photouncaging. Angew Chem Int Ed Engl 2023; 62:e202209975. [PMID: 36417319 PMCID: PMC10107135 DOI: 10.1002/anie.202209975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 11/24/2022]
Abstract
The 5' cap is a hallmark of eukaryotic mRNA involved in the initiation of translation. Its modification with a single photo-cleavable group can bring translation of mRNA under the control of light. However, UV irradiation causes cell stress and downregulation of translation. Furthermore, complex processes often involve timed expression of more than one gene. The approach would thus greatly benefit from the ability to photo-cleave by blue light and to control more than one mRNA at a time. We report the synthesis of a 5' cap modified with a 7-(diethylamino)coumarin (CouCap) and adapted conditions for in vitro transcription. Translation of the resulting CouCap-mRNA is muted in vitro and in mammalian cells, and can be initiated by irradiation with 450 nm. The native cap is restored and no non-natural residues nor sequence alterations remain in the mRNA. Multiplexing for two different mRNAs was achieved by combining cap analogs with coumarin- and ortho-nitrobenzyl-based photo-cleavable groups.
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Affiliation(s)
- Amarnath Bollu
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Petr Špaček
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Florian P Weissenboeck
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Sabine Hüwel
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
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6
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Klöcker N, Anhäuser L, Rentmeister A. Enzymatic Modification of the 5' Cap with Photocleavable ONB-Derivatives Using GlaTgs V34A. Chembiochem 2023; 24:e202200522. [PMID: 36408753 PMCID: PMC10108117 DOI: 10.1002/cbic.202200522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/22/2022]
Abstract
The 5' cap of mRNA plays a critical role in mRNA processing, quality control and turnover. Enzymatic availability of the 5' cap governs translation and could be a tool to investigate cell fate decisions and protein functions or develop protein replacement therapies. We have previously reported on the chemical synthesis of 5' cap analogues with photocleavable groups for this purpose. However, the synthesis is complex and post-synthetic enzymatic installation may make the technique more applicable to biological researchers. Common 5' cap analogues, like the cap 0, are commercially available and routinely used for in vitro transcription. Here, we report a facile enzymatic approach to attach photocleavable groups site-specifically to the N2 position of m7 G of the 5' cap. By expanding the substrate scope of the methyltransferase variant GlaTgs V34A and using synthetic co-substrate analogues, we could enzymatically photocage the 5' cap and recover it after irradiation.
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Affiliation(s)
- Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
| | - Lea Anhäuser
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
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7
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Chen L, Liu Y, Guo W, Liu Z. Light responsive nucleic acid for biomedical application. Exploration 2022; 2:20210099. [PMCID: PMC10190984 DOI: 10.1002/exp.20210099] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/03/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Liwei Chen
- Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Central South University Changsha Hunan Province P. R. China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Central South University Changsha Hunan Province P. R. China
| | - Weisheng Guo
- Department of Minimally Invasive Interventional Radiology Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & The Second Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong Province P. R. China
| | - Zhenbao Liu
- Department of Pharmaceutics Xiangya School of Pharmaceutical Sciences Central South University Changsha Hunan Province P. R. China
- Molecular Imaging Research Center of Central South University Changsha Hunan Province P. R. China
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8
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Rösner L, Reichert D, Rau K, Muthmann N, Rentmeister A. Sequence-specific targeting of RNA. Methods 2022; 205:73-82. [PMID: 35764247 DOI: 10.1016/j.ymeth.2022.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/10/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Post-transcriptional modifications play an important role in several processes, including translation, splicing, and RNA degradation in eukaryotic cells. To investigate the function of specific modifications it is of high interest to develop tools for sequence-specific RNA-targeting. This work focuses on two abundant modifications of eukaryotic mRNA, namely methylation of the guanine-N7 position of the 5'-cap and internal N6-methyladenosine (m6A). We describe the sequence-specific targeting of model RNA transcripts via RNA-binding proteins, such as nuclease-deficient RNA-targeting Cas9 (RCas9) and the Pumilio homology domain (PumHD) fused to two different effector enzymes, the dioxygenase FTO and the guanine-N7 methyltransferase Ecm1. With this tool, we were able to install and remove the methylation at the respective positions with high specificity.
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Affiliation(s)
- Lukas Rösner
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Dennis Reichert
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Kristina Rau
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Nils Muthmann
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Andrea Rentmeister
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, 48149 Münster, Germany
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9
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Klöcker N, Weissenboeck FP, van Dülmen M, Špaček P, Hüwel S, Rentmeister A. Photocaged 5' cap analogues for optical control of mRNA translation in cells. Nat Chem 2022. [PMID: 35725774 DOI: 10.1038/s41557-022-00972-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/11/2022] [Indexed: 11/08/2022]
Abstract
The translation of messenger RNA (mRNA) is a fundamental process in gene expression, and control of translation is important to regulate protein synthesis in cells. The primary hallmark of eukaryotic mRNAs is their 5′ cap, whose molecular contacts to the eukaryotic translation initiation factor eIF4E govern the initiation of translation. Here we report 5′ cap analogues with photo-cleavable groups (FlashCaps) that prohibit binding to eIF4E and resist cleavage by decapping enzymes. These compounds are compatible with the general and efficient production of mRNAs by in vitro transcription. In FlashCap-mRNAs, the single photocaging group abrogates translation in vitro and in mammalian cells without increasing immunogenicity. Irradiation restores the native cap, triggering efficient translation. FlashCaps overcome the problem of remaining sequence or structure changes in mRNA after irradiation that limited previous designs. Together, these results demonstrate that FlashCaps offer a route to regulate the expression of any given mRNA and to dose mRNA therapeutics with spatio-temporal control. ![]()
Analogues of mRNA 5′ caps containing a photo-cleavable group have now been developed. These so-called FlashCaps can be used for routine in vitro transcription to make long mRNAs containing a cap. In cells, the capped mRNAs are translationally muted; however, upon irradiation by light, the photo-cleavable group is removed without leaving any remaining modification and mRNA is then translated into the corresponding protein.
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10
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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.
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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
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11
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Rudenko AY, Mariasina SS, Sergiev PV, Polshakov VI. Analogs of S-Adenosyl-L-Methionine in Studies of Methyltransferases. Mol Biol 2022; 56:229-250. [PMID: 35440827 PMCID: PMC9009987 DOI: 10.1134/s002689332202011x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 01/02/2023]
Abstract
Methyltransferases (MTases) play an important role in the functioning of living systems, catalyzing the methylation reactions of DNA, RNA, proteins, and small molecules, including endogenous compounds and drugs. Many human diseases are associated with disturbances in the functioning of these enzymes; therefore, the study of MTases is an urgent and important task. Most MTases use the cofactor S‑adenosyl‑L‑methionine (SAM) as a methyl group donor. SAM analogs are widely applicable in the study of MTases: they are used in studies of the catalytic activity of these enzymes, in identification of substrates of new MTases, and for modification of the substrates or substrate linking to MTases. In this review, new synthetic analogs of SAM and the problems that can be solved with their usage are discussed.
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Affiliation(s)
- A. Yu. Rudenko
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
- Zelinsky Institute of Organic Chemistry, 119991 Moscow, Russia
| | - S. S. Mariasina
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
- Institute of Functional Genomics, Moscow State University, 119991 Moscow, Russia
| | - P. V. Sergiev
- Institute of Functional Genomics, Moscow State University, 119991 Moscow, Russia
| | - V. I. Polshakov
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
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12
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Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
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Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
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13
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Abdellaoui C, Hermanns V, Reinfelds M, Scheurer M, Dreuw A, Heckel A, Wachtveitl J. A long-lived fluorenyl cation: efficiency booster for uncaging and photobase properties. Phys Chem Chem Phys 2022; 24:5294-5300. [PMID: 35174833 DOI: 10.1039/d1cp05292f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photochemistry of fluorenols has been of special interest for many years. This is because both the fluorenol and the fluorenyl cation are antiaromatic in the ground state due to their 4n π-electrons according to the Hückel rule. The photolysis reaction of various fluorene derivatives takes place via a cation intermediate and is preferred due to its excited state aromaticity. Here we present an extremely long-lived fluorenyl cation and its effects on the uncaging of various leaving groups. We analyze the relationship between uncaging quantum yields of fluorene-based cages and the longevity of their fluorenyl cations with different spectroscopic methods in the steady state and on an ultrafast time scale and find that the uncaging quantum yield rises with the stability of the cation. In contrast to previous reports, the cation can be observed on a time scale of minutes, even in moderately protic solvents as methanol and ethanol. The stability of this cation depends on the dimethylamino-substituents on the fluorene scaffold and the properties of the solvent. In addition, with bis-dimethylamino fluorenol, a photobase is introduced that expands the small group of known photoinduced hydroxide emitters.
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Affiliation(s)
- Chahinez Abdellaoui
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany.
| | - Volker Hermanns
- Institute of Organic Chemistry, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany.
| | - Matiss Reinfelds
- Institute of Organic Chemistry, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany. .,Institute of Chemistry and Technology of Materials (ICTM), NAWI Graz, Graz University of Technology, Graz 8010, Austria.
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg 69120, Germany.
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg 69120, Germany.
| | - Alexander Heckel
- Institute of Organic Chemistry, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany.
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt am Main 60438, Germany.
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14
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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15
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Blümler A, Schwalbe H, Heckel A. Solid‐Phase‐Supported Chemoenzymatic Synthesis of a Light‐Activatable tRNA Derivative. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Anja Blümler
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance BMRZ Goethe University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt am Main Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
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16
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Blümler A, Schwalbe H, Heckel A. Solid-Phase-Supported Chemoenzymatic Synthesis of a Light-Activatable tRNA Derivative. Angew Chem Int Ed Engl 2021; 61:e202111613. [PMID: 34738704 PMCID: PMC9299214 DOI: 10.1002/anie.202111613] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 12/14/2022]
Abstract
Herein, we present a multi‐cycle chemoenzymatic synthesis of modified RNA with simplified solid‐phase handling to overcome size limitations of RNA synthesis. It combines the advantages of classical chemical solid‐phase synthesis and enzymatic synthesis using magnetic streptavidin beads and biotinylated RNA. Successful introduction of light‐controllable RNA nucleotides into the tRNAMet sequence was confirmed by gel electrophoresis and mass spectrometry. The methods tolerate modifications in the RNA phosphodiester backbone and allow introductions of photocaged and photoswitchable nucleotides as well as photocleavable strand breaks and fluorophores.
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Affiliation(s)
- Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany.,Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance BMRZ, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
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17
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Reichert D, Schepers H, Simke J, Lechner H, Dörner W, Höcker B, Ravoo BJ, Rentmeister A. Computational design and experimental characterization of a photo-controlled mRNA-cap guanine-N7 methyltransferase. RSC Chem Biol 2021; 2:1484-1490. [PMID: 34704053 PMCID: PMC8495969 DOI: 10.1039/d1cb00109d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/25/2021] [Indexed: 11/21/2022] Open
Abstract
The spatial and temporal control of gene expression at the post-transcriptional level is essential in eukaryotic cells and developing multicellular organisms. In recent years optochemical and optogenetic tools have enabled the manipulation and investigation of many steps in the involved processes. However, examples for light-mediated control of eukaryotic mRNA processing and the responsible enzymes are still rare. In particular, methylation of the 5′ cap of mRNA is required for ribosome assembly, and the responsible guanine-N7 methyltransferase (MTase) from E. cuniculi (Ecm1) proved suitable for activating translation. Here, we report on a photoswitchable MTase obtained by bridging the substrate-binding cleft of Ecm1 with a tetra-ortho-methoxy-azobenzene. This azobenzene derivative is characterized by efficient trans-to-cis isomerization using red light at 615 nm. Starting from a cysteine-free Ecm1 variant (ΔCys), we used a computational approach to identify suitable conjugation sites for the azobenzene moiety. We created and characterized the four best-ranked variants, each featuring two appropriately positioned cysteines close to the substrate-binding cleft. Conjugating and crosslinking the azobenzene between C149/C155 in a designed Ecm1 variant (VAR3-Az) enabled light-dependent modulation of the MTase activity and showed a 50% higher activity for the cis form than the trans-form of the azobenzene conjugated to VAR3-Az. Guided by computational design, we engineered a light-dependent 5' cap guanine-N7 methyltransferase by bridging the substrate-binding cleft with an azobenzene derivative.![]()
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Affiliation(s)
- Dennis Reichert
- Institute of Biochemistry, University of Münster, Correnstraße 36 Münster 48149 Germany .,Cells in Motion Interfaculty Center, University of Münster Münster 48149 Germany
| | - Helena Schepers
- Institute of Biochemistry, University of Münster, Correnstraße 36 Münster 48149 Germany
| | - Julian Simke
- Organic Chemistry Institute, University of Münster, Corrensstraße 36 Münster 48149 Germany
| | - Horst Lechner
- Department for Biochemistry, University of Bayreuth, Universitätsstraße 30 Bayreuth 95447 Germany.,Institute of Biochemistry, Graz University of Technology, Petersgasse 10-12/II Graz 8010 Austria
| | - Wolfgang Dörner
- Institute of Biochemistry, University of Münster, Correnstraße 36 Münster 48149 Germany
| | - Birte Höcker
- Department for Biochemistry, University of Bayreuth, Universitätsstraße 30 Bayreuth 95447 Germany
| | - Bart Jan Ravoo
- Cells in Motion Interfaculty Center, University of Münster Münster 48149 Germany.,Organic Chemistry Institute, University of Münster, Corrensstraße 36 Münster 48149 Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Correnstraße 36 Münster 48149 Germany .,Cells in Motion Interfaculty Center, University of Münster Münster 48149 Germany
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18
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Peters A, Herrmann E, Cornelissen NV, Klöcker N, Kümmel D, Rentmeister A. Visible-Light Removable Photocaging Groups Accepted by MjMAT Variant: Structural Basis and Compatibility with DNA and RNA Methyltransferases. Chembiochem 2021; 23:e202100437. [PMID: 34606675 PMCID: PMC9298006 DOI: 10.1002/cbic.202100437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/01/2021] [Indexed: 12/20/2022]
Abstract
Methylation and demethylation of DNA, RNA and proteins constitutes a major regulatory mechanism in epigenetic processes. Investigations would benefit from the ability to install photo‐cleavable groups at methyltransferase target sites that block interactions with reader proteins until removed by non‐damaging light in the visible spectrum. Engineered methionine adenosyltransferases (MATs) have been exploited in cascade reactions with methyltransferases (MTases) to modify biomolecules with non‐natural groups, including first evidence for accepting photo‐cleavable groups. We show that an engineered MAT from Methanocaldococcus jannaschii (PC‐MjMAT) is 308‐fold more efficient at converting ortho‐nitrobenzyl‐(ONB)‐homocysteine than the wildtype enzyme. PC‐MjMAT is active over a broad range of temperatures and compatible with MTases from mesophilic organisms. We solved the crystal structures of wildtype and PC‐MjMAT in complex with AdoONB and a red‐shifted derivative thereof. These structures reveal that aromatic stacking interactions within the ligands are key to accommodating the photocaging groups in PC‐MjMAT. The enlargement of the binding pocket eliminates steric clashes to enable AdoMet analogue binding. Importantly, PC‐MjMAT exhibits remarkable activity on methionine analogues with red‐shifted ONB‐derivatives enabling photo‐deprotection of modified DNA by visible light.
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Affiliation(s)
- Aileen Peters
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Eric Herrmann
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Nils Klöcker
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
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19
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Abstract
Conditionally activated ("caged") oligonucleotides provide useful spatiotemporal control for studying dynamic biological processes, e.g., regulating in vivo gene expression or probing specific oligonucleotide targets. This review summarizes recent advances in caging strategies, which involve different stimuli in the activation step. Oligo cyclization is a particularly attractive caging strategy, which simplifies the probe design and affords oligo stabilization. Our laboratory developed an efficient synthesis for circular caged oligos, and a circular caged antisense DNA oligo was successfully applied in gene regulation. A second technology is Transcriptome In Vivo Analysis (TIVA), where caged oligos enable mRNA isolation from single cells in living tissue. We highlight our development of TIVA probes with improved caging stability. Finally, we illustrate the first protease-activated oligo probe, which was designed for caspase-3. This expands the toolkit for investigating the transcriptome under a specific physiologic condition (e.g., apoptosis), particularly in specimens where light activation is impractical.
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Affiliation(s)
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA;
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20
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Abstract
Gene expression is tightly regulated in all domains of life, with post-transcriptional regulation being more pronounced in higher eukaryotes. Optochemical and optogenetic approaches enable the actuation of many underlying processes by light, which is an excellent tool to exert spatio-temporal control. However, light-mediated control of eukaryotic mRNA processing and the respective enzymes has not been reported. We used genetic code expansion to install a photo-caged tyrosine (Y) in the active site of the cap methyltransferase Ecm1. This enzyme is responsible for guanine N7 methylation of the 5′ cap, which is required for translation. Substituting Y284 with the photocaged ortho-nitrobenzyl-tyrosine (ONBY) almost completely abrogated the methylation activity of Ecm1. Irradiation with light removed the ONB group, restoring the native tyrosine and Ecm1 activity, yielding up to 97% conversion of the minimal substrate GpppA within 60 min after activation. Using luciferase- and eGFP-mRNAs as reporters, we could show that light actuates translation by inducing activation of Ecm1 ONBY284 in a eukaryotic in vitro translation system. A tyrosine in the active site of the 5′ cap methyltransferase Ecm1 was photocaged. Translation of mRNA could be triggered by light in eukaryotic cell lysate.![]()
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Affiliation(s)
- Dennis Reichert
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany .,Cells in Motion Interfaculty Center, University of Münster 48149 Münster Germany
| | - Henning D Mootz
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany .,Cells in Motion Interfaculty Center, University of Münster 48149 Münster Germany
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21
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Michailidou F, Rentmeister A. Harnessing methylation and AdoMet-utilising enzymes for selective modification in cascade reactions. Org Biomol Chem 2021; 19:3756-3762. [PMID: 33949607 DOI: 10.1039/d1ob00354b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Enzyme-mediated methylation is a very important reaction in nature, yielding a wide range of modified natural products, diversifying small molecules and fine-tuning the activity of biomacromolecules. The field has attracted much attention over the recent years and interesting applications of the dedicated enzymes in biocatalysis and biomolecular labelling have emerged. In this review article, we summarise the concepts and recent advances in developing (chemo)-enzymatic cascades for selective methylation, alkylation and photocaging as tools to study biological methylation and as biotransformations to generate site-specifically alkylated products.
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Affiliation(s)
- Freideriki Michailidou
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 481\49 Münster, Germany.
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 481\49 Münster, Germany.
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22
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Bollu A, Sharma NK. Biased photo cleavage of N-/N-nitrobenzyl from 2’-hydroxyethyl-adenosine and their DNA/RNA Caged-analogues. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.112864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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Cannalire R, Pelliccia S, Sancineto L, Novellino E, Tron GC, Giustiniano M. Visible light photocatalysis in the late-stage functionalization of pharmaceutically relevant compounds. Chem Soc Rev 2020; 50:766-897. [PMID: 33350402 DOI: 10.1039/d0cs00493f] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The late stage functionalization (LSF) of complex biorelevant compounds is a powerful tool to speed up the identification of structure-activity relationships (SARs) and to optimize ADME profiles. To this end, visible-light photocatalysis offers unique opportunities to achieve smooth and clean functionalization of drugs by unlocking site-specific reactivities under generally mild reaction conditions. This review offers a critical assessment of current literature, pointing out the recent developments in the field while emphasizing the expected future progress and potential applications. Along with paragraphs discussing the visible-light photocatalytic synthetic protocols so far available for LSF of drugs and drug candidates, useful and readily accessible synoptic tables of such transformations, divided by functional groups, will be provided, thus enabling a useful, fast, and easy reference to them.
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Affiliation(s)
- Rolando Cannalire
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Napoli, Italy.
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24
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Michailidou F, Klöcker N, Cornelissen NV, Singh RK, Peters A, Ovcharenko A, Kümmel D, Rentmeister A. Maßgeschneiderte SAM‐Synthetasen zur enzymatischen Herstellung von AdoMet‐Analoga mit Photoschutzgruppen und zur reversiblen DNA‐Modifizierung in Kaskadenreaktionen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Freideriki Michailidou
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
- Derzeitige Adresse: ETH Zürich Fachbereich Chemie und angewandte Biowissenschaften Laboratorium für Organische Chemie Vladimir-Prelog-Weg 1–5/10 8093 Zürich Schweiz
| | - Nils Klöcker
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Nicolas V. Cornelissen
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Rohit K. Singh
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Aileen Peters
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Anna Ovcharenko
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Daniel Kümmel
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
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25
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Michailidou F, Klöcker N, Cornelissen NV, Singh RK, Peters A, Ovcharenko A, Kümmel D, Rentmeister A. Engineered SAM Synthetases for Enzymatic Generation of AdoMet Analogs with Photocaging Groups and Reversible DNA Modification in Cascade Reactions. Angew Chem Int Ed Engl 2020; 60:480-485. [PMID: 33017502 PMCID: PMC7839696 DOI: 10.1002/anie.202012623] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Indexed: 12/17/2022]
Abstract
Methylation and demethylation of DNA, RNA and proteins has emerged as a major regulatory mechanism. Studying the function of these modifications would benefit from tools for their site‐specific inhibition and timed removal. S‐Adenosyl‐L‐methionine (AdoMet) analogs in combination with methyltransferases (MTases) have proven useful to map or block and release MTase target sites, however their enzymatic generation has been limited to aliphatic groups at the sulfur atom. We engineered a SAM synthetase from Cryptosporidium hominis (PC‐ChMAT) for efficient generation of AdoMet analogs with photocaging groups that are not accepted by any WT MAT reported to date. The crystal structure of PC‐ChMAT at 1.87 Å revealed how the photocaged AdoMet analog is accommodated and guided engineering of a thermostable MAT from Methanocaldococcus jannaschii. PC‐MATs were compatible with DNA‐ and RNA‐MTases, enabling sequence‐specific modification (“writing”) of plasmid DNA and light‐triggered removal (“erasing”).
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Affiliation(s)
- Freideriki Michailidou
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany.,Current address: ETH Zürich, Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Rohit K Singh
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Aileen Peters
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Anna Ovcharenko
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
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26
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Chakrapani A, Vaňková Hausnerová V, Ruiz-Larrabeiti O, Pohl R, Krásný L, Hocek M. Photocaged 5-(Hydroxymethyl)pyrimidine Nucleoside Phosphoramidites for Specific Photoactivatable Epigenetic Labeling of DNA. Org Lett 2020; 22:9081-9085. [PMID: 33156631 DOI: 10.1021/acs.orglett.0c03462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Hydroxymethylcytosine and uracil are epigenetic nucleobases, but their biological roles are still unclear. We present the synthesis of 2-nitrobenzyl photocaged 5-hydroxymethyl-2'-deoxycytidine and uridine 3'-O-phosphoramidites and their use in automated solid-phase synthesis of oligonucleotides (ONs) modified at specific positions. The ONs were used as primers for PCR to construct DNA templates modified in the promoter region that allowed switching of transcription through photochemical uncaging.
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Affiliation(s)
- Aswathi Chakrapani
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Viola Vaňková Hausnerová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Olatz Ruiz-Larrabeiti
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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27
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Abstract
Covering: up to the beginning of 2020Enzymes depending on cofactors are essential in many biosynthetic pathways of natural products. They are often involved in key steps: catalytic conversions that are difficult to achieve purely with synthetic organic chemistry. Hence, cofactor-dependent enzymes have great potential for biocatalysis, on the condition that a corresponding cofactor regeneration system is available. For some cofactors, these regeneration systems require multiple steps; such complex enzyme cascades/multi-enzyme systems are (still) challenging for in vitro biocatalysis. Further, artificial cofactor analogues have been synthesised that are more stable, show an altered reaction range, or act as inhibitors. The development of bio-orthogonal systems that can be used for the production of modified natural products in vivo is an ongoing challenge. In light of the recent progress in this field, this review aims to provide an overview of general strategies involving enzyme cofactors, cofactor analogues, and regeneration systems; highlighting the current possibilities for application of enzymes using some of the most common cofactors.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
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28
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Hassan MM, Olaoye OO. Recent Advances in Chemical Biology Using Benzophenones and Diazirines as Radical Precursors. Molecules 2020; 25:E2285. [PMID: 32414020 PMCID: PMC7288102 DOI: 10.3390/molecules25102285] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 12/19/2022] Open
Abstract
The use of light-activated chemical probes to study biological interactions was first discovered in the 1960s, and has since found many applications in studying diseases and gaining deeper insight into various cellular mechanisms involving protein-protein, protein-nucleic acid, protein-ligand (drug, probe), and protein-co-factor interactions, among others. This technique, often referred to as photoaffinity labelling, uses radical precursors that react almost instantaneously to yield spatial and temporal information about the nature of the interaction and the interacting partner(s). This review focuses on the recent advances in chemical biology in the use of benzophenones and diazirines, two of the most commonly known light-activatable radical precursors, with a focus on the last three years, and is intended to provide a solid understanding of their chemical and biological principles and their applications.
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Affiliation(s)
- Muhammad Murtaza Hassan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada;
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Olasunkanmi O. Olaoye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada;
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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29
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Anhäuser L, Klöcker N, Muttach F, Mäsing F, Špaček P, Studer A, Rentmeister A. A Benzophenone-Based Photocaging Strategy for the N7 Position of Guanosine. Angew Chem Int Ed Engl 2020; 59:3161-3165. [PMID: 31747109 PMCID: PMC7012642 DOI: 10.1002/anie.201914573] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Indexed: 12/11/2022]
Abstract
Selective modification of nucleobases with photolabile caging groups enables the study and control of processes and interactions of nucleic acids. Numerous positions on nucleobases have been targeted, but all involve formal substitution of a hydrogen atom with a photocaging group. Nature, however, also uses ring-nitrogen methylation, such as m7 G and m1 A, to change the electronic structure and properties of RNA and control biomolecular interactions essential for translation and turnover. We report that aryl ketones such as benzophenone and α-hydroxyalkyl ketone are photolabile caging groups if installed at the N7 position of guanosine or the N1 position of adenosine. Common photocaging groups derived from the ortho-nitrobenzyl moiety were not suitable. Both chemical and enzymatic methods for site-specific modification of N7G in nucleosides, dinucleotides, and RNA were developed, thereby opening the door to studying the molecular interactions of m7 G and m1 A with spatiotemporal control.
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Affiliation(s)
- Lea Anhäuser
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Nils Klöcker
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Fabian Muttach
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Florian Mäsing
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstrasse 4048149MünsterGermany
| | - Petr Špaček
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Armido Studer
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstrasse 4048149MünsterGermany
| | - Andrea Rentmeister
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
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