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Predicting small molecule binding pockets on diacylglycerol kinases using chemoproteomics and AlphaFold

16 Nov 2023

About this article

Diacylglycerol (DAG) lipids are important secondary messenger for cell signalling and cellular levels can be controlled through phosphorylation mediated by DAG kinases (DGK). Small molecule inhibitors of individual DGK proteins would be valuable tools to investigate DAG signalling but have been difficult to develop because of limited information on binding pockets available for targeting in cells.

An integrated chemical proteomics and AlphaFold strategy can predict unexpected binding regions for covalent inhibitor development.

 

Read the full article here.

 

 

About RSC Chemical Biology

Led by Hiroaki Suga (University of Tokyo), RSC Chemical Biology is dedicated to publishing and disseminating the most exceptionally significant, breakthrough findings of interest to the chemical biology community. All submissions are handled by our experienced and internationally recognised Associate Editors. For more information on the journal, please visit the journal homepage.

As a gold open access journal, there are no barriers to accessing content and your research article will reach an international audience. Please note that the article processing charges are waived until mid-2022, so the journal is currently free to publish in.

RSC Chemical Biology is now indexed in the Directory of Open Access Journals (DOAJ), PubMed Central, Scopus and Web of Science: Emerging Sources Citation Index.  Find out more about the journal and submit your work at rsc.li/rsc-chembio

 

RSC Chemical Biology

Royal Society of Chemistry

www.rsc.org

 

 

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The multivalent G-quadruplex (G4)-ligands MultiTASQs allow for versatile click chemistry-based investigations

23 Oct 2023

About this article

G-quadruplexes (or G4s) are four-stranded DNA and RNA structures that fold from guanine (G)-rich sequences. G4 are suspected to play key biological roles in human cells and diseases. Small molecules that selectively target G4s (or G4-ligands) can thus be used as modulators to gain insights into the cell circuitry where G4s are involved. While hundreds of G4-ligands have been designed, synthesized and used, most if not all of them are flat aromatic molecules prone to interact with the duplex-DNA (the major form of DNA within the nucleus), which mechanically decreases their specificity for G4s.

We have developed a brand new molecular design, following a biomimetic approach that hinges on the observation that G4s are stable secondary structures owing to the ability of Gs to self-associate to form G-quartets, and then of G-quartets to self-stack to form the columnar core of G4s. Therefore, using a synthetic G-quartet as a G4-ligand represents a unique example of biomimetic recognition of G4s, relying on a like-likes-like approach, which is the surest pledge for a very high G4-selectivity.

In this article, we report on the design, synthesis and use of synthetic G-quartet-based ligands, also referred to as TASQs (for template-assembled synthetic G-quartets). These TASQs are the latest prototypes of TASQs, being multivalent TASQs (that is why we refer to them as MultiTASQs) able to be functionalized in situ by click chemistry (both CuAAC and SPAAC) for optical imaging and affinity precipitation purposes. These bioorthogonal investigations thus provides unique information about G4 biology.

Click on the infographic to read the full paper!

G-quadruplexes (or G4s) are four-stranded DNA and RNA structures that fold from guanine (G)-rich sequences. G4 are suspected to play key biological roles in human cells and diseases. Small molecules that selectively target G4s (or G4-ligands) can thus be used as modulators to gain insights into the cell circuitry where G4s are involved. While hundreds of G4-ligands have been designed, synthesized and used, most if not all of them are flat aromatic molecules prone to interact with the duplex-DNA (the major form of DNA within the nucleus), which mechanically decreases their specificity for G4s.

 

About RSC Chemical Biology

Led by Hiroaki Suga (University of Tokyo), RSC Chemical Biology is dedicated to publishing and disseminating the most exceptionally significant, breakthrough findings of interest to the chemical biology community. All submissions are handled by our experienced and internationally recognised Associate Editors. For more information on the journal, please visit the journal homepage.

As a gold open access journal, there are no barriers to accessing content and your research article will reach an international audience. Please note that the article processing charges are waived until mid-2022, so the journal is currently free to publish in.

RSC Chemical Biology is now indexed in the Directory of Open Access Journals (DOAJ), PubMed Central, Scopus and Web of Science: Emerging Sources Citation Index.  Find out more about the journal and submit your work at rsc.li/rsc-chembio

 

RSC Chemical Biology

Royal Society of Chemistry

www.rsc.org

 

 

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New themed collection on ‘Chemical Proteomics’

19 Sep 2023

A slide summarising the information in this blog post, with images of the two Guest Editors

We’re pleased to announce that a new themed collection from RSC Chemical Biology on Chemical Proteomics has now been published online.

Read the collection

This collection, Guest Edited by Dr Keriann Backus (UCLA, USA) and Dr Stephan Hacker (Leiden University, Netherlands), highlights work on applications of chemoproteomics to study the targets and off-targets of covalent and non-covalent inhibitors, to study the reactivity of amino acids in the proteome, to develop new reactive groups for photocrosslinkers, covalent inhibitors and protein labeling as well as to study post-translational modifications and cofactor binding proteome-wide.

A listing of the articles has been provided below. All articles in RSC Chemical Biology are open access and free to read.

Perspective

Finding a vocation for validation: taking proteomics beyond association and location
Marcus J. C. Long, Jinmin Liu and Yimon Aye
RSC. Chem. Biol., 2023, 3, 110–120, DOI: 10.1039/D2CB00214K

Communications

Quantitative profiling of PTM stoichiometry by resolvable mass tags
Ying Chen, Baiyi Quan, Yuanpei Li, Yuan Liu, Wei Qin and Chu Wang
RSC. Chem. Biol., 2023, 3, 1320–1324, DOI: 10.1039/D2CB00179A

Chemoproteomic mapping of human milk oligosaccharide (HMO) interactions in cells
Abdullah A. Hassan, Jacob M. Wozniak, Zak Vilen, Weichao Li, Appaso Jadhav, Christopher G. Parker and Mia L. Huang
RSC. Chem. Biol., 2023, 3, 1369–1374, DOI: 10.1039/D2CB00176D

Papers

The covalent reactivity of functionalized 5-hydroxy-butyrolactams is the basis for targeting of fatty acid binding protein 5 (FABP5) by the neurotrophic agent MT-21
Esben B. Svenningsen, Rasmus N. Ottosen, Katrine H. Jørgensen, Marija Nisavic, Camilla K. Larsen, Bente K. Hansen, Yong Wang, Kresten Lindorff-Larsen, Thomas Tørring, Stephan M. Hacker, Johan Palmfeldt and Thomas B. Poulsen
RSC. Chem. Biol., 2023, 3, 1216–1229, DOI: 10.1039/D2CB00161F

A peptide-crosslinking approach identifies HSPA8 and PFKL as selective interactors of an actin-derived peptide containing reduced and oxidized methionine
Aaron Maurais and Eranthie Weerapana
RSC. Chem. Biol., 2023, 3, 1282–1289, DOI: 10.1039/D2CB00183G

Chemical proteomic analysis of bile acid-protein targets in Enterococcus faecium
Xinglin Yang, Xiaohui Zhao, Victor Chen and Howard C. Hang
RSC. Chem. Biol., 2023, 3, 1397–1402, DOI: 10.1039/D2CB00178K

Photoreactive bioorthogonal lipid probes and their applications in mammalian biology
Karthik Shanbhag, Kavita Sharma and Siddhesh S. Kamat
RSC. Chem. Biol., 2023, 3, 37–46, DOI: 10.1039/D2CB00174H

Predicting small molecule binding pockets on diacylglycerol kinases using chemoproteomics and AlphaFold
Roberto Mendez, Minhaj Shaikh, Michael C. Lemke, Kun Yuan, Adam H. Libby, Dina L. Bai, Mark M. Ross, Thurl E. Harris and Ku-Lung Hsu
RSC. Chem. Biol., 2023, 3, 422–430, DOI: 10.1039/D3CB00057E

We hope you enjoy this new themed collection from RSC Chemical Biology.

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A fluorescent photoaffinity probe for formyl peptide receptor 1 labelling in living cells

18 Sep 2023
About this article

The paper explores developing a chemical tool to label formyl peptide receptor 1 (FPR1) in cells. FPR1 is a sensor in the human innate immune system, which is our body’s ancient first-line response system to detect pathogens. FPR1 is found in our immune cells; it helps these cells move towards sites of infection by sensing peptides released from bacteria.

However, the role of FPR1 is not so simple. FPR1 has been reported in other cells, such as those lining our mucous membranes (gut, lungs etc.), where it presumably comes into contact with many of our friendly bacteria without causing widespread immune activation. This family of proteins (FPRs1-3) can recognise very different molecules, and how this occurs is only beginning to be explored. FPRs can also cause and suppress inflammation and have been linked to numerous diseases (cancer, autoimmune disease). However, it’s unclear how this occurs and how we might modulate it to treat diseases.

In this paper, we designed a tool to label or tag FPR1 with a dye so we can see this sensor on the surface of cells. Our tool also allows us to detect inhibitors that bind FPR1. A key feature of it, is that it permanently labels FPR1. We expect it will be useful to understand the fundamentals of FPR1 biology and explore how we can treat diseases through molecules that activate or repress this protein.

Image of the article

About RSC Chemical Biology

Led by Hiroaki Suga (University of Tokyo), RSC Chemical Biology is dedicated to publishing and disseminating the most exceptionally significant, breakthrough findings of interest to the chemical biology community. All submissions are handled by our experienced and internationally recognised Associate Editors. For more information on the journal, please visit the journal homepage.

As a gold open access journal, there are no barriers to accessing content and your research article will reach an international audience. Please note that the article processing charges are waived until mid-2022, so the journal is currently free to publish in.

RSC Chemical Biology is now indexed in the Directory of Open Access Journals (DOAJ), PubMed Central, Scopus and Web of Science: Emerging Sources Citation Index.  Find out more about the journal and submit your work at rsc.li/rsc-chembio

 

RSC Chemical Biology

Royal Society of Chemistry

www.rsc.org

 

 

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SREBP activation contributes to fatty acid accumulations in necroptosis

10 Aug 2023
About this article:

Necroptosis is a type of programmed cell death that is accompanied by extensive inflammatory activity. Previously, it has been shown that lipids accumulate in this process, and the accumulation exacerbates the membrane permeability and cell death in necroptosis.

However, the mechanisms that result in the accumulation of these lipids are unknown.

In this work, the authors used a global transcriptomics approach. They investigated the changes in the expression of proteins involved in lipid biosynthesis and transport to identify upstream mechanisms that cause lipid accumulation in necroptosis. Such a transcriptomics approach combined with further targeted experiments revealed the activation of a key regulatory mechanism of lipid production, namely sterol regulatory element binding proteins.

The authors showed that modulating the activation of sterol regulatory element binding proteins impacts necroptotic phenotype, demonstrating the functional role of these proteins in the accumulation of toxic lipids in necroptosis. Moreover, these results provide insights into mechanisms that regulate lipid production in cell death.

 

Infographic of SREBP activation contributes to fatty acid accumulations in necroptosis

About RSC Chemical Biology

Led by Hiroaki Suga (University of Tokyo), RSC Chemical Biology is dedicated to publishing and disseminating the most exceptionally significant, breakthrough findings of interest to the chemical biology community. All submissions are handled by our experienced and internationally recognised Associate Editors. For more information on the journal, please visit the journal homepage.

As a gold open access journal, there are no barriers to accessing content and your research article will reach an international audience. Please note that the article processing charges are waived until mid-2022, so the journal is currently free to publish in.

RSC Chemical Biology is now indexed in the Directory of Open Access Journals (DOAJ), PubMed Central, Scopus and Web of Science: Emerging Sources Citation Index.  Find out more about the journal and submit your work at rsc.li/rsc-chembio

 

RSC Chemical Biology

Royal Society of Chemistry

www.rsc.org

 

 

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A mechanistic study on the cellular uptake, intracellular trafficking, and antisense gene regulation of bottlebrush polymer-conjugated oligonucleotides

02 May 2023

A research infographic summarising the linked article.

Read the full article here.

RSC Chemical Biology is now indexed in the Directory of Open Access Journals (DOAJ), PubMed Central, Scopus and Web of Science: Emerging Sources Citation Index.  Find out more about the journal and submit your work at rsc.li/rsc-chembio

RSC Chemical Biology

Royal Society of Chemistry

www.rsc.org

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Photoreactive bioorthogonal lipid probes and their applications in mammalian biology

27 Mar 2023

Infographic Bioorthogonal lipid probes: unlocking a world of possibilities by Dr Kamat

 

Read the full article here.

 

 

RSC Chemical Biology is now indexed in the Directory of Open Access Journals (DOAJ), PubMed Central, Scopus and Web of Science: Emerging Sources Citation Index.  Find out more about the journal and submit your work at rsc.li/rsc-chembio

RSC Chemical Biology

Royal Society of Chemistry

www.rsc.org

 

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Methyltetrazine as a small live-cell compatible biorthogonal handle for imaging enzyme activities in situ

13 Mar 2023

Infographic about Methyltetrazine as a small live-cell compatible biorthogonal handle for imaging enzyme activities in situ

Read the full article by  Herman S. Overkleeft and  Sander I. van Kasteren here

 

RSC Chemical Biology is now indexed in the Directory of Open Access Journals (DOAJ), PubMed Central, Scopus and Web of Science: Emerging Sources Citation Index.  Find out more about the journal and submit your work at rsc.li/rsc-chembio

RSC Chemical Biology

Royal Society of Chemistry

www.rsc.org

 

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Efficient synthesis and replication of diverse sequence libraries composed of biostable nucleic acid analogues

13 Mar 2023

infographic of efficient synthesis and replication of diverse sequence libraries composed of biostable nucleic acid analogues

Read the full article by Phillip Holliger & Alexander Taylor here

 

RSC Chemical Biology is now indexed in the Directory of Open Access Journals (DOAJ), PubMed Central, Scopus and Web of Science: Emerging Sources Citation Index.  Find out more about the journal and submit your work at rsc.li/rsc-chembio

RSC Chemical Biology

Royal Society of Chemistry

www.rsc.org

 

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Photo-induced telomeric DNA damage in human cancer cells

10 Mar 2023

 

Read the full article by Dr Benjamin Elias & Dr Anabell Decottignies here

 

RSC Chemical Biology is now indexed in the Directory of Open Access Journals (DOAJ), PubMed Central, Scopus and Web of Science: Emerging Sources Citation Index.  Find out more about the journal and submit your work at rsc.li/rsc-chembio

RSC Chemical Biology

Royal Society of Chemistry

www.rsc.org

 

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