scholarly journals Influenza neuraminidase operates via a nucleophilic mechanism and can be targeted by covalent inhibitors

2013 ◽  
Vol 4 (1) ◽  
Author(s):  
Christopher J. Vavricka ◽  
Yue Liu ◽  
Hiromasa Kiyota ◽  
Nongluk Sriwilaijaroen ◽  
Jianxun Qi ◽  
...  
Keyword(s):  
Covalent Inhibitors ◽  
Nucleophilic Mechanism

Novel chemistry for covalent inhibitors

2020 ◽  
Vol 19 (11) ◽  
pp. 754-754
Author(s):  
Megan Cully
Keyword(s):  
Covalent Inhibitors

Isotopically Labeled Desthiobiotin Azide (isoDTB) Tags Enable Global Profiling of the Bacterial Cysteinome

2019 ◽  
Author(s):  
Patrick R. A. Zanon ◽  
Lisa Lewald ◽  
Stephan M. Hacker
Keyword(s):  
Binding Sites ◽  
Bacterial Resistance ◽  
Mevalonate Pathway ◽  
Rapid Development ◽  
High Reactivity ◽  
Functional Importance ◽  
Essential Proteins ◽  
Covalent Inhibitors ◽  
Druggable Targets ◽  
Covalent Ligands

Rapid development of bacterial resistance has led to an urgent need to find new druggable targets for antibiotics. In this context, residue-specific chemoproteomic approaches enable proteome-wide identification of binding sites for covalent inhibitors. Here, we describe isotopically labeled desthiobiotin azide (isoDTB) tags that are easily synthesized, shorten the chemoproteomic workflow and allow an increased coverage of cysteines in bacterial systems. We quantify 59% of all cysteines in essential proteins in <i>Staphylococcus aureus</i> and discover 88 cysteines with high reactivity, which correlates with functional importance. Furthermore, we identify 268 cysteines that are engaged by covalent ligands. We verify inhibition of HMG-CoA synthase, which will allow addressing the bacterial mevalonate pathway through a new target. Overall, a comprehensive map of the bacterial cysteinome is obtained, which will facilitate the development of antibiotics with novel modes-of-action.

Covalent-Fragment Screening of Brd4 Identifies a Ligandable Site Orthogonal to the Acetyl-Lysine Binding Sites

2019 ◽  
Author(s):  
Michael Olp ◽  
Daniel Sprague ◽  
Stefan Kathman ◽  
Ziyang Xu ◽  
Alexandar Statsyuk ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Binding Site ◽  
Binding Sites ◽  
Computational Prediction ◽  
Chemical Probes ◽  
Computational Docking ◽  
Fragment Screening ◽  
Covalent Inhibitors ◽  
Bet Protein ◽  
Proof Of Principle

<p>Brd4, a member of the bromodomain and extraterminal domain (BET) family, has emerged as a promising epigenetic target in cancer and inflammatory disorders. All reported BET family ligands bind within the bromodomain acetyl-lysine binding sites and competitively inhibit BET protein interaction with acetylated chromatin. Alternative chemical probes that act orthogonally to the highly-conserved acetyl-lysine binding sites may exhibit selectivity within the BET family and avoid recently reported toxicity in clinical trials of BET bromodomain inhibitors. Here, we report the first identification of a ligandable site on a bromodomain outside the acetyl-lysine binding site. Inspired by our computational prediction of hotspots adjacent to non-homologous cysteine residues within the <i>C</i>-terminal Brd4 bromodomain (Brd4-BD2), we performed a mid-throughput mass spectrometry screen to identify cysteine-reactive fragments that covalently and selectively modify Brd4. Subsequent mass spectrometry, NMR and computational docking analyses of electrophilic fragment hits revealed a novel ligandable site near Cys356 that is unique to Brd4 among all human bromodomains. This site is orthogonal to the Brd4-BD2 acetyl-lysine binding site as Cys356 modification did not impact binding of the pan-BET bromodomain inhibitor JQ1 in fluorescence polarization assays. Finally, we tethered covalent fragments to JQ1 and performed NanoBRET assays to provide proof of principle that this orthogonal site can be covalently targeted in intact human cells. Overall, we demonstrate the potential of targeting sites orthogonal to bromodomain acetyl-lysine binding sites to develop bivalent and covalent inhibitors that displace Brd4 from chromatin.</p>

Recent Progress in Chemosensors Using Aldehyde-bearing Fluorophores for the Detection of Specific Analytes and their Bioimaging

2019 ◽  
Vol 26 (21) ◽  
pp. 4003-4028 ◽  
Author(s):  
Fangjun Huo ◽  
Yaqiong Zhang ◽  
Caixia Yin
Keyword(s):  
Biomedical Research ◽  
Nucleophilic Addition ◽  
Recent Progress ◽  
Biological Imaging ◽  
Tissue Imaging ◽  
Fluorescence Probes ◽  
Biological Applications ◽  
Convenient Procedure ◽  
Nucleophilic Mechanism

In recent years, aldehyde-appended fluorescence probes have attracted increasing attention. Fluorescent biological imaging includes many modern applications for cell and tissue imaging in biomedical research. Meanwhile, the nucleophilic mechanism is a very simple and convenient procedure for the preparation of aldehyde-sensing probes. This tutorial review focuses on aldehyde-bearing chemosensors based on nucleophilic addition mechanism with biological applications.

scholarly journals FGFR-TKI resistance in cancer: current status and perspectives

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sitong Yue ◽  
Yukun Li ◽  
Xiaojuan Chen ◽  
Juan Wang ◽  
Meixiang Li ◽  
...  
Keyword(s):  
Gene Fusion ◽  
Kinase Inhibitors ◽  
Current Status ◽  
Great Success ◽  
Fibroblast Growth Factor Receptors ◽  
Pathway Activation ◽  
Tki Resistance ◽  
Covalent Inhibitors ◽  
And Migration ◽  
Dual Target

AbstractFibroblast growth factor receptors (FGFRs) play key roles in promoting the proliferation, differentiation, and migration of cancer cell. Inactivation of FGFRs by tyrosine kinase inhibitors (TKI) has achieved great success in tumor-targeted therapy. However, resistance to FGFR-TKI has become a concern. Here, we review the mechanisms of FGFR-TKI resistance in cancer, including gatekeeper mutations, alternative signaling pathway activation, lysosome-mediated TKI sequestration, and gene fusion. In addition, we summarize strategies to overcome resistance, including developing covalent inhibitors, developing dual-target inhibitors, adopting combination therapy, and targeting lysosomes, which will facilitate the transition to precision medicine and individualized treatment.

scholarly journals Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Haixia Su ◽  
Sheng Yao ◽  
Wenfeng Zhao ◽  
Yumin Zhang ◽  
Jia Liu ◽  
...  
Keyword(s):  
Theoretical Calculations ◽  
Cysteine Proteinase ◽  
Covalent Binding ◽  
Food Sources ◽  
Binding Mechanism ◽  
Covalent Inhibitors ◽  
Catalytic Cysteine ◽  
3Cl Protease ◽  
Covalent Ligands ◽  
Covalent Inhibitor

AbstractThe ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) urgently needs an effective cure. 3CL protease (3CLpro) is a highly conserved cysteine proteinase that is indispensable for coronavirus replication, providing an attractive target for developing broad-spectrum antiviral drugs. Here we describe the discovery of myricetin, a flavonoid found in many food sources, as a non-peptidomimetic and covalent inhibitor of the SARS-CoV-2 3CLpro. Crystal structures of the protease bound with myricetin and its derivatives unexpectedly revealed that the pyrogallol group worked as an electrophile to covalently modify the catalytic cysteine. Kinetic and selectivity characterization together with theoretical calculations comprehensively illustrated the covalent binding mechanism of myricetin with the protease and demonstrated that the pyrogallol can serve as an electrophile warhead. Structure-based optimization of myricetin led to the discovery of derivatives with good antiviral activity and the potential of oral administration. These results provide detailed mechanistic insights into the covalent mode of action by pyrogallol-containing natural products and a template for design of non-peptidomimetic covalent inhibitors against 3CLpros, highlighting the potential of pyrogallol as an alternative warhead in design of targeted covalent ligands.

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