Semi-synthesis of Ubiquitin-propargylamide for identifying deubiquitinase targeting inhibitors

Tan, Xiaodan; Bai, Jingsi; Ding, Shan; Ren, Yujing; Hong, Danning; Mei, Ziqing; Li, Yiming

doi:10.1016/j.cclet.2018.09.003

Cited by 11 publications

(7 citation statements)

References 29 publications

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“…49 The samples were prepared as previously reported (SI). 50 As the LOD of the BCA method was much higher than that of the present procedure, the samples were prepared at a high concentration of the analyte for the BCA method and then diluted 25 times. Figure 4d shows that the results of the present procedure are consistent with those of the BCA method.…”

Section: ■ Results and Discussionmentioning

confidence: 83%

“…The proposed strategy was also compared with the standard bicinchoninic acid (BCA) method (Figure d) . The samples were prepared as previously reported (SI) . As the LOD of the BCA method was much higher than that of the present procedure, the samples were prepared at a high concentration of the analyte for the BCA method and then diluted 25 times.…”

Section: Results and Discussionmentioning

confidence: 99%

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Can Direct-Immersion Aqueous–Aqueous Microextraction Be Achieved When Using a Single-Drop System?

et al. 2022

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For the analysis of biological analytes in complex matrices, it is difficult to achieve extraction of analytes and enrichment in an aqueous−aqueous single-drop microextraction system. In this study, we proposed a pH-dependent polydopamine (PDA)-coated vesicle/Fe 3 O 4 magnetic aqueous−aqueous in a single-drop microreactor (SDMR) for the direct fluorescence detection of glutathione S-transferase (GST), a metabolic enzyme involved with crucial biological processes, in biological samples. After extracting and enriching the GST target from an aqueous−aqueous single-drop interface, the extraction process was conducted rapidly in 6 s in the SDMR system. The GST was first extracted from the sample solution via the GST-Aptamer on the polydopamine-coated vesicle/ Fe 3 O 4 nanospheres (Fe 3 O 4 @PDA@GST-Aptamer). Then, as the pH changed from weakly acidic to weakly alkaline in the SDMR system, the GST and GST-Aptamer were released from Fe 3 O 4 @PDA@GST-Aptamer nanospheres and captured by polydiacetylene vesicles via the capture probe. These changes altered the effective conjugation length and angle of the vesicle trunk, generating a highly enhanced fluorescence signal. This not only achieved the purpose of target enrichment but also reduced interferences posed by matrix effects. The approach can be used for the direct detection of GST in genuine urine and blood without any sample pretreatment. The linear range was 0.005 to 0.5 μg/mL, and the limit of detection was 0.834 ng/mL. The recoveries of GST in genuine blood samples ranged from 90.8 to 108.0% and in urine from 91.6 to 102.8%. The method has the capability of handling complex samples directly by enabling microextraction in an aqueous−aqueous single-drop system.

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Section: ■ Results and Discussionmentioning

confidence: 83%

Section: Results and Discussionmentioning

confidence: 99%

Can Direct-Immersion Aqueous–Aqueous Microextraction Be Achieved When Using a Single-Drop System?

et al. 2022

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“…Orthogonally protected Fmoc‐Lys‐(Mtt)‐OH was loaded on to the N‐terminal of the caged Ub moiety, and after removal of the Mtt (methyltrityl) group, [19] the ϵ‐amine of the Lys residue was coupled with TER or D‐biotin to yield the caged Ub moiety bearing either the fluorophore or enrichment tag (Figure S8). We then installed the commonly used cell‐penetrating peptide cR10 (Figure S9) to the N‐terminus of the backbone‐modified Ub moiety, [20] and obtained probes 2 and 3 after the aforementioned propargylamine aminolysis (Figure 2a) [17] . The purity and identity of probes 2 and 3 were confirmed by HPLC, SDS‐PAGE and ESI‐MS analyses (Figure 2b, c and Figure S10).…”

Section: Resultsmentioning

confidence: 97%

“…We then installed the commonly used cellpenetrating peptide cR10 (Figure S9) to the N-terminus of the backbone-modified Ub moiety, [20] and obtained probes 2 and 3 after the aforementioned propargylamine aminolysis (Figure 2a). [17] The purity and identity of probes 2 and 3 were confirmed by HPLC, SDS-PAGE and ESI-MS analyses (Figure 2b, c and Figure S10).…”

Section: Synthesis Of a Cell-permeable Photocaged Ub-pa For In-cell L...mentioning

confidence: 85%

Photocaging of Activity‐Based Ubiquitin Probes via a C‐Terminal Backbone Modification Strategy

et al. 2022

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Photocaged, activity-based ubiquitin (Ub) probes (Ub-ABPs) have been developed for the time-resolved probing of deubiquitinating enzyme (DUB) activities, but many Ub-ABPs are still challenging to photocage because their warheads (e.g. propargylamide (PA) or dehydroalanine (Dha)) are difficult to temporally block and activate. Here, we describe a new C-terminal backbone modification strategy for the construction of photocaged Ub-ABPs in which a light-sensitive group is placed at the backbone amide bond of the Ub Gly75. This strategy enabled the facile generation of cell-permeable photocaged Ub-PA and Dha probes that could be activated to capture DUBs after photo-irradiation, and were used to profile DUBs in cells under specially designed conditions (e.g. in cells experiencing oxidative stress) or DUBs with isopeptide linkage selectivity. This backbone modification strategy is anticipated to provide a general solution for the development of photocaged Ub ABPs bearing any warheads for DUB profiling.

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“…Other screening efforts have included the use of DNA‐encoded libraries; [338] cyclic peptides; [339] peptide aldehyde inhibitors of M PRO or PL PRO ; [340] and large‐scale fragment screening by combined MS and crystallography. One such screen identified the N ‐chloroacetyl‐ N ’‐sulfonamidopiperazine or N ‐chlorocetylanilene motifs as frequent hits [341] . It also unveiled a 3‐bromopropargyl pharmacophore as an M PRO inhibiting motif.…”

Section: The Pipelinementioning

confidence: 99%

Science's Response to CoVID‐19

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2021

ChemMedChem

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CoVID‐19 is a multi‐symptomatic disease which has made a global impact due to its ability to spread rapidly, and its relatively high mortality rate. Beyond the heroic efforts to develop vaccines, which we do not discuss herein, the response of scientists and clinicians to this complex problem has reflected the need to detect CoVID‐19 rapidly, to diagnose patients likely to show adverse symptoms, and to treat severe and critical CoVID‐19. Here we aim to encapsulate these varied and sometimes conflicting approaches and the resulting data in terms of chemistry and biology. In the process we highlight emerging concepts, and potential future applications that may arise out of this immense effort.

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Semi-synthesis of Ubiquitin-propargylamide for identifying deubiquitinase targeting inhibitors

Cited by 11 publications

References 29 publications

Can Direct-Immersion Aqueous–Aqueous Microextraction Be Achieved When Using a Single-Drop System?

Can Direct-Immersion Aqueous–Aqueous Microextraction Be Achieved When Using a Single-Drop System?

Photocaging of Activity‐Based Ubiquitin Probes via a C‐Terminal Backbone Modification Strategy

Science's Response to CoVID‐19

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