- Improved synthesis of photo-leucine
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An improved and reproducible synthesis of photo-leucine [3-(3-methyl-3-diazirinyl)-alanine] is presented. Copyright Taylor & Francis Group, LLC.
- Ikeda, Yoshio,Behrman
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- Selective profiling of steviol-catalyzing UDP-glycosyltransferases with a metabolically synthesized probe
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Selective profiling of steviol-catalyzing UDP-glycosyltransferases in plants was accomplished with a probe metabolically synthesized from two substrate-derived components comprising an alkynylated sugar receptor (steviol) module and a diazirine-modified sugar donor (UDP-glucose) module, thereby illustrating a facile approach for harnessing biosynthetic enzymes of natural glycosides in plants for synthetic biology.
- Wong, Nai-Kei,Zhong, Suyun,Li, Weichao,Zhou, Fugui,Deng, Zhangshuang,Zhou, Yiqing
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- Diazirine-containing photoactivatable isoprenoid: Synthesis and application in studies with isoprenylcysteine carboxyl methyltransferase
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Photoaffinity labeling is a useful technique employed to identify protein-ligand and protein-protein noncovalent interactions. Photolabeling experiments have been particularly informative for probing membrane-bound proteins where structural information is difficult to obtain. The most widely used classes of photoactive functionalities include aryl azides, diazocarbonyls, diazirines, and benzophenones. Diazirines are intrinsically smaller than benzophenones and generate carbenes upon photolysis that react with a broader range of amino acid side chains compared with the benzophenone-derived diradical; this makes diazirines potentially more general photoaffinity-labeling agents. In this article, we describe the development and application of a new isoprenoid analogue containing a diazirine moiety that was prepared in six steps and incorporated into an a-factor-derived peptide produced via solid-phase synthesis. In addition to the diazirine moiety, fluorescein and biotin groups were also incorporated into the peptide to aid in the detection and enrichment of photo-cross-linked products. This multifuctional diazirine-containing peptide was a substrate for Ste14p, the yeast homologue of the potential anticancer target Icmt, with Km (6.6 μM) and Vmax (947 pmol min-1 mg-1) values comparable or better than a-factor peptides functionalized with benzophenone-based isoprenoids. Photo-cross-linking experiments demonstrated that the diazirine probe photo-cross-linked to Ste14p with observably higher efficiency than benzophenone-containing a-factor peptides.
- Vervacke, Jeffrey S.,Funk, Amy L.,Wang, Yen-Chih,Strom, Mark,Hrycyna, Christine A.,Distefano, Mark D.
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- Identification of Pyruvate Carboxylase as the Cellular Target of Natural Bibenzyls with Potent Anticancer Activity against Hepatocellular Carcinoma via Metabolic Reprogramming
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Cancer cell proliferation in some organs often depends on conversion of pyruvate to oxaloacetate via pyruvate carboxylase (PC) for replenishing the tricarboxylic acid cycle to support biomass production. In this study, PC was identified as the cellular target of erianin using the photoaffinity labeling-click chemistry-based probe strategy. Erianin potently inhibited the enzymatic activity of PC, which mediated the anticancer effect of erianin in human hepatocellular carcinoma (HCC). Erianin modulated cancer-related gene expression and induced changes in metabolic intermediates. Moreover, erianin promotes mitochondrial oxidative stress and inhibits glycolysis, leading to insufficient energy required for cell proliferation. Analysis of 14 natural analogs of erianin showed that some compounds exhibited potent inhibitory effects on PC. These results suggest that PC is a cellular target of erianin and reveal the unrecognized function of PC in HCC tumorigenesis; erianin along with its analogs warrants further development as a novel therapeutic strategy for the treatment of HCC.
- Sheng, Yuwen,Chen, Yuwen,Zeng, Zhongqiu,Wu, Wenbi,Wang, Jing,Ma, Yuling,Lin, Yuan,Zhang, Jichao,Huang, Yulan,Li, Wenhua,Zhu, Qiyu,Wei, Xiao,Li, Suiyan,Wisanwattana, Wisanee,Li, Fu,Liu, Wanli,Suksamrarn, Apichart,Zhang, Guolin,Jiao, Wei,Wang, Fei
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p. 460 - 484
(2022/01/03)
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- One-Pot Synthesis of Diazirines and 15N2-Diazirines from Ketones, Aldehydes and Derivatives: Development and Mechanistic Insight
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Broad scope one-pot diazirine synthesis strategies have been developed using two different oxidants depending on the nature of the starting material. In all cases, an inexpensive commercial solution of ammonia (NH3) in methanol (MeOH) was emplo
- Ibert, Quentin,Cauwel, Madeleine,Glachet, Thomas,Tite, Tony,Le Nahenec-Martel, Patricia,Lohier, Jean-Fran?ois,Renard, Pierre-Yves,Franck, Xavier,Reboul, Vincent,Sabot, Cyrille
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supporting information
p. 4390 - 4398
(2021/08/03)
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- Traceless Staudinger Ligation to Introduce Chemical Diversity on β-Lactamase Inhibitors of Second Generation
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We explored the traceless Staudinger ligation for the functionalization of the C2 position of second generation β-lactamase inhibitors based on a diazabicyclooctane (DBO) scaffold. Our strategy is based on the synthesis of phosphine phenol esters and thei
- Arthur, Michel,Atze, Heiner,Bouchet, Flavie,Ethève-Quelquejeu, Mélanie,Iannazzo, Laura
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supporting information
p. 7755 - 7758
(2021/10/25)
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- PHOTOPROXIMITY PROFILING OF PROTEIN-PROTEIN INTERACTIONS IN CELLS
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Photoactive probes and probe systems for detecting biological interactions are described. The photoactive probes include probes that combine both photocleavable and photoreactive moieties. The photoactive probe systems can include a first probe comprising a photocatalytic group and a second probe comprising a group that can act as a substrate for the reaction catalyzed by the photocatalytic group. The probes and probe systems can also include groups that can specifically bind to a binding partner on a biological entity of interest and a detectable group or a precursor thereof. The probes and probe systems can detect spatiotemporal interactions of proteins or cells. In some embodiments, the interactions can be detected in live cells. Also described are methods of detecting the biological interactions.
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Page/Page column 73; 75-77
(2021/04/01)
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- Live-Cell Protein Modification by Boronate-Assisted Hydroxamic Acid Catalysis
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Selective methods for introducing protein post-translational modifications (PTMs) within living cells have proven valuable for interrogating their biological function. In contrast to enzymatic methods, abiotic catalysis should offer access to diverse and new-to-nature PTMs. Herein, we report the boronate-assisted hydroxamic acid (BAHA) catalyst system, which comprises a protein ligand, a hydroxamic acid Lewis base, and a diol moiety. In concert with a boronic acid-bearing acyl donor, our catalyst leverages a local molarity effect to promote acyl transfer to a target lysine residue. Our catalyst system employs micromolar reagent concentrations and affords minimal off-target protein reactivity. Critically, BAHA is resistant to glutathione, a metabolite which has hampered many efforts toward abiotic chemistry within living cells. To showcase this methodology, we installed a variety of acyl groups inE. colidihydrofolate reductase expressed within human cells. Our results further establish the well-known boronic acid-diol complexation as abona fidebio-orthogonal reaction with applications in chemical biology and in-cell catalysis.
- Adamson, Christopher,Kajino, Hidetoshi,Kanai, Motomu,Kawashima, Shigehiro A.,Yamatsugu, Kenzo
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supporting information
p. 14976 - 14980
(2021/09/29)
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- Compounds and methods of use
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Compounds are provided according to Formula (I): and pharmaceutically acceptable salts thereof, and pharmaceutical compositions thereof; wherein X1, X2, X3, X4, Y, A, L1, L2, R1, R2, R5, m and n are as defined herein. Compounds of the present invention are contemplated useful for the prevention and treatment of a variety of conditions.
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Page/Page column 825; 826
(2021/08/04)
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- Photosensitive molecule and preparation method of surface-enhanced Raman detection substrate containing same
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The invention discloses a photosensitive molecule for constructing a photoresponse soft and hard substrate, and the structural general formula is as shown in the specification. R1 - X-R2 . and, The invention further discloses a prepa
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Paragraph 0112; 0114; 0121-0123
(2021/09/21)
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- Photoproximity Profiling of Protein-Protein Interactions in Cells
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We report a novel photoproximity protein interaction (PhotoPPI) profiling method to map protein-protein interactions in vitro and in live cells. This approach utilizes a bioorthogonal, multifunctional chemical probe that can be targeted to a genetically encoded protein of interest (POI) through a modular SNAP-Tag/benzylguanine covalent interaction. A first generation photoproximity probe, PP1, responds to 365 nm light to simultaneously cleave a central nitroveratryl linker and a peripheral diazirine group, resulting in diffusion of a highly reactive carbene nucleophile away from the POI. We demonstrate facile probe loading, and subsequent interaction- A nd light-dependent proximal labeling of a model protein-protein interaction (PPI) in vitro. Integration of the PhotoPPI workflow with quantitative LC-MS/MS enabled unbiased interaction mapping for the redox regulated sensor protein, KEAP1, for the first time in live cells. We validated known and novel interactions between KEAP1 and the proteins PGAM5 and HK2, among others, under basal cellular conditions. By contrast, comparison of PhotoPPI profiles in cells experiencing metabolic or redox stress confirmed that KEAP1 sheds many basal interactions and becomes associated with known lysosomal trafficking and proteolytic proteins like SQSTM1, CTSD, and LGMN. Together, these data establish PhotoPPI as a method capable of tracking the dynamic subcellular and protein interaction "social network" of a redox-sensitive protein in cells with high temporal resolution.
- Carlos, Anthony,Lee, Gihoon,McCutcheon, David C.,Moellering, Raymond E.,Montgomery, Jeffrey E.
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supporting information
p. 146 - 153
(2020/01/31)
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- Discovery of a Class of Potent and Selective Non-competitive Sentrin-Specific Protease 1 Inhibitors
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Sentrin-specific proteases (SENPs) are responsible for the maturation of small ubiquitin-like modifiers (SUMOs) and the deconjugation of SUMOs from their substrate proteins. Studies on prostate cancer revealed an overexpression of SENP1, which promotes prostate cancer progression as well as metastasis. Therefore, SENP1 has been identified as a novel drug target against prostate cancer. Herein, we report the discovery and biological evaluation of potent and selective SENP1 inhibitors. A structure-activity relationship (SAR) of the newly identified pyridone scaffold revealed allosteric inhibitors with very attractive in vitro ADMET properties regarding plasma binding and plasma stability for this challenging target. This study also emphasizes the importance of biochemical mode of inhibition studies for de novo designed inhibitors.
- Brand, Michael,Frasson, David,Gall, Flavio,Hunziker, Lukas,Kroslakova, Ivana,Lindenmann, Urs,Riedl, Rainer,Sievers, Martin
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supporting information
(2020/03/24)
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- BIS(DIAZIRINE) DERIVATIVES AS PHOTO-CROSSSLINKER FOR TREATING CORNEAL ECTATIC DISORDERS
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This disclosure features bis(diazirine) derivatives of the formulae (I) (l-a) or (l-b) that generate cross-linking in the cornea in response to exposure to an electromagnetic irradiation (e.g. UV-light). The compounds are useful, e.g. for treating a subje
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- Preparation method of disulfide bond-containing dual-response functional molecule and hydrogel microsphere and application thereof
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The invention discloses a disulfide bond-containing dual-response functional molecule, and the structural general formula of the disulfide bond-containing dual-response functional molecule is shown inthe specification. The invention also provides the dual
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Paragraph 0129-0134
(2020/09/23)
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- Unlocking a Diazirine Long-Lived Nuclear Singlet State via Photochemistry: NMR Detection and Lifetime of an Unstabilized Diazo-Compound
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Diazirines are important for photoaffinity labeling, and their photoisomerization is relatively well-known. This work shows how hyperpolarized NMR spectroscopy can be used to characterize an unstable diazo-compound formed via photoisomerization of a 15N2-labeled silyl-ether-substituted diazirine. This diazirine is prepared in a nuclear spin singlet state via catalytic transfer of spin order from para-hydrogen. The active hyperpolarization catalyst is characterized to provide insight into the mechanism. The photochemical isomerization of the diazirine into the diazo-analogue allows the NMR invisible nuclear singlet state of the parent compound to be probed. The identity of the diazo-species is confirmed by trapping with N-phenyl maleimide via a cycloaddition reaction to afford bicyclic pyrazolines that also show singlet state character. The presence of singlet states in the diazirine and the diazo-compound is validated by comparison of experimental nutation behavior with theoretical simulation. The magnetic state lifetime of the diazo-compound is determined as 12 ± 1 s in CD3OD solution at room temperature, whereas its chemical lifetime is measured as 100 ± 5 s by related hyperpolarized NMR studies. Indirect evidence for the generation of the photoproduct para-N2 is presented.
- Procacci, Barbara,Roy, Soumya S.,Norcott, Philip,Turner, Norman,Duckett, Simon B.
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supporting information
p. 16855 - 16864
(2018/12/11)
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- Dehydrogenation of the NH?NH Bond Triggered by Potassium tert-Butoxide in Liquid Ammonia
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A novel strategy for the dehydrogenation of the NH?NH bond is disclosed using potassium tert-butoxide (tBuOK) in liquid ammonia (NH3) under air at room temperature. Its synthetic value is well demonstrated by the highly efficient synthesis of aromatic azo compounds (up to 100 % yield, 3 min), heterocyclic azo compounds, and dehydrazination of phenylhydrazine. The broad application of this strategy and its benefit to chemical biology is proved by a novel, convenient, one-pot synthesis of aliphatic diazirines, which are important photoreactive agents for photoaffinity labeling.
- Wang, Lei,Ishida, Akiko,Hashidoko, Yasuyuki,Hashimoto, Makoto
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supporting information
p. 870 - 873
(2017/01/14)
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- Chemical Probes Unravel an Antimicrobial Defense Response Triggered by Binding of the Human Opioid Dynorphin to a Bacterial Sensor Kinase
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Host-microbe communication via small molecule signals is important for both symbiotic and pathogenic relationships, but is often poorly understood at the molecular level. Under conditions of host stress, levels of the human opioid peptide dynorphin are elevated, triggering virulence in the opportunistic pathogenic bacterium Pseudomonas aeruginosa via an unknown pathway. Here we apply a multilayered chemical biology strategy to unravel the mode of action of this putative interkingdom signal. We designed and applied dynorphin-inspired photoaffinity probes to reveal the protein targets of the peptide in live bacteria via chemical proteomics. ParS, a largely uncharacterized membrane sensor of a two-component system, was identified as the most promising hit. Subsequent full proteome studies revealed that dynorphin(1-13) induces an antimicrobial peptide-like response in Pseudomonas, with specific upregulation of membrane defense mechanisms. No such response was observed in a parS mutant, which was more susceptible to dynorphin-induced toxicity. Thus, P. aeruginosa exploits the ParS sensing machinery to defend itself against the host in response to dynorphin as a signal. This study highlights interkingdom communication as a potential essential strategy not only for induction of P. aeruginosa virulence but also for maintaining viability in the hostile environment of the host.
- Wright, Megan H.,Fetzer, Christian,Sieber, Stephan A.
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supporting information
p. 6152 - 6159
(2017/05/09)
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- Simple Light-Triggered Fluorescent Labeling of Silica Nanoparticles for Cellular Imaging Applications
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A simple and mild light-triggered fluorescent labeling approach, based on the photolysis and reactive carbene insertion of diazirine, to rapidly generate fluorescent nanoparticles is reported. Proof of concept studies demonstrated that the non-fluorescent SiNPs could be covalently labeled by diazirine-conjugated fluorescein (dFITC) upon photo irradiation (λ=365 nm) to afford fluorescent SiNPs with good fluorescent stability and low cytotoxicity. In vitro cellular imaging results indicated that the internalization of SiNPs into living cells could be readily visualized based on fluorescein-labeled SiNPs (F-SiNPs) in real time. We believe that the light-triggered labeling approach may offer a valuable method for surface modification of nanomaterials to achieve new functions.
- Sun, Rui,Yin, Ling,Zhang, Shaohua,He, Lei,Cheng, Xiaju,Wang, Anna,Xia, Huawei,Shi, Haibin
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supporting information
p. 13893 - 13896
(2017/09/14)
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- RNA Chemical Proteomics Reveals the N6-Methyladenosine (m6A)-Regulated Protein-RNA Interactome
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Epitranscriptomic RNA modifications can regulate mRNA function; however, there is a major gap in our understanding of the biochemical mechanisms mediating their effects. Here, we develop a chemical proteomics approach relying upon photo-cross-linking with synthetic diazirine-containing RNA probes and quantitative proteomics to profile RNA-protein interactions regulated by N6-methyladenosine (m6A), the most abundant internal modification in eukaryotic RNA. In addition to identifying YTH domain-containing proteins and ALKBH5, known interactors of this modification, we find that FMR1 and LRPPRC, two proteins associated with human disease, "read" this modification. Surprisingly, we also find that m6A disrupts RNA binding by the stress granule proteins G3BP1/2, USP10, CAPRIN1, and RBM42. Our work provides a general strategy for interrogating the interactome of RNA modifications and reveals the biochemical mechanisms underlying m6A function in the cell.
- Arguello, A. Emilia,Deliberto, Amanda N.,Kleiner, Ralph E.
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supporting information
p. 17249 - 17252
(2017/12/15)
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- Ultraviolet light mediated nano-particle self-assembly aggregate and preparation method and application thereof
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The invention discloses ultraviolet light mediated nano-particle self-assembly aggregate and a preparation method and application thereof. The preparation method includes the following steps that 1, PEG is modified on the surfaces of nano-particles; 2, an ultraviolet light sensitive cross-linking agent is modified on terminal amino of PEG; 3, the ultraviolet light mediated nano-particles are self-assembled. According to the method, the cross-linking agent with the small size is used for the first time, and precipitation of the nano-particles is avoided; controllable self-assembly is achieved by controlling the use amount of the cross-linking agent and illumination time; self-assembly of nano-particles of the same type or different types is achieved through ultraviolet light irradiation, and the application range of the method is widened. The ultraviolet light mediated nano-particle self-assembly aggregate obtained through the preparation method has low toxicity and a good photo-thermal treatment effect, is suitable for being developed into anti-tumor medicine based on the photo-thermal therapy, and has high scientific research and economic value.
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Paragraph 0027
(2017/07/20)
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- Base-mediated one-pot synthesis of aliphatic diazirines for photoaffinity labeling
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Aliphatic diazirines have been widely used as prominent photophores for photoaffinity labeling owing to their relatively small size which can reduce the steric effect on the natural interaction between ligands and proteins. Based on our continuous efforts
- Wang, Lei,Tachrim, Zetryana Puteri,Kurokawa, Natsumi,Ohashi, Fumina,Sakihama, Yasuko,Hashidoko, Yasuyuki,Hashimoto, Makoto
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- Discovery of a Highly Selective Cell-Active Inhibitor of the Histone Lysine Demethylases KDM2/7
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Histone lysine demethylases (KDMs) are of critical importance in the epigenetic regulation of gene expression, yet there are few selective, cell-permeable inhibitors or suitable tool compounds for these enzymes. We describe the discovery of a new class of inhibitor that is highly potent towards the histone lysine demethylases KDM2A/7A. A modular synthetic approach was used to explore the chemical space and accelerate the investigation of key structure–activity relationships, leading to the development of a small molecule with around 75-fold selectivity towards KDM2A/7A versus other KDMs, as well as cellular activity at low micromolar concentrations.
- Gerken, Philip A.,Wolstenhulme, Jamie R.,Tumber, Anthony,Hatch, Stephanie B.,Zhang, Yijia,Müller, Susanne,Chandler, Shane A.,Mair, Barbara,Li, Fengling,Nijman, Sebastian M. B.,Konietzny, Rebecca,Szommer, Tamas,Yapp, Clarence,Fedorov, Oleg,Benesch, Justin L. P.,Vedadi, Masoud,Kessler, Benedikt M.,Kawamura, Akane,Brennan, Paul E.,Smith, Martin D.
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supporting information
p. 15555 - 15559
(2017/12/02)
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- A diazirine-based photoaffinity probe for facile and efficient aptamer-protein covalent conjugation
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A photo-reactive functional labelling reagent, diazirine phosphoramidite, was designed and synthesized for easy and flexible site-specific labelling of oligonucleotides with the diazirine moiety. The new reagent allows facile photo-crosslinking of oligonu
- Zhang, Huimin,Song, Yanling,Zou, Yuan,Ge, Yun,An, Yuan,Ma, Yanli,Zhu, Zhi,Yang, Chaoyong James
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supporting information
p. 4891 - 4894
(2014/05/06)
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- Mapping the protein interaction landscape for fully functionalized small-molecule probes in human cells
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Phenotypic screening provides a means to discover small molecules that perturb cell biological processes. Discerning the proteins and biochemical pathways targeted by screening hits, however, remains technically challenging. We recently described the use of small molecules bearing photoreactive groups and latent affinity handles as fully functionalized probes for integrated phenotypic screening and target identification. The general utility of such probes, or, for that matter, any small-molecule screening library, depends on the scope of their protein interactions in cells, a parameter that remains largely unexplored. Here, we describe the synthesis of an ～60-member fully functionalized probe library, prepared from Ugi-azide condensation reactions to impart structural diversity and introduce diazirine and alkyne functionalities for target capture and enrichment, respectively. In-depth mass spectrometry-based analysis revealed a diverse array of probe targets in human cells, including enzymes, channels, adaptor and scaffolding proteins, and proteins of uncharacterized function. For many of these proteins, ligands have not yet been described. Most of the probe-protein interactions showed well-defined structure-activity relationships across the probe library and were blocked by small-molecule competitors in cells. These findings indicate that fully functionalized small molecules canvas diverse segments of the human proteome and hold promise as pharmacological probes of cell biology.
- Kambe, Tohru,Correia, Bruno E.,Niphakis, Micah J.,Cravatt, Benjamin F.
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supporting information
p. 10777 - 10782
(2014/08/18)
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- A traceless staudinger reagent to deliver diazirines
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A triarylphosphine reagent that reacts with organic azides to install amide-linked diazirines is reported. This traceless Staudinger reagent reacts with complex organic azides to yield amide-linked diazirines, thus expanding the scope of the utility of bo
- Ahad, Ali M.,Jensen, Stephanie M.,Jewett, John C.
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supporting information
p. 5060 - 5063
(2013/10/22)
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- Photoaffinity-labeled peptoids and depsipeptides by multicomponent reactions
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Photoaffinity tags can be incorporated easily into peptoids and congeners by the Ugi and Passerini multicomponent reactions. Products related to photo-methionine and photo-leucine can be accomplished by diazirine-containing building blocks. The same proto
- Henze, Michael,Kreye, Oliver,Brauch, Sebastian,Nitsche, Christoph,Naumann, Kai,Wessjohann, Ludger A.,Westermann, Bernhard
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experimental part
p. 2997 - 3003
(2010/10/21)
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- PHOTO ACTIVATABLE AMINO ACIDS
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This invention relates to an amino acid based on a naturally occurring non-polar, non-aromatic α-amino acid, wherein said amino acid differs from the naturally occurring counterpart in that the side chain contains a diazirine ring. Furthermore provided are methods of synthesizing a (poly)peptide with one or more amino acids of the invention incorporated, methods for cross-linking interacting molecules, methods of synthesizing the amino acids of the invention, and a kit comprising the amino acids of the invention.
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(2008/06/13)
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- The Thermal Decomposition of Diazirines: 3-(3-Methyldiazirin-3-yl)propan-1-ol and 3-(3-Methyldiazirin-3-yl)propanoic Acid
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The thermolyses of 3-(3-methyldiazirin-3-yl)propan-1-ol (1) and 3-(3-methyldiazirin-3-yl)propanoic acid (2) have been studied in solution over the temperature range 96-125 deg C.The reactions are unimolecular and fit linear Arrhenius plots with k(1)=1013.85+/-0.69exp-1/RT>s-1 and k(2)=1012.38+/-0.43exp-1/RT>s-1.The major products are the alkenes derived from the corresponding carbenes MeC2.CH2CH2CH2OH (3) and MeC2.CH2CH2CO2H (4).The new rate data, taken together with previous work, tend to confirm that diazirine thermolysis involves ring opening to a "complex" followed either by nitrogen loss or by isomerization to a diazo compound.Whereas (1) gives no product of closure onto oxygen, the acid (2) affords about 5percent γ-valerolactone.
- Stevens, Ian D. R.,Liu, Michael T. H.,Soundararajan, N.,Paike, N.
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p. 661 - 667
(2007/10/02)
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