Hydroxymethylated Dioxobilins in Senescent Arabidopsis thaliana Leaves: Sign of a Puzzling Biosynthetic Intermezzo of Chlorophyll Breakdown

1‐Formyl‐19‐oxobilin‐type tetrapyrroles are characteristic, abundant products of chlorophyll breakdown in senescent leaves. However, in some leaves, 1,19‐dioxobilin‐type chlorophyll catabolites (DCCs) lacking the formyl group accumulate instead. A P450 enzyme was identified in in vitro studies that removed the formyl group of a primary fluorescent chlorophyll catabolite (pFCC) and generated fluorescent DCCs. These DCCs are precursors of isomeric nonfluorescent DCCs (NDCCs). Here, we report a structural investigation of the NDCCs in senescent leaves of wild‐type Arabidopsis thaliana. Four new NDCCs were characterized, two of which carried a stereoselectively added hydroxymethyl group. Such formal DCC hydroxymethylations were previously found in DCCs in leaves of a mutant of A. thaliana. They are now indicated to be a feature of chlorophyll breakdown in A. thaliana, associated with the specific in vivo deformylation of pFCC en route to NDCCs.     

Hydroxymethylated Phyllobilins: A Puzzling New Feature of the Dioxobilin Branch of Chlorophyll Breakdown

Colorless nonfluorescent chlorophyll (Chl) catabolites (NCCs) are formyloxobilin‐type phyllobilins, which are considered the typical products of Chl breakdown in senescent leaves. However, in degreened leaves of some plants, dioxobilin‐type Chl catabolites (DCCs) predominate, which lack the formyl group of the NCCs, and which arise from Chl catabolites by oxidative removal of the formyl group by a P450 enzyme. Here a structural investigation of the DCCs in the methylesterase16 mutant of Arabidopsis thaliana is reported. Eight new DCCs were identified and characterized structurally. Strikingly, three of these DCCs carry stereospecifically added hydroxymethyl groups, and represent bilin‐type linear tetrapyrroles with an unprecedented modification. Indeed, DCCs show a remarkable structural parallel, otherwise, to the bilins from heme breakdown.     

Development of micro X-ray fluorescence spectrometer with multi excitation sources

X-ray fluorescence analysis (XRF) is a suitable technique for elemental analysis in nondestructive measurement. Recently, small area analysis by using the XRF technique has gained popularity. The synchrotron radiation source is responsible for the increase in the popularity of micro-XRF analysis. However, most people find it difficult to gain access to the synchrotron radiation facility. In this study, a micro-XRF system is developed for use in laboratories. To enable the use of this system, it is necessary to satisfy the following two conditions: (1) the excitation source must be optional for efficient excitation of the sample and (2) the X-rays must be focused. An X-ray tube with multi excitation sources has also been developed. In this tube, there are three targets, namely Cr, W, and Pd, on the anode, and each target can be excited sequentially. A doubly curved crystal (DCC) developed using a Si(111) crystal is used as the optics for focusing the X-rays into a beam with a diameter of less than 100 μm. A system composed of the X-ray tube and DCC optics is used to perform the small particle analysis of a Si wafer. The lower limit of detection (LLD) of the sample particle is estimated as 1.6 μm in diameter.     

Thermal properties of oxidized cellulose

Three series of oxidized celluloses – 2,3-dialdehyde celluloses (DACs), 2,3-dicarboxycelluloses (DCCs) and sodium 2,3-dicarboxycelluloses (NaDCCs) — were prepared, having incremental changes in their degrees of oxidation. Their thermogravimetric analysis (TG) and differential thermal analysis (DTA) were studied. It was found that oxidation generally destabilized cellulose at lower temperatures (below 250 °C), but at higher temperatures the oxidized products were found to be more stable. Cellulose, DACs, and DCCs all showed final weight losses in the region of 80–85%. However, 80% NaDCC and 98% NaDCC showed weight losses of only 30 and 37%, respectively.NCL Communication No. 6051.     

动态组合化学最新进展

动态组合化学是组合化学的一个新兴分支,在药物先导化合物的发现中有广阔的应用前景。在动态组合化学库中,利用靶标分子的诱导结合作用,通过可逆共价反应,能够选择性的筛选到与靶标分子存在强相互作用的优势化合物。本文按照动态组合化学方法简介、动态组合化学中的可逆共价化学、动态组合化学库的分类、动态组合化学库筛选方法的研究进展及动态组合化学在药物先导化合物发现过程中的应用等5个方面对动态组合化学进行了概述。     

Reaction of RF-palmitic acid-F13 with dicyclohexylcarbodiimide

The 1,3-dicyclohexylcarbodiimide (DCC) adduct of R_F-palmitic acid-F₁₃1 has been synthesized and characterized. The X-ray crystal structure shows that the product arises from an O- to N-acyl migration of an initially formed N,N′-dicyclohexyl-O-R_F-palmitoyl-F₁₃-isourea 2 to give 1-R_F-palmitoyl-F₁₃-1,3-dicyclohexylurea 3. X-ray data for an R_F-palmitic acid-F₁₃ unit are reported for the first time. The product of the reaction of DCC with palmitic acid is also the urea derivative which has been characterized by IR and NMR methods.     

全保护RGD三肽的合成方法研究

以两条路线、多种偶联试剂(DCC，EDCI，CDI，EEDQ)合成了全保护三肽Arg- Gly-Asp(RGD)．Boc-Arg(Tos)-OH经上述偶联剂短时活化，于合适条件下与Ts0H- G1y-OBzl缩合，均获得良好收率(43％-97％)．经Pd(OH)2／H2还原得到的Boc-Arg (Tos)-G1y-0H于22-27℃与HCl·Asp(OcHex)-OBzl偶联得到全保护三肽Boc-Arg (Tos)-Gly-Asp(OcHex)-OBzl(TM)，反应收率分别为76．4％(DCC／HOSu)，64．7％ -78．3％(DCC／HOBt)，66．7％-77．9％(EDCI／HOBt)．Boc-Gly-OH和HCl·Asp- (OcHex)-OBzl经DCC／HOBt或CDI活化，可得到碳端二肽Boc-Gly-Asp(OcHex)-OBzl (收率分别为81．2％，89．5％)，该二肽脱Boc后与Boc-Asp(Tos)-OH反应，经DCC ／HOBt，EDCI／HOBt，CDI，DCC／HOSu活化，均可生成目标分子TM，其反应收率分 别为40．4％，73．8％，67．8％，84．4％．     

Synthesis and Crystal Structure of 3,5-Dichloro-N-(2-methoxyphenyl)benzamide

<正>The title compound was synthesized by the direct reaction of 3,5-dichlorobenzoic acid with 2-methoxyaniline in the presence of DCC and HOBT. The structure was supported by the spectroscopic data and unambiguously confirmed by the single-crystal X-ray diffraction studies. It crystallizes from a methanol solution in the monoclinic space group P2_1/c with unit cell dimensions of a = 4.9369(16), b = 13.351(5), c = 20.168(7), β = 96.755(8)°, V = 1320.1(8)~3 and Z = 4.     

Resolving the problem of chromatographic overlap by 3D cross correlation (3DCC) processing of LC, MS and NMR data for characterization of complex glycan mixtures

Chromatographic overlap is a common problem in the analysis of complex mixtures. As a result, it is not possible to identify the components because each resulting NMR or MS spectrum contains multiple components. We introduce three-dimensional cross correlation (3DCC) that dissects NMR spectra of a mixture into spectra of the individual components without actually separating them. Correlation of peaks from MS and NMR profiles along a common LC time domain yields 3DCC NMR spectra of pure components correlated with a mass and a retention time. The method requires an LC run followed by fractionation and recording of MS and NMR spectra. The method is applicable to mixtures of any classes of molecules. Here, we demonstrate its application to a mixture of complex glycans obtained from a glycoprotein. Fourteen glycans eluting within only 3 min showed heavy overlap in the chromatographic run. 3DCC allowed their direct characterization without separation. Some of these structures from the glycoprotein bovine fibrinogen had not previously been described. The 3DCC procedure has been implemented in standard software. Actually, 3DCC can be used for any combination of separation techniques, like LC or GC, combined with two characterization methods like UV, IR, Raman, NMR or MS.     

新型噻吩席夫碱及其酯化产物合成与性能

以噻吩为起始原料,对工艺进行了优化合成出噻吩-2-甲醛,并由噻吩-2-甲醛与4-氨基苯酚缩合反应生成未见报道的噻吩-2-甲醛缩4-氨基苯酚席夫碱,进一步由DCC/DMAP高效酯化法与十一烯酸进行酯化反应。通过用纸片法测试了该席夫碱抑菌活性,结果表明具有较好的抑制作用;并通过偏光显微镜对酯化产物进行研究,观察到了较好的液晶相织构。     

Blood compatibility of polyurethane surface grafted copolymerization with sulfobetaine monomer

Surface modification is an effective way to improve the hemocompatibility and remain bulk properties of biomaterials. Recently, polymer tailed with zwitterions was found having good blood compatibility. In this study, the grafting copolymerization of sulfobetaine onto polyurethane surface was obtained through two steps. In the first step, polyurethane film coupled with vinyl groups was obtained through the reaction between the carboxyl group of acrylic acid (AA) and the NH-urethane group of polyurethane by dicyclohexylcarbodiimide (DCC). In the second step, sulfobetaine was grafted copolymerization on the surface using AIBN as an initiator. The reaction process was monitored with ATR-IR spectra and X-ray photoelectron spectroscopy (XPS) spectra. The wettability of films was investigated by water contact angle measurement. The blood compatibility of the grafted films was evaluated by platelet adhesion in platelet rich plasma (PRP) and protein absorption in bovine fibrinogen (BFG). Low platelet adhesion was observed on the grafted films incubated in PRP for 1 and 3 h, respectively. The protein absorption was reduced on the grafted films after incubated in bovine fibrinogen for 2 h. All of these results revealed that the improved blood compatibility was obtained by grafting copolymerization with zwitterionic monomer of sulfobetaine onto polyurethane film. In addition, introducing vinyl groups onto surface through DCC and AA is a novel method to functionalize polyurethane for further modification.     

聚硅氧烷接枝酯类手性固定相的制备与表征

以S-(-)-乳酸甲酯、S-(-)-α-苯乙醇、(S)-(+)-仲丁醇为手性源,N,N'-二环己基碳二亚胺(DCC)为缩水剂、4-二甲氨基吡啶为酰化催化剂,分别与上述三种不饱和酸进行酯化反应设计合成出新的手性不饱和酯类单体,提纯产物,用红外扫描、核磁共振及有机元素分析表征确定了得到了纯净的产物。然后,以聚硅氧烷接枝手性单体,制备手性固定相。     

Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment‐Based Drug Design Facilitated by Dynamic Combinatorial Chemistry

Fragment‐based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit‐identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease endothiapepsin. Based on X‐ray crystal structures of endothiapepsin in complex with fragments, we designed a library of bis‐acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC₅₀ value of 54 nm , which represents a 240‐fold improvement in potency compared to the parent hits. Subsequent X‐ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit‐identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit‐to‐lead optimization.     

Multiprotein Dynamic Combinatorial Chemistry: A Strategy for the Simultaneous Discovery of Subfamily‐Selective Inhibitors for Nucleic Acid Demethylases FTO and ALKBH3

Dynamic combinatorial chemistry (DCC) is a powerful supramolecular approach for discovering ligands for biomolecules. To date, most, if not all, biologically templated DCC systems employ only a single biomolecule to direct the self‐assembly process. To expand the scope of DCC, herein, a novel multiprotein DCC strategy has been developed that combines the discriminatory power of a zwitterionic “thermal tag” with the sensitivity of differential scanning fluorimetry. This strategy is highly sensitive and could differentiate the binding of ligands to structurally similar subfamily members. Through this strategy, it was possible to simultaneously identify subfamily‐selective probes against two clinically important epigenetic enzymes: FTO ( 7 ; IC₅₀=2.6 μm ) and ALKBH3 ( 8 ; IC₅₀=3.7 μm ). To date, this is the first report of a subfamily‐selective ALKBH3 inhibitor. The developed strategy could, in principle, be adapted to a broad range of proteins; thus it is of broad scientific interest.     

A NOVEL GAS SENSOR FROM POLYMER-GRAFTED CARBON BLACK: EFFECTS OF POLYMER,CRYSTALLINE ORGANIC COMPOUND,AND CARBON BLACK ON ELECTRIC RESPONSE TO TETRAHYDROFURAN VAPOR

The responsiveness of electric resistance of three types of composites, polyethylene (PE)/PE-grafted carbon black (CB) (CB-g-PE), N,N'-dicyclohexylcarbodiimide (DCC)/CB-g-PE and PE/DCC/CB-g-PE, to THF vapor was investigated. To modify the CB compatibility in the composite, PE was grafted onto a CB surface. Although responsiveness of composite DCC/CB-g-PE was the most sensitive to THF vapor among the three composites, the composite film is too weak to be of practical use. On the contrary, the responsiveness and the sensitivity of PE/CB-g-PE were too low to be used in many fields. However, through modification by the addition of DCC, responsiveness was greatly improved, and the sensitivity was considerably higher than that of PE/CB-g-PE. The effects of CB-g-PE and DCC content in the composites on the responsiveness to THF vapor was studied in detail. It was found that the responsiveness of electric resistance to THF vapor was caused by the change of the crystalline structure of the composite. A crystalline model was proposed to explain the response of the composite to solvent vapor.     

Structure elucidation of a condensation product of 4-aminopyrrole derivatives and dicyclohexylcarbodiimide

The chemical structure of the two condensation products of dicyclohexylcarbodiimide (DCC) with the precursors of the mono-pyrrole homologues of distamycin and with the mono and tri-pyrrole homologues of congocidine were established. The two products isolated were proven to be condensation products between 4-aminopyrrole derivatives and dicyclohexylcarbodiimide (DCC).     

DCC/AlCl_3体系引发异丁烯正离子聚合

研究以对-二枯基氯(DCC)/AlCl3体系引发异丁烯在CH2Cl2/Hex(40/60,V/V)混合溶剂中进行正离子聚合,探讨了DCC用量、给电子试剂,如三苯胺(TPA)、2,6-二甲基吡啶(DMPy)对异丁烯正离子聚合转化率、产物分子量及其分布的影响.结果表明,在无给电子试剂存在时,DCC和体系中微量水均可与AlCl3产生络合竞争引起相继的引发竞争,聚合产物GPC谱图呈双峰分布,分子量分布宽,需要大量的引发剂DCC(DCC/H2O=5.3)来减少体系中微量水的不可控引发;在少量上述给电子试剂存在下,可提高DCC的引发效率,减少向单体链转移反应,提高聚合产物的分子量和使分子量分布呈较窄的单峰分布,即使在较低DCC用量下也可基本抑制体系中微量水的不可控引发,达到DCC定量引发,并得到分子量分布相对较窄(Mw/Mn≈2.3)的聚异丁烯产物.     

Exploring the formation pathways of donor-acceptor catenanes in aqueous dynamic combinatorial libraries

The discovery through dynamic combinatorial chemistry (DCC) of a new generation of donor-acceptor [2]catenanes highlights the power of DCC to access unprecedented structures. While conventional thinking has limited the scope of donor-acceptor catenanes to strictly alternating stacks of donor (D) and acceptor (A) aromatic units, DCC is demonstrated in this paper to give access to unusual DAAD, DADD, and ADAA stacks. Each of these catenanes has specific structural requirements, allowing control of their formation. On the basis of these results, and on the observation that the catenanes represent kinetic bottlenecks in the reaction pathway, we propose a mechanism that explains and predicts the structures formed. Furthermore, the spontaneous assembly of catenanes in aqueous dynamic systems gives a fundamental insight into the role played by hydrophobic effect and donor-acceptor interactions when building such complex architectures.     

Micellar electrokinetic chromatography with laser-induced fluorescence detection for rapid and sensitive analysis of two new bioactive reagents using dynamic covalent coating

A simple, rapid, selective, and sensitive micellar electrokinetic chromatography (MEKC) with laser-induced fluorescence detection (LIF) method was developed, using hexamethyldisilazane (HMDS) as dynamic covalent coating (DCC), for the analysis of two new bioactive agents N-n-hexyl-N'-(sodium p-aminobenzenesulfonate) thiourea (HXPT) and N-n-undecyl-N'-(sodium p-aminobenzenesulfonate) thiourea (UPT) derivatized with 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole. MEKC methods both not using DCC and using DCC were investigated. In a series of optimization steps, DCC and a running buffer of 20 mM Na2B4O7 + 16 mM SDS + 8% acetonitrile were applied for determination of the derivatives. Linear relationships for HXPT and UPT were obtained in the range of 5 to 100 microM (correlation coefficient: 0.9986 for HXPT, 0.9978 for UPT), and the detection limits for HXPT and UPT were 16.5 and 39.0 ng mL(-1). The sensitivity was improved over that of fluorescence spectroscopy methods. The method was applied to the analysis of the two reagents in lab water waste with recoveries in the range of 95.6-107.5%.     

Structure‐Based Design of Inhibitors of the Aspartic Protease Endothiapepsin by Exploiting Dynamic Combinatorial Chemistry

Structure‐based design (SBD) can be used for the design and/or optimization of new inhibitors for a biological target. Whereas de novo SBD is rarely used, most reports on SBD are dealing with the optimization of an initial hit. Dynamic combinatorial chemistry (DCC) has emerged as a powerful strategy to identify bioactive ligands given that it enables the target to direct the synthesis of its strongest binder. We have designed a library of potential inhibitors (acylhydrazones) generated from five aldehydes and five hydrazides and used DCC to identify the best binder(s). After addition of the aspartic protease endothiapepsin, we characterized the protein‐bound library member(s) by saturation‐transfer difference NMR spectroscopy. Cocrystallization experiments validated the predicted binding mode of the two most potent inhibitors, thus demonstrating that the combination of de novo SBD and DCC constitutes an efficient starting point for hit identification and optimization.