Mannosylated G(0) dendrimers with nanomolar affinities to Escherichia coli FimH

Pentaerythritol and bis-pentaerythritol scaffolds were used for the preparation of first generation glycodendrimers bearing aryl alpha-D-mannopyranoside residues assembled using single-step Sonogashira and click chemistry. The carbohydrate precursors were built with either para-iodophenyl, propargyl, or 2-azidoethyl aglycones whereas the pentaerythritol moieties were built with terminal azide or propargyl groups, respectively. Cross-linking abilities of this series of glycodendrimers were first evaluated with the lectin from Canavalia ensiformis (Concanavalin A). Surface plasmon resonance measurements showed these two families of mannosylated clusters as the best ligands known to date toward Escherichia coli K12 FimH with subnanomolar affinities. Tetramer 4 had a K(d) of 0.45 nM. These clusters were 1000 times more potent than mannose for their capacity to inhibit the binding of E. coli to erythrocytes in vitro.     

Rapid Screening of Lectins for Multivalency Effects with a Glycodendrimer Microarray

Multivalency is an important phenomenon in protein–carbohydrate interactions. In order to evaluate glycodendrimers as multivalent inhibitors of carbohydrate binding proteins, we displayed them on a microarray surface. Valencies were varied from 1 to 8, and corrections were made for the valencies so that all surfaces contained the same amount of the sugar ligand. Five different carbohydrates were attached to the dendrimers. A series of fluorescent lectins was evaluated, and for each of them a binding profile was obtained from a single experiment showing both the specificity of the lectin for a certain sugar and whether it prefers multivalent ligands or not. Very distinct binding patterns were seen for the various lectins. The results were rationalized with respect to the interbinding distances of the lectins.     

Acetyl‐α‐d‐mannopyranose‐based cationic polymer via RAFT polymerization for lectin and nucleic acid bindings

Functional cationic polymers carrying mannose moieties were synthesized in a facile manner by employing RAFT polymerization. Initially, a protected carbohydrate based monomer, [2‐(2,3,4,6‐tetra‐O‐acetyl‐α‐d ‐mannopyranosyloxy)ethyl methacrylate (AcManEMA)], was prepared by the O‐glycosylation of 2‐hydroxyethyl methacrylate (HEMA). Subsequently, a macroRAFT agent of poly[2‐(dimethyl)amino ethyl methacrylate] (PDMAEMA) was generated, and a further chain extension polymerization with AcManEMA was carried out in dioxane to form a acetylated mannose cationic diblock copolymer, PDMAEMA‐b‐PAcManEMA. It was attained in high yields and displayed low dispersity (Ð). Acetylated mannose moieties on the polymer were deprotected with sodium methoxide and the amines from the DMAEMA block were protonated to yield a cationic diblock glycopolymer, PDMAEMA‐b‐PManEMA. The cationic property of polymers were characterized by mixing with a negatively charged siRNA duplex and a pDNA, and aggregates of 102 and 233 nm were obtained, respectively. Agarose gel shift assay revealed that the polymers were able to retain the nucleic acids as large polymer complexes. Lectin binding assay proved that the mannose residue on the polymers were only able to bind specifically with ConA. PNA lectin was employed as a control and did not show specific binding. The cationic glycopolymer could be advantageous in targeted nucleic acids delivery in specific cells. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017 , 134, 44947.     

Optimal modification of annexin V with fluorescent dyes

The many uses of chemically modified annexin Vs necessitate an understanding of the optimal degree of modification and modification sites of the protein. When reacted with the N-hydroxysuccinimide ester of Cy5.5, annexin V with one modification per mole of protein retained its affinity for phosphatidylserine of apoptotic cells, whereas modification with two dyes per mole of protein caused a complete loss of activity. A tryptic digest LC/MS method was used to identify the modification sites as either of two closely spaced lysine residues, in position 286 or 290. The crystal structure indicated the location of these lysines was distal to the phosphatidylserine binding sites on annexin V. These results can be used to develop active or inactive fluorescent control annexin V proteins and to suggest strategies for attaining higher levels of modification with retention of bioactivity.     

Palindromes in DNA—A Risk for Genome Stability and Implications in Cancer

A palindrome in DNA consists of two closely spaced or adjacent inverted repeats. Certain palindromes have important biological functions as parts of various cis-acting elements and protein binding sites. However, many palindromes are known as fragile sites in the genome, sites prone to chromosome breakage which can lead to various genetic rearrangements or even cell death. The ability of certain palindromes to initiate genetic recombination lies in their ability to form secondary structures in DNA which can cause replication stalling and double-strand breaks. Given their recombinogenic nature, it is not surprising that palindromes in the human genome are involved in genetic rearrangements in cancer cells as well as other known recurrent translocations and deletions associated with certain syndromes in humans. Here, we bring an overview of current understanding and knowledge on molecular mechanisms of palindrome recombinogenicity and discuss possible implications of DNA palindromes in carcinogenesis. Furthermore, we overview the data on known palindromic sequences in the human genome and efforts to estimate their number and distribution, as well as underlying mechanisms of genetic rearrangements specific palindromic sequences cause.     

Design and Synthesis of Galactosylated Bifurcated Ligands with Nanomolar Affinity for Lectin LecA from Pseudomonas aeruginosa

Lectin A (LecA) from Pseudomonas aeruginosa is an established virulence factor. Glycoclusters that target LecA and are able to compete with human glycoconjugates present on epithelial cells are promising candidates to treat P. aeruginosa infection. A family of 32 glycodendrimers of generation 0 and 1 based on a bifurcated bis‐galactoside motif have been designed to interact with LecA. The influences both of the central multivalent core and of the aglycon of these glycodendrimers on their affinity toward LecA have been evaluated by use of a microarray technique, both qualitatively for rapid screening of the binding properties and also quantitatively (K_d). This has led to high‐affinity LecA ligands with K_d values in the low nanomolar range (K_d=22 nm for the best one).     

Protein Sensing Device with Multi-Recognition Ability Composed of Self-Organized Glycopeptide Bundle

We designed and synthesized amphiphilic glycopeptides with glucose or galactose at the C-terminals. We observed the protein-induced structural changes of the amphiphilic glycopeptide assembly in the lipid bilayer membrane using transmission electron microscopy (TEM) and Fourier transform infrared reflection-absorption spectra (FTIR-RAS) measurements. The glycopeptides re-arranged to form a bundle that acted as an ion channel due to the interaction among the target protein and the terminal sugar groups of the glycopeptides. The bundle in the lipid bilayer membrane was fixed on a gold-deposited quartz crystal microbalance (QCM) electrode by the membrane fusion method. The protein-induced re-arrangement of the terminal sugar groups formed a binding site that acted as a receptor, and the re-binding of the target protein to the binding site induced the closing of the channel. We monitored the detection of target proteins by the changes of the electrochemical properties of the membrane. The response current of the membrane induced by the target protein recognition was expressed by an equivalent circuit consisting of resistors and capacitors when a triangular voltage was applied. We used peanut lectin (PNA) and concanavalin A (ConA) as target proteins. The sensing membrane induced by PNA shows the specific response to PNA, and the ConA-induced membrane responded selectively to ConA. Furthermore, PNA-induced sensing membranes showed relatively low recognition ability for lectin from Ricinus Agglutinin (RCA120) and mushroom lectin (ABA), which have galactose binding sites. The protein-induced self-organization formed the spatial arrangement of the sugar chains specific to the binding site of the target protein. These findings demonstrate the possibility of fabricating a sensing device with multi-recognition ability that can recognize proteins even if the structure is unknown, by the protein-induced self-organization process.     

人肝再生增强因子对人外周血单个核细胞增殖的影响及其机制

目的探讨人肝再生增强因子(hALR)对人外周血单个核细胞(PBMC)增殖的影响及其机制。方法梯度离心分离PBMC,将细胞分为正常对照组、刀豆蛋白A(ConA)(5mg/L)组和ConA(5mg/L)+hALR(30mg/L)组,分别培养10min、30min、1h、2h、4h后,MTT法检测各组各时间点细胞增殖水平,钙荧光指示剂法检测细胞内游离Ca2+浓度的变化,Western blot法检测细胞内胞外信号调节激酶(ERK)的磷酸化程度。结果4h内,各组细胞的增殖水平差异无统计学意义,但ConA组细胞增殖水平已表现出逐渐升高的趋势。正常对照组细胞内Ca2+浓度在加入Fluo-3/AM后2h达高峰,ConA组1h达高峰,ConA+hALR组10min达高峰。正常对照组细胞内磷酸化的ERK随培养时间的延长而逐渐减少;ConA组细胞内磷酸化的ERK在30min达高峰,之后逐渐降低;ConA+hALR组细胞内磷酸化的ERK在2h前明显低于ConA组。结论hALR可能通过影响细胞内Ca2+浓度的变化峰值和磷酸化的ERK,来抑制人PBMC的免疫功能,从而影响其增殖。     

Functional classification of protein kinase binding sites using Cavbase

Increasingly, drug-discovery processes focus on complete gene families. Tools for analyzing similarities and differences across protein families are important for the understanding of key functional features of proteins. Herein we present a method for classifying protein families on the basis of the properties of their active sites. We have developed Cavbase, a method for describing and comparing protein binding pockets, and show its application to the functional classification of the binding pockets of the protein family of protein kinases. A diverse set of kinase cavities is mutually compared and analyzed in terms of recurring functional recognition patterns in the active sites. We are able to propose a relevant classification based on the binding motifs in the active sites. The obtained classification provides a novel perspective on functional properties across protein space. The classification of the MAP and the c-Abl kinases is analyzed in detail, showing a clear separation of the respective kinase subfamilies. Remarkable cross-relations among protein kinases are detected, in contrast to sequence-based classifications, which are not able to detect these relations. Furthermore, our classification is able to highlight features important in the optimization of protein kinase inhibitors. Using small-molecule inhibition data we could rationalize cross-reactivities between unrelated kinases which become apparent in the structural comparison of their binding sites. This procedure helps in the identification of other possible kinase targets that behave similarly in "binding pocket space" to the kinase under consideration.     

On the reason why acid treatment of biomass enhances the biosorption capacity of cationic pollutants

The present work is aimed at understanding the effect of acid treatment and demonstrating the reason for its effect. For this, Corynebacterium glutamicum biomass was used as a model biomass. Two cationic (cadmium and Methylene Blue) and one anionic (Reactive Red 4) pollutants were used to evaluate the sorption capacity by the biomass. Isotherm experiments showed that acid treatment of the biomass increased the uptake of the cationic pollutants, but decreased that of the anionic pollutant. Through the results of FTIR and potentiometric titrations, it was found that carboxyl groups on the biomass increased after acid treatment. The carboxyl groups seem to be generated likely through hydrolysis of esters in the biomass under the acidic condition. Therefore, increase of the carboxyl groups provided the binding sites for cationic pollutants, whereas it may interfere with the binding of anionic pollutants.     

Comparative analysis of the surface interaction properties of the binding sites of CDK2, CDK4, and ERK2

Recently developed hydrogen-bonding and hydrophobic analysis algorithms were used to investigate the interaction properties of the ATP binding sites of CDK2, CDK4, and ERK2. We were able to prioritise those hydrogen-bonding groups that are observed to bind the native ATP ligand, as well as to identify other important groups found to bind inhibitors of these enzymes. However, as the hydrogen-bonding groups in the ATP binding sites of these enzymes are fairly well-conserved, we have confirmed that inhibitor selectivity may be predominantly due to differences in either the hydrophobic or steric properties of their binding sites. In particular, the hydrophobic properties of regions outside the specificity surface were observed to provide a rationale for the differences in specificity between various inhibitors to these enzymes. Our method was thus able to identify variations in hydrophobicity. The greater hydrophobicity of certain regions of CDK4 over analogous regions in CDK2 was detectable; likewise, it was possible to distinguish variations in hydrophobicity for regions of CDK2 against those in ERK2, despite the fact that these regions are largely composed of similar residue types.     

Novel hyperbranched glycomimetics recognized by the human mannose receptor: quinic or shikimic acid derivatives as mannose bioisosteres

The mannose receptor mediates the internalization of a wide range of molecules or microorganisms in a pattern recognition manner. Therefore, it represents an attractive entry for specific drug, gene, or antigen delivery to macrophages and dendritic cells. In an attempt to design novel effective synthetic mannose receptor ligands, quinic and shikimic acid were selected as putative mannose mimics on the basis of X-ray crystallographic data from the related rat mannose-binding lectin. As the mannose receptor preferentially binds to molecules displaying several sugar residues, fluorescein-labeled cluster quinic and shikimic acid derivatives with valencies of two to eight were synthesized. Their mannose receptor mediated uptake was assayed on monocyte-derived human dendritic cells by cytofluorimetric analysis. Mannose-receptor specificity was further assessed by competitive inhibition assays with mannan, by confocal microscopy analysis, and by expression of the mannose receptor in transfected Cos-1 cells. Constructs derived from both quinic and shikimic acid were efficiently recognized by the mannose receptor with an optimum affinity for the molecules with a valency of four. As a result, commercially available quinic and shikimic acids appear as stable mannose bioisosteres, which should prove valuable tools for specific cell delivery.     

A Synthetic MUC1 Anticancer Vaccine Containing Mannose Ligands for Targeting Macrophages and Dendritic Cells

A MUC1 anticancer vaccine equipped with covalently linked divalent mannose ligands was found to improve the antigen uptake and presentation by targeting mannose‐receptor‐positive macrophages and dendritic cells. It induced much stronger specific IgG immune responses in mice than the non‐mannosylated reference vaccine. Mannose coupling also led to increased numbers of macrophages, dendritic cells, and CD4⁺ T cells in the local lymph organs. Comparison of di‐ and tetravalent mannose ligands revealed an increased binding of the tetravalent version, suggesting that higher valency improves binding to the mannose receptor. The mannose‐coupled vaccine and the non‐mannosylated reference vaccine induced IgG antibodies that exhibited similar binding to human breast tumor cells.     

Duplex formation of the simplified nucleic acid GNA

Glycol nucleic acid (GNA) has an acyclic backbone of propylene glycol nucleosides that are connected by phosphodiester bonds. This paper characterizes the duplex-formation properties of this simplified nucleic acid. Although single and multiple GNA nucleotides are highly destabilizing if incorporated into DNA duplexes, the two enantiomeric oligomers (S)-GNA and (R)-GNA form antiparallel homoduplexes that are thermally and thermodynamically significantly more stable than analogous duplexes of DNA and RNA. The salt-dependence and Watson-Crick-pairing fidelity of GNA duplexes are similar to those of DNA duplexes, but, apparently, the 2'-deoxyribonucleotide and the propylene glycol backbones are not compatible with each other. This conclusion is further supported by cross-pairing experiments. Accordingly, both (S)- and (R)-GNA strands do not generally pair with DNA. However, (S)-GNA, but not (R)-GNA, forms stable heteroduplexes with RNA in sequences that are low in G:C content. Altogether, the high stability and fidelity of GNA duplex formation in combination with the economical accessibility of propylene glycol building blocks for oligonucleotide synthesis render GNA an attractive candidate for the design of self-assembling materials. They further suggest that GNA could be considered as a potential candidate for a predecessor of RNA during the evolution of life on Earth.     

Fluorescent labelled thiourea-bridged glycodendrons

GlcNAc-coated glycodendrimers, which are polyvalent glycomimetics, display strong in vitro affinity for the rat natural killer cell protein-1A (NKR-P1A), a C-type lectin-like receptor of natural killer (NK) cells in rats, humans and some strains of mice. Administration of these compounds in vivo results in a substantial increase in the antitumour activity with involvement of the natural cell immunity. To clarify the in vitro and in vivo fate of these molecules, we synthesized labelled glycodendron analogues of the previously studied glycodendrimers. Labelling with fluorescent tags enabled the localization of the glycodendrons in white blood cells, tumours and other tissues by using different imaging techniques such as fluorescence and confocal microscopy. These studies are useful for probing the mechanism of action and fate of artificial ligands and the cell receptors involved.     

白细胞介素-2脂质体的制备及其活性和稳定性的研究

利用逆相蒸发法制备出白细胞介素－2（IL－2）脂质体,其包封率为34．52±1．12％,在电镜下具有典型大单层脂体结构,大小为0．2μm左右。利用“ConA诱导T细胞微量测定法”对其活性进行了测定,结果表明IL－2脂质体,活性提高,稳定性好。     

Grafting of discontinuous sites: a protein modeling strategy

A strategy for modeling continuous as well as discontinuoussites in protein structures has been developed. Central to thismodeling strategy is the search algorithm of FITSITE, a programto search a given target structure for suitable combinationsof backbone positions mirroring as closely as possible the geometricrelationships of a source structural motif of interest. Alltarget sites detected by FITSITE are further refined to mimicthe source geometry. The side-chain rotamer library conceptfails to precisely describe side chains involved in coordinativebonding (e.g. metal binding sites). Therefore an algorithm usingdetailed database bonding parameter information was appliedfor the side-chain construction. The FITSITE program and thesubsequent processing of the program output are presented ina test case. The Rop protein, a four-helix bundle structure,served as the target protein. It was searched for candidatesites to model a variety of metal binding sites, with structuresextracted from Brookhaven Protein Database entries. The preliminaryprotein models were investigated for structural overlaps withneighboring residues by interactive computer graphics; if required,additional changes were performed. A set of parameters for energyminimization with AMBER (including metal ions) was developed,and the completed Rop variants were energy minimized. Finally,12 potentially metal binding Rop variants were selected forproduction via genetic engineering.     

Continuous CHO cell cultures with improved recombinant protein productivity by using mannose as carbon source: Metabolic analysis and scale-up simulation

The replacement of glucose by mannose as a means to improve recombinant protein productivity was studied for the first time in continuous cultures of Chinese hamster ovary (CHO) cells producing human recombinant tissue plasminogen activator (t-PA). Steady-state operation at two hexose levels in the inlet (2.5 and 10 mM) allowed comparing the effect of sugar type and concentration on cell metabolism and t-PA production independently of changes in specific growth rates produced by different culture conditions. An increase in biomass concentration (15–20%) was observed when using mannose instead of glucose. Moreover, specific hexose consumption rates were 20–25% lower in mannose cultures whereas specific production rates of lactate, an undesirable by-product, were 25–35% lower than in glucose control cultures. The volumetric productivity of t-PA increased up to 30% in 10 mM mannose cultures, without affecting the sialylation levels of the protein. This increase is manly explained by the higher cell concentration, and represents a substantial improvement in the t-PA production process using glucose. Under this condition, the oxygen uptake rate and the specific oxygen consumption rate, both estimated by a stoichiometric analysis, were about 10% and 25% lower in mannose cultures, respectively. These differences lead to significant differences at larger scales, as it was estimated by simulating cell cultures at different bioreactor sizes (5–5000 L). By assuming a set of regular operating conditions in this kind of process, it was determined that mannose-based cultures could allow culturing CHO cells up to 3000 L compared to only 80 L in glucose cultures at the same conditions. These facts indicate that mannose cultures may have a significant advantage over glucose cultures not only in terms of volumetric productivity of the recombinant protein but also for their potential application in large-scale productive processes.     

Inhibition of fat cell lipolysis by low FFA to albumin ratios

Epididymal fat cells isolated from chronically cold-exposed rats were used to study the inhibition of lipolysis with albumin bound FFA. It was demonstrated that lipolysis becomes inhibited as the class 2 binding sites on albumin are filled and that 50% inhibition occurs at free fatty acid (FFA) to albumin ratios between 4.6 and 4.0. Experiments with dibutyryl adenosine cyclic phosphate suggest that this is an effect on the fat cell lipases rather than the lipase activating system or phosphodiesterase. The results indicate that reesterification proceeds as a relatively constant percentage of the rate of lipolysis and, therefore, in the absence of exogenous FFA, conditions that reduce lipolysis reduce reesterification. On the other hand, high rates of reesterification can apparently be stimulated even when the class 1 binding sites on albumin are not filled.     

Use of click chemistry to define the substrate specificity of Leishmania beta-1,2-mannosyltransferases

Leishmania spp. are human pathogens that utilize a novel beta-1,2-mannan as their major carbohydrate reserve material. We describe a new approach that combines traditional substrate-modification methods and "click chemistry" to assemble a library of modified substrates that were used to qualitatively define the substrate tolerance of the Leishmania beta-1,2-mannosyltransferases responsible for beta-1,2-mannan biosynthesis. The library was assembled by using the highly selective copper(I)-catalysed cycloaddition reaction of azides and alkynes to couple an assortment of azide- and alkyne-functionalized small molecules with complementary alkyne- and azide-functionalized mannose derivatives. All mannose derivatives with alpha-orientated substituents on the anomeric carbon were found to act as substrates when incubated with a Leishmania mexicana particulate fraction containing GDP-mannose. In contrast, 6-substituted mannose derivatives were not substrates. Representative products formed from the library compounds were analysed by mass spectrometry, methylation linkage analysis and beta-mannosidase digestions and showed extension with up to four beta-1,2-linked mannosyl residues. This work provides insights into the substrate specificity of this new class of glycosyltransferases that can be applied to the development of highly specific tools and inhibitors for their study.