Synthetic Approaches of Epoxysuccinate Chemical Probes.

Synthetic chemical probes are powerful tools for investigating biological processes. They are particularly useful for proteomic studies such as activity-based protein profiling (ABPP). These chemical methods initially used mimics of natural substrates. As the techniques gained prominence, more and more elaborate chemical probes with increased specificity towards given enzyme/protein families and amenability to various reaction conditions were used. Among the chemical probes, peptidyl-epoxysuccinates represent one of the first types of compounds used to investigate the activity of the cysteine protease papain-like family of enzymes. Structurally derived from the natural substrate, a wide body of inhibitors and activity- or affinity-based probes bearing the electrophilic oxirane unit for covalent labeling of active enzymes now exists. Herein, we review the literature regarding the synthetic approaches to epoxysuccinate-based chemical probes together with their reported applications, from biological chemistry and inhibition studies to supramolecular chemistry and the formation of protein arrays.

Synthesis of Fluorescent Dansyl Derivatives of Methoxyamine and Diphenylhydrazine as Free Radical Precursors.

Starting from dansyl-chloride, in reaction with 1,1-diphenylhydrazine and methoxyamine, two new fluorescent derivatives 1 and 2 were obtained and characterized by NMR, IR, UV-Vis, HR-MS, and fluorescence spectroscopy. The single-crystal X-ray structure was obtained for compound 2. Both compounds generate free radicals by oxidation, as demonstrated by ESR spectroscopy. Compound 1 generates the corresponding hydrazyl-persistent free radical, evidenced directly by ESR spectroscopy, while compound 2 generates in the first instance the methoxyaminyl short-lived free radical, which decomposes rapidly with the formation of the methoxy radical, evidenced by the ESR spin-trapping technique. By oxidation of compounds 1 and 2, their fluorescence is quenched.

A novel adaptive fluorescent probe for cell labelling.

In this study we describe the synthesis and characterisation of a new hydrazone-based fluorescent compound that is able to selectively label the endoplasmic reticulum (ER) in yeast and mammalian living cells. The fluorescence properties of the compound depended on the DMSO/water ratio and on the pH. NMR experiments allowed determination of the conformation adopted in various environments. Apart from the convenient synthetic procedure, our compound displays low cell toxicity and blue emission compatible with filters routinely used in fluorescence microscopy.

Logical Reduction of Biological Networks to Their Most Determinative Components.

Boolean networks have been widely used as models for gene regulatory networks, signal transduction networks, or neural networks, among many others. One of the main difficulties in analyzing the dynamics of a Boolean network and its sensitivity to perturbations or mutations is the fact that it grows exponentially with the number of nodes. Therefore, various approaches for simplifying the computations and reducing the network to a subset of relevant nodes have been proposed in the past few years. We consider a recently introduced method for reducing a Boolean network to its most determinative nodes that yield the highest information gain. The determinative power of a node is obtained by a summation of all mutual information quantities over all nodes having the chosen node as a common input, thus representing a measure of information gain obtained by the knowledge of the node under consideration. The determinative power of nodes has been considered in the literature under the assumption that the inputs are independent in which case one can use the Bahadur orthonormal basis. In this article, we relax that assumption and use a standard orthonormal basis instead. We use techniques of Hilbert space operators and harmonic analysis to generate formulas for the sensitivity to perturbations of nodes, quantified by the notions of influence, average sensitivity, and strength. Since we work on finite-dimensional spaces, our formulas and estimates can be and are formulated in plain matrix algebra terminology. We analyze the determinative power of nodes for a Boolean model of a signal transduction network of a generic fibroblast cell. We also show the similarities and differences induced by the alternative complete orthonormal basis used. Among the similarities, we mention the fact that the knowledge of the states of the most determinative nodes reduces the entropy or uncertainty of the overall network significantly. In a special case, we obtain a stronger result than in previous works, showing that a large information gain from a set of input nodes generates increased sensitivity to perturbations of those inputs.

Selective host molecules obtained by dynamic adaptive chemistry.

Up till 20 years ago, in order to endow molecules with function there were two mainstream lines of thought. One was to rationally design the positioning of chemical functionalities within candidate molecules, followed by an iterative synthesis-optimization process. The second was the use of a "brutal force" approach of combinatorial chemistry coupled with advanced screening for function. Although both methods provided important results, "rational design" often resulted in time-consuming efforts of modeling and synthesis only to find that the candidate molecule was not performing the designed job. "Combinatorial chemistry" suffered from a fundamental limitation related to the focusing of the libraries employed, often using lead compounds that limit its scope. Dynamic constitutional chemistry has developed as a combination of the two approaches above. Through the rational use of reversible chemical bonds together with a large plethora of precursor libraries, one is now able to build functional structures, ranging from quite simple molecules up to large polymeric structures. Thus, by introduction of the dynamic component within the molecular recognition processes, a new perspective of deciphering the world of the molecular events has aroused together with a new field of chemistry. Since its birth dynamic constitutional chemistry has continuously gained attention, in particular due to its ability to easily create from scratch outstanding molecular structures as well as the addition of adaptive features. The fundamental concepts defining the dynamic constitutional chemistry have been continuously extended to currently place it at the intersection between the supramolecular chemistry and newly defined adaptive chemistry, a pivotal feature towards evolutive chemistry.

A Synthetic Approach for Oxadiazole-Decorated Azobenzene Photoswitches.

This work reports the design and synthesis of novel oxadiazole-decorated azobenzenes, structural analysis of the resulting compounds and behavior under light irradiation. The synthetic strategy involved constructing amino functionalized heterocyclic key intermediates which were used either to yield electrophilic diazonium salts able to react with phenol moieties or as nucleophilic partners in Bayer-Mills reaction with nitroso-substituted derivatives. The amino-derived oxadiazole intermediates were investigated by absorption and emission spectroscopy providing blue and green emitted light. The target oxadiazole-decorated azobenzenes were structurally characterized, including solid-state structures, and subsequently used in irradiation experiments in order to take advantage of the azo group known to provide photoswitching abilities. We noticed quenching of the emissive properties in presence of the azo group; however, all compounds were very stable to repeated cycles of light irradiation. In addition, according to structural diversification we could obtain half-lives of the meta stable isomers within hours to hundreds of hours range. The experimental results were very well correlated with DFT calculations.

Unexpected formation of N-(1-(2-aryl-hydrazono)isoindolin-2-yl)benzamides and their conversion into 1,2-(bis-1,3,4-oxadiazol-2-yl)benzenes.

Reaction between ortho-phthalaldehyde and various aroylhydrazines unexpectedly yields N-(1-(2-aryl-hydrazono)isoindolin-2-yl)benzamides as major products along with the predictable 1,2-bis-aroylhydrazones. NMR investigation of the major reaction products indicate the presence of a mixture of geometrical isomers, in various ratios. Single crystal X-ray diffraction confirms the proposed structure and indicates a Z configuration of the C═N double bond substitutents. Optimization of the condensation reaction conditions enabled quantitative isolation of the cyclic isomer. Oxidation of the isomers with bis(trifluoroacetoxy)iodobenzene (PIFA) leads to rapid formation of new highly fluorescent 1,2-bis(5-aryl-1,3,4-oxadiazol-2-yl)benzenes.

Glycine fluoromethylketones as SENP-specific activity based probes.

We report here the synthesis and biochemical properties of a new peptidyl activity-based probe 1 for SUMO proteases, SENPs. The activity-based probe has at its C terminus a glycine-derived fluoromethylketone moiety as a reactive group designed to target the active-site cysteine of SENPs. Based on a study of the interactions between SENPs and SUMOs, we introduced further design elements that allow the activity-based probe to selectively target SENPs at low micromolar to high nanomolar concentrations. Moreover, 1 out-competes SUMO1 from the reversible SUMO1-SENP1 complex, thus suggesting that 1 and SUMO1 share a common binding site on SENP1.

A general solid phase method for the synthesis of sequence independent peptidyl-fluoromethyl ketones.

We present here a new, general, solid phase strategy for the synthesis of sequence independent peptidyl-fluoromethyl ketones using standard Fmoc peptide chemistry. Our method is based on the synthesis of bifunctional linkers which allows the incorporation of amino acid fluoromethyl ketone unit at the C-terminal end of peptide sequences. Application of this approach for the synthesis of activity based probes for SENPs is also described.

Exploring Arylazo-3,5-Bis(trifluoromethyl)pyrazole Switches.

Arylazopyrazoles stand out among the azoheteroarene photoswitches due to their excellent properties in terms of stability of the least stable isomer and conversion between isomers, leading to their use in several interesting applications. We report herein the synthesis of arylazo-trifluoromethyl-substituted pyrazoles and their switching behavior under light irradiation. UV-vis and NMR experiments showed that arylazo-1H-3,5-bis(trifluoromethyl)pyrazoles displayed very long half-lives in DMSO (days), along with reasonable values of other parameters that characterize a photoswitch. Inclusion of naphthyl moieties as aryl counterparts of the arylazopyrazoles is beneficial only in combination with trifluoromethyl groups, while extending the conjugation by grafting the pyrazole moiety with electron-donating or -withdrawing substituents positively affects the photoswitching behavior, in terms of isomerization yield and half-lives of the least stable isomer. The experimental values were correlated with theoretical calculations indicating the valuable influence of the trifluoromethyl groups onto the photoswitching behavior.

Metal ion mediated self-assembly directed formation of protein arrays.

Self-assembled inorganic-protein arrays with well-defined and controllable size and structure were obtained through the Fe(II) complexation of protein-conjugated terpyridine units (ligand). The atom-level control of the ligand is obtained through residue-specific conjugation between the complexing unit (terpy) containing an activity-based probe and a corresponding active enzyme (papain). The Fe(II)-based self-assembly performed on this unique building block (ligand) leads to chemical species of unprecedented constitution. The first example presented herein opens the way to a shape and size regime usually reserved to polymers.

Protein-inorganic array construction: design and synthesis of the building blocks.

Herein we describe the design and synthesis of the first series of di-functional ligands for the directed construction of inorganic-protein frameworks. The synthesized ligands are composed of a metal-ion binding moiety (terpyridine-based) conjugated to an epoxysuccinyl peptide, known to covalently bind active cysteine proteases through the active-site cysteine. We explore and optimize two different conjugation chemistries between the di-functionalized metal-ion ligand and the epoxysuccinyl-containing peptide moiety: peptide-bond formation (with limited success) and Cu(I)-catalysed click chemistry (with good results). Further, the complexation of the synthesized ligands with Fe(II) and Ni(II) ions is investigated: the di-functional ligands are confirmed to behave similarly to the parent terpyridine. As designed, the peptidic moiety does not interfere with the complexation reaction, in spite of the presence of two triazole rings that result from the click reaction. ES-MS together with NMR and UV/Vis studies establish the structure, the stoichiometry of the complexation reactions, as well as the conditions under which chemically sensitive peptide-containing polypyridine ligands can undergo the self-assembly process. These results establish the versatility of our approach and open the way to the synthesis of di-functional ligands containing more elaborated polypyridine ligands as well as affinity labels for different enzyme families. As such, this paper is the first step towards the construction of robust supramolecular species that cover a size-regime and organization level previously unexplored.

Removing heavy metals from synthetic effluents using "kamikaze" Saccharomyces cerevisiae cells.

One key step of the bioremediation processes designed to clean up heavy metal contaminated environments is growing resistant cells that accumulate the heavy metals to ensure better removal through a combination of biosorption and continuous metabolic uptake after physical adsorption. Saccharomyces cerevisiae cells can easily act as cation biosorbents, but isolation of mutants that are both hyperaccumulating and tolerant to heavy metals proved extremely difficult. Instead, mutants that are hypersensitive to heavy metals due to increased and continuous uptake from the environment were considered, aiming to use such mutants to reduce the heavy metal content of contaminated waters. In this study, the heavy metal hypersensitive yeast strain pmr1Delta was investigated for the ability to remove Mn2+, Cu2+, Co2+, or Cd2+ from synthetic effluents. Due to increased metal accumulation, the mutant strain was more efficient than the wild-type in removing Mn2+, Cu2+, or Co2+ from synthetic effluents containing 1-2 mM cations, with a selectivity and also in removing Mn2+ and Cd2+ from synthetic effluents containing 20-50 microM cations, with a selectivity Mn2+ > Cd2+.

A polycarboxylic chelating ligand for efficient resin purification of His-tagged proteins expressed in mammalian systems.

We describe the synthesis of a novel polyamino polycarboxylic ligand, its ability to coordinate metal-ions and attachment to a solid support designed for protein purification through Immobilised Metal-ion Affinity Chromatography (IMAC). The resin was found to be highly efficient for purification of His-tagged HCV E2 glycoproteins expressed in 293T mammalian cells.

Spectroscopic investigations of the binding interaction of a new indanedione derivative with human and bovine serum albumins.

Binding of a newly synthesized indanedione derivative, 2-(2-hydroxy-3-ethoxybenzylidene)-1,3-indanedione (HEBID), to human and bovine serum albumins (HSA and BSA), under simulated physiological conditions was monitored by fluorescence spectroscopy. The binding parameters (binding constants and number of binding sites) and quenching constants were determined according to literature models. The quenching mechanism was assigned to a Förster non-radiative energy transfer due to the HEBID-SA complex formation. A slightly increased affinity of HEBID for HSA was found, while the number of binding sites is approximately one for both albumins. The molecular distance between donor (albumin) and acceptor (HEBID) and the energy transfer efficiency were estimated, in the view of Förster's theory. The effect of HEBID on the protein conformation was investigated using circular dichroism and synchronous fluorescence spectroscopies. The results revealed partial unfolding in the albumins upon interaction, as well as changes in the local polarity around the tryptophan residues.

Seasonal variation in trace metals concentrations in the Ialomita River, Romania.

Sampling streams for metals is an important aspect of water-quality monitoring. Using ICP-AES the concentration of some microelements in the Ialomita River (Romania) were determined. In order to grasp the different phases of the river regime, samples were collected from its water-sediment interface at seven locations along the river, during three campaigns: during snow melting periods in the mountain zones (April), the period of reduced flow and high water temperature (August) and the period of high precipitations (November). HNO3 was added to the samples for fixation. Cadmium and copper appear accidentally; lead was detected only in samples collected in the vicinity of roads; the MAC (maximum admitted concentration) for surface waters is exceeded for nickel and chromium in samples collected in April and respectively in April and November; zinc concentrations were usually above the MAC; molybdenum concentration was above the set reference value, especially for samples collected in April and November. Possible explanations are given for the presence of the investigated microelements along the river.

A novel profluorescent paramagnetic diaza-crown ether: synthesis, characterization and alkaline metal-ion complexation.

Starting from Kryptofix 22 two different branches were covalently attached through the nitrogen atoms, one containing a fluorescent moiety and the other the stable free radical TEMPO. The novel derivative exhibits fluorescence and paramagnetic properties, while the diaza-crown part ensures the affinity for alkaline metal-ions.

Identification of Biologically Essential Nodes via Determinative Power in Logical Models of Cellular Processes.

A variety of biological networks can be modeled as logical or Boolean networks. However, a simplification of the reality to binary states of the nodes does not ease the difficulty of analyzing the dynamics of large, complex networks, such as signal transduction networks, due to the exponential dependence of the state space on the number of nodes. This paper considers a recently introduced method for finding a fairly small subnetwork, representing a collection of nodes that determine the states of most other nodes with a reasonable level of entropy. The subnetwork contains the most determinative nodes that yield the highest information gain. One of the goals of this paper is to propose an algorithm for finding a suitable subnetwork size. The information gain is quantified by the so-called determinative power of the nodes, which is obtained via the mutual information, a concept originating in information theory. We find the most determinative nodes for 36 network models available in the online database Cell Collective (http://cellcollective.org). We provide statistical information that indicates a weak correlation between the subnetwork size and other variables, such as network size, or maximum and average determinative power of nodes. We observe that the proportion represented by the subnetwork in comparison to the whole network shows a weak tendency to decrease for larger networks. The determinative power of nodes is weakly correlated to the number of outputs of a node, and it appears to be independent of other topological measures such as closeness or betweenness centrality. Once the subnetwork of the most determinative nodes is identified, we generate a biological function analysis of its nodes for some of the 36 networks. The analysis shows that a large fraction of the most determinative nodes are essential and involved in crucial biological functions. The biological pathway analysis of the most determinative nodes shows that they are involved in important disease pathways.

Dynamics of asynchronous random Boolean networks with asynchrony generated by stochastic processes.

An asynchronous Boolean network with N nodes whose states at each time point are determined by certain parent nodes is considered. We make use of the models developed by Matache and Heidel [Matache, M.T., Heidel, J., 2005. Asynchronous random Boolean network model based on elementary cellular automata rule 126. Phys. Rev. E 71, 026232] for a constant number of parents, and Matache [Matache, M.T., 2006. Asynchronous random Boolean network model with variable number of parents based on elementary cellular automata rule 126. IJMPB 20 (8), 897-923] for a varying number of parents. In both these papers the authors consider an asynchronous updating of all nodes, with asynchrony generated by various random distributions. We supplement those results by using various stochastic processes as generators for the number of nodes to be updated at each time point. In this paper we use the following stochastic processes: Poisson process, random walk, birth and death process, Brownian motion, and fractional Brownian motion. We study the dynamics of the model through sensitivity of the orbits to initial values, bifurcation diagrams, and fixed-point analysis. The dynamics of the system show that the number of nodes to be updated at each time point is of great importance, especially for the random walk, the birth and death, and the Brownian motion processes. Small or moderate values for the number of updated nodes generate order, while large values may generate chaos depending on the underlying parameters. The Poisson process generates order. With fractional Brownian motion, as the values of the Hurst parameter increase, the system exhibits order for a wider range of combinations of the underlying parameters.

Long-lived states detect interactions between small molecules and diamagnetic metal ions.

Long-lived states of nuclear spin order were used for the first time to probe interactions between molecules and diamagnetic metal ions. Proton spin states with lifetimes twice as long as the spin-lattice relaxation time constants of the same nuclei were promoted on the methoxyphenyl and tolyl substituents of a 1,3,4-oxadiazole derivative. The transient interaction of this oxadiazole derivative with silver(I) ions significantly speeds up the relaxation rate constants of proton long-lived states. The interactions between silver and organic compounds lead to the formation of coordination polymers that can be used for the preparation of bio-compatible materials.