Predicting substrates by docking high-energy intermediates to enzyme structures

With the emergence of sequences and even structures for proteins of unknown function, structure-based prediction of enzyme activity has become a pragmatic as well as an interesting question. Here we investigate a method to predict substrates for enzymes of known structure by docking high-energy intermediate forms of the potential substrates. A database of such high-energy transition-state analogues was created from the KEGG metabolites. To reduce the number of possible reactions to consider, we restricted ourselves to enzymes of the amidohydrolase superfamily. We docked each metabolite into seven different amidohydrolases in both the ground-state and the high-energy intermediate forms. Docking the high-energy intermediates improved the discrimination between decoys and substrates significantly over the corresponding standard ground-state database, both by enrichment of the true substrates and by geometric fidelity. To test this method prospectively, we attempted to predict the enantioselectivity of a set of chiral substrates for phosphotriesterase, for both wild-type and mutant forms of this enzyme. The stereoselectivity ratios of the six enzymes considered for those four substrate enantiomer pairs differed over a range of 10- to 10,000-fold and underwent 20 switches in stereoselectivities for favored enantiomers, compared to the wild type. The docking of the high-energy intermediates correctly predicted the stereoselectivities for 18 of the 20 substrate/enzyme combinations when compared to subsequent experimental synthesis and testing. The possible applications of this approach to other enzymes are considered.     

Photochemical Transformation of Colchicine: A Kinetic Study

Spectroscopic methods and theoretical calculations were used to study the photophysical properties of colchicine (1). The characteristic bands of colchicine (1) transitions occurring at ∼245 nm and 350 nm arise from n–π ^* and π–π ^* transitions, and were found to be blue shifted with increasing polarity index of the solvent and red shifted (bathocrhomic) with increasing acidity of the media. Solvent type and polarity were found to affect both the rate constant and photo conversion yield. Excitation of colchicine (1) at 366 nm populates the S1 orbital, from which the photoreaction of colchicine (1) initially produces lumicolchicine directly in its ground state by a concerted disrotatory electrocyclization (i.e., 4π electrocyclization involving the tropolone ring). The acidity of the media affects both rate constants and conversion yield; both of these were inversely proportional to the acid concentration. The presence of acid decreases the photo conversion yield of colchicine (1) from 90% to 40%. The ionic strength affects both the rate constants and the photo conversion yield; rate constants are inversely related to the ionic strength. The photochemistry of colchicine (1) is explained on the basis of the initial formation of a solvation complex in the ground state.     

Daptomycin: A Novel Macrocyclic Antibiotic as a Chiral Selector in an Organic Polymer Monolithic Capillary for the Enantioselective Analysis of a Set of Pharmaceuticals

Daptomycin, a macrocyclic antibiotic, is here used as a new chiral selector in preparation of chiral stationary phase (CSP) in a recently prepared polymer monolithic capillary. The latter is prepared using the copolymerization of the monomers glycidyl methacrylate (GMA) and ethylene glycol dimethacrylate (EGDMA) in the presence of daptomycin in water. Under reversed phase conditions (RP), the prepared capillaries were tested for the enantioselective nanoliquid chromatographic separation of fifty of the racemic drugs of different pharmacological groups, such as adrenergic blockers, H1-blockers, NSAIDs, antifungal drugs, and others. Baseline separation was attained for many drugs under RP-HPLC. Daptomycin expands the horizon of chiral selectors in HPLC.     

The utility of cyclodextrins in lipase-catalyzed transesterification in organic solvents: enhanced reaction rate and enantioselectivity

The use of enzymes as valuable catalysts in organic solvents has been well documented. However, some of their features limit their application in organic synthesis, especially the frequently lower enzyme activity under nonaqueous conditions, which constitutes a major drawback in the application of enzymes in organic solvents. In addition, many enzymatic reactions are subject to substrate or product inhibition, leading to a decrease in the reaction rate and enantioselectivity. To overcome these drawbacks and to make enzymes more appealing to organic chemists, we demonstrate the use of cyclodextrins as regulators for the Pseudomonas cepacia lipase (PSL) and macrocyclic additives to enhance the reaction rate and enantioselectivity E in lipase-catalyzed enantioselective transesterification of 1-(2-furyl)ethanol in organic solvents. Both reaction rate and enantioselectivity were significantly enhanced by several orders of magnitude when using co-lyophilized lipase in the presence of cyclodextrins. The effect of cyclodextrin derivatives as well as solvents on the improvement of the reaction parameters has been studied. The observed enhancement was tentatively interpreted in terms of their ability to give a certain flexibility to the enzyme and to form a host-guest complex, thus avoiding product inhibition and leading to enhancement of the reaction rate and enantioselectivity. The effect of cyclodextrin additives on the enzyme morphology has been studied using scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) of the co-lyophilized lipase with cyclodextrins. The ability of cyclodextrins to form a host-guest complex to avoid product inhibition, which leads to the observed enhancement, has been proved by NOESY, COSY, 13C and 1H NMR.     

Light-driven tyrosine radical formation in a ruthenium-tyrosine complex attached to nanoparticle TiO2

We demonstrate a possibility of multistep electron transfer in a supramolecular complex adsorbed on the surface of nanocrystalline TiO(2). The complex mimics the function of the tyrosine(Z)() and chlorophyll unit P(680) in natural photosystem II (PSII). A ruthenium(II) tris(bipyridyl) complex covalently linked to a L-tyrosine ethyl ester through an amide bond was attached to the surface of nanocrystalline TiO(2) via carboxylic acid groups linked to the bpy ligands. Synthesis and characterization of this complex are described. Excitation (450 nm) of the complex promotes an electron to a metal-to-ligand charge-transfer (MLCT) excited state, from which the electron is injected into TiO(2). The photogeneration of Ru(III) is followed by an intramolecular electron transfer from tyrosine to Ru(III), regenerating the photosensitizer Ru(II) and forming the tyrosyl radical. The tyrosyl radical is formed in less than 5 micros with a yield of 15%. This rather low yield is a result of a fast back electron transfer reaction from the nanocrystalline TiO(2) to the photogenerated Ru(III).     

Radiation effects on polymers—IV: Straight radiation vulcanization of styrene-butadiene rubber mixes

Vulcanization of styrene-butadiene rubbers was carried out by gamma radiation in air. For unloaded unextracted rubbers, the dose required for optimum cross-linking was about 40 megaroentgens (MR). Elimination of foreign materials and stabilizers and also incorporation of filler affected the vulcanization. Loaded samples gave vulcanizates with best complex physico-mechanical properties for filler content of 50 (phr) and a dose of 30 MR. Evaluation of various fillers has shown that the best properties were obtained with HAF among the black fillers and silica in the case of white fillers.     

Radiation effects on polymers—V: Vulcanization of styrene-butadiene rubber (SBR) with gamma radiation and coagents

Possible enhancement of the radiation-induced vulcanization of SBR by polyfunctional allyl and vinyl monomers, was tested. Polyfunctional allyl esters did not enhance the radiation vulcanization; in fact they retarded the process and so can be considered as “antirads”. Di- and tri-vinyl monomers acted individually as effective radiation coagents. In their presence, the dose required for satisfactory curing was 7–10 MR instead of 40 MR in the case of unenhanced vulcanization. The results indicate that vinyl esters are more effective coagents than vinyl amides. The physico-mechanical properties of vulcanizates, obtained in the presence of 10–30 parts of vinyl coagents per 100 parts of SBR. are of the same level as those obtained by conventional sulphur vulcanization.     

Metal–metal bonded alkaline-earth distannyls

The first families of alkaline-earth stannylides [Ae(SnPh₃)₂·(thf)_x] (Ae = Ca, x = 3, 1; Sr, x = 3, 2; Ba, x = 4, 3) and [Ae{Sn(SiMe₃)₃}₂·(thf)_x] (Ae = Ca, x = 4, 4; Sr, x = 4, 5; Ba, x = 4, 6), where Ae is a large alkaline earth with direct Ae–Sn bonds, are presented. All complexes have been characterised by high-resolution solution NMR spectroscopy, including ¹¹⁹Sn NMR, and by X-ray diffraction crystallography. The molecular structures of [Ca(SnPh₃)₂·(thf)₄] (1′), [Sr(SnPh₃)₂·(thf)₄] (2′), [Ba(SnPh₃)₂·(thf)₅] (3′), 4, 5 and [Ba{Sn(SiMe₃)₃}₂·(thf)₅] (6′), most of which crystallised as higher thf solvates than their parents 1–6, were established by XRD analysis; the experimentally determined Sn–Ae–Sn′ angles lie in the range 158.10(3)–179.33(4)°. In a given series, the ¹¹⁹Sn NMR chemical shifts are slightly deshielded upon descending group 2 from Ca to Ba, while the silyl-substituted stannyls are much more shielded than the phenyl ones (δ¹¹⁹Sn/ppm: 1′, −133.4; 2′, −123.6; 3′, −95.5; 4, −856.8; 5, −848.2; 6′, −792.7). The bonding and electronic properties of these complexes were also analysed by DFT calculations. The combined spectroscopic, crystallographic and computational analysis of these complexes provide some insight into the main features of these unique families of homoleptic complexes. A comprehensive DFT study (Wiberg bond index, QTAIM and energy decomposition analysis) points at a primarily ionic Ae–Sn bonding, with a small covalent contribution, in these series of complexes; the Sn–Ae–Sn′ angle is associated with a flat energy potential surface around its minimum, consistent with the broad range of values determined by experimental and computational methods.

The complete series of heterobimetallic alkaline-earth distannyls [Ae{SnR₃}₂·(thf)_x] (Ae = Ca, Sr, Ba) have been prepared for R = Ph and SiMe₃, and their bonding and electronic properties have been comprehensively investigated.     

Design and synthesis of some new pyranoxanthenones with cytotoxic activity

As part of a research program directed towards the design and synthesis of pyranoxanthones structurally related to acronycine, we present here the synthesis and cytotoxic activity of the pyranoxanthones 3 and 4 (X= H, Br; R= H, OMe; R'= H, Ac). Some of these compounds inhibit L1210 cell proliferation.