Synthesis of some biologically relevant beta-C-glycoconjugates

[reaction: see text] An esterification-RCM approach to a variety of biologically relevant beta-C-glycoconjugates is reported herein. A range of carboxylic acids were coupled with several different olefin alcohols 1 to provide esters 3. The esters were then converted to the final ring-closed product 6 in three steps in 49-60% overall yield. The formed compounds are biologically relevant and serve as stable carbohydrate mimics of the corresponding O-glycosides.     

Capillary electrochromatography of biologically relevant flavonoids

Flavonoids were separated utilizing CEC technique. Baseline separation of biologically relevant flavonoids was obtained using a 100 microm ID fused-silica capillary filled with 3 microm Silica-C18 material and an optimized mobile phase comprising of 20 mM Tris-HCl (pH 6.5), ACN and water at a ratio of 10/40/50 v/v/v. Separations were carried out at 25 kV and a column temperature of 25 degrees C. The influence of relevant parameters for the CEC separation, such as buffer concentration, pH, separation voltage, and ACN concentration, was investigated and optimized. Dependencies of the electroendoosmotic flow (EOF) on these parameters and effects on the resolution of the analytes were studied. During analyses the solvents used for dissolving the samples turned out to have significant effects on the separation of flavonoids. The optimized system was then successfully used for the separation of the flavonoids epicatechin, myricetin, quercetin, naringenin, and hesperetin. CEC turned out to be a useful complementary tool for the economic analysis of flavonoids in addition to common HPLC, muHPLC, and CE methodologies. This method can be used for real applications in phytomics.     

A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins

A three-step approach for multiscale modeling of protein conformational changes is presented that incorporates information about preferred directions of protein motions into a geometric simulation algorithm. The first two steps are based on a rigid cluster normal-mode analysis (RCNMA). Low-frequency normal modes are used in the third step (NMSim) to extend the recently introduced idea of constrained geometric simulations of diffusive motions in proteins by biasing backbone motions of the protein, whereas side-chain motions are biased toward favorable rotamer states. The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. When applied to a data set of proteins with experimentally observed conformational changes, conformational variabilities are reproduced very well for 4 out of 5 proteins that show domain motions, with correlation coefficients r > 0.70 and as high as r = 0.92 in the case of adenylate kinase. In 7 out of 8 cases, NMSim simulations starting from unbound structures are able to sample conformations that are similar (root-mean-square deviation = 1.0-3.1 ?) to ligand bound conformations. An NMSim generated pathway of conformational change of adenylate kinase correctly describes the sequence of domain closing. The NMSim approach is a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or as starting points for more sophisticated sampling techniques.     

Weak exchange interaction supported by a biologically relevant long chemical bridge in a Cu-peptide model compound

The copper complex of the dipeptide L-alanyl-L-phenylalanine, catena-(L-alaninate-L-phenylalaninate-copper(II) monohydrate), identified as Cu(II)Ala-Phe, provides a convenient system to study a weak exchange interaction between unpaired spins transmitted through a biologically relevant long chemical bridge (18.34 A). In this complex, the copper ions are arranged in two symmetry-related anisotropic layers parallel to the ab plane at 13.17 A, separated by a double layer of water molecules. The equatorial-equatorial bridge considered as the most relevant path for exchange interactions between copper ions in neighbor layers contains 11 diamagnetic atoms (including three hydrogens), with two covalent amidate bridges plus three weak and moderate H bonds that go across the water layer. This interaction was studied using electron paramagnetic resonance in single-crystal samples, at 9.5 and 34.5 GHz. The measured magnitude of the interlayer interaction, |J3|/kB = 1.7(2) x 10(-3) K, is discussed in terms of values obtained for similar paths in other model compounds and in proteins. These results in model systems provide information that may be important in understanding biological functions at the molecular level.     

Nonradiative decay mechanisms of the biologically relevant tautomer of guanine

We present the excited-state potential energy profiles of the biologically relevant 9H-keto-amino tautomer of guanine with respect to the radiationless decay via the out-of-plane deformation of the six-membered ring as well as the dissociation of NH bonds. The CASPT2//CASSCF method is employed for the reaction-path calculations. The reaction path for the out-of-plane deformation in the (1)pi pi* state leads in a barrierless way to a conical intersection with the electronic ground state. For the NH dissociation via the (1)pi sigma* state, the 9H-keto-amino tautomer is shown to have lower energy barriers than the 7H tautomers which we have studied recently. These two radiationless decay mechanisms explain the unexpected missing of the biologically relevant form in the resonant two-photon ionization spectrum of guanine in a supersonic jet. It is suggested that these ultrafast deactivation processes provide the biologically relevant tautomer of guanine with a high degree of photostability.     

Applications of X-ray absorption spectroscopy to biologically relevant metal-based chemistry

Recent developments in the understanding of the biosynthesis of the active site of the nitrogenase enzyme, the structure of the iron centre of [Fe]-hydrogenase and the structure and biomimetic chemistry of the [FeFe] hydrogenase H-cluster as deduced by application of X-ray spectroscopy are reviewed. The techniques central to this work include X-ray absorption spectroscopy either in the form of extended X-ray absorption fine structure (EXAFS), X-ray absorption near-edge structure (XANES) and nuclear resonant vibrational spectroscopy (NRVS). Examples of the advances in the understanding of the chemistry of the system through integration of a range of spectroscopic and computational techniques with X-ray spectroscopy are highlighted. The critical role played by ab initio calculation of structural and spectroscopic properties of transition-metal compounds using density functional theory (DFT) is illustrated both by the calculation of nuclear resonance vibrational spectroscopy (NRVS) spectra and the structures and spectra of intermediates through the catalytic reactions of hydrogenase model compounds.     

Synthesis of glycophostones: cyclic phosphonate analogues of biologically relevant sugars

Analogues of L-fucose, N-acetyl-D-glucosamine, N-acetyl-D-mannosamine, and N-acetyl neuraminic acid in which the anomeric carbon atom was replaced by a phosphonyl group (phostones or cyclic phosphonates) were synthesized by stereocontrolled methods relying on the Abramov reaction.     

The interaction of Bromophenol Blue with proteins in acidic solution

The interactions of Bromophenol Blue (BPB) with bovine serum albumin and gamma-globulin in acidic solutions were investigated by a spectrophotometric method. It was considered that the electrostatic force is the main binding force, and that the color change during the combination is due to the transformation of dye species of free acidic form into bound basic form as well as to the bathochromic and hyperchromic effects of conjugation. The formation of an isosbestic point in the absorption spectra was explained based on a new consideration about the solution equilibria. Two conditional constants, apparent binding constant and maximum binding number, were defined to express the binding ability of a dye to a certain protein under a given set of conditions, and two linear regression equations were derived to determine these two parameters and the molar absorptivity of bound dye. The Scatchard model is not appropriate in the treatment of data obtained here. The factors which influence the sensitivity of a dye binding protein assay were discussed, and the Sandell index was used to express the sensitivity of protein detection. It was found that sodium chloride concentration and acidity of the solutions have significant effect on the sensitivity of BPB protein assay.     

Mechanicochemical interaction of plant proanthocyanidins with drugs

The possibility has been studied of regulating the solubility properties of deoxypeganine by binding it with plant proanthocyanidins (katatsin, kavergal, yantapsin).Institute of the Chemistry of Plant Substances, Academy of Sciences of the Republic of Uzbekistan, Tashkent, fax (3712) 89 14 75. Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 226–228, March-April, 1995. Original article submitted April 14, 1994.     

Dehydrogenative Heck coupling of biologically relevant N-heteroarenes with alkenes: discovery of fluorescent core frameworks

A Pd/Cu-catalyzed dehydrogenative Heck coupling is established that allows direct alkenylation of various biologically relevant N-heteroarenes with alkenes. The resulting π-extended alkenylated N-heteroarenes exhibit interesting fluorescent properties and have proven to be potentially useful fluorescent probes for bioimaging.     

Solution and biologically relevant conformations of enantiomeric 11-cis-locked cyclopropyl retinals

To gain information on the conformation of the 11-cis-retinylidene chromophore bound to bovine opsin, the enantiomeric pair (2a and 2b) of 11-cis-locked bicyclo[5.1.0]octyl retinal (retCPr) 2 was prepared and its conformation was investigated by NMR, geometry optimization, and CD calculations. This compound is also of interest since it contains a unique moiety in which a chiral cyclopropyl group is flanked by triene and enal chromophores, and hence would clarify the little-known chiroptical contribution of a cyclopropyl ring linked to polyene systems. NMR revealed that the seven-membered ring of retCPr adopts a twist chair conformation. The NMR-derived structure constraints were then used for optimizing the geometry of 2 with molecular mechanics and ab initio methods. This revealed that enantiomer 2a with a 11 beta,12 beta-cyclopropyl group exists as two populations of diastereomers depending on the twist around the 6-s bond; however, the sense of twist around the 12-s is positive in both rotamers. The theoretical Boltzmann-weighted CD obtained with the pi-SCF-CI-DV MO method and experimental spectra were consistent, thus suggesting that the conjugative effect of the cyclopropyl moiety is minimal. It was found that only the beta-cyclopropyl enantiomer 2a, but not the alpha-enantiomer 2b, binds to opsin. This observation, together with earlier retinal analogues incorporation results, led to the conclusion that the chromophore sinks into the N-terminal of the opsin receptor from the side of the 4-methylene and 15-aldehyde, and that the binding cleft accommodates 11-cis-retinal with a slightly positive twist around C12/C13. A reinterpretation of the previously published negative CD couplet of 11,12-dihydrorhodopsin also leads to a chromophoric C12/C13 twist conformation with the 13-Me in front as in 1b. Such a conformation for the chromophore accounts for both the observed biostereoselectivity of retCPr 2a and the observed negative couplet of 11,12-dihydro-Rh7.     

In vitro anticancer activity and biologically relevant metabolization of organometallic ruthenium complexes with carbohydrate-based ligands

The synthesis and in vitro anticancer activity of dihalogenido(eta6-p-cymene)(3,5,6-bicyclophosphite-alpha-D-glucofuranoside)ruthenium(II) complexes are described. The compounds were characterized by NMR spectroscopy and ESI mass spectrometry, and the molecular structures of dichlorido-, dibromido- and diiodido(eta6-p-cymene)(3,5,6-bicyclophosphite-1,2-O-isopropylidene-alpha-D-glucofuranoside)ruthenium(II) were determined by X-ray diffraction analysis. The complexes were shown to undergo aquation of the first halido ligand in aqueous solution, followed by hydrolysis of a P--O bond of the phosphite ligand, and finally formation of dinuclear species. The hydrolysis mechanism was confirmed by DFT calculations. The aquation of the complexes was markedly suppressed in 100 mM NaCl solution, and notably only very slow hydrolysis of the P--O bond was observed. The complexes showed affinity towards albumin and transferrin and monoadduct formation with 9-ethylguanine. In vitro studies revealed that the 3,5,6-bicyclophosphite-1,2-O-cyclohexylidene-alpha-D-glucofuranoside complex is the most cytotoxic compound in human cancer cell lines (IC50 values from 30 to 300 microM depending on the cell line).     

Structural study of AOT reverse micelles containing native or modified proteins: influence of surfactant-enzyme interaction

In this paper, the solubilization effect of different proteins in sodium di(2-ethylhexyl)sulfosuccinate (AOT) reverse micelles is studied. From results obtained with chemically modified proteins, it is shown that the nature of the surfactant-protein interaction controls the intermicellar potential, not the location of the proteins within the droplets. By binding hydrophobic molecules onto the surface of -chymotrypsin and ribonuclease, we force these hydrophobic enzymes to interact, via hydrophobic forces, with the droplet's interface. Small-angle X-ray scattering (SAXS) and conductivity measurements suggest that modification of the intermicellar potential is not required when the enzymes are modified. Conversely, electrostatic forces play an important role, as is observed using cytochrome c and its derivatives differing in their superficial charge.     

Thermodynamic and kinetic studies on reactions of Pt(II) complexes with biologically relevant nucleophiles

The effect of different N-N spectator ligands on the reactivity of platinum(II) complexes was investigated by studying the water lability of [Pt(diaminocyclohexane)(H2O)2]2+ (Pt(dach)), [Pt(ethylenediamine)(H2O)2]2+ (Pt(en)), [Pt(aminomethylpyridine)(H2O)2]2+ (Pt(amp)), and [Pt(N,N'-bipyridine)(H2O)2]2+ (Pt(bpy)). Some of the selected N-N chelates form part of the coordination sphere of Pt(II) drugs in clinical use, as in Pt(dach) (oxaliplatin), or are models, regarding the nature of the amines, with higher stability in terms of substitution and hydrolysis of the diamine moiety, as in Pt(en) (cisplatin) and Pt(amp) (AMD473). The effect of pi-acceptors on the reactivity was investigated by introducing one (Pt(amp)) or two pyridine rings (Pt(bpy)) in the system. The pK(a) values for the two water molecules (viz., Pt(dach) (pK(a1) = 6.01, pK(a2) = 7.69), Pt(en) (pK(a1) = 5.97, pK(a2) = 7.47), Pt(amp) (pK(a1) = 5.82, pK(a2) = 6.83), Pt(bpy) (pK(a1) = 4.80, pK(a2) = 6.32) show a decrease in the order Pt(dach) > Pt(en) > Pt(amp) > Pt(bpy). The substitution of both coordinated water molecules by a series of nucleophiles (viz., thiourea (tu), L-methionine (L-Met), and guanosine-5'-monophosphate (5'GMP-) was investigated under pseudo-first-order conditions as a function of concentration, temperature, and pressure using UV-vis spectrophotometric and stopped-flow techniques and was found to occur in two subsequent reaction steps. The following k1 values for Pt(dach), Pt(en), Pt(amp), and Pt(bpy) were found: tu (25 degrees C, M(-1) s(-1)) 21 +/- 1, 34.0 +/- 0.4, 233 +/- 5, 5081 +/- 275; L-Met (25 degrees C) 0.85 +/- 0.01, 0.70 +/- 0.03, 2.15 +/- 0.05, 21.8 +/- 0.6; 5'GMP- (40 degrees C) 5.8 +/- 0.2, 3.9 +/- 0.1, 12.5 +/- 0.5, 24.4 +/- 0.3. The results for k2 for Pt(dach), Pt(en), Pt(amp), and Pt(bpy) are as follows: tu (25 degrees C, M(-1) s(-1)) 11.5 +/- 0.5, 10.2 +/- 0.2, 38 +/- 1, 1119 +/- 22; L-Met (25 degrees C, s(-1)) 2.5 +/- 0.1, 2.0 +/- 0.2, 1.2 +/- 0.3, 290 +/- 4; 5'GMP- (40 degrees C, M(-1) s(-1)) 0.21 +/- 0.02, 0.38 +/- 0.02, 0.97 +/- 0.02, 24 +/- 1. The activation parameters for all reactions suggest an associative substitution mechanism. The pK(a) values and substitution rates of the complexes studied can be tuned through the nature of the N-N chelate, which is important in the development of new active compounds for cancer therapy.     

Next generation techniques in the high resolution spectroscopy of biologically relevant molecules

Recent advances in the technology of test and measurement equipment driven by the computer and telecommunications industries have made possible the development of a new broadband, Fourier-transform microwave spectrometer that operates on principles similar to FTNMR. This technique uses a high sample-rate arbitrary waveform generator to construct a phase-locked chirped microwave pulse that gives a linear frequency sweep over a wide frequency range in 1 μs. The chirped pulse efficiently polarizes the molecular sample at all frequencies lying within this band. The subsequent free induction decay of this polarization is measured with a high-speed digitizer and then fast Fourier-transformed to yield a broadband, frequency-resolved rotational spectrum, spanning up to 11.5 GHz and containing lines that are as narrow as 100 kHz. This new technique is called chirped-pulse Fourier transform microwave (CP-FTMW) spectroscopy. The technique offers the potential to determine the structural and dynamical properties of very large molecules solely from fully resolved pure rotational spectra. FTMW double resonance techniques employing a low-resolution UV laser facilitate an easy assignment of overlapping spectra produced by different conformers in the sample. Of particular interest are the energy landscapes of conformationally flexible molecules of biological importance, including studies of their interaction with solvent and/or other weakly bound molecules. An example is provided from the authors' work on p-methoxyphenethylamine, a neurotransmitter, and its complexes with water.