Searching the "biologically relevant"conformation of dopamine: a computational approach

We report here an exhaustive and complete conformational study on the conformational potential energy hypersurface (PEHS) of dopamine (DA) interacting with the dopamine D2 receptor (D2-DR). A reduced 3D model for the binding pocket of the human D2-DR was constructed on the basis of the theoretical model structure of bacteriorhodopsin. In our reduced model system, only 13 amino acids were included to perform the quantum mechanics calculations. To obtain the different complexes of DA/D2-DR, we combined semiempirical (PM6), DFT (B3LYP/6-31G(d)), and QTAIM calculations. The molecular flexibility of DA interacting with the D2-DR was evaluated from potential energy surfaces and potential energy curves. A comparative study between the molecular flexibility of DA in the gas phase and at D2-DR was carried out. In addition, several molecular dynamics simulations were carried out to evaluate the molecular flexibility of the different complexes obtained. Our results allow us to postulate the complexes of type A as the "biologically relevant conformations" of DA. In addition, the theoretical calculations reported here suggested that a mechanistic stepwise process takes place for DA in which the protonated nitrogen group (in any conformation) acts as the anchoring portion, and this process is followed by a rapid rearrangement of the conformation allowing the interaction of the catecholic OH groups.     

Ultrafast relaxation dynamics of a biologically relevant probe dansyl at the micellar surface

We report picosecond-resolved measurement of the fluorescence of a well-known biologically relevant probe, dansyl chromophore at the surface of a cationic micelle (cetyltrimethylammonium bromide, CTAB). The dansyl chromophore has environmentally sensitive fluorescence quantum yields and emission maxima, along with large Stokes shift. In order to study the solvation dynamics of the micellar environment, we measured the fluorescence of dansyl chromophore attached to the micellar surface. The fluorescence transients were observed to decay (with time constant approximately 350 ps) in the blue end and rise with similar timescale in the red end, indicative of solvation dynamics of the environment. The solvation correlation function is measured to decay with time constant 338 ps, which is much slower than that of ordinary bulk water. Time-resolved anisotropy of the dansyl chromophore shows a bi-exponential decay with time constants 413 ps (23%) and 1.3 ns (77%), which is considerably slower than that in free solvents revealing the rigidity of the dansyl-micelle complex. Time-resolved area-normalized emission spectroscopic (TRANES) analysis of the time dependent emission spectra of the dansyl chromophore in the micellar environment shows an isoemissive point at 21066 cm-1. This indicates the fluorescence of the chromophore contains emission from two kinds of excited states namely locally excited state (prior to charge transfer) and charge transfer state. The nature of the solvation dynamics in the micellar environments is therefore explored from the time-resolved anisotropy measurement coupled with the TRANES analysis of the fluorescence transients. The time scale of the solvation is important for the mechanism of molecular recognition.     

Synthesis of new transglycosidically tethered 5'-nucleotides constrained to a highly biologically relevant profile

A new motif for restricting 5'-nucleotides to highly biologically relevant conformations has been developed. The 5',6-oxomethylene transglycosidically tethered versions of uridine 5'-monophosphate and 2'-deoxyuridine 5'-monophosphate (1 and 2, respectively) were synthesized in 10-11 steps from their respective natural nucleoside precursors along routes general to the preparation of tethered versions of a wide variety of 5'-nucleotide-based compounds. In both routes, a shelf-stable 6-hydroxymethyl pyrimidine nucleoside 5'-carboxaldehyde is the key intermediate. It exists in a carbohydrate-like fashion in a cyclic hemiacetal form under aprotic conditions. The phosphorylated cyclic hemiacetals 1 and 2 were isolated as binary mixtures of 5'-diastereomers differing principally in the trajectory of the phosphate group with respect to the carbohydrate. By (1)H NMR, both 1 and 2 were demonstrated to be stable to hydrolysis at ambient temperature in D(2)O solution for at least 2 months. The oxomethylene transglycosidic tether as deployed in 1 and 2 leaves all of the native 5'-nucleotide molecular recognition sites intact while it restricts the framework to a low-energy anti glycosyl conformation and an extended phosphate disposition. This provides a spatial presence that approximates nearly three-quarters of the protein-bound 5'-nucleotide ligands described in the Protein Data Bank. The tether has a low structural and electronic impact, occupies a region of space (over the beta-face of the furan ring) seldom penetrated by proteins, and should be accommodated as readily on purine-based 5'-nucleotide frameworks as on pyrimidine-based ones. Because of its unique and attractive features, this new motif for the conformational restriction of 5'-nucleotides is expected to be useful for producing probes of structure/function relationships and in assessing the conformational binding requirements that enzymes and receptor sites have for their natural 5'-nucleotide-based ligands.     

Development of a biologically relevant calcium phosphate substrate for sum frequency generation vibrational spectroscopy

A novel biologically relevant composite substrate has been prepared consisting of a calcium phosphate (CaP) layer formed by magnetron sputter-coating from a hydroxyapatite (HA) target onto a gold-coated silicon substrate. The CaP layer is intended to mimic tooth and bone surfaces and allows polymers used in oral care to be deposited in a procedure analogous to that used for dental surfaces. The polymer cetyl dimethicone copolyol (CDC) was deposited onto the CaP surface of the substrate by Langmuir Blodgett deposition, and the structure of the adsorbed layer was investigated by the surface specific technique of sum frequency generation (SFG) vibrational spectroscopy. The gold sublayer provides enhancement of the SFG signal arising from the polymer but plays no part in the adsorption of the polymer. The surface morphology of the substrate was investigated using SEM and AFM. The surface roughness was commensurate with that of the thermally evaporated gold sublayer and uniform over areas of at least 36 mum(2). The chemical composition of the CaP-coated surface was determined by FTIR and TOF-SIMS. It was concluded that the surface is primarily calcium phosphate present as a mixture of amorphous, non-hydroxylated phases rather than solely stoichiometric hydroxyapatite. The SFG spectra from CDC on CaP were closely similar, both in resonance wavenumbers and in their relative intensities, with spectra of thin films of CDC recorded directly on gold. Application of previous analysis of the spectra of CDC on gold therefore enabled interpretation of the polymer orientation and conformation on the CaP substrate.     

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.     

Iron(III) complexes with a biologically relevant aroylhydrazone: crystallographic evidence for coordination versatility

Complexation of iron(III) with the heterodonor chelating agent 3,5-di-tert-butylsalicylidene benzoylhydrazine, H2(3,5-tBu2)salbh, in the absence or presence of a base affords the complex cation [Fe{H(3,5-tBu2)salbh}2]+ or the neutral compound [Fe{H(3,5-tBu2)salbh}{(3,5-tBu2)salbh}], respectively, as revealed by single-crystal X-ray analyses. Such a synthetic and crystallographic demonstration of the coordination versatility of an aroylhydrazone toward iron is uncommon. The oxidation and spin states of the iron have been verified with magnetic and spectroscopic measurements.     

Advanced glycation end products: a highly complex set of biologically relevant compounds detected by mass spectrometry

Structural information on 'AGE-peptides,' a class of substances belonging to advanced glycation end products (AGE) and originating by proteolysis of glycated proteins, was gained through various analytical approaches on the mixture produced by proteinase K digestion of in vitro glycated bovine serum albumin. Both matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and high-performance liquid chromatography/electrospray ionization mass spectrometry (HPLC/ESI-MS) were employed, and the results were compared with those from conventional spectroscopic methods (UV, fluorescence, gel permeation). The data acquired by the various techniques all depict the digestion mixtures as highly complex, with components exhibiting molecular mass in the range 300-3500 Da. In the analysis of HPLC/ESI-MS data, identification of AGE-peptides was facilitated by 3D mapping. Structural information was gained by means of multiple mass spectrometric experiments.     

Effect of molecular size on the threshold energy producing a51Cr hot atom

The lowest retention values of⁵¹Cr hot atom in various forms of the -diketonetype complexes, Cr(bzac)₃, Cr(dpm)₃ and Cr(dbm)₃, as well as Cr(acac)₃ as a reference, were obtained in the experimental condition in which they are regarded as the primary retentions. From these retention values, the threshold energies for producing a hot atom, the appearance energies, were estimated using the calculated relationship between the primary retention and appearance energy, which was obtained by the recoil energy spectra computed by the method recently developed by us. The appearance energy increased steeply with increasing molecular weight of the complex. A theoretical interpretation for this result was attempted by setting a model in which a hot atom is produced in the center of the complex and receives the stopping action by the surrounding ligand molecule. The agreement between the observed and calculated values was good.     

The synthesis of biologically relevant 4(5)-phosphono-5(4)-aminoimidazoles using a Pd-catalyzed coupling reaction

Regiochemically defined 1-benzyl-4-phosphono-5-carboalkoxyimidazoles were synthesized from the corresponding 4-bromoimidazoles using a tetrakis(triphenylphosphine)palladium(0)-catalyzed coupling reaction with diethyl phosphite. The corresponding Michaelis-Arbusov reaction failed to give a phospho-nylated product. The carbomethoxy moiety was converted to an amino group using a Curtius rearrangement to afford 1-benzyl-4-phosphono-5-amino-imidazoles. Following deprotection and hydrolysis, phos-phonic acid-linked aminoimidazoles were accessed that resemble intermediates formed during purine biosynthesis.     

Site-selective electron transfer from purines to electrocatalysts: voltammetric detection of a biologically relevant deletion in hybridized DNA duplexes.

BACKGROUND: The one-electron oxidation of guanine nucleobases is of interest for understanding the mechanisms of mutagenesis, probing electron-transfer reactions in DNA, and developing sensing schemes for nucleic acids. The electron-transfer rates for oxidation of guanine by exogenous redox catalysts depend on the base paired to the guanine. An important goal in developing the mismatch sensitivity is to identify a means for monitoring the current resulting from electron transfer at a single base in the presence of native oligonucleotides that contain all four bases. RESULTS: The nucleobase 8-oxo-guanine (8G) is selectively oxidized by the redox catalyst Os(bpy)(3)(3+/2+) (bpy = 2,2'-bipyridine) in the presence of native guanine. Cyclic voltammograms of Os(bpy)(3)(2+) show current enhancements indicative of nucleobase oxidation upon addition of oligonucleotides that contain 8G, but not in the presence of native guanine. As expected, similar experiments with Ru(bpy)(3)(2+) show enhancement with both guanine and 8G. The current enhancements for the 8G/Os(III) reaction increase in the order 8G-C approximately 8G.T < 8G.G < 8G.A < 8G, the same order as that observed for guanine/Ru(III). This site-selective mismatch sensitivity can be applied to detection of a TTT deletion, which is important in cystic fibrosis. CONCLUSIONS: The base 8G can be effectively used in conjunction with a low-potential redox catalyst as a probe for selective electron transfer at a single site. Because of the high selectivity for 8G, rate constants can be obtained that reflect the oxidation of only one base. The mismatch sensitivity can be used to detect biologically relevant abnormalities in DNA.     

NMR studies of solvent-assisted proton transfer in a biologically relevant Schiff base: toward a distinction of geometric and equilibrium H-bond isotope effects

The tautomeric equilibrium in a Schiff base, N-(3,5-dibromosalicylidene)-methylamine 1, a model for the hydrogen bonded structure of the cofactor pyridoxal-5'-phosphate PLP which is located in the active site of the enzyme, was measured by means of 1H and 15N NMR and deuterium isotope effects on 15N chemical shifts at variable temperature and in different organic solvents. The position of the equilibrium was estimated using the one-bond 1J(OHN) and vicinal 3J(H(alpha)CNH) scalar coupling constants. Additionally, DFT calculations of a series of Schiff bases, N-(R1-salicylidene)-alkyl(R2)amines, were performed to obtain the hydrogen bond geometries. The latter made it possible to investigate a broad range of equilibrium positions. The increase of the polarity of the aprotic solvent shifts the proton in the intramolecular OHN hydrogen bond closer to the nitrogen. The addition of methanol and of hexafluoro-2-propanol to 1 in aprotic solvents models the PLP-water interaction in the enzymatic active site. The alcohols, which vary in acidity and change the polarity around the hydrogen bond, also stabilize the equilibrium, so that the proton is shifted to the nitrogen.     

Inkjet printing of gold nanoparticles onto a biologically relevant matrix to create quantitative test materials for time-of-flight secondary ion mass spectrometry

This study describes the use of inkjet printing for the preparation of test materials containing gold nanoparticles (AuNPs) on a biologically relevant matrix and discusses the methods of using time-of-flight secondary ion mass spectrometry (ToF-SIMS) for their spatially resolved quantification. Evaluation of test materials containing AuNPs with nominal diameters of (30, 80, 100, and 150) nm deposited onto gelatin with loadings ranging from 34 fg up to 67 000 fg per spot suggests that ToF-SIMS has the sensitivity and the dynamic range to quantify NP deposits in a biological matrix at toxicologically relevant concentrations, although it was not capable of reliably determining the size of the AuNPs from the intensity data. Regardless, the ability to extract intensity data from individual regions of interest (ROIs) showed that spatially resolved quantification is possible, even when multiple features exist in a single image and in a single depth profile. The argon gas cluster source used for sputtering led to a matrix removal effect where the matrix surrounding the AuNPs became negligible, which may facilitate the preparation of quantitative test materials.     

Solid-phase synthesis of phenolic steroids: from optimization studies to a convenient procedure for combinatorial synthesis of biologically relevant estradiol derivatives

During the course of our studies on therapeutic agents for the treatment of breast cancer, we became interested in the solid-phase combinatorial synthesis of estradiol derivatives that contain a functionalized side chain at either position 16 beta or 7 alpha. Both types of compounds have already demonstrated inhibitory activity toward both biosynthesis and action of estradiol. As a first step, two versatile precursors bearing an azidoalkyl side chain at either position 16 beta or 7 alpha of estradiol were synthesized using standard solution-phase methods. Afterward, the effectiveness of five linkers to attach the phenolic function of these estradiol derivatives to a polystyrene resin was investigated; they were benzylic ether (Merrifield), 4-alkoxy-benzylic ethers (Wang, Sheppard), tetrahydropyranyl ether (Ellman), benzoic ester, and o-nitrobenzyl ether. To test the linker in a synthetic context, a short sequence of reactions, including reduction of the azide and acylation of the corresponding amine, was performed on the polymer-bound estradiol derivative. While all of the tested linkers proved effective in attaching the phenol functionality of the precursor, only the o-nitrobenzyl ether photolabile linker enabled the release of the final products in acceptable purities. Consequently, this linker was used to perform successfully the solid-phase synthesis of four different classes of estradiol derivatives in acceptable yields and excellent purities. This study was preliminary to the combinatorial synthesis of larger libraries of biologically relevant estradiol derivatives.     

Palladium(II) complex taken as a model of an antitumour agent: Synthesis and equilibrium investigation involving biologically relevant ligands

Pd(DHP)Cl₂ and Pd(DHP)(CBDCA) complexes (DHP = 1,3-diamino-2-hydroxopropane and CBDCA = 1,1-cyclobutanedicarboxylate), were synthesized and characterized by elemental analysis, IR and NMR spectral measurements. The coordination of [Pd(DHP)(H₂O)₂]²⁺ with some selected bio-relevant ligands, containing different functional groups was investigated. The ligands used are amino acids, peptides, DNA constituents and dicarboxylic acids. Stoichiometry and stability constants of the complexes formed are reported at 25 °C and 0.1 M ionic strength. The results show the formation of 1:1 complexes with amino acids and dicarboxylic acids. DNA constituents form 1:1 and 1:2 complexes. Peptides form both 1:1 complexes and the corresponding deprotonated amide species. The effect of chloride ion concentration and dioxane on the acid dissociation constants of 1,1-cyclobutane dicarboxylic acid (CBDCAH₂) and the formation constant of its complex with Pd(DHP)²⁺ was reported. The equilibrium constants for the displacement of coordinated ligands as uracil, glycine or methionine by cysteine are calculated. The results are expected to contribute to the chemistry of antitumour agents.     

Structural organization of gold nanoparticles onto the ITO surface and its optical properties as a function of ensemble size

Self-assembly of citrate-stabilized gold nanoparticles (AuNPs) onto an optically transparent indium tin oxide (ITO) surface followed by neutralization of these particles using dodecanethiol as a surfactant have been demonstrated. X-ray photoelectron spectroscopic (XPS) studies revealed the partial removal of citrate ions from the immobilized AuNPs, which advances the dilution of electrostatic attraction between AuNPs and the APS (amino-terminated monolayer)-functionalized ITO surface. The resultant AuNPs restore their mobility to some extent and form small ensembles. Some of the immobilized AuNPs were completely removed from the surface due to neutralization, as confirmed by XPS studies. Interparticle distance and size of ensembles were manipulated by consecutive cycles of immobilization and neutralization of AuNPs. Controlled nanostructural fabrication progression, which leads to two-dimensional lateral growth of AuNPs, provides a method for systematically shifting the surface plasmon resonance band based on the increase in plasmon coupling among the closely placed AuNPs of an ensemble. The magnitude of shift increases with the size of ensemble. This manipulated chemical strategy offers a convenient and simple method to tune the optical properties of materials on a nanoscale.     

Sensing of biologically relevant d-metal ions using a Eu(III)-cyclen based luminescent displacement assay in aqueous pH 7.4 buffered solution

1·Eu·BPS was developed as a luminescent lanthanide sensor for use in displacement assays for detection of d-metal ions by monitoring the changes in the europium emission, which was quenched for iron(II), with a detection limit of ～10 pM (0.002 μg L(-1)) for Fe(II) in buffered pH 7.4 solution.     

Energetics of Zn2+ binding to a series of biologically relevant ligands: A molecular mechanics investigation grounded on ab initio self-consistent field supermolecular computations

Detailed investigations are performed of the binding energetics of Zn²⁺ to a series of neutral and anionic ligands making up the sidechains of amino acid residues of proteins, as well as ligands which can be involved in Zn²⁺ binding during enzymatic activation: imidazole, formamide, methanethiol, methanethiolate, methoxy, and hydroxy. The computations are performed using the SIBFA molecular mechanics procedure (SMM), which expresses the interaction energy under the form of four separate contributions related to the corresponding ab initio supermolecular ones: electrostatic, short-range repulsion, polarization, and charge transfer. Recent refinements to this procedure are first exposed. To test the reliability of this procedure in large-scale simulations of inhibitor binding to metalloenzyme cavities, we undertake systematic comparisons of the SMM results with those of recent large basis set ab initio self-consistent field (SCF) supermolecule computations, in which a decomposition of the total ΔE into its four corresponding components is done (N. Gresh, W. Stevens, and M. Krauss, J. Comp. Chem., 16 , 843, 1995). For each complex, the evolution of each individual SMM energy component as a function of radial and in- and out-of-plane angular variations of the Zn²⁺ position reproduces with good accuracy the behavior of the corresponding SCF term. Computations performed subsequently on di- and oligoligated complexes of Zn²⁺ show that the SIBFA molecular mechanics (SMM) functionals, E_pol and E_ct, closely account for the nonadditive behaviors of the corresponding second-order energy contributions determined from the ab initio SCF calculations on these complexes and their nonlinear dependence on the number of ligands. Thus, the total intermolecular interaction energies computed with this procedure reproduce, with good accuracy, the corresponding SCF ones without the need for additional, extraneous terms in the intermolecular potential of polyligated complexes of divalent cations. © 1995 by John Wiley & Sons, Inc.