Binding of α-hydroxy-β-amino acid inhibitors to methionine aminopeptidase. The performance of two types of scoring functions

The binding mode of a recently described set of -hydroxy--amino acid inhibitors of methionine aminopeptidase type 2 is suggested in the present work. The binding mode is supported by analysis of published structures of transition state analogues co-crystallised with E. coli methionine aminopeptidase and by a comparison of molecular interaction fields calculated using GRID for E. coli and human methionine aminopeptidase. Based on the suggested binding mode two types of scoring functions have been evaluated and compared. These are the commercially available consensus score, CScore, and scoring of the ligands employing energies calculated using the Merck Molecular Force Field (MMFF). Enriched subsets of ligands were obtained when using CScore, but these scores could not be used to assess the relative affinities of individual compounds. Although still not sufficiently accurate for reliable predictive purposes, an improved correlation was obtained between structure and affinity using a combined force field energy including contributions from solvation and conformational energy penalty for binding.     

Metal ion interaction with dimethyl phosphate anion

The influence of metal ions on the conformation of dimethyl phosphate anion around its O-P bonds, has been studied theoretically. The perturbation caused due to metal ions like Na⁺ and Mg²⁺ seems to affect the free dimethyl phosphate anion conformation to a considerable extent. In particular, the fully extended conformation becomes much more favourable in the metal ion dimethyl phosphate complex.     

Photochemical addition of diethyl ether to β,β,β',β'-tetrakis(trifluoromethyl)divinyl ether

The 1:1 adducts of diethyl and ,,','-tetrakis(trifluoromethyl)divinyl ether (1),i.e., 3,5-(ee)-bis[2,2,2-trifluoro-1-(trifluoromethyl)ethyl]-2,6-dimethyl-1,4-dioxane (2) (3 isomers) and 4-ethoxy-1,1,1-trifluoro-2-trifluoromethyl-3-[3,3,3-trifluoro-2(trifluoromethyl)propenyloxy]pentane (3), have been obtained by UV-irradiation of a solution of divinyl ether1 in diethyl ether. The X-ray structural investigation of the all-(e)-isomer of dioxane (2) has been carried out.Deceased.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 85–88, January, 1994.     

Synthesis,Structure and Property of Oxo-Bridged Binuclear Iron(III) Complex [Fe(phen)(H<Subscript>2</Subscript>O)<Subscript>3</Subscript>]<Subscript>2</Subscript>O⋅2SO<Subscript>4</Subscript>

An oxo-bridged binuclear iron(III) complex, [Fe(phen)(H₂O)₃]₂O2SO₄, has been synthesized and structurally characterized by elemental analysis (EA), IR, TG-DSC and X-ray. Its crystal structure has been determined by X-ray crystallography. It crystallizes in the orthorhombic system, space group P2₁2₁2, with lattice parameters a = 17.650(4), b = 8.5133(17), c = 9.971(2) Å; V = 1498.2(5) ų, _calcd = 1.763 g/cm³ and Z = 4 for R₁ = 0.0601. The crystal structure indicated that two octahedrally coordinated iron(III) ions bridged with oxygen atoms formed a non-linear complex. The bond angle of Fe–O–Fe is 163.9(4). The data of EA and IR are in good agreement with the crystal structure. The thermal gravity (TG) data indicate that there are four decomposition steps with three endothermic peaks. The final product of the thermal decomposition may be Fe(C₂H₈N₂)SO₄.     

A prediction of the three-dimensional structure of maize NADP+-dependent malate dehydrogenase which explains aspects of light-dependent regulation unique to plant enzymes

Summary A model has been built for the plant NADP-malate dehydrogenase from Zea mays, a key enzyme in photosynthesis, which undergoes light-dependent regulation. The model was based on sequence and presumed structural homology to the known three-dimensional structure of mammalian porcine cytosolic NAD-malate dehydrogenase. A cystine-loop present in an extended C-terminal region of plant NADP-malate dehydrogenases was modelled using molecular mechanics and computer graphical methods, based on the assumption that a disulphide bridge exists in the inactive form of the enzyme between Cys³⁵¹ and Cys³⁶³. The predicted conformation of the intact C-terminal cystine-loop suggests that the extended polypeptide will bind in the active centre and inhibit enzyme activity. Another ionizable cysteine residue in the active site is predicted to control the charge of the catalytic His²¹⁵ and might be responsible for the uniquely tight binding of the positively charged nicotinamide ring of NADP⁺ in this and other C4 and C3 plant NADP-malate dehydrogenases.     

Synthesis of a Calix[4]arene Containing 'Hard' and 'Soft' Metal Ion Binding Sites

Co-receptor 1,3-calix[4]-di(aza-benzo)crown-crown-6 (1-H) designed with one calix[4]arene in a 1,3-alternate conformation and hard and soft metal ion binding sites has been prepared according to three pathways (A-C). Pathway B, consisting of two different 1 + 1 condensations with ditosylate derivatives, was shown to be the most efficient.     

Room temperature phosphorescence optosensing for gadolinium

An optosensing method for gadolinium based on the room-temperature phosphorescence behavior in aqueous solution induced by the transient adsorption of the complex formed by 1,4-bis (1-phenyl-3-methyl-5-pyrazolone-4-)butanedione (1,4) with Gd (III) on the chelating resin Chelex 100 (packed in a flow cell) is proposed. The proposed optosensing is satisfactory for the determination of the gadolinium ion in the range 8 × 10^–7–5 × 10^–5 M with a correlation coefficient of 0.995. The relative standard deviation was 2.0% for determination of 5× 10^–6 M gadolinium ion (n = 10). The response mechanism of the optosensing and the interferences of other lanthanide ions were also investigated. The method has been used to determine gadolinium ion in synthetic sample.     

The effect of Fe(II) ions on the 1,10-phenanthroline and neocuproine intercalates of γ-zirconium phosphate

1,10-Phenanthroline (phen), 2,9-dimethyl-1,10-phenanthroline (neocuproine), and 4,7-dimethyl-1,10-phenanthroline have been intercalated between layers of -zirconium phosphate (-ZrP). The observed interlayer distances are not a simple function of the size of guest molecules. Despite the fact that -ZrP takes up very few Fe²⁺ ions, the phen and neocuproine intercalates do take up some Fe²⁺ ions without further changes in the interlayer distances. The chemical environments around Fe²⁺ ions between layers of the intercalates were investigated by⁵⁷Fe Mössbauer spectroscopy. A fairly large fraction of the Fe²⁺ ions was found to be in a high-spin state. The low-spin [Fe(phen)₃]²⁺ ions are also ion exchanged on -ZrP, with the expansion of the interlayer up to 19.9 Å.     

The μ-and δ-opioid pharmacophore conformations of cyclic β-casomorphin analogues indicate docking of the Phe3 residue to different domains of the opioid receptors

Summary Cyclic -casomorphin analogues with a d-configured amino acid residue in position 2, such as Tyr-c[-Xaa-Phe-Pro-Gly-] and Tyr-c[-Xaa-Phe-d-Pro-Gly-] (Xaa=d-A₂bu, d-Orn, d-Lys) were found to bind to the -opioid receptor as well as to the -opioid receptor, whereas the corresponding l-Xaa² derivatives are nearly inactive at both. Low-energy conformers of both active and nearly inactive derivatives have been determined in a systematic conformational search or by molecular dynamics simulations using the TRIPOS force field. The obatained conformations were compared with regard to a model for -selective opiates developed by Brandt et al. [Drug Des. Discov., 10 (1993) 257]. Superpositions as well as electrostatic, lipophilic and hydrogen bonding similarities with the -opioid receptor pharmacophore conformation of t-Hpp-JOM-13 proposed by Mosberg et al. [J. Med. Chem., 37 (1994) 4371, 4384] were used to establish the probable -pharmacophoric cyclic -casomorphin conformations. These conformations were also compared with a -opioid agonist (SNC 80) and the highly potent antagonist naltrindole. These investigations led to a prediction of the -and -pharmacophore structures for the cyclic -casomorphins. Interestingly, for the inactive compounds such conformations could not be detected. The comparison between the -and -pharmacophore conformations of the cyclic -casomorphins demonstrates not only differences in spatial orientation of both aromatic groups, but also in the backbone conformations of the ring part. In particular, the differences in ² and ² (70°,-80°; 165°,55°) cause a completely different spatial arrangement of the cyclized peptide rings when all compounds are matched with regard to maximal spatial overlap of the tyrosine residue. Assuming that both the -and -pharmacophore conformations bind with the tyrosine residue in a similar orientation at the same transmembrane domain X of their receptors, the side chain of Phe³ as a second binding site has to dock with different domains.This paper is based on a presentation given at the 14th Molecular Graphics and Modelling Society Conference, held in Cairns, Australia, August 27–September 1, 1995.     

Charge-transfer complexes betweenp-toluidine and iodine in solution: A kinetic study

The kinetics of charge-transfer interaction betweenp-toluidine and iodine in methylene chloride was investigated in depth. Thethermal process of formation of theinner complex was found to proceed to an equilibrium. Thephotochemical process follows a different reaction coordinate, going through the formation of an exciplex between the excitedouter complex and the amine ground state. In both cases the same ionic complex (Am ₂I⁺I ₃ ^– , whereAm stands forp-toluidine) was detected as the final product.

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Kinetische Untersuchung der Charge-Transfer-Komplexe zwischenp-Toluidin und Jod

Zusammenfassung Die Kinetik der Charge-Transfer-Wechselwirkung zwischenp-Toluidin und Jod in Methylenchlorid wurde ausführlich untersucht. Derthermische Prozeß, der zur Bildung desinner-Komplexes führt, geht bis zu einem Gleichgewicht. Derphotochemische Prozeß folgt einer unterschiedlichen Reaktionskoordinate und verläuft über die Bildung eines Exziplexes zwischen dem angeregtenouter-Komplex und dem Amin im Grundzustand. In beiden Fällen wurde derselbe ionische Komplex (Am ₂I⁺I ₃ ^– , wobeiAm fürp-Toluidin steht) als Endprodukt festgestellt.

     

Colloidal copper in aqueous solutions: radiation-chemical reduction,mechanism of formation,and properties

Colloidal copper has been obtained by -irradiation of aqueous solutions of copper (II) perchlorate in the presence of alcohol and polyethyleneimine (PEI). The sols are spherical particles about 4 nm in diameter, which are quickly oxidized by oxygen or other oxidants. When Cu^II is not entirely incorporated into the complex with PEI, disproportionation of Cu^I aqua complexes formed affords the metal, along with Cu₂O. Reduction of the PEI complex of Cu^I by hydrated electrons gives only colloidal copper. The copper ions can be reduced on the surface of silver sols. Optical parameters of the resulting bimetallic particles have been studied. The presence of copper ions leads to broadening of the absorption band associated with the silver sols and shifts it to the UV region, which is due to the transfer of electrons from copper to silver. Three copper monolayers are enough to cause plasmon absorption of colloidal copper.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 25–30, January, 1994.     

Effect of medium on the equilibrium of cationic σ- and π-complexes: interconversion of 1-pentafluorophenylthio-1,2-dimethyl-acenaphthylenium and 1,2-dimethylacenaphtylene-1,2-S-pentafluorophenylepisulphonium ions

The equilibrium of 1-pentafluorophenylthio-1,2-dimethylacenaphthylenium and 1,2-dimethylacenaphthylene-1, 2-S-pentafluorophenylepisulphonium ions in different media has been investigated by¹H and¹³C NMR spectroscopy using isotope perturbation. It has been found that this equilibrium is weakly sensitive to variation in the medium.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1057–1060, June, 1993.     

Synthesis of Platinum-Triruthenium Clusters Using the Zero-Valent Platinum Reagent Pt(nb)3: X-Ray Crystal Structures of Ru3Pt(CO)11(P-iPr3)2, Ru3Pt(μ-H)(μ3-η3-MeCCHCMe)(CO)9(P-iPr3), Ru3Pt(μ3-η2-PhCCPh)(CO)10(P-iPr3), Ru3Pt(μ-H)(μ4-N)(CO)10(P-iPr3) and Ru3Pt(μ-H)(μ4-η2-NO)(CO)10(P-iPr3)

The complexes Pt(nb)_3-n(P-iPr₃)_n (n=1, 2, nb=bicyclo[2.2.1]hept-2-ene), prepared in situ from Pt(nb)₃, are useful reagents for addition of Pt(P-iPr₃)_n fragments to saturated triruthenium clusters. The complexes Ru₃Pt(CO)₁₁(P-iPr₃)₂ (1), Ru₃Pt(-H)(₃-³-MeCCHCMe)(CO)₉(P-iPr₃) (2), Ru₃Pt(₃-²-PhCCPh)(CO)₁₀(P-iPr₃) (3), Ru₃Pt(-H)(₄-N)(CO)₁₀(P-iPr₃) (4) and Ru₃Pt(-H)(₄-²-NO)(CO)₁₀(P-iPr₃) (5) have been prepared in this fashion. All complexes have been characterized spectroscopically and by single crystal X-ray determinations. Clusters 1–3 all have 60 cluster valence electrons (CVE) but exhibit differing metal skeletal geometries. Cluster 1 exhibits a planar-rhomboidal metal skeleton with 5 metal–metal bonds and with minor disorder in the metal atoms. Cluster 2 has a distorted tetrahedral metal arrangement, while cluster 3 has a butterfly framework (butterfly angle=118.93(2)°). Clusters 4 and 5 posseses 62 CVE and spiked triangular metal frameworks. Cluster 4 contains a ₄-nitrido ligand, while cluster 5 has a highly unusual ₄-²-nitrosyl ligand with a very long nitrosyl N–O distance of 1.366(5) Å.     

Chemie der Pleuromutiline, 11. Mitt.: Konfigurationsumkehr der Vinylgruppe am Kohlenstoff 12 durch reversible Retro-En-Spaltung

The reaction of pleuromutilin-22-0-tosylat(2) withEtZnI afforded a mixture of the 12-epimeric compounds2 and3. A reversible retro-en-reaction of the homoallylic system is discussed as a possible mechanistic pathway. The structure assignment is based on¹H- and¹³C-NMR spectroscopic data.

Für Verbindungen dieser Substanzklasse, die auf ihre antibakterielle Aktivität geprüft werden, ist erfahrungsgemäß eine basisch substituierte Acylgruppierung in Position 14 erforderlich⁴. Heterocyclische Acylgruppierungen erwiesen sich dabei als besonders wirkungsvoll.     

Synthesis of Co3(CO)7(μ-η3-Allyl)(μ3-X) Complexes (X=S, Se) and Structure of the Selenium Derivative

The complexes Co₃(CO)₉( ₃-X) (X=S, Se) can be reduced to the corresponding anionic species [Co₃(CO)₉( ₃-X)]^–, which react with allyl bromide to give Co₃(CO)₇(- ³-C₃H₅)( ₃-X) (X=S, Se). These are the first two cobalt complexes containing the bridging - ³-allyl ligand. The structure of the selenium complex was determined by X-ray crystallography. Crystal data for Co₃(CO)₇(- ³-C₃H₅)( ₃-Se) are as follows: space group P2₁/c, a=9.051(2) Å, b=8.102(2) Å, c=21.27(4) Å, =93.82(3)°, Z=4, and R=0.0565 for 2491 observed reflections.     

Theory of isomer shift in hemin

Using the self-consistent charge extended Hückel procedure, the charge density difference at Fe⁵⁷ nucleus, between hemin and Fe⁺³ ion is calculated. This is combined with the recent value of the calibration constant, –0.23±0.02a ₀ ³ mm/sec to obtain an isomer shift of –0.374 mm/sec between hemin and Fe⁺³ in good agreement with the value –0.392 mm/sec derived from experimental data and the calculated value of the isomer shift of Fe⁺³ with respect to K₃FeF₆ from first principle covalency investigations in the latter compound. is composed of contributions from core and valence electrons of the same order of magnitude, with the latter being more than one-half of the former. The core contribution is composed of a number of terms of comparable magnitude and differing signs, whose significance is discussed.Supported by grant HL 15196-02 from the Heart and Lung Institute of National Institute of Health.     

Organomineral sorbents based on clinoptilolite-containing tuffs

The anion-exchange properties of a new organomineral sorbent obtained by modification of clinoptilolite-containing tuffs by polyhexamethyleneguanidine have been studied after different periods of storage (time after synthesis) and numbers of sorption-regeneration cycles. The sorbent can be used as a cation- and an anion-exchanger simultaneously. Selectivity coefficients (exchange constants) for F^–, SO₄ ^2–, and HPO₄ ^2– ionsvs. Cl^– ions on modified clinoptilolite-containing tuffs have been determined. The modification improves the mechanical properties of clinoptilolite tuffs.For part 1, see Ref. 1.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1554–1556, September, 1994.     

Cation-binding to biomolecules

Ab initio SCF computations indicate that Mg²⁺ should bind essentially to the oxygen atoms of uracil, the remaining part of the base being rather repulsive towards such an interaction. The Coulombic component predominates in the interaction, the essential feature of which may thus be deduced from the study of the molecular electrostatic potential of uracil. These ab initio results contradict an earlier CNDO prediction that the binding of uracil and Mg²⁺ should occur preferentially at the C₅=C₆ double bond of the base. It is shown that the CNDO result is an artifact due to an exaggeration by this method of the charge transfer between the ligand and the cation. The small amount of available experimental data seem in favor of the ab initio results.     

Direct spectrometric determination of proteins in body fluids using a near-infrared cyanine dye

A new near-infrared (NIR) dye, 1,1-disulfobutyl-3,3,3,3-tetramethylindotricarbocyanine (DTCY) has been developed for the quantitation of proteins in solution. The method is based on the binding of DTCY to proteins under acidic conditions. The binding of DTCY to proteins causes a new band at 814 nm. The maximum binding number of bovine serum albumin (BSA) with DTCY was measured as 100. The linear range is 0.3–40 g mL^–1 for BSA and human serum albumin (HSA), respectively. Except for Fe²⁺, Cu²⁺, and cetyltrimethylammonium bromide, all of the examined coexisting substances show no interference in the assay. The method has been applied to the quantitation of proteins in serum and urine with recoveries between 96 and 105%.