Structure determination of protein-ligand complexes by transferred paramagnetic shifts

Rational drug design depends on the knowledge of the three-dimensional (3D) structure of complexes between proteins and lead compounds of low molecular weight. A novel nuclear magnetic resonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allows the rapid determination of the 3D structure of a small ligand molecule bound to its protein target in solution and, simultaneously, its location and orientation with respect to the protein. The method relies on the presence of a lanthanide ion in the protein target and on fast exchange between bound and free ligand. The binding affinity of the ligand and the paramagnetic effects experienced in the bound state are derived from concentration-dependent (1)H and (13)C spectra of the ligand at natural isotopic abundance. Combined with prior knowledge of the crystal or solution structure of the protein and of the magnetic susceptibility tensor of the lanthanide ion, the paramagnetic data define the location and orientation of the bound ligand molecule with respect to the protein from simple 1D NMR spectra. The method was verified with the ternary 30 kDa complex between the lanthanide-labeled N-terminal domain of the epsilon exonuclease subunit from the Escherichia coli DNA polymerase III, the subunit theta, and thymidine. The binding mode of thymidine was found to be very similar to that of thymidine monophosphate present in the crystal structure.     

Photoreactivity of psoralen derivatives in micelles: the roles of hydrophobicity and heavy atom substitution

Intersystem crossing quantum yields of two psoralen derivatives, bromopsoralen (BrMOP) and hexylpsoralen (8-HOP) were measured in ethanol and water by means of laser flash photolysis. Compared to 8-methoxypsoralen (8-MOP), the triplet quantum yields of BrMOP and 8-HOP in ethanol are increased by a factor of 5 and 30, respectively, while BrMOP in aqueous solution shows a twofold enhancement with respect to 8-MOP. Radical cations and hydrated electrons were generated by photoionization in micellar solution upon excitation at 266nm. A nonlinear relationship between transient yield and photon fluence was obtained for each compound, indicating that a two-photon mechanism is predominant in the photoionization of the sensitizers. The photoionization efficiencies are significantly higher in anionic sodium dodecyl sulfate (SDS) than in cationic cetyltrimethylammonium bromide (CTAB) micelles, reflecting the influence of micelle charge on the efficiency of the separation of the photoproduced charge carriers. The photoionization efficiencies of 8-HOP and 8-MOP are similar. It is concluded that the intersystem crossing properties of BrMOP show a substantial heavy atom effect, whereas the effects of hydrophobic substitution on photoionization efficiency are minor.     

ω-Hydroxyalkyl-phosphonium salts as “instant-ylid” components : extremely convenient and highly cis-selective synthesis of alkenol-type pheromones

In less than 2 hours, (Z)-alkenols of 97 – 98% stereoisomeric purity may be prepared and isolated (!) if a new type of “instant-ylids” is used.     

Synthesis of ferrocenyl-1,2-diketones and related compounds: Crystal and molecular structures of 1,2-diferrocenylethanedione and 1-ferrocenyl-2-(4-biphenylyl) ethanedione

Ferrocenyl-1,2-diketones FcCOCOR, 3, [Fc = (C₅H₅)Fe(C₅H₄)] can be prepared by oxidation of acylferrocenes FcCOCH₂R or, more efficiently, by oxidation of the isomeric ketones FcCH₂COR, 2. The ketones 2 are in turn readily synthesized from the salt (FcCH₂PPh₃)⁺I⁻ via the acylated salts [FcCH(COR)PPh₃]⁺I⁻. The haloacylferocenes FcCOCCl_x H_3−x (x = 1, 2, 3, of which the x = 2 example is synthetically equivalent to a diketone) are synthesized by Friedel—Crafts acylation of ferrocene using CCl_xH_3−xCOCl/AlCl₃, but the reaction proceeds via two parallel pathways, one giving the normal acyl derivatives FcCOCCl_xH_3−x and the other giving the reduced products FcCOCCl_x−1H_4−x. Two diketones FcCOCOFc 3b and FcCOCOC₆H₄Ph 3c have been structurally characterised by single-crystal X-ray diffraction.     

Stereoselective Ring Opening of Electronically Excited Cyclohexa-2, 4-dienones: Cause and effect

The two conformers of a cyclohexa-2, 4-dienone with different substituents at C(6) on irradiation are believed to undergo ring opening stereospecifically affording a mixture of two configurationally isomeric diene-ketenes (and descendents thereof)- Exceptions are generally found for those dienones with one C and one O substituent or even with two C substituents, if one of them carries a polar group at a site able to interact through space with the ring C?O group. In these cases, only one of the two anticipated diene-ketenes (and descendents thereof) is produced. A thorough investigation of the photochemistry of a series of structurally different cyclohexa-2, 4-dienones on analytical as well as on preparative scale extends our mechanistic knowledge of the various routes from diene-ketenes into a variety of compound classes. Novel compound classes accessible to diene-ketenes are seven-membered carbocycles (by intramolecular aldolization of the zwitterion of appropriately substituted, transiently formed diene-(N, O)-ketene acetals) and β-lactams (by Staudinger reaction).     

Identification of protein surfaces by NMR measurements with a pramagnetic Gd(III) chelate.

Gd-diethylenetriamine pentaacetic acid-bismethylamide, Gd(DTPA-BMA), is shown to be a reagent suitable for the identification of protein surfaces. Compared to the conventionally used spin-label TEMPOL, Gd(DTPA-BMA) is a stronger relaxation agent, requiring lesser concentrations to achieve the same paramagnetic relaxation enhancement of solvent-exposed protein protons. It is also less hydrophobic and therefore less prone to specific binding to proteins. Relaxation enhancements predicted by a second-sphere interaction model correlated with experimental data recorded with ubiquitin, while the correlation with corresponding data recorded with TEMPOL was poor.     

Comparative enantioseparations with native beta-cyclodextrin,randomly acetylated beta-cyclodextrin and heptakis-(2,3-di-O-acetyl)-beta-cyclodextrin in capillary electrophoresis

Comparative enantioseparations were performed with three neutral cyclodextrins (CDs) in capillary electrophoresis (CE). In particular, native beta-CD was compared with single component heptakis(2,3-di-O-acetyl)-beta-CD (HDA-beta-CD) and randomly acetylated beta-CD (Ac-beta-CD) with the emphasis on the enantiomer migration order. The opposite affinity of the enantiomers of several chiral analytes was observed towards native beta-CD and its acetylated derivatives. The enantiomer affinity pattern of some chiral analytes was also opposite towards the two acetylated derivatives of beta-CD. In the case of the chiral drug clenbuterol (CL) an attempt was made to evaluate the possible structural reasons of the affinity reversal using one- and two-dimensional as well as transverse rotating frame nuclear Overhauser effect spectroscopy (ROESY). Significant differences were observed between the structure of the CL complexes with beta-CD and HDA-beta-CD.     

Enantioseparation of glutethimide and its 5-OH-metabolite in capillary electrophoresis and study of selector-selectand interactions using one-dimensional rotating frame nuclear Overhauser and exchange spectroscopy

Enantioseparation of glutethimide (GT) and its 5-hydroxy metabolite (5-OH-GT) has been studied with several charged cyclodextrin (CD) derivatives. The emphasis was made on the enantiomer migration order of GT and simultaneous enantioseparation of GT and 5-OH-GT. The possible structural differences of GT complexes with three different single isomer charged CD derivatives were studied using one-dimensional rotating frame nuclear Overhauser and exchange spectroscopy (1-D ROESY).