Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.     

Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.     

Synthesis of 6-(perfluoroalkyl)salicylates by [3+3] cyclization of 1,3-bis(silyl enol ethers) with 3-ethoxy-1-(perfluoroalkyl)prop-2-en-1-ones

6-(Perfluoroalkyl)salicylates were prepared by [3+3] cyclization of 1,3-bis(silyl enol ethers) with 3-ethoxy-1-(perfluoroalkyl)prop-2-en-1-ones.     

Synthesis of helix 69 of Escherichia coli 23S rRNA containing its natural modified nucleosides,m(3)Psi and Psi

The synthesis of 3-methylpseudouridine (m(3)Psi) phosphoramidite, 5'-O-[benzhydryloxybis(trimethylsilyloxy)silyl]-2'-O-[bis(2-acetoxyethoxy)methyl]-3-methylpseudouridine-3'-(methyl-N,N-diisopropyl)phosphoramidite, is reported. Selective pivaloyloxymethyl protection of the Psi N1 followed by methylation at N3 was used to generate the naturally occurring pseudouridine analogue. The m(3)Psi phosphoramidite was used in combination with pseudouridine (Psi) and standard base phosphoramidites to synthesize a 19-nucleotide RNA representing helix 69 of Escherichia coli 23S ribosomal RNA (rRNA) (residues 1906-1924), containing a single m(3)Psi at position 1915 and two Psi's at positions 1911 and 1917. Our synthesis of the fully modified helix 69 RNA demonstrates the ability to make milligram quantities of RNA that can be used for further high-resolution structure studies. Site-selective introduction of the methyl group at the N3 position of pseudouridine at position 1915 causes a slight increase in the thermodynamic stability of the RNA hairpin relative to pseudouridine; RNAs containing either uridine or 3-methyluridine at position 1915 have similar stability. One-dimensional imino proton NMR and circular dichroism spectra of the modified RNAs reveal that the methyl group does not cause any substantial changes in the RNA hairpin structure.     

Synthesis of bipyridine and terpyridine based ruthenium metallosynthons for grafting of multiple pyrene auxiliaries

The synthesis of novel ruthenium(II) bipyridine or terpyridine complexes bearing an increasing number of pyrene or toluyl moieties is described. The ruthenium complexes are constructed in a first step with ligands bearing the required bromine functions, followed in a second step by stepwise grafting of 1-ethynylpyrene or 4-ethynyltoluene promoted by Pd(0). A complex bearing a protected triethylsilylacetylene function was also prepared. In situ deprotection of this function with K₂CO₃ and cross-coupling with 1-bromopyrene afforded a soluble complex in which two pyrene moieties are linearly linked via ethynyl spacers to one of the bipyridine ligands. These highly coloured complexes exhibit well defined absorption and emission properties in solution at both rt and 77 K.     

Nuclear quadrupole hyperfine structure in the microwave spectrum of HCl-N2O: electric field gradient perturbation of N2O by HCl

The microwave spectra of six isotopomers of HCl-N(2)O have been obtained in the 7-19 GHz region with a pulsed molecular beam, Fourier transform microwave spectrometer. The nuclear quadrupole hyperfine structure due to all quadrupolar nuclei is resolved and the spectra are analyzed using the Watson S-reduced Hamiltonian with the inclusion of nuclear quadrupole coupling interactions. The spectroscopic constants determined include rotational constants, quartic and sextic centrifugal distortion constants, and nuclear quadrupole coupling constants for each quadrupolar nucleus. Due to correlations of the structural parameters, the effective structure of the complex cannot be obtained by fitting to the spectroscopic constants of the six isotopomers. Instead, the parameters for each isotopomer are calculated from the A and C rotational constants and the chlorine nuclear quadrupole coupling constant along the a-axis, chi(aa). There are two possible structures; the one in which hydrogen of HCl interacts with the more electronegative oxygen of N(2)O is taken to represent the complex. The two subunits are approximately slipped parallel. For H (35)Cl-(14)N(2)O, the distance between the central nitrogen and chlorine is 3.5153 A and the N(2)O and HCl subunits form angles of 72.30 degrees and 119.44 degrees with this N-Cl axis, respectively. The chlorine and oxygen atoms occupy the opposite, obtuse vertices of the quadrilateral formed by O, central N, Cl, and H. Nuclear quadrupole coupling constants show that while the electric field gradient of the HCl subunit remains essentially unchanged upon complexation, there is electronic rearrangement about the two nitrogen nuclei in N(2)O.     

Lanthanide-transition-metal carbonyl complexes. 1. Syntheses and structures of ytterbium(II) solvent-separated ion pairs and isocarbonyl polymeric arrays of tetracarbonylcobaltate

Transmetalation reactions of metallic ytterbium with Hg[Co(CO)(4)](2) in the coordinating solvents pyridine and THF yield the solvent-separated ion pairs [Yb(L)(6)] [Co(CO)(4)](2) (1a, L = Pyr; 2a, L = THF). The IR spectrum of 1a in pyridine indicates that the tetracarbonylcobaltate anion is not directly bonded to the divalent Yb cation owing to the strong coordinating ability of pyridine. On the other hand, IR spectra of 2a in THF are concentration dependent. In dilute solutions there is an equilibrium between the solvent-separated ion pair and a weak contact ion pair. Higher concentrations of 2a facilitate the formation of a tight ion pair that has a low-frequency isocarbonyl absorption. Remarkably, complexes 1a and 2a are easily transformed in toluene into the two-dimensional sheetlike arrays [(Pyr)(4)Yb[(mu-CO)(2)Co(CO)(2)](2)](infinity) (1b) and [(THF)(2)Yb[(mu-CO)(3)Co(CO)](2).Tol](infinity) (2b). The two-dimensional frameworks are supported by isocarbonyl linkages. Infrared spectra of toluene solutions substantiate the existence of the isocarbonyl bridges with low-frequency absorptions at 1780 cm(-1). Compounds 1b and 2b belong to a rare class of lanthanide-transition-metal carbonyl extended arrays, only three others of which have been structurally established. Dissolving 1b in pyridine regenerates 1a, but the complete conversion of 2b into 2a cannot be achieved. Crystal data: 1a.Pyr is monoclinic, P2(1)/c, a = 11.171(1) A, b = 11.925(1) A, c = 33.978(1) A, beta = 95.10(1) degrees, Z = 4; 2a is monoclinic, C2/c, a = 17.724(1) A, b = 12.468(1) A, c = 18.413(1) A, beta = 100.34(1) degrees, Z = 4; 1b is monoclinic, C2/c, a = 11.047(1) A, b = 13.423(1) A, c = 21.933(1) A, beta = 103.49(1) degrees, Z = 4; 2b is monoclinic, C2/c, a = 28.589(1) A, b = 7.223(1) A, c = 14.983(1) A, beta = 118.90(1) degrees, Z = 4.     

17O NMR Investigation of Chemical Homogeneity in Hybrid Systems

¹⁷O NMR experiments using enriched water were performed to followthe hydrolysis-condensation process of dimethyldiethoxysilanetetraethoxysilane and a 1/1 mixture of dimethyldiethoxysilane andtetraethoxysilane (H₂O/OEt = 0.5; pH = 2). The spectrarecorded over several hours time period were simulated to followquantitatively the variations of residual water, hydroxyl groups(Si–¹⁷ H) and oxo bridges (Si–¹⁷ –Si). Presence of a resonance signal due oxo bridges between di- andtetrafunctional Si units clearly demonstrates that co-condensationreactions occur to a large extent between the two alkoxides, and that thesebonds are stable during the aging period.     

Bioterrorism: impact on external quality assessment service delivery

Safety issues related to the design, production and distribution of simulated specimens for microbiology external quality assessment (EQA) have occupied scheme organisers for many years. Since the anthrax attacks in Washington, USA in October 2001, there has been heightened awareness in the public domain regarding the transport of infectious substances. For instance, in direct response to the anthrax incident in the US, microbiology institutes in the UK that handle dangerous pathogens (like the Health Protection Agency) are registered with the national police force and are inspected regularly to ensure compliance with current legislation covering the control of these pathogens. The fear of a complete ban on the movement of infectious substances following the anthrax incident has not yet been realised, but remains a serious risk. Many countries such as the UK, USA, and Australia have introduced measures for the control, transportation, and health and safety aspects of handling and distribution of infectious materials. The national postal services of many countries do not accept infectious materials by mail. There are a limited number of courier services willing to transport dangerous goods, especially division 6.2 (infectious substances) and these services are costly. Measures can be implemented by scheme organisers to ensure best practice; for instance, by having sufficient and trained staff, with knowledge, expertise and use of computerised systems in the shipping/export department. Ensuring compliance with national and international health and safety legislation by providing safety data sheets and by carrying out product risk assessments is required to ensure transparency and to demonstrate duty of care. Organisers of microbiology EQA face uncertainty about the future survival of schemes in the current climate. It is imperative that practices and procedures are put into place that meet with the legislation and enable us to continue to support quality in laboratory medicine.     

Theoretical evaluation of atomic charges to be integrated into conformational analyses of neutral lipids

Conformational analyses of large molecules as fatty acids and triglycerides are usually amenable by molecular mechanics. A correct evaluation of the electrostatic energy term is thus crucial in determining reliable results. In this contribution, we have considered the most abundant fatty acids in biomembranes, i.e., lauric, stearic, oleic, and elaidic acid, and the corresponding triglycerides, i.e., trilaurin, tristearin, triolein, and trielaidin, and estimated the Mulliken and potential-derived charges both at the semiempirical AM 1 and ab initio HF MO STO -3G level. Atomic charges obtained by the Mulliken population analysis do not take into account the full geometry of the molecule. On the contrary, the change of conformation, due to different chains length or the presence of a trans or cis double bond, greatly influences the repartition of the potential-derived charges. A systematic comparative analysis shows that charges calculated by AM 1 are not suitable because as they do not reproduce potential-derived charges obtained by ab initio. © 1993 John Wiley & Sons, Inc.