Molecularly imprinted polymers in the drug discovery process

Since molecularly imprinted polymers (MIPs) are designed to have a memory for their molecular templates it is easy to draw parallels with the affinity between biological receptors and their substrates. Could MIPs take the place of natural receptors in the selection of potential drug molecules from synthetic compound libraries? To answer that question this review discusses the results of MIP studies which attempt to emulate natural receptors. In addition the possible use of MIPs to guide a compound library synthesis towards a desired biological activity is highlighted. © 2005 Elsevier B.V. All rights reserved.

Increased diversity of libraries from libraries: chemoinformatic analysis of bis-diazacyclic libraries

Combinatorial libraries continue to play a key role in drug discovery. To increase structural diversity, several experimental methods have been developed. However, limited efforts have been performed so far to quantify the diversity of the broadly used diversity-oriented synthetic (DOS) libraries. Herein we report a comprehensive characterization of 15 bis-diazacyclic combinatorial libraries obtained through libraries from libraries, which is a DOS approach. Using MACCS keys, radial and different pharmacophoric fingerprints as well as six molecular properties, it was demonstrated the increased structural and property diversity of the libraries from libraries over the individual libraries. Comparison of the libraries to existing drugs, NCI Diversity and the Molecular Libraries Small Molecule Repository revealed the structural uniqueness of the combinatorial libraries (mean similarity < 0.5 for any fingerprint representation). In particular, bis-cyclic thiourea libraries were the most structurally dissimilar to drugs retaining drug-like character in property space. This study represents the first comprehensive quantification of the diversity of libraries from libraries providing a solid quantitative approach to compare and contrast the diversity of DOS libraries with existing drugs or any other compound collection.

Managing the quality, value and impact of academic libraries: the role of external standards

Purpose – The purpose of this paper is to explore the role and relevance of external standards in demonstrating the value and impact of academic library services to their stakeholders. Design/methodology/approach – Two UK standards, Charter Mark and Customer Service Excellence, are evaluated via an exploratory case study, employing multiple data collection techniques. Methods and results of phases 1-2 of a three phase research project are outlined. Findings – Despite some limitations, standards may assist the manager in demonstrating the value, impact and quality of academic libraries in a recessional environment. Active engagement and partnership with customers is imperative if academic libraries are to be viewed as vital to their parent organisations and thus survive. Originality/value – This paper provides a systematic evaluation of the role of external accreditation standards in measuring academic library service value and impact.

Investigation of the effects of low energy high dose ion bombardment in metals and compound semiconductors

The effect of low energy nitrogen molecular ion beam bombardment on metals and compound semiconductors has been studied, with the aim to investigate at the effects of ion and target properties. For this purpose, nitrogen ion implantation in aluminium, iron, copper, gold, GaAs and AIGaAs is studied using XPS and Angle Resolve XPS. A series of experimental studies on N+2 bombardment induced compositional changes, especially the amount of nitrogen retained in the target, were accomplished. Both monoenergetic implantation and non-monoenergetic ion implantation were investigated, using the VG Scientific ESCALAB 200D system and a d. c. plasma cell, respectively. When the samples, with the exception of gold, are exposed to air, native oxide layers are formed on the surfaces. In the case of monoenergetic implantation, the surfaces were cleaned using Ar+ beam bombardment prior to implantation. The materials were then bombarded with N2+ beam and eight sets of successful experiments were performed on each sample, using a rastered N2+ ion beam of energy of 2, 3, 4 and 5 keV with current densities of 1 μA/cm2 and 5 μA/cm22 for each energy. The bombarded samples were examined by ARXPS. After each complete implantation, XPS depth profiles were created using Ar+ beam at energy 2 ke V and current density 2 μA/cm2 . As the current density was chosen as one of the parameters, accurate determination of current density was very important. In the case of glow discharge, two sets of successful experiments were performed in each case, by exposing the samples to nitrogen plasma for the two conditions: at low pressure and high voltage and high pressure and low voltage. These samples were then examined by ARXPS. On the theoretical side, the major problem was prediction of the number of ions of an element that can be implanted in a given matrix. Although the programme is essentially on experimental study, but an attempt is being made to understand the current theoretical models, such as SATVAL, SUSPRE and TRIM. The experimental results were compared with theoretical predictions, in order to gain a better understanding of the mechanisms responsible. From the experimental results, considering possible experimental uncertainties, there is no evidence of significant variation in nitrogen saturation concentration with ion energy or ion current density in the range of 2-5 ke V, however, the retention characteristics of implantant seem to strongly depend on the chemical reactivity between ion species and target material. The experimental data suggests the presence of at least one thermal process. The discrepancy between the theoretical and experimental results could be the inability of the codes to account for molecular ion impact and thermal processes.

Ion bombardment induced compositional changes in compound semiconductor surfaces studied by XPS combined with LEISS

Surface compositional change of GaP, GaAs, GaSb, InP, InAs, InSb, GeSi and CdSe single crystals due to low keV noble gas ion beam bombardment has been investigated by combining X-ray Photoelectron Spectroscopy (XPS) and Low Energy Ion Scattering Spectroscopy (LEISS). The purpose of using this complementary analytical method is to obtain more complete experimental evidence of ion beam modification in surfaces of compound semiconductors and GeSi alloy to improve the understanding of the mechanisms responsible for these effects. Before ion bombardment the sample surfaces were analysed nondestructively by Angular Resolved XPS (ARXPS) and LEISS to get the initial distribution of surface composition. Ion bombardment experiments were carried out using 3keV argon ions with beam current of 1μA for a period of 50 minutes, compositional changes in the surfaces of compound semiconductors and GeSi alloy were monitored with normal XPS. After ion bombardment the surfaces were re-examined with ARXPS and LEISS. Both XPS and LEISS results showed clearly that ion bombardment will change the compositional distribution in the compound semiconductor and GeSi surfaces. In order to explain the observed experimental results, two major theories in this field, Sigmund linear collision cascade theory and the thermodynamic models based on bombardment induced Gibbsian surface segregation and diffusion, were investigated. Computer simulation using TRIM code was also carried out for assistance to the theoretical analysis. Combined the results obtained from XPS and LEISS analyses, ion bombardment induced compositional changes in compound semiconductor and GeSi surfaces are explained in terms of the bombardment induced Gibbsian surface segregation and diffusion.

Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing:identification of novel zinc finger proteins.

We have successfully linked protein library screening directly with the identification of active proteins, without the need for individual purification, display technologies or physical linkage between the protein and its encoding sequence. By using 'MAX' randomization we have rapidly constructed 60 overlapping gene libraries that encode zinc finger proteins, randomized variously at the three principal DNA-contacting residues. Expression and screening of the libraries against five possible target DNA sequences generated data points covering a potential 40,000 individual interactions. Comparative analysis of the resulting data enabled direct identification of active proteins. Accuracy of this library analysis methodology was confirmed by both in vitro and in vivo analyses of identified proteins to yield novel zinc finger proteins that bind to their target sequences with high affinity, as indicated by low nanomolar apparent dissociation constants.

Removing the redundancy from randomised gene libraries

Amino acid substitution plays a vital role in both the molecular engineering of proteins and analysis of structure-activity relationships. High-throughput substitution is achieved by codon randomisation, which generates a library of mutants (a randomised gene library) in a single experiment. For full randomisation, key codons are typically replaced with NNN (64 sequences) or NNG CorT (32 sequences). This obligates cloning of redundant codons alongside those required to encode the 20 amino acids. As the number of randomised codons increases, there is therefore a progressive loss of randomisation efficiency; the number of genes required per protein rises exponentially. The redundant codons cause amino acids to be represented unevenly; for example, methionine is encoded just once within NNN, whilst arginine is encoded six times. Finally, the organisation of the genetic code makes it impossible to encode functional subsets of amino acids (e.g. polar residues only) in a single experiment. Here, we present a novel solution to randomisation where genetic redundancy is eliminated; the number of different genes equals the number of encoded proteins, regardless of codon number. There is no inherent amino acid bias and any required subset of amino acids may be encoded in one experiment. This generic approach should be widely applicable in studies involving randomisation of proteins. © 2003 Elsevier Ltd. All rights reserved.

A new randomization assay reveals Unexpected elements of sequence bias in model 'randomized' gene libraries:Implications for biopanning

Although techniques such as biopanning rely heavily upon the screening of randomized gene libraries, there is surprisingly little information available on the construction of those libraries. In general, it is based on the cloning of 'randomized' synthetic oligonucleotides, in which given position(s) contain an equal mixture of all four bases. Yet, many supposedly 'randomized' libraries contain significant elements of bias and/or omission. Here, we report the development and validation of a new, PCR-based assay that enables rapid examination of library composition both prior to and after cloning. By using our assay to analyse model libraries, we demonstrate that the cloning of a given distribution of sequences does not necessarily result in a similarly composed library of clones. Thus, while bias in randomized synthetic oligonucleotide mixtures can be virtually eliminated by using unequal ratios of the four phosphoramidites, the use of such mixtures does not ensure retrieval of a truly randomized library. We propose that in the absence of a technique to control cloning frequencies, the ability to analyse the composition of libraries after cloning will enhance significantly the quality of information derived from those libraries. (C) 2000 Published by Elsevier Science B.V. All rights reserved.

Public libraries, citizens and the post democracy

This essay explores the relationship between the development of public libraries in the context of an increasingly market-dominated economy and marketised society. It argues that although neo-liberalism as a policy goal and practice has taken different forms over time, there are common themes in terms of its emphasis on market values, privatisation, and the support of measures that reduce the role of public funding and the state in the provision of public services. This has led some commentators to express concerns that the meaning and practice of citizenship and democracy is being transformed, managed or otherwise diminished. These concerns are compounded by changes effected by new digital technology. Imbricated with this issue are debates surrounding the future of the public library, and attempts by librarians and others to reinvent and reimagine its purpose. With reference to some innovative initiatives in the USA and Scandinavia, it is suggested that public libraries, through their service and spatial rearticulation, can conceivably help strengthen and revitalise public democracy and the public sphere.

Solid-supported boronic acid conjugates for sugar and glycopeptide recognition

The Fmoc synthetic strategy was employed to synthesise two identical combinatorial peptide libraries on a hydrophilic PEG-PS resin. One library was appended with boronic acid moieties at two positionally-fixed locations. Successful inclusion of the boronic acid units was confirmed using a novel UV fluorescent colorimetric assay employing carminic acid as the dye compound. A study of the effect had by the resin-bound peptides bearing boronic acid groups on the binding characteristics of vancomycin, a medically relevant antibiotic glycoprotein, was conducted. In all, 132 library compounds were tested for their binding affinity with vancomycin, via immobilisation of the glycopeptide onto the solid support through hydrogen bonding or complexation with the boronic acid moieties. Subsequent cleavage via acidolysis afforded vancomycin containing solutions which were quantified by growth inhibition of methicillin susceptible Staphylococcus aureus. Comparison of the diameters of the resultant zones of inhibition and those produced by vancomycin of known concentrations afforded a means of calculating the vancomycin concentration of the cleavage solutions, and thereby determining the binding affinity of vancomycin to each peptide sequence. Five peptide sequences and twenty one of the peptidyl-boronic acid sequences showed zones of inhibition, demonstrating their reversible affinity for vancomycin. Three peptide sequences showed zones of inhibition in both libraries. The presence of boronic acid was therefore shown to impart, enhance, detract and remove the affinity of vancomycin to a range of resin-bound peptide sequences.

A new 3-D polymeric spin transition compound: [tris(1,4-bis-(tetrazol-1-yl) butane-N1,N1′)iron(II)] bis(perchlorate)

A series of novel polymeric compounds of formula [M(btzb)3][ClO4]2 (Mll = Fe, Ni or Cu) with btzb = 1,4-bis-(tetrazol-1-yl)butane have been prepared and their physical properties investigated. The btzb ligand has been prepared and its crystal structure determined, together with a tentative crystal structure of the 3-D compound [Fe(btzb)3][ClO4]2. The model of the latter shows two symmetry-related, interpenetrating Fe-btzb networks in which the iron(II) ions approach each other as close as 8.3 and 9.1 Å. This supramolecular catenane undergoes a sharp thermal spin transition around 160 K with hysteresis (20 K) along with a pronounced thermochromic effect. The spin crossover behaviour has been followed by magnetic, DSC, optical spectroscopy and 57Fe Mössbauer spectroscopy measurements. Irradiation with green light at low temperature leads to population of the metastable high-spin state for the thermally active iron(ll) ions. The nature of the spin crossover behaviour has been discussed in detail.

Structure and physical properties of [µ-Tris(1,4-bis(tetrazol-1-yl)butane-N4,N4‘')iron(II)] Bis(hexafluorophosphate), a new Fe(II) spin-crossover compound with a three-dimensional threefold interlocked crystal lattice

[μ-Tris(1,4-bis(tetrazol-1-yl)butane-N4,N4‘)iron(II)] bis(hexafluorophosphate), [Fe(btzb)3](PF6)2, crystallizes in a three-dimensional 3-fold interlocked structure featuring a sharp two-step spin-crossover behavior. The spin conversion takes place between 164 and 182 K showing a discontinuity at about T1/2 = 174 K and a hysteresis of about 4 K between T1/2 and the low-spin state. The spin transition has been independently followed by magnetic susceptibility measurements, 57Fe-Mössbauer spectroscopy, and variable temperature far and midrange FTIR spectroscopy. The title compound crystallizes in the trigonal space group P30¯(No. 147) with a unit cell content of one formula unit plus a small amount of disordered solvent. The lattice parameters were determined by X-ray diffraction at several temperatures between 100 and 300 K. Complete crystal structures were resolved for 9 of these temperatures between 100 (only low spin, LS) and 300 K (only high spin, HS), Z = 1 [Fe(btzb)3](PF  6)2:  300 K (HS), a = 11.258(6) Å, c = 8.948(6) Å, V = 982.2(10) Å3; 100 K (LS), a = 10.989(3) Å, c = 8.702(2) Å, V = 910.1(4) Å3. The molecular structure consists of octahedral coordinated iron(II) centers bridged by six N4,N4‘ coordinating bis(tetrazole) ligands to form three 3-dimensional networks. Each of these three networks is symmetry related and interpenetrates each other within a unit cell to form the interlocked structure. The Fe−N bond lengths change between 1.993(1) Å at 100 K in the LS state and 2.193(2) Å at 300 K in the HS state. The nearest Fe separation is along the c-axis and identical with the lattice parameter c.