Academic librarians at play in the field of cheminformatics: building the case for chemistry research data management

There are compelling needs from a variety of camps for more chemistry data to be available. While there are funder and government mandates for depositing research data in the United States and Europe, this does not mean it will be done well or expediently. Chemists themselves do not appear overly engaged at this stage and chemistry librarians who work directly with chemists and their local information environments are interested in helping with this challenge. Our unique understanding of organizing data and information enables us to contribute to building necessary infrastructure and establishing standards and best practices across the full research data cycle. As not many support structures focused on chemistry currently exist, we are initiating explorations through a few case studies and focused pilot projects presented here, with an aim of identifying opportunities for increased collaboration among chemists, chemistry librarians, cheminformaticians and other chemistry professionals.     

Immunoassays: biological tools for high throughput screening and characterisation of combinatorial libraries

In the demanding field of proteomics, there is an urgent need for affinity-catcher molecules to implement effective and high throughput methods for analysing the human proteome or parts of it. Antibodies have an essential role in this endeavour, and selection, isolation and characterisation of specific antibodies represent a key issue to meet success. Alternatively, it is expected that new, well-characterised affinity reagents generated in rapid and cost-effective manners will also be used to facilitate the deciphering of the function, location and interactions of the high number of encoded protein products. Combinatorial approaches combined with high throughput screening (HTS) technologies have become essential for the generation and identification of robust affinity reagents from biological combinatorial libraries and the lead discovery of active/mimic molecules in large chemical libraries. Phage and yeast display provide the means for engineering a multitude of antibody-like molecules against any desired antigen. The construction of peptide libraries is commonly used for the identification and characterisation of ligand-receptor specific interactions, and the search for novel ligands for protein purification. Further improvement of chemical and biological resistance of affinity ligands encouraged the "intelligent" design and synthesis of chemical libraries of low-molecular-weight bio-inspired mimic compounds. No matter what the ligand source, selection and characterisation of leads is a most relevant task. Immunological assays, in microtiter plates, biosensors or microarrays, are a biological tool of inestimable value for the iterative screening of combinatorial ligand libraries for tailored specificities, and improved affinities. Particularly, enzyme-linked immunosorbent assays are frequently the method of choice in a large number of screening strategies, for both biological and chemical libraries.     

Quality control in combinatorial chemistry: determination of the quantity,purity, and quantitative purity of compounds in combinatorial libraries

The quality of combinatorial libraries determines the success of biological screening in drug discovery programs. In this paper, we evaluate and compare various methods for measuring identity, purity, and quantity (yield) of combinatorial libraries. Determination of quantitative purity reveals the true library quality and often indicates potential quality problems before full-scale library production. The relative purity can be determined for every member in a large library in a high-throughput mode, but must be cautiously interpreted. In particular, many impurities are not observable by relative purity measurements using detectors such as UV(214), UV(254), and evaporative light-scattering detection. These "invisible" impurities may constitute a significant portion of the sample weight. We found that TFA, plastic extracts, inorganic compounds, and resin washout are among these impurities. With compelling evidence, we reach a conclusion that purification is the only way to remove "invisible" impurities and improve the quantitative purity of any compound even though some compounds may have a high relative purity before purification.     

Solid electrodes in electroanalytical chemistry: present applications and prospects for high throughput screening of drug compounds

This review summarizes recent progress in the development and application of solid electrodes to the screening of pharmaceutical dosage forms and biological fluids. Recent trends and advances in the electroanalytical chemistry of solid electrodes, microelectrodes and electrochemical sensors are reviewed. The varieties of solid electrodes and their basic physico-chemical properties and some specific characteristics including some supramolecular phenomena at their surface are surveyed. This review also includes some selected designs and their applications. Despite many reviews about individual solid electrodes in the literature, this review offers the first comprehensive report on all forms of solid electrodes. Special attention is paid to the possibilities of solid electrodes in high throughput electroanalytical investigation of drug dosage forms and biological samples using modern electroanalytical techniques. Various selected studies on these subjects since 1996 are reviewed in this paper.     

Application of artificial intelligence on the CO2 capture: a review

Journal of Thermal Analysis and Calorimetry - Unleashing greenhouse gases especially CO2 has been proven to be detrimental in many aspects both globally and individually. Numerous techniques and...     

Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulators with Forecaster, a novel platform for drug discovery

As part of a large medicinal chemistry program, we wish to develop novel selective estrogen receptor modulators (SERMs) as potential breast cancer treatments using a combination of experimental and computational approaches. However, one of the remaining difficulties nowadays is to fully integrate computational (i.e., virtual, theoretical) and medicinal (i.e., experimental, intuitive) chemistry to take advantage of the full potential of both. For this purpose, we have developed a Web-based platform, Forecaster, and a number of programs (e.g., Prepare, React, Select) with the aim of combining computational chemistry and medicinal chemistry expertise to facilitate drug discovery and development and more specifically to integrate synthesis into computer-aided drug design. In our quest for potent SERMs, this platform was used to build virtual combinatorial libraries, filter and extract a highly diverse library from the NCI database, and dock them to the estrogen receptor (ER), with all of these steps being fully automated by computational chemists for use by medicinal chemists. As a result, virtual screening of a diverse library seeded with active compounds followed by a search for analogs yielded an enrichment factor of 129, with 98% of the seeded active compounds recovered, while the screening of a designed virtual combinatorial library including known actives yielded an area under the receiver operating characteristic (AU-ROC) of 0.78. The lead optimization proved less successful, further demonstrating the challenge to simulate structure activity relationship studies.     

Dynamic combinatorial chemistry as a tool for the design of functional materials and devices

This tutorial review presents emerging lines of investigations directed towards the development of dynamic combinatorial materials and devices. These can be defined as multi-component chemical systems which, thanks to the reversibility of their interconnections within networks of competing reactions, and thanks to their sensitivity to environmental parameters, aim at performing modular functional tasks by responding to external stimuli. The behaviour of such dynamic materials is by essence more complex than the one produced by their static or single-component counterparts and as such, they hold higher potentialities in terms of information processing and functionality tuning. Key examples are selected here to illustrate the variety of their chemical nature and physical properties which can be implemented for the fabrication of devices as diverse as sensors, ion channels, self-healable materials, mesophases for the controlled release of bioactive compounds, or dynamic functional nanostructures.     

Interplay of thermochemistry and structural chemistry, the journal (volume 15, 2004) and the discipline

As practiced disciplines, structural chemistry, and thermochemistry need not necessarily be related. Yet such relationships, ranging from minor to very close, can help our overall understanding and detailed analyses of the species and methods under consideration. In the current study, these relations are made more evident from among the contents of the journal “Structural Chemistry” (Vol. 15) for the year 2004. The year’s articles have been reviewed, giving to most of those appearing therein a thermochemical commentary, “spin” or “slant.” A special emphasis is made on raising questions or noting possible future research topics that arise when looking at the relations noted earlier.     

Gelators for organic liquids based on self-assembly: a new facet of supramolecular and combinatorial chemistry

The recent years have been witness to a rapidly growing interest in the self-assembly phenomenon of low molecular weight organogelators. Herein, we highlight the recent developments in the discovery of new gelator systems and the potential methods for useful stabilisation of gels. Additionally, the recent progress in gel-characterisation with novel analytical methods and the practical application of gel systems are also reviewed.     

K-Screen: a free application for high throughput screening data analysis, visualization, and laboratory information management

High throughput screening (HTS) has emerged as an important technique for allowing researchers to rapidly profile very large numbers of chemicals against drug targets. As recent and future advances make HTS cheaper to perform on even larger scales, the amount of data that has to be processed, analyzed, and searched will only grow larger in size and harder for researchers to manually sift through. It is therefore an unavoidable requirement that institutions utilizing HTS technology will need to begin looking for effective solutions in the maturing area of laboratory information management systems like many other types of labs have already done. K-Screen is one such solution. Our initial goal with K-Screen was to have an integrated application environment that supported data analysis, management, and presentation so we could efficiently perform client requested screens and searches as well as generate detailed reports on the results of those. Previously, we had attempted but failed to locate an existing software suite that sufficiently addressed all our requirements. K-Screen is a web accessible application that offers the ability to host a large chemical structure library, process and store single-dose (primary) and dose response (secondary) screening data, perform searches based on screening results, plate coordinates, and structure, substructure and structure similarity. It uses heat maps and histograms to visualize screen or plate level statistics. Interfaces to external searches against PubChem and ZINC databases are also provided. We feel that these features make K-Screen a practical and effective alternative to other commercial or academic HTS LIMS systems.     

Oxidation of a biomarker for phenol carcinogen exposure: expanding the redox chemistry of 2'-deoxyguanosine

A biomarker for phenolic carcinogen exposure, 8-(4'-hydroxyphenyl)-2'-deoxyguanosine, has been found to undergo oxidative coupling in the presence of Na2IrCl6 to afford ortho-ortho C-C-coupled polyphenols through the intermediacy of a phenoxyl radical. One can envision using such unique chemistry to oxidatively couple strands of DNA for the generation of new biomaterials. Our results also demonstrate the potential for phenolic adducts of DNA to undergo further oxidation reactions that may contribute to phenol-mediated cytotoxicity and genotoxicity.     

Direct-injection NMR (DI-NMR): a flow NMR technique for the analysis of combinatorial chemistry libraries

A new tool for analyzing compound libraries by NMR has been developed. Aliquots of solution-state samples (between 120 and 350 microL) are directly injected, using a standard liquids handler, into an NMR (LC-NMR) flow probe. Automated NMR software tracks--and suppresses--intense signals arising from the nondeuterated solvents used (if any) and acquires high-sensitivity one-dimensional 1H NMR spectra. An 88-member combinatorial library, dissolved in DMSO and stored in a 96-well microtiter plate, has been analyzed a number of ways using this technique. This nondestructive technique, which we call direct-injection NMR (DI-NMR) and which is embodied in our versatile automated sample changer (VAST) hardware, has proven to be both routine and robust. Our success in automatically acquiring the NMR data for entire plates of library compounds (within 4-8 h) has caused us to develop new ways to display and analyze the resulting NMR data, as will be shown here.     

A new [4]carceplex, and a crystal structure and dynamic combinatorial chemistry of a [5]carceplex

A new [4]carceplex (2·guest) is reported. It is composed of two cavitands linked by four disulfide bonds. It forms twistomers, which interconvert on a millisecond timescale. The energy barrier for interconversion of twistomers is guest-dependent. Formation of [4]carceplex 2·guest is template dependent. The selectivity in templates is flat relative to most previous related template work. Larger kin [5]carceplex 1·guests were reinvestigated. A crystal structure confirms the twist between the hemispherical cavitands. Use of a redox buffer allowed dynamic combinatorial chemistry to be performed between pairs of templates.     

A "single-sample concept" (SSC): a new approach to the combinatorial chemistry of inorganic materials

Combinatorial estimations show that, within an unreacted ceramic sample prepared by mixing N different starting materials MxOy with average particle size approximately 1 microm, there are about 10(12) grains per cubic centimeter, sufficient for local reactions to occur that may produce a larger number of product oxides than presently accessible by 2D plate techniques. The "single-sample concept" (SSC) is proposed for performing property-directed syntheses for the preparation of ferri-/ferromagnetic or superconducting compounds. Because of the magnetic properties of the products, libraries of product grains can be sorted by means of magnetic separation techniques. For materials with a large magnetization, the separation efficiency is so high that traces of products can be isolated. The SSC concept was tested experimentally to prepare Fe-based oxides (N=17, 24, 30). The large yields (<75 wt %, N=17) of product grains agree with the literature data, which indicate that 3d metal magnetic oxide phases (Tc>300 K) are most probably Fe oxides. In combination with magnetic separation techniques, SSC seems particularly adapted for exploring the solid-state chemistry of metallic lead elements that form ferri-/ferromagnetic or superconducting oxide phases difficult to detect systematically within the large phase space of theoretically existing compounds.     

Design of new plasmepsin inhibitors: a virtual high throughput screening approach on the EGEE grid

Though different species of the genus Plasmodium may be responsible for malaria, the variant caused by P. falciparum is often very dangerous and even fatal if untreated. Hemoglobin degradation is one of the key metabolic processes for the survival of the Plasmodium parasite in its host. Plasmepsins, a family of aspartic proteases encoded by the Plasmodium genome, play a prominent role in host hemoglobin cleavage. In this paper we demonstrate the use of virtual screening, in particular molecular docking, employed at a very large scale to identify novel inhibitors for plasmepsins II and IV. A large grid infrastructure, the EGEE grid, was used to address the problem of large computation resources required for docking hundreds of thousands of chemical compounds on different plasmepsin targets of P. falciparum. A large compound library of about 1 million chemical compounds was docked on 5 different targets of plasmepsins using two different docking software, namely FlexX and AutoDock. Several strategies were employed to analyze the results of this virtual screening approach including docking scores, ideal binding modes, and interactions to key residues of the protein. Three different classes of structures with thiourea, diphenylurea, and guanidino scaffolds were identified to be promising hits. While the identification of diphenylurea compounds is in accordance with the literature and thus provides a sort of "positive control", the identification of novel compounds with a guanidino scaffold proves that high throughput docking can be effectively used to identify novel potential inhibitors of P. falciparum plasmepsins. Thus, with the work presented here, we do not only demonstrate the relevance of computational grids in drug discovery but also identify several promising small molecules which have the potential to serve as candidate inhibitors for P. falciparum plasmepsins. With the use of the EGEE grid infrastructure for the virtual screening campaign against the malaria causing parasite P. falciparum we have demonstrated that resource sharing on an eScience infrastructure such as EGEE provides a new model for doing collaborative research to fight diseases of the poor.     

[1,2]-Aryl migration in the synthesis of substituted indoles: scope, mechanism, and high throughput experimentation

A mild regioselective synthesis of substituted indoles from readily accessible 1-(2-aminophenyl)-2-chloroethanones is described. Addition of a range of carbon nucleophiles to α-chloro acetophenones 1 generates 2-substituted indoles 2 in moderate to excellent yields. A reaction mechanism involving a [1,2]-aryl migration is proposed. This useful transformation is further examined using high throughput experimentation.     

Preparation and improved stability of N-Boc-alpha-amino-5-acyl Meldrum's acids,a versatile class of building blocks for combinatorial chemistry

The preparation of novel N-Boc-alpha-amino-5-acyl Meldrum's acids is described. The synthetic inaccessibility and instability of several of these products have led to the development of a protocol that allows the synthesis of their corresponding 4-(dimethylamino)pyridine (DMAP) salts (5-AMA-DMAP's), which exhibit superior stability compared to that of the free 5-AMA. A simple and expedient ion-exchange method was developed for the quantitative removal of DMAP to liberate the synthetically useful DMAP-free form when needed.     

One-armed artificial receptors for the binding of polar tetrapeptides in water: probing the substrate selectivity of a combinatorial receptor library

We have recently developed a new class of one-armed artificial receptors 1 for the binding of the polar tetrapeptide N-Ac-D-Glu-L-Lys-D-Ala-D-Ala-OH (EKAA) 2 in water using a combined combinatorial and statistical approach. We have now further probed the substrate selectivity of this receptor library 1 by screening a second tetrapeptide substrate (3) with the inverse sequence N-Ac-D-Ala-D-Ala-L-Lys-D-Glu-OH (AAKE). This "inverse" substrate is also efficiently bound by our receptors, with K(ass) approximately 6000 M(-1) for the best receptors, as determined both by a quantitative on-bead binding assay and by UV and fluorescence titration studies in free solution. Hence, the inverse tetrapeptide 3 is in general bound two to three times less efficiently than the "normal" peptide 2 (K(ass) approximately 17,000 M(-1)), even though the complexation mainly involves long-range electrostatic interactions and both the receptor and substrate are rather flexible. Molecular modeling and ab initio calculations have been used to rationalize the observed substrate selectivity and to analyze the various binding interactions within the complex.     

A personal account of some dinitrogen and organometallic chemistry research at the University of Sussex

This article reviews the development of dinitrogen chemistry and some associated organometallic chemistry at the University of Sussex with which the author was directly involved. The establishment of the basic heavy-element halide phosphine chemistry laid the ground for the discovery of dinitrogen complexes of rhenium, osmium, molybdenum and tungsten. From there, some of the first well-defined reactions of coordinated dinitrogen (especially protonation and alkylation) were discovered and the essential mechanisms of such reactions were established. This allowed the development of models for the action of nitrogenases that are still probably the best available. Later work has produced similar models in iron chemistry and a range of organometallic chemistry has been uncovered in the effort to discover parallels between the basic organometallic chemistry of substances such as metal carbonyls, dinitrogen complexes and hydrides in their interactions with acetylenes and cyclpropene.