Knowledge discovery and data mining in toxicology

Knowledge discovery and data mining tools are gaining increasing importance for the analysis of toxicological databases. This paper gives a survey of algorithms, capable to derive interpretable models from toxicological data, and presents the most important application areas. The majority of techniques in this area were derived from symbolic machine learning, one commercial product was developed especially for toxicological applications. The main application area is presently the detection of structure-activity relationships, very few authors have used these techniques to solve problems in epidemiological and clinical toxicology. Although the discussed algorithms are very flexible and powerful, further research is required to adopt the algorithms to the specific learning problems in this area, to develop improved representations of chemical and biological data and to enhance the interpretability of the derived models for toxicological experts.     

Managing laboratory automation: integration and informatics in drug discovery

Drug discovery today requires the focused use of laboratory automation and other resources in combinatorial chemistry and high-throughput screening (HTS). The ultimate value of both combinatorial chemistry and HTS technologies and the lasting impact they will have on the drug discovery process is a chapter that remains to be written. Central to their success and impact is how well they are integrated with each other and with the rest of the drug discovery processes-informatics is key to this success. This presentation focuses on informatics and the integration of the disciplines of combinatorial chemistry and HTS in modern drug discovery. Examples from experiences at Neurogen from the last five years are described.     

Functionalized carbon nanotubes in drug design and discovery

Carbon nanotubes (CNTs) have been proposed and actively explored as multipurpose innovative carriers for drug delivery and diagnostic applications. Their versatile physicochemical features enable the covalent and noncovalent introduction of several pharmaceutically relevant entities and allow for rational design of novel candidate nanoscale constructs for drug development. CNTs can be functionalized with different functional groups to carry simultaneously several moieties for targeting, imaging, and therapy. Among the most interesting examples of such multimodal CNT constructs described in this Account is one carrying a fluorescein probe together with the antifungal drug amphotericin B or fluorescein and the antitumor agent methotrexate. The biological action of the drug in these cases is retained or, as in the case of amphotericin B constructs, enhanced, while CNTs are able to reduce the unwanted toxicity of the drug administered alone. Ammonium-functionalized CNTs can also be considered very promising vectors for gene-encoding nucleic acids. Indeed, we have formed stable complexes between cationic CNTs and plasmid DNA and demonstrated the enhancement of the gene therapeutic capacity in comparison to DNA alone. On the other hand, CNTs conjugated with antigenic peptides can be developed as a new and effective system for synthetic vaccine applications. What makes CNTs quite unique is their ability, first shown by our groups in 2004, to passively cross membranes of many different types of cells following a translocation mechanism that has been termed the nanoneedle mechanism. In that way, CNTs open innumerable possibilities for future drug discovery based on intracellular targets that have been hard to reach until today. Moreover, adequately functionalized CNTs as those shown in this Account can be rapidly eliminated from the body following systemic administration offering further encouragment for their development. CNT excretion rates and accumulation in organs and any reactivity with the immune system will determine the CNT safety profile and, consequently, any further pharmaceutical development. Caution is advised about the need for systematic data on the long-term fate of these very interesting and versatile nano-objects in correlation with the type of CNT material used. CNTs are gradually plyaing a bigger and more important role in the emerging field of nanomedicine; however, we need to guarantee that the great opportunities they offer will be translated into feasible and safe constructs to be included in drug discovery and development pipelines.     

Intrinsically disordered proteins: from sequence and conformational properties toward drug discovery

Structural disorder of functional proteins under physiological conditions is widespread within eukaryotic proteomes. The lack of stable tertiary and secondary structure offers a variety of functional advantages to intrinsically disordered proteins (IDPs): their malleability of interaction with different partners, specific but low-affinity binding, and their fine modulation by post-translational modifications. IDPs are therefore central players in key processes such as cell-cycle control and signal-transduction pathways, and impairment of their function is associated with many disease states such as cancer and neurodegenerative disorders. Fascinating progress in the experimental characterization of IDPs has been made in the last decade, especially in NMR spectroscopy and small-angle X-ray scattering as well as in single-molecule techniques. It has been accompanied by the development of powerful computational tools to translate experimental results in explicit ensemble representations of IDPs. With the aid of bioinformatics tools, these advances have paved the way to targeting IDP interactions in rational drug-discovery projects.     

A study of the mobility and trapping of minor hydrogen concentrations in diamond in three dimensions using quantitative ERDA microscopy

Two direct and two indirect nuclear methods are used for the analysis of hydrogen in diamond of different types. Exploiting the power of two-dimensional position sensitive detectors, the distribution of hydrogen in and on diamond in three dimensions has been measured by elastic recoil detection analysis, supplementing the earlier resonant nuclear techniques. Indirect methods of muonium spin rotation and time differential perturbed angular distribution measurements prove to be very informative. In a series of dynamic experiments, hydrogen has been implanted and the diffusion thereof sought as a function of temperature. Unlike the equivalent case for silicon, no migration of the hydrogen in diamond is found up to 1473 K. This striking result is considered in regard to existing theoretical calculations. It is concluded that the implanted hydrogen is self-trapped. Arguments are presented as to the location of hydrogen in natural diamond, in diamond grown at high pressure and high temperature, and in diamond grown by chemical vapour deposition.     

Looplure efficacy and electrophysiological responses in three plusiinae species

Source concentration differences of (Z)-7-dodecen-1-ol acetate, or looplure, were evaluated for field trapping efficiency and electrophysiological responses with malePseudoplusia includens (Walker),Trichoplusia ni (Hubner) andRachiplusia ou (Guenné) (Lepidoptera: Noctuidae). Sticky traps baited with 1000 g of the lure captured a significantly greater (P < 0.05) number of maleP. includens andT. ni than any other concentration;R. ou males were caught at a greater rate in traps baited with 100 g of looplure, significantly more (P < 0.05) than with 1000 g. Electroantennogram (EAG) studies demonstrated that antennae of maleP. includens have a lower response threshold to looplure than eitherT. ni orR. ou antennae, the latter demonstrating the highest significant threshold of response. No differences in the stimulus-response functions of the three species were detected.Lepidoptera: Noctuidae.     

Multi-step usage of in vivo models during rational drug design and discovery

In this article we propose a systematic development method for rational drug design while reviewing paradigms in industry, emerging techniques and technologies in the field. Although the process of drug development today has been accelerated by emergence of computational methodologies, it is a herculean challenge requiring exorbitant resources; and often fails to yield clinically viable results. The current paradigm of target based drug design is often misguided and tends to yield compounds that have poor absorption, distribution, metabolism, and excretion, toxicology (ADMET) properties. Therefore, an in vivo organism based approach allowing for a multidisciplinary inquiry into potent and selective molecules is an excellent place to begin rational drug design. We will review how organisms like the zebrafish and Caenorhabditis elegans can not only be starting points, but can be used at various steps of the drug development process from target identification to pre-clinical trial models. This systems biology based approach paired with the power of computational biology; genetics and developmental biology provide a methodological framework to avoid the pitfalls of traditional target based drug design.     

Discrete element simulations of stress distributions in silos: crossover from two to three dimensions

The transition from two-dimensional (2D) to three-dimensional (3D) granular packings is studied using large-scale discrete element computer simulations. We focus on vertical stress profiles and examine how they change with dimensionality. We compare results for packings in 2D, quasi-2D packings between flat plates, and 3D packings. Analysis of these packings suggests that the Janssen theory does not fully describe these packings, especially at the top of the piles, where a hydrostaticlike region of vertical stress is visible in all cases. We find that the interior of the packing is far from incipient failure, while, in general, the forces at the walls are close to incipient failure.     

Explorations in cell biology and pharmacology using synthetic polymers

We have used synthetic polymers as tools to probe endocytosis and lysosome function. Their particular value lies in their well-defined chemical constitution and in the possibility to custom-synthesize molecules with desired characteristics. Polyvinylpyrrolidone, Percoll and polystyrene beads have been ¹²⁵I-labelled and used to explore the borderland of pinocytosis and phagocytosis. Derivatized poly(aspartamide), poly(hydroxypropylmethacrylamide) and a polylysine-poly(ethylene oxide) block copolymer have been used to investigate the effects of hydrophobic moieties and sugar residues on substrate-selection in pinocytosis. The effect of cationic moieties has been studied using vinylpyrrolidone-vinylamine copolymers. Poly(hydroxypropylmethacrylamide) with certain oligopeptide side---chains have been shown to be susceptible to lysosomal peptidases. Ethylene glycol oligomers are being used to study the basal permeability of the lysosome membrane. Soluble macromolecules have considerable potential in targeted drug-delivery. Drugs attached to appropriate polymers by covalent links that are susceptible to lysosomal enzymes can deliver drug to target cells and avoid unwanted sideeffects. Synthetic macromolecules have several advantages over their natural counterparts: they are chemically more robust, less immunogenic, and easier and cheaper to prepare in bulk.     

A journey in structure-based drug discovery: from designed peptides to protein surface topomimetics as antibiotic and antiangiogenic agents

Most biological events are mediated through molecular interactions by proteins, and because proteins are composed of structural units like helices, beta-sheets and turns, small peptides and peptidomimetics may be used to mimic their biological effects and even as therapeutic agents in the clinic. Here, we present a structure-based, scaffold-driven approach to design bioactive peptides and peptidomimetics. Initially, we designed a novel series of beta-sheet-forming peptides that mimic the activities of both antibiotic bacterial membrane disrupting peptides and antiangiogenic proteins. We subsequently used structure-activity relationships to reduce the design to partial peptide mimetics and then to fully nonpeptide topomimetics. Some of these agents are currently in extensive preclinical studies for further development as drug candidates against infectious disease and cancer.     

反应性高分子的制备、表征测试及其在药物合成中的应用

介绍了反应性高分子的合成方法及测试表征手段,特别对微米级聚合物试剂进行了较全面的研究。同时对其在药物合成中的应用进行了综述。     

Tandem oxidation processes using manganese dioxide: discovery, applications, and current studies

"One-pot" processes in which alcohol oxidations are combined with further elaboration of the carbonyl intermediate are reviewed. Sequential processes are briefly discussed, but most attention is centered on tandem processes; that is, oxidations carried out in the presence of a nucleophilic trapping agent, rather than those in which the trapping agent is added after the oxidation is complete. As part of this Account, a comprehensive review of the discovery of tandem oxidation processes (TOP) will be given together with applications in alkene-forming reactions, cyclopropanations, and imine, oxime, amine, and heterocycle formation.     

Development of natural and synthetic polymer-based semi-interpenetrating polymer network for controlled drug delivery: optimization and in vitro evaluation studies

This research paper describes the development, optimization and in vitro characterization of chemically cross-linked pectin–polyvinyl alcohol-co-poly(2-Acrylamido-2-methylpropane sulfonic acid) semi-interpenetrating polymer network hydrogel [pectin–PVA-co-poly(AMPS) semi-IPN hydrogel] for controlled delivery of model drug tramadol HCl. Response surface methodology based on 3² factorial design was used for optimization and investigating the effect of independent factors: polymer-blend ratio (pectin:PVA = X ₁) and monomer (AMPS = X ₂) concentration on the dependent variables, swelling ratio (q _18th), percent drug release (R _18th, %), time required for 80 % drug release (t _{80 %}, h), drug encapsulation efficiency (DEE, %) and drug loaded contents (DLC, mg/g) in pectin-PVA-co-poly(AMPS) gels prepared by free radical polymerization. The optimized semi-IPN gel (FPP-10) showed controlled in vitro drug release (R _18th) of 56.34 % in 18 h, t _{80 %} of 30 h, and DEE of 23.40 %. These semi-IPN hydrogels were also characterized through SEM, FTIR, sol–gel analysis, swelling studies and drug release characteristics. Therefore, this newly synthesized polymeric network could be a potential polymeric system for controlled drug delivery of tramadol HCl for prolonged drug release.