Chemical genomics: a challenge for de novo drug design.

De novo design provides an in silico toolkit for the design of novel small molecular structures to a set of specified structural constraints. With the avalanche of bioinformatics data, de novo design is ideally suited for exploring molecules that could be useful for chemical genomics. The design process involves manipulation of the input, modification of structural constraints, and further processing of the de novo generated molecules using various modular toolkits. The development of a theoretical framework for each of these stages will provide novel practical solutions to the problem of creating compounds with maximal chemical diversity. This short review describes the fundamental problems encountered in the application of novel chemical design technologies to chemical genomics by means of a formal representation. This notation helps to outline and clarify ideas and hypotheses that can then be explored using mathematical algorithms. It is only by developing this rigorous foundation that in silico design can progress in a rational way.

Recent advances in structure-based rational drug design.

Two approaches to structure-based drug design, that is, the docking of known compounds into a target protein and molecular assembly in situ, are seen to be merging technologies. The need for structural information about drug-protein complexes is now fundamental for drug discovery.

Industrial-scale, genomics-based drug design and discovery.

The demands on drug discovery organizations have increased dramatically in recent years, partly because of the need to identify novel targets that are both relevant to disease and chemically tractable. This is leading to an industrial approach to traditional biology and chemistry, inspired in part by the revolution in genomics. The purpose of this article is to highlight the flow of investigation from gene sequence of potential therapeutic targets, through mRNA and protein expression, to protein structure and drug design. To deal with this scale of activity, many commercial and public organizations have been established and some of the key players will be listed in this article.

Development of a pharmacophore model for histamine H3 receptor antagonists, using the newly developed molecular modeling program SLATE.

New molecular modeling tools were developed to construct a qualitative pharmacophore model for histamine H3 receptor antagonists. The program SLATE superposes ligands assuming optimum hydrogen bond geometry. One or two ligands are allowed to flex in the procedure, thereby enabling the determination of the bioactive conformation of flexible H3 antagonists. In the derived model, four hydrogen-bonding site points and two hydrophobic pockets available for binding antagonists are revealed. The model results in a better understanding of the structure-activity relationships of H3 antagonists. To validate the model, a series of new antagonists was synthesized. The compounds were designed to interact with all four hydrogen-bonding site points and the two hydrophobic pockets simultaneously. These ligands have high H3 receptor affinity, thereby illustrating how the model can be used in the design of new classes of H3 antagonists.

Drug-receptor recognition: electrostatic field lines at the receptor and dielectric effects.

1. In this paper the directional component of the vector electrostatic field emanating from a drug receptor is analysed in the three orthogonal planes. 2. B-DNA with an alternating guanine-cytosine sequence was chosen for a receptor model and the lines of force constructed for two dielectric conditions, namely the cases where firstly the dielectric is homogeneous and a constant throughout the space surrounding the receptor, and secondly where the dielectric is inhomogeneous and is treated as a vector quantity. 3. Electric field line maps indicate marked differences in the local fields situated in the helical wide and narrow grooves for the different sequences of cytosine and guanine; these variations are enhanced when the dielectric is handled as a vector. 4. The significance of electric field lines in interpreting receptor-induced ligand orientation effects is discussed since the direction of the lines is related to the torque that a receptor would impose on an attacking drug molecule.

Drug-receptor recognition: molecular orientation and dielectric effects.

1 The orientation of ethidium and its carboxyphenyl derivative was computed at various positions around one turn of the B-DNA helical receptor. 2 Dielectric effects of solvent were included using values for the bulk constant and a dielectric vector to simulate dielectric inhomogeneities. 3 From the electrostatic energy values for the orientations, the corresponding Boltzmann distributions were obtained to assess the orientation restriction to the drug imposed by the receptor. 4 A correlation was observed between the direction of the drug molecular dipole and the local line of force generated by the receptor vector field. 5 These findings are discussed with respect to the phenomenon of drug-receptor recognition.

Inhibition of alloxan-induced hyperglycaemia by compounds of similar molecular structure.

In this study we have shown that a range of compounds that are structurally similar to alloxan are able to protect mice against the diabetogenic effect of alloxan. The compounds include a group of five barbiturates, a group of five hydantoins, the methylxanthines caffeine and theophylline, the related compound uric acid, and ethosuximide. They were injected intraperitoneally prior to intravenous injection of alloxan, and blood glucose concentration was used as an index of alloxan toxicity. The salient structural feature possessed by all of these protective compounds is a pair of carbonyl oxygen atoms separated by a distance of 4.5 A and projecting from an approximately planar heterocyclic five- or six-membered ring; in all cases the carbonyl groups are separated by a ring nitrogen. We suggest that this feature is required for the protective effect of these compounds. In order to test further the requirement for two ring carbonyl groups, we also examined the effects of two compounds containing hydroxyl groups projecting from a six-membered ring, inositol and glucuronic acid. In agreement with previous studies on hexoses, we found that the effects of compounds such as these are unpredictable, with inositol protecting against alloxan toxicity but glucuronic acid not. We are unable to identify the critical difference in structure between these two compounds.

Toffee clearance and lingual sensory and motor activities in normal children and in children with articulation problems of speech.

The rate at which a standardized mouthful of toffee containing technetium (99mTc) tin colloid was cleared from the mouth during and after chewing was measured by counting the residual radioactivity in the mouth at short time intervals by external gamma counting. The clearance curve was resolved into three phases for each subject--chewing time (1), which coincided with the time to reach 10% of the initial counting rate, scavenging time (2), and a final slow diffusion phase (3). Although the mean chewing time was only 1.9 min, the technique allowed the pattern of clearance during this phase to be assessed for each of 10 normal children (mean age 11.1 yr) and 7 children (mean age 11.0 yr) diagnosed as having delayed articulation. Two measurements of sensory and motor functions of the tongue were made on the same subjects. These measurements were of oral stereognosis and tongue-tip manipulation. Within the control group, only the correlation between stereognosis error scores and the duration of phase 1 or phases 1 and 2 combined was statistically significant. The mean stereognosis and tongue manipulation scores were significantly lower in the poor articulation group than in normal children but, with one notable exception, the clearance curves were similar.

The impact of epilepsy surgery on quality of life in children.

OBJECTIVE: To determine if epilepsy surgery is effective in improving the quality of life (QOL) of children with intractable seizures using the Quality of Life in Childhood Epilepsy Questionnaire (QOLCE). METHODS: The authors conducted a prospective study of the families of 35 children with intractable epilepsy who underwent epilepsy surgery. Parents completed the QOLCE preoperatively and again 6 to 18 months after surgery. At both assessment dates parents indicated the severity of their child's seizures during the past 6 months and the frequency of their child's seizures during the past 4 weeks on Likert-type scales. Children were split into two groups according to surgery outcome: seizure free vs persistent seizures. Statistical analyses were conducted to determine if children rendered seizure free showed a greater improvement in QOL compared to those with persistent seizures postoperatively. RESULTS: Greater improvement in QOL was documented for children rendered seizure free vs children with persistent seizures. This was significant for the overall QOLCE QOL score and subscales assessing cognitive, social, emotional, behavioral, and physical domains of life. CONCLUSIONS: Epilepsy surgery improves the quality of life of children rendered seizure free. Families can be counseled preoperatively of the potential benefits of surgery beyond seizure reduction.

Recent advances in drug design methods: where will they lead?

Drug design methods have made significant new advances over the last ten years, mainly in the areas of molecular modelling. In more recent times important developments in theory have led to a different type of modelling becoming possible, the so-called de novo or automated design algorithms. In this new method the programs perform much of the chemist's thinking, in finding appropriately sized chemical groups to fit into a target site. However this is a combinatoric problem which has no general analytical solution; it is ripe for optimization. Other advances, such as combinatorial chemical synthesis and screening, will dramatically influence the search for new lead structures for target sites, which at present are poorly understood. Already these methods are being applied to peptide libraries. Peptides do not make good drug compounds because of their poor bioavailability; further, their flexibility reduces their affinity. In some cases peptide backbones can be removed and replaced with rigid non-peptide scaffolds.

The kinetics of beta-granule formation: a morphometric study.

The rate of formation of beta-granules in mouse islet cells has been studied by morphometry using experimental conditions in which insulin secretion is known to be blocked. The number of beta-granules in a cell is increased by 120%, 45 minutes after a continued glucose stimulus of 16.7 mM. The implications of the results are discussed with respect to the construction of kinetic models for the secretion of insulin by exocytosis.