Mini-Review:
Computational Structure-Based Design of Inhibitors that Target Protein Surfaces.
Pp. 355-362
Molecular Descriptors in Chemoinformatics, Computational Combinatorial
Chemistry, and Virtual Screening. Pp.
363-372.
Ling Xue and
Jürgen Bajorath
Targeting of Phage Display Vectors to
Mammalian Cells. Pp. 373-392.
Asko Uppala
and Erkki Koivunen
High Throughput Mutation Screening by
Automated Capillary Electrophoresis. Pp. 393-409.
Lars Allan
Larsen, Michael Christiansen, Jens Vuust and Paal Skytt Andersen
High Throughput and Global Approaches to
Gene Expression. Pp. 411-420.
David Ghosh
Forecasting Roles of Combinatorial
Chemistry in the Age of Genomically Derived Drug Discovery Targets. Pp. 421-436.
David S.
Thorpe
Fluorescence Polarization is a Useful
Technology for Reagent Reduction in Assay Miniaturization. Pp. 437-444.
Thomas J. Kowski
and Jinzi J. Wu
[Back to top] Mini-Review:
Computational Structure-Based Design of Inhibitors that Target Protein Surfaces.
Jun Zeng
Finding drugs
that inhibit protein-protein interactions is usually difficult. While
computer-aided design is used widely to facilitate the drug discovery process
for protein targets with well-defined binding pockets, its application to the
design of inhibitors targeting a protein surface is very limited. In this
mini-review we address two aspects of this issue: firstly, we overview the
current state of design methodology for inhibitors specifically targeting
protein surfaces, and secondly, we briefly outline recent advances in
computational methods for structure-based drug design. These methods are
closely related to protein docking and protein recognition, the difference
being that in ligand design, ligands are built on a fragment-by-fragment basis.
A novel scheme of computational combinatorial ligand design developed for the
design of inhibitors that interfere with protein-protein interaction is
described in detail. Current applications and limitations of this methodology,
as well as its future prospects, are discussed.
[Back to top]
Molecular
Descriptors in Chemoinformatics, Computational Combinatorial Chemistry, and
Virtual Screening.
Many contemporary applications
in computer-aided drug discovery and chemoinformatics depend on representations
of molecules by descriptors that capture their structural characteristics and
properties. Such applications include, among others, diversity analysis,
library design, and virtual screening. Hundreds of molecular descriptors have
been reported in the literature, ranging from simple bulk properties to
elaborate three-dimensional formulations and complex molecular fingerprints, which
sometimes consist of thousands of bit positions. Knowledge-based selection of
descriptors that are suitable for specific applications is an important task in
chemoinformatics research. If descriptors are to be selected on rational
grounds, rather than guesses or chemical intuition, detailed evaluation of
their performance is required. A number of studies have been reported that
investigate the performance of molecular descriptors in specific applications
and/or introduce novel types of descriptors. Progress made in this area is
reviewed here in the context of other computational developments in
combinatorial chemistry and compound screening.
[Back to top]
Targeting of
Phage Display Vectors to Mammalian Cells.
Phage display
libraries offer a strategy to isolate peptide ligands to target proteins and to
define potential interaction sites between proteins. Recent studies have
indicated a novel utility for phage display in that bacteriophage engineered to
express peptide ligands to specific cell surface receptors are internalized by
mammalian cells. Thus, reporter genes such as green fluorescent protein and
lacZ harbored in the phage genome can be delivered to mammalian cells using
targeting peptides displayed on the surface of phage. There is also the
possibility to generate novel types of peptide libraries expressed
intracellularly using a phage capable of inducing expression of its coding
genes in human cells.
[Back to top] High
Throughput Mutation Screening by Automated Capillary Electrophoresis.
Molecular diagnosis of complex
inherited disorders, population screening of genetic diseases, studies of the
genetic basis of variable drug response (pharmacogenetics) as well as discovery
and investigation of new drug targets (pharmacogenomics) involve screening for
mutations in multiple DNA samples. Furthermore, the development of a third
generation of the human genome map, based on single nucleotide polymorphisms
(SNPs), requires screening for allelic variants through all of the three
billion basepairs in the human genome. Thus, the need for high throughput
mutation screening methods is great and is rapidly increasing. Traditional
methods for mutation screening often involve slab-gel electrophoresis analyses
which are laborious and difficult to automate. However, recent developments in
capillary electrophoresis systems for DNA fragment analysis have made fully
automated mutation screening possible and have dramatically increased the
possible sample throughput. This review describes the recent advances in
capillary electrophoresis of DNA and summarize the various methods for mutation
screening based on this technique.
[Back to top] High
Throughput and Global Approaches to Gene Expression.
David Ghosh
In the past several years, a new
set of technologies based on whole genome analysis have revolutionized the
study of gene expression. These microarray or "gene chip"
technologies, which arose out of the development of large-scale sequencing
approaches, are now coming into increasing use, generating a far greater volume
of data than the data representing the sequences themselves. This review
focuses on the current state of development of these technologies, and the
available approaches to manage and analyze the information they generate. The
applicability of this technology to general problems in biomedicine is also
discussed.
[Back to top] Forecasting
Roles of Combinatorial Chemistry in the Age of Genomically Derived Drug
Discovery Targets.
David S.
Thorpe
Genomics has caused an explosion
in the number of potential therapeutic targets with varying degrees of
validated pathophysiology. Among the first applications of combinatorial
chemistry in genomics-driven drug discovery is the search for surrogate ligands
or substrates. In the event that no surrogate is found for molecular assays,
more exotic functional screens in whole cells or model organisms are used.
Protein-protein interaction mapping by yeast and mammalian two-hybrid systems
dominates empirical functional genomics, and this will lead to a bias for
screening projects targeting this type of interaction. Drug discovery for
protein-protein interactions has a poor track record, and this will challenge
prevailing views on the design of combinatorial libraries. Genomics based on
structural homology will yield many putative kinases, receptors, enzymes,
transporter proteins, ion channels and GPCRs. Most of these projects will
require new surrogate agonists, ligands or substrates, and then
pharmaceutically useful agonists or antagonists will need to be found. Again,
combinatorial chemistry might be essential to these studies. Given the need to
screen hundreds of targets at great risk of irrelevance to pathophysiology,
combined with the challenge of finding surrogate or natural ligands for these
new targets, there is an urgent need for efficiency. Different groups are
addressing these concerns by developing biologically-driven combinatorial
libraries in order to achieve a higher density of bioactivity. Early efforts in
this regard will be described.
[Back to top] Fluorescence
Polarization is a Useful Technology for Reagent Reduction in Assay
Miniaturization.
Thomas
J. Kowski and Jinzi J. Wu
The use of
fluorescence polarization (FP) has increased significantly in the development
of sensitive and robust assays for high throughput screening of chemical
compound libraries during the past few years. In this study, we show that FP is
a useful assay miniaturization technology for reagent reduction during high
throughput screening. We developed and optimized several FP assays for binding
to estrogen receptor a and two protein
kinases with an assay volume of 100 ml.
Without any re-optimization, a consistent signal window was maintained in 384-
or 1536-well format when the assay volume varied from 2.5-100 ml at constant concentrations of all assay
components. In contrast, the signal window decreased with decreasing assay
volume at constant reagent concentration in the protein kinase C scintillation
proximity assay (SPA) and prompt fluorescence assay. In addition, the effect of
evaporation on the signal window was minimal for the FP assays. Our study
suggests that FP is superior to SPA and prompt fluorescence in terms of reagent
reduction in the miniaturized assay format.