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Combinatorial Chemistry &
High Throughput Screening
ISSN: 1386-2073
Combinatorial Chemistry &
High Throughput Screening
Volume 10, Number 4, May 2007
Contents
The Relative Transcription Index: A Gene
Expression Based Metric for Prioritization of Drug Candidates
Pp. 239-245
Sujoy Ghosh, Mike A. Watson and Jon L. Collins
[Abstract]
Oligonucleotide Profiling for Discriminating Bacteria
in Bacterial Communities Pp. 247-255
Ping-An He and Li Xia
[Abstract]
Traceless Synthesis of 3-N-Substituted-2-Thioxoquinazoline-4
Ones on a Soluble Polymeric Support Pp. 257-260
Hongdan Peng, Yanling Huang, Jianhong Yang, Zuxing Chen
and Guichun Yang
[Abstract]
Development of Self-Indicating Resin Pp.
261-267
Osamu Ichihara, David Sampson, Mark Whittaker, Mark Bradley
and Jin Ku Cho
[Abstract]
Oligonucleotide Fingerprinting of Arrayed Genomic
DNA Sequences Using LNA-Modified Hybridization Probes
Pp. 269-276
Jian-Ping Liu, Mario Drungowski, Lajos Nyársik,
Regine Schwartz, Hans Lehrach, Ralf Herwig and Michal Janitz
[Abstract]
A Naturally Logical Representation for DNA Primary
Sequences Pp. 277-281
Chun Li and Jun Wang
[Abstract]
Compound Hub: Efficiency Gains Through Innovative
Sample Management Processes Pp. 283-287
Ulrich Schopfer, Marc R.M. Andreae, Matthieu Hueber, Andreas
Saur, Marcel O. Kummer, Michel Girod, Desmond Fox, Thomas
Steiner, Maxim Popov and Robert Smith
[Abstract]
Fluorescence-Based Adenylyl Cyclase Assay Adaptable
to High Throughput Screening Pp. 289-298
Kannan Vadakkadathmeethal, Jennifer M. Cunliffe, Jennifer
Swift, Robert T. Kennedy, Richard R. Neubig and Roger K. Sunahara
[Abstract]
Abstracts
[Back to top]
The Relative Transcription Index: A Gene
Expression Based Metric for Prioritization of Drug Candidates
Sujoy Ghosh, Mike A. Watson and Jon L. Collins
Efficient compound selection remains a key challenge in drug
discovery today. The goal is to identify developable drug
candidates early in the screening process while simultaneously
flagging compounds with off-target effects indicative of liabilities
or alternate indications. This goal overlaps but is distinct
from the goal of toxicogenomics which is focused primarily
on identifying toxicity signatures of lead candidates in key
tissues. We propose a framework where global changes in gene
expression levels in response to compounds can be used as
an objective metric for early compound prioritization. We
call this metric the Relative Transcription Index (RTI). RTI
is a measure of the relative activity of compounds as ascertained
by their effects on transcription at a genome-wide level.
Compounds with a low RTI affect the expression of only a few
genes whereas compounds with a high RTI affect the expression
of a large number of genes. This information is useful for
differentiating compounds that, based on phenotypic assays
alone, may appear to be equally efficacious. Since compounds
with high RTI are more likely to display off-target effects,
the RTI metric, if implemented early in the screening process,
can become a valuable tool for compound selection. The utility
of the RTI metric is demonstrated by its application to two
different gene expression datasets - one involving modulators
of the liver X receptor (LXR) and the other concerning antibacterial
compounds belonging to diverse mechanistic classes.
[Back to top]
Oligonucleotide Profiling for Discriminating Bacteria
in Bacterial Communities
Ping-An He and Li Xia
Based on the relative ratios of di- and tri-nucleotides in
the DNA sequences, the profiles of 164 genome sequences from
152 representative microbial organisms were computed. By comparing
the profiles of the genomes and their substrings with length
500 bps, the fluctuations of the relative abundances of di-
and tri-nucleotides of these genomic sequences were analyzed.
A new method to discriminate the origins of orphan DNA sequences
was proposed, and the origins of 17 uncultured bacterium sequences
from a bacterial community in the human gut were postulated
and discussed.
[Back to top]
Traceless Synthesis of 3-N-Substituted-2-Thioxoquinazoline-4
Ones on a Soluble Polymeric Support
Hongdan Peng, Yanling Huang, Jianhong Yang, Zuxing Chen
and Guichun Yang
The synthesis of 3-N-substituted-2-thioxoquinazoline-4-ones
is described with a traceless linker strategy using poly(ethylene
glycol) (PEG) as a soluble polymeric support. Staudinger-Aza-Wittig
reaction of PEG-supported azide with Ph3P and CS2
gave the corresponding PEG-supported phenyl isothiocyanate.
Treatment of the phenyl isothiocyanate with different primary
amines led, via intramolecular cyclization and simultaneous
cleavage from PEG, to 2-thioxoquinazoline-4-ones with of moderate
to excellent yields.
[Back to top]
Development of Self-Indicating Resin
Osamu Ichihara, David Sampson, Mark Whittaker, Mark Bradley
and Jin Ku Cho
Previously, we have reported the development and application
of self-indicating resins (SIR), materials which can indicate
presence or absence of amines in the reaction solution by
the conspicuous color change of a phenolsulfophthalein type
dye immobilized on resin beads [2a]. Although the functionality
necessary for attaching the dye to the resins could be readily
introduced by the Suzuki-Miyaura coupling during the synthesis
of the SIR 1, this approach was only applicable
to the dyes containing suitable functionality for the cross-coupling
reaction. In this article we describe a new approach of immobilizing
the indicating dyes onto the resin support. The dyes suitable
for loading onto aminomethyl polystyrene (PS) resin were prepared
by Friedel-Crafts reaction of 2-sulfoterephthalic anhydride
with a wide range of phenols. Using this new route, the SIR
6c was readily prepared in >100g quantities.
Use of the SIR 6c in the synthesis of a 144
member urea library was demonstrated and the SIR successfully
indicated the endpoint of the reaction between amines and
isocyanates.
[Back to top]
Oligonucleotide Fingerprinting of Arrayed Genomic
DNA Sequences Using LNA-Modified Hybridization Probes
Jian-Ping Liu, Mario Drungowski, Lajos Nyársik,
Regine Schwartz, Hans Lehrach, Ralf Herwig and Michal Janitz
Recently, we established a robust method for the detection
of hybridization events using a DNA microarray deposited on
a nanoporous membrane. Here, in a follow-up study, we demonstrate
the performance of this approach on a larger set of LNA-modified
oligoprobes and genomic DNA sequences. Twenty-six different
LNA-modified 7-mer oligoprobes were hybridized to a set of
66 randomly selected human genomic DNA clones spotted on a
nanoporous membrane slide. Subsequently, assay sensitivity
analysis was performed using receiver operating characteristic
(ROC) curves. Comparison of LNA-modified heptamers and DNA
heptamers revealed that the LNA modification clearly improved
sensitivity and specificity of hybridization experiment. Clustering
analysis was applied in order to test practical performance
of hybridization experiments with LNA-modified oligoprobes
in recognizing similarity of genomic DNA sequences. Comparing
the results with the theoretical sequence clusters, we conclude
that the application of LNA-modified oligoprobes allows for
reliable clustering of DNA sequences which reflects the underlying
sequence homology. Our results show that LNA-modified oligoprobes
can be used effectively to unravel sequence similarity of
DNA sequences and thus, to characterize the content of unknown
DNA libraries.
[Back to top]
A Naturally Logical Representation for DNA Primary
Sequences
Chun Li and Jun Wang
In this paper, we (1) introduce a logical representation (LR)
for DNA primary sequences; (2) show relations between LR and
some other representations including the characteristic sequences
of a DNA sequence, Randic’s 2-D, 4-D representations,
and Z-curve (a 3-D graphical representation); and (3) outline
the constructions of the S/S matrix specific for a logical
sequence and its 2*2 condensed matrix.
[Back to top]
Compound Hub: Efficiency Gains Through Innovative
Sample Management Processes
Ulrich Schopfer, Marc R.M. Andreae, Matthieu Hueber, Andreas
Saur, Marcel O. Kummer, Michel Girod, Desmond Fox, Thomas
Steiner, Maxim Popov and Robert Smith
While significant investments are made across the industry
and increasingly also in academia to enhance or build a compound
file, the efficient sourcing of compounds from in-house medical
chemistry is frequently seen as a challenge. This article
introduces the Compound Hub strategy developed at the Novartis
Compound Archive. Central Compound Hubs in Basel and Cambridge
were combined with web-based ordering of compounds and assays,
providing assay-ready, solubilized samples to labs anywhere
in the global research organization. Relieving scientists
from time-intensive sample preparation tasks, error rates
could be reduced through electronic processing and tracking
of compounds/assays and the capture of medicinal chemistry
compounds for the compound library could be increased by 75%.
[Back to top]
Fluorescence-Based Adenylyl Cyclase Assay Adaptable
to High Throughput Screening
Kannan Vadakkadathmeethal, Jennifer M. Cunliffe, Jennifer
Swift, Robert T. Kennedy, Richard R. Neubig and Roger K. Sunahara
The second messenger cAMP has been implicated in numerous
cellular processes such as glycogen metabolism, muscle contraction,
learning and memory, and differentiation and development.
Genetic evidence suggests that the enzyme that produces cAMP,
adenylyl cyclase (AC), may be involved in pathogenesis in
many of these cellular processes. In addition, these data
suggest that membrane-bound ACs may be valuable targets for
therapeutics to treat pathogenesis of these processes. The
development of a robust real-time adenylyl cyclase assay that
can be scalable to high-throughput screening could help in
the development of novel therapeutics. Here we report a novel
fluorescence-based cyclase assay using Bodipy FL GTPγS
(BGTPγS).
The fluorescence of the Bodipy™ moiety of BGTPγS
was dramatically enhanced by incubation with the minimal catalytic
core of wild-type-AC (wt-AC) and a mutant with decreased purine
selectivity (mut-AC), in an AC activation-dependent manner.
No increase in fluorescence was observed using Bodipy FL ATPγS
(BATPγS)
as substrate for either wt-AC or mut-AC. Using BGTPγS,
forskolin, Gsγα•GTPγS
and the divalent cation Mn2+
potently enhanced the rate of fluorescence increase in a concentration-dependent
manner. The fluorescence enhancement of the Bodipy moiety
was inhibited by known inhibitors of AC such as 2'deoxy,3'AMP
and 2',5'-dideoxy-3'ATP. Furthermore, the fluorescence assay
is adaptable to 96-well and 384-well multiplate format and
is thus applicable to high throughput screening methodologies.
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