Combinatorial
Chemistry & High Throughput Screening
ISSN: 1386-2073
Combinatorial Chemistry &
High Throughput Screening
Volume 13, Number 1, January 2010
Contents
Editorial Pp. 1-2
High Content Screening of CXCR2-Dependent Signalling Pathways
Pp. 3-15
Michael Wolff, Simone Kredel, Dorothea Haasen, Jörg
Wiedenmann, G. Ulrich Nienhaus, Barbara Kistler, Franz Oswald and Ralf Heilker
[Abstract] [Full
Text Article] [PMID: 20214572 PubMed - indexed for MEDLINE]
Efficient Identification of Novel Leads by Dynamic Focused
Screening: PDK1 Case Study Pp. 16-26
Dongyu Sun, Joon Jung, Thomas S. Rush III, Zangwei
Xu, Michael J. Weber, Ekaterina Bobkova, Alan Northrup and
Ilona Kariv
[Abstract] [Full Text Article] [PMID: 20214573 PubMed - indexed for MEDLINE]
A Universal, Fully Automated High Throughput Screening Assay
for Pyrophosphate and Phosphate Release from Enzymatic Reactions
Pp. 27-38
Scott D. Pegan, Yang Tian, Valerie Sershon and
Andrew D. Mesecar
[Abstract] [Full Text Article] [PMID: 20201823 PubMed - indexed for MEDLINE]
Prediction of Critical Micelle Concentration
of Nonionic Surfactants by a Quantitative Structure –
Property Relationship Pp. 39-44
Anna Mozrzymas and Bozenna Rózycka-Roszak
[Abstract] [Full Text Article] [PMID: 20201824 PubMed - indexed for MEDLINE]
Tagging Molecules with Linear Polymers:
Biocatalytic Transformation of Substrates Anchored on Soluble
Macromolecules Pp. 45-53
Claudio Cornaggia and Dario Pasini
[Abstract] [Full Text Article] [PMID: 20214574 PubMed - indexed for MEDLINE]
Applications of Integrated Data Mining
Methods to Exploring Natural Product Space for Acetylcholinesterase
Inhibitors Pp. 54-66
Daniela Schuster, Lisa Kern, Dimitar P. Hristozov, Lothar
Terfloth, Bruno Bienfait, Christian Laggner, Johannes Kirchmair,
Ulrike Grienke, Gerhard Wolber, Thierry Langer, Hermann Stuppner,
Johann Gasteiger and Judith M. Rollinger
[Abstract] [Full Text Article] [PMID: 20214575 PubMed - indexed for MEDLINE]
High Throughput Synthesis and Screening
of New Catalytic Materials for the Direct Epoxidation of Propylene
Pp. 67-74
Michael Kahn, Anusorn Seubsai, Isik Onal and
Selim Senkan
[Abstract] [Full Text Article] [PMID: 20201825 PubMed - indexed for MEDLINE]
Phage-Displayed Combinatorial Peptide Libraries in
Fusion to β-Lactamase
as Reporter for an Accelerated Clone Screening: Potential
Uses of Selected Enzyme-Linked Affinity Reagents in Downstream
Applications Pp. 75-87
Girja S. Shukla and David N. Krag
[Abstract] [Full Text Article] [PMID: 20214576
PubMed - indexed for MEDLINE]
Abstracts
[Back to top]
Editorial:
After serving as Editor-in-Chief of Combinatorial
Chemistry & High Throughput Screening since the beginning
of its publication in 1998 and overseeing the first 12 volumes,
I am stepping down from this position with the beginning of
CCHTS volume 13. Since I will remain on the Editorial
Board, I will still be involved with CCHTS. The new
Editor-in-Chief of CCHTS will be Dr. Rathnam Chaguturu
who directs the High Throughput Screening Laboratories at
the University of Kansas. Since the publication of manuscripts
takes several months and includes peer review, revision and
proof reading under the oversight of the Editor-in-Chief followed
by redacting, printing and publication by the production department,
most of the articles in the next several issues of CCHTS
will still have been prepared under my oversight. Gradually
during the year, the transition to the new Editor-in-Chief
will become complete.
In a 2007 editorial [1], I reviewed the early years of CCHTS
and listed the top ten most cited papers from the first 10
years of publication. It seems appropriate to update the list
of our ten most cited papers since there have been some changes.
At the top of the list this year is a paper from the laboratory
of Prof. John Pezzuto concerning the screening of natural
products for antioxidants. The honor of being first is appropriate
since Prof. Pezzuto was involved in the founding of CCHTS.
The second and tenth most cited papers in our top-ten list
concern peptides and peptide therapeutic agents. In the first
of these papers, Schulz-Knappe and colleagues coined the term
“peptidomics” as a corollary to proteomics, recognizing
that many peptides are biochemically, pharmacologically and
therapeutically important. The other paper by Lohner and Blondelle
is new to this list at position 10 and describes the rational
design of peptide antibiotic agents targeting bacterial membranes.
The popularity of these articles is a testament to the importance
of proteomics and biological therapeutic agents in biomedical
research today.
The articles occupying the third and fifth positions of our
top-ten list review the use of multicomponent reactions such
as the Ugi reaction in combinatorial synthesis. It is no surprise
that Prof. Ugi is an author of one of these review articles
and his former student Prof. Dömling is author of the
other paper. The article by Xue and Bajorath rose from fifth
to fourth place and is the only article on the top ten list
addressing virtual screening, which has been a popular topic
for many articles published in CCHTS. The paper by
Naser and Jolley reviews the use of fluorescence polarization
in high-throughput screening, which has been another popular
topic. At position six for the second time in a row, the paper
by Masimirembwa, et al., reviews how high throughput
screening is being applied to drug development with a focus
on drug metabolism. This is an important step in bringing
new drugs to clinical trials that can be a bottleneck and
a frequent cause of lead compound failure. The articles occupying
positions eight and nine are new to the top ten list this
year. The article by DeSimone, et al., at position
nine concerns the discovery of scaffolds known as privileged
structures which usually exhibit good drug-like properties
and are useful for drug discovery. Finally, the paper by Yarrow
and co-workers describes the use of fluorescent probes and
cell imaging to screen combinatorial libraries for physiological
changes in cells. The wide range of topics represented by
these articles, which cover combinatorial synthesis, virtual
screening, high-throughput screening, and drug development,
is faithful to the scope and purpose of CCHTS which
is to publish articles on all aspects of combinatorial chemistry
and high-throughput screening.
When my grandfather John van Breemen emigrated from the Netherlands
to the Unites States of America more than 100 years ago, he
became an apprentice in a Chicago print shop. He said that
he learned English by reading what he printed. Later, my grandfather
ran his own print shop in which my father learned the trade,
too. Although my father became a university professor, he
occasionally moonlighted in a print shop and sometimes let
me help. Because of my heritage in printing, I have taken
great pride in my job as editor of CCHTS.
During the first several years of production, much of the
correspondence for CCHTS was carried out by mail,
telephone and Fax. Authors had to submit their articles in
both print and electronic formats. Although the peer reviewed
and accepted versions of all figures and text were submitted
to our printing department in electronic form, it was still
necessary to supply printed copies and photo ready art in
case of problems with the electronic versions. I even had
to mail a color slide of the cover art for each issue to our
production department. After an issue went to press, only
printed reprints were available in the early years, and electronic
copies were not supplied. In fact, reprints of the first two
volumes are CCHTS are still not available in electronic
form. Gradually, the transition to electronic media was completed,
and today, no printed material or slides need to be submitted
by authors. The peer review process is also carried out electronically.
Today, the accepted manuscripts, figures and even the cover
art are transmitted electronically to our production department.
Articles are available for download via the internet as soon
as the printed versions are released. By the time my successor
retires from this position, the print versions of CCHTS
and perhaps most scientific journals might have been discontinued.
I would like to thank all the members of the Editorial Board
of CCHTS, most of whom have served since the formation
of this journal, for providing their time and expertise in
the peer review of articles under consideration for publication.
I would also like to thank Regional Editors Dr. Andy Merritt,
Prof. Peter Nielsen and Prof. Ikuo Fujii for handling the
peer review of countless manuscripts of the years. Of course
I am most grateful for the service of our publications department
whose names do not appear on the inside cover of CCHTS
and whose members include the printers of CCHTS.
The 10 most cited papers appearing in Combinatorial Chemistry
& High Throughput Screening from 1998 to 2008 (according
to the Web-of-Science, produced by Thomson Reuters; accessed
on-line November 20, 2009 at http://apps.isiknowledge.com/
are as follows:
2008
|
2006
|
|
| Rank
|
Rank
|
|
1
|
2
|
Lee SK, Mbwambo ZH, Chung HS, Luyengi L, Gamez EJC,
Mehta RG, Kinghorn AD, Pezzuto JM. Evaluation of the
antioxidant potential of natural products. Comb.
Chem. High. Throughput Screen.,1998,
1 (1), 35-46. Times cited 110.
|
2
|
1
|
Schulz-Knappe P, Zucht HD, Heine C, Jurgens M, Hess
R, Schrader M. Peptidomics: The comprehensive analysis
of peptides in complex biological mixtures. Comb.
Chem. High. Throughput Screen., 2001,
4 (2), 207-217. Times cited 97. |
3
|
8
|
Ugi I, Heck S. The multicomponent reactions and their
libraries for natural and preparative chemistry. Comb.
Chem. High. Throughput Screen., 2001,
4 (1), 1-34. Times cited 72. |
4
|
5
|
Xue L, Bajorath J. Molecular descriptors in chemoinformatics,
computational combinatorial chemistry, and virtual screening.
Comb. Chem. High. Throughput Screen.,2000,
3 (5), 363-372. Times cited 71. |
5
|
4
|
Domling A. Isocyanide based multicomponent reactions
in combinatorial chemistry. Comb. Chem. High. Throughput
Screen.,1998, 1 (1),
1-22. Times cited 71. |
6
|
6
|
Masimirembwa CM, Thompson R, Andersson TB. In
vitro high throughput screening of compounds for
favorable metabolic properties in drug discovery. Comb.
Chem. High. Throughput Screen., 2001,
4 (3), 245-263. Times cited 65. |
7
|
3
|
Nasir MS, Jolley ME. Fluorescence polarization: An
analytical tool for immunoassay and drug discovery.
Comb. Chem. High. Throughput Screen., 1999,
2 (4), 177-190. Times cited 65. |
8
|
>10
|
DeSimone RW, Currie KS, Mitchell SA, Darrow JW, Pippin
DA. Privileged structures: applications in drug discovery.
Comb. Chem. High. Throughput Screen., 2004,
7 (5), 473-493. Times cited 64. |
9
|
>10
|
Yarrow JC, Feng Y, Perlman ZE, Kirchhausen T, Mitchison
TF. Phenotypic screening of small molecule libraries
by high throughput cell imaging. Comb. Chem. High.
Throughput Screen.,2003, 6
(4), 279-286. Times cited 60. |
10
|
>10
|
Lohner K, Blondelle SE. Molecular mechanisms of membrane
perturbation by antimicrobial peptides and the use of
biophysical studies in the design of novel peptide antibiotics.
Comb. Chem. High. Throughput Screen., 2005,
8 (3), 241-256. Times cited 59. |
LITERATURE CITED
[1] van Breemen RB. Comb Chem High Throughput Screen. 2007,
10 (1), 1-2.
Richard B. van Breemen
(Editor-in-Chief)
University of Illinois
College of Pharmacy
833 S. Wood Street
Chicago
IL 60612
USA
E-mail: breemen@uic.edu
[Back to top] [Full Text Article] [PMID: 20214572 PubMed - indexed for MEDLINE]
High Content Screening of CXCR2-Dependent Signalling Pathways
Michael Wolff, Simone Kredel, Dorothea Haasen, Jörg
Wiedenmann, G. Ulrich Nienhaus, Barbara Kistler, Franz Oswald and Ralf Heilker
Stimulation of CXC-type chemokine receptor 2 (CXCR2)-transfected
cells by Gro-α
or IL-8 induced (i) CXCR2 internalization, (ii) phosphorylation
of ERK1/2 (pERK) and (iii) translocation of nuclear factor
of activated T cells (NFAT) into the nucleus. Employing high
content screening (HCS; i.e. fluorimetric imaging combined
with image analysis) these three ligand-induced events were
quantified by using a CXCR2-specific antibody, an antibody
recognizing phosphorylated ERK1/2 (pERK) and a red fluorescent
protein (RFP) in fusion to transiently overexpressed NFAT,
respectively. As an RFP, we applied a recently developed mutant
of an Entacmaea quadricolor fluorescent protein with
favorable properties for HCS, such as high fluorescence brightness,
photostability, large Stokes shift, and stability with regard
to formaldehyde.
Receptor internalization was closely coupled with ERK signalling
both when analyzed in regard of stimulation by physiological
CXCR2 ligands and when observed in the presence of antagonistic
test compounds. A means of increasing the throughput or of
broadening the pharmacological characterization of test compounds
is the use of multiplexed imaging. Indeed, CXCR2 internalization
could be multiplexed with the NFAT nuclear translocation by
fixation at ~45
min after Gro-α
stimulation. This multiplexing demonstrated that Gro-α-induced
CXCR2 internalization was tightly correlated with Gro-α-induced
NFAT translocation, also on the single cell level.
The analysis of ERK phosphorylation, NFAT translocation and
receptor internalization enabled the profiling of antagonistic
test compounds with respect to G-protein signalling and possible
receptor desensitization liabilities.
[Back to top] [Full Text Article] [PMID: 20214573 PubMed - indexed for MEDLINE]
Efficient Identification of Novel Leads by Dynamic Focused
Screening: PDK1 Case Study
Dongyu Sun, Joon Jung, Thomas S. Rush III, Zangwei
Xu, Michael J. Weber, Ekaterina Bobkova, Alan Northrup and
Ilona Kariv
A dynamic, focused screening strategy that utilized
a limited but diversified set of target-specific compounds
was explored as an efficient means for the identification
of inhibitors of the protein kinase PDK1. Approximately 21,500
compounds, including a 19,000 molecule kinase-focused compound
collection (KFCC), were screened at two concentrations to
identify initial leads. The KFCC included several empirically-derived,
general kinase libraries and molecules chosen by PDK1-specific
virtual screens. As was expected, this initial screen mostly
identified potent leads with limited novelty. In order to
overcome this limitation, the data from the screen were used
to drive several rounds of a customized iterative focused
screening (IFS) campaign. A machine-learning technique was
used to build a predictive model to identify compounds to
be screened in subsequent rounds. Molecules deemed not to
be novel were removed from the training set for the next round,
which allowed this campaign to progressively walk away from
the chemical space covered by the KFCC. This resulted in the
identification of PDK1 inhibitors which are uniquely different
from publicly known chemotypes after just three rounds of
screenings. A retrospective analysis of this IFS approach
against an ultra-high throughput screen (uHTS) indicated that
while uHTS is still the most prolific paradigm for lead identification,
this dynamic, focused screening approach was successful in
discovering novel scaffolds for a medicinal chemistry effort.
Finally, a theoretical optimization suggested the dynamic,
focused screening approaches could provide either a complementary
or alternative approach to uHTS for the efficient and rapid
lead identification.
[Back to top] [Full Text Article] [PMID: 20201823 PubMed - indexed for MEDLINE]
A Universal, Fully Automated High Throughput Screening Assay
for Pyrophosphate and Phosphate Release from Enzymatic Reactions
Scott D. Pegan, Yang Tian, Valerie Sershon and
Andrew D. Mesecar
The malachite green assay is often used for measuring
the presence of inorganic mono-phosphate concentrations. Some
studies have adapted this assay for use in monitoring enzymatic
reactions and have suggested its potential use in high throughput
screening (HTS). With the increasing availability of laboratory
automation, some studies are starting to explore the possibility
of conducting limited, semi-automated versions of the assay.
Here we report the optimization and complete adaptation of
the malachite green assay to a fully automated, HTS platform
that can be performed unattended with standard, commercially
available, automated liquid-handling systems. The assay is
universal for the majority of enzymes that release phosphate
or pyrophosphate. Moreover, the assay is fully scalable from
smaller drug screening efforts (~20,000
wells per day) to ultra-high throughput environments (~200,000
wells per day). The assay uses cost-effective, commercially
available reagents, and can be used to perform automated IC50
value and kinetic parameter determination. Finally, we demonstrate
the utility of the assay via the initial, primary
screening of 100,080 compounds against two target enzymes
from Bacillus anthracis, O-succinylbenzoyl-CoA synthetase
and nicotinate mononucleotide adenylyltransferase.
[Back to top] [Full Text Article] [PMID: 20201824 PubMed - indexed for MEDLINE]
Prediction of Critical Micelle Concentration of Nonionic Surfactants
by a Quantitative Structure – Property Relationship
Anna Mozrzymas and Bozenna Rózycka-Roszak
A quantitative structure – property relationship
(QSPR) was used to predict the critical micelle concentration
(cmc) of nonionic surfactants. The relation was developed
for a diverse set of 23 nonionic surfactants (r =
0.99, F-test = 1042.5) employing the connectivity
and valence connectivity indices only. The molecular connectivity
indices were calculated for the whole molecule which was a
simple and general approach.
[Back to top] [Full Text Article] [PMID: 20214574 PubMed - indexed for MEDLINE]
Tagging Molecules with Linear Polymers: Biocatalytic Transformation
of Substrates Anchored on Soluble Macromolecules
Claudio Cornaggia and Dario Pasini
With the increasingly available technology in automated
synthesis and screening protocols, the combination of polymer-supported
chemistry and biocatalysis, with their respective advantages
over classical organic synthesis, has become more scientifically
attractive, yet remains challenging. Since the development
of solid-phase synthesis and its rapid expansion in combination
with the advent of combinatorial techniques, a variety of
alternative methodologies have been proposed and demonstrated
to be viable for applications in high-throughput and multistep
syntheses of the desired products. These alternative methodologies
overcome the disadvantages of crosslinked polymer beads, which,
as a consequence of their insolubility and their being necessarily
heterogeneous in the reaction mixture, do have operational
drawbacks. They often rely on a common strategy: tagging the
target substrate of interest with other fragments (fluorous
synthons, macromolecules, "precipitons") in such
a way that the tag-substrate covalent ensemble is then easily
separated from the reaction mixture by physical methods (liquid-liquid
extraction, precipitation, etc.). The efficiency of enzymes
in transforming substrates is often enhanced when the stability
limitations of the biocatalyst in unnatural conditions (i.e.
organic solvents, high temperatures) are avoided by the use
of immobilization-stabilization techniques. We comment here,
with recent examples, on the use of linear macromolecules
as recyclable tags capable of acting as covalent supports
in combination with a biocatalyzed reaction.
[Back to top] [Full Text Article] [PMID: 20214575 PubMed - indexed for MEDLINE]
Applications of Integrated Data Mining Methods to Exploring
Natural Product Space for Acetylcholinesterase Inhibitors
Daniela Schuster, Lisa Kern, Dimitar P. Hristozov, Lothar
Terfloth, Bruno Bienfait, Christian Laggner, Johannes Kirchmair,
Ulrike Grienke, Gerhard Wolber, Thierry Langer, Hermann Stuppner,
Johann Gasteiger and Judith M. Rollinger
Nature, especially the plant kingdom, is a rich source
for novel bioactive compounds that can be used as lead compounds
for drug development. In order to exploit this resource, the
two neural network-based virtual screening techniques novelty
detection with self-organizing maps (SOMs) and counterpropagation
neural network were evaluated as tools for efficient lead
structure discovery. As application scenario, significant
descriptors for acetylcholinesterase (AChE) inhibitors were
determined and used for model building, theoretical model
validation, and virtual screening. Top-ranked virtual hits
from both approaches were docked into the AChE binding site
to approve the initial hits. Finally, in vitro testing of
selected compounds led to the identification of forsythoside
A and (+)-sesamolin as novel AChE inhibitors.
[Back to top] [Full Text Article] [PMID: 20201825 PubMed - indexed for MEDLINE]
High Throughput Synthesis and Screening
of New Catalytic Materials for the Direct Epoxidation of Propylene
Michael Kahn, Anusorn Seubsai, Isik Onal and
Selim Senkan
Nanoparticles of 35 individual metals as well as their
binary combinations were synthesized using High Throughput
pulsed laser ablation (PLA), and collected on Al2O3,
CeO2, SiO2,
TiO2, and ZrO2
pellets. These materials were then screened for their catalytic
activities and selectivities for the partial oxidation of
propylene, in particular for propylene oxide (PO), using array
channel microreactors. Reaction conditions were the following:
1 atm pressure, gas hourly space velocity (GHSV) of 20,000
h-1, temperature 300°C,
333°C,
and 367°C,
and feed gas composition 20 vol% O2,
20 vol% C3H6
and balance He. Initial screening experiments resulted in
the discovery of SiO2 supported
Cr, Mn, Cu, Ru, Pd, Ag, Sn, and Ir as the most promising leads
for PO synthesis. Subsequent experiments pointed to bimetallic
Cu-on-Mn/SiO2, for which
the PO yields increased several fold over single metal catalysts.
For multimetallic materials, the sequence of deposition of
the active metals was shown to have a significant effect on
the resulting catalytic activity and selectivity.
[Back to top]
[Full Text Article] [PMID: 20214576
PubMed - indexed for MEDLINE]
Phage-Displayed Combinatorial Peptide Libraries
in Fusion to β-Lactamase
as Reporter for an Accelerated Clone Screening: Potential
Uses of Selected Enzyme-Linked Affinity Reagents in Downstream
Applications
Girja S. Shukla and David N. Krag
Phage-display selection of combinatorial libraries is
a powerful technique for identifying binding ligands against
desired targets. Evaluation of target binding capacity of
multiple clones recovered from phage display selection to
a specific target is laborious, time-consuming, and a rate-limiting
step. We constructed phage-display combinatorial peptide libraries
in fusion with a β-lactamase
enzyme, which acts as a reporter. Linear dodecapeptide and
cysteine-constrained decapeptide libraries were created at
the amino-terminus of the Enterobacter cloacae P99
cephalosporinase molecule (P99 β-lactamase).
The overall and positional diversity of amino acids in both
libraries was similar to other phage-display systems. The
libraries were selected against the extracellular domain of
ErbB2 receptor (ErbB2ECD).
The target-selected clones were already conjugated to an enzyme
reporter, therefore, did not require subcloning or any other
post-panning modifications. We used β-lactamase
enzyme activity-based assays for sample normalizations and
clone binding evaluation. Clones were identified that bound
to purified ErbB2ECD and
ErbB2-overexpressing cell-lines. The peptide sequences of
the selected binding clones shared significant motifs with
several rationally designed peptide mimetics and phage-display
derived peptides that have been reported to bind ErbB2ECD.
β-Lactamase
fusion to peptides saved time and resources otherwise required
by the phage-ELISA of a typical phage display screening protocol.
The β-lactamase
enzyme assay protocols is a one-step process that does not
require secondary proteins, several steps of lengthy incubations,
or washings and can be finished in a few minutes instead of
hours. The clone screening protocol can be adopted for a high
throughput platform. Target-specific β-lactamase-linked
affinity reagents selected by this procedure can be produced
in bulk, purified, and used, without any modification, for
a variety of downstream applications, including targeted prodrug
therapy.
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