Post-Panning
Computer-Aided Analysis of Phagotope Collections Selected with
Neurocysticercosis Patient Polyclonal Antibodies: Separation of
Disease-Relevant and Irrelevant Peptide Sequences
Synthase
Pp. 221-235
K.G. Gazarian , M.J.
Rowleyb, T.G. Gazarianc, J. Sotelod, E. García-Mendozad and
R. Hernándeza
Identification
of Inhibitors of DNA Topoisomerase II from a Synthetic Library of
Glycoconjugates
Pp. 237-244
R.P. Tripathi, S.K.
Rastogi, B. Kundu, J.K. Saxenaa, V.J.M. Reddya, S. Srivastavab,
S. Chandrab and A.P. Bhaduri
In
Vitro High Throughput Screening of Compounds for Favorable
Metabolic Properties in Drug Discovery Pp. 245-263
Collen M. Masimirembwa,
Richard Thompson and Tommy B. Andersson
[Abstract]
Cystic
Fibrosis and Fragile X Syndrome: The Arguments for Antenatal Screening
Pp. 65-72
Jenni Murray and Howard
Cuckle
[Abstract]
Helma Wennemers
On-line
Sample Preparation for High Throughput Reversed-phase LC/MS Analysis of
Combinatorial Chemistry Libraries Pp. 287-293
Liang Tang , William L.
Fitch , Peter Smith , David Tumelty , Kathy Cao and Steven W. Ferla
Virtual
Darwinian Drug Design: QSAR Inverse Problem, Virtual Combinatorial Chemistry,
and Computational Screening Pp. 295-310
J. V. de Julián-Ortiz
Estimation of Aqueous Solubility in Drug Design
Pp. 311-316
Jarmo Huuskonen
[Back to top] Post-Panning Computer-Aided
Analysis of Phagotope Collections Selected with Neurocysticercosis Patient
Polyclonal Antibodies: Separation of Disease-Relevant and Irrelevant Peptide
Sequences
K.G. Gazarian M.J.Rowleyb, T.G.Gazarianc, J. Sotelod,
E. García-Mendozad and R.Hernándeza
The homology of peptide sequences selected from a 7mer phage display library with antibodies elicited by the multicelled parasite Taenia solium in cerebrospinal fluid and serum of neurocysticercosis (NCC) patients and by antibodies of uninfected control patients with similar neurological complications of other ethiology (non-NCC) were analyzed using a PILEUP-Tudos sequence alignments program. The analysis generated dendrograms bearing two types of sequence clusters, those containing (1) only NCC patients-derived peptides and (2) both NCC- and control non-NCC – patient derivatives. By using ELISA, peptides that were selected by the antibodies were identified predominantly in the NCC-derived clusters. In repeated analysis in which sequences were added or removed, the first type of clusters maintained their structure, while the second type of clusters were split into many separate homology units dispersed throughout the guide tree. These results are interpreted as the ability of the analysis to segregate NCC-specific peptide sequences from other sequences. Altogether, this study demonstrates the high potential of the PILEUP-Tudos computer program to analyze phagotope collections recovered through biopanning with polyclonal antibodies elicited in patients by complex and as yet unknown multiple pathogenic antigens and to separate all phagotopes that are disease-relevant on the basis of the sequence homology.
[Back to top]
Identification of Inhibitors of DNA Topoisomerase II from a
Synthetic Library of Glycoconjugates
R.P. Tripathi, S.K. Rastogi, B. Kundu, J.K. Saxenaa, V.J.M.
Reddya, S. Srivastavab, S.
Chandrab and A.P. Bhaduri
A library of 24 glycoconjugates related to glycosylated b-amino acid derivative (I) was been prepared and screened against DNA topoisomerase-II of the filarial parasite S. cervi. Among these, compound 6 was found to be a potent inhibitor of DNA topoisomerase-II with 95% inhibition at 1.09mM. Furthermore, compound 6 was at least three times more potent than the lead compound, glycosylated b-amino acid derivative I.
[Back to top]
In Vitro High Throughput Screening of Compounds for Favorable
Metabolic Properties in Drug Discovery
Collen M. Masimirembwa, Richard Thompson and Tommy B. Andersson
Drug
metabolism can have profound effects on the pharmacological and toxicological
profile of therapeutic agents. In the pharmaceutical industry, many in vitro
techniques are in place or under development to screen and optimize compounds
for favorable metabolic properties in the drug discovery phase. These in vitro
technologies are meant to address important issues such as: (1) is the compound
a potent inhibitor of drug metabolising enzymes (DMEs)? (2) does the compound
induce the expression of DMEs? (3) how labile is the compound to metabolic
degradation? (4) which specific enzyme(s) is responsible for the compound’s
biotransformation? and (5) to which metabolites is the compound metabolized?
Answers to these questions provide a basis for judging whether a compound is
likely to have acceptable pharmacokinetic properties in vivo. To address these
issues on the increasing number of compounds inundating the drug discovery
programs, high throughput assays are essential. A combination of biochemical
advances in the understanding of the function and regulation of DMEs (in
particular, cytochromes P450, CYPs) and automated analytical technologies are
revolutionizing drug metabolism research. Automated LC-MS based metabolic
stability, fluorescence, radiometric and LC-MS based CYP inhibition assays are
now in routine use. Automatible models for studying CYP induction based on
enzyme activity, quantitative RT-PCR and reporter gene systems are being
developed. We will review the utility and limitations of these HTS approaches and
highlight on-going developments and emerging technologies to answer metabolism
questions at the different stages of the drug discovery process.
[Back to top]
Cystic Fibrosis and Fragile X Syndrome: The Arguments for
Antenatal Screening
Jenni Murray and Howard Cuckle
The ultimate public health aim of genetic screening is prevention. This can be achieved by reducing birth prevalence through primary or secondary methods such as pre-conceptional or antenatal screening. Tertiary prevention by neonatal screening is also an option where there is direct unbiased evidence for a substantial improvement in prognosis. In addition to this, the information provided during screening is also of value, enabling individuals to make choices that otherwise would not have been available. Having elucidated the natural histories and genetic defects underlying two common, serious genetic disorders, cystic fibrosis and fragile X syndrome, considerable efforts have been channelled into ascertaining the most efficacious method of prevention. To date there is only indirect evidence to suggest that neonatal screening improves prognosis in cystic fibrosis. Similarly, treatment for fragile X syndrome is limited and therefore early identification of the disorder by neonatal screening is unlikely to improve long term outlook. Thus the focus of this review is on primary and secondary preventive methods.
[Back to top]
Combinatorial Chemistry: A Tool for the Discovery of New
Catalysts
Helma Wennemers
The discovery of new reactions and catalysts has always presented an intriguing challenge to scientists. With the rise of combinatorial chemistry, a new method has emerged that holds considerable promise to facilitate the task since it allows for the simultaneous generation and testing of a large number of compounds. The crucial difficulty lies in establishing general technologies for rapid and reliable screening of libraries to determine the catalytic activity of their members. Several recent publications have addressed this question by using infrared thermography, colorimetric assays and fluorescence spectroscopy. These techniques have not only been applied successfully to the high-throughput screening of parallel compound arrays but also to the screening of one-bead-one-compound libraries. This demonstrates that combinatorial chemistry possesses indeed the potential to establish itself as a powerful tool for the discovery of new catalysts. This review describes the methodologies used so far for the detection of catalytic events and will place particular emphasis on the on-bead screening of one-bead-one-compound libraries.
[Back to top]
On-line Sample Preparation for High Throughput Reversed-phase LC/MS Analysis of Combinatorial Chemistry Libraries
Liang Tang, William L. Fitch, Peter Smith, David Tumelty,
Kathy Cao and Steven W. Ferla
An on-line sample preparation method utilizing a
time-programmed autosampler is described for high throughput liquid
chromatography/mass spectrometry (LC/MS). This approach is particularly helpful
for the LC/MS analysis of samples which require solvents incompatible with HPLC
in the sample preparation process. The on-line sample preparation approach
minimizes a bottleneck in throughput and improves sample recovery under some
circumstances.
[Back to top]
Virtual Darwinian Drug Design: QSAR Inverse Problem, Virtual
Combinatorial Chemistry, and Computational Screening
J. V. de Julián-Ortiz
The generation of diversity and its further selection
by an external system is a common mechanism for the evolution of the living
species and for the current drug design methods. This assumption allows us to
label the methods based on generation and selection of molecular diversity as
“Darwinian” ones, and to distinguish them from the structure-based,
structure-modulation approaches. An example of a Darwinian method is the
inverse QSAR. It consists of the computational generation of candidate chemical
structures and their selection according to a previously established QSAR
model. New trends in the field of combinatorial chemical syntheses comprise the
concepts of virtual combinatorial synthesis and virtual or computational
screening. Virtual combinatorial synthesis, closely related to inverse QSAR,
can be defined as the computational simulation of the generation of new
chemical structures by using a combinatorial strategy to generate a virtual
library. Virtual screening is the selection of chemical structures having
potential desirable properties from a database or virtual library in order to
be synthesized and assayed. This review is mainly focused on graph theoretical
drug design approaches, but a survey with key references is provided that
covers other simulation methods
[Back to top]
Estimation of Aqueous Solubility in Drug Design
Jarmo Huuskonen
The solubility of drugs in water is of central importance in
the process of drug discovery and development from molecular design to
pharmaceutical formulation and biopharmacy. The ability to estimate the aqueous
solubility and other properties of a promising lead compound affecting its
pharmacokinetics is a prerequisite to rational drug design, although it has
received much less attention than the prediction of drug-receptor interactions.
In this review, methods for the estimation of aqueous solubility of organic
compounds are described and limited to approaches, which might be used in the
early stage of drug design and development.