Random Sequence Libraries Displayed on
Phage: Identification of Biologically
Important Molecules Pp.1-14
Christopher G. Adda, Robin F. Anders, Leann Tilley and Michael Foley
Mimotopes of Viral Antigens and Biologically
Important Molecules as Candidate Vaccines and Potential Immunotherapeutics Pp.15-27
C. D. Partidos and M.W. Steward
Rapid Determination of Pharmacokinetic
Properties of New Chemical Entities: In vivo Approaches Pp.29-37
Kathleen A. Cox, Ronald E. White and Walter
A. Korfmacher
A Systematic SAR Study of C10 Modified
Paclitaxel Analogues Using a Combinatorial Approach Pp.39-48
Yanbin Liu, Syed M. Ali, Thomas C. Boge,
Gunda I. Georg, Samuel Victory, Jan
Zygmunt Rebecca T. Marquez and Richard H. Himes
Molecular Diversity Sample Generation on the Basis
of Quantum-Mechanical Computations and Principal Component Analysis
Pp.49-57
H. G.-de-Terán, J. J. Lozano, V. Segarra and
F. Sanz
Screening Drugs for Metabolic Stability Using
Pulsed Ultrafiltration Mass Spectrometry
Pp.59-64
Young Geun Shin, Judy L. Bolton and Richard
B. van Breemen
Evaluation of a Micro Volume Pulsed
Ultrafiltration Cell for Screening
Ligands in Non-Covalent Complexes Pp.65-73
Michael B. Beverly, Paul West and Randy K.
Julian
Solid-Phase and Solution-Phase Parallel
Synthesis of Tetrahydro-isoquinolines via Pictet-Spengler Reaction
Pp.75-81
Qun Sun and Donald J. Kyle
Recognition of Multiple Substrate Motifs by
the c-ABL Protein Tyrosine Kinase Pp.83-91
Jinzi J. Wu, Daniel E. H. Afar, Hoang Phan,
Owen N. Witte and Kit S. Lam
Solid Phase Synthesis of Structurally Diverse
Tetra Substituted Pyrimidines for
Potential Use in Combinatorial Chemistry Pp.93-95
P.M.S. Chauhan and Arun Kumar
[Back to top] Random Sequence Libraries Displayed on
Phage: Identification of Biologically Important Molecules
Christopher G. Adda, Robin F. Anders, Leann
Tilley and Michael Foley
Phage display has become a
widely used tool for the identification of proteins or peptides with affinity
for a variety of biomolecules. The versatility, simplicity and cost
effectiveness of this application has pervaded a wide variety of research
areas. Although not without its limitations, phage display has provided a
convenient methodology for obtaining ligands to study the function, structure
and diagnostic or therapeutic potential of various macromolecules. This review
highlights some recent research employing this technology that serves to
illustrate its utility in various research and clinical applications.
[Back to top] Mimotopes of Viral
Antigens and Biologically Important Molecules as Candidate Vaccines and
Potential Immunotherapeutics
C. D. Partidos and M.W. Steward
Antigen recognition by antibodies or ligand-receptor
interactions involve small areas of the molecule named epitopes that are
normally conformational in nature. The availability of combinatorial peptide
libraries has provided a powerful tool for selecting novel sequences which
mimic conformational epitopes (mimotopes) either structurally and/or
immunologically. These mimotopes can be particularly useful in a number of
situations, including: the development of vaccines against tumors, infectious
diseases or allergic conditions; the design of molecules which can act as
agonists or antagonists of various biologically-important molecules; and for
the development of diagnostic assays. This article reviews the authors’ work on
the application of combinatorial peptide libraries to identify mimotopes of
protective B-cell epitopes from various pathogens, and the search for molecules
able to block the biological activities of TNF-a, a cytokine which plays
a key role in inflammation.
[Back to top]
Rapid Determination of Pharmacokinetic
Properties of New Chemical Entities: In vivo Approaches
Kathleen A. Cox, Ronald E. White and Walter
A. Korfmacher
There is a continuing need for increased throughput in the
evaluation of new chemical entities in terms of their pharmacokinetic (PK)
parameters as part of new drug discovery. This review summarizes various
approaches that have been used to increase throughput in this area. The article
divides the approaches into two areas: assay enhancement and sample reduction.
[Back to top] A
Systematic SAR Study of C10 Modified Paclitaxel Analogues Using a
Combinatorial Approach
Yanbin Liu, Syed M. Ali, Thomas C. Boge, Gunda I. Georg, Samuel Victory, Jan Zygmunt Rebecca T. Marquez and Richard H. Himes
A library with 63 paclitaxel analogues modified at the C10
position of paclitaxel has been prepared using parallel solution phase
synthesis. Most of the C10 analogues were slightly less active than paclitaxel
in the tubulin assembly assay and had reduced potency in the B16 melanoma and
MCF-7 cell line cytotoxicity assays. These modifications at C10, however, did
not lead to the total loss of activity, indicating that the C10 moiety of
paclitaxel may not be directly involved in the drug-microtubule interactions,
but could influence its binding affinity to P-glycoprotein. Approximately 50%
of the analogues demonstrated better activity against the drug resistant cell
line MCF7-ADR. However, the increase in activity was 10-fold at most. This
result demonstrates that the cytotoxicity against this drug resistant cancer
cell line is sensitive to structural changes at the C10 position of paclitaxel.
It was also found that the presence of a nitrogen atom in the C10 substituent
might play a role in the interaction of analogues with microtubules.
[Back to top] Molecular Diversity Sample Generation on
the Basis of Quantum- Mechanical
Computations and Principal Component Analysis
H. G.-de-Terán, J. J. Lozano, V. Segarra and
F. Sanz
The present study introduces a new strategy of selection of a maximum diversity sample of n compounds from N available in a molecular database. This strategy can be useful in pharmacological screening, combinatorial chemistry or parallel synthesis planning. It consists of first describing the compounds by means of parameters derived from quantum mechanical computations (water solvation DG, benzene solvation DG, octanol solvation DG, dipolar moment), as well as standard molecular parameters such as solvent-accessible surface area and molecular weight. Solvation parameters are used because of the importance of this phenomenon in the pharmacological behaviour. Redundant information in the description of the compounds is eliminated by using principal components (PC) instead of the original descriptors. Based on the similarity between the N compounds in the PC space, they are classified into n groups by k-means cluster analysis. The compounds that are nearest to the centroid of each cluster constituted the maximum diversity sample. When practical difficulties exist for the use of one of the proposed compounds, another also close to the cluster centroid can substitute for it. This strategy has been tested in the selection of a sample of 50 amines from the 923 available in the Aldrich catalogue. The results have been contrasted with those obtained from an optimal, distance-based experimental design, resulting in an 86% of agreement between both approaches. An R2-like diversity coefficient has been used to assess the quality of the proposed solutions.
[Back to top] Screening Drugs for Metabolic Stability Using Pulsed Ultrafiltration Mass Spectrometry
Young Geun Shin, Judy L. Bolton and Richard
B. van Breemen
A pulsed ultrafiltration-mass spectrometric screening
method has been developed to evaluate the metabolic stability of drugs. Pooled
human liver microsomes containing cytochrome P450 enzymes were trapped by an
ultrafiltration membrane in a stirred flow-through chamber, and eight b-blocker
drugs including acebutolol, alprenolol, atenolol, metoprolol, oxprenolol,
pindolol, propranolol, and timolol were flow-injected through the chamber along
with the cofactor NADPH. The ultrafiltrate was collected, concentrated and
analyzed by using liquid chromatography-tandem mass spectrometry (LC-MS-MS) in
order to quantitate the unmetabolized fraction of each drug. The metabolic
stability of each b-blocker was determined based on the difference between the
corresponding LC-MS-MS peak areas of an experimental incubation and a control
without NADPH. A flow-through incubation method, pulsed ultrafiltration
metabolic screening minimizes the potential for product feed back inhibition of
cytochrome P450 enzymes. The importance of this phenomenon was illustrated by
the observation that the metabolic stability of the set of b-blocker drugs
measured using pulsed ultrafiltration more closely resembled the in vivo
stability than that determined using a conventional batch incubation with
microsomes or an incubation with human hepatocytes. Since a mixture of
compounds was analyzed, the relative metabolic stability of each compound could
be assessed by comparison to the other compounds in the incubation. This
approach might be particularly useful for the ranking of a directed library of
drug leads with respect to metabolic stability and then the selection of lead
compounds for further drug development.
[Back to top] Evaluation
of a Micro Volume Pulsed Ultrafiltration Cell for Screening Ligands in
Non-Covalent Complexes
Michael B. Beverly, Paul West and Randy K.
Julian
A pulsed ultrafiltration cell with
a 35 mL binding chamber was evaluated for its ability to screen
ligands that formed non-covalent complexes with protein targets. The cell was
tested with ligands to the targets of carbonic anhydrase and serum albumin.
Non-covalent ligand binding to both of these targets was observed and bound
ligands were eluted from the cell in less than five min. The cell was also
demonstrated to effectively screen a methanolic fermentation broth extract
spiked with a known inhibitor to carbonic anhydrase. In addition to detecting
specific binding events, the pulsed ultrafiltration method was investigated for
its ability to distinguish non-specific binding events. Using carbonic
anhydrase with the zinc-binding site removed, it was found that non-specific
complexes observed when using electrospray ionization alone were not detected
when using the pulsed ultrafiltration mass spectrometry method.
[Back to top] Solid-Phase and Solution-Phase Parallel Synthesis of Tetrahydro- isoquinolines via Pictet-Spengler Reaction
Qun Sun and Donald J. Kyle
An efficient parallel synthesis of
6,7-dimethoxytetrahydroisoquinolines is reported. The key reaction step is
3,4-dimethoxyphenethylimines reacting with acid chlorides to form an
N-acyliminium ion intermediate, which undergoes Pictet-Spengler condensation to
give the desired products in >80% yield. Both solution-phase and solid-phase
synthesis of 6,7-dimethoxytetrahydroisoquinolines are described.
[Back to top] Recognition of Multiple Substrate Motifs by the c-ABL Protein
Tyrosine Kinase
Jinzi J. Wu, Daniel E. H. Afar, Hoang Phan,
Owen N. Witte and Kit S. Lam
Using a combinatorial peptide library that is based on the
one-bead one-peptide approach we identified 14 peptide substrates for the c-ABL
protein tyrosine kinase, which define three distinct consensus sequence groups.
This is distinct from many serine/threonine kinases, which often phosphorylate
only one major consensus sequence. The three consensus sequences accurately
predict phosphorylation sites in cellular ABL substrates proven to play a role
in cell signaling. Our data suggest that protein tyrosine kinases have evolved
to recognize multiple substrate motifs.
[Back to top] Solid Phase Synthesis of Structurally Diverse Tetra
Substituted Pyrimidines for Potential Use in Combinatorial Chemistry
P.M.S. Chauhan and Arun Kumar