Combinatorial Chemistry & High Throughput Screening - Volume 5, Issue 1, 2002

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.

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-α, a cytokine which plays a key role in inflammation.

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.

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 percentof 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.

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 ΔG, benzene solvation ΔG, octanol solvation ΔG, 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 percent of agreement between both approaches. An R²-like diversity coefficient has been used to assess the quality of the proposed solutions.

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 β-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 β-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 β-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.

A pulsed ultrafiltration cell with a 35 μL 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.

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 percent yield. Both solution-phase and solid-phase synthesis of 6,7-dimethoxytetrahydroisoquinolines are described.

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.

A new pyrimidine based scaffold has been identified for generation of combinatorial libraries using solid phase technique.The utility of the scaffolds was demonstrated by synthesizing small libraries of 12 substituted pyrimidines (4a-4l).