Combinatorial Chemistry & High Throughput Screening - Volume 6, Issue 5, 2003

Libraries of displayed antibodies have been increasingly used to select or screen antibodies. It is generally well recognized that large libraries provide high probability of finding a given antibody. In this review, the factors that limit the sizes of current in vivo and ribosome-based in vitro display libraries to be around 10 11 members are first discussed. An analysis resulting in a quantitative correlation between the library size and the antibody affinity is then presented. This analysis underscores the importance of large libraries in not only increasing the probability of finding a given antibody, but also enhancing the quality of a given antibody. Recent advances in preparing state-of-the-art large display libraries are then reviewed. Finally, potential improvements to current library technologies to generate libraries as large as 10 12 and their rationales are explored in length.

The Nobel Prize in Chemistry 1902 was given to Hermann Emil Fischer “in recognition of the extraordinary services he had rendered by his work on sugar and purine synthesis”. This truly great chemist of all time named a group of bicyclic nitrogenous structures as purines, discovered the synthesis of glucose, fructose and mannose starting from glycerol, and further created the basis for glucoside-, amino acid-, and enzyme chemistry. To honour his discoveries, and to celebrate the 100 year since his Nobel Prize, we decided to write a short review article on the latest discoveries in the fields of purine / pyrimidine and sugar chemistry beeing performed on solid support. The review summarizes most of the material beeing published in the field since 1960, and ends by giving a picture of future directions for the field of drug discovery based on sugar and purine chemistry.

High-throughput ligand-based proton NMR screening performed in the presence of a spy molecule and a control molecule is a valuable tool for identifying drug leads. A limitation of the technique is represented by the severe overlap encountered in the screening of large chemical mixtures. An approach for overcoming this overlap problem is the use of multi-selective R1 filtered and COSY or TOCSY experiments. Application of this methodology to compounds binding to the Sudlow site I of human serum albumin is presented. The screening is performed by simply monitoring the intensity of two signals. The precise measurement of the relative intensity of the two resonances permits determination of the binding constant of the NMR-hit. For a simple competition binding mechanism, the rapidly-derived NMR binding constants are in good agreement with the values derived from full-titration ITC and fluorescence spectroscopy measurements.

In solid tumors the predominant genetic mechanism for oncogene activation is through amplification of genes. The HER-2 (also known as ErbB2 / c-erbB2 / HER-2 / neu) oncogene is the most frequently amplified oncogene in breast cancer and is also commonly amplified in other forms of cancer. Alongside its important role in tumor induction, growth and progression, HER-2 is also a target for a new form of chemotherapy. Since 1998, breast cancer patients have been treated with considerable success with Herceptin (trastuzumab), a recombinant antibody designed to block signaling through the HER-2 receptor. In addition to Herceptin, a large number of various HER-2 directed immunological and genetic approaches, either targeting the HER-2 receptor, its signaling pathways or both HER-2 and epidermal growth factor receptor (EGFR) together, have demonstrated promising pre-clinical potential towards HER-2 amplified carcinomas. Moreover, the HER-2 amplicon contains other genes with altered copy numbers that could be used as targets for chemotherapy. The topoisomerase II α (topoII α) gene (TOP2A) is located adjacent to the HER-2 oncogene at the chromosome location 17q12-q21 and is either amplified or deleted, with equal frequency, in almost 90% of HER-2 amplified primary breast tumors. Recent data suggest that amplification or deletion of TOP2A may account for both sensitivity or resistance to topoII-inhibitor-chemotherapy, depending on the specific genetic defect at the TOP2A locus. The understanding of HER-2 amplification and its role in the pathogenesis of cancer is expanding. The number of therapeutic strategies targeting HER-2 signaling pathways will most probably be introduced in the treatment of HER-2 amplified tumors within the next few years. Combining HER-2 targeting therapies with conventional forms of cytotoxic chemotherapy, where additional diagnostics tests such as those ascertaining topoII α status, may be helpful for the ideal selection of patients for the combination therapy of a HER-2 targeting drug together with a cytotoxic drug. The clinical and therapeutic importance of the HER-2 and TOPO2A status of tumor cells in cancer management will only increase within the next few years.

A solution phase strategy for the multiple parallel synthesis of a demonstration library of indazoles is described by which regio-selectivity problems inherent to previous syntheses of this nucleus are largely overcome. Synthesis of selected components proceeded satisfactorily indicating that a fully realized library of indazole analogs could readily be produced using this methodology. Simple modifications of the basic nucleophilic aromatic substitution route unambiguously produce a range of N-1 substitutions (alkyl, aryl and aralkyl) in 50-75% yields. Next a range of substituents was introduced at the C-3 position in 50-80% yields by O-alkylation. Careful choice of reagents and reaction conditions were required to prevent by-product formation due to competing alkylation at N-2 (trace to 15% yields). When present, these contaminants were readily removed by chromofiltration. A third diversity site was sketched in at C-5 in 75-90% yield by reductive alkylation or acylation. Screening of some of the demonstration library members in vitro revealed highly active antioxidants suggesting that producing a full library would be worthwhile.

A biased chemical library containing 91 differentially substituted thiazolidinones was prepared in an effort to improve the pharmacology of a known anticonvulsant agent V102862. The collection was prepared in a single step multi-component condensation reaction that produced good yields and very high crude purity (75%-85%). Seven compounds, identified within the library were shown to be more potent than V102862, our parent reference compound, in an electrophysiological assay measuring sodium channel antagonism. The most potent compound, 3-(2-piperidinylethyl)-2-(3-(3-trifluoromethylphenoxy)phenyl)thiazolidinone, has a Ki of 90 nM.