The rapid evolution of combinatorial chemistry in recent years has led to a dramatic improvement in synthetic capabilities. The goal is to accelerate the discovery of molecules showing affinity against a target, such as an enzyme or a receptor, through the simultaneous synthesis of a great number of structurally diverse compounds. This is done by generating combinatorial libraries containing as many as hundreds or thousands of compounds. The need to test all these compounds led to the development of high-throughput screening (HTS) techniques, and also high-throughput analytical techniques capable of assessing the occurrence, structure and purity of the products. In order to be applied effectively to the characterization of combinatorial libraries, an analytical technique must be adequately sensitive (to analyse samples which are typically produced in nanomole amounts or less), fast, affordable and easy to automate (to minimize analysis time and operator intervention). Although no method alone can meet all the analytical challenges underlying this task, the recent progress in mass spectrometric (MS) instrumentation renders this technique an essential tool for scientists working in this area. We describe here relevant aspects of the use of MS in combinatorial technologies, such as current methods of characterization, purification and screening of libraries. Some examples from our laboratory deal with the analysis of pooled oligomeric libraries containing n x 324(n = 1, 2) compounds, using both on-line high-performance liquid chromatography/MS with an ion trap mass spectrometer, and direct infusion into a triple quadrupole instrument. In the first approach, MS and product ion MS/MS with automatic selection of the precursor were performed in one run, allowing library confirmation and structural elucidation of unexpected by-products. The second approach used MS scans to characterize the entire library and also precursor ion and neutral loss scans to detect selectively components with given structural characteristics.

The large-scale solid-phase continuous flow synthesis of the bicyclic peptide MEN 10627, a new potent Neurokinin A receptor antagonist, is described using the Fmoc-polyamide method on both macrosorb 125 and Macrosorb 250 resin. A new synthesizer designed in-house was realized by assembling Whitey valves and Waters pump in order to allow small-scale (0.0001 mol; 1 x 10 cm Omnifit columns) synthetic studies which were strongly predictive of the conditions required for large-scale (0.01-0.10 mol; 3.6 or 5.9 x 46 cm Büchi columns) production, performed on the same apparatus.

A preparative method for the preparation of large peptides is described. An advantageous theoretical weight of peptide/weight of starting resin ratio (tPw/Rw) of about 0.3 was successfully experimented. The esterification of the first amino acid was realized with a racemization of less than 1%. The study of the coupling conditions led to the use of a diluted acylating mixture that allowed a 56% consumption of the amino acid derivatives (percentage use of amino acids) introduced in the synthesis. The cost analysis of the synthesis showed that the recovery of the amino acid derivatives was not worthwhile.

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The large-scale solid-phase continuous flow synthesis of the bicyclic peptide MEN 10627, a new potent Neurokinin A receptor antagonist, is described using the Fmoc-polyamide method on both macrosorb 125 and Macrosorb 250 resin. A new synthesizer designed in-house was realized by assembling Whitey valves and Waters pump in order to allow small-scale (0.0001 mol; 1 x 10 cm Omnifit columns) synthetic studies which were strongly predictive of the conditions required for large-scale (0.01-0.10 mol; 3.6 or 5.9 x 46 cm Büchi columns) production, performed on the same apparatus.