Combinatorial libraries side products

Many acid-labile linkers are used to assemble combinatorial libraries. Compounds are cleaved in the final step by TFA/DCM solution with various concentrations for a certain period of time. Mild cleavage conditions may lead to incomplete cleavage of the desired compound from a solid support. On the other hand harsh conditions may cause compound degradation and side reactions. Harsh conditions will also cause the partial breakdown of resin and the leaching of unidentified impurities into the final products. Harsh cleavage conditions demand the stabihty of all compounds under such conditions. This may limit the scope of combinatorial synthesis... 

In LC/MS analysis of combinatorial libraries, the MS determines the product identity and its purity is determined by other on-line detection techniques such as UV, evaporative light scattering detection (ELSD), and chemiluminescent nitrogen detection (CLND).17-20 UV detection is used here to assess product purity based on the assumption of similar absorption coefficients at 214 nm for the desired product and the side-products. 

Any MS experiment begins with ionization of molecules of analyte. Numerous ionization techniques (electron ionization, fast atom bombardment, plasma desorption, electrospray ionization, etc.) allow MS analysis of a wide range of organic molecules. In most cases the characterization of combinatorial libraries means analysis of crude compounds i.e. one can expect not only the intended compound to be present in the analyte, but also products of side... 

Flow injection analysis mass spectrometry (FIA-MS) has been reported to be a fast method for the characterization of combinatorial libraries (55,56). The method verifies the presence of the molecular ions of the expected product and side products or impurities but does not provide information on the quality of the analyzed samples. Significant improvements related to the increased analytical throughput, obtained by reducing the time between each injection without increasing the intersample carry-over from each analysis, were recently reported (57, 58). When coupled with RP-HPLC, FIA-MS allows the separation and the determination of the molecular weight of the components of each sample. This is normally enough to unequivocally attribute the structure of the expected library component and of any side products from a library synthesis. 

LiBrain (103) is a collection of software modules for automated combinatorial library design, including the incorporation of desirable pharmacophoric features and the optimization of the diversity of designed libraries. A Chemistry Simulation Engine module is trained by chemists to determine the suitability of reactants for a specified reaction, to recognize the risk of undesirable side reactions, and to predict the structures of the most likely reaction products, so as to circumvent major bottlenecks associated with automating the process. 

A very important use of MS in combinatorial chemistry is in quality control of combinatorial libraries. As much as possible, we would like to have pure compounds generated in high yield, with no side reactions or by-products. We also need to verify that every component actually exists in a library (i.c.. that no reactions failed). Only MS provides the sensitivity and versatility to perform this checking with both solid-pha.se and solution-phase libraries... 

Capillary electrophoresis (CE) is a powerful separation technique. It is especially useful for separation of ionic compounds and chiral mixtures. Mass spectrometry has been coupled with CE to provide a powerful platform for separation and detection of complex mixtures such as combinatorial libraries. However, the full potential of CE in the application of routine analysis of samples has yet to be realized. This is in part due to perceived difficulty in the use of the CE technique compared to the more mature techniques of HPLC and even SFC. Dunayevskiy et al. [136] analyzed a library of 171 theoretically disubstituted xanthene derivatives with a CE/ESI-MS system. The method allowed the purity and makeup of the library to be determined 160 of the expected compounds were found to be present, and 12 side products were also detected in the mixture. Due to the ability of CE to separate analytes on the basis of charge, most of the xanthene derivatives could be resolved by simple CE-MS procedures even though 124 of the 171 theoretical compounds were isobaric with at least one other molecule in the mixture. Any remaining unresolved peaks were resolved by MS/MS experiments. The method shows promise for the analysis of small combinatorial libraries with fewer than 1000 components. Boutin et al. [137] used CE-MS along with NMR and MS/MS to characterize combinatorial peptide libraries that contain 3 variable positions. The CE-MS method was used to provide a rapid and routine method for initial assessment of the construction of the library. Simms et al. [138] developed a micellar electrokinetic chromatography method for the analysis of combinatorial libraries with an open-tube capillary and UV detection. The quick analysis time of the method made it suitable for the analysis of combinatorial library samples. CE-MS was also used in the analysis... 

The design of enzyme inhibitors has included random screening of synthetic chemical agents, natural products, and combinatorial libraries followed by molecular optimization or structure-activity relationships of so-called lead structures as well as bio-isosteric analogues of the enzyme substrates themselves. Drugs (e.g., finasteride) also have been developed for one indication but, based on observed side effects, have lead to other uses. 

Libraries of synthetic combinatorial chemicals complement libraries of natural product metabolites, but do not duplicate or replace them. Examples of side-by-side screening of synthetic combinatorial chemicals and microbial fermentation extracts indicate that both sets of chemical diversity can provide unique leads. The quantity of leads generated by each method is irrelevant, if the quality of the lead is not considered. Therefore, scientific research should be focussed not on which type of library is better, but rather how to take advantage of both resources in a cost-effective and timely manner. 

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