Multiple-Component Condensation Strategies for Combinatorial Library Synthesis

Historically, the paradigm of drug development has followed an iterative cycle of screening and synthesis, involving the manipulation of individual structures. The feedstock of molecules for this process has traditionally incorporated both natural products and proprietary and commercial compound collections. The latter usually represent a collectively monumental effort of synthesis over a period of many years. The introduction of high-throughput biological screening and the accelerated discovery of new biological targets has increased the demand on synthetic chemists to produce new compounds for testing. One response to this demand has been the development of techniques to greatly increase the speed and efficiency of compound synthesis. In the case of peptides1-4 and oligonucleotides,5,6 combinatorial libraries containing large numbers of individual components have afforded high-affinity ligands and potent inhibitors to a variety of targets. However, synthetic methods for these biopolymers are well-established, and it is only recently that chemists have applied some of these strategies to the currently more difficult task of generating libraries of small-molecule therapeutics. In this Account, we will focus on multiple-component condensations (MCCs) as one subset of strategies for the generation of compound libraries. While most libraries have been generated using a linear, multistep process, MCCs provide a complementary approach to a number of structures and should find applications in library generation. Multiple-component condensations are those reactions in which three or more reactants come together in a single reaction vessel to form a new product which contains portions of all the components. These reactions may be carried out in solution or on a solid support. A catalyst or other additive which might facilitate the coupling of two other components in a reaction but which does not structurally contribute to the product is not considered a component in an MCC reaction. It is not necessary that all components condense in a mechanistically concerted fashion; however, the MCC reactions considered herein do not require extensive manipulations: they are one-pot reactions. In this and the succeeding section, it is instructive to contrast this approach with linear synthesis to highlight the differences in methods, potential library size, and output format. For example, an MCC reaction with four components provides, in a single step, a molecular scaffold characterized by a core set of atoms common to the condensation reaction and displaying aspects of the four components. In contrast, to achieve the same structure in a linear fashion, multiple steps with attendant workup cycles may be required. It is our belief that the methods used to synthesize a particular library are dictated by (1) the need for a specific core structure and (2) the commercial availability or ease of access to inputs which give the structural variability to the core. Approaches to desired core structures vary greatly, and the chosen route may be a linear synthesis, an MCC, or a combination of the two. The term linear synthesis as used in this Account refers to a multistep process requiring the isolation of intermediates or washing of the solid support resin and re-exposure to new reagents for each step of the synthesis. While synthetic chemists may be more familiar with the distinction between “linear” and “convergent” when applied to synthetic strategies, in this Account we refer to as linear any library strategy that builds up the target molecule one step at a time. By this definition, both a solid-phase peptide synthesis and, for example, Ellman’s 1,4-benzodiazepine synthesis7 (Figure 1) constitute linear syntheses, because each constructs the target skeleton in a stepwise manner. We define “linear” in this manner as a means of distinguishing the MCC strategy, which we feel is an underutilized tool for library synthesis.8 This Account will focus on two related core struc-