Diversity-oriented synthetic libraries

The split-and-pool synthesis not only simplifies the complexity of the combinatorial synthetic process, but also offers additional important benefits. To undertake a full range of solid-phase chemical reactions, elaborate reaction conditions are needed for some chemical transformations. These include, but are not limited to, low temperature and inert atmosphere conditions. Parallel synthesis of a thousand compounds requires handling of a thousand reaction vessels. The timely addition of sensitive reagents (e.g., butyl lithium) at low temperature (—78°) under inert atmosphere during parallel synthesis is not a trivial task. It can be done if sophisticated automated synthesizer equipment is designed to handle and tolerate such reaction conditions. Such a synthesis can alternatively be performed easily in a manual fashion using a split-and-pool method that requires only a limited number of reaction vessels. Examples from Nicolaou s17 and Schrei-ber s18,19 laboratories have shown that the split-and-pool method is the methodology of choice for the synthesis of complex and diversity-oriented combinatorial libraries. 

In term of diversity-oriented strategies, multicomponent reactions (MCR) represent an attractive and rapid access to libraries of macrocycles inspired by biologically active natural products. Combined with Passerini and Ugi reactions, M-RCM has already shown promising synthetic potential, as illustrated by the pioneering work of Domling and coworkers [46]. Condensation of isocyanide 69 with carboxylic acid 70 in the presence of paraformaldehyde leads to bis-olefin 71, which is subsequently submitted to RCM in the presence of G1 and titanium isopropoxide to give the 22-membered macrocycle 72 (Scheme 2.27). 

Contributions by R. Joseph and P. Arya as well as M. A. Koch and H. Waldmann focus on synthetic aspects towards lead structures originating from natural product-derived scaffolds. R. Joseph and P. Arya refer to two complementary approaches, the synthetic access to focussed libraries around bioactive natural product cores, and diversity-oriented synthesis aiming at 3D scaffold diversity for hit generation, respectively. On the other hand, M. A. Koch and H. Waldmann emphasise the correlation of natural product-based library concepts with structural features of targeted protein domains, thus strengthening the privileged structure concept from a bioorganic viewpoint. 

Most commonly, a commercial library, containing a subset of compounds that matches a desired set of properties (if known), is screened in an initial study. Once hits are obtained and verified, a small library of compounds is synthesized to produce a set of compounds in the same chemical-stmctural space as the original hit stmcture. This process allows for hits with higher potency and elucidates information of the structure-activity relationship within the system of interest. Such synthetic libraries of chemically diverse compounds have been made possible through combinatorial chemistry (52-56) and diversity-oriented synthesis (52). 

There are a few library concepts originating from synthetic feasibility considerations. Multicomponent reactions, click chemistry, and diversity-oriented synthesis will now be discussed in more detail. 

Figure 4.1. Planning strategies and end goals involved in target-oriented synthesis, focused library synthesis (combinatorial synthesis), and diversity-oriented synthesis. The first two approaches use retrosynthetic analysis to design the synthesis of target compounds. Diversity-oriented synthesis uses forward synthetic analysis to produce libraries that occupy diffuse regions of chemical space.

Principal component analysis (PCA) is a mathematical method for dimensionality reduction that allows for multidimensional datasets to be visualized using two- or three-dimensional plots with minimal loss of information [1,2]. When applied in the context of diversity-oriented synthesis, PCA is primarily used to visualize similarities and differences within collections of compounds based on structural and physicochemical parameters, and can be leveraged in library design [3]. Molecular weight, stereocenters, rotatable bonds, hydrophobicity, and aqueous solubility are a few examples of parameters commonly included in such analyses. Herein, we selected 20 structural and physicochemical parameters for analysis based on previously identified correlations of these parameters with oral bioavailability, cell permeability, solubility, and binding selectivity, as well as their ability to distinguish synthetic drugs... 

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