Comprehensive survey of combinatorial library synthesis: 1999

ADVANCES IN CHEMICAL GENETICS

Chemical genetics is an emerging approach for studying biological systems using chemical tools. This strategy aims to reveal the macromolecules responsible for regulating biological systems; thus, the approach shares much in common with genetics. In both strategies, one must (a) develop an assay that reports on a biological process of interest, (b) perturb this process systematically (with mutations or small molecules), and (c) determine the target of each perturbation to reveal macromolecules (i.e., proteins and genes) regulating the process of interest. In this review, we discuss advances and challenges in this field that have emerged over the past four years. Several technologies have converged, raising the hope that it may be possible to systematically apply chemical probes to biological processes.

Solid-supported reagents and catalysts for the preparation of large ring compounds

Parallel combinatorial synthesis in solution using immobilized reagents, catalysts, and scavengers has emerged as a powerful technique for the preparation of diverse libraries of compounds. This technique has only recently been applied to the synthesis of large-ring compounds. In this comprehensive review several strategies are presented and discussed, including Pd-catalyzed allylic alkylation, Stille-coupling, macrolactonization and macrolactamization using solid supported reagents and catalysts. In several cases site isolation has allowed operation, of these macrocyclization reactions in concentrated solution (pseudo-dilution effect).

A very large diversity space of synthetically accessible compounds for use with drug design programs

We have constructed a very large virtual diversity space containing more than 10(13) chemical compounds. The diversity space is built from about 400 combinatorial libraries, which have been expanded by choosing sizeable collections of suitable R-groups that can be attached to each link point of their scaffolds. These R-group collections have been created by selecting reagents that have drug-like properties from catalogs of available chemicals. As members of known combinatorial libraries, the compounds in the diversity space are in general synthetically accessible and useful as potential drug leads. Hence, the diversity space can be used as a vast source of compounds by a de novo drug design program. For example, we have used such a program to generate inhibitors of HIV integrase enzyme that exhibited activity in the micromolar range.

Small molecule biaryl FSH receptor agonists. Part 1: Lead discovery via encoded combinatorial synthesis

High-throughput screening of two million compounds in 37 distinct encoded combinatorial libraries using FSH receptor transfected cells provided small molecule agonists such as 1 (EC(50)=3 microM) and 2 (EC(50)=3.9 microM), based on which a focused combinatorial library with a total of 31372 compounds was designed, synthesized, and screened to reveal 72 novel biaryl FSH receptor agonists such as 8a-c as well as a unique combinatorial SAR.

Privileged structure-based combinatorial libraries targeting G protein-coupled receptors

Combinatorial chemistry has become a key component of today's drug discovery process. Privileged structures, with their inherent affinity for diverse biological receptors, represent an ideal source of core scaffolds and capping fragments for the design and synthesis of combinatorial libraries targeted at various receptors. GPCRs-distributed widely in the body and involved in many physiological and pathophysiological processes-have been historically among the most popular targets for drug discovery. Numerous privileged structure-based combinatorial libraries have been designed and synthesized, and these libraries have proved to be an extremely powerful tool to aid the rapid discovery and optimization of potent and selective ligands for a wide variety of GPCR targets. This review focuses on recent developments in applying privileged structure-based combinatorial libraries for the discovery and optimization of GPCR ligands and critically evaluates the advantages of the various types of GPCR-targeted libraries.

Ring-closing metathesis: development of a cyclisation-cleavage strategy for the solid-phase synthesis of cyclic sulfonamides

A series of novel 7-membered cyclic sulfonamides have been synthesised using a solid-phase cyclisation-cleavage RCM strategy. Model solution studies indicated the sulfonamides were suitable substrates for RCM using the Grubbs' catalyst 2. Starting from either 2-carboxyethyl polystyrene (21) or Merrifield resin, various seven-membered sulfonamides were prepared in good to excellent yields at low catalyst loadings (2.5-5 mol%) using a flexible spacer between the polymer and the substrate. In addition, a novel double-armed linker was shown to allow efficient RCM cleavage of sulfonamides with as little as 1 mol% of the ruthenium alkylidene complex 2.

Solid phase synthesis and application of trisubstituted thioureas

Resin-bound amines 1a-e condense with isothiocyanates to give thiourea resins 2a-i. Resins 2a-g subsequently react with iodomethane followed by cleavage affording S-methyl isothioureas 4a-g, and resins 2a-b,h-i react with acyl chlorides to afford N-acylated thioureas 6a-d. N-Acylthioureas 8a-f (R(2) = H) were prepared directly from resin-bound amines 1a-d with acyl isothiocyanates. N-Acylthioureas 8a-d,f(R(2) = H) were used for the preparation of S-methyl-N-acylisothioureas 10a-e. Alkylation was performed using methyl iodide. Resin-bound S-methyl-N-acylisothioureas 10a,b,d are converted by an action of hydrazines into 3-amino-1,2,4-triazoles 13a-d. Condensation of resins 8a-e (R(2) = H) with 2-bromoacetophenones in the presence of TEA affords thiazoles 15 a-e. All transformations proceeded in high yields and gave products of good purities.

Molecular shape diversity of combinatorial libraries: a prerequisite for broad bioactivity

A computational method to rapidly assess and visualize the diversity in molecular shape associated with a given compound set has been developed. Normalized ratios of principal moments of inertia are plotted into two-dimensional triangular graphs and then used to compare the shape space covered by different compound sets, such as combinatorial libraries of varying size and composition. We have further developed a computational method to analyze interset similarity in terms of shape space coverage, which allows the shape redundancy between the different subsets of a given compound collection to be analyzed in a quantitative way. The shape space coverage has been found to originate mainly from the nature and the 3D-geometry (but not the size) of the central scaffold, while the number and nature of the peripheral substituents and conformational aspects were shown to be of minor importance. Substantial shape space coverage has been correlated with broad biological activity by applying the same shape analysis to collections of known bioactive compounds, such as MDDR and the GOLD-set. The aggregate of our results corroborates the intuitive notion that molecular shape is intimately linked to biological activity and that a high degree of shape (hence scaffold) diversity in screening collections will increase the odds of addressing a broad range of biological targets.

Ammonium hydrogencarbonate, an excellent buffer for the analysis of basic drugs by liquid chromatography-mass spectrometry at high pH

Ammonium hydrogencarbonate buffer has been found to be especially useful for high-pH HPLC analysis of samples from both combinatorial and medicinal chemistry sources. Satisfactory results were obtained by the standard diode array, evaporative light-scattering, and MS detection by using this buffer at a concentration of 10 mM. From a practical standpoint, ammonium hydrogencarbonate is an ideal buffer for chromatographers since it provides excellent chromatographic behaviour and reproducible separation. In addition to this, its volatility makes it an essential tool for rapid LC-MS product identification. Ammonium hydrogencarbonate was tested for a number of drug-like compounds analysed as mixtures, and data obtained were compared to those from the classical and MS-friendly buffers widely used by chromatographers: trifluoroacetic and formic acids. The results of this study revealed the suitability of this buffer for routine HPLC application in research laboratories.

Generation and cycloaddition of polymer-supported azomethine ylide via a 1,2-silatropic shift of alpha-silylimines: traceless synthesis of pyrrolidine derivatives

The 1,3-dipolar cycloaddition of polymer-supported azomethine ylides to dipolarophiles gave pyrrolidine derivatives in good yields. The azomethine ylides were generated from resin-bound alpha-silylimines via a 1,2-silatropic shift. The features of this method are not only a traceless synthesis but also a unique solid-phase route to pyrrolidines with extensive diversity. [reaction: see text]

A multidetachable sulfamate linker successfully used in a solid-Phase strategy to generate libraries of sulfamate and phenol derivatives

The sulfamates and phenols constitute two families of compounds with numerous interesting biological properties. Using the ability of a new multidetachable sulfamate linker to generate these two families of compounds from the same resin, we designed and synthesized libraries of estradiol derivatives, sulfamoylated or not. A C-16beta side chain was then judiciously diversified to target two key steroidogenic enzymes, the steroid sulfates and the type 1 17beta-HSD. Four libraries of sulfamate and phenol derivatives were easily obtained by solid-phase parallel synthesis in good crude overall yields (13-62%) and HPLC purities (85-96%). Such strategy using the new two-in-line sulfamate linker could be also extended to other therapeutic targets than steroidogenic enzymes, thus adding to its potential.

Combinatorial chemistry and high-throughput screening in drug discovery: different strategies and formats

Different strategies for the discovery of novel leads interacting with therapeutically relevant targets are thoroughly presented and discussed, using also three recent examples. Emphasis is given to approaches which do not require extensive resources and budgets, but rather prove how cleverness and creativity can provide active compounds in drug discovery.

Combinatorial synthesis of unsymmetrical secondary amines. Application to arylethanolamines, arylpropanolamines and aryloxypropanolamines

Combinatorial libraries of unsymmetrical secondary amines: arylethanolamine, arylpropanolamines and aryloxypropanolamines [1], in particular have been synthesized by four different routes using styrenes, aldehydes, hydroxyaromatic acids and bromoaliphatic acids. The structurally diverse libraries were generated in parallel format using solid phase methodology. The compounds corresponding to prototype I-IV were obtained in high yields and purities.

New tools and concepts for modern organic synthesis

The increasing need to efficiently assemble small molecules as potential modulators of therapeutic targets that are emerging from genomics and proteomics is driving the development of novel technologies for small-molecule synthesis. Here, we describe some of the general applications and approaches to synthesis using one such technology--solid-supported reagents--that has been shown to significantly improve productivity in the generation of combinatorial libraries and complex target molecules.

Principles of docking: An overview of search algorithms and a guide to scoring functions

The docking field has come of age. The time is ripe to present the principles of docking, reviewing the current state of the field. Two reasons are largely responsible for the maturity of the computational docking area. First, the early optimism that the very presence of the "correct" native conformation within the list of predicted docked conformations signals a near solution to the docking problem, has been replaced by the stark realization of the extreme difficulty of the next scoring/ranking step. Second, in the last couple of years more realistic approaches to handling molecular flexibility in docking schemes have emerged. As in folding, these derive from concepts abstracted from statistical mechanics, namely, populations. Docking and folding are interrelated. From the purely physical standpoint, binding and folding are analogous processes, with similar underlying principles. Computationally, the tools developed for docking will be tremendously useful for folding. For large, multidomain proteins, domain docking is probably the only rational way, mimicking the hierarchical nature of protein folding. The complexity of the problem is huge. Here we divide the computational docking problem into its two separate components. As in folding, solving the docking problem involves efficient search (and matching) algorithms, which cover the relevant conformational space, and selective scoring functions, which are both efficient and effectively discriminate between native and non-native solutions. It is universally recognized that docking of drugs is immensely important. However, protein-protein docking is equally so, relating to recognition, cellular pathways, and macromolecular assemblies. Proteins function when they are bound to other molecules. Consequently, we present the review from both the computational and the biological points of view. Although large, it covers only partially the extensive body of literature, relating to small (drug) and to large protein-protein molecule docking, to rigid and to flexible. Unfortunately, when reviewing these, a major difficulty in assessing the results is the non-uniformity in the formats in which they are presented in the literature. Consequently, we further propose a way to rectify it here.

Single-bead analysis in combinatorial chemistry

Notable limitations have previously prevented the wide application of split synthesis. However, recent developments in highly condensed and miniaturized biological screening and single-bead analysis methods have argued for a revival of split combinatorial synthesis. Although there are still many challenges, we are now in a much better position to accomplish high-throughput analysis and screening of one-bead-one-compound libraries.

Novel chemistry of alpha-tosyloxy ketones: applications to the solution- and solid-phase synthesis of privileged heterocycle and enediyne libraries

New synthetic technologies for the preparation and elaboration of alpha-tosyloxy ketones in solution- and on solid-phase are described. Both olefins and ketones serve as precursors to these relatively stable chemical entities: olefins via a novel one-pot epoxidation, arylsulfonic acid displacement, and oxidation sequence, and ketones by direct exposure to arylsulfonic acids in the presence of diacetoxy iodobenzene. Reaction of these substrates with O-, S-, or N-centered nucleophiles leads to incorporation of the nucleophile with concomitant expulsion of the sulfonate, while exposure to bis-functional nucleophiles furnishes annulated heterocyclic systems. In addition, the reactions of carbon-centered nucleophiles with alpha-tosylyloxy ketones are also explored. The collated data for all these nucleophiles provide compelling evidence for the proposal that different reaction pathways are followed when alpha-tosyloxy ketones are engaged by "hard" versus "soft" nucleophiles. The accessibility and site-selectivity of the chemistry demonstrated herein offer the promise of an expanded use for this moiety in solid-phase library construction, in particular, and in the field of organic synthesis, in general.

Current practices in generation of small molecule new leads

The current drug discovery processes in many pharmaceutical companies require large and growing collections of high quality lead structures for use in high throughput screening assays. Collections of small molecules with diverse structures and "drug-like" properties have, in the past, been acquired by several means: by archive of previous internal lead optimization efforts, by purchase from compound vendors, and by union of separate collections following company mergers. More recently, many drug discovery companies have established dedicated efforts to effect synthesis by internal and/or outsourcing efforts of targeted compound libraries for new lead generation. Although high throughput/combinatorial chemistry is an important component in the process of new lead generation, the selection of library designs for synthesis and the subsequent design of library members has evolved to a new level of challenge and importance. The potential benefits of screening multiple small molecule compound library designs against multiple biological targets offers substantial opportunity to discover new lead structures. Subsequent optimization of such compounds is often accelerated because of the structure-activity relationship (SAR) information encoded in these lead generation libraries. Lead optimization is often facilitated due to the ready applicability of high-throughput chemistry (HTC) methods for follow-up synthesis. Some of the strategies, trends, and critical issues central to the success of lead generation processes are discussed below.

Liquid-phase combinatorial synthesis of aminobenzimidazoles

Liquid-phase synthesis of 2-arylaminobenzimidazoles using soluble polymer support strategy is first described. The key step to benzimidazole skeleton is achieved in the presence of diisopropylcarbodimide (DICDI) and isothiocyanates. A mechanism study for one-pot cyclodesulfurization is also investigated on the support. A wide range of benzimidazole derivatives is synthesized in excellent yield and purity just by simple wash and precipitation.

Soluble polymer-supported synthesis of benzodiazepinones

Soluble polymer-supported synthetic method provides a highly efficient route for the construction of biologically important 1,5-benzodiazepin-2-ones. A library of N-substituted benzodiazepinones can be readily assembled utilizing S(N)Ar reaction, reduction of nitro group and one-pot cyclization following N-alkylation as the key step in the synthesis. All reactions in the sequence were performed at room temperature to facilitate the generation of libraries in a parallel fashion. The crude products were obtained in 80-95% yield with 60-96% HPLC purity.

Color test for the detection of resin-bound aldehyde in solid-phase combinatorial synthesis

We report the development of a sensitive and specific color test for the detection of the presence of resin-bound aldehyde groups using 4-amino-3-hydrazino-5-mercapto-1,2,4-triazole (Purpald). Aldehyde resin turns dark-brown to purple after a 5 min reaction followed by a 10 min air oxidation period. Resins that possess other functional groups (i.e., ketone, ester, amide, alcohol, and carboxylic acid) do not change color under the same conditions. The detection limit is 20 micromol/g for polystyrene-based aldehyde resins.

A combinatorial scaffold approach toward kinase-directed heterocycle libraries

A novel strategy for efficient synthesis of various substituted heterocycles as kinase-directed combinatorial libraries is described. The general scheme involves capture of various dichloroheterocycles onto solid support and further elaborations by aromatic substitution with amines at elevated temperature or by anilines, boronic acids, and phenols via palladium-catalyzed cross-coupling reactions, thus the scaffold itself is transformed into a diversity element within the combinatorial scheme. Libraries consisting of discrete and highly diverse heterocyclic small molecules constructed with these chemistries are currently being evaluated in a variety of cell and protein-based assays.

Toward high-throughput synthesis of complex natural product-like compounds in the genomics and proteomics age

In the age of high-throughput biology, novel genes and proteins are emerging quickly. The need for developing organic synthesis-derived methods that allow rapid access to polyfunctional, complex natural product-like compounds is growing constantly, largely because these small-molecule-based compounds serve as smart, powerful tools both in understanding the roles and functions of emerging biological targets and in validating their biological responses. Developing asymmetric synthesis-derived organic reactions on solid phase allows the synthesis of complex natural product-like compounds in a high-throughput manner. Solid phase organic synthesis is now commonly utilized in the library synthesis of rather simple compounds (i.e., compounds with no multiple stereogenic centers). With few exceptions, the synthesis of complex natural product-like derivatives is still in its infancy. Some recent efforts made in this area indicate opportunities yet to be explored.

Novel strategies for solid-phase construction of small-molecule combinatorial libraries

During the past decade we witnessed a rapid advance in the new field of chemical science, combinatorial chemistry. The pharmaceutical industries invested heavily in accelerating the development of this new technology. As a result, it has become an extremely important tool in lead identification and optimization in current pharmaceutical research. It also quickly crossed the boundaries of the original chemical discipline and demonstrated great potential in many other important areas, such as searching for novel and highly efficient catalysts and superconductive material. Researchers from both academic and industrial laboratories have directed great effort towards the development of novel strategies for combinatorial synthesis.

A one-bead, one-stock solution approach to chemical genetics: part 1

BACKGROUND

In chemical genetics, small molecules instead of genetic mutations are used to modulate the functions of proteins rapidly and conditionally, thereby allowing many biological processes to be explored. This approach requires the identification of compounds that regulate pathways and bind to proteins with high specificity. Structurally complex and diverse small molecules can be prepared using diversity-oriented synthesis, and the split-pool strategy allows their spatial segregation on individual polymer beads, but typically in quantities that limit their usefulness.

RESULTS

We report full details of the first phase of our platform development, including the synthesis of a high-capacity solid-phase bead/linker system, the development of a reliable library encoding strategy, and the design of compound decoding methods both from macrobeads and stock solutions. This phase was validated by the analysis of an enantioselective, diversity-oriented synthesis resulting in an encoded 4320-member library of structurally complex dihydropyrancarboxamides.

CONCLUSIONS

An efficient and accessible approach to split-pool, diversity-oriented synthesis using high-capacity macrobeads as individual microreactors has been developed. Each macrobead contains sufficient compound to generate a stock solution amenable to many biological assays, and reliable library encoding allows for rapid compound structure elucidation post-synthesis. This 'one-bead, one-stock solution' strategy is a central element of a technology platform aimed at advancing chemical genetics.

Combinatorial libraries and biological discovery

Combinatorial chemistry has become a popular tool for the preparation of collections of compounds that can be used to find inhibitors and substrates for different protein targets. It has evolved to provide small molecule libraries, which, with the concomittant use of affinity chromatography, gene expression profiling and complementation, can be used to identify compounds and their protein targets in biological systems, including the neurological system.

Combinatorial synthesis through disulfide exchange: discovery of potent psammaplin A type antibacterial agents active against methicillin-resistant Staphylococcus aureus (MRSA)

Psammaplin A is a symmetrical bromotyrosine-derived disulfide natural product isolated from the Psammaplysilla sponge, which exhibits in vitro antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). Inspired by the structure of this marine natural product, a combinatorial scrambling strategy for the construction of heterodimeric disulfide analogues was developed and applied to the construction of a 3828-membered library starting from 88 homodimeric disulfides. These psammaplin A analogues were screened directly against various gram positive bacterial strains leading to the discovery of a series of potent antibacterial agents active against methicillin-resistant Staphylococcus aureus (MRSA). Among the most active leads derived from these studies are compounds 104, 105, 113, 115, 123, and 128. The present, catalytically-induced, disulfide exchange strategy may be extendable to other types of building blocks bearing thiol groups facilitating the construction of diverse discovery-oriented combinatorial libraries.