Solid-Phase Synthesis and Combinatorial Technologies

8.1 SOLUTIONVERSUS SOLID-PHASE SYNTHETIC LIBRARIES: WHICH ONES TO USE? 343

Figure 8.2 Scaffolds 8.1–8.12 for solution-phase pool library synthesis.

this reason more attention has been payed to the preparation of SP pool libraries to create valuable primary libraries.

Two intriguing, recent reports took advantage of different reaction pathways from mixtures of reagents to generate some predictable pool diversity in solution. Boger et al. (35) validated the synthesis of solution pool libraries of biaryls, obtained through the coupling of equimolar quantities of trisubstituted aryl iodides 8.13a–e to give 2- to 15-member mixtures of biaryls 8.14 in predictable relative abundancies; the HPLC traces of the reaction products confirmed the presence of all the expected compounds in roughly the predicted amounts (Fig. 8.3). Boger et al. recently exploited further this chemistry and prepared a 64,980-member solution-phase pool library containing both

344 SYNTHETIC ORGANIC LIBRARIES: SOLUTION-PHASE LIBRARIES

Figure 8.3 Chemistry assessment for the synthesis of a solution pool library of biaryls: synthesis of 8.14.

biaryls from Pd-catalyzed iodoarene couplings and acetylene-connected biaryls from Stille couplings (36). Klumpp et al. (37) validated the synthesis of pool libraries of 3,3-diaryloxindoles in solution via the condensation of isatins 8.15 with substituted benzenes 8.16 (Fig. 8.4); as an example, the condensation between one equivalent of the isatins 8.15a,b and two equivalents of the aromatics 8.16a–d produced all the 20 expected isomers 8.17 (not including enantiomers) as confirmed by GC-MS. For both approaches additional building blocks would allow the synthesis of larger libraries, and the introduction of modifiable substituents on the aromatic rings would allow further diversification of the libraries. Nevertheless, substantial work has to be done

(enantiomers not included)

a: mixture of 8.15 (1 eq.), mixture of 8.16 (2 eqs.), triflic acid, rt, 12 hrs.

Figure 8.4 Chemistry assessment for the synthesis of a solution pool library of 3,3-diarylox- indoles: synthesis of 8.17.

346 SYNTHETIC ORGANIC LIBRARIES: SOLUTION-PHASE LIBRARIES

8.2 SOLUTION-PHASE DISCRETE LIBRARIES

8.2.1 Design and Synthesis of Solution-Phase Discrete Libraries

Synthesis of solution-phase libraries is similar to the synthesis of single compounds in classical organic chemistry protocols, although the overall throughput is increased by simultaneous handling of multiple solutions that are treated with reagents, worked up, and purified according to a common reaction scheme. The majority of the steps that are relevant to prepare a high-quality SP library (see Chapter 3) are the same as for the preparation of a high-quality solution-phase library and are summarized in Fig. 8.5.

The design of a library that is project dependent and identical for both solution and solid phases, involves the identification of a suitable structural motif together with its randomization points, which are available for generation of diversity (Fig. 8.6, top) and the overall definition of library size. A retrosynthetic study follows in which a reasonable synthetic route in solution is determined, while work on SP requires the choice of a suitable support and of a linker as well (Fig. 8.6, bottom).

The next phase for SP is the validation of the selected route in solution. It is useful to check the outcome of the reaction on several compounds to uncover potential weaknesses. This step is obviously redundant in the solution phase, because it corresponds to the following chemical assessment step, even though the synthesis of a few more fully characterized discretes may be desirable (Fig. 8.7, top). Typically, the assessment of the chemistry in solution takes several weeks to check a few representative monomers with different reactivities in order to discard unsuitable monomer

TARGET LIBRARY DESIGN

RETROSYNTHESIS

SYNTHESIS VALIDATION

CHEMICAL ASSESSMENT

MONOMER SELECTION

AND REHEARSAL

MODEL LIBRARY

SYNTHESIS

LIBRARY SYNTHESIS

Figure 8.5 Logical steps to a successful solution-phase library synthesis.

8.2 SOLUTION-PHASE DISCRETE LIBRARIES 347

SOLUTION-PHASE

Figure 8.6 Design of a synthetic organic library and retrosynthetic studies: solutionversus solid-phase formats.

subclasses, refine the chemical route and experimental conditions leading to highquality final compounds, and select simple handling and purification procedures for intermediates (if and when necessary) and final compounds. The same step on SP (Fig. 8.7, bottom) that has been shown in previous chapters is the most time-consuming and effort-requiring phase. Typically, the transfer and optimization of reaction conditions from solution phase to SP to give a reliable synthetic scheme requires several months to be successfully completed.

The optimized reaction conditions to make the same library in solution or on SP differ significantly in most examples because of the influence exerted by the heterogeneous support (see Chapter 1), which may lead to different purities and yields of the final compounds. When the chemistry assessment, either in solution or on solid phase, does not give satisfactory results after having exploited all the reasonable experimental conditions, the other phase should at least be considered before abandoning the library synthesis.

Potential representative monomers are then selected from commercially available compounds or from internal collections, possibly through the application of computational methods to select only the most significant examples, and the chemistry is rehearsed using these. The process is identical both in SP and in solution, but the support makes monitoring of the reactions, the precise determination of yields and purities of the reaction products, and the structure and the quantity of impurities more difficult and time consuming in the SP (Fig. 8.8). If the proper analytical equipment and expertise for working in SP are not available, the selection or rejection of a monomer candidate may be more difficult, less accurate, or even wrong.

Monomer rehearsal is strongly influenced by the selection of the phase. The higher flexibility in terms of conditions in solution may allow the successful rehearsal of more monomers, whereas the solid support or the linker may interfere with reactive mono-

348 SYNTHETIC ORGANIC LIBRARIES: SOLUTION-PHASE LIBRARIES

-validation of the synthetic route

-synthesis of several discretes

-reaction monitoring (TLC)

-characterization of discretes (yield, purity) in solution

SOLID-PHASE

L

Figure 8.7 Chemical assessment: solutionversus solid-phase formats.

mers and premature cleavage from the resin may sometimes interfere. Reactions with poorly reactive monomers are driven to completion on SP by addition of a large excess of the monomer, and SP site isolation (see Section 1.1.5) may prevent double reactions of bifunctional monomers. The planning of a library synthesis should take into account these issues related to the choice of monomers and should accordingly privilege one of the phases for the synthesis of the library. A large monomer class may be split into subclasses, and two libraries in the two different phases may be designed. An example of this approach could be a subclass of stable, unreactive monomers that must be used in large excess, in which case SP would be preferred, and a subclass of reactive monomers that can be used stoichiometrically, in which case the solution is preferred.

The next step is the synthesis of a model library and the goal of both solid and solution phases is to use the same protocols for the library synthesis as were determined during rehearsal and to check if problems related to parallelization of the synthesis arise. This information is acquired much more easily in solution, and the overall process of solution-phase library synthesis is accelerated. However, a major additional step for the optimization of the synthesis is the testing of the handling and purification procedures in parallel, which must eventually yield a set of high-quality final discretes. This study identifies the essential purification steps, taking into account the planned size of the final library. In general, accurate methods with low throughput are not

8.2 SOLUTION-PHASE DISCRETE LIBRARIES 349

SOLUTION-PHASE

Figure 8.8 Monomer rehearsal: soluitionversus solid-phase fonnats.

suitable for medium to large solution-phase discrete libraries and must be replaced by high-throughput, less accurate but procedurally more simple protocols.

Finally, the library synthesis is performed and both solution-phase and SP synthesis lead to high-quality discrete libraries using the appropriate reaction conditions, monomer sets, and analytical and synthetic instrumentation. It is clear, though, that smallto medium-size libraries in solution require less effort and time for their preparation (providing that the library is not a focused expansion of a primary SP library) and the faster acquisition of information derived from screening them for activity is highly desirable.

Some recent reviews that thoroughly cover solution-phase combinatorial libraries are provided in references 2 and 38–45. Two examples will be described in details in the following sections and only a few recent reports will be cited here. Stewart et al. (46) have reported the preparation of a focused, 48-member phenothiazine amide