Chemical Library Purification Strategies Based on Principles of Complementary Molecular Reactivity and Molecular Recognition

ROMP-generated oligomeric sulfonyl chlorides as versatile soluble scavenging agents

[reaction: see text] A new method for homogeneous nucleophilic scavenging employing oligomeric sulfonyl chloride (OSC) reagents is described. The method utilizes OSC to rapidly scavenge a variety of amines that are present in excess. The OSC reagents are generated from ROM polymerization of 2-chlorosulfonyl-5-norbornene utilizing the second generation Grubbs catalyst to produce oligomers of varying size as stable, free-flowing powders. Following the scavenging event, these oligomers are precipitated with ethyl acetate leaving products in excellent yield and purity.

A tandem three-phase reaction for preparing secondary amines with minimal side products

[reaction: see text] A new method for the preparation of secondary amines has been reported. Complementary solution-phase and solid-phase synthesis highlight the process. Amines are obtained in good yields free from the usual byproducts of reductive amination. Secondary amines are unreactive, so overalkylation does not occur. The procedure can be used interchangeably for traditional or parallel synthesis settings.

Realities of high-throughput liquid chromatography/mass spectrometry purification of large combinatorial libraries: a report on overall sample throughput using parallel purification

We report on the development of a validated, streamlined high-throughput process for the purification of parallel-synthesis-derived combinatorial libraries. The steps involved in this library purification process include dissolution of dry films of crude synthetic material, dual-column LC/MS purification, dual-column postpurification analysis, quantitation, reformatting, and submission of pure compounds for registration. Although the purification and postpurification analysis times decreased essentially linearly as a function of the number of HPLC columns employed, it was not possible to decrease the total purification process time linearly as a function of the number of columns employed in the system. This was due primarily to the fact that numerous steps in the total purification process are independent of sample analysis and purification (e.g., evaporation, reconstitution, and reformatting, etc.). Additionally, experiments were also performed to assess whether separate gradient pumps were necessary for each channel of this two-channel LC/MS or if acceptable results could be reliably obtained by splitting the flow from one set of gradient pumps between two HPLC columns. On the basis of the parallel, two-column LC/MS system employed in this work, throughput estimates were extrapolated to more massively parallel systems (e.g., four-channel LC/MS).

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.

Solution-phase parallel synthesis of substituted benzimidazoles

A solution-phase parallel synthesis of o-phenylenediamines is described. These intermediates were then subsequently converted to benzimidazole scaffolds (three-point diversity) in excellent purities and yields. High-throughput purification of this multistep synthetic sequence was accomplished using polymer-bound scavengers and reagents and liquid-liquid extraction protocols.

High-throughput mass-directed parallel purification incorporating a multiplexed single quadrupole mass spectrometer

We report on the development of a parallel HPLC/MS purification system incorporating an indexed (i.e., multiplexed) ion source. In the method described, each of the flow streams from a parallel array of HPLC columns is directed toward the multiplexed (MUX) ion source and sampled in a time-dependent, parallel manner. A visual basic application has been developed and monitors in real-time the extracted ion current from each sprayer channel. Mass-directed fraction collection is initiated into a parallel array of fraction collectors specific for each of the spray channels. In the first embodiment of this technique, we report on a four-column semipreparative parallel LC/MS system incorporating MUX detection. In this parallel LC/MS application (in which sample loads between 1 and 10 mg on-column are typically made), no cross talk was observed. Ion signals from each of the channels were found reproducible over 192 injections, with interchannel signal variations between 11 and 17%. The visual basic fraction collection application permits preset individual start collection and end collection thresholds for each channel, thereby compensating for the slight variation in signal between sprayers. By incorporating postfraction collector UV detection, we have been able to optimize the valve-triggering delay time with precut transfer tubing between the mass spectrometer and fraction collectors and achieve recoveries greater than 80%. Examples of the MUX-guided, mass-directed fraction purification of both standards and real library reaction mixtures are presented within.

Scavenge-ROMP-filter: a facile strategy for soluble scavenging via norbornenyl tagging of electrophilic Reagents

[reaction: see text] A new "chemical tagging" method for homogeneous electrophilic scavenging is described. The method utilizes 5-norbornene-2-methanol to scavenge/tag a variety of electrophiles that are present in excess. Once tagging is complete, the crude reaction mixture is subjected to a rapid ROM polymerization event utilizing the second generation Grubbs catalyst. This process yields a polymer that can be precipitated with methanol or ether/hexane, leaving products in excellent yield and purity.

Solid-supported reagents for multi-step organic synthesis: preparation and application

Since the early days of combinatorial chemistry solid-phase organic synthesis has been the method of choice for the production of large libraries. Solution-phase synthesis is again gaining importance especially for the synthesis of parallel arrays of smaller, focussed libraries containing single compounds with high degrees of purity. In the field of solution-phase library generation, the use of solid-supported reagents, catalysts and scavengers is emerging as a leading strategy, combining the advantages of both solid-phase organic synthesis (e.g. allowing the employment of an excess of reagent without the need for additional purification steps) and solution-phase chemistry (e.g. the ease of monitoring the progress of the reactions by applying LC-MS, TLC or standard NMR techniques). An account of some of the most recent advances in this area of research will be presented.

Capture-ROMP-release: application for the synthesis of O-alkylhydroxylamines

[reaction: see text] A new capture-ROMP-release method for chromatography-free purification of N-hydroxysuccinimde Mitsunobu reactions is described. The Mitsunobu reaction captures a variety of alcohols onto a norbornenyl N-hydroxysuccinimide monomer. Subjection of the resulting crude reaction mixture to ROM-polymerization generates a polymer that can be precipitated with methanol and filtered from the Mitsunobu byproducts. Treatment of the polymer with hydrazine releases the substrate from the water-soluble polymer, producing a variety of O-alkylhydroxylamines with good purity.

Polymer-supported O-methylisourea: a new reagent for the O-methylation of carboxylic acids

[reaction: see text] A solid-supported O-methylisourea reagent has been prepared in one step starting from commercially available solid-supported carbodiimide. The isourea reagent has been successfully used for the preparation of methyl esters from the corresponding carboxylic acids. The crude products obtained after resin filtration and solvent evaporation are generally obtained in >98% purity.

Controlling chemoselectivity in vinyl and allylic C-X bond activation with palladium catalysis: a pK(a)-based electronic switch

It has been demonstrated that the same Pd catalyst can be used to effect allylic substitution or vinylic cross-coupling reactions selectively and interchangeably on polyfunctionalized olefin building blocks despite the differences in reaction mechanism. This was achieved by altering the pK(a) of the conjugate acid of the allylic leaving group while keeping the vinyl coupling partner constant. In the case of 2,3-dibromo-1-propene, Pd-catalyzed allylic ionization with malonate nucleophile proceeded selectively and quantitatively in the presence of the Suzuki reaction components necessary for cross-coupling. Conversely, the bromide of 2-bromo-1-(4-ethylphenoxy)-2-propene could be cross-coupled selectively without activation of the allylic phenoxy substituent. In both reactions, the same catalyst could then be used to complete the sequence, which typically involved heating as the trigger to promote the second, more reluctant reaction. Mechanistic considerations as well as synthetic applications demonstrating the value of this interchangeable catalyzed sequence are presented.

Design, synthesis, and biological evaluation of a library of 1-(2-thiazolyl)-5-(trifluoromethyl)pyrazole-4-carboxamides

A library of 422 1-(2-thiazolyl)-5-(trifluoromethyl)pyrazole-4-carboxamides was prepared in five steps using solution-phase chemistry. The first step in the synthesis was the reaction of ethyl 2-ethoxymethylene-3-oxo-4,4,4-trifluorobutanoate with thiosemicarbazide, which is reported in the literature to afford a 1:1 mixture of ethyl 1-thiocarbamoyl-5-(trifluoromethyl)pyrazole-4-carboxylate and ethyl 1-thiocarbamoyl-3-(trifluoromethyl)pyrazole-4-carboxylate. We reassigned the structure of the product to be a single compound, ethyl 5-hydroxy-1-thiocarbamoyl-5-(trifluoromethyl)-4,5-dihydro-1H-pyrazole-4-carboxylate. This common intermediate was diversified by reaction with 17 alpha-bromoketones affording, in two steps, 17 1-(2-thiazolyl)-5-(trifluoromethyl)pyrazole-4-carboxylic acids. Scavenger resins were used to facilitate formation and purification of up to 27 amides from each of these acids in the last step. In addition, the Curtius reaction was applied to 12 of the acids followed by quenching with alcohols to afford a 108-member carbamate library. Certain compounds in the two libraries were toxic to C. elegans.

Work-up strategies for high-throughput solution synthesis

The key bottleneck in parallel synthesis has, in truth, always been the isolation and purification of the reaction products, rather than carrying out the reactions themselves. Solution-phase chemistry for parallel synthesis has recently been re-emphasized and has stimulated the development of a wide-range of practical tools for efficient high-throughput work-up, which are gaining increasing acceptance in medicinal chemistry groups.

Solution-phase synthesis of an aminomethyl-substituted biaryl library via sequential amine N-alkylation and Suzuki cross-coupling

Described herein is the semiautomated preparation of a 20-member aminomethyl-substituted biaryl library. The two-step solution-phase synthesis was achieved via sequential N-alkylation of various amines with either 3- or 4-bromobenzyl bromide and Suzuki cross-coupling of the resultant aryl bromides with various boronic acids.

Identification of potent non-peptide somatostatin antagonists with sst(3) selectivity

Using a solution-phase parallel synthesis strategy, a series of non-peptide somatostatin analogues were prepared, and their binding affinities to the five human somatostatin receptor subtypes (sst(1-5)) were determined. Imidazolyl derivatives 2 were found to bind with moderate affinity but with high selectivity to the sst(3) receptor subtype. Further modifications of these structures led to a more potent class of ligands, the tetrahydro-beta-carboline derivatives 4. Among these, compounds 4k (BN81644) and 4n (BN81674) bind selectively and with high affinity to the sst(3) receptor subtype (K(i) = 0.64 and 0.92 nM, respectively). Furthermore, 4k and 4n reverse the inhibition of cyclic AMP accumulation induced by 1 nM somatostatin via sst(3) receptors, with IC(50) = 2.7 and 0.84 nM, respectively. The most potent compound 4n was shown to be a competitive antagonist of human sst(3) receptors by increasing the EC(50) of SRIF-14-mediated inhibition of cAMP accumulation with a K(B) of 2.8 nM (where K(B) is the concentration of antagonist that shifts the agonist dose-response 2-fold). These new derivatives are, to our knowledge, the first potent and highly selective non-peptide human sst(3) antagonists known and, as such, are useful tools for investigating the physiological role of sst(3) receptors.

Structure-based design and in-parallel synthesis of inhibitors of AmpC beta-lactamase

BACKGROUND

Group I beta-lactamases are a major cause of antibiotic resistance to beta-lactams such as penicillins and cephalosporins. These enzymes are only modestly affected by classic beta-lactam-based inhibitors, such as clavulanic acid. Conversely, small arylboronic acids inhibit these enzymes at sub-micromolar concentrations. Structural studies suggest these inhibitors bind to a well-defined cleft in the group I beta-lactamase AmpC; this cleft binds the ubiquitous R1 side chain of beta-lactams. Intriguingly, much of this cleft is left unoccupied by the small arylboronic acids.

RESULTS

To investigate if larger boronic acids might take advantage of this cleft, structure-guided in-parallel synthesis was used to explore new inhibitors of AmpC. Twenty-eight derivatives of the lead compound, 3-aminophenylboronic acid, led to an inhibitor with 80-fold better binding (2; K(i) 83 nM). Molecular docking suggested orientations for this compound in the R1 cleft. Based on the docking results, 12 derivatives of 2 were synthesized, leading to inhibitors with K(i) values of 60 nM and with improved solubility. Several of these inhibitors reversed the resistance of nosocomial Gram-positive bacteria, though they showed little activity against Gram-negative bacteria. The X-ray crystal structure of compound 2 in complex with AmpC was subsequently determined to 2.1 A resolution. The placement of the proximal two-thirds of the inhibitor in the experimental structure corresponds with the docked structure, but a bond rotation leads to a distinctly different placement of the distal part of the inhibitor. In the experimental structure, the inhibitor interacts with conserved residues in the R1 cleft whose role in recognition has not been previously explored.

CONCLUSIONS

Combining structure-based design with in-parallel synthesis allowed for the rapid exploration of inhibitor functionality in the R1 cleft of AmpC. The resulting inhibitors differ considerably from beta-lactams but nevertheless inhibit the enzyme well. The crystal structure of 2 (K(i) 83 nM) in complex with AmpC may guide exploration of a highly conserved, largely unexplored cleft, providing a template for further design against AmpC beta-lactamase.

Grafted macroporous polymer monolithic disks: a new format of scavengers for solution-phase combinatorial chemistry

Polyethylene encased porous poly(chloromethylstyrene-co-divinylbenzene) disks have been prepared by polymerization in a cylindrical glass mold and cut to a disk format. Following attachment of a free radical azo initiator 4,4'-azobis(4-cyanovaleric acid) to available functionalities at the surface of the pores, the polymerization of 2-vinyl-4,4-dimethylazlactone was initiated from the surface. To avoid an undesirable increase in flow resistance and to improve the yield of grafting, divinylbenzene was added to the polymerization mixture in order to form a layer of swellable reactive polymer gel within the pores. The use of these disks as scavenging filters to remove various amines from solutions in flow-through operations was demonstrated by effective removal of amines in a very short period of time from their solutions in a variety of solvents, even including alcohols and water.

Solution phase synthesis of libraries of variably substituted olefin scaffolds: a library of allylic amines

The synthesis of allylic amine libraries derived from olefin templates is described. The two-step, solution phase reaction sequence consists of amination of the template followed by Suzuki coupling and expedited purification via ion exchange chromatography. The methodology has been used to synthesize a 1344-member allylic amine library.

Column asymmetric catalysis for beta-lactam synthesis

[structure] A catalytic asymmetric reaction process was designed involving the use of solid-phase reagents and catalysts that constitute the packing of a series of "reaction columns". This process was applied to the catalytic asymmetric synthesis of beta-lactams, yielding pure product after crystallization with exceptional enantio- and diastereoselectivity.

ROMPGEL scavengers: a high-loading supported anhydride for sequestering amines and hydrazines

[reaction: see text]A versatile method for sequestering excess amines and hydrazines is reported using a high-loading ROMPGEL anhydride polymer.

3,5-Bis(trifluoromethyl)pyrazoles: a novel class of NFAT transcription factor regulator

A series of bis(trifluoromethyl)pyrazoles (BTPs) has been found to be a novel inhibitor of cytokine production. Identified initially as inhibitors of IL-2 synthesis, the BTPs have been optimized in this regard and even inhibit IL-2 production with a 10-fold enhancement over cyclosporine in an ex vivo assay. Additionally, the BTPs show inhibition of IL-4, IL-5, IL-8, and eotaxin production. Unlike the IL-2 inhibitors, cyclosporine and FK506, the BTPs do not directly inhibit the dephosphorylation of NFAT by calcineurin.

Solid-phase extraction for combinatorial libraries

Solid-phase extraction (SPE) has during the last three years emerged as a convenient method for the purification of compound libraries prepared by solution synthesis. The widespread use of SPE in combinatorial chemistry can be explained by straightforward SPE method development facilitated by the availability of numerous commercial SPE resins. High-speed automated SPE is readily accomplished by taking advantage of commercial laboratory robot systems. The present review summarizes and discusses advancements made in the use of different SPE resins and molecule tagging techniques for optimization of ion-exchange, reversed-phase, normal-phase and fluorous-phase SPE in combinatorial chemistry.

Euclidean shape-encoded combinatorial chemical libraries

A method for the encoding of split/mix combinatorial chemical libraries based on Euclidean shapes is described. The shapes are fashioned from a polymeric matrix designed to swell in common organic solvents while retaining their unique forms, and exhibit good mechanical strength. The lightly crosslinked gel-type polymer was processed into an array of Euclidean forms that serve as encoding elements in the synthesis of combinatorial chemical libraries by using the split/pool methodology. To assess the viability of this approach, a library of compounds based on a urea scaffold was prepared. The validity of this methodology was demonstrated through correct deconvolution of the library mixture by shape discrimination. Furthermore, because the shapes used have a large surface area to volume ratio, each monolith can act as an independent chemical reactor. This simplifies the analytical identification process because each compound can be prepared in significant quantities and isolated as single entities. Given the high loading capacity of the monoliths and the conceptually simple encoding strategy, it is envisioned that these Euclidean forms will find significant application in combinatorial and high-throughput synthetic chemistry.

Polyaromatic Scavenger Reagents (PAHSR): A New Methodology for Rapid Purification in Solution-Phase Combinatorial Synthesis

A new method of purification of solution-phase combinatorial libraries has been developed. Development of a chemically inert polyaromatic anchor with a reactive "scavenger reagent" (PAHSR) allows unreacted reagents and impurities to be removed from a reaction by absorption of the PAHSR to charcoal and simple filtration.

Are porphyrin mixtures favorable photodynamic anticancer drugs? A model study with combinatorial libraries of tetraphenylporphyrins

Reported here is the preparation of tetraphenylporphyrin libraries via efficient combinatorial solution-phase syntheses, their purification, and preliminary results from a bioorganic study on their uptake in liposome membranes. Libraries with up to 666 components were prepared with substituents including Br, CF3, Cl, CN, CO2Me, Et, F, OAc, and Ph. Further, a first example for the synthesis of more diverse libraries via a "latent libraries" approach is presented. This involves masking polar groups with lipophilic protecting groups. After purification of the latent library, the masking protecting groups are removed in a quantitative reaction that produces the library compounds as the only non-volatile components. Libraries were characterized by laser desorption time-of-flight mass spectrometry, NMR, and UV-vis spectroscopy. In vitro uptake into membranes of small sonicated liposomes was measured, both in terms of total porphyrin incorporation and in terms of structure-incorporation relationships. The latter were determined from isotopically-resolved laser-desorption mass spectra under conditions that yield quantitative results. Smaller libraries showed increased uptake of porphyrins bearing OH and CF3 substituents and lower uptake of ester-, alkyl-, and halide-bearing porphyrins. This structure-dependent selectivity disappears for larger libraries, however, where uniformly high uptake is observed, i.e., at a constant lipid:porphyrin ratio the total porphyrin incorporation is higher for libraries than for single compounds of similar polarity. We propose that the decreased concentration of individual compounds in large libraries is responsible for this effect. Membrane incorporation has previously been shown to correlate with photodynamic activity in vitro and in vivo.16 Therefore, these results may help to explain why photodynamic therapy of tumors, a modern anti-cancer treatment modality, is successfully performed with a complex mixture of porphyrins.

Combinatorial chemistry as a tool for drug discovery

The question 'will combinatorial chemistry deliver real medicines' has been posed [96]. First it is important to realise that the chemical part of the drug discovery process cannot stand alone; the integration of synthesis and biological assays is fundamental to the combinatorial approach. The results presented in Tables 3.1 to 3.8 suggest that so far smaller directed combinatorial libraries have obtained equivalent results to those obtained previously from traditional medicinal chemistry analogue programs. Unfortunately, because of the long time it takes to develop pharmaceutical drugs there are no examples yet of marketed drugs discovered by combinatorial methods. There are interesting examples where active leads have been discovered from the screening of the same library against multiple targets (e.g. libraries 13, 39, 43, 66, 71 and 76). It is now possible to handle much larger libraries of non-oligomeric structures and the chemistry required for such applications is becoming available. Whether combinatorial approaches can also be adapted to deal with all the other requirements of a successful pharmaceutical (lack of toxicity, bioavailability etc.) is open to question but there are already examples such as cassette dosing [235-237]. However we can still be optimistic about the possibility of larger libraries producing avenues of investigation for the medicinal chemist to develop into real drugs. Combinatorial chemistry is an important tool for the medicinal chemist.

Polymer-assisted solution-phase (PASP) library synthesis of alpha-ketoamides

A parallel solution-phase library synthesis of alpha-ketoamides is described. The two-step library synthesis is accomplished using polymer-assisted solution-phase (PASP) synthesis techniques. This high-yielding, multi-step sequence utilizes sequestering resins for the removal of reactants, reactant by-products, and tagged reagents. The first step of the library synthesis utilizes PASP resins to mediate the amide coupling of an alpha-hydroxy acid with an amine. The second step uses PASP resins for the periodinane oxidation of the alpha-hydroxy acid to an alpha-ketoamide leaving highly pure products after simple filtration and evaporation.

"Reactive filtration": use of functionalized porous polymer monoliths as scavengers in solution-phase synthesis

[reaction: see text] Solid functionalized porous monolithic disks with reactive polymer chains grafted to their inner pore surface have been developed for scavenging excess reagents from reaction mixtures. A poly(chloromethylstyrene-co-divinylbenzene) monolith was cut into disks and activated by graft polymerizing 4-vinyl-2,2-dimethylazlactone to its pore surface. In contrast to the direct copolymerization of reactive monomers, grafting increases the accessibility of the reactive groups. Application of the reactive disks is demonstrated in the scavenging of excess amines from reaction mixtures in different solvents.

Preparation of trifluoromethylpyridine libraries

S-Alkylation followed by heterocyclization of trifluoromethyl-3-cyano-2(1H)-pyridinethiones was used for preparation of libraries of S-alkyl trifluoromethylpyridines and thieno[2,3-b]pyridines. The S-alkylation (in water--DMF mixtures) was successful for all 18 alkylating agents employed (yields typically > 50%). S-Alkyl derivatives were further converted to corresponding thieno[2,3-b]pyridines via heterocyclization in base conditions (yields > 65%). Structures of new compounds were elucidated by a combination of IR and 1H NMR spectroscopy and elemental analysis and were confirmed by means of single-crystal X-ray diffraction analysis.