DIVERSOMERTM technology: Solid phase synthesis, automation, and integration for the generation of chemical diversity

Development and Commercialization of the MiniBlock Synthesizer Family: A Historical Case Study

An internal development project at Bristol-Myers Squibb (BMS) led to invention of a family of organic chemistry synthesis blocks for both parallel synthesis in drug discovery and parallel reaction optimization in pharmaceutical development. The internal demand for these synthesis blocks became so great that the original development team was challenged by the burden of ongoing manufacture, support, and supply chain management. As a result, BMS entered into a unique industry partnership with Mettler-Toledo AutoChem (MT), Newark, DE, formerly Bohdan Automation, to commercialize the reactor blocks and extend the product family, now known as the MiniBlock line. This manuscript describes the initial development drivers, the overall technical design, and the ultimate successful commercialization of the MiniBlock synthesis family.

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.

Screening for novel antimicrobials from encoded combinatorial libraries by using a two-dimensional agar format

A sensitive lawn-based format has been developed to screen bead-tethered combinatorial chemical libraries for antimicrobial activity. This method has been validated with beads linked to penicillin V via a photocleavable chemical linker in several analyses including a spike-and-recover experiment. The lawn-based screen sensitivity was modified to detect antibacterial compounds of modest potency, and a demonstration experiment with a naive combinatorial library of over 46,000 individual triazines was evaluated for antibacterial activity. Numerous hits were identified, and both active and inactive compounds were resynthesized and confirmed in traditional broth assays. This demonstration experiment suggests that novel antimicrobial compounds can be easily identified from very large combinatorial libraries of small, nonpeptidic compounds.

Development of Weiner et al. force field parameters suitable for conformational studies of [1,4]-benzodiazepines and related compounds

A set of force field parameters capable of reproducing the preferred conformations of the biologically important [1,4]-benzodiazepines was developed for AMBER and other molecular modeling programs that utilize the Weiner et al. force field. Equilibrium parameters were obtained from representative model compounds found in the Cambridge Structural Database, and bond stretching and torsion potential force constants were estimated using AM1 and PM3 semiempirical Hamiltonians. Parameters obtained with the two semiempirical methods and the existing linear interpolation method are compared. Molecular mechanics and dynamic simulations showed that AM1 derived parameters, together with MNDO ESP fitted atomic charges, predicted the X-ray structure of a number of representative [1,4]-benzodiazepines within 0.01 A, 0.8 degree, and 5 degrees, from observed bond lengths, bond angles, and bond torsions, respectively.

Versatile Acylation of N-Nucleophiles Using a New Polymer-Supported 1-Hydroxybenzotriazole Derivative

The synthesis of a new polymer-supported coupling reagent derived from 1-hydroxybenzotriazole is described. An aminomethylated polystyrene was functionalized by reaction with 3-nitro-4-chlorobenzenesulfonyl chloride (2) followed by treatement with hydrazine hydrate, to give the polymeric N-benzyl-1-hydroxybenzotriazole-6-sulfonamide (4).The polymeric reagent 4 was shown to be highly efficient for the synthesis of amides. The efficiency of 4 could be attributed to its high acidity, conferred by the sulfonyl moiety. The procedure for amide synthesis involves the formation of an activated ester on the derivatized polymer followed, in a second step, by treatment with an amine to generate the amide in solution. Simple filtration allows the separation of the product from the polymeric reagent which in this case plays the role of leaving group. An optimization study of this two-step procedure was performed. As amides are obtained in solution free of reaction byproducts, this method can be used in an automated procedure to recover them directly into a 96 well plate, ready to be used in high throughput screening assays. Thus 4 was shown to be particularly suitable for the high throughput parallel synthesis of amides libraries.

Synthesis and screening of an indexed motif-library containing non-proteinogenic amino acids

In an effort to increase the probability of finding novel peptides in resin-bound combinatorial libraries displaying affinity to various macromolecular targets, we increased the diversity of a solid-phase library considerably by synthesizing multiple structures on each bead - a motif-library - including 45 building blocks. The building blocks consist of L-aa, D-aa and eight hydrophobic non-proteinogenic alpha-amino acids. A library with the format O-Z0-1-O-Z0-1-O-XX-resin was synthesized giving the four motifs OOOXX, OZOOXX, OOZOXX, OZOZOXX corresponding to 364.500 different motifs (45(3) x 4 theoretical combinations). The positions O are defined amino acids while Z represents three mixtures pi, omega, phi, where pi is a mixture of polar and charged residues, omega is a mixture of aliphatic residues and phi is a mixture of aromatic residues. X represents a mixture of all 45 residues. The library was screened with the macromolecular target streptavidin which served as a model receptor. Binding peptides were sequenced by microsequencing. We included small amounts of norvaline and norleucine in the library, which served as index residues to be able to distinguish between LD-amino acids and other residues with the same retention time in the HPLC system. Beads that interact with the receptor were found, and the binding motifs that appeared had no homology to known binding motifs found in either L-aa or D-aa libraries, instead motifs with the non-proteinogenic residues L-phenylglycine, O-benzyl-L-hydroxyproline and O-benzyl-L-tyrosine dominated. The novel peptides inhibit binding of biotin to streptavidin but do not bind to avidin, and the affinity is higher than the peptides found in linear all L-aa peptide libraries.

Quantitation of combinatorial libraries of small organic molecules by normal-phase HPLC with evaporative light-scattering detection

The advantages of evaporative light-scattering detection over UV detection for the quantitation of combinatorial libraries composed of small organic compounds by HPLC are described. The detector's response is independent of the sample chromophore, which makes it well-suited to chromatographic analyses of mixtures of dissimilar solutes. Thus, HPLC with evaporative light-scattering detection offers to potential for reducing false positive or false negative results in screening assays, because of its ability to detect the presence of impurities that absorb poorly in the UV (e.g., those impurities originating from the polymeric support). Furthermore, the evaporative light-scattering detector exhibits a nearly equivalent response to compounds of similar structural class. Hence, rapid quantitation of compound libraries may be carried out with the use of a single external standard. For example, the quantitation errors, based on a single external standard, for a series of steroids, hydantoins, and BOC- and Fmoc-protected amino acids by normal-phase HPLC with evaporative light-scattering detection average approximately +/-10%. The application of the evaporative light-scattering detector to the quantitation of low-level sample impurities and the detector's compatibility with gradient elution are also described.

Structurally homogeneous and heterogeneous synthetic combinatorial libraries

We have designed and synthesized structurally homogeneous and heterogeneous nonpeptide libraries. Structurally homogeneous libraries are characterized by the presence of one common structural unit, a scaffold, in all library compounds (e.g. cyclopentane, cyclohexane, diketopiperazine, thiazolidine). In structurally heterogeneous libraries different organic reactions (acylation, etherification, reductive amination, nucleophilic displacement) were applied to connect bifunctional building blocks unrelated in structure (aromatic hydroxy acids, aromatic hydroxy aldehydes, amino alcohols, diamines, and amino acids). The focus of this communication is to document the use of bifunctional building blocks for the design and synthesis of structurally heterogeneous libraries of N-(alkoxy acyl)amino acids, N,N'-bis-(alkoxy acyl)diamino acids, N-acylamino ethers, N-(alkoxy acyl)amino alcohols, N-alkylamino ethers, and N-(alkoxy aryl)diamines.

Bifunctional scaffolds as templates for synthetic combinatorial libraries

A small-molecule synthetic combinatorial library was designed and synthesized that features potential pharmacophores attached to a variety of small cyclic scaffolds. The synthesis of the library involved randomization of three types of building blocks: 20 amino acids, 10 aromatic hydroxy acids and 21 alcohols, totaling a library complexity of 4200 compounds. Mitsunobu polymer-supported etherification was used in the last randomization. The library compounds were attached to beads via an ester-bond linkage enabling both on-bead as well as in-solution screening. When the library was tested against a model target, streptavidin, specific binders were found. The structures of the most active compounds were determined from the fragmentation pattern in MS/MS experiments.

The impact of polystyrene resins in solid-phase organic synthesis

A major objective of the DIVERSOMER technology is to provide pure and characterized compounds for biological testing in order to prevent 'false negatives' in our libraries. On several occasions, analysis of the final products by 1H-NMR and MS, has revealed by-products from the polystyrene solid support. Subsequently, three alternative methods were studied to remove polystyrene by-products; (i) prewashing of the resin prior to execution of the synthesis; (ii) pretreatment of the resin with the cleavage conditions consistent with the solid-phase synthesis reaction scheme; and (iii) parallel purification.

Automated synthesis and combinatorial chemistry

The advent of combinatorial chemistry for the high-throughput synthesis of compounds has driven the advancement of new and emerging technologies for synthetic chemistry laboratories. Automated methods for reaction design, information management, chemical synthesis, compound analysis, and biological testing are necessary to realize the full potential of combinatorial chemistry efforts.

Combinatorial drug discovery: which methods will produce the greatest value?

Combinatorial strategies are important new approaches to drug discovery, and it seems quite likely that they will result in the discovery of interesting potential pharmaceuticals. However, it is less clear whether combinatorial approaches will result in quantum advances in therapeutics. Nor is there general agreement about the factors most important in defining how combinatorial strategies will provide value to the discovery of lead and therapeutic compounds. In this review, we propose criteria that define the value of combinatorial strategies and categorize the various approaches by: (a) the type of chemical space to be searched, (b) the tactics employed to synthesize and screen libraries, and (c) the structures of individual molecules in libraries. We evaluate the strengths and weaknesses of the various strategies and suggest milestones that can help to track their success.