Transformation of low-affinity lead compounds into high-affinity protein capture agents

A simple and potentially general approach to the isolation of high-affinity and -specificity protein binding synthetic molecules is presented. A modest affinity lead compound is appended to the end of each molecule in a combinatorial library of oligomeric compounds, such as peptides or peptoids. The library is then screened under conditions too demanding for the lead to support robust binding to the protein target. It was anticipated that this procedure would select for bivalent ligands in which the oligomer library provides both a second binding element as well as an appropriate linker between this element and the lead compound. We report here synthetic ligands for the Mdm2 protein and ubiquitin able to capture their target proteins from dilute solutions in the presence of a large excess of other proteins.     

Design and synthesis of a tetracyclic pyrimidine-fused benzodiazepine library

Method development for a heterocyclic library which entails novel scaffolds of benzodiazepines fused with various heterocycles, such as pyrimidines, indolines, and tetrahydroquinolines, was accomplished. The new synthetic strategy is based on an electrophilic cyclization reaction involving an iminium intermediate formed by the corresponding aminopyrimidine with a carbonyl compound to give the desired heterocycles in high yields. Subsequent replacement of the chloro group in the resulted structures with a nucleophile, such as boronic acids, amines, alcohols and thiols, led to a library of privileged compounds with up to eight accessible diversity points.     

Synthetic compound libraries displayed on the surface of encoded bacteriophage

We describe a technology for attaching libraries of synthetic compounds to coat proteins of bacteriophage particles such that the identity of the chemical structure is encoded in the genome of the phage, analogous to peptides displayed on phage surfaces by conventional phage-display techniques. This format allows a library of synthetic compounds to be screened very efficiently as a single pool. Encoded phage serve as extremely robust reporters of the presence of each compound, providing exquisite sensitivity for identification of active compounds engaged in complex biological processes such as receptor-mediated endocytosis and transcytosis. To evaluate this approach, we constructed a library of 980 analogs of folic acid displayed on T7 phage, and demonstrated rapid identification of compounds that bind to folate receptor and direct endocytosis of associated phage particles into cells that express the targeted receptor.     

High-resolution analysis of a 144-membered pyrazole library from combinatorial solid phase synthesis by using electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry

A compound library consisting of 144 pyrazole carboxylic acids and six sublibraries consisting of 24 components was analysed using electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). The library was synthesised by the split-mix method and investigated by direct infusion analysis by which 134 compounds were detected. FTICR-MS is predestined for the direct characterisation of complex compound libraries because of its outstanding mass resolution and mass accuracy. However, discrimination within the electrospray ionisation process sometimes leads to signal suppression and thus to misinterpretation of the synthetic results. Using micro-HPLC/MS we were able to assign all 144 compounds including all pairs of isobaric pyrazoles. We also show that, due to partial separation, FTICR-MS is indispensable for proper detection of co-eluting compounds.     

Exploration of structure--activity relationships among foldamer ligands for a specific protein binding site via parallel and split-and-mix library synthesis

We describe the use of parallel and split-and-mix library synthesis strategies for exploration of structure-activity relationships among peptidic foldamer ligands for the BH3-recognition cleft of the anti-apoptotic protein Bcl-xL. This effort began with a chimeric (alpha/beta+alpha)-peptide oligomer (composed of an alpha/beta-peptide segment and an alpha-peptide segment) that we previously identified to bind tightly to the target cleft on Bcl-xL. The side chains that interact with Bcl-xL were varied in a 1000-member one-bead-one-compound library. Fluorescence polarization (FP) screening identified four new analogues with binding affinities similar to that of the lead compound but no analogues with enhanced affinity. These results suggested that significant improvements in affinity were unlikely in this series. We then used library synthesis to examine backbone variations in the C-terminal alpha-peptide segment of the lead compound. These studies provided an opportunity for direct comparison of parallel and split-and-mix synthesis formats for foldamer libraries with respect to synthetic variability and assay sensitivity. We found that compounds from both the parallel and one-bead-one-compound libraries could be reliably screened in a competition FP assay without purification of library members. Our findings should facilitate the use of combinatorial library synthesis for exploration of foldamers as inhibitors of protein-protein interactions.     

Chemoinformatics methods for systematic comparison of molecules from natural and synthetic sources and design of hybrid libraries

Until recently, the field of diversity and library design has more or less ignored natural products as a compound source. This is probably due to at least two reasons. First, combinatorial and reaction-based approaches have been major focal points in the early days of computational library design. In addition, a widespread view is that natural products are often highly complex and not amenable to medicinal chemistry efforts. This contribution introduces recent computational approaches to systematically analyze natural molecules and bridge the gap between natural products and synthetic chemistry programs. Large scale comparisons of natural and synthetic molecules are discussed as well as studies designed to identify `synthetic mimics' of natural products with specific activity. In addition, a concept for the design of natural/synthetic hybrid libraries is introduced. Although research in this area is still in its early stages, an important lesson to be learned from computational analyses is that there is no need to a priori `shy away' from natural products as a source for molecular design.     

Beyond mere diversity: tailoring combinatorial libraries for drug discovery

Combinatorial library design attempts to choose the best set of substituents for a combinatorial synthetic scheme to maximize the chances of finding a useful compound, such as a drug lead. Initial efforts were focused primarily on maximizing diversity, perhaps allowing some bias by the inclusion of a small, fixed set of pharmacophoric substituents. However, many factors besides diversity impact good library design for drug discovery. A library can be better "tailored" by assigning the candidate substituents to categories such as polar, pharmacophoric, rigid, low molecular weight, and expensive. Stratified sampling by successive steps of D-optimal design generates diverse designs which are also consistent with desirable profiles of these properties. Comparing the diversity scores among design profiles reveals the tradeoffs between diversity, physical property distributions, synthetic difficulty, expense, and pharmacophoric bias. The diversity scores can be calibrated by scoring the best designs from subsets of the candidates made either from specific classes of substituents or by randomly eliminating candidates. This procedure shows how poor random designs are compared even to highly biased optimal designs. Library design requires a synergistic effort between computational and synthetic medicinal chemists, so specialized interactive software has been developed to integrate substructure searching, display, and statistical experimental design to facilitate this interaction for the effective design of well-tailored libraries.     

The Symbiotic Relationship Between Drug Discovery and Organic Chemistry

All pharmaceutical products contain organic molecules; the source may be a natural product or a fully synthetic molecule, or a combination of both. Thus, it follows that organic chemistry underpins both existing and upcoming pharmaceutical products. The reverse relationship has also affected organic synthesis, changing its landscape towards increasingly complex targets. This Review article sets out to give a concise appraisal of this symbiotic relationship between organic chemistry and drug discovery, along with a discussion of the design concepts and highlighting key milestones along the journey. In particular, criteria for a high-quality compound library design enabling efficient virtual navigation of chemical space, as well as rise and fall of concepts for its synthetic exploration (such as combinatorial chemistry; diversity-, biology-, lead-, or fragment-oriented syntheses; and DNA-encoded libraries) are critically surveyed.     

A practical microwave method for the synthesis of fluoromethy 4-methylbenzenesulfonate in tert-amyl alcohol

Fluorine substitution is an established tool in medicinal chemistry to favourably alter the molecular properties of a lead compound of interest. However, gaps still exist in the library of synthetic methods for accessing certain fluorine-substituted motifs. One such area is the fluoromethyl group, particularly when required in a fluoroalkylating capacity. The cold fluorination of methylene ditosylate is under evaluated in the literature, often proceeding with low yields or harsh conditions. This report describes a novel microwave method for the rapid nucleophilic fluorination of methylene ditosylate using inexpensive reagents in good isolated yield (65%).     

Analysis and prediction of combinatorial chemistry synthesis and screening data

The goal of combinatorial chemistry is to simultaneously synthesize sets of compounds possessing properties that are then distinguished through screening. As the size of a compound set increases, data analysis becomes more challenging. Analysis of Variance (ANOVA) is an accepted statistical method that offers a straightforward solution to this problem. Two steps encountered by combinatorial scientists appear well suited to ANOVA: the prediction of synthetic outcomes (purity and yield) of set members and the analysis of screening data to identify combinations of reagent inputs that result in molecules with a desired property. To illustrate, a subset of a combinatorial array, referred to as a reaction rehearsal set, is evaluated to create a model predictive of the individual synthetic outcomes of the full matrix. In a second exercise, the biochemical screening data obtained from a combinatorial library is analyzed to identify reagent interactions that result in molecules possessing the sought activity.     

Solution- and solid-phase syntheses of substituted guanidinocarboxylic acids

A library of guanidine-based compounds was produced to mimic the lead compound 1, which is a substance known to have intensely sweet-taste characteristics. Libraries of guanidinocarboxylic acids were therefore prepared via two synthetic methods. The solid-phase method involving trapping of solution-phase carbodiimides by supported amines was used to produce N,N'-dialkyl derivatives (Scheme 1). The second solid-phase method, featuring supported carbodiimides and solution-phase amines (Scheme 2), was devised to prepare N,N'-disubstituted and N,N',N'-trisubstituted guanidinocarboxylic acids. A small collection of guanadinoacetic acid dimers and trimers was also prepared, but this time via a solution-phase coupling of carbodiimides to a polyamine linker.     

Chemical substructure identification by mass spectral library searching

A library-search procedure that identifies structural features of an unknown compound from its electron-ionization mass spectrum is described. Like other methods, this procedure first retrieves library compounds whose spectra are most similar to the spectrum of an unknown compound. It then deduces structural features of the unknown compound from the chemical structures of the retrievals. Unlike other methods, the significance of each retrieved spectrum is weighted according to its similarity to the spectrum of the unknown compound. Also, a “peaks-in-common” screening step serves to reduce search times and an optimized dot product function provides the match factor. If the molecular weight of the unknown compound is provided, the identification of certain substructures can be improved by including “neutral loss” peaks. Correlations between the presence of a substructure in a test compound and its presence among library retrievals were derived from the results of searching the NIST/EPA/NIH reference library with a 7891 compound test set. These correlations allow the estimation of probabilities of substructure occurrence and absence in an unknown compound from the results of a library search. This method may be viewed as an optimization of the “K-nearest neighbor” method of Isenhour and co-workers, with improvements that arise from spectrum screening, peak scaling, an optimal distance measure, a relative-distance weighting scheme, and a larger reference library.     

Naturally occurring scaffolds for compound library design: convenient access to bis-aryl 1-azaadamantanes carrying a vicinal amino alcohol motif

The vast majority of scaffolds found in natural products are absent from the currently available compound collections for biological screening. At the same time, scaffolds derived from natural products may have a distinct advantage over non-natural cores in terms of providing compounds endowed with biological activities and should be used extensively in screening library design. We have developed a synthetic approach to merging a naturally occurring 1-azaadamantane core with a vicinal amino alcohol moiety that is also common in natural product chemical space. The synthesis features diastereoselective epoxidation of racemic chiral 2,6-diaryl-4-methylene 1-azaadamantanes with subsequent S_N2-type epoxide opening in aqueous isopropanol.     

A solid phase approach to PDMP analogs：A general strategy for combinatorial library

The present work reports the first solid phase synthesis of biologically interesting D-threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol(D-threo-PDMP)derivatives.This synthetic strategy includes facile preparation of versatile azido intermediate(5) in a relatively short sequence and the subsequent derivatization of 5,which led to a series of sulfonamide,urea and heterocycle substituted PDMP analogs(10 and 10’).With this method,a 5280-member compound library has been successfully built by IRORI Nanokan? system.     

Affinity screening by packed capillary high-performance liquid chromatography using molecular imprinted sorbents. I. Demonstration of feasibility

Molecular imprint polymers (MIPs) are synthetic polymers capable of selectively binding a template molecule. In this work, the potential utility of MIP-based chromatographic sorbents for affinity screening of structurally similar compounds was investigated as alternatives to in vitro bioassays and biological targets bound to chromatographic supports. A group of structurally similar tricyclic antidepressant drugs and related compounds were used to simulate a combinatorial library. One of the antidepressants, nortriptyline (NOR), was selected as the template species. Using capillary HPLC columns packed with NOR-imprinted MIP particles, the simulated library was screened and the degree of selective interaction of each compound was determined. This correlated with each compound's affinity for the NOR binding site in the polymer. The results of the study revealed that library species which possess the major structural features of the template, specifically the ring structure and pendant secondary amine, were best "recognized" by the MIP, while the most structurally dissimilar compounds exhibited the least selective interaction. An investigation of the retention mechanism on these MIPs provided evidence that hydrogen bonding between the pendant amine group on the antidepressants and a methacrylic acid moiety on the polymer surface was critical in the molecular recognition process.     

Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4

Combinatorial synthesis and large scale screening methods are being used increasingly in drug discovery, particularly for finding novel lead compounds. Although these "random" methods sample larger areas of chemical space than traditional synthetic approaches, only a relatively small percentage of all possible compounds are practically accessible. It is therefore helpful to select regions of chemical space that have greater likelihood of yielding useful leads. When three-dimensional structural data are available for the target molecule this can be achieved by applying structure-based computational design methods to focus the combinatorial library. This is advantageous over the standard usage of computational methods to design a small number of specific novel ligands, because here computation is employed as part of the combinatorial design process and so is required only to determine a propensity for binding of certain chemical moieties in regions of the target molecule. This paper describes the application of the Multiple Copy Simultaneous Search (MCSS) method, an active site mapping and de novo structure-based design tool, to design a focused combinatorial library for the class II MHC protein HLA-DR4. Methods for the synthesizing and screening the computationally designed library are presented; evidence is provided to show that binding was achieved. Although the structure of the protein-ligand complex could not be determined, experimental results including cross-exclusion of a known HLA-DR4 peptide ligand (HA) by a compound from the library. Computational model building suggest that at least one of the ligands designed and identified by the methods described binds in a mode similar to that of native peptides.     

Encoding method for OBOC small molecule libraries using a biphasic approach for ladder-synthesis of coding tags

In the "one-bead one-compound" (OBOC) combinatorial library method, each compound bead displays only one compound entity. Hundreds of thousands to millions of compound beads can be synthesized rapidly and screened simultaneously. Positive compound beads are then isolated for structural analysis. To fully exploit the power of OBOC combinatorial small molecule libraries, a robust and high throughput encoding method is needed to decode the positive compound beads. In this paper, we report on the development of a novel encoding strategy that combines the concepts of ladder-synthesis and chemical encoding on bilayer beads. In these encoded libraries, small molecule compounds are displayed on the bead surface, and cleavable coding tags consisting of a series of truncated molecules reside in the bead interior. Such a library can be easily constructed using the biphasic approach (J. Am. Chem. Soc.2002, 124, 7678) to topologically segregate the functionalities of the beads during library synthesis. The ladder members and coding tags are then released for MALDI-TOF-MS analysis. To simplify the interpretation of the mass spectra, we purposely add bromine into the cleavable linker so that the cleavage products generate a characteristic isotope fingerprint. The chemical structure of library compounds can be determined by analyzing the mass differences between adjacent peaks on the mass spectra. This encoding strategy also provides valuable information on the quality of the testing compound on the surface of the bead. To validate this methodology, a model OBOC small molecule library with 12,288 members was synthesized on TentaGel beads and screened against streptavidin. The chemical structures of the compound on each positive bead were unambiguously identified.     

Synthesis of serine-based glycolipids as potential TLR4 activators

A new series of monosaccharide-based glycolipids devoid of phosphate groups and with two lipid chains were rationally designed by varying the lipid chain lengths and saccharide structure of a α-GalCer-derived lead compound (CCL-34) that is a potent TLR4 agonist. The NF-κB activity of a 60-membered galactosyl serine-based synthetic library containing compounds with various lipid chain lengths was measured in a HEK293 cell line that stably expressed human TLR4, MD2, and CD14 (293-hTLR4/MD2-CD14). The results showed that the optimal carbon chain lengths for the lipid amine and fatty acid to activate TLR4 were 10-11 and 12, respectively. Evaluation of a 20-membered synthetic glycosyl serine-based lipid library containing compounds with various saccharide moieties and fixed lipid chain lengths revealed that the galactose moiety in CCL-34 could be replaced by glucose without loss of activity (CCL-34-S3 and CCL-34-S16). Changing the orientation of the anomeric glycosidic bond of CCL-34 resulted in a complete loss of activity (β-CCL34). Surprisingly, a change in configuration of the anomeric glycosidic bond in a glucosyl glycolipid is tolerable (CCL-34-S14). Another noteworthy observation is that the activity of a l-fucosyl derived glycolipid (CCL-34-S13) was comparable to that of CCL-34. In sum, this study determines the structural features that are crucial for an optimal TLR4-stimulating activity. It also provides several molecules with immunostimulating potential.     

Identification of novel thiourea-stilbene-triazine conjugates as persuasive lymphoid tyrosine phosphatase inhibitors

A library of novel thiourea-based symmetrical stilbene-triazines ( 5a-i ) was synthesized in an effort to develop new protein tyrosine phosphatase LYP inhibitors. The versatile nature of 2,4,6-trichloro-1,3,5-triazine allows considerable scope for derivatization and hence exploration of structure activity relationships. A convenient and versatile three-step synthetic approach involved the successive replacement of the two chloro groups of 2,4,6-trichloro-1,3,5-triazine by a variety of substituents for structural modification. The newly synthesized derivatives were subjected to tyrosine phosphatase LYP inhibition studies. The results for the in vitro bioassays were promising with the identification of compound 5k and 5l having a 4-methyl and 4-methoxy substituent on phenyl ring, as the lead and selective candidate for LYP inhibition with an IC₅₀ value of 2.1 ± 0.05 μM and 28 ± 3.3 μM, respectively. Moreover, docking studies were carried out to determine the possible interaction sites of thiourea-based stilbene-triazine compounds with Lymphoid Tyrosine Phosphatase. Results of docking computations further ascertained the inhibitory potential of compound 5k and 5l . The results indicated that the compound 5k may serve as a structural model for the design of most potent LYP inhibitors.