Stereochemical and skeletal diversity employing pipecolate ester scaffolds

[structure: see text] The stereocontrolled synthesis of pyridooxazinones by Mg(OTf)2-promoted epoxide ring-opening with use of chiral pipecolates as nucleophiles is described. Pyridooxazinone products derived from azido-epoxides can be further rearranged to seven-membered pyridodiazepinones by azide reduction. The sequence of functional group interconversions generates diversity through topological and stereochemical variation.     

The immune diversity in a test tube--non-immunised antibody libraries and functional variability in defined protein scaffolds

Technologies to develop and evolve the function of proteins and, in particular, antibodies have developed rapidly since the introduction of phage display. Importantly, it has become possible to identify molecules with binding properties that cannot be found by other means. A range of different approaches to create general libraries that are useful for the selection of such molecules specific for essentially any kind of target have emerged. We herein review some of the most prominent approaches in the field and in particular discuss specific features related to the development of antibody libraries based on single antibody framework scaffolds. This approach not only permits identification of a range of specific binders, but also facilitates further evolution of initially derived molecules into molecules with optimised functions.     

Combinatorial libraries of bis-heterocyclic compounds with skeletal diversity

Combinatorial solid-phase synthesis of bis-heterocyclic compounds, characterized by the presence of two heterocyclic cores connected by a spacer of variable length/structure, provided structurally heterogeneous libraries with skeletal diversity. Both heterocyclic rings were assembled on resin in a combinatorial fashion.     

Fluorous mixture synthesis of two libraries with hydantoin-, and benzodiazepinedione-fused heterocyclic scaffolds

Diversity-oriented synthesis (DOS) and fluorous mixture synthesis (FMS) are two aspects of combinatorial chemistry. DOS generates library scaffolds with skeletal, substitution, and stereochemistry variations, whereas FMS is a highly efficient tool for library production. The combination of these two aspects in solution-phase synthesis of two novel heterocyclic compound libraries is presented in this paper. Mixtures of different fluorous amino acids undergo [3 + 2] cycloadditions followed by postcondensation reactions. The mixtures are then demixed by fluorous HPLC. Fluorous tags are removed by cyclization to afford hydantoin- and benzodiazepinedione-fused heterocyclic compounds as individual, pure, and structurally defined molecules. The application of MS-directed HPLC purification and parallel four-channel LC/MS analysis further increases the efficiency of FMS.     

Highly ordered structures of peptides by using molecular scaffolds

Protein secondary structures such as alpha-helices, beta-sheets, and beta-turns are important in inducing the three-dimensional structure and biological activity of proteins. Designing secondary structure mimics composed of short peptides has attracted much attention not only to gain fundamental insight into the factors affecting protein folding but also to develop pharmacologically useful compounds, artificial receptors, asymmetric catalysts, and new materials. In this tutorial review, we focus on molecular scaffolds employed to induce beta-sheet-like structure in attached peptide chains, thereby creating highly ordered molecular structures, and discuss the versatility of these molecular scaffolds to regulate the attached peptide strands in the appropriate dimensions.     

Skeletal diversity by sequential one-pot and stepwise routes using morpholine ester scaffolds

A skeletal diversity approach starting from morpholine acetals has been achieved by tuning a three-step process from stepwise to sequential one-pot to provide diverse scaffolds containing either a 2-oxopiperazine or a diketopiperazine skeleton.     

Scaffold architecture and pharmacophoric properties of natural products and trade drugs: application in the design of natural product-based combinatorial libraries

Natural products were analyzed to determine whether they contain appealing novel scaffold architectures for potential use in combinatorial chemistry. Ring systems were extracted and clustered on the basis of structural similarity. Several such potential scaffolds for combinatorial chemistry were identified that are not present in current trade drugs. For one of these scaffolds a virtual combinatorial library was generated. Pharmacophoric properties of natural products, trade drugs, and the virtual combinatorial library were assessed using a self-organizing map. Obviously, current trade drugs and natural products have several topological pharmacophore patterns in common. These features can be systematically explored with selected combinatorial libraries based on a combination of natural product-derived and synthetic molecular building blocks.     

Informational complexity and functional activity of RNA structures

Very little is known about the distribution of functional DNA, RNA, and protein molecules in sequence space. The question of how the number and complexity of distinct solutions to a particular biochemical problem varies with activity is an important aspect of this general problem. Here we present a comparison of the structures and activities of eleven distinct GTP-binding RNAs (aptamers). By experimentally measuring the amount of information required to specify each optimal binding structure, we show that defining a structure capable of 10-fold tighter binding requires approximately 10 additional bits of information. This increase in information content is equivalent to specifying the identity of five additional nucleotide positions and corresponds to an approximately 1000-fold decrease in abundance in a sample of random sequences. We observe a similar relationship between structural complexity and activity in a comparison of two catalytic RNAs (ribozyme ligases), raising the possibility of a general relationship between the complexity of RNA structures and their functional activity. Describing how information varies with activity in other heteropolymers, both biological and synthetic, may lead to an objective means of comparing their functional properties. This approach could be useful in predicting the functional utility of novel heteropolymers.     

Dimolybdenum-containing molecular triangles and squares with diamidate linkers: structural diversity and complexity

By employing cis-Mo2(DAniF)2(2+) (DAniF = N,N'-di(p-anisyl)formamidinate) as the vertex building block and terephthaloyldiamidate as the linker, four dimolybdenum-containing cyclic oligomers have been synthesized and structurally characterized. In these compounds, described by the general formula [cis-Mo2(DAniF)2((ArNOC)2C6H4)2]n, n = 3 and 4, the geometry and composition of the products are affected by the identity of the aromatic groups of the linker. When Ar = phenyl, n = 3 (1a and 1b); however, n = 4 for Ar = p-trifluoromethylphenyl (2) and when Ar = m-trifluoromethylphenyl (3). All these compounds have a central cavity, shaped by the diamidate linker, that is capable of serving as host to guest molecules in a selective manner. For compounds 2 and 3, self-assembly that takes place in the crystalline state entails intermolecular C-H...F-C interactions. Such interactions generate a one-dimensional network with a tunnel cross section of 10 x 10 A(2) in 2, whereas in 3, they result in a cage in which two THF molecules are encapsulated. The F...H distances vary in a broad range from 2.38 to 2.70 A.     

Generation of submicrometer structures by photolithography using arrays of spherical microlenses

This paper describes the fabrication of arrays of spherical microlenses by self-assembly of microspheres and the use of these arrays for nearfield photolithography to generate repetitive microstructures in photoresist. We used these arrays of microspheres to fabricate two types of elastomeric membranes: (i) membranes that have microspheres embedded in their surface and (ii) membranes that have hemispherical wells in their surface. Both types of membranes act as amplitude masks that pattern the intensity of illumination in the near field incident on the photoresist. Microspheres in the first type of membrane act as convergent lenses that generate recessed microstructures in positive photoresist. Hemispherical wells in the second type of membrane act as divergent lenses that produce protrusive microstructures in positive photoresist. This method can generate dense, regular arrays of microstructures with a variety of profiles--circular or hexagonal holes, circular posts, hollow posts, and cones--depending on the sizes and refractive indices of the spherical lenses and the distance between the lenses and the photoresist. This technique provides a simple route to large areas (>4 cm2) of repetitive, simple microstructures.     

Nonamorphism in flufenamic acid and a new record for a polymorphic compound with solved structures

The unprecedented polymorphism of the non-steroidal anti-inflammatory drug (NSAID) flufenamic acid (FFA) is described here. Nine polymorphs were accessed through the use of polymer-induced heteronucleation (PIHn) and solid-solid transformation at low temperature. Structural elucidation of six of these forms, in addition to the two previously known forms, makes FFA indisputably octamorphic. Although the structure of at least one other form of FFA remains elusive, the occurrence of most of these polymorphs under one crystallization condition through PIHn illustrates that a fine interplay exists among the kinetic factors that lead to phase selection in this NSAID.     

Selection of diverse polymorphic structures from a small dynamic molecular network controlled by the environment

The complex interplay between systems and their environment plays an important role in processes ranging from self-assembly to evolution. Polymorphism, where, from the same ingredients different products can be formed, is likely to be an important enabler for evolutionary adaptation. Environmental pressures may induce polymorphic behaviour, where different pressures result in different structural organisation. Here we show that by combining covalent and non-covalent bond formation three distinct polymorphs can emerge from the same small dynamic molecular network: vesicular aggregates, self-replicating fibres and nanoribbons, depending on the nature of the solvent environment. Additionally, a particular set of conditions allows the transient co-existence of both vesicles and fibres.

The solvent environment dictates assembly morphology and molecular constitution allowing access to a remarkable variety of self-assembled structures.     

gamma-Hydroxyalkynyl ketones as useful scaffolds for the preparation of combinatorial libraries of furans, isoxazoles and pyrazoles

Using 5-hydroxy-hex-3-yne-2-one (9) as a model substrate, the utility of the gamma-hydroxyl alkynyl ketone scaffold for the preparation of combinatorial libraries of furans, isoxazoles, and pyrazoles is described. The addition of hydrazoic acid to the acetylenic ketone 9 forms in a single step both 3-azido-2,5-dimethyl furan (10) and alpha,5-dimethyl-3-isoxazolemethanol (11). Reaction of a mixture of (E)- and (Z)-bromoenediones (5 and 6), accessible from 3-bromo-2,5-dimethyl furan (17), with 1,1-dimethylhydrazine afforded a nearly quantitative yield of 1,3-dimethyl-5-acetylpyrazole (18). When the (E)- and (Z)-vinyl bromides 5 and 6 were reacted with sodium azide, 3-acetyl-5-methylisoxazole (7) formed via the intermediate (Z)-3-azido-3-hexene-2,5-dione (4), was the only product.     

Generation of molecular complexity from cyclooctatetraene using dienyliron and olefin metathesis methodology

Transformation of the simple hydrocarbon cyclooctatetraene into a variety of polycyclic skeletons was achieved by sequential coordination to iron, reaction with electrophiles followed by allylated nucleophiles, decomplexation and olefin metathesis.     

Visual characterization and diversity quantification of chemical libraries: 2. Analysis and selection of size-independent, subspace-specific diversity indices

High Throughput Screening (HTS) is a standard technique widely used to find hit compounds in drug discovery projects. The high costs associated with such experiments have highlighted the need to carefully design screening libraries in order to avoid wasting resources. Molecular diversity is an established concept that has been used to this end for many years. In this article, a new approach to quantify the molecular diversity of screening libraries is presented. The approach is based on the Delimited Reference Chemical Subspace (DRCS) methodology, a new method that can be used to delimit the densest subspace spanned by a reference library in a reduced 2D continuous space. A total of 22 diversity indices were implemented or adapted to this methodology, which is used here to remove outliers and obtain a relevant cell-based partition of the subspace. The behavior of these indices was assessed and compared in various extreme situations and with respect to a set of theoretical rules that a diversity function should satisfy when libraries of different sizes have to be compared. Some gold standard indices are found inappropriate in such a context, while none of the tested indices behave perfectly in all cases. Five DRCS-based indices accounting for different aspects of diversity were finally selected, and a simple framework is proposed to use them effectively. Various libraries have been profiled with respect to more specific subspaces, which further illustrate the interest of the method.     

Generation of anti-colorectal cancer fab phage display libraries with a high percentage of diverse antigen-reactive clones

A combinatorial Fab phage display library was generated from the antibody variable region genes of each of 2 BALB/c mice immunized with the human colorectal cancer cell lines SW480, SW948, and SW837. These libraries were shown to be diverse by nucleotide sequencing and diagnostic restriction enzyme digestion (fingerprinting) of individual members. The two libraries were combined and selected for binding to a suspension of formaldehyde-fixed human colorectal cancer cells in two successive rounds of selection and phage amplification by infection of bacteria. Analysis of the selected libraries as well as individual library clones by ELISA, showed binding to the cancer cell lines in both formaldehyde-fixed and native forms. Fifty five percent and 94% of library clones were positive for colorectal cancer cell binding after the first and second rounds of selection, respectively. Fingerprinting of individual clones showed the first round selected library to be very diverse and the second round selected library to be of more limited diversity. After absorption with normal human cell types, these anti-cancer selected libraries could be used to develop therapeutic and/or diagnostic agents.