Heteroaromatic rings of the future

A selective intramolecular 5-exo-dig or 6-endo-dig cyclization en route to 2-furanone or 2-pyrone containing tricyclic scaffolds

Ringfused bicyclic 2-pyridones exhibit interesting biological properties against pili assembly in uropathogenic Escherichia coli (Pinkner, J. S. et al. Proc. Natl. Acad. Sci. U. S. A.2006, 103, 17897-17902; Åberg, V. et al. Org. Biomol. Chem.2007, 5, 1827-1834) as well as curli formation (Cegelski, L. et al. Nat. Chem. Biol.2009, 5, 913-919). In the search for new ring-fused central fragments, highly selective synthetic routes to the 2-furanone or 2-pyrone containing tricyclic scaffolds 1 and 2 have been developed.

Scaffold diversity of exemplified medicinal chemistry space

The scaffold diversity of 7 representative commercial and proprietary compound libraries is explored for the first time using both Murcko frameworks and Scaffold Trees. We show that Level 1 of the Scaffold Tree is useful for the characterization of scaffold diversity in compound libraries and offers advantages over the use of Murcko frameworks. This analysis also demonstrates that the majority of compounds in the libraries we analyzed contain only a small number of well represented scaffolds and that a high percentage of singleton scaffolds represent the remaining compounds. We use Tree Maps to clearly visualize the scaffold space of representative compound libraries, for example, to display highly populated scaffolds and clusters of structurally similar scaffolds. This study further highlights the need for diversification of compound libraries used in hit discovery by focusing library enrichment on the synthesis of compounds with novel or underrepresented scaffolds.

Novel chiral skeletons for drug discovery: antibacterial tetramic acids

Modification of the ring nucleus of tetramic acids derived from serine gives chiral heterocyclic libraries that exhibit antibacterial activity, and correlation with various physicochemical parameters indicates that chiral tetramic acids may provide a potentially valuable non-aromatic skeleton for fragment-based drug discovery.

A facile, metal- and solvent-free, autoxidative coupling of quinolines with indoles and pyrroles

A simple, solvent-free, one-pot autoxidative coupling reaction between quinoline and indoles or pyrroles is reported. This atom economic method requires only a stoichiometric amount of inexpensive hydrochloric acid and does not require a catalyst.

Recent trends and observations in the design of high-quality screening collections

The design of a high-quality screening collection is of utmost importance for the early drug-discovery process and provides, in combination with high-quality assay systems, the foundation of future discoveries. Herein, we review recent trends and observations to successfully expand the access to bioactive chemical space, including the feedback from hit assessment interviews of high-throughput screening campaigns; recent successes with chemogenomics target family approaches, the identification of new relevant target/domain families, diversity-oriented synthesis and new emerging compound classes, and non-classical approaches, such as fragment-based screening and DNA-encoded chemical libraries. The role of in silico library design approaches are emphasized.

Microwave-promoted synthesis of 3-amino-substituted 1,2-benzisoxazoles

BACKGROUND

1,2-benzisoxazole derivatives have been the focus of numerous studies, due to their biological and chemical interest.

RESULTS

We demonstrate an efficient synthesis of a series of 3-amino-substituted 1,2-benzisoxazoles from a 3-chloro-1,2-benzisoxazole by microwave-promoted nucleophilic aromatic substitution. The 3-amino-1,2-benzisoxazoles prepared were obtained in 1-6 h in good-to-high yields of 54-90%. The 3-chloro-1,2-benzisoxazoles were also prepared by heating with microwave irradiation in quantitative yields in 2 h, from the corresponding 3-hydroxy-1,2-benzisoxazoles.

CONCLUSION

This efficient microwave-assisted pathway could be applied to a variety of substrates in the further development of substituted 1,2-benzisoxazoles.

Challenges and perspectives of chemical biology, a successful multidisciplinary field of natural sciences

Objects, goals, and main methods as well as perspectives of chemical biology are discussed. This review is focused on the fundamental aspects of this emerging field of life sciences: chemical space, the small molecule library and chemical sensibilization (small molecule microassays).

Combinatorial library design from reagent pharmacophore fingerprints

Combinatorial and parallel chemical synthesis technologies are powerful tools in early drug discovery projects. Over the past couple of years an increased emphasis on targeted lead generation libraries and focussed screening libraries in the pharmaceutical industry has driven a surge in computational methods to explore molecular frameworks to establish new chemical equity. In this chapter we describe a complementary technique in the library design process, termed ProSAR, to effectively cover the accessible pharmacophore space around a given scaffold. With this method reagents are selected such that each R-group on the scaffold has an optimal coverage of pharmacophoric features. This is achieved by optimising the Shannon entropy, i.e. the information content, of the topological pharmacophore distribution for the reagents. As this method enumerates compounds with a systematic variation of user-defined pharmacophores to the attachment point on the scaffold, the enumerated compounds may serve as a good starting point for deriving a structure-activity relationship (SAR).

Synthesis and preliminary evaluation of curcumin analogues as cytotoxic agents

A series of curcumin analogues with different substituents at the 4-position of the phenyl group were synthesized and screened for in vitro cytotoxicity against a panel of human cancer cell lines. Several novel curcumin analogues, especially 32 and 34, exhibited selective and potent cytotoxic activity against human epidermoid carcinoma cell line A-431 and human glioblastoma cell line U-251, implying their specific potential in the chemoprevention and chemotherapy of skin cancer and glioma. The preliminary SAR information extracted from the results suggested that introduction of appropriate substituents to the 4'-positions could be a promising approach for the development of new cytotoxic curcumin analogues with special selectivity for A-431 and U-251 cell lines.

Design and evaluation of 3,6-di(hetero)aryl imidazo[1,2-a]pyrazines as inhibitors of checkpoint and other kinases

A range of 3,6-di(hetero)arylimidazo[1,2-a]pyrazine ATP-competitive inhibitors of CHK1 were developed by scaffold hopping from a weakly active screening hit. Efficient synthetic routes for parallel synthesis were developed to prepare analogues with improved potency and ligand efficiency against CHK1. Kinase profiling showed that the imidazo[1,2-a]pyrazines could inhibit other kinases, including CHK2 and ABL, with equivalent or better potency depending on the pendant substitution. These 3,6-di(hetero)aryl imidazo[1,2-a]pyrazines appear to represent a general kinase inhibitor scaffold.

9,10-Dioxa-1,2-diaza-anthracene derivatives from tetrafluoropyridazine

Reaction of tetrafluoropyridazine with catechol gives a tricyclic 9,10-dioxa-1,2-diaza-anthracene system by a sequential nucleophilic aromatic substitution ring annelation process, further extending the use of perfluoroheteroaromatic derivatives for the synthesis of unusual polyfunctional heterocyclic architectures. The tricyclic scaffold reacts with amines and sodium ethoxide providing a short series of functional 9,10-dioxa-1,2-diaza-anthracene systems.

Bioisosteric Replacement and Scaffold Hopping in Lead Generation and Optimization

Bioisosteric replacement and scaffold hopping are twin methods used in drug design to improve the synthetic accessibility, potency and drug like properties of a compound and to move into novel chemical space. Bioisosteric replacement involves swapping functional groups of a molecule with other functional groups that have similar biological properties. Scaffold hopping is the replacement of the core framework of a molecule with another scaffold that will improve the properties of the molecule or to find similar potent compounds that exist in novel chemical space. This review outlines the key concepts, importance and challenges of both methods using examples and comparisons of techniques available for finding bioisosteric replacements and scaffold hops. There are many methods available for bioisosteric replacement and scaffold hopping, all with their own advantages and disadvantages. Drug design projects would benefit from a combination of these methods to retrieve diverse and complimentary results. Continuing progress in these fields will allow further validation of both methods as well as the accumulation of knowledge on bioisosteres and possible scaffold replacements.

Annular tautomerism: experimental observations and quantum mechanics calculations

The use of MP2 level quantum mechanical (QM) calculations on isolated heteroaromatic ring systems for the prediction of the tautomeric propensities of whole molecules in a crystalline environment was examined. A Polarisable Continuum Model was used in the calculations to account for environment effects on the tautomeric relative stabilities. The calculated relative energies of tautomers were compared to relative abundances within the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB). The work was focussed on 84 annular tautomeric forms of 34 common ring systems. Good agreement was found between the calculations and the experimental data even if the quantity of these data was limited in many cases. The QM results were compared to those produced by much faster semiempirical calculations. In a search for other sources of the useful experimental data, the relative numbers of known compounds in which prototropic positions were often substituted by heavy atoms were also analysed. A scheme which groups all annular tautomeric transformations into 10 classes was developed. The scheme was designed to encompass a comprehensive set of known and theoretically possible tautomeric ring systems generated as part of a previous study. General trends across analogous ring systems were detected as a result. The calculations and statistics collected on crystallographic data as well as the general trends observed should be useful for the better modelling of annular tautomerism in the applications such as computer-aided drug design, small molecule crystal structure prediction, the naming of compounds and the interpretation of protein-small molecule crystal structures.

The scaffold tree: an efficient navigation in the scaffold universe

The Scaffold Tree algorithm (J Chem Inf Model 47:47-58, 2007) allows to organize large molecular data sets by arranging sets of molecules into a unique tree hierarchy based on their scaffolds, with scaffolds forming leaf nodes of such tree. The hierarchy is created by iterative removal of rings from more complex scaffolds using chemically meaningful set of rules, until a single, root ring is obtained. The classification is deterministic, data set independent, and scales linearly with the number of compounds included in the data set. In this review we summarize the basic principles of the Scaffold Tree methodology and review its applications, which appeared in recent medicinal chemistry literature, including the use of Scaffold Trees for visualization of large chemical data sets, compound clustering, and the identification of novel bioactive molecules. References to several computer programs, including also free tools available on the Internet, allowing to perform classification and visualization of molecules based on their scaffolds are also provided.