Ligand-based molecular modeling study on a chemically diverse series of cholecystokinin-B/gastrin receptor antagonists: generation of predictive model

Pharmacophore hypotheses were developed for six structurally diverse series of cholecystokinin-B/gastrin receptor (CCK-BR) antagonists. A training set consisting of 33 compounds was carefully selected. The activity spread of the training set molecules was from 0.1 to 2100 nM. The most predictive pharmacophore model (hypothesis 1), consisting of four features, namely, two hydrogen bond donors, one hydrophobic aliphatic, and one hydrophobic aromatic feature, had a correlation (r) of 0.884 and a root-mean-square deviation of 1.1526, and the cost difference between null cost and fixed cost was 81.5 bits. The model was validated on a test set consisting of six different series of 27 structurally diverse compounds and performed well in classifying active and inactive molecules correctly. This validation approach provides confidence in the utility of the predictive pharmacophore model developed in this work as a 3D query tool in the virtual screening of drug-like molecules to retrieve new chemical entities as potent CCK-BR antagonists. The model can also be used to predict the biological activities of compounds prior to their costly and time-consuming synthesis.     

Diversity-oriented synthesis of biaryl-containing medium rings using a one bead/one stock solution platform

Diversity-oriented synthesis of structurally complex and diverse small molecules can be used as the first step in a process to explore cellular and organismal pathways. The success of this process is likely going to be dependent on advances in the synthesis of small molecules having natural product-like structures in an efficient and stereoselective manner. The development, scope, and mechanism of the oxidation of organocuprates was investigated and exploited in the atropdiastereoselective synthesis of biaryl-containing medium rings (9-, 10-, and 11-membered rings). The methodology was performed on high-capacity, large polystyrene beads by metalating aryl bromides with i-PrBu(2)MgLi, followed by transmetalating with CuCN x 2LiBr and then oxidizing with 1,3-dinitrobenzene, and was used in a diversity-oriented synthesis of biaryl-containing medium rings (library total theoretical maximum 1412 members). The high capacity beads were arrayed into 384-well plates and, using a process optimized during the development of a one bead/one stock solution technology platform, converted into arrays of stock solutions, with each stock solution containing largely one compound. These stock solutions were used in numerous phenotypic and protein-binding assays. The process described outlines a pathway that we feel will contribute to a comprehensive and systematic chemical approach to exploring biology (chemical genetics).     

Catalyst‐Dependent Selectivity in the Relay Catalytic Branching Cascade

The synthesis of small organic molecules as probes for discovering new therapeutic agents has been an important aspect of chemical biology. One of the best ways to access collections of small molecules is to use various techniques in diversity‐oriented synthesis (DOS). Recently, a new form of DOS, namely “relay catalytic branching cascades” (RCBCs), has been introduced, wherein a common type of starting material reacts with several scaffold‐building agents (SBAs) to obtain structurally diverse molecular scaffolds under the influence of catalysts. Herein, the RCBC reaction of a common type of substrate with SBAs is reported to give two different types of molecular scaffolds and their formation is essentially dependent on the type of catalyst used.     

Electrooxidative dearomatization of biaryls: synthesis of tri- and difluoromethylated spiro[5.5]trienones

Radical spirocyclization via dearomatization has emerged as an attractive strategy for the rapid synthesis of structurally diverse spiro molecules. We report the use of electrochemistry to perform an oxidative dearomatization of biaryls leading to tri- and difluoromethylated spiro[5.5]trienones in a user friendly undivided cell set-up and a constant current mode. The catalyst- and chemical oxidant-free dearomatization procedure features ample scope, and employs electricity as the green and sole oxidant.

Radical spirocyclization via dearomatization has emerged as an attractive strategy for the rapid synthesis of structurally diverse spiro molecules.     

Pathway development and pilot library realization in diversity-oriented synthesis: exploring Ferrier and Pauson-Khand reactions on a glycal template

Through a correlation of the ability of small molecules to bind biological macromolecules and their ability to modulate cellular and organismal processes, chemistry can inform biology and vice versa. Diversity-oriented organic synthesis (DOS), which aims to provide structurally complex and diverse small molecules efficiently, can play a key role in such chemical genetic studies. Here we illustrate the trial-and-error experimentation that can refine an initial pathway-planning exercise and result eventually in an effective diversity pathway. By exploring Ferrier and Pauson-Khand reactions on a glycal template, we have developed efficient and stereoselective syntheses of tricyclic compounds. In this pathway, diversity results from the substituents and their spatial relationships about the tricyclic rings. A pilot split-pool library synthesis of 2500 tricyclic compounds highlights the use of planning considerations in DOS and a "one-bead, one-stock solution" technology platform. Additionally, it illustrates a promising synthetic pathway for future chemical genetic studies.     

Combinatorial discovery of fluorescent pharmacophores by multicomponent reactions in droplet arrays

Fluorescence imaging in clinical diagnostics and biomedical research relies to a great extent on the use of small organic fluorescent probes. Because of the difficulty of combining fluorescent and molecular-recognition properties, the development of such probes has been severely restricted to a number of well-known fluorescent scaffolds. Here we demonstrate that autofluorescing druglike molecules are a valuable source of bioimaging probes. Combinatorial synthesis and screening of chemical libraries in droplet microarrays allowed the identification of new types of fluorophores. Their concise and clean assembly by a multicomponent reaction presents a unique potential for the one-step synthesis of thousands of structurally diverse fluorescent molecules. Because they are based upon a druglike scaffold, these fluorophores retain their molecular recognition potential and can be used to design specific imaging probes.     

Nickel‐Catalyzed Carbofluoroalkylation of 1,3‐Enynes to Access Structurally Diverse Fluoroalkylated Allenes

A nickel‐catalyzed 1,4‐carbofluoroalkylation of 1,3‐enynes to access structurally diverse fluoroalkylated allenes has been established. This method has demonstrated high catalytic reactivity, mild reaction conditions, broad substrate scope, and excellent functional‐group tolerance. The key to success is the use of a nickel catalyst to generate different fluoroalkyl radicals from readily available and structurally diverse fluoroalkyl halides to access 1,4‐difunctionalization of 1,3‐enynes by a radical relay. This strategy provides facile synthesis of structurally diverse multisubstituted allenes, and offers a solution for batch production of various fluorinated bioactive molecules for drug discovery by further transformations.     

Skeletal diversity via a branched pathway: efficient synthesis of 29 400 discrete,polycyclic compounds and their arraying into stock solutions

We report the synthesis and arraying of 29 400 structurally diverse and complex polycyclic carbocycles using diversity-oriented synthesis (DOS) and the "one bead-one stock solution" technology platform. Skeletal diversity, a difficult challenge in DOS, was achieved with a branching reaction pathway using one or two Diels-Alder reactions. This pathway yields small molecules having 10 different skeletons.     

Chemical genetics approach to identify new small molecule modulators of cell growth by phenotypic screening of Saccharomyces cerevisiae strains with a library of morpholine-derived compounds

A chemical genetics approach has been applied in the screening of yeast deletants strains with a pool of morpholine-derived compounds in order to identify candidate small molecules able to produce phenotypic effects on yeast cells. The analysis of the effects of structurally diverse molecules towards cell growth rate in both exponential and stationary phases provides a tool to select candidate compounds for subsequent assays to identify new chemical entities as chemical probes for drug discovery.     

Diversity-oriented synthesis; a challenge for synthetic chemists

The efficient, simultaneous synthesis of structurally diverse compounds, better known as diversity-oriented synthesis (DOS), is not obvious, and remains a challenge to synthetic chemistry. This personal account details why DOS has such enormous implications for the discovery of small molecules with desired properties, such as catalysts, synthetic reagents, biological probes and new drugs, Also, I describe the evolution behind the current state-of-play of DOS.     

An Efficient Synthesis of Benzazocines by Gold(I)‐Catalyzed Tandem 1,2‐Acyloxy Shift/[3+2] Cycloaddition of Terminal 1,9‐Enynyl Esters

An effective synthesis of structurally diverse benzazocines was accomplished in good to excellent chemical yields (55–82 %) through a gold(I)‐catalyzed cascade reaction involving tandem 1,2‐acyloxy shift/[3+2] cycloaddition of terminal 1,9‐enynyl esters. The reaction proceeds under extremely mild conditions and represents one of the relatively few transition‐metal‐catalyzed intramolecular cycloaddition reactions for the synthesis of benzazocines.     

Selective Monomethylation of Amines with Methanol as the C1 Source

The N‐monomethyl functionality is a common motif in a variety of synthetic and natural compounds. However, facile access to such compounds remains a fundamental challenge in organic synthesis owing to selectivity issues caused by overmethylation. To address this issue, we have developed a method for the selective, catalytic monomethylation of various structurally and functionally diverse amines, including typically problematic primary aliphatic amines, using methanol as the methylating agent, which is a sustainable chemical feedstock. Kinetic control of the aliphatic amine monomethylation was achieved by using a readily available ruthenium catalyst at an adequate temperature under hydrogen pressure. Various substrates including bio‐related molecules and pharmaceuticals were selectively monomethylated, demonstrating the general utility of the developed method.     

Soluble polymer supported divergent synthesis of tetracyclic benzene-fused pyrazino/diazepino indoles: an advanced synthetic approach to bioactive scaffolds

The synthesis of indoline substituted nitrobenzene on a PEG support and its further elaboration to structurally diverse benzene-fused pyrazino/diazepino indoles is disclosed. A reagent based diversification approach coupled with Pictet-Spengler type condensation reactions furnished these fused polycyclic scaffolds. Microwave irradiation was used as a means of rate acceleration for soluble polymer-supported reactions. The efficiency of these fused heterocyclic molecules to inhibit the vascular endothelial growth factor receptor 3 (VEGFR-3) was examined in vitro using kinase receptor activation enzyme-linked immunosorbant assay (KIRA-ELISA). Based on the preliminary results obtained, a small set of potential drug candidates were identified as novel leads in this therapeutic area to be further explored as anti-metastatic agents.     

Amaryllidaceae and Sceletium alkaloids

Structurally diverse alkaloids, which show significant biological activities, are abundant in the plants of the family Amaryllidaceae. The latest progress on the isolation, identification, biological activity, and chemical synthesis of Amaryllidaceae alkaloids and the structurally close Sceletium alkaloids is summarized in this review.     

Synthesis and characteristics of sugar-phosphoramidates: A spectroscopic study

Phosphoramidate-incorporated scaffolds are structurally important targets owing to their diverse applications, particularly in medicinal chemistry. Herein we report the synthesis of several sugar phosphoramidates in excellent yields. NMR analyses were undertaken to examine their intramolecular H-bonding, stability under acidic conditions, and chemical shift effects.     

A modified Prins reaction for the facile synthesis of structurally diverse substituted 5-(2-hydroxyethyl)-3,3-dihydrofurane-2(3H)-ones

Furanones are important synthetic intermediates commonly found in natural products, receptor ligands, and drug molecules. Unacceptable yields of substituted furanones obtained using a previously reported Prins reaction led to the development of a modified approach. Readily prepared substituted allylic esters were reacted under Prins reaction conditions catalyzed by a protic acid to provide structurally diverse substituted furanones in modest to good yields. The reaction goes through a protected caprolactone intermediate that was isolated and characterized for selected compounds. The approach supplies an efficient, versatile, and higher yield method for the synthesis of these important heterocyclic intermediates.     

A Copper‐Catalyzed Multicomponent Reaction and ‘Click Strategy’ for the Stereoselective Synthesis of a New Series of Oxazolone Peptidomimetics with α‐Acylamino Amide and β‐Amido Ketone Structures

A novel ‘click ligation’ strategy for the stereoselective synthesis of a medium‐size library of structurally complex and functionally diverse oxazolone peptidomimetics, which contain α‐acylamino carboxamide or β‐amido ketone residues, is presented. Most of these molecules have lipophilicity constant values (log P) in the qualifying range for cell permeability, and that indicates the possibilities of these new molecules to be used in the search for potential inhibitors for a broad spectrum of enzymes.     

BRUTUS: optimization of a grid-based similarity function for rigid-body molecular superposition. II. Description and characterization

Finding novel lead molecules is one of the primary goals in early phases of drug discovery projects. However, structurally dissimilar compounds may exhibit similar biological activity, and finding new and structurally diverse lead compounds is difficult for computer algorithms. Molecular energy fields are appropriate for finding structurally novel molecules, but they are demanding to calculate and this limits their usefulness in virtual screening of large chemical databases. In our approach, energy fields are computed only once per superposition and a simple interpolation scheme is devised to allow coarse energy field lattices having fewer grid points to be used without any significant loss of accuracy. The resulting processing speed of about 0.25 s per conformation on a 2.4 GHz Intel Pentium processor allows the method to be used for virtual screening on commonly available desktop machines. Moreover, the results indicate that grid-based superposition methods could be efficiently used for the virtual screening of compound libraries.     

Chemical Biology of Glycosylphosphatidylinositol Anchors

Glycosylphosphatidylinositols (GPIs) are complex glycolipids that are covalently linked to the C‐terminus of proteins as a posttranslational modification. They anchor the attached protein to the cell membrane and are essential for normal functioning of eukaryotic cells. GPI‐anchored proteins are structurally and functionally diverse. Many GPIs have been structurally characterized but comprehension of their biological functions, beyond the simple physical anchoring, remains largely speculative. Work on functional elucidation at a molecular level is still limited. This Review focuses on the roles of GPI unraveled by using synthetic molecules and summarizes the structural diversity of GPIs, as well as their biological and chemical syntheses.     

Carbohydrate chemistry in drug discovery

The multitude of roles that carbohydrates and their glyco-conjugates play in biological processes has stimulated great interest in determining the nature of their interactions in both normal and diseased states. Manipulating such interactions will provide leads for drug discovery. Of the major classes of biomolecule, carbohydrates are the most structurally diverse. This hetereogeneity makes isolation of pure samples, and in sufficient amounts, from biological sources extremely difficult. Chemical synthesis offers the advantage of producing pure and structurally defined oligosaccharides for biological investigations. Although the complex nature of carbohydrates means that this is challenging, recent advances in the field have facilitated access to these molecules. The synthesis and isolation of oligosaccharides combined with progress in glycoarray technology have aided the identification of new carbohydrate-binding drug targets. This review aims to provide an overview of the latest advancements in carbohydrate chemistry and the role of these complex molecules in drug discovery, focusing particularly on synthetic methodologies, glycosaminoglycans, glycoprotein synthesis and vaccine development over the last few years.