The combinatorial synthesis of bicyclic privileged structures or privileged substructures

Do benzodiazepines mimic reverse-turn structures?

The role of benzodiazepine derivatives (BZD) as a privileged scaffold that mimics beta-turn structures (Ripka et al. (1993) Tetrahedron 49:3593-3608) in peptide/protein recognition was reexamined in detail. Stable BZD ring conformers were determined with MM3, and experimental reverse-turn structures were extracted from the basis set of protein crystal structures previously defined by Ripka et al. Ideal beta-turns were also modeled and similarly compared with BZD conformers. Huge numbers of conformers were generated by systematically scanning the torsional degrees of freedom for BZDs, as well as those of ideal beta-turns for comparison. Using these structures, conformers of BZDs were fit to experimental structures as suggested by Ripka et al., or modeled classical beta-turn conformers, and the root-mean-square deviation (RMSD) values were calculated for each pairwise comparison. Pairs of conformers with the smallest RMSD values for overlap of the four alpha-beta side-chain orientations were selected. All overlaps of BZD conformers with experimental beta-turns yielded one or more comparisons where the least RMSD was significantly small, 0.48-0.86 angstroms, as previously suggested. Utilizing a different methodology, the overall conclusion that benzodiazepines could serve as reverse-turn mimetics of Ripka et al. is justified. The least RMSD values for the overlap of BZDs and modeled classical beta-turns were also less than 1 angstrom. When comparing BZDs with experimental or classical beta-turns, the set of experimental beta-turns selected by Ripka et al. fit the BZD scaffolds better than modeled classical beta-turns; however, all the experimental beta-turns did not fit a particular BZD scaffold better. A single BZD ring conformation, and/or chiral orientation, can mimic some, but not all, of the experimental beta-turn structures. BZD has two central ring conformations and one chiral center that explains why the four variations of the BZD scaffold can mimic all types of beta-turn structure examined. It was found, moreover, that the BZD scaffold also mimics each of the nine clusters of experimental orientations of side chains of reverse turns in the Protein Data Bank, when the new classification scheme for the four side-chain directions (the relative orientations of alpha-beta vectors of residues i through i+3) was considered (Tran et al. (2005) J Comput-Aided Mol Des 19:551-566).

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.

Synthesis, characterization, and DNA-binding properties of the Ln(III) complexes with 6-hydroxy chromone-3-carbaldehyde-(2′-hydroxy) benzoyl hydrazone

A new ligand, 6-hydroxy chromone-3-carbaldehyde-(2'-hydroxy) benzoyl hydrazone (L), was prepared by condensation of 6-hydroxy-3-carbaldehyde chromone (CDC) with 2-hydroxy benzoyl hydrazine. Its four rare earth complexes have been synthesized and characterized on the basis of elemental analyses, molar conductivities, mass spectra, 1H NMR, thermogravimetry/differential thermal analysis (TG-DTA), UV-vis spectra, fluorescence spectra, and IR spectra. The general formula of the complexes is [LnL2.(NO3)2].NO3 [Ln=La(1), Sm(2), Dy(3), Eu(4)]. Spectrometric titration, ethidium bromide displacement experiments, and viscosity measurements indicate that Eu(III) complex and ligand, especially the Eu(III) complex, strongly bind with calf-thymus DNA, presumably via an intercalation mechanism. The intrinsic binding constants of Eu(III) complex and ligand with DNA were 3.55 x 10(6) and 1.33 x 10(6)M(-1) through fluorescence titration data, respectively. In addition, the suppression ratio for O2-* and OH* of the ligand and its complexes was studied by spectrophotometric methods. The experimental results show that La (1), Sm (2), and Eu (4) complexes are better effective inhibitor for OH* than that of mannitol. It indicates that the complexes have the activity to suppress O2-* and OH* and exhibit more effective antioxidants than ligand alone.

Microwave-Enhanced High-Speed Fluorous Synthesis

Increasing reaction speed and simplifying product purification are two major ways to improve the efficiency of organic synthesis. A new technology for high-speed solution-phase synthesis has been developed by combination of microwave heating and fluorous purification. This review describes different techniques for microwave-enhanced fluorous synthesis and their applications in Pd-catalyzed cross-coupling reactions, free-radical reactions, multicomponent reactions, and compound library synthesis.

Synthesis of Biaryls via Catalytic Decarboxylative Coupling

We present a safe and convenient cross-coupling strategy for the large-scale synthesis of biaryls, commercially important structures often found in biologically active molecules. In contrast to traditional cross-couplings, which require the prior preparation of organometallic reagents, we use a copper catalyst to generate the carbon nucleophiles in situ, via decarboxylation of easily accessible arylcarboxylic acid salts. The scope and potential economic impact of the reaction are demonstrated by the synthesis of 26 biaryls, one of which is an intermediate in the large-scale production of the agricultural fungicide Boscalid.

Asymmetric multicomponent reactions (AMCRs): the new frontier

Asymmetric multicomponent reactions involve the preparation of chiral compounds by the reaction of three or more reagents added simultaneously. This kind of addition and reaction has some advantages over classic divergent reaction strategies, such as lower costs, time, and energy, as well as environmentally friendlier aspects. All these advantages, together with the high level of stereoselectivity attained in some of these reactions, will force chemists in industry as in academia to adopt this new strategy of synthesis, or at least to consider it as a viable option. The positive aspects as well as the drawbacks of this strategy are discussed in this Review.

Design, synthesis, and biological evaluation of indole derivatives as novel nociceptin/orphanin FQ (N/OFQ) receptor antagonists

A novel series of 2-(1,2,4-oxadiazol-5-yl)-1H-indole derivatives as nociceptin/orphanin FQ (N/OFQ) receptor antagonists was discovered. Systematic modification of our original lead by changing the pendant functional groups, linker, heterocyclic core, and basic side chain revealed the structure-activity requirements for this novel template and resulted in the identification of more potent analog with improved potency as compared to the parent compound.

Efficient solid-phase synthesis of highly functionalized 1,4-benzodiazepin-5-one derivatives and related compounds by intramolecular aza-Wittig reactions

Due to their widespread biological activities and favorable pharmacokinetic properties, benzodiazepines were among the first classes of small molecules to be synthesized on solid supports. Since then, there have been numerous reports on the synthesis of similar skeletons. We have employed the T1 triazene linker to yield 1,4-benzodiazepin-5-one. Starting from various substituted triazene resins, cleavage in the presence of an azide donor, such as trimethylsilylazide, gave rise to aryl azides. Intramolecular aza-Wittig reactions produced the appropriately functionalized N-heterocycles. By using this route, the natural product deoxyvasicinone and related compounds were prepared.

Liquid-Phase Parallel Synthesis of Combinatorial Libraries of Substituted 6-Carbamoyl-3,4-dihydro-2H-benzo[1,4]thiazines

In this work, we explored several original combinatorial derivatization patterns for the 3,4-dihydro-2H-1,4-benzothiazine scaffold. The synthesis begins with commercially available 4-chloro- and 4-fluoro-3-nitrobenzoates and employs a sequence of moderate and high-yielding reactions that display a relatively high substituent tolerance. Simple manual techniques for parallel reactions were coupled with easy workup and purification procedures to give high-purity final products. The developed approach was easily adaptable for parallel synthesis of more than 2600 novel 2H-benzo[1,4]thiazine-6-carboxylic acid amides, which were efficiently prepared in a semiautomatic fashion using special CombiSyn synthesizers.

Electron ionization-induced fragmentation of some new dibenzo(d, f)(1,3)dioxepine derivatives

The mass spectrometric behaviour of a series of 6,6-disubstituted dibenzo(d,f)(1,3)dioxepine derivatives have been studied. The fragmentation patterns were described and discussed in detail with the aid of labelled compounds, accurate mass measurements and collisionally induced dissociation experiments performed using an ion trap.

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.

A one-pot entry to a novel 3-H-benzo[d]pyrazolo[1,5-b]isothiazole ring system

The phosphorus ylide obtained from the reaction between 2-aminobenzo[d]isothiazol-3-one and dimethyl acetylenedicarboxylate in the presence of triphenylphosphine undergoes a smooth intramolecular Wittig-type reaction to produce, in a one-pot reaction, 3-H-benzo[d]pyrazolo[1,5-b]isothiazole-2,3a-dicarboxylic acid dimethyl ester, a novel functionalized heterocyclic compound.

Practical Thiol Surrogates and Protective Groups for Arylthiols for Suzuki−Miyaura Conditions

We have developed practical thiol surrogates and arylthiol protective groups for the Suzuki-Miyaura reaction. 2-Ethylhexyl-3-mercaptopropionate and 4-(2'-mercaptoethyl)pyridine were shown to be not only good thiol surrogates but also good protective groups for thiol. We have demonstrated toleration of these protective groups under aqueous Suzuki-Miyaura conditions.

Are Target-Family-Privileged Substructures Truly Privileged?

One of the early and effective approaches to G-coupled protein receptor target family library design was the analysis of a set of ligands for frequently occurring chemical moieties or substructures. Various methods ranging from frameworks analysis to pharmacophores have been employed to find these so-called target-family-privileged substructures. Although the use of these substructures is common practice in combinatorial library design and has produced leads, the methods used for finding them rarely verified their selectivity for the particular target family from which they were derived. The frequency of occurrence among ligands associated with a target receptor family is not a sufficient criterion for those substructures to receive the label of target-family-privileged substructure. This study explores the question of selectivity of ClassPharmer generated fragments for a series of target families: GPCRs, nuclear hormone receptors, serine proteases, protein kinases, and ligand-gated ion channels. In addition, a GPCR focused library and a random set of 10k compounds are examined in terms of their target-family-privileged-substructure composition. The results challenge the combinatorial chemistry concept of target-family-privileged substructures and suggest that many of these fragments may simply be drug-like or attractive for various receptors in accordance with the original definition of privileged substructures.

Diversity-oriented synthesis: exploring the intersections between chemistry and biology

Diversity-oriented synthesis (DOS) is an emerging field involving the synthesis of combinatorial libraries of diverse small molecules for biological screening. Rather than being directed toward a single biological target, DOS libraries can be used to identify new ligands for a variety of targets. Several different strategies for library design have been developed to target the biologically relevant regions of chemical structure space. DOS has provided powerful probes to investigate biological mechanisms and also served as a new driving force for advancing synthetic organic chemistry.

Privileged structure-based quinazolinone natural product-templated libraries: Identification of novel tubulin polymerization inhibitors

A focused quinazolinone natural product-templated library was designed and synthesized. Compounds from this privileged structure-based library were identified as antimitotic agents acting through destabilization of tubulin polymerization. The results suggested that 2 could be a privileged substructure.

5-Aminooxazole as an Internal Traceless Activator of C-Terminal Carboxylic Acid: Rapid Access to Diversely Functionalized Cyclodepsipeptides

A conceptually novel macrolactonization protocol has been developed. It is a domino process involving a sequence of: 1) protonation of 5-aminooxazole leading to the electrophilic iminium salt; 2) trapping of the iminium species by the neighboring C-terminal carboxylic acid leading to a putative spirolactone; and 3) intramolecular nucleophilic addition of the tethered alcohol to the spirolactone followed by fragmentation. The strategically incorporated 5-aminooxazole serves as an internal traceless activator of the neighboring C-terminal carboxylic acid, since it became an integral part of the peptide backbone after cyclization. No coupling reagent is required and the entire sequence is triggered by just a few equivalents of trifluoroacetic acid under very mild conditions (MeCN as the solvent at room temperature). The spirolactone as an activated form of the carboxylic acid has been evidenced by a sulfur-migration experiment. By combining with a three-component synthesis of 5-aminooxazole, a two-step synthesis of structurally complex cyclodepsipeptides from readily accessible starting materials was developed.

Diversity-Oriented Synthesis of 3-Iodochromones and Heteroatom Analogues via ICl-Induced Cyclization

The ICl-induced cyclization of heteroatom-substituted alkynones provides a simple, highly efficient approach to various 3-iodochromones and analogues. This process is run under mild conditions, tolerates various functional groups, and generally provides chromones in good to excellent yields. Subsequent palladium-catalyzed transformations afford a rapid increase in molecular complexity and a convenient preparation of a wide range of functionally substituted chromones, furans, and polycyclic compounds. Iodothiochromenones and iodoquinolinones are also prepared by similar ICl-induced cyclizations.

Solid-phase synthesis of an alkylaminobenzanilide library

The synthesis of a library of 2- and 3-substituted benzanilides has been achieved on solid phase. Attachment of anilines to formyldimethoxyphenyl (FDMP) resin via reductive amination was optimized to allow a wide range of anilines to be used. Acylation of this resin-bound aniline was accomplished with 2- or 3-nitrobenzoyl chloride to yield nitrobenzanilides. Following reduction of the nitro group, the resulting amine was alkylated using aromatic and heteroaromatic aldehydes in the presence of NaBH(OAc)(3) under controlled conditions. Finally, the products were cleaved from the resin using trifluoroacetic acid to produce a 10 800-member library.

Structural modifications of the cannabinoid side chain towards C3-aryl and 1',1'-cycloalkyl-1'-cyano cannabinoids

The compounds reported in this study are Delta(8)-THC analogues in which the C3 five-carbon linear side chain of Delta(8)-THC was replaced with aryl and 1',1'-cycloalkyl substituents. Of the compounds described here analogues 2d (CB(1), K(i)=11.7 nM. CB(2), K(i)=9.39 nM) and 2f (CB(1), K(i)=8.26 nM. CB(2), K(i)=3.86 nM) exhibited enhanced binding affinities for CB(1) and CB(2), exceeding that of Delta(8)-THC. Efficient procedures for the synthesis of these novel cannabinoid analogues are described.

Concise and diversity-oriented synthesis of novel scaffolds embedded with privileged benzopyran motif

A branching DOS strategy for an unbiased natural product-like library with embedded privileged benzopyran motif was established to provide complexity and diversity of resulting heterocycles with desired drug-likeness. The importance of skeletal diversity conducted on a privileged substructure was demonstrated through the biological evaluation of a small molecule library representing 22 unique core skeletons via in vitro cytotoxicity assay.

Mechanistic study on the coupling reaction of aryl bromides with arylboronic acids catalyzed by (iminophosphine)palladium(0) complexes. Detection of a palladium(ii) intermediate with a coordinated boron anion

The complexes [Pd(eta2-dmfu)(P-N)] [P-N = 2-(PPh2)C6H4-1-CH=NR, R = C(6)H(4)OMe-4; CHMe2; C6H3Me2-2,6; C6H3(CHMe2)-2,6] react with an excess of BrC6H4R1-4 (R1= CF3; Me) yielding the oxidative addition products [PdBr(C6H4R1-4)(P-N)] at different rates depending on R [C6H4OMe-4 > C6H3(CHMe2)-2,6 > CHMe2 approximately C6H3Me2-2,6] and R1 (CF3>> Me). In the presence of K2CO3 and activated olefins (ol = dmfu, fn), the latter compounds react with an excess of 4-R2C6H4B(OH)2 (R2= H, Me, OMe, Cl) to give [Pd(eta2-ol)(P-N)] and the corresponding biaryl through transmetallation and fast reductive elimination. The transmetallation proceeds via a palladium(II) intermediate with an O-bonded boron anion, the formation of which is markedly retarded by increasing the bulkiness of R. The intermediate was isolated for R = CHMe2, R1 = CF3 and R2= H. The boron anion is formulated as a diphenylborinate anion associated with phenylboronic acid and/or as a phenylboronate anion associated with diphenylborinic acid. In general, the oxidative addition proceeds at a lower rate than transmetallation and represents the rate-determining-step in the coupling reaction of aryl bromides with arylboronic acids catalyzed by [Pd(eta2-dmfu)(P-N)].

Topological side-chain classification of β-turns: Ideal motifs for peptidomimetic development

Beta-turns are important topological motifs for biological recognition of proteins and peptides. Organic molecules that sample the side chain positions of beta-turns have shown broad binding capacity to multiple different receptors, for example benzodiazepines. Beta-turns have traditionally been classified into various types based on the backbone dihedral angles (phi2, psi2, phi3 and psi3). Indeed, 57-68% of beta-turns are currently classified into 8 different backbone families (Type I, Type II, Type I', Type II', Type VIII, Type VIa1, Type VIa2 and Type VIb and Type IV which represents unclassified beta-turns). Although this classification of beta-turns has been useful, the resulting beta-turn types are not ideal for the design of beta-turn mimetics as they do not reflect topological features of the recognition elements, the side chains. To overcome this, we have extracted beta-turns from a data set of non-homologous and high-resolution protein crystal structures. The side chain positions, as defined by C(alpha)-C(beta) vectors, of these turns have been clustered using the kth nearest neighbor clustering and filtered nearest centroid sorting algorithms. Nine clusters were obtained that cluster 90% of the data, and the average intra-cluster RMSD of the four C(alpha)-C(beta) vectors is 0.36. The nine clusters therefore represent the topology of the side chain scaffold architecture of the vast majority of beta-turns. The mean structures of the nine clusters are useful for the development of beta-turn mimetics and as biological descriptors for focusing combinatorial chemistry towards biologically relevant topological space.

Discovery of a potent and selective 5-ht5A receptor antagonist by high-throughput chemistry

High-throughput screening of an array of biphenylmethylamines synthesised by high-throughput solid-phase chemistry resulted in the identification of compounds with high-affinity for the 5-ht5A receptor. The structure-activity relationship within this series and further array synthesis led to the identification of the biphenylmethylamine derivative 11, a potent and selective 5-ht5A receptor antagonist.

Annulation of Primary Amines to Piperazines and Diazaspirocycles Utilizing α-Methyl Benzyl Resin

The microwave-assisted solid-phase synthesis of piperazines, 3,9-diazaspiro[5.5]undecanes and 2,9-diazaspiro[5.5]undecanes is reported. The synthesis relies on the direct annulation of primary amines with resin-bound bismesylates. Critical to the success of this chemistry was the development of alpha-methyl benzyl carbamate resin linker. This resin permits the cleavage of the heterocycles under mildly acidic conditions, free of contaminating linker-derived N-alkylated byproducts.

Multicomponent One-Pot Procedure for the Synthesis of Free α-Chiral Amines from Aldehydes

[reaction: see text] The synthesis of free alpha-chiral amines by a one-pot multicomponent procedure from commercially available starting materials is described. This enantioselective reaction involves a catalytic asymmetric addition of dialkylzinc reagents to N-diphenylphosphinoylimines with use of an air-stable precatalyst complex 1. The alpha-chiral amines are prepared with a one-pot procedure from alkyl and aryl aldehydes in good yield (41-90%) and with excellent enantioselectivity (90-97% ee).

Synthesis of Novel Tricyclic Pyrimido[4,5-b][1,4]benzothiazepines via Bischler−Napieralski-Type Reactions

[reaction: see text] Novel tricyclic pyrimido[4,5-b][1,4]benzothiazepines were readily prepared from 5-amino-4,6-bis(arylthio)pyrimidines and carboxylic acids via Bischler-Napieralski-type reactions. The 6-aryl sulfide group of the resulting pyrimido[4,5-b][1,4]benzothiazepines could be selectively oxidized to its corresponding sulfoxide, which underwent facile substitution reactions when treated with nucleophiles such as an amine. This synthetic strategy provides an efficient way to access a library of novel heterocyclic compounds that are of interest in drug discovery.

Identifying Biologically Active Compound Classes Using Phenotypic Screening Data and Sampling Statistics

Scoring the activity of compounds in phenotypic high-throughput assays presents a unique challenge because of the limited resolution and inherent measurement error of these assays. Techniques that leverage the structural similarity of compounds within an assay can be used to improve the hit-recovery rate from screening data. A technique is presented that uses clustering and sampling statistics to predict likely compound activity by scoring entire structural classes. A set of phenotypic assays performed against a commercially available compound library was used as a test set. Using the class-scoring technique, the resultant activity prediction scores were more reproducible than individual assay measurements, and class scoring recovered known active compounds more efficiently than individual assay measurements because class scoring had fewer false positives. Known biologically active compounds were recovered 87% of the time using class scores, suggesting a low false-negative rate that compared well to individual assay measurements. In addition, many weak and potentially novel classes of active compounds, overlooked by individual assay measurements, were suggested.

A review of melanocortin receptor small molecule ligands

The melanocortin system (MC) is implicated in the regulation of a variety of physiological pathways including pigmentation, steroid function, energy homeostasis, food intake, obesity, cardiovascular, sexual function, and normal gland regulation. The melanocortin system consists of five receptors identified to date (MC1-5R), melanocortin agonists derived from the pro-opiomelanocortin prohormone (POMC) and two naturally existing antagonists. Melanocortin receptor ligand structure-activity studies have been performed since the 1960s, primarily focused on the pigmentation aspect of physiology. During the 1990s, the melanocortin-4 receptor was identified to play a significant physiological role in the regulation of both food intake and obesity. Subsequently, a concerted drug design effort has focused on the design and discovery of melanocortin receptor small molecules. Herein, we present an overview of melanocortin receptor heterocyclic small molecules.

Solid-Phase Synthesis of 2-Aminoquinazolinone Derivatives with Two- and Three-Point Diversity

A versatile solid-phase method for the synthesis of various substituted 2-amino-4(3H)-quinazolinones with two- and three-point diversity is described. The synthesis commenced with the generation of polymer-bound S-methylisothiourea followed by N-acylation with different substituted o-nitrobenzoic acid. Finally, reduction of the nitro group triggered intramolecular cyclization via formation of guanidine to afford 2-amino-4(3H)-quinazolinone and its derivatives in high yields and purities.

Selection of heterocycles for drug design

A method has been devised to obtain heterocyclic ring systems suitable for use in drug design and library design, with an emphasis on the selection of systems with good absorption, distribution, metabolism, excretion and toxicity (ADMET) properties in man. This has been achieved by extraction of the ring systems found in drugs that have reached Phase II or later stages of drug development and launch. Properties have been calculated for these ring systems to enable them to be rationally selected from the database, including descriptors based on molecular size, shape, hydrogen bonding and orbital properties. In many cases, the properties have been calculated for different attachment points of the same heterocycle. Principal components analysis has been used to enable visualization of the set of heterocycles in a useful "chemical space". Using this space, it is possible to select heterocycles for drug design to explore specific aspects of the properties of the heterocycle, such as size or hydrogen bonding, while maintaining other parameters near constant, or to select heterocycles with extreme values of these properties but which are nonetheless likely to be acceptable in a drug. The differences between the properties calculated for the most- and least-frequently used heterocycles from the late-phase drug set have been analyzed, and may suggest that heterocycles in successful drugs are more likely to have calculated quantities associated with lower chemical reactivity.