The combinatorial synthesis of bicyclic privileged structures or privileged substructures

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.

Reversion of Human Pgp-Dependent Multidrug Resistance by New Sesquiterpenes from Zinowiewia costaricensis

In an intensive study of South American medicinal plants, herein we report the isolation, structure elucidation and biological activity of fourteen new and five known dihydro-beta-agarofuran sesquiterpenes from the leaves of Zinowiewia costaricensis (1-19). Their structures were determined by means of (1)H and (13)C NMR spectroscopic studies, including homonuclear and heteronuclear correlation experiments. The absolute configurations of the new compounds were determined by CD studies, chemical correlations or biogenetic grounds. All the natural compounds and derivative 20 have been tested on human MDR1-transfected NIH-3T3 cells, to determine their ability to revert the multidrug resistance phenotype due to P-glycoprotein overexpression. Six compounds from this series (1, 8, 11, 12, 13 and 14) showed similar effectiveness to the classical P-glycoprotein modulator verapamil when reversing resistance to daunorubicin, but it is up to sixteen times greater than that of verapamil when reversing resistance to vinblastine. The structure-activity relationships are discussed.

Solid-Phase Synthesis of Pyrroloisoquinolines via the Intramolecular N-Acyliminium Pictet−Spengler Reaction

In the present investigation, solid-phase routes toward 1,5,6,10b-tetrahydro-2H-pyrrolo[2,1-a]isoquinolin-3-ones via the intramolecular N-acyliminium Pictet-Spengler reaction are established. Peptide aldehydes generated from their parent N-Boc 1,3-oxazines by acidic reaction conditions undergo intramolecular condensation reactions with the amide N of a solid-supported peptide backbone, thus forming a 1:1 epimeric mixture of a cyclic 5-hydroxylactam, which in turn is in equilibrium with the corresponding intermediate N-acyliminium ion. Provided appropriate acidic reaction conditions, a second ring may be appended via Pictet-Spengler cyclization from the aromatic ring of a neighboring phenylalanine derivative in the peptide sequence. The aromatic substitution pattern of the nucleophilic benzene ring of the phenylalanine derivative and the nature of the acidic reaction media are critically important for the course of the reaction, and both Lewis and Brønsted acids may be employed to effect the cyclization process. This intramolecular reaction is under strict control of stereoselectivity, and only a single stereoisomer is detected in the crude products. A range of mono-, di-, and trisubstituted phenylalanines with diverse sets of electron-donating and electron-withdrawing substituents, pyrene, and naphthalenes have successfully been brought within the scope of the reaction, thus providing a unique scaffold for combinatorial library synthesis.

Potential protease inhibitors based on a functionalized cyclic sulfamide scaffold

Exploratory studies related to the design and synthesis of functionalized cyclic sulfamides (I) as potential inhibitors of proteolytic enzymes were carried out. The structural motif and three diversity sites embodied in the scaffold render it amenable to combinatorial parallel synthesis and the facile generation of lead discovery prospecting libraries. The scaffold was readily assembled starting with (DL) serine methyl ester, and a series of compounds was generated and screened against human leukocyte elastase. Modification of the P(1) recognition element, believed to be accommodated at the primary specificity site (S(1) subsite) of the enzyme, yielded compounds that inhibited the enzyme by an apparent hyperbolic partial mixed-type inhibition.

A Versatile Synthetic Approach to Peptidyl Privileged Structures Using a “Safety-Catch” Linker

Peptidyl privileged structures have been widely used by many groups to discover biologically active molecules. In this context, privileged substructures are used as "hydrophobic anchors", to which peptide functionality is appended to gain specificity. Utilization of this concept has led to the discovery of many different active compounds at a wide range of biological receptors. A synthetic approach to these compounds has been developed on a "safety-catch" linker that allows rapid preparation of large libraries of these molecules. Importantly, amide bond formation/cleavage through treatment with amines is the final step; it is a linker strategy that allows significant diversification to be easily incorporated, and it only requires the inclusion of an amide bond. In addition, chemistry has been developed that permits the urea moiety to be inserted at the N-terminus of the peptide, allowing the same set of amines (either privileged substructures or amino acid analogues) to be used at both the N- and C-termini of the molecule. To show the robustness of this approach, a small library of peptidyl privileged structures were synthesized, illustrating that large combinatorial libraries can be synthesized using these technologies.

Molecular Diversity via Amino Acid Derived α-Amino Nitriles: Synthesis of Spirocyclic 2,6-Dioxopiperazine Derivatives

[reaction: see text] Chiral spirocyclic 2,6-dioxopiperazines were synthesized from amino acid derived alpha-quaternary alpha-amino nitriles via H(2)SO(4)-promoted cyano hydration, followed by base-mediated cyclization and N-alkylation. This methodology, requiring the previous preparation of the amino nitrile by a modified Strecker reaction, was applied to Phe, Trp, Pro, Asp, Glu, and Ser derivatives. In the case of the Trp-derived amino nitrile the major product of the treatment with H(2)SO(4) was not the expected carboxamide, but a new tetracyclic indoline derivative containing the novel heterocyclic system hexahydropyrrolo[1',2',3':1,9a,9]imidazo[1,2-a]indole, as a result of a domino tautomerization. The treatment of this indoline derivative with refluxing 1 N HCl led to a Trp-derived 2,6-dioxopiperazine. The 2,6-dioxopiperazine ring opened under the reaction conditions of methyl ester saponification, giving N-(carboxyalkyl)amino acid derivatives. Therefore, the synthesis of 2,6-dioxopiperazines containing free carboxylic acids from the respective methyl esters required transesterification to benzyl esters, followed by hydrogenolysis.

Synthesis of Tricyclic 4-Chloro-pyrimido[4,5-b][1,4]benzodiazepines

[reaction: see text] A novel methodology was developed for the efficient synthesis of 4-chloro-pyrimido[4,5-b][1,4]benzodiazepines. The key is the intramolecular Friedel-Crafts cyclization of 5-amino-4-(N-substituted)anilino-6-chloropyrimidine with either a carboxylic acid or its derivatives to construct the 4-chloro-pyrimido[4,5-b][1,4]benzodiazepine core. Subsequent nucleophilic substitution allows the introduction of one more diversity point in the target molecules. This strategy provides an efficient method to access a library of compounds based on privileged substructures that are of great interest in drug discovery.

Antitumor-Promoting Effects of New Sesquiterpenes fromCrossopetalum tonduzii

Seven new sesquiterpenes (1-7) with a 'dihydro-beta-agarofuran' (= 5,11-epoxy-5beta,10alpha-eudesmane) skeleton were isolated from Crossopetalum tonduzii. Their structures were elucidated spectroscopically, especially by means of homo- and heteronuclear NMR correlation (COSY, ROESY, HSQC, and HMBC). The absolute configurations of the new compounds were determined by circular dichroism (CD) studies and by chemical correlations via the derivatives 8-11. The new compounds showed moderate antitumor-promoting effects with respect to the activation of the Epstein-Barr virus early antigen (EBV-EA).

Solution-phase parallel synthesis of an N-alkylated dihydropteridinone library from fluorous amino acids

Parallel synthesis of an N-alkylated dihydropteridinone library has been accomplished in five steps starting from two displacement reactions of 4,6-dichloro-5-nitropyrimidine, first with fluorous amino acids, then with secondary amines. The hydrogenation of the nitro group followed by microwave-assisted cyclization gave the dihydropteridinones. Further diversification was achieved by the reaction of dihydropteridinones with benzyl halides to afford mono-N-alkylated products. All the reaction intermediates and final products were purified by SPE or precipitation without the need to perform chromatography.

A safety catch linker for Fmoc-based assembly of constrained cyclic peptides

A new safety-catch linker for Fmoc solid-phase peptide synthesis of cyclic peptides is reported. The linear precursors were assembled on a tert-butyl protected catechol derivative using optimized conditions for Fmoc-removal. After activation of the linker using TFA, neutralization of the N-terminal amine induced cyclization with concomitant cleavage from the resin yielding the cyclic peptides in DMF solution. Several constrained cyclic peptides were synthesized in excellent yields and purities.

Using surface plasmon resonance to directly identify molecules in a tripeptide library that bind tightly to a vancomycin chip

This paper describes a procedure, based on direct binding, for identifying tight-binding ligands for a receptor immobilized on a sensor chip from an array of equimolar tripeptides using surface plasmon resonance. Vancomycin and a library of 96 tripeptides, with molecular weight ranging from 316 to 560 Da, were used as a model system to illustrate the procedure. A consensus structure of the strongest interacting peptides consisted of D-Ala at the C terminus and aromatic amino acid in the penultimate position. Ligands having this structure bound more tightly to vancomycin than the known D-Ala-D-Ala peptide. The throughput of our continuous assay is 96 compounds in 3.3 h, and the sample consumption is less than 2 microg per peptide and 1 ng for vancomycin. This procedure should be applicable to peptide libraries of greater complexity than that used here and to mixtures of small organic compounds.

Capter 11 Filtering in Drug Discovery

This chapter discusses the concept of filtering in drug discovery. Multiple filters may be incorporated into a definition of drug-likeness and this leads to tradeoffs among compound properties in compounds intended for screening. The optimization of compound properties may require some type of multiparameter optimization scheme in library design. Fingerprint algorithms can be used to guide diversity. Filters also need to be employed in the chemistry synthesis planning process so that good quality compounds are made. Differences in property ranges between oral and injectable drugs are summarized in the chapter. Oral drugs are lower in MWT and have fewer H-bond donors, acceptors, and rotatable bonds. A scheme for separating central nervous system (CNS)- from non-CNS-active drugs in the WDI allowed the discovery of simple parameters relating to passive blood brain barrier (BBB) permeability and the prediction of p-glycoprotein (PGP) affinity. The PGP transporter is a major barrier to the entry of compounds to the CNS. Appropriately determined PGP efflux ratios can be used as a measure of compound affinity to PGP.

Synthesis and derivatisation of a novel spiro[1-benzofuran-2,4′-piperidin]-3-one scaffold

The synthesis of a novel spiro[1-benzofuran-2,4'-piperidin]-3-one scaffold has been achieved in five steps with an overall yield of 47%. The versatility of the spiropiperidine scaffold in the context of library synthesis is exemplified by selective and sequential derivatisation of the amino and aryl bromide functional groups, including the development of multi-step telescope reaction matrices.

Palladium catalyzed alkenyl amination: from enamines to heterocyclic synthesis

The most recent advances in the Pd catalyzed amination of alkenyl halides directed towards the synthesis of imines and enamines are reviewed. The application of this cross-coupling reaction in the synthesis of heterocycles appears to be a potentially powerful methodology. The few examples already available are also discussed.

Solution-Phase Parallel Synthesis of Spirohydantoins

Spirohydantoins are considered privileged structures, making them attractive for the preparation of compound libraries with the potential for diverse biological activity. However, very few modifications of this scaffold have been reported to date. The spirohydantoin template was elaborated into a library of 168 compounds through a two-step solution-phase parallel synthesis starting from various N-substituted piperidinones. The Strecker reaction was employed to generate alpha-amino nitriles from aniline and TMSCN (or KCN). Subsequent reaction of the anilido nitrogen with a diverse set of isocyanates, followed by refluxing under acidic conditions, afforded the title library in high yield and purity.

Versatile Solid-Phase Synthesis of Trisubstituted 1H-Pyrido[2,3-d]pyrimidin-4-ones and Related Heterocycles

A solid-phase synthesis of trisubstituted 1H-pyrido[2,3-d]pyrimidin-4-ones has been developed. The synthesis utilizes solid-phase bound N-2,6-dichloronicotinoyl-1H-benzotriazole-1-carboximidamides as key intermediates. Sequential substitution of benzotriazole and the two chlorines furnishes the title compounds with regioselectivity and high purity. Application of the method to various disubstituted analogues is also demonstrated.

The role of natural product chemistry in drug discovery

Although traditionally natural products have played an important role in drug discovery, in the past few years most Big Pharma companies have either terminated or considerably scaled down their natural product operations. This is despite a significant number of natural product-derived drugs being ranked in the top 35 worldwide selling ethical drugs in 2000, 2001, and 2002. There were 15 new natural product-derived drugs launched from 2000 to 2003, as well as 15 natural product-derived compounds in Phase III clinical trials or registration at the end of 2003. Recently, there has been a renewed interest in natural product research due to the failure of alternative drug discovery methods to deliver many lead compounds in key therapeutic areas such as immunosuppression, anti-infectives, and metabolic diseases. To continue to be competitive with other drug discovery methods, natural product research needs to continually improve the speed of the screening, isolation, and structure elucidation processes, as well addressing the suitability of screens for natural product extracts and dealing with issues involved with large-scale compound supply.

Solid-Phase Synthesis of the 2(1H)-Pyrazinone Scaffold: A New Approach toward Diversely Substituted Heterocycles

The first solid-phase synthesis of the 2(1H)-pyrazinone scaffold is described. The diversity at position C6 of the pyrazinone ring is determined by the choice of the starting aldehyde. Microwave-enhanced transition metal-catalyzed reactions allow easy introduction of a variety of substituents at the C3 position. This opens a way for the generation of libraries of diversely substituted 2(1H)-pyrazinones that will be screened for biological activities.

Parallel Solid-Phase Syntheses of 1,3,4-Thiadiazolium-2-Aminides

An efficient and advantageous solid-phase strategy has been developed to synthesize 1,3,4-thiadiazolium-2-aminides. The title compounds were prepared in parallel fashion according to the following compact route: (i) anchoring of aromatic aldehydes to the solid support; (ii) solution preparation of 1,4-disubstituted thiosemicarbazides from hydrazines plus isothiocyanates; (iii) trimethylsilyl chloride-promoted cyclization between the resin-bound aldehydes and 1,4-disubstituted thiosemicarbazides; and (iv) removal of the products from the solid support by acid treatment. The products (17 made in all) were cleaved with high initial purities (90-98%) and obtained in generally good isolated yields (53-94%, with one exception).

Privileged scaffolds for blocking protein-protein interactions: 1,4-disubstituted naphthalene antagonists of transcription factor complex HOX-PBX/DNA

Structure-based-design studies, with the crystal structure of the HOXB1-PBX1/DNA transcription factor complex, were used to identify 1,4-disubstituted naphthalenes as potential antagonists. An initial library of 32 analogs was synthesized, two of which were found to be more potent than the reported activity for a 12 amino acid peptide antagonist. Antagonists were also identified of the related BRN1/DNA and BRN2/DNA transcription factor complexes indicating that a 1,4-disubstituted naphthalene may be a privileged scaffold for preparing screening libraries targeting this family of transcription factor complexes.

Unprecedented Stereospecific Synthesis of a Novel Tetracyclic Ring System, a Hybrid of Tetrahydropyrrolo[2,3-b]indole and Tetrahydroimidazo[1,2-a]indole, via a Domino Reaction upon a Tryptophan-Derived Amino Nitrile

Compounds containing a novel tetracyclic ring system, a hybrid of tetrahydropyrrolo[2,3-b]indole and tetrahydroimidazo[1,2-a]indole, are synthesized via an acid-mediated stereospecific domino tautomerization of a tryptophan-derived alpha-amino nitrile. Characterization of these new compounds and preliminary studies on the reactivity of the tetracyclic heterocyclic system are reported. [reaction: see text]

Ligand identification for G-protein-coupled receptors: a lead generation perspective

This review addresses strategies for the generation of ligands for G-protein-coupled receptors outside classical high-throughput screening and literature based approaches. These range from the chemical intuition-based strategies of endogenous ligand elaboration and privileged structure decoration to the in silico approaches of virtual screening and de novo design. Examples are cited where supporting pharmacological data has been presented.

Synthesis of fused tetrazole derivatives via a tandem cycloaddition and N-allylation reaction and parallel synthesis of fused tetrazole amines

A method for the synthesis of novel fused tricyclic tetrazoles from allylic bromides generated by the recently discovered DiazAll reaction has been developed. This new tandem reaction comprises a cycloaddition between a nitrile and (TMS)N(3) followed by an intramolecular N-allylation. The variation of functionalities in the benzene moiety was well-tolerated, and only a moderate difference in yield and degree of purity was noticed. An exo-methylene group in these new compounds permitted further derivatization. Structural resemblance with substances which possess important pharmacological properties motivated the synthesis of a series of ketones and a small library of amines.

Combinatorial Synthesis of Substituted Biaryls and Heterocyclic Arylamines

In this paper, we report very general conditions that enable palladium-mediated coupling reactions on the solid support. A wide variety of biaryls and arylamines (including pyrimidines) have been synthesized using this protocol. The chemistry facilitates a combinatorial approach to the production of large numbers of medicinally relevant heterocyclic structures.

A Versatile Stereoselective Synthesis of endo,exo-Furofuranones: Application to the Enantioselective Synthesis of Furofuran Lignans

A new stereoselective route to endo,exo-2,6-diarylfurofuranones has been developed using Mn(III)-mediated intramolecular cyclopropanation and C-H insertion reactions as key C-C bond-forming steps. Mn(III)-mediated oxidative cyclization of acetoacetate derivative 11 afforded 1-acetyl-4-aryl-3-oxabicyclo[3.1.0]hexan-2-one (12) with excellent diastereocontrol (d.r. 22:1). Subsequent Lewis acid-catalyzed opening of the activated cyclopropane ring present in 12 with benzylic alcohols then gave alpha-acetyl-gamma-butyrolactones 16 and 18-20, which reacted efficiently with in situ-generated TfN(3) to secure the key alpha-diazo-gamma-butyrolactones 22-25. Highly stereoselective rhodium-catalyzed C-H insertion reactions of diazolactones 22-25 completed the synthesis of endo,exo-2,6-diarylfurofuranones 26-29 in overall yields ranging from 41 to 48% from 1-phenylallyl alcohol (+/-)-10. The approach developed for the furofuranones 26-29 was then applied to the asymmetric syntheses of four furofuran lignans, (+)-xanthoxylol (1), (+)-methylxanthoxylol (2), (+)-epipinoresinol (3), and (+)-epieudesmin (4), starting from enantiomerically enriched 1-arylallyl alcohol (S)-31.

Switchable Catalysis: Modular Synthesis of Functionalized Pyrimidinones via Selective Sulfide and Halide Cross-Coupling Chemistry

[reaction: see text] A general demonstration of orthogonal selectivity of the Liebeskind-Srogl cross-coupling protocol compared to the Suzuki-Miyaura and Stille variants is reported.

5-Endo-dig electrophilic cyclization of alpha-alkynyl carbonyl compounds: synthesis of novel bicyclic 5-iodo- and 5-bromofuranopyrimidine nucleosides

5-Endo-dig electrophilic cyclization of 5-alkynyl-2'-deoxyuridines with N-iodosuccinimide or N-bromosuccinimide in acetone at room temperature gives 3-(2'-deoxy-beta-D-ribofuranosyl)-5-halo-2,3-dihydrofuro[2,3-d]pyrimidin-2-ones that usually precipitate from the reaction mixture (86-74%).

Difficult macrocyclizations: new strategies for synthesizing highly strained cyclic tetrapeptides

[reaction: see text] Cyclic tetrapeptides are an intriguing class of natural products. To synthesize highly strained cyclic tetrapeptides we developed a macrocyclization strategy that involves the inclusion of 2-hydroxy-6-nitrobenzyl (HnB) group at the N-terminus and in the "middle" of the sequence. The N-terminal auxiliary performs a ring closure/ring contraction role, and the backbone auxiliary promotes cis amide bonds to facilitate the otherwise difficult ring contraction. Following this route, the all-L cyclic tetrapeptide cyclo-[Tyr-Arg-Phe-Ala] was successfully prepared.