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.     

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.     

Synthesis of Molecular Frameworks Containing Two Distinct Heterocycles Connected in a Single Molecule with Enhanced Three‐Dimensional Shape Diversity

Herein, we report the synthesis of fused‐triazole scaffolds that are connected by pyrimidines, pyrazoles, or pyrazolopyrimidines through carbohydrate‐derived stereodivergent linkers. Pyrimidine‐, pyrazole‐, or pyrazolopyrimidine‐based carbohybrids were constructed through condensations of the key intermediates, 2‐C‐formyl glycals, with various dinucleophiles. Fused‐triazole scaffolds were obtained through intramolecular 1,3‐dipolar cycloadditions after selective functionalization of the carbohybrid polyol moieties with azide and alkyne functionalities using S_N2‐type alkylations or Mitsunobu reactions. Overall, this synthetic method affords two distinct privileged substructures in a single molecule, connected by stereodivergent diol linkers derived from abundant natural chiral sources, namely, carbohydrates. The resulting vicinal diols in the linker were further modified to achieve unique connectivities between the two privileged structures for maximized three‐dimensional shape diversity, which we called the linker diversification strategy.     

Combinatorial synthesis of oligo(phenylene ethynylene)s

The combinatorial synthesis of oligo(phenylene ethynylene) tetramers, both in solution and on solid support, is described. These products are of interest for molecular electronics applications. An iterative sequence, coupling of aryl halides to alkynes under Sonogashira conditions, was used. Five monomers functionalized with electron-donating or electron-withdrawing groups were synthesized, and used to generate a library of 25 trimers in a solution-phase based process. A library of 24 tetramers was prepared by subsequent protodesilylation and coupling with the alligator clip 4-iodo-1-thioacetylbenzene. The solution-phase based sequence was successfully adapted to a higher yielding directed split-and-pool solid-phase process, with average yields of 78–86% for each step over seven steps. A triazene linker group was used to attach the starting monomer to the polymer beads. At the completion of the solid-phase-based process, traceless cleavage of trimers from the resin was achieved by sonication of the resin in 10% HCl/THF solution. The released products were then poised for the final step in the sequence, attachment of the alligator clip.     

Solid-phase approach to tetrahydroquinolones using a sulfur linker cleaved by SmI2

[reaction: see text] A sulfur alpha-heteroatom-substituted carbonyl (HASC) linker has been utilized in a solid-phase approach to tetrahydroquinolones. The route illustrates the compatibility of the linker system with palladium-catalyzed transformations and its utility for library synthesis. The linker is cleaved by electron transfer from samarium(II) iodide.     

Antibacterial single-bead screening

Triazine based antibiotics were prepared by the attachment of cyanuric chloride onto a Marshall-type safety catch linker, followed by successive aromatic nucleophilic substitutions, linker activation and nucleophilic cleavage. High-loading dendrimer beads allowed the release of sufficient amount of compound from a single bead to give clear inhibition.     

Using covalent dimers of human carbonic anhydrase II to model bivalency in immunoglobulins

This paper describes the development of a new bivalent system comprising synthetic dimers of carbonic anhydrase linked chemically through thiol groups of cysteine residues introduced by site-directed mutagenesis. These compounds serve as models with which to study the interaction of bivalent proteins with ligands presented at the surface of mixed self-assembled monolayers (SAMs). Monovalent carbonic anhydrase (CA) binds to benzenesulfonamide ligands presented on the surface of the SAM with K(d)(surf) = 89 nM. The synthetic bivalent proteins--inspired by the structure of immunoglobulins--bind bivalently to the sulfonamide-functionalized SAMs with low nanomolar avidities (K(d)(avidity,surf) = 1-3 nM); this difference represents a ~50-fold enhancement of bivalent over monovalent association. The paper describes dimers of CA having (i) different lengths of the covalent linker that joined the two proteins and (ii) different points of attachment of the linker to the protein (either near the active site (C133) or distal to the active site (C185)). Comparison of the thermodynamics of their interactions with SAMs presenting arylsulfonamide groups demonstrated that varying the length of the linker between the molecules of CA had virtually no effect on the rate of association, or on the avidity of these dimers with ligand-presenting surfaces. Varying the point of attachment of the linker between monomeric CA's also had almost no effect on the avidity of the dimers, although changing the point of attachment affected the rates of binding and unbinding. These observations indicate that the avidities of these bivalent proteins, and by inference the avidities of structurally similar bivalent proteins such as IgG, are unexpectedly insensitive to the structure of the linker connecting them.     

Practical synthesis of a dithiane-protected 3',5'-dialkoxybenzoin photolabile safety-catch linker for solid-phase organic synthesis.

The solution-phase preparation of the 3',5'-dialkoxybenzoin photolabile safety-catch linker 16 is described. Pivotal to this convenient synthesis is the selection of appropriate orthogonal protecting groups for the alkoxy functionalities present. The new linker can be readily loaded onto any standard amine-terminating resin under peptide-coupling conditions, without the need to protect the secondary alcohol functionality, and subsequently loaded with substrate. Alternatively, the loading efficiency of sterically hindered substrates can be enhanced by preloading the semiprotected linker variant 10 in solution prior to immobilization onto the resin. This second generation of benzoin photolabile safety-catch linkers provides greater control of both linker loading and resin attachment and should prove to be a more versatile and convenient form of the linker.     

Solid phase approaches to N-heterocycles using a sulfur linker cleaved by SmI2

A sulfur HASC (alpha-hetero-atom substituted carbonyl) linker has been utilized in solid-phase approaches to oxindoles and tetrahydroquinolones. The route to oxindoles employs the first Pummerer cyclizations on solid phase, whereas the route to tetrahydroquinolones involves a microwave-assisted Heck reaction followed by a Michael cyclization. In both cases, the linker is cleaved in a traceless fashion by electron transfer from samarium(II) iodide. The routes illustrate the compatibility of the linker system with a number of reaction types and its utility for library synthesis.     

Constructing virtual combinatorial fragment libraries based upon MDL Drug Data Report database

Structural analysis of known drugs or drug-like compounds provides important information for drug design. The 142553 drug molecules in the MDL Drug Data Report database were analyzed, and then the common structural features were extracted. According to the common structural features, drug molecules were segmented into 32017 fragments, including 13642 ring fragments, 10076 linker fragments, and 8299 side chain fragments. These fragments were further used to establish three types of virtual combinatorial fragment libraries: a basic framework library containing 13574 rings; a linker library of 8051 linkers and a pharmacophore library of 34244 fragments combined by rings and side chains. After energy minimization, all fragments in the above three libraries maintain reasonable geometrical features and spatial conformations, and would be useful for building a virtual combinatorial database and de novo drug design.     

A solid-supported,enantioselective synthesis suitable for the rapid preparation of large numbers of diverse structural analogues of (-)-saframycin A

A 10-step solid-supported, enantioselective synthesis suitable for the rapid preparation of large numbers of diverse structural analogues of saframycin A is described. The synthetic route, which bears analogy to solid-phase peptide synthesis, involves the directed condensation of N-protected alpha-amino aldehyde reactants. A novel dual linker was developed for attachment of intermediates to the solid support via a C-protective group, a substituted morpholino nitrile derivative. The route employs a novel diastereospecific cyclorelease mechanism, supports structural variation at multiple sites in the saframycin core, and obviates the need for chromatographic purification of the products or any intermediate. To demonstrate the feasibility of structural variation at multiple sites, a matrix of 16 saframycin A analogues was prepared by parallel synthesis with simultaneous variation of two sites. This work is notable not only as a preliminary step toward large-scale library construction but also as an example of the use of sequential stereoselective C-C bond-forming reactions on the solid phase for the preparation of natural product analogues.     

Parallel solid-phase synthesis and structural characterization of a library of highly substituted chiral 1,3-oxazolidines

The rapid parallel synthesis and characterization of diverse chirally defined 1,3-oxazolidines is reported. Three diversity elements were incorporated in a 6 x 4 x 4 block approach to generate a 96-member 1,3-oxazolidine library. The synthetic route involved initial attachment of six nonracemic phenylglycidols, (2S,3S)1A-C and (2R,3R)-2A-C, to 2% cross-linked polystyrene resin via a chlorodiethylsilane linker (PS-DES), followed by regio- and stereoselective oxirane ring opening with four primary amines (3a-d). The key condensation reaction between the resulting polymer-bound beta-amino alcohols and four aldehydes (4a-d) was found to occur optimally in warm benzene (60 degrees C) in the presence of anhydrous magnesium sulfate. Cleavage of the oxazolidines from the resin support was achieved with TBAF to give the individual members (2R,4R,5R)-5Aaa-Cdd and (2S,4S,5S)-6Aaa-Cdd in good to excellent yields (51-99%) based on mass recovery. Purities of all these crude products was generally >85% (as measured by LCMS). 1H, 13C NMR, and 1D difference nOe of the library members confirmed the structural and stereochemical integrity of the substituents around the 1,3-oxazolidine core. The asymmetric induction at C-2 (cis or trans to the C-4 substituent) ratio ranged from 4 to I to 49 to 1 across the library. This report highlights the versatility of the 1,3-oxazolidine heterocycle as a scaffold for concise parallel library construction and opens the way for high-throughput screening of such compounds in the biological sphere.     

Cleavable hydrophilic linker for one-bead-one-compound sequencing of oligomer libraries by tandem mass spectrometry

We have developed a method for the rapid and unambiguous identification of sequences of hit compounds from one-bead-one-compound combinatorial libraries of peptide and peptoid ligands. The approach uses a cleavable linker that is hydrophilic to help reduce nonspecific binding to biological samples and allows for the attachment of a halogen tag, which greatly facilitates post-screening sequencing by tandem mass spectrometry (MS/MS). The linker is based on a tartaric acid unit, which, upon cleavage from resin, generates a C-terminal aldehyde. This aldehyde can then be derivatized with a bromine-containing amino-oxy compound that serves as an isotope tag for subsequent MS/MS analysis of y-ion fragments. We have applied this linker and method to the syntheses of a number of peptoids that vary in sequence and length and have also demonstrated single-bead sequencing of a peptoid pentamer. The linker is also shown to have very low levels of nonspecific binding to proteins.     

A design strategy for drug-like polyheterocycles with privileged substructures for discovery of specific small-molecule modulators

We demonstrated the importance of maximized skeletal diversity of privileged substructures for the construction of a drug-like small-molecule library through a series of high-throughput screening and subsequent bioevaluations. Our divergent pDOS strategy can provide an efficient approach for the discovery of novel small-molecule modulators with excellent specificity.     

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.     

An oxidatively-activated safety catch linker for solid phase synthesis

A N-benzyl-4-amino-2,2-dimethylbutanoic acid-based system has been developed as a new oxidatively activated safety catch linker for reaction monitoring and optimisation on solid support. The CAN promoted oxidative debenzylation of the tertiary N-benzylamine moiety, followed by concomitant cyclisation and release of alcohols and amines has been demonstrated both in solution phase model studies and on the solid phase. The linker system has been applied to the solid phase synthesis of a collection of phenol derivatives, and to the demonstration of the attachment and release of a chiral auxiliary from a solid support.     

Solid-phase combinatorial synthesis of benzothiazoles, benzimidazoles, and benzoxazoles using a traceless linker

New methodology for the solid-phase synthesis of benzothiazoles, benzimidazoles, and benzoxazoles has been developed by using a traceless 4-alkoxy-aniline linker. The desired products were released from the polymer support by imine-exchange process coupled with air oxidation. Combinatorial library consisting of 36 members has been synthesized using this linker. The yields are low to good, which highly depend on the building blocks. Recycling of the polymer support was also investigated.     

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.     

TRAM linker: a safety-catch linker for the traceless release of acrylamides

[reaction: see text] A novel safety-catch linker for the solid-phase synthesis of small-molecule libraries containing electrophilic reactive groups has been developed. Upon cleavage from solid support, the linker generates a Michael acceptor (an acrylamide) on each library member. Utilization of a two-resin system in the final cleavage step provides crude products in high purity, allowing direct use in biological assays following filtration and evaporation.     

Solid-Phase Synthesis of Oligosaccharides: Construction of a Dodecasaccharide

Complicated oligosaccharides such as dodecasaccharide 1 can be constructed by a new solid-phase strategy. The attachment to the polymeric support (gray sphere) is through a photolabile linker (structure I ), and thioglycosides serve as carbohydrate donors. Bn=benzyl, Bz=benzoyl.