Urea Substituents Research Articles

Intramolecular Nucleophilic Vinylic Substitution (SNV) by Carbon Nucleophiles: Conformationally Directed Formation of Dienes from N,N'-Diallyl Ureas.

Nucleophilic vinylic substitution (SNV) by carbon nucleophiles allows the formation of vinylic C-C bonds without transition metal catalysts. In this paper, we show that tethering two alkenes together through a urea linkage can lead to the formation of a diene by an intramolecular SNV reaction. The starting materials are fully substituted N,N'-diallyl ureas; the reaction proceeds in the presence of base, and entails a cascade of deprotonations, reprotonations, and an SNV reaction of an allylic carbanion on a rare electrophile: a vinylic urea. As a result, two allylic substituents couple to form a diene, despite the fact that neither is activated towards electrophilic attack. The reaction is tolerant of significant steric bulk, and exhibits regioselectivity with unsymmetrical diallyl ureas: β-substituted allyl groups invariably behave as nucleophiles, while electrophilic behavior may be enforced by the use of an E-vinylic urea substituent that cannot be deprotonated under the reaction conditions.

Fullerene Complexation in a Hydrogen-Bonded Porphyrin Receptor via Induced-Fit: Cooperative Action of Tautomerization and C-H···π Interactions.

A supramolecular chiral hydrogen-bonded tetrameric aggregate possessing a large cavity and tetraarylporphyrin substituents was assembled using alternating 4H- and 2H-bonds between ureidopyrimidinone and isocytosine units, respectively. The aggregation mode was rationally shifted from social to narcissistic self-sorting by changing urea substituent size only. The H-bonded tetramer forms a strong complex with C60 guest, at the same time undergoing remarkable structural changes. Namely, the cavity adjusts to the guest via keto-to-enol tautomerization of the ureidopyrimidinone unit and as a result, porphyrin substituents move apart from each other in a scissor blade-like opening fashion. The rearrangement is accompanied by C-H···π interaction between the alkyl solubilizing groups and the nearby placed porphyrin π-systems. The latter interaction was found to be crucial for the guest complexation event, providing energetic compensation for otherwise costly tautomerization. We showed that only the systems possessing sufficiently long alkyl chains capable of interacting with a porphyrin ring are able to form a complex with C60. The structural rearrangement of the tetramer was quantitatively characterized by electron paramagnetic resonance pulsed dipolar spectroscopy measurements using photogenerated triplets of porphyrin and C60 as spin probes. Further exploring the C-H···π interaction as a decisive element for the C60 recognition, we investigated the guest-induced self-sorting phenomenon using scrambled tetramer assemblies composed of two types of monomers possessing alkyl chains of different lengths. The presence of the fullerene guest has enabled the selective scavenging of monomers capable of C-H···π interaction to form homo-tetrameric aggregates.

Selective Carboxylate Recognition Using Urea-Functionalized Unclosed Cryptands: Mild Synthesis and Complexation Studies.

Herein we present the synthesis and evaluation of anion-binding properties of 12 new receptors from the unclosed cryptand family. Their core is built on the stable 26-membered tetraamidic macrocyclic scaffold, whereas various alkyl and aryl urea substituents were introduced after a yield-limiting macrocyclization step (65–98%). The receptors strongly bind anions, in particular carboxylates, even in a highly competitive solvent mixture (DMSO-d6 + H2O 95:5 v/v).

Pan-NS3 protease inhibitors of hepatitis C virus based on an R3-elongated pyrazinone scaffold

Herein, we present the design and synthesis of 2(1H)-pyrazinone based HCV NS3 protease inhibitors and show that elongated R3 urea substituents were associated with increased inhibitory potencies over several NS3 protein variants. The inhibitors are believed to rely on β-sheet mimicking hydrogen bonds which are similar over different genotypes and current drug resistant variants and correspond to the β-sheet interactions of the natural peptide substrate. Inhibitor 36, for example, with a urea substituent including a cyclic imide showed balanced nanomolar inhibitory potencies against genotype 1a, both wild-type (Ki = 30 nM) and R155K (Ki = 2 nM), and genotype 3a (Ki = 5 nM).

Structure-guided design of purine-based probes for selective Nek2 inhibition.

Nek2 (NIMA-related kinase 2) is a cell cycle-dependent serine/threonine protein kinase that regulates centrosome separation at the onset of mitosis. Overexpression of Nek2 is common in human cancers and suppression can restrict tumor cell growth and promote apoptosis. Nek2 inhibition with small molecules, therefore, offers the prospect of a new therapy for cancer. To achieve this goal, a better understanding of the requirements for selective-inhibition of Nek2 is required. 6-Alkoxypurines were identified as ATP-competitive inhibitors of Nek2 and CDK2. Comparison with CDK2-inhibitor structures indicated that judicious modification of the 6-alkoxy and 2-arylamino substituents could achieve discrimination between Nek2 and CDK2. In this study, a library of 6-cyclohexylmethoxy-2-arylaminopurines bearing carboxamide, sulfonamide and urea substituents on the 2-arylamino ring was synthesized. Few of these compounds were selective for Nek2 over CDK2, with the best result being obtained for 3-((6-(cyclohexylmethoxy)-9H-purin-2-yl)amino)-N,N-dimethylbenzamide (CDK2 IC50 = 7.0 μM; Nek2 IC50 = 0.62 μM) with >10-fold selectivity. Deletion of the 6-substituent abrogated activity against both Nek2 and CDK2. Nine compounds containing an (E)-dialkylaminovinyl substituent at C-6, all showed selectivity for Nek2, e.g. (E)-6-(2-(azepan-1-yl)vinyl)-N-phenyl-9H-purin-2-amine (CDK2 IC50 = 2.70 μM; Nek2 IC50 = 0.27 μM). Structural biology of selected compounds enabled a partial rationalization of the observed structure activity relationships and mechanism of Nek2 activation. This showed that carboxamide 11 is the first reported inhibitor of Nek2 in the DFG-in conformation.

Design, synthesis and in vitro pharmacology of GluK1 and GluK3 antagonists. Studies towards the design of subtype-selective antagonists through 2-carboxyethyl-phenylalanines with substituents interacting with non-conserved residues in the GluK binding sites

In order to identify compounds selective for the GluK1 and GluK3 subtypes of kainate receptors we have designed and synthesized a series of (S)-2-amino-3-((2-carboxyethyl)phenyl)propanoic acid analogs with hydrogen bond donating and accepting substituents on the aromatic ring. Based on crystal structures of GluK1 in complex with related ligands, the compounds were designed to explore possible interactions with non-conserved residues outside the glutamate ligand binding site and challenge the water binding network. Apart from obtaining GluK1 selective antagonists one analog with a phenyl-substituted urea (compound 31) showed some preference for GluK3 over GluK1-receptors. Docking studies indicate that this preference may be attributed to contacts between the NH of the urea substituent and non-conserved Ser741 and Ser761 residues.

ChemInform Abstract: Protecting Group Free Synthesis of Carboxyl‐Substituted Dihydropyrimidines Through Biginelli Reaction.

Chlorotrimethylsilane-promoted Biginelli-type reaction of benzaldehyde, acetoacetic acid derivatives, and various carboxyl-containing ureas was explored. It was found that the steric load of the urea substituents influenced strongly the reaction outcome; in particular, the method was efficient only in the case of unbranched mono-substituted ureas bearing either aliphatic or aromatic groups. The method allows performing a one-pot, protecting group free synthesis of dihydropyrimidines possessing carboxylic functionality.

Thiophene carboxamide inhibitors of JAK2 as potential treatments for myleoproliferative neoplasms

A series of carboxamide-substituted thiophenes demonstrating inhibition of JAK2 is described. Development of this chemical series began with the bioisosteric replacement of a urea substituent by a pyridyl ring. Issues of chemical and metabolic stability were solved using the results of both in vitro and in vivo studies, ultimately delivering compounds such as 24 and 25 that performed well in an acute PK/PD model measuring p-STAT5 inhibition.

Protecting Group Free Synthesis of Carboxyl-substituted Dihydropyrimidines Through Biginelli Reaction

Chlorotrimethylsilane-promoted Biginelli-type reaction of benzaldehyde, acetoacetic acid derivatives, and various carboxyl-containing ureas was explored. It was found that the steric load of the urea substituents influenced strongly the reaction outcome; in particular, the method was efficient only in the case of unbranched mono-substituted ureas bearing either aliphatic or aromatic groups. The method allows performing a one-pot, protecting group free synthesis of dihydropyrimidines possessing carboxylic functionality.

Heteroaryl urea inhibitors of fatty acid amide hydrolase: Structure–mutagenicity relationships for arylamine metabolites

The structure–activity relationships for a series of heteroaryl urea inhibitors of fatty acid amide hydrolase (FAAH) are described. Members of this class of inhibitors have been shown to inactivate FAAH by covalent modification of an active site serine with subsequent release of an aromatic amine from the urea electrophile. Systematic Ames II testing guided the optimization of urea substituents by defining the structure–mutagenicity relationships for the released aromatic amine metabolites. Potent FAAH inhibitors were identified having heteroaryl amine leaving groups that were non-mutagenic in the Ames II assay.

SupraBox: Chiral Supramolecular Oxazoline Ligands

AbstractA new class of oxazoline ligands, named SupraBox, was studied. These ligands possess an additional urea functionality to generate supramolecular bidentate ligands in transition‐metal complexes, by the establishment of hydrogen bonds between the urea N‐hydrogens of one ligand and the carbonyl oxygen of a second one. A library of 16 SupraBox ligands was prepared using 5 differently substituted oxazoline nuclei, 4 linkers and 3 different urea substituents. The formation of copper(II) and palladium(II) complexes was investigated by MS, UV/Vis and 1H‐NMR spectroscopy. The SupraBox library was screened in the copper‐catalyzed asymmetric benzoylation of vic‐diols. Good selectivities were obtained in the kinetic resolution of racemic hydrobenzoin [up to 86 % ee and selectivity (s) = 28] and in the desymmetrization of meso‐hydrobenzoin (up to 88 % ee).

Molecular Basis for Binding and Subtype Selectivity of 1,4-Benzodiazepine Antagonist Ligands of the Cholecystokinin Receptor

Allosteric binding pockets in peptide-binding G protein-coupled receptors create opportunities for the development of small molecule drugs with substantial benefits over orthosteric ligands. To gain insights into molecular determinants for this pocket within type 1 and 2 cholecystokinin receptors (CCK1R and CCK2R), we prepared a series of receptor constructs in which six distinct residues in TM2, -3, -6, and -7 were reversed. Two novel iodinated CCK1R- and CCK2R-selective 1,4-benzodiazepine antagonists, differing only in stereochemistry at C3, were used. When all six residues within CCK1R were mutated to corresponding CCK2R residues, benzodiazepine selectivity was reversed, yet peptide binding selectivity was unaffected. Detailed analysis, including observations of gain of function, demonstrated that residues 6.51, 6.52, and 7.39 were most important for binding the CCK1R-selective ligand, whereas residues 2.61 and 7.39 were most important for binding CCK2R-selective ligand, although the effect of substitution of residue 2.61 was likely indirect. Ligand-guided homology modeling was applied to wild type receptors and those reversing benzodiazepine binding selectivity. The models had high predictive power in enriching known receptor-selective ligands from related decoys, indicating a high degree of precision in pocket definition. The benzodiazepines docked in similar poses in both receptors, with C3 urea substituents pointing upward, whereas different stereochemistry at C3 directed the C5 phenyl rings and N1 methyl groups into opposite orientations. The geometry of the binding pockets and specific interactions predicted for ligand docking in these models provide a molecular framework for understanding ligand selectivity at these receptor subtypes. Furthermore, the strong predictive power of these models suggests their usefulness in the discovery of lead compounds and in drug development programs.

The Mechanism of the Stereospecific Intramolecular Arylation of Lithiated Ureas: The Role of Li+ Probed by Electronic Structure Calculations, and by NMR and IR Spectroscopy

AbstractIn situ NMR and IR spectroscopy studies were carried out on the rearrangement of lithiated N‐benzyl‐N′‐aryl ureas, which involves N‐to‐C aryl transfer with retention of configuration. The IR spectroscopy studies revealed that initial benzylic lithiation was followed by migration of the aryl ring to yield a lithiated urea product without a detectable dearomatised intermediate. Similar results were obtained by NMR spectroscopy, but when 1,3‐dimethyl‐3,4,5,6‐tetrahydro‐2(1H)‐pyrimidinone (DMPU) was added to the solvent mixture, a transient dearomatised intermediate was detectable during migration of a 1‐naphthyl ring. DFT calculations highlight the importance of coordinated lithium cations, and their migration from one site to another, in the rearrangement. Rearrangement is initiated by migration of a solvated lithium cation from the anionic centre of the starting organolithium to a site close the adjacent phenyl ring, allowing retentive attack of the anionic centre on the more remote ring with movement of the solvated lithium cation to the remote ring stabilising the developing negative charge. A short‐lived spirocyclic intermediate is predicted to undergo elimination by loss of the urea substituent, completing the migration. Coordination of the carbonyl group to a second solvated lithium cation appears to be essential for this step. Calculated shifts for this intermediate when a 1‐naphthyl ring is migrating are consistent with the transient signals observed by NMR spectroscopy. Alternative pathways involving (1) invertive migration and (2) attack on the urea C=O group were also calculated and were found to require significantly higher energy transition states.

Identification of MK-5710 ((8aS)-8a-methyl-1,3-dioxo-2-[(1S,2R)-2-phenylcyclopropyl]-N-(1-phenyl-1H-pyrazol-5-yl)hexahydroimid azo[1,5-a]pyrazine-7(1H)-carboxamide), a potent smoothened antagonist for use in Hedgehog pathway dependent malignancies, Part 1

The Hedgehog (Hh-) signaling pathway is a key developmental pathway which controls patterning, growth and cell migration in most tissues, but evidence has accumulated showing that many human tumors aberrantly reactivate this pathway. Smoothened antagonists offer opportunities for the treatment of malignancies dependent on the Hh pathway, and the most advanced clinical candidates are demonstrating encourage initial results. A novel series of [6,5]-bicyclic tetrahydroimidazo[1,5-a]pyrazine-1,3(2H,5H)-dione smoothened antagonists has been identified, and the series has been extensively explored to ascertain the key detriments for activity, demonstrating that the trans-2-phenylcyclopropyl and hydantoin ring systems are critical for potency, while a variety of urea substituents can be tolerated. The combination of these optimal groups gives smoothened antagonists with activity in the low nanomolar range.

Drug Development for Eradication with InclusionComplex of Multifunctional-modifiedβCD

We studied the properties of an inclusion complex of amoxicillin (AMPC) in a multifunctional-modified β-cyclodextrin (mf-βCD) having an affinity for bacteria. The mf-βCDs used were βCDs modified by the introduction, on the end of a hydrocarbon chain linker, of a saccharide or urea substituent group expected to have affinity for bacteria. Using quantum chemical methods, we showed that the use of mf-βCD stabilizes AMPC against acid, and that formation of an inclusion complex should produce bacterial affinity and improve bactericidal efficiency. The chemical stabilization of AMPC by mf-βCD was tested by hydrolysis. We also showed that in order to form a 1:1 complex of AMPC and mf-βCD (AMPC-mf-βCD) functioning as a drug delivery system (DDS), the optimal conditions require mixing mf-βCD with AMPC at a molar ratio between 1:5 and 1:10 (AMPC:mf-βCD). We used Gaussian program to determine the precedence of inclusion of AMPC by mf-βCDs and to obtain optimized structures of the complex. We demonstrated the importance of orbital interactions and electronic correlations during complexation for the emergence of chemotaxis in Helicobacter pylori1) toward the urea substituent on mf-βCDs. We further used the self-consistent reaction field (SCRF) method to study the effects of solvent. Using the optimized structures under solvent-free conditions, we calculated the energies of each AMPC-mf-βCD complex in water by the SCRF method using B3LYP/6-31G* levels.

Anomeric Effect of the Nitrogen Atom in the Isocyano and Urea Groups

AbstractThe anomeric effect associated with the nitrogen atom in the isocyano group was investigated by using 1H NMR spectroscopic analysis of an anomeric pair of xylopyranosyl isocyanides 8 and 7. We found that β‐anomer 7 prefers to exist in the 1C4 conformation in which the nitrogen atom in the isocyano group adopts an axial orientation. This observation, coupled with the results of X‐ray crystallographic analysis establishes that the nitrogen atom in the isocyano group displays the anomeric effect. Furthermore, xylopyranosyl isocyanides 8 and 7 were transformed into the corresponding xylopyranosyl ureas 10 and 11. In the case of the urea group, a normal sterically determined preference is observed in which the bulky urea substituents at the pyranose anomeric position occupy the equatorial position.

Synthesis and Anion‐Binding Properties of Novel Redox‐Active Calixarene Receptors

AbstractA novel synthetic approach towards redox‐active calixarene‐based receptors is described in which ferrocene fragments were introduced at the lower rim through anion‐binding urea or amide connections. These derivatives were prepared in one pot by treating an amine‐containing calixarene with ferrocenecarboxylic acid in the presence of diphenylphosphoryl azide and diisopropylethylamine. This method allows a convergent approach to these receptors and is readily adaptable to the introduction of other urea substituents. The anion‐binding properties of these artificial receptors have been revealed by NMR spectroscopy and thoroughly investigated by electrochemical methods. We have assessed the importance of the urea–phosphate bonds in the observed electrochemical response by studying receptors in which the ferrocene reporters and binding fragments are closely associated or fully disconnected through a long alkyl chain. The experimental results clearly show the utmost importance of ion‐pairing effects in the electrochemical recognition process, which account for most of the transduction signal in organic apolar media. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)

Potent Inhibitors of the Hedgehog Signaling Pathway

A small family of phenyl quinazolinone ureas is reported as potent modulators of Hedgehog protein function. Preliminary SAR studies of the urea substituent led to a nanomolar Hedgehog antagonist.

Corrosion-protective properties of 1-phenacylmethyl-2-arylcarbamido(arylthiocarbamido)pyridinium bromides

Inhibiting effect of 1-phenacylmethylpyridinium bromides containing urea or thiourea substituents in the pyridinium ring on steel and zinc corrosion in sulfuric acid solutions was studied.

Structure-Based Organic Synthesis of a Tricyclic N-Malayamycin Analogue

The solid-state structure of crystalline malayamycin A reveals a urea substituent that bisects the plane of the chairlike tetrahydropyran subunit. On the basis of this topological feature, we synthesized a tricyclic N-nucleoside analogue in which an ethano bridge linked the urea NH group with the ring junction of the bicyclic tetrahydrofuropyran unit.