Urea Derivatives in Modern Drug Discovery and Medicinal Chemistry

The urea functionality is inherent to numerous bioactive compounds, including a variety of clinically approved therapies. Urea containing compounds are increasingly used in medicinal chemistry and drug design in order to establish key drug-target interactions and fine-tune crucial drug-like properties. In this perspective, we highlight physicochemical and conformational properties of urea derivatives. We provide outlines of traditional reagents and chemical procedures for the preparation of ureas. Also, we discuss newly developed methodologies mainly aimed at overcoming safety issues associated with traditional synthesis. Finally, we provide a broad overview of urea-based medicinally relevant compounds, ranging from approved drugs to recent medicinal chemistry developments.

Quantification of Stereochemical Communication in Metal-Organic Assemblies

The derivation and application of a statistical mechanical model to quantify stereochemical communication in metal-organic assemblies is reported. The factors affecting the stereochemical communication within and between the metal stereocenters of the assemblies were experimentally studied by optical spectroscopy and analyzed in terms of a free energy penalty per "incorrect" amine enantiomer incorporated, and a free energy of coupling between stereocenters. These intra- and inter-vertex coupling constants are used to track the degree of stereochemical communication across a range of metal-organic assemblies (employing different ligands, peripheral amines, and metals); temperature-dependent equilibria between diastereomeric cages are also quantified. The model thus provides a unified understanding of the factors that shape the chirotopic void spaces enclosed by metal-organic container molecules.

Quantification of Stereochemical Communication in Metal-Organic Assemblies

The derivation and application of a statistical mechanical model to quantify stereochemical communication in metal-organic assemblies is reported. The factors affecting the stereochemical communication within and between the metal stereocenters of the assemblies were experimentally studied by optical spectroscopy and analyzed in terms of a free energy penalty per "incorrect" amine enantiomer incorporated, and a free energy of coupling between stereocenters. These intra- and inter-vertex coupling constants are used to track the degree of stereochemical communication across a range of metal-organic assemblies (employing different ligands, peripheral amines, and metals); temperature-dependent equilibria between diastereomeric cages are also quantified. The model thus provides a unified understanding of the factors that shape the chirotopic void spaces enclosed by metal-organic container molecules.

Remote stereoselective deconjugation of α,β-unsaturated esters by simple amidation reactions

The thermodynamically disfavored isomerization of α,β-unsaturated esters to deconjugated β,γ-unsaturated analogues occurs readily when coupled to an amidation. Within the framework of macrocyclic derivatives, it is shown that 15, 16, and 18 membered macrocycles react with tBuOK and anilines to generate, in one-pot, β,γ-unsaturated amides (yields up to 88%). Importantly, single (chiral) diastereomers are isolated (d.r. > 49 : 1, ¹H NMR) irrespective of the size and nature of the rings, showing an effective transmission of remote stereochemistry during the isomerization process. CSP-chromatographic resolution and absolute configuration determination by VCD are achieved.

Corrole–imide dyads — Synthesis and optical properties

Two rarely seen building blocks have been incorporated into light absorbing arrays: corroles and 2,3-naphthalimides. General synthetic strategy consisting in direct condensation of formyl substituted aromatic imides with dipyrranes led to diverse range of trans-A2B-corroles in acceptable yields. Spectroscopic properties of all five dyads studied suggest that regardless the imide's structure, components are weakly electronically coupled. Positioning 2,3-naphthalimide unit partially above the corrole core leads to slight alteration of their optical properties. Dyads bearing blue-absorbing imide components display different behavior depending on their structure. In corrole linked with naphthalenyl-naphthalene-1,8-carboximide a 100% effective energy transfer reaction from the imide component to the corrole component occurred. On the contrary, in small, strongly polarized amino-cyano-phthalimide neither efficient energy-nor electron-transfer could be detected and excitation leads to fluorescence from both components.

Flaws in foldamers: conformational uniformity and signal decay in achiral helical peptide oligomers

Although foldamers, by definition, are extended molecular structures with a well-defined conformation, minor conformers must be populated at least to some extent in solution. We present a quantitative analysis of these minor conformers for a series of helical oligomers built from achiral but helicogenic α-amino acids. By measuring the chain length dependence or chain position dependence of NMR or CD quantities that measure screw-sense preference in a helical oligomer, we quantify values for the decay constant of a conformational signal as it passes through the molecular structure. This conformational signal is a perturbation of the racemic mixture of M and P helices that such oligomers typically adopt by the inclusion of an N or C terminal chiral inducer. We show that decay constants may be very low (<1% signal loss per residue) in non-polar solvents, and we evaluate the increase in decay constant that results in polar solvents, at higher temperatures, and with more conformationally flexible residues such as Gly. Decay constants are independent of whether the signal originates from the N or the C terminus. By interpreting the decay constant in terms of the probability with which conformations containing a screw-sense reversal are populated, we quantify the populations of these alternative minor conformers within the overall ensemble of secondary structures adopted by the foldamer. We deduce helical persistence lengths for Aib polymers that allow us to show that in a non-polar solvent a peptide helix, even in the absence of chiral residues, may continue with the same screw sense for approximately 200 residues.

Conformational cooperativity between helical domains of differing geometry in oligoamide–oligourea foldamer chimeras

Two foldamer domains of different classes (urea and amide) remain in conformational communication, and adopt a well-defined global structure in solution, provided the interdomain hydrogen-bonds are suitably orientated.

Conformation-determined through-bond versus through-space electronic communication in mixed-valence systems with a cross-conjugated urea bridge

Bis-triarylamine 2 and cyclometalated diruthenium 6(PF6)2 with a linear trans,trans-urea bridge have been prepared, together with the bis-triarylamine 3 and cyclometalated diruthenium 8(PF6)2 with a folded cis,cis-N,N-dimethylurea bridge. The linear or folded conformations of these molecules are supported by single-crystal X-ray structures of 2, 3, and other related compounds. These compounds display two consecutive anodic redox waves (N(·+/0) or Ru(III/II) processes) with a potential separation of 110-170 mV. This suggests that an efficient electronic coupling is present between two redox termini through the cross-conjugated urea bridge. The degree of electronic coupling has been investigated by using spectroelectrochemical measurements. Distinct intervalence charge-transfer (IVCT) transitions have been observed for mixed-valent (MV) compounds with a linear conformation. The IVCT transitions can also be identified for the folded MV compounds, albeit with a much weaker intensity. DFT results support that the electronic communication occurs by a through-bond and through-space pathway for the linear and folded compounds, respectively. The IVCT transitions of the MV compounds have been reproduced by TDDFT calculations. For the purpose of comparison, a bistriarylamine and a diruthenium complex with an imidazolidin-2-one bridge and a urea-containing mono-triarylamine and monoruthenium complex have been synthesized and studied.

Synthesis of enantiomerically enriched (R)-C-labelled 2-aminoisobutyric acid (Aib) by conformational memory in the alkylation of a derivative of L-alanine

The method of Kouklovsky and coworkers for the enantioselective alkylation of cyclic N-naphthoyl derivatives of amino acids was used to introduce a ¹³C label into one of the two enantiotopic methyl groups of 2-aminoisobutyric acid (Aib) by retentive alkylation of L-alanine with ¹³CH₃I. Conditions were identified for optimization of yield and enantiomeric purity, and the absolute configuration of the labelled product was established.