Conformational study into N-alkyl-N′-aryl ureas to inform drug discovery

Abstract

Ureas are an important functional group in small molecule drugs as well as having wider applications in organic chemistry. Understanding of their conformation is of critical importance for rational design of urea-containing bioactive compounds. Whilst the conformational preferences of biaryl ureas have been extensively studied, very little attention has been paid to alkylated analogues. We carried out a systematic study of N-aryl (phenyl and pyridyl)-N′-cyclopentyl ureas with differing N-methylation patterns using Well Tempered Metadynamics at a semi-empirical level in implicit water (GBSA) using Well-Tempered Metadynamics to generate their conformational free-energy landscapes. Geometries and energetics of the most relevant configurations are further refined using DFT level of theory. Validation for the computation was obtained by synthesis of all 8 analogues followed by conformational studies by X-ray crystallography and NMR. These findings reveal that the methylation pattern significantly affects the conformational preference of the system. Most notably, N-phenyl-N′-cyclopentyl urea is shown to adopt both the trans–trans, and cis–trans conformations with equal energy and that the cis–trans conformation can be significantly stabilised by the presence of an internal hydrogen bond to the N′-hydrogen. This study will be of utility for the design of N-alkyl-N′-aryl ureas as drug candidates.