Synthesis and Characterization of New Functionalized Pyrimidine (Hetero)Cyclic Molecular Hybrids as Chiral Heterocyclic Amino Acid Derivatives

Heterocyclic unnatural amino acids and their biheterocyclic derivatives represent invaluable structural scaffolds in modern medicinal chemistry and peptidomimetics due to their ability to induce conformational constraints and modulate pharmacokinetic profiles. While saturated nitrogen heterocycles and monocycle heteroaromatic systems are well-established pharmacophores, research on linear biheterocyclic amino acid frameworks remains significantly underrepresented in the literature. Addressing this structural gap, this study aims to synthesize and characterize a novel series of functionalized pyrimidine (hetero)cyclic molecular hybrids acting as chiral heterocyclic amino acid derivatives. The target pyrimidine-5-carboxylates and pyrimidine-4-carboxylic acid derivatives were prepared from β-dicarbonyl compounds and their corresponding enamine analogues via cyclocondensation approaches. Particular attention was paid to reaction optimization, substrate scope exploration, and stereochemical integrity preservation, utilizing chiral HPLC analysis to evaluate enantiomeric retention. Pyrimidine-5-carboxylates prepared from β-enamino keto esters retained high enantiomeric excess (90.2–100% ee), whereas cyclization of β-diketones under strongly basic conditions at elevated temperature resulted in complete racemization (ee < 1%). Modification of the synthetic route and application of milder cyclization conditions partially suppressed racemization, affording pyrimidine derivatives with 61.8–65.5% ee. These findings suggest that substrate structure influences stereochemical integrity during pyrimidine synthesis.