A set of newer generation pyrimidine hydroxamic acid derivatives were designed, synthesized, and evaluated for antiproliferative activity against breast cancer cell line and in-vitro alpha-amylase activity. The design of the molecules was fully dependent upon the structural features of suberoyl anilide hydroxamic acid. Then all the designed molecules (S1-S100) were docked with 4LXZ HDAC2 enzyme and S1, S2, S16 showed good docking interaction scores as compared to SAHA. The interacting residues of (S1, S2, S16) and 4LXZ showed similar amino acid lining as present in the active site. The synthetic procedure of the molecules (S1, S2, S16) was divided into three parts such as synthesis of chalcone derivative using aromatic aldehyde and acetophenone, the reaction between chalcone and thiourea to form substituted pyrimidine-2-thiol, then finally substituted pyrimidine-2-thiol and 2-chloro-N-hydroxyacetamide reacted in the presence of dimethylformamide to obtain the best-docked molecules. All the molecules showed characteristic peaks in fourier-transform infrared (FTIR), proton nuclear magnetic resonance (1H-NMR) and mass spectrometry with sharp melting points and single peak in thin layer chromatography (TLC) plate. Finally antiproliferative activity against MCF-7 and in-vitro alpha amylase activity data confirmed that S1 was the best molecule among all the synthesized molecules.