Investigation of novel 4-substituted piperazine-pyrrolo[2,3-d]pyrimidine N-phenylacetamides as MELK-targeted anticancer agents for breast cancer therapy.
Makwana Shivangi S, Pandey Vivek V, Shah Umang U, Imran Mohd M et al.
The study reports design and synthesis of two series of pyrrolo[2,3-d]pyrimidine-N-phenylacetamide derivatives based on 1-(2,3-dichlorophenyl) piperazine (9a-f) and 1-((4-chlorophenyl) (phenyl)methyl) piperazine (10a-f). Compounds were characterized using 1H NMR, 19F NMR, 13C NMR, and HRMS spectral analyses. Post-chemical characterization, UALCAN analysis revealed elevated expression of MELK at both RNA and protein level in breast cancer, hence studies were conducted in MCF-7 cells. Of the two derivatives, piperazine-substituted compounds 9a-f (dichlorophenyl) showed better activity than 10a-f (chlorobenzhydryl) in the MTT assay. 9b and 9d exhibited modest IC50 of 13.84 ± 1.02 μM and 13.5 ± 1.29 μM, respectively, compared to routine drug 5-fluorouracil, which showed an IC50 of 17.77 ± 1.59 μM. However, a series 10a-f exhibited good to moderate to average cytotoxicity. Further analysis revealed both 9b and 9d exert an inhibitory effect by causing cell death, S-phase cell cycle arrest, and inhibiting migratory potential by upregulating E-Cadherin and downregulating the MMP-9. Molecular docking with the MELK protein revealed favorable binding to key active-site residues. Additionally, 100 ns molecular dynamics simulations confirmed conformational stability and dynamic behavior stable ligand-protein complex throughout the simulation, further western blotting analysis showed direct action of 9b and 9d on MELK expression with later being more prominent. In silico ADME study predicts that compound 9b demonstrates more favorable pharmacokinetic properties than 9d, including adherence to Lipinski's rule, improved oral absorption, enhanced Caco-2/MDCK permeability, and favorable BBB, skin permeability, and plasma protein binding, suggesting their potential as MELK- targeted leads for anticancer candidates.