A one-pot multicomponent approach was established for site selective synthesis of novel 1,3,6-trisubstituted 3,6-diunsaturated (3Z,6Z)-2,5-diketopiperazine derivatives with high stereoselectivity. The computational studies revealed that the steric hindrances between the 2-hydrogen atoms on the aromatic rings and the carbonyl, as well as the steric repulsions between the hydrogen atoms of the CH group in the benzylidene and the CH2 group in the N-alkylative part might be responsible for the Z/E selectivity. Compound (3Z,6Z)-3h (IC50=11 nM) has a close activity to the positive compound plinabulin (IC50=15 nM) against the cancer cell line HL60. (C) 2015 Elsevier Ltd. All rights reserved.