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2,5-Diketopiperazines: A New Class of Poly(ADP-ribose)polymerase Inhibitors

D. K. Nilov1, K. I. Yashina2, I. V. Gushchina2, A. L. Zakharenko3, M. V. Sukhanova3, O. I. Lavrik3, and V. K. Švedas1,2*

1Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, 119991 Moscow, Russia; E-mail: vytas@belozersky.msu.ru

2Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, 119991 Moscow, Russia

3Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia

* To whom correspondence should be addressed.

Received July 11, 2017; Revision received October 3, 2017
We show for the first time that natural 2,5-diketopiperazines (cyclic dipeptides) can suppress the activity of the important anticancer target poly(ADP-ribose)polymerase (PARP). Cyclo(L-Ala-L-Ala) and cyclo(L-Ala-D-Ala) can interact with the key residues of the PARP-1 active site, as demonstrated using docking and molecular dynamics simulations. One of the amide groups of cyclo(L-Ala-L-Ala) and cyclo(L-Ala-D-Ala) forms hydrogen bonds with the Gly863 residue, while the second amide group can form a hydrogen bond with the catalytic residue Glu988, and the side chain can make a hydrophobic contact with Ala898. Newly identified diketopiperazine inhibitors are promising basic structures for the design of more effective inhibitors of PARP family enzymes. The piperazine core with two chiral centers provides many opportunities for structural optimization.
KEY WORDS: diketopiperazine, piperazinedione, poly(ADP-ribose)polymerase, inhibitor, molecular modeling, docking, molecular dynamics

DOI: 10.1134/S0006297918020074