Structure based design of inhibitory peptides targeting ornithine decarboxylase dimeric interface and in vitro validation in human retinoblastoma Y79 cells

Abstract

Polyamine synthesis in human cells is initiated by catalytic action of Ornithine decarboxylase (ODC) on Ornithine. Elevated levels of polyamines are manifested proliferating cancer cells and are found to promote tumour cell adhesion. Di-flouro methyl orninthine is a known inhibitor of ODC, however its usage is limited due its low affinity quick clearance and incompetent cellular uptake, thus posing a need for potential inhibitors. Currently, peptides are substituting drugs, as these are highly selective, specific and potent. Hence, in this study, the interacting interfaces of native homodimeric form of ODC and its heterodimer with Antizyme were probed to design inhibitory peptides targeting ODC. The designed peptides were validated for structural fitness by extensive molecular dynamics simulations and Circular dichroism studies. Finally, these peptides were validated in Y79 retinoblastoma cells for impact on ODC activity, cytotoxicity cell cycle and cell adhesion. On collective analysis, Peptide3 (Pep 3) and Peptide4 (Pep 4) were found to be potentially targeting ODC, as these peptides showed significant decrease in intracellular polyamine levels, cell adhesion and cell cycle perturbation in Y79 cells. Thus, Pep 3 and Pep 4 shall be favourably considered as therapeutic agents for targeting ODC mediated proliferation in retinoblastoma.

Communicated by Ramaswamy H. Sarma

Keywords:

• Ornithine decarboxylase
• retinoblastoma
• antizyme
• peptide inhibitor
• cell adhesion
• docking

Acknowledgements

Dr. K.N. Sulochana & Dr. V. Umashankar thank CSIR, New Delhi. Project sanctions order No: 02 (0105)/12/EMR-II and dated on 01/11/12. The authors thank, Vision Research Foundation for supporting the research. Muthukumaran thanks ICMR for providing fellowship (CMB-BMS/2017-2298). The authors also thank Indian Institute of Technology (IIT) Madras for helping with the CD spectroscopy facility.

Disclosure statement

The authors declare no conflict of interest.