Telomere holds special mechanism for solving end repair problems and maintaining genomic stability. Protection of telomeres 1 (POT1) which belongs to shelterin family is identified as a key protein that recruits telomerase by interacting with telomere repeat binding factors (TRB1-3). Since, deciphering the mechanism through which POT assembles telomerase is of great interest, computational approaches have been undertaken to understand the mechanism in a well- developed model system - Arabidopsis thaliana. As a first step, an untraditional approach was mediated to locate the active site residues on modeled AtPOT1b protein by interaction studies using molecular docking. To keep in trend with the recent developments, peptide construction and validation was promoted as the next step via molecular dynamics simulation studies. Finally, the validated peptides based on propensity score was evaluated for its efficacy as a potent inhibitor for POT and TRB1-3 interactions. The best peptide, namely, (1-2-d) out of 30 designed peptides, was proved to be vital inhibitor by weakening the interacting complexes.