Exploiting the chemical diversity space of phosphopeptide binding to nasopharyngeal carcinoma PLK1 PBD domain with unnatural amino acid building blocks by using QSAR-based genetic optimization.

Human polo-like kinase 1 (PLK1) has been recognized as an attractive therapeutic target against nasopharyngeal carcinoma (NPC). The kinase contains a conserved polo-box domain (PBD) that exhibits a wide specificity across various substrates. Previously, we explored natural amino acid preference in PLK1 PBD-binding phosphopeptides. However, limited to the short sequence only natural amino acids cannot guarantee the sufficient exploitation of chemical and structural diversity of the phosphopeptides. Here, we described a genetic optimization (GO) strategy to systematically optimize a 10⁴-sized 6-mer phosphopeptide array towards increasing affinity to PLK1 PBD domain by using 20 natural plus 34 unnatural amino acids as basic building blocks. A QSAR predictor was created to guide the GO optimization and then evaluated rigorously at molecular and cellular levels. Three unnatural phosphopeptides uPP8, uPP15 and uPP20 were designed as potent binders with K_d = 0.18, 0.42 and 0.08 μM, respectively, in which the uPP20 also possessed a good anti-tumor activity against human NPC cells when fused with cell permeation sequence. In addition, we defined a relaxed 6-mer motif for the preferential PLK1 PBD-binding phosphosites, namely [Φ/П]-3-[ζ]-2-[ζ]-1-[pT/pS]0-[Φ/П]+1-[Φ]+2, where the symbols Φ, ζ and П represent hydrophobic, polar and aromatic amino acid types, respectively.  .