Conformational restrictions in ligand binding to the human intestinal di-/tripeptide transporter: implications for design of hPEPT1 targeted prodrugs Original Research Article

The aim of the present study was to develop a computational method aiding the design of dipeptidomimetic pro-moieties targeting the human intestinal di-/tripeptide transporter hPEPT1. First, the conformation in which substrates bind to hPEPT1 (the bioactive conformation) was identified by conformational analysis and 2D dihedral driving analysis of 15 hPEPT1 substrates, which suggested that ψ1 ∼ 165°, ω1 ∼ 180°, and ϕ2 ∼ 280° were descriptive of the bioactive conformation. Subsequently, the conformational energy required to change the peptide backbone conformation (ΔEbbone) from the global energy minimum conformation to the identified bioactive conformation was calculated for 20 hPEPT1 targeted model prodrugs with known Ki values. Quantitatively, an inverse linear relationship (r2 = 0.81, q2 = 0.80) was obtained between ΔEbbone and log 1/Ki, showing that ΔEbbone contributes significantly to the experimentally observed affinity for hPEPT1 ligands. Qualitatively, the results revealed that compounds classified as high affinity ligands (Ki < 0.5 mM) all have a calculated ΔEbbone < 1 kcal/mol, whereas medium and low-affinity compounds (0.5 mM < Ki < 15 mM) have ΔEbbone values in the range 1–3 kcal/mol. The findings also shed new light on the basis for the experimentally observed stereoselectivity of hPEPT1.