In silico panning for a non-competitive peptide inhibitor.
BACKGROUND
Peptide ligands have tremendous therapeutic potential as efficacious drugs. Currently, more than 40 peptides are available in the market for a drug. However, since costly and time-consuming synthesis procedures represent a problem for high-throughput screening, novel procedures to reduce the time and labor involved in screening peptide ligands are required. We propose the novel approach of 'in silico panning' which consists of a two-stage screening, involving affinity selection by docking simulation and evolution of the peptide ligand using genetic algorithms (GAs). In silico panning was successfully applied to the selection of peptide inhibitor for water-soluble quinoprotein glucose dehydrogenase (PQQGDH).


RESULTS
The evolution of peptide ligands for a target enzyme was achieved by combining a docking simulation with evolution of the peptide ligand using genetic algorithms (GAs), which mimic Darwinian evolution. Designation of the target area as next to the substrate-binding site of the enzyme in the docking simulation enabled the selection of a non-competitive inhibitor. In all, four rounds of selection were carried out on the computer; the distribution of the docking energy decreased gradually for each generation and improvements in the docking energy were observed over the four rounds of selection. One of the top three selected peptides with the lowest docking energy, 'SERG' showed an inhibitory effect with Ki value of 20 microM. PQQGDH activity, in terms of the Vmax value, was 3-fold lower than that of the wild-type enzyme in the presence of this peptide. The mechanism of the SERG blockage of the enzyme was identified as non-competitive inhibition. We confirmed the specific binding of the peptide, and its equilibrium dissociation constant (KD) value was calculated as 60 microM by surface plasmon resonance (SPR) analysis.


CONCLUSIONS
We demonstrate an effective methodology of in silico panning for the selection of a non-competitive peptide inhibitor from small virtual peptide library. This study is the first to demonstrate the usefulness of in silico evolution using experimental data. Our study highlights the usefulness of this strategy for structure-based screening of enzyme inhibitors.
Yagi
Yukiko
Y
Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-13 Naka-machi, Koganei, Tokyo, Japan. yagimay@hotmail.com <yagimay@hotmail.com>
Terada
Kotaro
K
Noma
Takahisa
T
Ikebukuro
Kazunori
K
Sode
Koji
K
D016954:Acinetobacter calcoaceticus / Q000201:enzymology; D000495:Allosteric Site / Q000235:genetics; D001667:Binding, Competitive / Q000235:genetics; D020650:Combinatorial Chemistry Techniques / Q000379:methods; D019020:Directed Molecular Evolution / Q000379:methods; D042843:Glucose 1-Dehydrogenase / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D008024:Ligands; D019151:Peptide Library; D010455:Peptides / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding / Q000235:genetics; D017433:Protein Structure, Secondary / Q000235:genetics; D020349:Surface Plasmon Resonance
D008024:Ligands; D019151:Peptide Library; D010455:Peptides; D042843:Glucose 1-Dehydrogenase