Protein And Ligand Interaction Studies And Small Peptide Inhibitor Design Method In China

In present paper, some new results about studies of protein-ligand interactions through electronic structure calculations and applications of the statistics method on peptide inhibitor design are reported.Understanding the ruling principles of protein-ligand interactions is of paramount importance in drug discovery efforts. However, we still lack a clear molecular mechanism to explain the protein-ligand interactions on the basis of electronic structures. By combining the calculation of the full electronic structure of a protein along with its hydrophobic pocket and the perturbation theory, we found out two rules on the protein-ligand interactions. One rule is that protein-ligand interactions only occur between the lowest unoccupied molecular orbitals (LUMOs) of a protein and the highest occupied molecular orbital (HOMO) of its ligand, not between the HOMOs of a protein and the LUMO of its ligand. The other rule is that only those residues or atoms located in both the LUMOs of a protein and a surface pocket of a protein are active residues or active atoms of the protein, and the corresponding pocket is the ligand binding site. These two rules are derived from the structure of energy levels of a protein and could be one of important criterions for the drug design. They were validated on complex Cyclophilin A (CypA) bound with Cyclosporine A (CsA) and complex 12-kDa FK506 binding protein (FKBP12) bound with FK506. Moreover, the protein/ligand complex FKBP12/FK506 was studied by combining molecular dynamic simulations and electronic structure calculations. The protein FKBP12 was found to have the strongest biological activity at room temperature (302 K) due to the smallest band gap. The active residues and active atoms of the FKBP12 identified by our method are in good agreement with experimental findings. During the molecular dynamics simulations, the root mean square deviations of these active residues were found to be smaller than that of the rest residues. It indicates the active regions are more stable.The peptide-based drug design is becoming a hot research subject since 1990s for the easy synthesis of peptides. In this paper, we proposed two methods for peptide inhibitor design:the mathematical model for screening (MMS) and the rational-designed database for screening (RDS). The MMS combines the two rules on protein-ligand interactions, Miyazawa-Jernigan (MJ) matrix and Hidden Markov Model (HMM). The MMS was applied to predict peptide inhibitors Ala-Gly-Pro (AGP) and Gly-Gln for protein CypA and KFBP12, respectively. The other method RDS was applied to predict a potent peptide inhibitor Trp-Gly-Pro (TGP) for CypA through screening from a rationally built database of 40 peptides. Peptide TGP showed comparable ability of inhibition as the positive control CsA on the PPlase activity of CypA (IC50 values of 33.11 nM and 10.25 nM, respectively). The peptide TGP was also demonstrated by surface plasmon resonance analysis to have same order of binding affinity with CsA with a dissociation equilibrium constant KD of 3.41×10-6 M, while CsA of 6.42×10-6 M. Moreover, the peptide TGP has no immunosuppressive activity and its high ligand efficiency (-0.37) permits enough room for further lead optimization and clinical applications. The results are encouraging, and point out that our methods are reliable for peptide inhibitor design.