Peptidomimetic inhibitors of human immunodeficiency virus protease (HIV-PR): Design, enzyme binding and selectivity, antiviral efficacy, and cell permeability properties

In Silico Peptide Ligation: Iterative Residue Docking and Linking as a New Approach to Predict Protein-Peptide Interactions

Peptide⁻protein interactions are corner-stones of living functions involved in essential mechanisms, such as cell signaling. Given the difficulty of obtaining direct experimental structural biology data, prediction of those interactions is of crucial interest for the rational development of new drugs, notably to fight diseases, such as cancer or Alzheimer's disease. Because of the high flexibility of natural unconstrained linear peptides, prediction of their binding mode in a protein cavity remains challenging. Several theoretical approaches have been developed in the last decade to address this issue. Nevertheless, improvements are needed, such as the conformation prediction of peptide side-chains, which are dependent on peptide length and flexibility. Here, we present a novel in silico method, Iterative Residue Docking and Linking (IRDL), to efficiently predict peptide⁻protein interactions. In order to reduce the conformational space, this innovative method splits peptides into several short segments. Then, it uses the performance of intramolecular covalent docking to rebuild, sequentially, the complete peptide in the active site of its protein target. Once the peptide is constructed, a rescoring step is applied in order to correctly rank all IRDL solutions. Applied on a set of 11 crystallized peptide⁻protein complexes, the IRDL method shows promising results, since it is able to retrieve experimental binding conformations with a Root Mean Square Deviation (RMSD) below 2 Å in the top five ranked solutions. For some complexes, IRDL method outperforms two other docking protocols evaluated in this study. Hence, IRDL is a new tool that could be used in drug design projects to predict peptide⁻protein interactions.

Characterization of dynamic state inhibitors of HIV-1 protease

The inhibitory behavior of simple N-protected amino acids containing a dysfunctional enol group was analyzed. Pseudo-Hill coefficients below 0.5 were obtained for the enol compounds. The active moiety of the enols described herein is involved in an equilibrium between keto and enol forms. The enol in its E form interacts strongly with the enzyme and we suggest that the Z form is expelled from the active site, as suggested by molecular modeling studies using the docking technique. Also, tetrahedral intermediate mimicry is achieved by the enol form, but not by the corresponding keto form. A pseudo-Hill coefficient of 0.25 has been determined for the Boc-phenylalanine enol, and by multiplying the concentration of inhibitor by its pseudo-Hill coefficient, a Ki of 0.82 microM has been determined for the inhibitory E-enol form. Boc-tyrosine enol generated a Ki of 0.39 microM. The requirements at the P1' position to achieve good inhibition are also described.