A CRYSTALLOGRAPHIC AND MOLECULAR MODELLING STUDY OF THE POTENCIES OF FOUR DIASTEREOISOMERS OF PEPTIDOMIMETIC INHIBITORS OF HIV-1 PROTEASE
Jeroen Mesters1, Alexander Hillisch1, Carlo Ciatto1, Iva Pichová2, Jan Konvalinka2, Milan Soucek2, Juraj Sedlácek2 and Rolf Hilgenfeld1
1 Institute of Molecular
Biotechnology, Department of Structural Biology and
Crystallography, Beutenbergstr. 11, D-07745 Jena, Germany,
e-mail: jmesters@imb-jena.de
2 Academy of Sciences
of the Czech Republic, 166 10 Prague 6, Czech Republic.
Keywords: HIV protease, molecular modelling, inhibitor
The human immunodeficiency virus protease (HIV-Pr) processes the polyprotein products of the gag and gag-pol genes, a crucial step in the propagation of infectious virus particles. A combination chemotherapy targeted at both the HIV reverse transcriptase and the protease currently appears to be the most promising approach against AIDS. However, the long-term use of these drugs will lead to viral resistance and new potent inhibitors are urgently needed to broaden the spectrum of anti-AIDS chemotherapeutic compounds. The future success of designing new drugs fully depends on a detailed understanding of the binding mode of known inhibitors to the proteins.
We have started a crystallographic study of a series of four diastereoisomers of peptidomimetic inhibitors with large differences (3 orders of magnitude) in the binding affinity towards HIV-Pr (see (1)). Recently, we succeeded (under novel cryo-conditions) to collect complete datasets with a resolution of better than 1.9 A in house. The three-dimensional models for all four inhibitor-HIV-Pr complexes are currently in the final stage of refinement.
The hydroxyethylene isoster group, in our BocPhe[CHOHCH2]PheGlnPheNH2 inhibitors, is one of the most effective scissile bond replacements since it closely resembles the transition state of a hydrolysed amide bond. Most interestingly, the main differences in the binding modes between the four inhibitors are found in the S1 and the S1' pockets. In particular, the positioning of the hydroxyl group seems to be a key player in dictating the binding affinities.
Independent of the crystallographic
investigations, we started a molecular modelling study. An energy
minimised conformation was used as input for a genetic algorithm
driven docking procedure with the FlexiDock program in SYBYL (2).
All torsion angles of the inhibitors and the contacting amino
acids in the protein were left flexible. The r.m.s. deviation
calculated from a superposition of the predicted conformations
with those of the crystal structures is less than 1 A.