Structure of HOE/BAY 793 Complexed to Human Immunodeficiency Virus (HIV‐1) Protease in Two Different Crystal Forms Structure/Function Relationship and Influence of Crystal Packing

Abstract

Human immunodeficiency virus 1 (HIV-1) protease is a prime target in the search for drugs to combat the AIDS virus. The enzyme functions as a C,-symmetric dimer, cleaving the gag and gag-pol viral polyproteins at distinct sites. The possession of a twofold axis passing through the active site, has led to the design of C,-symmetrical inhibitors in the form of substrate-based transition-state analogs. The structure of this inhibitor bound to HIV-1 protease, in two different crystal forms, has been solved at 0.24-nm resolution using X-ray crystallography. In both forms, the details of the inhibitor-protease interactions revealed an overall asymmetric binding mode, especially between the central diol unit and the active-site aspartates. The main binding interactions comprise several specific H-bonds and hydrophobic contacts, which rationalize many of the characteristics of the structure/ activity relationship in the class of vicinal diol inhibitors. In a general analysis of the mobility of the flap regions, which cover the active site and participate directly in binding, using our structures and the HTV protease models present in the Brookhaven databank, we found that in most structures the flexibility of the flaps is limited by local crystal contacts. However, in one of the structures presented here, no significant crystal contacts to the flap regions were present, and as a result the flexibility of the inhibitor bound flaps increased significantly. This suggests that the mobility and conformational flexibility of the flap residues are important in the functioning of HIV-1 protease, and must be considered in the future design of drugs against HIV protease and in structure-based drug design in general.

Targeting structural flexibility in HIV-1 protease inhibitor binding

“…Although large scale flap opening is presumably required for normal substrate access to the active site (Figure 1c), no crystallographic structures representing such an open configuration have been reported. Despite the four available crystal structures of unbound HIV PR [16][17][18][19] all show the semi-open conformation, it was not entirely clear whether this reflects the preferred flap conformation or crystal packing effects [10,20,21]. However it is known from NMR experiments [22,23] that the flap region has a high degree of flexibility.…”

4D-QSAR Models of HOE/BAY-793 Analogues as HIV-1 Protease Inhibitors

“…Therefore, the bioactive conformation of compound 32 was selected from Models 2 and 7 (a unique conformation), and it was assumed to be the bioactive conformation for this compound in this series of inhibitors. In addition, the postulated bioactive conformation of 32 was docked ( Figures 5 and 6) into the region occupied by the crystallographic structure of 32 (HOE/BAY-793) complexed with HIV-1 protease [20].…”

“…We superimposed the bioactive conformation of compound 32 and its complexed crystallographic structure [20], as shown in Figure 5, considering the four carbon atoms from the carbonyl groups ( Figure 1). We observed a very similar orientation for the P1', P2' and P3' substituents.…”

“…Hydrogen atoms were added to the crystallographic structure of HOE/BAY-793 and HIV-1 protease complex obtained from the Protein Data Bank (PDB code: 1VIJ) [20]. Energy minimization, using steepest descent and conjugate gradient algorithms, were carried out until a gradient of 0.1 kcal · mol À 1 · A À 1 was reached.…”

“…The HOE/BAY-793 ( Figure 1) crystallographic conformation was retrieved from the Protein Data Bank (PDB code: 1VIJ) [20] and used for modeling the 32 compounds of the training and test sets. Three-dimensional models of each of the 32 compounds reported in Table 1 were constructed inside the active site of HIV-1 protease, using Builder module of INSIGHTII software [21].…”