Structural Role of the 30's Loop in Determining the Ligand Specificity of the Human Immunodeficiency Virus Protease^,

Abstract

The structural basis of ligand specificity in human immunodeficiency virus (HIV) protease has been investigated by determining the crystal structures of three chimeric HIV proteases complexed with SB203386, a tripeptide analogue inhibitor. The chimeras are constructed by substituting amino acid residues in the HIV type 1 (HIV-1) protease sequence with the corresponding residues from HIV type 2 (HIV-2) in the region spanning residues 31-37 and in the active site cavity. SB203386 is a potent inhibitor of HIV-1 protease (Ki = 18 nM) but has a decreased affinity for HIV-2 protease (Ki = 1280 nM). Crystallographic analysis reveals that substitution of residues 31-37 (30's loop) with those of HIV-2 protease renders the chimera similar to HIV-2 protease in both the inhibitor binding affinity and mode of binding (two inhibitor molecules per protease dimer). However, further substitution of active site residues 47 and 82 has a compensatory effect which restores the HIV-1-like inhibitor binding mode (one inhibitor molecule in the center of the protease active site) and partially restores the affinity. Comparison of the three chimeric protease structures with those of HIV-1 and SIV proteases complexed with the same inhibitor reveals structural changes in the flap regions and the 80's loops, as well as changes in the dimensions of the active site cavity. The study provides structural evidence of the role of the 30's loop in conferring inhibitor specificity in HIV proteases.

Atomic resolution crystal structures of HIV‐1 protease and mutants V82A and I84V with saquinavir

“…Similar flexibility of this region was described for the 9X mutant structure 24. Other flexible areas in the PR have been suggested, such as the residues 15–21, the 30s loop, the flap region and both termini 38–41. The flexibility of the PR structure may play an important role in its function in viral replication 42, 43.…”

Critical differences in HIV‐1 and HIV‐2 protease specificity for clinical inhibitors

“…Previously, differences in residues 31-37 were shown to make a major contribution to the inhibition and unusual mode of binding of a tripeptide analog in studies of chimeric enzymes. 17 In fact, residues 33-44 vary in sequence and conformation among different groups and subtypes of PR 1 although little effect on inhibition has been reported. [29][30][31] Structurally, PR 1M resembles PR 1 more than PR 2 .…”

“…Earlier studies showed that PR 1 bearing the substitutions, V32I, I47V, and V82I, altered the inhibition but not the binding mode of a tripeptide inhibitor. 16,17 These residues are the sites of drug resistance mutations V32I, I47V, and various substitutions of Val82 in HIV-1 (Fig. 1).…”

Mechanism of Drug Resistance Revealed by the Crystal Structure of the Unliganded HIV-1 Protease with F53L Mutation

“…Mutations of residues forming the active-site cavity can directly alter the PR interactions with inhibitor leading to the diminished affinity of the inhibitor to the mutated protease. 6,[8][9][10] Other mutations have been shown to alter the dimer interface and the dimer stability of the protease. 11,12 Finally, compensatory mutations such as K20R or A71V in distal regions are selected in the protease in order to restore and increase its catalytic efficiency.…”