Gag Mutations Strongly Contribute to HIV-1 Resistance to Protease Inhibitors in Highly Drug-Experienced Patients besides Compensating for Fitness Loss

Abstract

Human immunodeficiency virus type 1 (HIV-1) resistance to protease inhibitors (PI) results from mutations in the viral protease (PR) that reduce PI binding but also decrease viral replicative capacity (RC). Additional mutations compensating for the RC loss subsequently accumulate within PR and in Gag substrate cleavage sites. We examined the respective contribution of mutations in PR and Gag to PI resistance and RC and their interdependence using a panel of HIV-1 molecular clones carrying different sequences from six patients who had failed multiple lines of treatment. Mutations in Gag strongly and directly contributed to PI resistance besides compensating for fitness loss. This effect was essentially carried by the C-terminal region of Gag (containing NC-SP2-p6) with little or no contribution from MA, CA, and SP1. The effect of Gag on resistance depended on the presence of cleavage site mutations A431V or I437V in NC-SP2-p6 and correlated with processing of the NC/SP2 cleavage site. By contrast, reverting the A431V or I437V mutation in these highly evolved sequences had little effect on RC. Mutations in the NC-SP2-p6 region of Gag can be dually selected as compensatory and as direct PI resistance mutations, with cleavage at the NC-SP2 site behaving as a rate-limiting step in PI resistance. Further compensatory mutations render viral RC independent of the A431V or I437V mutations while their effect on resistance persists.

Generation of Infectious Feline Immunodeficiency Virus (FIV) Encoding FIV/Human Immunodeficiency Virus Chimeric Protease

“…However, efficient processing at the NC-p2 junction to produce mature NC and p2 is required for FIV infectivity. The processing efficiency of the equivalent HIV-1 NC-p1-p6 cleavage junctions has been extensively examined, and proper temporal cleavage at these sites correlates with viral fitness, replication capacity, and drug resistance (11,40,45,47,49,52). The findings of the current study reinforce the notion that the cleavage and maturation of NC-p2 in FIV and of the equivalent NC-p1-p6 in HIV-1 offer a new potential therapeutic target.…”

“…1B). The clinical drugs against HIV-1 PR are very poor inhibitors for wild-type (WT) FIV PR, and interestingly, eight of the drug resistance mutations in HIV-1 PR mentioned above, namely, V11I, K20I, V32I, I50V, I62V, A71I, N88D, and L90M, are already present in the structurally equivalent positions of FIV PR (16 11 I, 25 20 I, 37 32 I, 59 50 V, 71 62 V, 85 71 I, 105 88 D, and 107 90 M [FIV numbering is given, with equivalent HIV-1 numbering in superscript]) (7,24).…”

Genetic Changes in HIV-1 Gag-Protease Associated with Protease Inhibitor-Based Therapy Failure in Pediatric Patients

“…For 10 patients (5,7,11,13,(15)(16)(17)(18)(19)(20) there were no changes in protease at failure, although nine had baseline protease polymorphisms.…”

“…8 Studies have shown that mutations in Gag cleavage sites (CS) also contribute to PI resistance development. [9][10][11][12] HIV-1 PR recognizes and cleaves the Gag and Gag Pol polyproteins to release the structural components: matrix (MA), capsid (CA), p6, nucleocapsid (NC), enzymes protease, reverse transcriptase, RNase H, integrase, the small polypeptides p1 and p2, as well as transframe protein (TFP). 13 Cleavage sites in Gag comprise five amino acids flanking either side of the scissile bond, with position 1 (P1) located immediately upstream and position 1 prime (P1¢) located immediately downstream of the cleavage point.…”

“…[9][10][11] While these sites are the most commonly described, substitutions at all CS have been observed at PI failure. 9,10,15 In addition, studies have shown that certain non-CS mutations in Gag can contribute to reduced susceptibility to PIs in the presence of major PR mutations in vitro.…”