Structure-Analysis of the HIV-1 Integrase Y143C/R Raltegravir Resistance Mutation in Association with the Secondary Mutation T97A

Abstract

In the strand transfer assay, the IN Y143C or R mutation combined with the secondary mutation T97A severely impaired susceptibility to RAL compared to results with the IN Y143C or R mutation alone. Assays without RAL suggested that the T97A mutation could rescue the catalytic activity which was impaired by the presence of the Y143C/R mutation. The combination of the T97A mutation with the primary RAL resistance mutations Y143C/R strongly reduces the susceptibility to RAL and rescues the catalytic defect due to the Y143C/R mutation. This result indicates that the emergence of the Y143C/R/T97A double-mutation pattern in patients is a signature of a high resistance level.

Impact of Primary Elvitegravir Resistance-Associated Mutations in HIV-1 Integrase on Drug Susceptibility and Viral Replication Fitness

“…These results demonstrated a ranked order among primary EVG RAMs whereby the most common clinically observed primary IN mutations (E92Q, Q148R, and N155H) exhibited the greatest reduction in EVG susceptibility, consistent with previous reports (10,11,30). The finding that T97A showed only very-lowlevel reduced EVG susceptibility in the multicycle assay is similar to its effect on RAL susceptibility in patients experiencing virologic failure on RAL-containing regimens (32,37). This special case of a primary EVG RAM suggests that additional amino acid substitutions may serve an accessory role for T97A to further reduce phenotypic susceptibility.…”

“…3). HIV-1 IN enzymes with the Q148R or N155H mutation were the most attenuated in both 3=-processing and strand transfer activities, consistent with previous biochemical assessments of recombinant IN enzymes possessing primary RAL RAMs (11,13,14,(30)(31)(32). Other primary EVG RAMs (T66I, E92Q, and S147G) exhibited marginal impairment of 3=-processing activity (80 to 87% of WT activity), with substantial impairment of strand transfer activity (ϳ40 to 75% of WT activity).…”

“…Importantly, E92Q and T97A have also been observed in HIV-1-infected patients experiencing virologic failure on RAL, either independently or in association with N155H and Y143R/ H/C, respectively (18,(39)(40)(41)(42). While E92Q is often referred to as a secondary RAL RAM (16,32,37), our data indicate a significant impact on EVG and RAL resistance, independent of other mutations. Small geometric differences between the interactions of EVG and those of RAL within IN may account for the observed variability in cross-resistance (T66K, E92Q, and Q148R/H/K) and why certain primary EVG RAMs (T66I/A, E92G, and S147G) retain susceptibility to RAL while certain primary RAL RAMs (Y143R/H/C) retain susceptibility to EVG.…”

Multiple Genetic Pathways Involving Amino Acid Position 143 of HIV-1 Integrase Are Preferentially Associated with Specific Secondary Amino Acid Substitutions and Confer Resistance to Raltegravir and Cross-Resistance to Elvitegravir

“…In addition, L74I,M, E92Q, E138K, V151I, G163R, I203M, and S230R have been associated with RAL treatment failure (31). G140S and T97A substitutions rescue the catalytic defect conferred by Q148H and Y143C,R substitutions, respectively (29,30).…”

“…For example, E92Q and G140A, S are associated with N155H and Q148H,K,R, respectively (16,29), whereas T97A is associated with Y143C,R (27,30). In addition, L74I,M, E92Q, E138K, V151I, G163R, I203M, and S230R have been associated with RAL treatment failure (31).…”