Characterization and Structural Analysis of HIV-1 Integrase Conservation

The HIV-1 integrase, responsible for the chromosomal integration of the newly synthesized doublestrandedviral DNA into the host genomic DNA, represents a new and important target of potentialclinical relevance. For instance, two integrase inhibitors, raltegravir and elvitegravir, have been shownto be promising in clinical trials, and the first has been recently made available for clinical practice.As is the case for other antiviral drugs, drug resistance to integrase inhibitors occurs both in vitroand/or in vivo through the selection of mutations within the HIV genome. Indeed, many integrasemutations have already been associated with resistance to all the different integrase inhibitors testedin in vitro and/or in vivo studies. Among them, about 40 substitutions have been specificallyassociated with the development of resistance to raltegravir and/or elvitegravir; some of them werealso found in vivo in patients failing such integrase inhibitors.The relevance of integrase mutations in clinical practice has yet to be defined, in light of the lack oflong-term follow-up of treated patients and the limited data about the prevalence of integrase inhibitorassociatedmutations in integrase inhibitor-naive patients (either untreated, or treated with antiretroviralsnot containing integrase inhibitors).Therefore, by structural analysis elaboration and literature discussion, the aim of this review is to characterizethe conserved residues and regions of HIV-1 integrase and the prevalence of mutations associated withintegrase inhibitor resistance, by matching data originated from a well-defined cohort of HIV-1 B subtypeinfectedindividuals (untreated and antiretroviral-treated) and data originated from the public LosAlamos Database available in the literature (all patients integrase inhibitor-naive by definition).In integrase inhibitor-naive patients, 180 out of 288 HIV-1 integrase residues (62.5%) are conserved(< 1% variability). Residues involved in protein stability, multimerization, DNA binding, catalytic activity,and in the binding with the human cellular cofactor LEDGF/p75 are fully conserved. Some of theseresidues clustered into large defined regions of consecutive invariant amino acids, suggesting thatconsecutive residues in specific structural domains are required for the correct performance of HIV-1integrase functions.All primary signature mutations emerging in patients failing raltegravir (Y143R, Q148H/K/R, N155H) orelvitegravir (T66I, E92Q, S147G, Q148H/K/R, N155H), as well as secondary mutations (H51Y, T66A/K,E138K, G140S/A/C, Y143C/H, K160N, R166S, E170A, S230R, D232N, R263K) were completely absent orhighly infrequent (< 0.5%) in integrase inhibitor-naive patients, either infected with HIV-1 B subtype(drug-naive or antiretroviral-treated), or non-B subtypes/group N and O. Differently, other mutations (L74M, T97A, S119G/R, V151I, K156N, E157Q, G163K/R, V165I, I203M, T206S,S230N) occurred as natural polymorphisms with a different prevalence according to different HIV-1subtype/circulating recombinant form/group.In conclusion, the HIV-1 integrase in vivo is an enzyme requiring the full preservation of almosttwo-thirds of its amino acids in the absence of specific integrase inhibitor pressure. Primary mutationsassociated with resistance to integrase inhibitors clinically relevant today are absent or highly infrequentin integrase inhibitor-naive patients. The characterization of the highly conserved residues (involved inprotein stability, multimerization, DNA binding, catalytic activity, LEDGF binding, and some with stillpoorly understood function) could help in the rational design of new HIV-1 inhibitors with alternativemechanisms of action and more favorable resistance profiles.