Natural Variation of HIV-1 Group M Integrase: Implications For a New Class of Antiretroviral Inhibitors

Soo-Yon Rhee; Tommy F Liu; Mark Kiuchi; Rafael Zioni; Robert J Gifford; Susan P Holmes; Robert W Shafer



In This Article

Abstract and Introduction


HIV-1 integrase is the third enzymatic target of antiretroviral (ARV) therapy. However, few data have been published on the distribution of naturally occurring amino acid variation in this enzyme. We therefore characterized the distribution of integrase variants among more than 1,800 published group M HIV-1 isolates from more than 1,500 integrase inhibitor (INI)-nave individuals. Polymorphism rates equal or above 0.5% were found for 34% of the central core domain positions, 42% of the C-terminal domain positions, and 50% of the N-terminal domain positions. Among 727 ARV-nave individuals in whom the complete pol gene was sequenced, integrase displayed significantly decreased inter- and intra-subtype diversity and a lower Shannon's entropy than protease or RT. All primary INI-resistance mutations with the exception of E157Q – which was present in 1.1% of sequences - were nonpolymorphic. Several accessory INI-resistance mutations including L74M, T97A, V151I, G163R, and S230N were also polymorphic with polymorphism rates ranging between 0.5% to 2.0%.


HIV-1 integrase contains 288 amino acids encoded by the 3' end of the HIV-1 pol gene. It catalyzes the cleavage of the conserved 3' dinucleotide CA (3' processing) and the ligation of the viral 3'-OH ends to the 5'-DNA of host chromosomal DNA (strand transfer). Integrase also plays a role in stabilizing a pre-integration complex (PIC), which consists of the 3'-processed genome and one or more cellular co-factors involved in nuclear transfer of the PIC (reviewed in [1,2,3,4]).

HIV-1 integrase is composed of three functional domains: the N-terminal domain (NTD), which encompasses amino acids 1-50 and contains a histidine-histidine-cysteine-cysteine (HHCC) motif that coordinates zinc binding, the catalytic core domain (CCD) which encompasses amino acids 51-212 and contains the catalytic triad D64, D116, and E152, known as the DDE motif, and the C-terminal domain (CTD), which encompasses amino acids 213-288 and is involved in host DNA binding.

Crystal structures of the CCD plus CTD domains[5] and the CCD plus NTD domains[6] have been solved, but the relative conformation of the three domains and of the active multimeric form of the enzyme are not known. There is one published crystal structure of the CCD bound to an early prototype diketo acid inhibitor (5CITEP)[7] but no structures of the CCD bound to one of the integrase inhibitors (INIs) in clinical use or to a DNA template. Because of the difficulties in obtaining structures of the most biologically relevant forms of the enzyme and of most integrase-INI structures, much of the functional roles of different integrase residues have been identified through biochemical and systematic amino acid replacement studies (reviewed in [8]).

One INI, raltegravir, has been licensed for the treatment of HIV-1 infection and a second INI, elvitegravir, is in advanced clinical trials. Mutations associated with resistance to these inhibitors have been identified through in vitro and in vivo selection studies (reviewed in [9]) and through in vitro susceptibility testing. The purpose of this study is to supplement the structural and biochemical assessment of integrase function and INI resistance by summarizing naturally occurring variation in published sequences of group M integrase, particularly as this variation applies to positions associated with INI resistance.


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