A conformational escape reaction of HIV-1 against an allosteric integrase inhibitor.

HIV-1 often acquires drug-resistant mutations in spite of the benefits of antiretroviral therapy (ART). HIV-1 integrase (IN) is essential for concerted integration of HIV-1 DNA into the host genome. IN further contributes to HIV-1 RNA binding, which is required for HIV-1 maturation. Non-catalytic site integrase inhibitors (NCINIs) have been developed as allosteric IN inhibitors, which performs anti-HIV-1 activity by a multimodal mode of action such as inhibition of IN-LEDGF/p75 interaction in the early stage and disruption of functional IN multimerization in the late stage of HIV-1 replication. Here, we show that IN undergoes an adaptable conformational change to escape from NCINIs. We observed that NCINI-resistant HIV-1 variants have accumulated four amino acid (AA) mutations by passage 26 (P26) in the IN-encoding region. We employed HPLC, thermal stability assay, and X-ray crystallographic analysis to show that some AA mutations affect the stability and/or dimerization interface of the IN catalytic core domains (CCD), potentially resulting in severely decreased multimerization of full-length IN proteins (IN under-multimerization). This under-multimerized IN via the NCINI-related mutations was stabilized by HIV-1 RNA and restored to the same level as HIV-1 wild type in the viral particles. Recombinant HIV-1 clones with IN under-multimerization propagated similarly as HIV-1 wild type. Our study revealed that HIV-1 can eventually countervail NCINI-induced IN over-multimerization by IN under-multimerization as one of the escape mechanisms. Our findings provide information on the understanding of IN multimerization with or without HIV-1 RNA and may influence the development of anti-HIV-1 strategies.IMPORTANCE Understanding the mechanism of HIV-1 resistance to anti-HIV-1 drugs would lead to the development of novel drugs with increased efficiency, resulting in more effective ART. ART composed of more potent and long-acting anti-HIV-1 drugs can greatly improve drug adherence and also provide HIV-1 prevention such as pre-exposure prophylaxis. NCINIs with the multimodal mode of action exert potent anti-HIV-1 effects through IN over-multimerization during HIV-1 maturation. However, HIV-1 can acquire some mutations which cause IN under-multimerization to alleviate NCINI-induced IN over-multimerization. This under-multimerized IN was efficiently stabilized by HIV-1 RNA and restored to the same level as HIV-1 wild type. Our findings revealed that HIV-1 eventually acquires such conformational escape reaction to overcome the unique NCINI actions. The investigation into the drug-resistant mutations associated with HIV-1 protein multimerization may facilitate the elucidation of its molecular mechanism and functional multimerization, allowing us to develop more potent anti-HIV-1 drugs and unique treatment strategies.