HIV-1 integrase is the enzyme responsible for integrating the viral DNA into the host genome and is one of the main targets for antiretroviral therapy; however, there are documented cases of resistance against all the currently used integrase strand transfer inhibitors (INSTIs). While some resistance-related mutations occur near the inhibitor’s binding site, the mutation N155H occurs on the opposite side of the drug-interacting Mg²⁺ ions, thus, not interacting directly with the drug molecules and currently lacking an explanation for its resistance mechanism. Moreover, mutation N155H and the resistance-related mutation Q148H are mutually exclusive for unknown reasons. In the present study, we use molecular dynamics simulations to understand the impact of the N155H mutation in the HIV-1 integrase structure and dynamics, when alone or in combination with Q148H. Our findings suggest that the Mg²⁺ ions of the active site adopt different orientations in each of the mutants, causing the catalytic triad residues involved in the ion coordination to adapt their side-chain configurations, completely changing the INSTIs binding site. The change in the ion coordination also seems to affect the flexibility of the terminal viral DNA nucleotide near the active site, potentially impairing the induced-fit mechanism of the drugs. The explanations obtained from our simulations corroborate previous hypotheses drawn from crystallographic studies. The proposed resistance mechanism can also explain the resistance caused by other mutations that take place in the same region of the integrase and help uncover the structural details of other HIV-1 resistance mechanisms.

HIV-1整合酶是负责将病毒DNA整合到宿主基因组中的酶，并且是抗逆转录病毒疗法的主要目标之一。然而，有文献证明对所有目前使用的整合酶链转移抑制剂（INSTI）有抗药性。虽然一些抗药性相关突变发生在抑制剂的结合位点附近，但突变N155H发生在与药物相互作用的Mg ²⁺的另一侧因此，离子并不直接与药物分子相互作用，目前尚缺乏对其耐药机制的解释。此外，由于未知原因，突变N155H和与抗性有关的突变Q148H是互斥的。在本研究中，我们单独或与Q148H结合使用分子动力学模拟来了解N155H突变对HIV-1整合酶结构和动力学的影响。我们的发现表明，Mg ²⁺活性位点的离子在每个突变体中采用不同的方向，从而导致参与离子配位的催化三联体残基适应其侧链构型，从而完全改变了INSTIs的结合位点。离子配位的变化似乎也影响了活性位点附近的末端病毒DNA核苷酸的柔韧性，有可能损害药物的诱导拟合机制。从我们的模拟中获得的解释证实了先前从晶体学研究中得出的假设。提出的抗药性机制还可以解释由整合酶同一区域中发生的其他突变引起的抗药性，并有助于揭示其他HIV-1抗药性机制的结构细节。