Molecular Dynamics Approaches Estimate the Binding Energy of HIV-1 Integrase Inhibitors and Correlate with In Vitro Activity

Abstract

The design of novel integrase (IN) inhibitors has been aided by recent crystal structures revealing the binding mode of these compounds with a full-length prototype foamy virus (PFV) IN and synthetic viral DNA ends. Earlier docking studies relied on incomplete structures and did not include the contribution of the viral DNA to inhibitor binding. Using the structure of PFV IN as the starting point, we generated a model of the corresponding HIV-1 complex and developed a molecular dynamics (MD)-based approach that correlates with the in vitro activities of novel compounds. Four well-characterized compounds (raltegravir, elvitegravir, MK-0536, and dolutegravir) were used as a training set, and the data for their in vitro activity against the Y143R, N155H, and G140S/Q148H mutants were used in addition to the wild-type (WT) IN data. Three additional compounds were docked into the IN-DNA complex model and subjected to MD simulations. All three gave interaction potentials within 1 standard deviation of values estimated from the training set, and the most active compound was identified. Additional MD analysis of the raltegravir-and dolutegravir-bound complexes gave internal and interaction energy values that closely match the experimental binding energy of a compound related to raltegravir that has similar activity. These approaches can be used to gain a deeper understanding of the interactions of the inhibitors with the HIV-1 intasome and to identify promising scaffolds for novel integrase inhibitors, in particular, compounds that retain activity against a range of drug-resistant mutants, making it possible to streamline synthesis and testing. . This leaves a conserved CA sequence with a free hydroxyl on each of the 3= ends of the viral DNA and a 2-nucleotide overhang on each of the 5= ends. In the second reaction, IN uses the newly created 3= hydroxyl to attack the phosphodiester backbone of the host genome (strand transfer [ST]). Depending on the retrovirus, the two viral ends are inserted 4 to 6 bases apart, creating a small duplication in the target DNA flanking the provirus (5 nucleotides in the case of HIV-1 and 4 for prototype foamy virus [PFV]) (50). Cellular enzymes repair the gaps, leaving the double-stranded proviral DNA stably integrated into the genome of the infected cell.Integrases consist of three functionally distinct domains that have been characterized by biochemical and mutational analyses. The N-terminal domain (NTD; residues 1 to 50) contains a zincbinding HHCC motif and contributes to multimer formation (7,8). The C-terminal domain (CTD; identified as residues 212 to 288 in deletion studies) nonspecifically binds DNA (18,20,34,42). The catalytic core domain (CCD; residues 50 to 212) contains the catalytic triad DD35E motif that is well conserved among the retroviral integrase superfamily (7,11,19,32). This active site coordinates two metal ions and binds one viral DNA end. Although IN complexes exist in solution in different multimeric states, recent crystallographic data confirmed that the functi...

Biochemical Analysis of the Role of G118R-Linked Dolutegravir Drug Resistance Substitutions in HIV-1 Integrase

“…DTG (8,(16)(17)(18)(19)(20)(21)(22)(23) also binds to integrase protein with a longer residence time than either RAL and EVG (24) and has yet to select for resistance substitutions in HIV-positive previously antiretroviral (ARV)-naive patients receiving ARVs for the first time, despite having been used over a period of 96 weeks (20,21,25). It is important to better understand the resistance profile of DTG as well as to determine whether differences in HIV subtype might ultimately affect the clinical performance of this drug.…”

Selectivity for strand-transfer over 3′-processing and susceptibility to clinical resistance of HIV-1 integrase inhibitors are driven by key enzyme–DNA interactions in the active site

“…We also investigated potential protein–nucleic acid interactions using our HIV-1 IN molecular model (26,27) pointing to a previously unreported role for residue Q146 in viral DNA end recognition. Finally, we describe a correlation between the ability of INSTIs to overcome drug resistance and their potency in the 3′-P reaction.…”

The elvitegravir Quad pill: the first once-daily dual-target anti-HIV tablet

“…Dolutegravir (formerly S/GSK1349572, Shionogi-GlaxoSmithKline Pharmaceuticals, LLC, now Shionogi-ViiV Healthcare, LLC) is the most recent INSTI in clinical development with an effective 50 mg once-daily unboosted administration [12]. Dolutegravir seems to have a higher barrier to resistance when compared to raltegravir as demonstrated by in vitro work [13] and suggested by preliminary in vivo data [12]. Dolutegravir was co-crystallized with the PFV integrase and retroviral DNA and was found to bind similarly to raltegravir and elvitegravir [14].…”