Theoretical study on the HIV-1 integrase inhibitor 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-propenone (5CITEP)

The Effect of Geometrical Isomerism of 3,5-Dicaffeoylquinic Acid on Its Binding Affinity to HIV-Integrase Enzyme: A Molecular Docking Study

A potent plant-derived HIV-1 inhibitor, 3,5-dicaffeoylquinic acid (diCQA), has been shown to undergo isomerisation upon UV exposure where the naturally occurring 3 ^trans ,5 ^trans -diCQA isomer gives rise to the 3 ^cis ,5 ^trans -diCQA, 3 ^trans ,5 ^cis -diCQA, and 3 ^cis ,5 ^cis -diCQA isomers. In this study, inhibition of HIV-1 INT by UV-induced isomers was investigated using molecular docking methods. Here, density functional theory (DFT) models were used for geometry optimization of the 3,5-diCQA isomers. The YASARA and Autodock VINA software packages were then used to determine the binding interactions between the HIV-1 INT catalytic domain and the 3,5-diCQA isomers and the Discovery Studio suite was used to visualise the interactions between the isomers and the protein. The geometrical isomers of 3,5-diCQA were all found to bind to the catalytic core domain of the INT enzyme. Moreover, the cis geometrical isomers were found to interact with the metal cofactor of HIV-1INT, a phenomenon which has been linked to antiviral potency. Furthermore, the 3 ^trans ,5 ^cis -diCQA isomer was also found to interact with both LYS156 and LYS159 which are important residues for viral DNA integration. The differences in binding modes of these naturally coexisting isomers may allow wider synergistic activity which may be beneficial in comparison to the activities of each individual isomer.

Use of a hexasubstituted benzene scaffold in the development of multivalent HIV-1 integrase inhibitors

The highly directional hexasubstituted benzene moiety was used as the central scaffold to create new human immunodeficiency virus (HIV)-1 integrase inhibitors through the attachment of multiple active groups. A series of potential inhibitors having substituted polyhydroxylated mono, bis and tris-cinnamoyl derivatives connected on the scaffold were prepared through Claisen-Schmidt condensations with substituted benzaldehydes, followed by partial demethylation to uncover the active phenolic groups required for the interactions with the integrase enzyme active sites. Using a multiplate integration assay method, four compounds carrying at least two sets of interacting moieties were found to be relatively potent integrase inhibitors with IC50 values in the low micromolar range. The results confirmed that multiple polyhydroxylated groups were required on the platform in order to effectively interact with the enzyme. The results from molecular docking studies consistently complemented the experimental results and revealed the nature of the potential key binding interactions responsible for the apparent activity of the active compounds.

HIV-1 IN alternative molecular recognition of DNA induced by raltegravir resistance mutations

Virologic failure during treatment with raltegravir, the first effective drug targeting HIV integrase, is associated with two exclusive pathways involving either Q148H/R/K, G140S/A or N155H mutations. We carried out a detailed analysis of the molecular and structural effects of these mutations. We observed no topological change in the integrase core domain, with conservation of a newly identified Omega-shaped hairpin containing the Q148 residue, in particular. In contrast, the mutations greatly altered the specificity of DNA recognition by integrase. The native residues displayed a clear preference for adenine, whereas the mutant residues strongly favored pyrimidines. Raltegravir may bind to N155 and/or Q148 residues as an adenine bioisoster. This may account for the selected mutations impairing raltegravir binding while allowing alternative DNA recognition by integrase. This study opens up new opportunities for the design of integrase inhibitors active against raltegravir-resistant viruses.