DB-02, a C-6-cyclohexylmethyl substituted pyrimidinone HIV-1 reverse transcriptase inhibitor with nanomolar activity, displays an improved sensitivity against K103N or Y181C than S-DABOs

Abstract

6-(cyclohexylmethyl)-5-ethyl-2-((2-oxo-2-phenylethyl)thio)pyrimidin-4(3H)-one (DB-02) is a member of the newly reported synthetic anti-HIV-1 compounds dihydro-aryl/alkylsulfanyl-cyclohexylmethyl-oxopyrimidines, S-DACOs. In vitro anti-HIV-1 activity and resistance profile studies have suggested that DB-02 has very low cytotoxicity (CC50>1mM) to cell lines and peripheral blood mononuclear cells (PBMCs). It displays potent anti-HIV-1 activity against laboratory adapted strains and primary isolated strains including different subtypes and tropism strains (EC50s range from 2.40 to 41.8 nM). Studies on site-directed mutagenesis, genotypic resistance profiles revealed that V106A was the major resistance contributor for the compound. Molecular docking analysis showed that DB-02 located in the hydrophobic pocket with interactions of Lys101, Val106, Leu234, His235. DB-02 also showed non-antagonistic effects to four approved antiretroviral drugs. All studies indicated that DB-02 would be a potential NNRTI with low cytotoxicity and improved activity.

Figure 1. Structures of S-DABO and DB-02.

Figure 2. Cytotoxicity of DB-02 in C8166, MT-4 and PBMC using MTT methods.

DB-02 showed low cytotoxicity to all the three types of aforementioned cells above. CC₅₀ of these cells were all >1000μM, respectively.

Figure 3. RT activity of DB-2 in vitro.

The RT activity was measured by ELISA using DIG-labeled dNTPs, which were incorporated into the newly synthesized cDNA. The figure represents three independent experiments.

Figure 4. Molecular docking of DB-02.

(A) Superimposition of the docked conformations of DB-02 (green-colored carbon atoms) and TNK-651 (grey). The docking results are showed by PyMOL. The backbone is represented by ribbons, and amino acid residues important for binding interactions are labeled. Dotted lines show the interactions between HIV-1 RT and DB-02. (B) The two-dimension representations of the interactions between the NNIBP and DB-02 (green) or TNK-651 (grey) are presented after the docking.