Guanine α-carboxy nucleoside phosphonate (G-α-CNP) shows a different inhibitory kinetic profile against the DNA polymerases of human immunodeficiency virus (HIV) and herpes viruses

Abstract

α-Carboxy nucleoside phosphonates (α-CNPs) are modified nucleotides that represent a novel class of nucleotide-competing reverse transcriptase (RT) inhibitors (NcRTIs). They were designed to act directly against HIV-1 RT without the need for prior activation (phosphorylation). In this respect, they differ from the nucleoside or nucleotide RTIs [N(t)RTIs] that require conversion to their triphosphate forms before being inhibitory to HIV-1 RT. The guanine derivative (G-α-CNP) has now been synthesized and investigated for the first time. The (L)-(+)-enantiomer of G-α-CNP directly and competitively inhibits HIV-1 RT by interacting with the substrate active site of the enzyme. The (D)-(−)-enantiomer proved inactive against HIV-1 RT. In contrast, the (+)- and (−)-enantiomers of G-α-CNP inhibited herpes (i.e. HSV-1, HCMV) DNA polymerases in a non- or uncompetitive manner, strongly indicating interaction of the (L)-(+)- and the (D)-(−)-G-α-CNPs at a location different from the polymerase substrate active site of the herpes enzymes. Such entirely different inhibition profile of viral polymerases is unprecedented for a single antiviral drug molecule. Moreover, within the class of α-CNPs, subtle differences in their sensitivity to mutant HIV-1 RT enzymes were observed depending on the nature of the nucleobase in the α-CNP molecules. The unique properties of the -CNPs make this class of compounds, including G-α-CNP, direct acting inhibitors of multiple viral DNA polymerases.

Overview of Biologically Active Nucleoside Phosphonates

“…In contrast, alpha-carboxynucleoside phosphonates (α-CNPs) are a class of structural mimics of natural 2′-deoxynucleotide 5′-triphosphates that were conceived to enable direct inhibition of viral DNA polymerases without the need for prior metabolic activation. This concept is best illustrated by cyclopentyl α-CNPs containing either a pyrimidine or purine base ( 43a–e , Figure 4 ), whose ability to be efficiently recognized and strongly inhibit HIV-1 reverse transcriptase (IC 50 = 0.19–4.3 μM) was demonstrated in a cell-free HIV-1-RT assay (Keane et al, 2015 ; Balzarini et al, 2017 ). Both the phosphonate and carboxyl groups were found to be required for activity, which resided in the L-enantiomer of the compounds.…”

Alpha-Carboxynucleoside Phosphonates: Direct-Acting Inhibitors of Viral DNA Polymerases

“…base present in the template overhang. In this respect, the α-CNPs behave similarly as the NRTIs and N(t)RTIs with respect of HIV RT recognition and inhibition [31,37]. The α-CNPs generally proved equally potent inhibitors of HIV-1 RT as their corresponding 2 ,3 -dideoxynucleotide analogs, such as AZT-TP, ddCTP, ddATP and ddGTP.…”

“…Their IC 50 values were in the middle micromolar range. Only the G-α-CNP analog had an IC 50 in the low micromolar range [37]. Strikingly, both the cellular DNA polymerases α and β were poorly inhibited by the cyclic α-CNPs (IC 50 >100 μM).…”

“…Later on, compounds were also designed to replace the cyclopentyl by an acyclic aliphatic entity, preferably a butenyl group since this moiety, which replaces the 2-deoxyribose in nucleotide analogs, had previously been shown to generate compounds with antiherpetic activity (Figure 4) [35]. All natural nucleobases, in addition to several unnatural nucleobases and modifications in the carboxy phosphonate part, have been designed and synthesized using the α-CNP concept [30,32,[36][37][38].…”

“…An interesting feature was observed for the acyclic (butenyl) α-CNPs. Whereas the cyclic α-CNPs inhibited HIV-1 RT in a highly selective manner (specific competition in the presence of a natural dNTP containing a similar nucleobase as the α-CNP), the acyclic (butenyl) α-CNPs behaved clearly differently [37]. They efficiently inhibited the herpetic DNA polymerases (i.e., HCMV and VZV DNA polymerases) irrespective of the nature of the nucleobase in the competing dNTP (Table 5).…”