Relationship between Conformation and Antiviral Activity-II. 5-Methoxymethyl-2′-deoxycytidine and 5-methoxymethyl-N⁴-methyl-2′-deoxycytidine

5-methoxymethyl-N 4 -methyl-2′-deoxycytidine (N 4 -Me-MMdCyd) and 5-methoxymethyl-N 4 -methyl-2′-deoxycytidine-5′-monophosphate (N 4 -Me-MMdCMP) were synthesized to confer resistance to deamination by deaminating enzymes. N 4 -Me-MMdCyd and N 4 -Me-MMdCMP were inactive against Herpes simplex virus type 1 (HSV-1) and also nontoxic to VERO cells up to 1796 μM (highest concentration tested). 5-methoxymethyl-2′-deoxycytidine-5′-monophosphate (MMdCMP) was more potent than the nucleoside against HSV-1 in VERO cells. In HSV-infected VERO cells (10 PFU/cell), N 4 -Me-MMdCyd caused only slight perturbations of deoxyribonucleoside triphosphate pools. 5-methoxymethyl-N 4 -methyl-2′-deoxycytidine-5′-triphosphate (N 4 -Me-MMdCTP) was synthesized and the nature of interaction of N 4 -Me-MMdCTP and dCTP with DNA polymerase of Escherichia coli, HSV-1 and human α was investigated. N 4 -Me-MMdCTP was neither an effective substrate nor a strong inhibitor of Escherichia coli, HSV-1 or human α DNA polymerase. The relationship between molecular conformation and antiviral activity for MMdCyd and N 4 -Me-MMdCyd is discussed. The conformation of the deoxyribofuranose ring in MMdCyd and N 4 -Me-MMdCyd are different. In N 4 -Me-MMdCyd, the exocyciic C(5′) side chain has the t conformation whereas MMdCyd has the g + rotomer conformation. The orientation of the N 4 -methyl group may also impede binding to the HSV-induced kinase by steric hindrance and/or by hindering hydrogen bonding between the enzyme and the lone pair of electrons at N(3). The results suggest that attempts to render resistance to deamination by alkylation at the N(4) position of the cytosine moiety is not likely to yield compounds with activity against HSV.