The alternating conformation of analogues of poly[d(AT)]

Anti-Herpes Virus Activity of 5-Methoxymethyl-2′-Deoxycytidine in Combination with Deaminase Inhibitors

5-Methoxymethyl-2′-deoxycytidine (MMdCyd) is an anti-metabolite with selective anti-herpes activity and low cytotoxicity. MMdCyd is dependent upon initial activation by the viral-induced deoxythymidine-deoxycytidine (dThd/dCyd) kinase for its activity against herpes simplex virus (HSV). Antiviral activity of MMdCyd is cell-dependent and is influenced by the deaminase content of the cell line used for assays. The antiviral potency against HSV-1 in this study was higher in RK-13 cells (ED50 3–5 μm) than in Vero and HEP-2 cells (ED50 14–26 μm). The potency of MMdCyd increased approximately 20-fold against HSV-1 and twofold against HSV-2 in the presence of tetrahydrodeoxyuridine (H4dUrd; which inhibits both dCyd deaminase and dCMP deaminase) in Vero cells. MdCyd in combination with H4dUrd was effective in preventing the cytopathogenic effect of HSV-1 and decreasing the production of infectious virus particles. The IC99 (concentration required to reduce the yield of infectious virus obtained 72 h after infection by 99% relative to control cultures) was 1.6 μm. In combination with tetrahydrouridine (H4Urd; an inhibitor of Cyd/dCyd deaminase) the potency of MMdCyd was only slightly enhanced (ED50 7–8 μm). Dihydrodeoxyuridine and deoxyuridine reversed the antiviral activity of MMdCyd. The minimum cytotoxic concentration for rapidly dividing cells (RK-13, HEP-2 and Vero) for MMdCyd was greater than 3 mm. H4Urd and H4dUrd were devoid of cytotoxicity and antiviral activity up to 2.12 mm (the highest concentration tested). Diacetyl-MMdCyd (pro-drug form) was approximatewly 20 times less potent than MMdCyd.

Interaction of 5-Methoxymethyl-2′-Deoxyuridine Triphosphate with DNA Polymerases: Effects of the 5-Substituent and Comparison with the Deoxycytidine Derivative

5-Methoxymethyl-2′-deoxyuridine (MMdUrd) is a selective anti-herpes agent that is dependent upon initial phosphorylation by Herpes simplex virus-induced deoxythymidine kinase. In order to determine its mechanism of action, MMdUrd was converted to the 5′-triphosphate (MMdUTP) and the nature of interaction of MMdUTP and dTTP with DNA polymerase of E. coli, HSV-1, and human α was investigated. The order of utilization of deoxyuridine analogues by bacterial and HSV-1 DNA polymerases for DNA synthesis was: dTTP > MMdUTP. In contrast, 5-methoxymethyl-2′-deoxycytidine-5′-triphosphate (MMdCTP) was a better substrate for HSV DNA polymerase compared to dCTP. MMdUTP is a competitive inhibitor of HSV-1 DNA polymerase with respect to dTTP incorporation (Ki = 2.9 × 10−6M). The IC50 values of MMdUTP for both HSV and human αDNA polymerases were 4.5 × 10 −6M. These data suggest that the selective activity of MMdUrd is due to its preferential phosphorylation by viral thymidine kinase and not at the DNA polymerase level. These results may also account for the difference in anti-HSV activity between MMdUrd and its deoxycytidine analogue.

Inhibition of human DNA topoisomerase I by new DNA minor groove ligands: derivatives of oligo-1,3-thiazolecarboxamides

A series of novel thiazole-containing oligopeptides (oligo-1,3-thiazolecarboxamides) interesting specifically with the minor groove of DNA was shown to inhibit human DNA topoisomerase I (topo I). Inhibitory effects of thiazole-containing oligopeptides (TCO) increase with the number of thiazole units in such compounds. Inhibitory properties of TCO containing 3 or 4 thiazole units were shown to be 3-10 times better than those of the well-known natural antibiotic, distamycin A containing pyrrole rings. The structure of various additional groups attached to the N-terminus and C-terminus of TCO had no significant effect on TCO interaction with the complex of DNA and topo I. TCO were shown to be capable of binding with double-stranded DNA (dsDNA), and the majority of TCO analyzed were more effective in binding with dsDNA than distamycin A. Possible reasons for the different effects of distamycin A and TCO on the reaction of relaxation catalyzed by topo I are discussed.

Synthesis and evaluation of oligo-1,3-thiazolecarboxamide derivatives as HIV-1 reverse transcriptase inhibitors

A set of oligo-1,3-thiazolecarboxamide derivatives able to interact with the minor groove of nucleic acids was synthesized. These oligopeptides contained different numbers of thiazole units presenting dimethylaminopropyl or EDTA moieties on the C-terminus, and aminohexanoyl or EDTA moieties on the N-terminus. The inhibition of such compounds on HIV-1 reverse transcriptase activity was evaluated using different model template primer duplexes: DNA x DNA, RNA x DNA, DNA x RNA and RNA x RNA. The biological properties of the thiazolecarboxamide derivatives were compared to those of distamycin, another minor groove binder which contains three pyrrole rings. Similar to distamycin, the thiazole containing oligopeptides were good inhibitors of the reverse transcription reaction in the presence of DNA x DNA. But in contrast to distamycin, the oligothiazolide derivatives were able to inhibit reverse transcription in the presence of RNA x DNA or DNA x RNA template primers. Both distamycin and oligothiazolecarboxamides had low affinity for RNA x RNA duplexes. The inhibition obtained with the newly synthesized thiazolecarboxamides showed that these compounds were more powerful and versatile inhibitors of the RT-dependent polymerization than the natural minor groove binder distamycin.

NMR studies of copper speciation in the bovine rumen environment

Dietary copper supplements containing complexed copper have been asserted to be more bioavailable than 'inorganic' supplements. Since bioavailability is intimately related to the particular metal ion species that exist in any given environment, studies of solution speciation can be used to examine this assertion. In a previous study, our computer modeling of copper speciation in bovine saliva indicated that when a lysine-complexed copper supplement is used, the complex will not persist. In the present study, these conclusions are supplemented and extended using 1H NMR experiments. Lysine and the copper(II)-lysine system are characterized, and chemical shifts of the individual species obtained. Chemical shift values for the copper(II)-lysine-bovine saliva system can then be predicted. Results show good agreement with experimental values. The scope of the computer modeling is then expanded to include the major low molar mass ligands present in the rumen. Implications of the results are discussed. The validity of this rumen model is further evaluated by NMR investigations on biological samples. The study provides further evidence that complexes such as copper(II)-lysine would disintegrate in the gastrointestinal tract, and are unlikely to be absorbed intact.

The algorithm of estimation of the Km values for primers in DNA synthesis catalyzed by human DNA polymerase alpha

DNA synthesis with various deoxyribo homo- and heterooligoprimers in the presence of complementary templates was investigated. The lengthening of d(pN)n, primers (n = 1-10) by a unit resulted in an increase of the primer affinity and a maximal rate of polymerization. The coefficient of the affinity enhancement of primers due to formation of one hydrogen bond between primer and template was found to be 1.35. The dependence of the primer affinity and polymerization rate on template-primer structure in solution was analyzed and the objective laws of the changes of the KM and Vmax values were revealed.

Structures of oligonucleotides containing 5-(methoxymethyl)-2'-deoxyuridine determined by NMR spectroscopy

Base pairing of 5-(methoxymethyl)-2'-deoxyuridine (MMdU) opposite either adenine or guanine in a seven base pair oligonucleotide duplex has been studied by NMR spectroscopy. When paired with A, we observe that the MMdU.A base pair adopts Watson-Crick geometry. The methoxymethyl substituent is not held in a fixed conformation and may rotate around the C5-CH2 and CH2-O bonds. Examination of the potential energy as a function of rotation around these bonds indicates the presence of four low energy conformations. No hydrogen bonding is indicated for the methoxymethyl substituent, and the four potential minima result from reduced steric clash. For the MMdU.G base pair, the two bases adopt a wobble geometry which does not change with increasing solvent pH. Similarly, we find four low energy conformations for the methoxymethyl substituent in the major groove of the DNA helix.

Functional analysis of primers and templates in the synthesis of DNA catalyzed by human immunodeficiency virus type 1 reverse transcriptase

The kinetics of copying of poly(A).(dT)n, poly(A).(U)n, poly(dA).(dT)n and poly(A).(dT)9-U by reverse transcriptase of human immunodeficiency virus-1 (HIV-1) has been studied and the binding affinity of the enzyme, for template or primer, determined. Short oligonucleotides and dTTP served as primers in the HIV-1 reverse-transcriptase-dependent DNA synthesis. Km and Vmax were measured as functions of the primer chain length; the logarithm of the values of both Km and Vmax increased linearly up to 10. For longer primers (n = 11 to n = 24) the increase of those values changes very little. The enhanced affinity of the primers, (dT)n or (U)n due to the formation of one complementary pair, A.dT, dA.dT, A.U was estimated as a factor of 2. A specific property of HIV-1 reverse transcriptase compared with other DNA polymerases (procaryotes, eucaryotes, other retroviruses and archaebacteria) was its higher affinity to riboprimers as compared to deoxyriboprimers. Relative initial rates when copying poly(A) or poly(dA) templates using different primers and various conditions were compared; the optimal temperature for the reaction of polymerization with poly(A) or poly(dA) templates and (U)10, (dT)10 or (dT)9-U primers was determined. The maximal activity of the enzyme in the case of poly(A) and decanucleotide primers was found at temperatures between 27-31 degrees C. An increase in the primer length results in the stabilization of the template.primer duplex complexed to the enzyme, thus increasing to more than 40 degrees C the optimal temperature of polymerization. The activation energy (Ea) values of the polymerization reaction for different template.primer complexes were evaluated.

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

5-methoxymethyl-N4-methyl-2′-deoxycytidine (N4-Me-MMdCyd) and 5-methoxymethyl-N4-methyl-2′-deoxycytidine-5′-monophosphate (N4-Me-MMdCMP) were synthesized to confer resistance to deamination by deaminating enzymes. N4-Me-MMdCyd and N4-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), N4-Me-MMdCyd caused only slight perturbations of deoxyribonucleoside triphosphate pools. 5-methoxymethyl-N4-methyl-2′-deoxycytidine-5′-triphosphate (N4-Me-MMdCTP) was synthesized and the nature of interaction of N4-Me-MMdCTP and dCTP with DNA polymerase of Escherichia coli, HSV-1 and human α was investigated. N4-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 N4-Me-MMdCyd is discussed. The conformation of the deoxyribofuranose ring in MMdCyd and N4-Me-MMdCyd are different. In N4-Me-MMdCyd, the exocyciic C(5′) side chain has the t conformation whereas MMdCyd has the g+rotomer conformation. The orientation of the N4-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.

Destabilization of the duplex and the high-salt Z-form of poly(dG-methyl5dC) by substitution of ethyl for the 5-methyl group

The B-to-Z conformational transition of poly(dG-dC) is highly promoted by 5-methyl substitution of the dC moiety, i.e. in poly(dG-methyl5dC). By the synthesis of a new poly(dG-dC) analogue, poly(dG-ethyl5dC), the effect of a longer alkyl-chain substituent of dC on structure and conformation has been studied with ultraviolet absorption melting profiles and circular dichroism spectroscopy. The 5-ethyl substituent in poly(dG-ethyl5dC) destabilizes the duplex structure against thermal denaturation compared with both poly(dG-methyl5dC) and poly(dG-dC). C.d. studies also reveal that for the high-salt B-Z transition of poly(dG-ethyl5dC) a higher NaCl concentration is required than for that of poly(dG-methyl5dC), although much lower than for poly(dG-dC). However low-salt Z-DNA in poly(dG-ethyl5dC) shows unique features, e.g. it needs no divalent cations to be stable. The low-salt B-Z transition of poly(dG-ethyl5dC) can also be observed by the absorption-temperature melting profile, in contrast to both poly(dG-methyl5dC) and poly(dG-dC). The effects of MgCl2 concentration, temperature, acid pH and trifluorethanol on the conformation of poly(dG-ethyl5dC) have also been determined.