Structural insights by molecular dynamics simulations into differential repair efficiency for ethano-A versus etheno-A adducts by the human alkylpurine-DNA N-glycosylase

1,N⁶-ethenoadenine adducts (εA) are formed by known environmental carcinogens and found to be removed by human alkylpurine-DNA N-glycosylase (APNG). 1,N⁶-ethanoadenine (ΕA) adducts differ from εA by change of a double bond to a single bond in the 5-member exocyclic ring and are formed by chloroethyl nitrosoureas, which are used in cancer therapy. In this work, using purified recombinant human APNG, we show that ΕA is a substrate for the enzyme. However, the excision efficiency of ΕA was 65-fold lower than that of εA. Molecular dynamics simulation produced similar structural motifs for εA and ΕA when incorporated into a DNA duplex, suggesting that there are no specific conformational features in the DNA duplex which can account for the differences in repair efficiency. However, when ΕA was modeled into the APNG active site, based on the APNG/εA-DNA crystallographic coordinates, in structures produced by 2 ns molecular dynamics simulation, we observed weakening in the stacking interaction between ΕA and aromatic side chains of the key amino acids in the active site. In contrast, the planar εA is better stacked at the enzyme active site. We propose that the observed destabilization of the ΕA adduct at the active site, such as reduced stacking interactions, could account for the biochemically observed weaker recognition of ΕA by APNG as compared to εA.     

Substrate specificity of human thymine-DNA glycosylase on exocyclic cytosine adducts

The environmental carcinogen glycidaldehyde (GDA) and therapeutic chloroethylnitrosoureas (CNUs) can form hydroxymethyl etheno and ring-saturated ethano bases, respectively. The mutagenic potential of these adducts relies on their miscoding properties and repair efficiency. In this work, the ability of human thymine-DNA glycosylase (TDG) to excise 8-(hydroxymethyl)-3,N(4)-ethenocytosine (8-hm-varepsilonC) and 3,N(4)-ethanocytosine (EC) was investigated and compared with varepsilonC, a known substrate for TDG. When tested using defined oligonucleotides containing a single adduct, TDG is able to excise 8-hm-varepsilonC but not EC. The 8-hm-varepsilonC activity mainly depends on guanine pairing with the adduct. TDG removes 8-hm-varepsilonC less efficiently than varepsilonC but its activity can be significantly enhanced by human AP endonuclease 1 (APE1), a downstream enzyme in the base excision repair. TDG did not show any detectable activity toward EC when placed in various neighboring sequences, including the 5'-CpG site. Molecular modeling revealed a possible steric clash between the non-planar EC exocyclic ring and residue Asn 191 within the TDG active site, which could account for the lack of TDG activity toward EC. TDG was not active against the bulkier exocyclic adduct 3,N(4)-benzethenocytosine, nor the two adenine derivatives with same modifications as the cytosine derivatives, 7-hm-varepsilonA and EA. These findings expand the TDG substrate range and aid in understanding the structural requirements for TDG substrate specificity.     

Inhibition of leucyl-tRNA-synthetases by modified ATP analogs

The interaction between modifying ATP analogs containing alkylating or phosphorylating groups in the polyphosphate moiety of the ATP molecule and leucyl-tRNA synthetases from cytoplasm and chloroplasts of Euglena gracilis (strain Z) was studied. It was shown that most of the ATP analogs irreversibly inhibit the cytoplasmic enzyme, having no inhibiting effect on the chloroplast synthetase. The kinetic constants K1 and k2 for the interaction between the most effective irreversible inhibitors and the cytoplasmic enzyme were determined. The data on the protection of the enzyme activity by substrates against irreversible inhibition suggest, that the effect of the adenosine 5'-(beta-chloroethyl phosphate) is directed to the ATP-binding site of the cytoplasmic enzyme, whereas the mixed anhydride of AMP and mesithylene carbonic acid acts predominantly on the binding site of 3'-terminal adenosine of the tRNALeu molecule. ATP analogs may be effectively used for affinity labelling of the cytoplasmic leucyl-tRNA synthetase.     

Effect of alkylating derivatives of cyclic adenosine-3' ,5'-monophosphate on proliferation of mouse bone marrow stem cells

The effect of the physiological concentration of cyclic adenosine-3' ,5'-monophosphate (cAMP) analogues on the proliferation of mouse bone marrow stem hemopoietic cells (CFUs) was examined. The stimulating effect was estimated from the decrease in CFUs expressed in the percentage derived from comparing the number of spleen colonies in the control and experimental groups treated with hydroxyurea 10(-3) M (incubation with hydroxyurea resuted in the cell death in S-phase). Cyclic AMP stimulted the proliferation of CFUs by 60%, while its analogues such as 8-(N-chloroacetylaminoethylamino)-cAMP, 1-(N-chloroacetylaminoethyoxy)-cAMP and 1-(N-(p-fluorosulfonyl)-benzoylaminoethoxy)-cAMP stimulated the proliferation by 39.2%, 32.4% and 21.9%, respectively. Therefore, the synthetic analogues of cAMP were not only far from inhibiting the proliferation of CFUs but, on the contrary, exerted a stimualting effect unlike most antineoplastic alkylating drugs that depress hemopoiesis up to its total aplasia.     

8-(Hydroxymethyl)-3,N(4)-etheno-C, a potential carcinogenic glycidaldehyde product, miscodes in vitro using mammalian DNA polymerases

8-(Hydroxymethyl)-3,N(4)-etheno-C (8-HM-epsilonC) is an exocyclic adduct resulting from the reaction of dC with glycidaldehyde, a mutagen and animal carcinogen. This compound has now been synthesized and its phosphoramidite incorporated site-specifically into a defined 25-mer oligonucleotide. In this study, the mutagenic potential of this adduct in the 25-mer oligonucleotide was investigated in an in vitro primer-template extension assay using four mammalian DNA polymerases. The miscoding potentials were also compared to those of an analogous derivative, 3,N(4)-etheno C (epsilonC), in the same sequence. Both adducts primarily blocked replication by calf thymus DNA polymerase alpha at the modified base, while human polymerase beta catalyzed measurable replication synthesis through both adducts. Nucleotide insertion experiments showed that dA and dC were incorporated by pol beta opposite either adduct, which would result in a C --> T transition or C --> G transversion. Human polymerase eta, a product of the xeroderma pigmentosum variant (XP-V) gene, catalyzed the most efficient bypass of the two lesions with 25% and 32% for 8-HM-epsilonC and epsilonC bypassed after 15 min. Varying amounts of all four bases opposite the modified bases resulted with pol eta. Human polymerase kappa primarily blocked synthesis at the base prior to the adduct. However, some specific misincorporation of dT resulted, forming an epsilonC.T or 8-HM-epsilonC.T pair. From these data, we conclude that the newly synthesized glycidaldehyde-derived adduct, 8-HM-epsilonC, is a miscoding lesion. The bypass efficiency and insertion specificity of 8-HM-epsilonC and epsilonC were similar for all four polymerases tested, which could be attributed to the similar planarity and sugar conformations for these two derivatives as demonstrated by molecular modeling studies.     

Stages in the improvement of drug therapy at a polyclinic]

Within 1968-1997 the authors studied the steps of introduction of the achievements of the medical science, technology and pharmacology to therapy of exacerbations and complications of peptic ulcer (PU). The scientific and practical value of endoscopic, histological, biochemical and bacteriological examinations in the improvement of the methods of pharmacotherapy of exacerbations and complications of PU was shown. Three phases of the PU development were indicated by the clinical signs and results of esophagogastroduodenoscopy, target biopsy and histological examinations. These data and available scientific achievements were assumed as a basis for the design of optimal drug combinations and their introduction to the medical practice. The use of such combinations made it possible to prevent relapses and life-threatening complications of the disease in the overwhelming majority of the patients. The best results of the pharmacotherapy were recorded in the years (1988-1997) when the drug combinations began to be used. The combinations provided eradication of Helicobacter pylori in the gastroduodenal mucosa and it was proved that in all the patients with PU and the relapsing lesions in the duodenum and in the overwhelming majority of the patients with gastric ulcer the disease developed at the background of chronic active gastroduodenitis associated with H.pylori. The success of the pharmacotherapy in the patients with PU was due to the use of the rational combinations of antibacterial and antisecretory agents.     

Spectral anisotropy of chloroplasts, subchloroplast particles and pigment-protein complexes

Anisotropic properties of pea chloroplasts, subchloroplast fragments (photosystem 1 particles and pigment-protein complexes) and the blue-green algae oriented in polyacrylamide gel were investigated. It was shown that linear dichroism spectra of chloroplasts are the superposition of the corresponding spectra for the main light harvesting complex (HMLC) and P 700 chlorophyll a--protein complex (CP 1). Anisotropic properties of the photosystem 1 particles and blue-green algae are mainly caused by CP 1 anisotropy. Qy-transition moments tend to perpendicular orientation to the membrane plane for the Chl. b 649, Chl. a 660 and parallel orientation--for Chl. b 654, Chl. a 682. The degree of Qy-transition moments parallel orientation is higher for the longwave forms (Chl. a 690, Chl. a 702, Chl. a 712), than for the shortwave ones and coincides with this degree for the reaction centre pigment P 700 transition moment. It is suggested that the specific orientation of the pigment-protein complexes in the chloroplast membrane is important for the regulation of the spillover between two photosystems.