Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity.

We report the results of an in vitro screening assay targeting the intraerythrocytic form of the malaria parasite Plasmodium falciparum using a library of 560 prenyl-synthase inhibitors. Based on "growth-rescue" and enzyme-inhibition experiments, geranylgeranyl diphosphate synthase (GGPPS) is shown to be a major target for the most potent leads, BPH-703 and BPH-811, lipophilic analogs of the bone-resorption drugs zoledronate and risedronate. We determined the crystal structures of these inhibitors bound to a Plasmodium GGPPS finding that their head groups bind to the [Mg(2+)](3) cluster in the active site in a similar manner to that found with their more hydrophilic parents, whereas their hydrophobic tails occupy a long-hydrophobic tunnel spanning both molecules in the dimer. The results of isothermal-titration-calorimetric experiments show that both lipophilic bisphosphonates bind to GGPPS with, on average, a ΔG of -9 kcal mol(-1), only 0.5 kcal mol(-1) worse than the parent bisphosphonates, consistent with the observation that conversion to the lipophilic species has only a minor effect on enzyme activity. However, only the lipophilic species are active in cells. We also tested both compounds in mice, finding major decreases in parasitemia and 100% survival. These results are of broad general interest because they indicate that it may be possible to overcome barriers to cell penetration of existing bisphosphonate drugs in this and other systems by simple covalent modification to form lipophilic analogs that retain their enzyme-inhibition activity and are also effective in vitro and in vivo.

Base pair opening kinetics study of the aegPNA:DNA hydrid duplex containing a site-specific GNA-like chiral PNA monomer.

Peptide nucleic acids (PNA) are one of the most widely used synthetic DNA mimics where the four bases are attached to a N-(2-aminoethyl)glycine (aeg) backbone instead of the negative-charged phosphate backbone in DNA. We have developed a chimeric PNA (chiPNA), in which a chiral GNA-like γ(3)T monomer is incorporated into aegPNA backbone. The base pair opening kinetics of the aegPNA:DNA and chiPNA:DNA hybrid duplexes were studied by NMR hydrogen exchange experiments. This study revealed that the aegPNA:DNA hybrid is much more stable duplex and is less dynamic compared to DNA duplex, meaning that base pairs are opened and reclosed much more slowly. The site-specific incorporation of γ(3)T monomer in the aegPNA:DNA hybrid can destabilize a specific base pair and its neighbors, maintaining the thermal stabilities and dynamic properties of other base pairs. Our hydrogen exchange study firstly revealed the unique kinetic features of base pairs in the aegPNA:DNA and chiPNA:DNA hybrids, which will provide an insight into the development of methodology for specific DNA recognition using PNA fragments.

CYP2D6- and CYP3A-dependent enantioselective plasma concentrations of ondansetron in postanesthesia care.

BACKGROUND: An influence of polymorphic cytochromes P450 (CYP) 2D6 genetic variants on antiemetic efficacy of ondansetron has been suggested. However, the role of CYP3A in ondansetron metabolism and efficacy has been unclear. In this study, we evaluated the hypothesis that genotype-dependent CYP2D6 and CYP3A activity selectively influences plasma concentrations of ondansetron enantiomers. Additionally, the effects of doubling the ondansetron dose on genotype-dependent plasma concentrations were investigated. METHODS: Patients received IV ondansetron 4 or 8 mg for emesis prophylaxis before emergence from anesthesia. The CYP2D6-dependent activity score representing no, decreased, normal, or increased CYP2D6 enzyme activity as well as CYP3A low (CYP3A5*3/*3) and high expressor status (CYP3A5 wt/wt or wt/*3) were determined. Plasma concentrations of R- and S-ondansetron enantiomers were measured by liquid chromatography-tandem mass spectrometry. Area under the plasma concentration-time curves (AUCs) of R- and S-ondansetron were associated with CYP2D6 and CYP3A5 genotype-dependent enzyme activity. RESULTS: Complete data of 141 subjects were analyzed. Concentrations of S-ondansetron differed between CYP2D6 activity groups (P = 0.01) with highest values in patients with no CYP2D6 activity (mean [95% confidence interval]: 362.5 [238.3/486.7] h · ng/mL) and lowest values in those with increased activity (149.6 [114.5/184.8] h · ng/mL) compared with subjects displaying genotypes resulting in reduced or normal CYP2D6 activity (263.6 [228.8/298.8], 255.4 [228.2/282.7] h · ng/mL). AUC of R-ondansetron was 2 times higher in CYP3A5 low expressors compared with high expressors (281.5 [248.6/314.3] vs 142.5 [92.4/192.7] h · ng/mL; P = 0.003). Doubling the ondansetron dose increased plasma concentrations only in individuals with low CYP3A activity, but not in individuals with high enzyme activity (P < 0.001). CONCLUSIONS: The metabolism of ondansetron seems to be enantioselective. In this postoperative setting, CYP2D6 activity scores correlated with concentrations of S-ondansetron, whereas CYP3A5 expressor status mainly influenced concentrations of R-ondansetron. Genetically and environmentally determined CYP2D6 and CYP3A enzyme activity might have implications for antiemetic efficacy.

Prioritising Risk Factors for Prescription Drug Overdose among Older Adults in South Korea: A Multi-Method Study.

Older adults are vulnerable to drug overdose. We used a multi-method approach to prioritise risk factors for prescription drug overdose among older adults. The study was conducted in two stages. First, risk factors for drug overdose were classified according to importance and changeability through literature review, determined through 2-phase expert surveys. Second, prescription drug overdose cases during 2011-2015 were selected from a national cohort; the prevalence of 'more important' or 'more changeable' factors determined in stage one was investigated. Scores were assigned according to the Basic Priority Rating Scale formula, reflecting the problem size and seriousness and intervention effectiveness. In the first stage, polypharmacy, old-old age, female sex, chronic disease, psychiatric disease, and low socioeconomic status (SES) were selected as risk factors. In the second stage, 93.9% of cases enrolled had chronic medical disease; 78.3% were using multiple drugs. Low SES was more prevalent than other risk factors. As per the scoring formula, chronic medical disease, polypharmacy, psychiatric disease, low SES, female sex, and old-old age were the most important risk factors in order of priority. Patients with chronic medical disease and those using multiple medications should be prioritised in overdose prevention interventions among older adults.

NMR spectroscopic elucidation of the B-Z transition of a DNA double helix induced by the Z alpha domain of human ADAR1.

The human RNA editing enzyme ADAR1 (double-stranded RNA deaminase I) deaminates adenine in pre-mRNA to yield inosine, which codes as guanine. ADAR1 has two left-handed Z-DNA binding domains, Z alpha and Z beta, at its NH(2)-terminus and preferentially binds Z-DNA, rather than B-DNA, with high binding affinity. The cocrystal structure of Z alpha(ADAR1) complexed to Z-DNA showed that one monomeric Z alpha(ADAR1) domain binds to one strand of double-stranded DNA and a second Z alpha(ADAR1) monomer binds to the opposite strand with 2-fold symmetry with respect to DNA helical axis. It remains unclear how Z alpha(ADAR1) protein specifically recognizes Z-DNA sequence in a sea of B-DNA to produce the stable Z alpha(ADAR1)-Z-DNA complex during the B-Z transition induced by Z alpha(ADAR1). In order to characterize the molecular recognition of Z-DNA by Z alpha(ADAR1), we performed circular dichroism (CD) and NMR experiments with complexes of Zalpha(ADAR1) bound to d(CGCGCG)(2) (referred to as CG6) produced at a variety of protein-to-DNA molar ratios. From this study, we identified the intermediate states of the CG6-Z alpha(ADAR1) complex and calculated their relative populations as a function of the Z alpha(ADAR1) concentration. These findings support an active B-Z transition mechanism in which the Z alpha(ADAR1) protein first binds to B-DNA and then converts it to left-handed Z-DNA, a conformation that is then stabilized by the additional binding of a second Z alpha(ADAR1) molecule.

Binding of NUFIP2 to Roquin promotes recognition and regulation of ICOS mRNA.

The ubiquitously expressed RNA-binding proteins Roquin-1 and Roquin-2 are essential for appropriate immune cell function and postnatal survival of mice. Roquin proteins repress target mRNAs by recognizing secondary structures in their 3'-UTRs and by inducing mRNA decay. However, it is unknown if other cellular proteins contribute to target control. To identify cofactors of Roquin, we used RNA interference to screen ~1500 genes involved in RNA-binding or mRNA degradation, and identified NUFIP2 as a cofactor of Roquin-induced mRNA decay. NUFIP2 binds directly and with high affinity to Roquin, which stabilizes NUFIP2 in cells. Post-transcriptional repression of human ICOS by endogenous Roquin proteins requires two neighboring non-canonical stem-loops in the ICOS 3'-UTR. This unconventional cis-element as well as another tandem loop known to confer Roquin-mediated regulation of the Ox40 3'-UTR, are bound cooperatively by Roquin and NUFIP2. NUFIP2 therefore emerges as a cofactor that contributes to mRNA target recognition by Roquin.

Repellency of aromatic medicinal plant extracts and a steam distillate to Aedes aegypti.

The repellent activity of methanol extracts from 23 aromatic medicinal plant species and a steam distillate against female blood-starved Aedes aegypti was examined in the laboratory by skin test and compared with that of N,N-diethyl-m-toluamide (deet). Responses varied according to plant species. At a dose of 0.1 mg/cm2, the repellency of extracts of Cinnamomum cassia bark (91%), Nardostachys chinensis rhizome (81%), Paeonia suffruticosa root bark (80%), and Cinnamomum camphora steam distillate (94%) was comparable to deet (82%). The duration of the effectiveness for extracts from C. cassia bark and N. chinensis rhizome was comparable to deet and lasted for approximately 1 h. Relatively short duration of repellency was observed in P. suffruticosa root bark extract and C. camphora steam distillate. The plants described merit further study as potential mosquito repellent agents.

NMR investigation on the DNA binding and B-Z transition pathway of the Zα domain of human ADAR1.

Human ADAR1, which has two left-handed Z-DNA binding domains, preferentially binds Z-DNA rather than B-DNA with a high binding affinity. Z-DNA can be induced in long genomic DNA by Z-DNA binding proteins through the formation of two B-Z junctions with the extrusion of one base pair from each junction. We performed NMR experiments on complexes of Zα(ADAR1) with three DNA duplexes at a variety of protein-to-DNA molar ratios. This study confirmed that the Zα(ADAR1) first binds to an 8-bp CG-rich DNA segment via a unique conformation during B-Z transition and the neighboring AT-rich region becomes destabilized. We also found that, when DNA duplexes have only 6-bp CG-rich segment, the interaction with Zα(ADAR1) did not affect the thermal stabilities of the 6-bp CG-rich segment as well as the neighboring two A·T base pairs. These results indicate that four Zα(ADAR1) proteins interact with the 8-bp DNA sequence containing a 6-bp CG-repeat segment as well as a dinucleotide step, even though the dinucleotid step contains A∙T base pairs. Thus this study suggests that the length of the CG-rich region is more important than the specific DNA sequence for determining which base-pair is extruded from the B-Z junction structure. This study also found that the Zα(ADAR1) in complex with a 11-bp DNA duplex exhibits a Z-DNA-bound conformation distinct from that of free Zα(ADAR1) and the initial contact conformations of Zα(ADAR1) complexed with 13-bp DNA duplexes.

A pyrene-imidazolium derivative that selectively recognizes G-quadruplex DNA.

G-quadruplexes, formed of four stranded guanine bases stabilized by monovalent cations, serve important role in cancer cell growth and control gene expression in telomere. Since there are various types of quadruplex structures, rapid and simple screening methods with high selectivity, sensitivity and nontoxicity are required for understanding about the biological roles of quadruplex DNA as well as in designing therapeutics. Herein, we report a pyrene-imidazolium derivative, JY-1, which can with high selectivity recognize G-quadruplex using fluorescence and NMR spectroscopy. This is the first example based on the imidazolium derivative, which can detect the G-quadruplex directly to utilize the excimer/monomer emission change in pyrene fluorophore. The selectivity of strong binding to a specific sequence can allow for quadruplex sensing and the detection method presented here is very simple, using fluorescence and NMR study. Also, the groove binding characteristic of JY-1 to the G-quadruplex has a relatively low nonspecific toxicity and the structure-specific differences in fluorescent character between DNA duplex and G-quadruplex may offer more discovery and application in biological study.

HIV-1 Integrase Inhibitor-Inspired Antibacterials Targeting Isoprenoid Biosynthesis.

We report the discovery of antibacterial leads, keto- and diketo-acids, targeting two prenyl transferases: undecaprenyl diphosphate synthase (UPPS) and dehydrosqualene synthase (CrtM). The leads were suggested by the observation that keto- and diketo-acids bind to the active site Mg(2+)/Asp domain in HIV-1 integrase, and similar domains are present in prenyl transferases. We report the x-ray crystallographic structures of one diketo-acid and one keto-acid bound to CrtM, which supports the Mg(2+) binding hypothesis, together with the x-ray structure of one diketo-acid bound to UPPS. In all cases, the inhibitors bind to a farnesyl diphosphate substrate-binding site. Compound 45 had cell growth inhibition MIC(90) values of ~250-500 ng/mL against S. aureus, 500 ng/mL against Bacillus anthracis, 4 µg/mL against Listeria monocytogenes and Enterococcus faecium, and 1 µg/mL against Streptococcus pyogenes M1, but very little activity against E. coli (DH5α, K12) or human cell lines.

The Zß domain of human DAI binds to Z-DNA via a novel B-Z transition pathway.

The human DNA-dependent activator of IFN-regulatory factor (DAI) protein, which activates the innate immune response in response to DNA, contains two tandem Z-DNA binding domains (Zα and Zß) at the NH(2) terminus. The hZß(DAI) structure is similar to other Z-DNA binding proteins, although it demonstrates an unusual Z-DNA recognition. We performed NMR experiments on complexes of hZß(DAI) with DNA duplex, d(CGCGCG)(2), at a variety of protein-to-DNA molar ratios. The results suggest that hZß(DAI) binds to Z-DNA via an active-di B-Z transition mechanism, where two hZß(DAI) proteins bind to B-DNA to form the hZß(DAI)-B-DNA complex; the B-DNA is subsequently converted to left-handed Z-DNA. This novel mechanism of DNA binding and B-Z conversion is distinct from Z-DNA binding of the human ADAR1 protein.

Antagonistic effects of ondansetron and tramadol? A randomized placebo and active drug controlled study.

UNLABELLED: Opposing effects of ondansetron and tramadol on the serotonin pathway have been suggested which possibly increase tramadol consumption and emesis when co-administered. In a randomized, double-blinded study, 179 patients received intravenous ondansetron, metoclopramide, or placebo for emesis prophylaxis. Analgesic regimen consisted of tramadol intraoperative loading and subsequent patient-controlled analgesia. Tramadol consumption and response to antiemetic treatment were compared. Additionally, plasma concentrations of ondansetron and (+)O-demethyltramadol and CYP2D6 genetic variants were analyzed as possible confounders influencing analgesic and antiemetic efficacy. Tramadol consumption did not differ between the groups. Response rate to antiemetic prophylaxis was superior in patients receiving ondansetron (85.0%) compared with placebo (66.7%, P = .046), with no difference to metoclopramide (69.5%). Less vomiting was reported in the immediate postoperative hours in the verum groups (ondansetron 5.0%, metoclopramide 5.1%) compared with placebo (18.6%; P = .01). Whereas plasma concentrations of (+)O-demethyltramadol were significantly correlated to CYP2D6 genotype, no influence was detected for ondansetron. Co-administration of ondansetron neither increased tramadol consumption nor frequency of PONV in this postoperative setting. PERSPECTIVE: Controversial findings were reported for efficacy of tramadol and ondansetron when co-administered due to their opposing serotonergic effects. Co-medication of these drugs neither increased postoperative analgesic consumption nor frequency of emesis in this study enrolling patients recovering from major surgery.

NMR study of hydrogen exchange during the B-Z transition of a DNA duplex induced by the Zα domains of yatapoxvirus E3L.

The Yaba-like disease viruses (YLDV) are members of the Yatapoxvirus family and have double-stranded DNA genomes. The E3L protein, which is essential for pathogenesis in the vaccinia virus, consists of two domains: an N-terminal Z-DNA binding domain and a C-terminal RNA binding domain. The crystal structure of the E3L orthologue of YLDV (yabZα(E3L)) bound to Z-DNA revealed that the overall structure of yabZα(E3L) and its interaction with Z-DNA are very similar to those of hZα(ADAR1). Here we have performed NMR hydrogen exchange experiments on the complexes between yabZα(E3L) and d(CGCGCG)(2) with a variety of protein-to-DNA molar ratios. This study revealed that yabZα(E3L) could efficiently change the B-form helix of the d(CGCGCG)(2) to left-handed Z-DNA via the active-mono B-Z transition pathway like hZα(ADAR1).

Sequence discrimination of the Zα domain of human ADAR1 during B-Z transition of DNA duplexes.

The Zα domain of human ADAR1 (Zα(ADAR1)) preferentially binds Z-DNA rather than B-DNA with high binding affinity. Zα(ADAR1) binds to the Z-conformation of both non-CG-repeat DNA duplexes and a d(CGCGCG)(2) duplex similarly. We performed NMR experiments on complexes between the Zα(ADAR1) and non-CG-repeat DNA duplexes, d(CACGTG)(2) or d(CGTACG)(2), with a variety of protein-DNA molar ratios. Comparison of these results with those from the analysis of d(CGCGCG)(2) in the previous study suggests that Zα(ADAR1) exhibits the sequence preference of d(CGCGCG)(2)≫d(CACGTG)(2)>d(CGTACG)(2) through multiple sequence discrimination steps during the B-Z transition.

Cell-penetrating autoantibody induces caspase-mediated apoptosis through catalytic hydrolysis of DNA.

In the present study, we investigated the substrate specificity of catalytic activity of a cytotoxic anti-DNA monoclonal autoantibody, G1-5, which was obtained from an MRL-lpr/lpr mouse by hybridoma technology. The antibody catalyzed hydrolysis of single- and double-stranded DNA with a higher substrate specificity for thymine than adenine by either beta-glycosidic or phosphodiester bond cleavage. The hydrolysis rate (kcat) showed maximum at acidic pH conditions, suggesting that the catalytic site of the antibody contains essential carboxylic group(s). Treatment of cells with the antibody promoted cell death and induced the activation of caspases. The cell death induced by the antibody was inhibited by the pan-caspase inhibitor. Furthermore, the antibody binds to cell membrane and penetrates into the cells. Our results suggest that the cell death is initiated by antibodies penetrating to cells and nucleus, hydrolyzing considerable amount of DNA, and mediating the caspase-dependent apoptotic pathway.