A derivative of the natural compound kakuol affects DNA relaxation of topoisomerase IB inhibiting the cleavage reaction

Topoisomerases IB are anticancer and antimicrobial targets whose inhibition by several natural and synthetic compounds has been documented over the last three decades. Here we show that kakuol, a natural compound isolated from the rhizomes of Asarum sieboldii, and a derivative analogue are able to inhibit the DNA relaxation mediated by the human enzyme. The analogue is the most efficient one and the inhibitory effect is enhanced upon pre-incubation with the enzyme. Analysis of the different steps of the catalytic cycle indicates that the inhibition occurs at the cleavage level and does not prevent DNA binding. Molecular docking shows that the compound preferentially binds near the active site at the bottom of the catalytic residue Tyr723, providing an atomistic explanation for its inhibitory activity.

Zinc ion coordination as a modulating factor of the ZnuA histidine-rich loop flexibility: a molecular modeling and fluorescence spectroscopy study

ZnuA is the soluble component of the high-affinity ZnuABC zinc transporter belonging to the ATP-binding cassette-type periplasmic Zn-binding proteins. The zinc transporter ZnuABC is composed by three proteins: ZnuB, the membrane permease, ZnuC, the ATPase component and ZnuA, the soluble periplasmic metal-binding protein which captures Zn and delivers it to ZnuB. The ZnuA protein contains a charged flexible loop, rich in histidines and acidic residues, showing significant species-specific differences. Various studies have established that this loop contributes to the formation of a secondary zinc binding site, which has been proposed to be important in the acquisition of periplasmic Zn for its delivery to ZnuB or for regulation of zinc uptake. Due to its high mobility the structure of the histidine-rich loop has never been solved by X-ray diffraction studies. In this paper, through a combined use of molecular modeling, mutagenesis and fluorescence spectroscopy, we confirm the presence of two zinc binding sites characterized by different affinities for the metal ion and show that the flexibility of the loop is modulated by the binding of the zinc ions to the protein. The data obtained by fluorescence spectroscopy have then be used to validate a 3D model including the unsolved histidine-rich loop.

Evidences of a natively unfolded state for the human topoisomerase IB N-terminal domain

The N-terminal domain of human topoisomerase IB has been expressed, purified and characterized by spectroscopic techniques. CD spectra as a function of concentration and pH indicate that the domain does not possess any defined secondary structure. The protein is probably in a natively unfolded state since its denaturation curve is indicative of a non-cooperative transition. Evidence of a partially folded structure comes from the fluorescence spectrum of ANS, whose intensity increases in presence of the domain. Indication of a partial structural arrangement of the domain comes also from the endogenous fluorescence of tryptophans that is centred at 350 nm in the native and shifts to 354 nm in the fully denaturated protein. Interestingly despite the poor structural degree, as also confirmed by a predictive approach, the domain efficiently binds DNA, suggesting that the absence of a defined 3D structure has a functional meaning that permits the domain to be available for the interaction with different molecular partners.

UV-vis spectra of the anticancer camptothecin family drugs in aqueous solution: specific spectroscopic signatures unraveled by a combined computational and experimental study

The ultraviolet-visible absorption spectrum of camptothecin (CPT) has been been recorded in aqueous solution at pH 5.3, where the equilibrium among the different CPT forms is shifted toward the lactonic one. Time-dependent density functional theory (TD-DFT) computations lead to a remarkable reproduction of the experimental spectrum only upon addition of explicit water molecules in interaction with specific moieties of the camptothecin molecule. Molecular dynamics (MD) simulations enforcing boundary periodic conditions for CPT embedded with 865 water molecules, with a force field derived from DFT computations, show that the experimental spectrum is due to the contributions of CPT molecules with different solvation patterns. A similar solvent effect is observed for several CPT derivatives, including the clinically relevant SN-38 and topotecan drugs. The quantitative agreement between TD-DFT/MD computations and experimental data allow us to identify specific spectroscopic signatures diagnostic of the drug environment and to develop procedures that can be used to monitor the drug-DNA/protein interaction.

Conjugated eicosapentaenoic acid inhibits human topoisomerase IB with a mechanism different from camptothecin

Conjugated eicosapentaenoic acid (cEPA) has been found to have antitumor effects which has been ascribed to their ability to inhibit DNA topoisomerases and DNA polymerases. We here show that cEPA inhibits the catalytic activity of human topoisomerase I, but unlike camptothecin it does not stabilize the cleavable complex, indicating a different mechanism of action. cEPA inhibits topoisomerase by impeding the catalytic cleavage of the DNA substrate as demonstrated using specific oligonucleotide substrates, and prevents the stabilization of the cleavable complex by camptothecin. Preincubation of the inhibitor with the enzyme is required to obtain complete inhibition. Molecular docking simulations indicate that the preferred cEPA binding site is proximal to the active site with the carboxylic group strongly interacting with the positively charged K443 and K587. Taken together the results indicate that cEPA inhibitor does not prevent DNA binding but inhibits DNA cleavage, binding in a region close to the topoisomerase active site.

Role of flexibility and long range communication on the function of human topoisomerase I

Eukaryotic topoisomerase I is an essential enzyme that regulates the changes in DNA topology, relaxing the superhelical tension associated with DNA replication, transcription and recombination. Human topoisomerase I is of significant medical interest being the only target of the antitumor drug camptothecin. The enzyme undergoes large conformational changes during its catalytic cycle and the knowedge of the degree of flexibility of the different regions provides an useful guide to the understanding of such movements. Molecular dynamics simulation is a well consolidated method for the investigation of structural and dynamic properties of proteins and nucleic acids and has been successfully applied to study the dynamical properties of the DNA-human topoisomerase complex. This review highlights some structural and dynamic properties of topoisomerase, obtained by MD simulations, that permits to explain the importance of flexibility in the modulation of the functional properties of the enzyme and in the transmission of communication between domains located far away one from each other.

The different cleavage DNA sequence specificity explains the camptothecin resistance of the human topoisomerase I Glu418Lys mutant

Yeast cells expressing the Glu418Lys human topoisomerase I mutant display a camptothecin resistance that slowly decreases as a function of time. Molecular characterization of the single steps of the catalytic cycle of the purified mutant indicates that it has a relaxation activity identical to the wild-type protein but a different DNA sequence specificity for the cleavage sites when compared to the wild-type enzyme, as assayed on several substrates. In particular the mutant has a low specificity for CPT sensitive cleavable sites. In fact, the mutant has, at variance of the wild-type enzyme, a reduced preference for cleavage sites having a thymine base in position −1 of the scissile strand. This preference, together with the strict requirement for a thymine base in position −1 for an efficient camptothecin binding, explains the temporary camptothecin resistance of the yeast cell expressing the mutant and points out the importance of the DNA sequence in the binding of the camptothecin drug.

Chemical characterization of different typologies of mucilaginous aggregates in the Northern Adriatic Sea

The chemical composition of mucilage aggregates found during summer 2000, 2001 and 2002 in the North Adriatic Sea depends on the nature of the organic matter during aggregation, on the environmental conditions of the site of formation and on the transformations during ageing. The mucilages were composed of organic matter, together with a significant inorganic fraction. Elemental analysis revealed 12.5-32.2% of organic carbon, 0-7.3% of inorganic carbon and 1.0-3.7% of nitrogen. The C(org)/N ratios of most aggregates were between 7.5 and 12.6, values close to those found in the suspended matter; higher ratios were found in large-size (>5 m) aggregates which are probably older. The content of carbohydrates and proteins determined in the aggregates, respectively, 15.4+/-8.9% and 7.9+/-4.8%, w/w, showed a prevalence of carbohydrates over proteins. Neutral carbohydrate analysis of purified polysaccharides from mucilage samples showed very similar signatures with high relative abundance of galactose and glucose. Humic, fulvic and humin substances extracted from the mucilages constitute an important fraction of the organic matter in the aggregates. The humin (a fraction insoluble in acidic and basic media) was present in all mucilage samples, indicating the refractory nature of a part of the organic matter in the mucilage. The iron and calcium could play a role during the aggregation process to form a complex with polysaccharides and humic fractions. The C(org)/N ratio 10+/-2 found in the humic acids extracted from the Adriatic aggregates disclosed a marine origin. The low phosphorus content and the high C(org)/P ratio found in the aggregates might depend from high bacteria activity or from the aggregation of organic fractions depleted of phosphorus. The principal inorganic species contained aluminium and silicon, part of which was of biogenic origin and was more significant in the offshore mucilage aggregates than in the coastal ones. The Si(biog)/C(org) ratio showed that diatoms were always present in the aggregates, although it cannot be established whether these are the producers or these develop within the aggregates.

New Hints on the pH-Driven Tautomeric Equilibria of the Topotecan Anticancer Drug in Aqueous Solutions from an Integrated Spectroscopic and Quantum-Mechanical Approach

The equilibria between the different forms of the topotecan anticancer drug have been studied at moderately acidic and physiological pH by an integrated computational tool rooted in the density functional theory and its time-dependent extension together with the polarizable continuum model. The results allow an unbiased selection between the different possible tautomeric forms and provide invaluable complements to experimental data. The ultraviolet-visible topotecan spectrum, recorded at moderately acidic pH, is accurately reproduced only by TD-DFT computations including solvent effects. Comparison of the experimental and calculated bands of the UV-vis spectrum at physiological pH indicates the presence of an equilibrium among different forms that is tuned by the microenvironment embedding the drug. The quantitative agreement between TD-DFT/PCM computations and experiments allows the identification of unequivocal spectroscopic signatures for different forms of topotecan.

Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study

The functional and dynamical properties of the human topoisomerase I Thr718Ala mutant have been compared to that of the wild-type enzyme using functional assays and molecular dynamics (MD) simulations. At physiological ionic strength, the cleavage and religation rates, evaluated on oligonucleotides containing the preferred topoisomerase I DNA sequence, are almost identical for the wild-type and the mutated enzymes, as is the cleavage/religation equilibrium. On the other hand, the Thr718Ala mutant shows a decreased efficiency in a DNA plasmid relaxation assay. The MD simulation, carried out on the enzyme complexed with its preferred DNA substrate, indicates that the mutant has a different dynamic behavior compared to the wild-type enzyme. Interestingly, no changes are observed in the proximity of the mutation site, whilst a different flexibility is detected in regions contacting the DNA scissile strand, such as the linker and the V-shaped α helices. Taken together, the functional and simulation results indicate a direct communication between the mutation site and regions located relatively far away, such as the linker domain, that with their altered flexibility confer a reduced DNA relaxation efficiency. These results provide evidence that the comprehension of the topoisomerase I dynamical properties are an important element in the understanding of its complex catalytic cycle.

Experimental and simulative dissociation of dimeric Cu,Zn superoxide dismutase doubly mutated at the intersubunit surface

The equilibrium properties of dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase mutant bearing two negative charges in the amino acid clusters at the association interface has been studied, experimentally and computationally, and compared to those of the native enzyme. Pressure-dependent dissociation is observed for the mutant, as observed by the fluorescence shift of the unique tryptophan residue located at the intersubunit surface. The spectral shift occurs slowly, reaching a plateau after 15-20 min, and is fully reversible. Measurement of the degree of dissociation allows us to calculate the standard volume variation upon association and the dissociation constant at atmospheric pressure. On the other hand the native protein is undissociable at any pressure. In the simulative approach, the dissociation free energy has been calculated through the blue moon calculation method for the case of a multidimensional reaction coordinate, corrected for the rotational contribution within the semiclassical approximation for a free rigid-body rotor. The scheme permits to define a definite path for the rupture of the dimer and to calculate the effective force involved in the process. The calculated free energy difference is close to the experimental one, and the value obtained for the mutant is well below that obtained for the native protein, indicating that the theoretical reaction scheme is able to reproduce the experimental trend. Moreover, we find that, when the separation distance increases, the protein structure of the monomer is stable in line with the fast recovery of the original fluorescence properties after decompression, which excludes the presence of partly unfolded intermediates during the dimer-monomer transition.

Active-site copper and zinc ions modulate the quaternary structure of prokaryotic Cu,Zn superoxide dismutase

The influence of the constitutive metal ions on the equilibrium properties of dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase has been studied for the wild-type and for two mutant protein forms bearing a negative charge in the amino acid clusters at the dimer association interface. Depletion of copper and zinc dissociates the two mutant proteins into monomers, which reassemble toward the dimeric state upon addition of stoichiometric amounts of zinc. Pressure-dependent dissociation is observed for the copper-depleted wild-type and mutated enzymes, as monitored by the fluorescence shift of a unique tryptophan residue located at the subunit association interface. The spectral shift occurs slowly, reaching a plateau after 15-20 minutes, and is fully reversible. The recovery of the original fluorescence properties, after decompression, is fast (less than four minutes), suggesting that the isolated subunit has a relatively stable structure, and excluding the presence of stable intermediates during the dimer-monomer transition. The dimer dissociation process is still incomplete at 6.5 kbar for the copper-depleted wild-type and mutated enzymes, at variance with what is generally observed for oligomeric proteins that dissociate below 3 kbar. Measurement of the degree of dissociation, at two different protein concentrations, allows us to calculate the standard volume variation upon association, Delta V, and the dissociation constant K(d0), at atmospheric pressure, (25 ml/mol and 3 x 10(-7)M, respectively). The holoprotein is fully dimeric even at 6.5 kbar, which allows us to evaluate a lower Delta G degrees limit of 11.5 kcal/mol, corresponding to a dissociation constant K(d0)<10(-9)M.

Specific combinations of zein genes and genetic backgrounds influence the transcription of the heavy-chain zein genes in maize opaque-2 endosperms

The transcript levels of heavy-chain zein genes (zH1 and zH2) and the occurrence of the zH polypeptides in different opaque-2 (o2) lines were investigated by RNA-blot analyses and by sodium dodecylsulfate-polyacrylamide gel electrophoresis or two-dimensional gel electrophoresis protein fractionations. Four mutant alleles o2R, o2T, o2It, and o2-676 introgressed into different genetic backgrounds (GBs) were considered. The mono-dimensional gel electrophoresis zein pattern can be either conserved or different among the various GBs carrying the same o2 allele. Likewise, in the identical GB carrying different o2 alleles, the zein pattern can be either conserved or differentially affected by the different mutant allele. Zein protein analysis of reciprocal crosses between lines with different o2 alleles or the same o2 showed in some case a more than additive zH pattern in respect to the o2 parent lines. Electrophoretic mobility shift assay approaches, with O2-binding oligonucleotide and endosperm extracts from the above o2 lines, failed to reveal o2-specific retarded band in any of the o2 extracts. The results suggest that the promoter of some zH1 and zH2 contains motif(s) that can respond to factors other than O2.

[The effectiveness and acceptance of a medical device for the treatment of aphthous stomatitis. Clinical observation in pediatric age]

BACKGROUND

To evaluate the efficacy of a new bioadhesive patch, Aloe vera hydrogel, for the treatment of aphthous stomatitis.

METHODS

An open, not controlled study was performed in 31 pediatric out-patients, aged 6-14 years, affected by mouth ulcers were enrolled consecutively in the 3 Gps Depts+ of San Marino Republic. For each case, data on case history and clinical profile, patterns of the lesion, presence of spontaneous or provoked pain were collected at baseline, and a bioadhesive patch ("Alovex patch") was administered on the basis of a daily regimen of < or = 3 patches for 4 days. Data on modification of the above-mentioned parameters, with patients and physicians opinion on the therapeutical efficacy, were collected during a control visit (4 days later). Moreover, by means of a daily diary, patients recorded information on the course of the symptoms during the 4 days and were also asked to compare the current treatment with other previous therapies.

RESULTS

At the control visit 77% of the patients have shown a marked resolution of spontaneous pain, while in the other patients, pain was significantly decreased to a "mild" or "moderate" level. No one child declared to suffer from severe pain. Also provoked pain resulted to be significantly decreased after treatment Global efficacy was judged positively, being the therapeutical effect in more than 80% of cases "evident or of absolute improvement" both by physicians and patients opinion. A positive improvement of symptomatology started within the 2nd day of treatment in 74% of the patients. The compliance (adhesivity, acceptability and palatability) of the formulation was judged largely favourable in more than 90% of the patients.

CONCLUSIONS

The results of this study underline the good efficacy and compliance of the patch for the treatment of the aphtous stomatitis; also the limit of topical available therapies, linked to the "contact time", to develop their therapeutical action, seems not to be evinced on the basis of this study, so the application of this patch seems to be more easy and beneficial.

[Syncopal pathology in childhood (I)]

Syncope is a common phenomenon, well-known to all pediatricians: it is defined as a sudden transient loss of consciousness associated with inability to maintain postural tone that is incompatible with a seizure disorder, vertigo, dizziness, coma, shock or other states of altered consciousness. The purpose of this study are to analyse the multiple causes of syncope, to determine the characteristics of pediatric patients with syncope, to define the pathophysiologic mechanisms that result in neurally mediated syncope.

[Postpartum myoglobin blood monitoring in newborns. Correlations with renal function in the first 48 hours of life]

BACKGROUND

Myoglobin is a muscular tissue protein, and it is a very early damage index. As the newborn "thin mass" is less than that of the adult and knowing the renal dynamics of this protein clearance, the authors have analyzed the correlation between myoglobinemia and transitory renal failure, which is frequently present in newborns with fetal distress.

METHODS

We examined a random population of 56 newborns (33 eutocic deliveries 14 caeserotomy, 9 various degrees of fetal distress) to which, after having had the parents' informed consent, the microsamples pattern was fixed at 0, 6, 12, 24, 48 hours from birth at the same time of ordinary exams to gauge: myoglobin with nephelometric method, CPK, creatininemia, azotemia and transaminase. The same exams were camed out on the mother at the beginning of labor and after delivery.

RESULTS

We found that the placenta is not permeable to mother myoglobin, at the sixth hour from birth we have the highest value, while CPK is lower to increase, myoglobinemia associated with myoglobin variations.

CONCLUSIONS

Myoglobinemia might be monitored to prevent distressed newborns from transitory renal tubular defect, justifying forced diuresis and urinary alkalosis.

Effect of patient characteristics on hospital costs for cirrhosis: implications for the disease-related group (DRG) reimbursement system

The Prospective Payment System uses Diagnosis-Related Groups (DRG) as a reimbursement system. DRG 202 is a disease-related group including liver cirrhosis as a whole. Patients referring to the inpatient unit complain of variable severity and complications of cirrhosis, possibly implying different expenditure of resources. Aim of the investigation was to identify factors affecting cost variability in patients with cirrhosis. A total of 73 consecutive, DRG 202-assigned, cirrhotic patients classified according to demographic and clinical variables were evaluated for length and costs of hospitalization calculated on a full-cost basis. Mean length of hospitalization was 10.2 +/- 7 days. Mean cost of hospitalization was Lit. 4.348.000 +/- 2.718.000. Medical, nursing, diagnostic, drug and general charges accounted for 13%, 29%, 37%, 5% and 16% of the cost, respectively. Child-Pugh score significantly correlated with drug consumption (p < 0.005), length (p < 0.01) and costs (p < 0.001) of hospitalization, but not with cost per day. Age, sex, admission status, referral reason, associated diseases and liver transplant susceptibility did not correlate with duration and costs of hospitalization. Disease severity significantly modifies costs of hospital admission in cirrhotic patients mostly on account of longer hospital stay. Surrogate indexes of disease severity, derived from ISTAT/DRG records, cannot identify patients consuming larger resources. In liver cirrhosis, the DRG system could be improved by introducing parameters, such as Child-Pugh score, directly taking into account disease severity.

Relationship between hydration of lean body mass and visceral adipose tissue. A clinical study of women

OBJECT

To study the relationship between hydration of lean body mass and adipose tissue location.

DESIGN

Cross-sectional, clinical study of visceral adipose tissue area and total body water as a percentage of lean body mass.

PATIENTS

Seventy-two adult, overweight, women, 52 pre- and 20 post-menopausal (age: 18-72 years, body mass index: 26-52).

MEASUREMENTS

Total body water was obtained by electrical impedance measurement; visceral adipose tissue and lean body mass were obtained by computed tomography measurement of visceral adipose tissue area at the level of the 4th-5th lumbar vertebra.

RESULTS

Visceral adipose tissue was found, by multiple regression analysis, to be the only predictor of the hydration of the lean body mass. The other independent variables: age, menopausal status, body mass index, glucose and insulin both fasting and after glucose load were not able to significantly improve the predictive power.

CONCLUSION

Results of this study confirm the existence of a relationship between visceral adipose tissue content and hydration of the lean body mass.

[Assessment of lead blood levels in children living in Lucca (Italy) in 1993. The study was conducted as part of the project METOS, in accordance with the decree 496 of June 1982 which adopted the directive CEE No.77/312]

OBJECTIVE

Lead poisoning is a major cause of environmental concern in all countries worldwide. Saturnism in children, especially if young and neglected, represents a peculiar phenomenon both in terms of the biology of growing subjects and the epidemiological nature of poisoning. In under five-year-olds, in addition to lead levels in the atmosphere, it is equally important to evaluate the presence of contaminated dust in the house, hand-to-mouth activities and the level of care provided by parents. It has been demonstrated that, in the presence of equivalent environmental lead levels, dust removal from the house and prevention of hand-to-mouth activities can successfully reduce lead blood levels (PbB) in children.

AIM

The aim of this study was to evaluate the risk of chronic lead poisoning in children attending Local Health Unit 6 in Piana di Lucca and to assess the need for a possible health education campaign aimed at eliminating the specific pediatric risk for lead poisoning.

MATERIALS AND METHODS

Assay of lead blood levels in 172 children from 0 to 14 years old consecutively attending the Emergency Ward at Campo di Marte Hospital in Lucca for reasons not relating to lead poisoning.

RESULTS

Mean lead blood levels in children were 57.2 +/- 30.2 mg/l (mean 50 mg/l) without significant differences between the various age brackets (0-5, 6-10, 11-14 years old). Only one child presented pathological PbB levels (280 mg/l when first measured; 360 mg/l a few months later with normal values of erythrocytic Zn-protoporphyrin, 24-h urinary lead excretion and 24-h urinary delta-aminolevulinic acid). An epidemiological study is now being made of the causes. The general population within the same area presented mean PbB levels of 70.4 +/- 36.9 mg/l (mean 60 mg/l), measured in a total of 471 subjects (adults and children).

DISCUSSION AND CONCLUSIONS

The PbB levels currently found in children resident in Lucca confirm a low-risk environmental situation. Preventive measures specifically aimed at children do not therefore appear to be justified at present.

Measured and predicted total and visceral adipose tissue in women. Correlations with metabolic parameters

The aim of this study was the verification of the clinical utility of predictive equations for total and intra-abdominal adipose tissue areas. Formulas were calculated using computed tomography (CT) as the gold standard. Ninety-three females were randomly divided into two groups. The predictive equation group was used to calculate the predictive equations for computed tomography adipose tissue areas at the L4-L5 level. These equations were then used to predict total and intra-abdominal adipose tissue area in the validation group. Correlations were made between metabolic parameters and both measured and calculated areas and single predictors. The following measurements were carried out: age, weight/height ratio, body mass index, waist, hip, waist/hip ratio, ultrasound measurement of intra-abdominal distance between abdominal muscle and aorta, sagittal abdominal diameter by CT, adipose tissue intra-abdominal area by CT, total abdominal adipose tissue area by CT. Blood glucose and insulin both fasting and after glucose load. Fasting cholesterol and triglycerides. The best predictors of total and visceral adipose tissue areas were, respectively: weight/height ratio and ultrasound intra-abdominal measurement. Correlations between metabolic parameters and adipose tissue areas both as measured and as calculated by predictive equations were quite similar. Correlations between metabolic parameters and single best predictors of measured adipose tissue areas also gave the same results. Some simple and safe anthropometric measurements can be used, instead of total and visceral adipose tissue area as assessed by CT, when studying associations between adipose tissue and metabolic parameters on sufficiently large groups of patients.