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Biomedical subjects

J Florián

Publications and source records attributed to J Florián.

8 recordsLinked to original sources
PubMed2003

Sequential doxorubicin and docetaxel as first-line treatment in metastatic breast cancer: a GEICAM-9801 phase II study.

PURPOSE: To evaluate the efficacy and the toxicity profile of the sequential administration of doxorubicin and docetaxel as first-line chemotherapy in metastatic breast cancer (MBC). PATIENTS AND METHODS: Eighty-one patients received a total of 436 cycles of chemotherapy: 236 of doxorubicin (75 mg/m2) and 200 of docetaxel (100 mg/m2 every 21 days). The first 35 patients received doxorubicin every 14 days with G-CSF support, and in the other 46 cases doxorubicin was administered every 21 days without G-CSF. RESULTS: After entire treatment the overall response rate was 65% (18 complete responses). With a median follow-up of 19 months (range, 1-48 months), the median time to progression was 11.3 months and the median survival time was 31 months. As expected, febrile neutropenia was the most important toxicity and it appeared in 26 cycles (6%) and 19 patients (23%). In the patients that received doxorubicin every 14 days, the febrile neutropenia incidence was higher during docetaxel treatment, especially after its first administration. CONCLUSIONS: The dose and schedule of doxorubicin and docetaxel used in this trial seems to be active in first-line treatment of patients with MBC. The toxicity profile appears to be better than observed with concomitant schedules.

Adult↗
PubMed2003

Gemcitabine/vinorelbine in metastatic breast cancer patients previously treated with anthracyclines: results of a phase II trial.

This phase II study was designed to evaluate the response rate (RR) and toxicity of gemcitabine/vinorelbine in patients with metastatic breast cancer. All patients had previously received anthracyclines. Treatment consisted of gemcitabine 1200 mg/m2 and vinorelbine 30 mg/m2 on days 1 and 8, every 3 weeks. Twenty-five patients were enrolled. Median age was 59 years (range, 33-73 years). Ten patients had received only adjuvant therapy with anthracyclines. The remaining 15 patients had received chemotherapy for metastatic disease, including taxanes in 11 cases. Four patients could not be evaluated for response. By intent-to-treat analysis, the overall RR was 44% (95% CI, 24.4%-65%). Median duration of response and median time to treatment failure were 21 and 17 weeks, respectively. The main toxicity was hematologic, with grade 3/4 neutropenia occurring in 13 patients and 1 patient developing febrile neutropenia. Two deaths from pneumonia occurred. These results reveal an encouraging activity with a reasonable toxicity profile in a patient population with an unfavorable prognosis. Our group is conducting a randomized study to compare this combination with vinorelbine alone in patients with metastatic breast cancer after failure to respond to anthracyclines and taxanes

Adult↗
PubMed2000

Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)(2) B<-->A intermediate crystal structure.

The crystal structure of d(CATGGGCCCATG)(2) shows unique stacking patterns of a stable B<-->A-DNA intermediate. We evaluated intrinsic base stacking energies in this crystal structure using an ab initio quantum mechanical method. We found that all crystal base pair steps have stacking energies close to their values in the standard and crystal B-DNA geometries. Thus, naturally occurring stacking geometries were essentially isoenergetic while individual base pair steps differed substantially in the balance of intra-strand and inter-strand stacking terms. Also, relative dispersion, electrostatic and polarization contributions to the stability of different base pair steps were very sensitive to base composition and sequence context. A large stacking flexibility is most apparent for the CpA step, while the GpG step is characterized by weak intra-strand stacking. Hydration effects were estimated using the Langevin dipoles solvation model. These calculations showed that an aqueous environment efficiently compensates for electrostatic stacking contributions. Finally, we have carried out explicit solvent molecular dynamics simulation of the d(CATGGGCCCATG)(2) duplex in water. Here the DNA conformation did not retain the initial crystal geometry, but moved from the B<-->A intermediate towards the B-DNA structure. The base stacking energy improved in the course of this simulation. Our findings indicate that intrinsic base stacking interactions are not sufficient to stabilize the local conformational variations in crystals.

Base Composition↗
PubMed2000

Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization.

The remarkable rate enhancement of orotidine 5'-phosphate decarboxylase (ODCase) has been attributed to ground-state destabilization (GSD) by desolvation and more recently to GSD by electrostatic stress. Here we reiterate our previous arguments that the GSD mechanisms are not likely to play a major role in enzyme catalysis and analyze quantitatively the origin of the rate enhancement of ODCase. This analysis involves energy considerations and computer simulations. Our energy considerations show that (i) the previously proposed desolvation mechanism is based on an improper reference state; (ii) a nonpolar active site cannot account for the catalytic effect of the enzyme; (iii) the focus on the role of the negatively charged protein residues in the electrostatic stress GSD mechanism overlooks the fact that the positively charged Lys72 strongly stabilizes the substrate; (iv) although the previous calculation of the actual enzymatic reaction correctly reproduced the observed rate enhancement, it could not obtain this rate enhancement from the calculated binding energies (which are the relevant quantities for determining GSD effects); (v) the GSD mechanism is inconsistent with the observed binding energy of the phosphoribosyl part of the substrate; and (vi) the presumably unstable substrate (orotate) can be stabilized, at equilibrium, by accepting a proton from the solvent. Our computer simulation studies involve two set of calculations. First, we study the catalytic reaction by using an empirical valence bond potential surface calibrated by ab initio calculations of the reference solution reaction. This calculation reproduces the observed catalytic effect of the enzyme. Next, we use free-energy perturbation calculations and evaluated the electrostatic contributions to the binding energies of the ground state and transition state (TS). These calculations show that the rate enhancement in ODCase is due to the TS stabilization rather than to GSD. The differences between our own and the previous theoretical analyses stem from both the selection of the reacting system and the treatment of the long-range electrostatic contributions to the binding energy. The reacting system was previously assumed to encompass only the orotate. However, this selection does not allow proper description of the reaction catalyzed by the enzyme (i.e., [Orotate(-) + LysH(+)] if [uracil + Lys + CO(2)]). Therefore, the reacting system should include both orotate and the general acid in the form of the protonated Lys72 protein residue. This selection leads to a simple and consistent interpretation of the catalytic effect where the electrostatic stabilization of the transition state is due to the fact that the two negatively charged aspartic residues are already placed near the reactive lysine so that they do not have to reorganize significantly during the reaction. Interestingly, even calculations with only orotate(-) as the reacting system do not produce sufficient destabilization to account for a GSD mechanism. In summary, we conclude, in agreement with previous workers, that ODCase catalyzes its reaction by electrostatic effects. However, we show that these effects are associated with TS stabilization due to a reduction in the protein-protein reorganization energy and not with protein-substrate destabilization effects.

Catalysis↗
PubMed1998

Computer simulations of enzyme catalysis: finding out what has been optimized by evolution.

The origin of the catalytic power of enzymes is discussed, paying attention to evolutionary constraints. It is pointed out that enzyme catalysis reflects energy contributions that cannot be determined uniquely by current experimental approaches without augmenting the analysis by computer simulation studies. The use of energy considerations and computer simulations allows one to exclude many of the popular proposals for the way enzymes work. It appears that the standard approaches used by organic chemists to catalyze reactions in solutions are not used by enzymes. This point is illustrated by considering the desolvation hypothesis and showing that it cannot account for a large increase in kcat relative to the corresponding kcage for the reference reaction in a solvent cage. The problems associated with other frequently invoked mechanisms also are outlined. Furthermore, it is pointed out that mutation studies are inconsistent with ground state destabilization mechanisms. After considering factors that were not optimized by evolution, we review computer simulation studies that reproduced the overall catalytic effect of different enzymes. These studies pointed toward electrostatic effects as the most important catalytic contributions. The nature of this electrostatic stabilization mechanism is far from being obvious because the electrostatic interaction between the reacting system and the surrounding area is similar in enzymes and in solution. However, the difference is that enzymes have a preorganized dipolar environment that does not have to pay the reorganization energy for stabilizing the relevant transition states. Apparently, the catalytic power of enzymes is stored in their folding energy in the form of the preorganized polar environment.

Animals↗
PubMed1996

Nonplanar DNA base pairs.

Three-dimensional structures of a representative set of more than 30 hydrogen-bonded nucleic acids pairs have been studied by reliable ab initio quantum mechanical methods. We show that many hydrogen-bonded nucleic acid base pairs are intrinsically nonplanar, mainly due to the partial sp3 hybridization of nitrogen atoms of their amino groups and secondary electrostatic interactions. This finding extends the variability of intermolecular interactions of DNA bases in that i) flexibility of the base pairs is larger than has been assumed before, and ii) attractive proton-proton acceptor interactions oriented out of the base pair plane are allowed. For example, all four G-A mismatch base pairs are propeller twisted, and the energy preferences for the nonplanar structures range from less than 0.1 kcal/mol to 1.8 kcal/mol. We predict that nonplanarity of the amino group of guanine in the G(anti)...A(anti) pair of the ApG step of the d(CCAAGATTGG)2 crystal structure is an important stabilizing factor that improves the energy of this structure by almost 3 kcal/mol. Currently used empirical potentials are not accurate enough to properly cover the interactions associated with amino-group and base-pair nonplanarity.

Base Composition↗
PubMed1995

Theoretical investigation of the molecular structure of the pi kappa DNA base pair.

The structure of the nonclassical pi kappa base pair (7-methyl-oxoformycin B. . .2,4-diaminopyrimidine) was studied at the ab initio Hartree-Fock (HF) and MP2 levels using the 6-31G* and 6-31G** basis sets. The pi kappa base pair is bound by three parallel hydrogen bonds with the donor-acceptor-donor recognition pattern. Recently, these bases were proposed as an extension of the genetic alphabet from four to six letters (Piccirilli et al, Nature 343,33 (1990)). By the HF/6-31G* method with full geometry optimization we calculated the 12 degree propeller twist for the minimum energy structure of this complex. The linearity of hydrogen bonds is preserved in the twisted structure by virtue of the pyramidal arrangement of the kappa-base amino groups. The rings of both the pi and kappa molecules remain nearly planar. This nonplanar structure of the pi kappa base pair is only 0.1 kcal/mol more stable than the planar (Cs) conformation. The HF/6-31G* level gas-phase interaction energy of pi kappa (-13.5 kcal/mol) calculated by us turned out to be nearly the same as the interaction energy obtained previously for the adenine-thymine base pair (-13.4 kcal/mol) at the same computational level. The inclusion of p-polarization functions on hydrogens, electron correlation effects (MP2/6-31G** level), and the correction for the basis set superposition error (BSSE) increase this energy to -14.0 kcal/mol.

Base Composition↗