Enhancement of energy decomposition analysis in fragment molecular orbital calculations.

Energy decomposition analysis is one of the most attractive features of fragment molecular orbital (FMO) calculations from the point of view of practical applications. Here we report some enhancements for PIEDA in the ABINIT-MP program. One is a separation of the dispersion-type stabilization from the electron correlation energy, traditionally referred to as the "dispersion interaction" (DI). Another is an alternative evaluation of the electrostatic (ES) interaction using the restrained electrostatic potential (RESP) charges. The GA:CT stacked base pair and the Trp-Cage miniprotein were used as illustrative examples.

Pharmacokinetics and pharmacodynamics of amiodarone in patients with hypertriglyceridemia: Two case reports.

BACKGROUND: The antiarrhythmic drug amiodarone has noncardiac adverse effects, leading to restrictive therapeutic plasma ranges. Despite the significant positive correlation between triglyceride and amiodarone levels, the effect of fluctuations in amiodarone levels in patients with hypertriglyceridemia on amiodarone therapy has not been fully characterized. This study is the first to report on the effect of hypertriglyceridemia on the efficacy and safety of amiodarone therapy. CASE PRESENTATION: The first patient was a 58-year-old man with hypertriglyceridemia who was diagnosed with ventricular fibrillation (patient #1). The second patient with hypertriglyceridemia was a 72-year-old man with sustained ventricular tachycardia (patient #2). Both patients received implantable cardioverter-defibrillator therapy. During the study period, amiodarone and N-desethylamiodarone concentrations were measured 12 times in patient #1 and 26 times in patient #2. Triglyceride concentrations in patient #1 and patient #2 ranged from 102 to 765 mg/dL and from 125 to 752 mg/dL, respectively. For both patients, amiodarone dosage was maintained at 100 mg/day, and the administration of concomitant drugs that could affect amiodarone pharmacokinetics was neither initiated nor discontinued. However, amiodarone concentrations fluctuated (patient #1, 0.52 - 1.86 µg/mL; patient #2, 0.73 - 2.82 µg/mL). Although amiodarone concentrations fluctuated, neither of the patients had defibrillation shocks to stop the abnormal rhythm via an implantable cardioverter-defibrillator, and laboratory data showed that thyroid-stimulating hormone, free thyroxine, KL-6, and surfactant protein-D remained close to normal. CONCLUSION: In patients with hypertriglyceridemia, it may be necessary for clinicians to pay more attention to the clinical symptoms along with fluctuations in amiodarone levels and accordingly adjust amiodarone dosage.

Relationship between serum bepridil concentration and corrected QT interval.

OBJECTIVE: Bepridil prolongs the QT interval and can induce torsade de pointes. Although increased bepridil concentration may be a primary cause of prolonged QT, the relationship between serum bepridil concentration and prolonged QT remains unclear. We investigated the relationship between serum bepridil concentration and the corrected QT (QTc) interval in patients treated with bepridil. MATERIALS AND METHODS: A retrospective study was performed at the National Cerebral and Cardiovascular Center in Japan. Patients with atrial fibrillation who were treated with bepridil from January 2014 to December 2015 were enrolled in the study. Serum bepridil concentrations and electrocardiogram data collected more than 21 days after the initiation of bepridil were used for analysis. RESULTS: A total of 60 patients were included in this study. There was a significant difference in mean QTc interval before and after initiation of bepridil (p < 0.0001). A significant relationship was observed between bepridil dose (p = 0.014) or serum bepridil concentration (p < 0.001) and QTc interval. Additionally, a significant relationship was observed between serum bepridil concentration and ΔQTc (p = 0.034). In the study, 4 patients developed QTc prolongation ≥ 500 ms after the initiation of bepridil. Serum bepridil concentration in this group was significantly higher compared with the group that did not display prolonged QTc (973 ± 651 vs. 526 ± 310 ng/mL, p = 0.01). CONCLUSION: This study revealed that the QTc interval was significantly associated with serum bepridil concentration. Serum bepridil concentration beyond a therapeutic range may be a critical risk factor for developing QTc prolongation.

Association between vancomycin pharmacokinetic/pharmacodynamic parameters, patient characteristics, and mortality in patients with bacteremia caused by vancomycin-susceptible Enterococcus faecium: a single-center retrospective study.

BACKGROUND: Vancomycin is commonly used to treat Enterococcus faecium (E. faecium) bacteremia. However, there are very few studies on the association between the trough concentration, area under the curve from 0 to 24 h /minimum inhibitory concentration (AUC24/MIC) ratio, and the therapeutic effect of vancomycin on E. faecium bacteremia. This study aimed to investigate the associations between vancomycin pharmacokinetic/pharmacodynamic parameters, patient characteristics, and mortality in patients with E. faecium bacteremia. METHODS: This retrospective study included patients with E. faecium bacteremia who received vancomycin between April 2012 and February 2018 at a single acute care hospital in Japan. Patients who received renal replacement therapy (hemodialysis or continuous hemodiafiltration), had an unmeasured serum vancomycin concentration, with unmeasured laboratory values, or received other antibiotics for treating E. faecium bacteremia were excluded from the study. The bivariate associations between 30-day all-cause mortality and patient characteristics were assessed. RESULTS: Among 87 patients diagnosed with E. faecium bacteremia, 45 were included in the final analysis. Of these, 12 (26.7%) died within 30 days of the diagnosis. The vancomycin trough concentration was higher in the 30-day all-cause mortality patients than in the survival patients (20.5 vs. 14.6 µg/mL; P = 0.022). There was no significant difference in the proportion of patients with a vancomycin AUC24/MIC ≤389 between the groups. The 30-day all-cause mortality patients showed a higher Charlson Comorbidity Index (CCI) and Sequential Organ Failure Assessment score at the first measurement of the vancomycin trough concentration than the survival patients. The same finding was observed among patients with a high CCI score (≥5 points). CONCLUSIONS: Whereas the vancomycin trough concentration and AUC24/MIC ratio were not associated with mortality in patients with E. faecium bacteremia, disease severity was associated with mortality in these patients.

RI-MP3 calculations of biomolecules based on the fragment molecular orbital method.

In this study, the third-order Møller-Plesset perturbation (MP3) theory using the resolution of the identity (RI) approximation was combined with the fragment molecular orbital (FMO) method to efficiently calculate a high-order electron correlation energy of biomolecular systems. We developed a new algorithm for the RI-MP3 calculation, which can be used with the FMO scheme. After test calculations using a small molecule, the FMO-RI-MP3 calculations were performed for two biomolecular systems comprising a protein and a ligand. The computational cost of these calculations was only around 5 and 4 times higher than those of the FMO-RHF calculations. The error associated with the RI approximation was around 2.0% of the third-order correlation contribution to the total energy. However, the RI approximation error in the interaction energy between the protein and ligand molecule was insignificantly small, which reflected the negligible error in the inter fragment interaction energy. © 2018 Wiley Periodicals, Inc.

IMP-6 Carbapenemase-Producing Enterobacteriaceae Bacteremia Successfully Treated with Amikacin-Meropenem in Two Patients.

Infections caused by carbapenemase-producing Enterobacteriaceae (CPE) are becoming increasingly common worldwide. Although CPE infections can be fatal, few reports in the literature have described effective and successful treatments for infectious diseases caused by several types of IMP CPE, and, to our knowledge, no reports have described the successful treatment of IMP-6 CPE infections. We describe two patients who developed bacteremia caused by IMP-6 CPE after surgery for cancer who were successfully treated with amikacin plus high-dose prolonged-infusion meropenem. Both patients were treated over a 2-week period using amikacin 15 mg/kg at various intervals based on therapeutic drug monitoring and meropenem 2000 mg infused over 3 hours every 12 hours. The dosages of amikacin and meropenem were determined based on the creatinine clearance of each patient. Both patients were cured of their bacteremia and did not experience any antibiotic-related adverse effects. Based on the outcomes of these patients, it appears that amikacin plus high-dose prolonged-infusion meropenem may be safe and effective for the treatment of bacteremia caused by IMP-6 CPE.

Experimental and theoretical study on the intermolecular complex formation between trehalose and benzene compounds in aqueous solution.

The uniqueness of trehalose as a stress protectant may exist in its potential amphiphilic character capable of interacting with both hydrophilic and hydrophobic partners in aqueous solution. To address this issue, we here investigated the interaction between trehalose and aromatic compounds. NMR measurements, including (1)H-(1)H NOESY spectra, provide direct evidence for the formation of stable intermolecular complexes of trehalose with benzene (or p-cresol) in aqueous solution. In addition, corresponding theoretical evidence is provided by calculating the potential mean force as a function of the distance between trehalose and benzene. In the energy minimum structure, the benzene molecule is located only around the hydrophobic side of trehalose where the first hydration shell is not formed. Therefore, it can be concluded that benzene binds to trehalose in a fashion in which dehydration penalty is minimized. Finally, we discuss the possible biological roles of the trehalose-benzene interaction discovered here.

Defining lipid-binding regions of human serum amyloid A using its fragment peptides.

Human serum amyloid A (SAA) protein is an apolipoprotein predominantly present in the high-density lipoprotein fraction of plasma. Despite its critical roles in lipid metabolism, especially in acute phases, systematic understanding of the lipid interaction of this protein is limited. Lipid-binding properties of synthetic fragment peptides corresponding to the N-terminal (residues 1-27), central (residues 43-63), and C-terminal (residues 77-104) parts of SAA molecule were examined. SAA (1-27) peptide binds to lipid forming an alpha-helical structure, whereas SAA (43-63) and (77-104) peptides do not display binding to lipid with any conformational changes. These results indicate that the N-terminal region of SAA is important for lipid interaction. In addition, the finding that deletion of or proline substitution in the most N-terminal region (residues 1-11) markedly decreased the binding to lipid further suggests that the alpha-helical structure in residues 1-11 is essential for lipid binding of SAA.

Intra- and intermolecular interaction inducing pyramidalization on both sides of a proline dipeptide during isomerization: an ab initio QM/MM molecular dynamics simulation study in explicit water.

The cis-trans isomerization of the peptide bond preceding a proline plays important roles in protein folding and biological function. Although many experimental and theoretical studies have been done, the mechanism has not yet been clearly elucidated. We studied the cis-trans isomerization of the proline dipeptide (Ace-Pro-NMe) in explicit water by molecular dynamics simulations using a combined potential derived from ab initio quantum mechanics and empirical molecular mechanics. We obtained the free energy landscape during the isomerization by using the umbrella sampling method. The free energy landscape is in good accordance with previous experimental and theoretical values. We observed that in the middle of the isomerization, the prolyl nitrogen transiently takes pyramidal conformations in two polarized directions and that, simultaneously, the prolyl C-N bond extends. We show that these geometrical changes cooperatively transform the prolyl nitrogen from a sp(2)-hybridized electronic state into a sp(3)-hybridized one, and thus realize a transition state that reduces the rotational barriers separating the cis- and trans-states. We also found that the hydration of the prolyl nitrogen stabilizes the negative pyramidal conformation, while an intramolecular interaction mainly stabilizes the positive one. Fluctuations in the polarity and magnitude of the pyramidal conformation during the isomerization are interpreted as a competition between the hydrogen-bonding partners for the prolyl nitrogen between different sides of the pyrrolidine ring.