Comparison of On-the-Fly Probability Enhanced Sampling and Parallel Tempering Combined with Metadynamics for Atomistic Simulations of RNA Tetraloop Folding.

Atomistic simulations with reliable models are extremely useful in providing exquisitely detailed pictures of biomolecular phenomena that are not always accessible to experiments. One such biomolecular phenomenon is RNA folding, which often requires exhaustive simulations with combined advanced sampling techniques. In this work, we employed the multithermal-multiumbrella on-the-fly probability enhanced sampling (MM-OPES) technique and compared it against combined parallel tempering and metadynamics simulations. We found that MM-OPES simulations were successful in reproducing the free energy surfaces from combined parallel tempering and metadynamics simulations. Importantly, we also investigated a wide range of temperature sets (minimum and maximum temperatures) for MM-OPES simulations in order to identify some guidelines for deciding the temperature limits for an accurate and efficient exploration of the free energy landscapes. We found that most temperature sets yielded almost the same accuracy in reproducing the free energy surface at the ambient conditions as long as (i) the maximum temperature is reasonably high, (ii) the temperature at which we run the simulation is reasonably high (in our simulations, running temperature is defined as [minimum temperature + maximum temperature]/2), and (iii) the effective sample size at the temperature of interest is statistically reasonable. In terms of the computational cost, all MM-OPES simulations were nearly 4 times less costly than the combined parallel tempering and metadynamics simulations. We concluded that the demanding combined parallel tempering and metadynamics simulations can safely be replaced with approximately 4 times less costly MM-OPES simulations (with carefully selected temperature limits) to obtain the same information.

Cardioprotective effects of deferoxamine in acute and subacute cardiotoxicities of doxorubicin: a randomized clinical trial.

BACKGROUND: Cardiotoxicity is a major concern following doxorubicin (DOX) use in the treatment of malignancies. We aimed to investigate whether deferoxamine (DFO) can prevent acute cardiotoxicity in children with cancer who were treated with DOX as part of their chemotherapy. RESULTS: Sixty-two newly-diagnosed pediatric cancer patients aged 2-18 years with DOX as part of their treatment regimens were assigned to three groups: group 1 (no intervention, n = 21), group II (Deferoxamine (DFO) 10 times DOX dose, n = 20), and group III (DFO 50 mg/kg, n = 21). Patients in the intervention groups were pretreated with DFO 8-h intravenous infusion in each chemotherapy course during and after completion of DOX infusion. Conventional and tissue Doppler echocardiography, serum concentrations of human brain natriuretic peptide (BNP), and cardiac troponin I (cTnI) were checked after the last course of chemotherapy. Sixty patients were analyzed. The level of cTnI was < 0.01 in all patients. Serum BNP was significantly lower in group 3 compared to control subjects (P = 0.036). No significant differences were observed in the parameters of Doppler echocardiography. Significant lower values of tissue Doppler late diastolic velocity at the lateral annulus of the tricuspid valve were noticed in group 3 in comparison with controls. By using Pearson analysis, tissue Doppler systolic velocity of the septum showed a marginally significant negative correlation with DOX dose (P = 0.05, r = - 0.308). No adverse effect was reported in the intervention groups. CONCLUSIONS: High-dose DFO (50 mg/kg) may serve as a promising cardioprotective agent at least at the molecular level in cancer patients treated with DOX. Further multicenter trials with longer follow-ups are needed to investigate its protective role in delayed DOX-induced cardiac damage. Trial registration IRCT, IRCT2016080615666N5. Registered 6 September 2016, http://www.irct.ir/IRCT2016080615666N5 .