Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning.

Metalloproteins require metal ions as cofactors to catalyze specific reactions with remarkable efficiency and specificity. In various electron transfer reactions, metals in the active sites change their oxidation states to facilitate the biochemical reactions. Cryogenic electron microscopy, X-ray, and X-ray free electron laser (XFEL) crystallography are used to image metalloproteins to understand the reaction mechanisms. However, radiation damage in cryoEM and X-ray crystallography, and the challenge of generating homogeneous crystals and keeping the appropriate experimental conditions for all the crystals in XFEL crystallography, may alter the oxidation states. Here, we build machine learning models trained on a large data set from the Cambridge Crystallographic Data Center to evaluate the metal oxidation states. The models yield high accuracy scores (from 82% to 94%) for all metals in the small molecules. Then, they were used to predict the oxidation states of more than 30 000 metal clusters in metalloproteins with Fe, Mn, Co, and Cu in their active sites. We found that most of the metals exist in the lower oxidation states (Fe2+ 77%, Mn2+ 85%, Co2+ 65%, and Cu+ 64%), and these populations correlate with the standard reduction potentials of the metal ions. Furthermore, we found no clear correlation between these populations and the resolution of the structures, which suggests no significant dependence of these predictions on the resolution. Our models represent a valuable tool for evaluating the oxidation states of the metals in metalloproteins imaged with different techniques. The data files and the machine learning code are available in a public GitHub repository: https://github.com/mamin03/OxitationStatesMetalloprotein.git.

Examining participant representation by sex, race, ethnicity and age in United States blood donation and blood transfusion clinical trials.

Significant inequities based on sex, race, ethnicity, and age exist among participants in clinical trials dedicated to investigating medical disease states. While general demographic data regarding blood donors and blood transfusion recipients have been studied extensively, the demographics of participants involved in blood donation and blood transfusion clinical trials are unknown. We performed a cross-sectional analysis of United States (U.S.) -based interventional blood donation and blood transfusion clinical trials registered with Clinicaltrials.gov to ascertain the composition of participants' sex, race, ethnicity, and age, as well as diagnostic conditions and geographic trial locations.Eligible trials were undertaken between July 2003 and August 2020. Thirty-eight of the one hundred and fifty-two blood donation and blood transfusion clinical trials met inclusion criteria (seven blood donation and thirty-one blood transfusion trials). While the participant dataset from trial reports were incomplete, 100 % of blood donation trials reported sex and age, 71.4 % reported race, and 42.3 % reported ethnicity. 96.8 % of blood transfusion trials reported sex, 51.6 % reported race, 38.7 % reported ethnicity, and 100 % reported age. Among 2720 participants enrolled in the seven blood donation trials, females were underrepresented (28.5 %) compared to U.S. Census data. Conversely, female (50.8 %) and male participants (49.2 %) were equally represented in blood transfusion trials (9255 participants). White participants were overrepresented in blood donation trials (73.4 %), while Hispanic or Latinos were underrepresented in both blood donation (7.7 %) and blood transfusion (8.2 %) trials compared to 2019 U.S.Census data. Only 8.3 % of blood transfusion clinical trials open to adults reported including older adults (i.e., ≥ 65yo). Despite mandatory reporting requirements and an already established framework, researchers frequently failed to report complete demographics of blood donation and blood transfusion clinical trial participants. Furthermore, various demographic groups were underrepresented in blood donation and/or blood transfusion clinical trials, including females, Hispanic or Latino individuals, and older adults. These findings demonstrate the need for implementation of strategies to ensure equitable representation of individuals in blood donation and transfusion clinical trials.

Evaluation of urinary acetaminophen metabolites and its association with the genetic polymorphisms of the metabolising enzymes, and serum acetaminophen concentrations in preterm neonates with patent ductus arteriosus.

Acetaminophen is gaining importance as a first-line drug for treating patent ductus arteriosus (PDA) in neonates. Predominant metabolites of acetaminophen in preterm neonates vary from that of adults; and the drug is predominantly metabolised by conjugation and partly by Cytochrome P450 (CYP) enzymes.We carried out the present study to identify the principal urine metabolites of acetaminophen (glucuronide/sulphate) in preterm neonates with hemodynamically significant PDA receiving intravenous acetaminophen, and to evaluate the prevalence of single nucleotide polymorphisms (SNPs) in the key CYP enzymes (CYP1A2*3, CYP1A2*4, CYP1A2*1C, CYP1A2*1K, CYP1A2*6, CYP2D6*10, CYP2E1*2, CYP2E1*5B, CYP3A4*1B, CYP3A4*2, CYP3A4*3, CYP3A5*3, CYP3A5*7, and CYP3A5*11) and their effect on urinary metabolites and serum acetaminophen concentrations.Nineteen (32.8%) neonates had heterozygous CYP1A2*1C, two (3.3%) with heterozygous CYP1A2*1K, 15 (27.8%) and two (3.7%) had heterozygous and homozygous CYP2D6*10, two (3.7%) had heterozygous CYP2E1*5B, seven (12.3%) and three (5.3%) had heterozygous and homozygous CYP3A4*1B, and three (5.5%) had CYP3A5*7 amongst the study population. Acetaminophen sulphate predominated over glucuronide metabolite at all time points. Postnatal days of life was significantly associated with an increase in the urine acetaminophen metabolites with decreased serum acetaminophen concentrations.A significant prevalence of SNPs in the key CYP enzymes related to acetaminophen metabolism was observed in our neonatal population. Population pharmacokinetic-pharmacodynamic modelling incorporating genetic and metabolite data is urgently needed for implementation of precision medicine in this vulnerable population.

Bacteriology of pediatric breast abscesses beyond the neonatal period.

BACKGROUND: Limited data exist regarding the presentation and bacteriology of nonneonatal pediatric breast abscess. OBJECTIVE: To determine the bacteriology and characteristic presentation of pediatric breast abscesses in a tertiary care center. METHODS: Cross-sectional study of patients age 1 month to 21 years admitted to a pediatric Emergency Department (ED) between 1996 and 2018 with a breast abscess. Patients with pre-existing conditions were excluded. Records were reviewed to determine demographics, history, physical exam findings, wound culture results, imaging and ED disposition. We used descriptive statistics to describe prevalence of different bacteria. RESULTS: We identified 210 patients who met study criteria. Median age was 13.6 years [IQR 6.6, 17.4], and 91% (191/210) were females. Ninety-two patients (43.8%) were 'pre-treated' with antibiotics prior to ED visit, and 33/210 (16%) were febrile. Ultrasound was obtained in 85 patients (40.5%), 69 patients had a single abscess and 16 had multiple abscesses. Most patients were treated with antibiotics and 100 had a surgical intervention, of these 89 had I&D and 11 a needle aspiration. Admission rate was 45%. Culture results were available for 75 (75%). Thirty-three (44%) had a negative culture, or grew non-aureus staphylococci or other skin flora. Culture were positive for MSSA 21 (28%), MRSA 13 (17%), Proteus mirabilis 2 (2.6%), Serratia 1 (1.3%). Other organisms include Gram-negative bacilli, group A Streptococcus and enterococcus. CONCLUSIONS: Non-neonatal pediatric breast abscess bacteriology is no different than data published on other skin abscesses. MRSA coverage should be considered based on local prevalence in skin infections.

Intravenous acetaminophen (at 15 mg/kg/dose every 6 hours) in critically ill preterm neonates with patent ductus arteriosus: A prospective study.

WHAT IS KNOWN AND OBJECTIVES: Acetaminophen has been increasingly used in treating patent ductus arteriosus (PDA) in preterm neonates. Variations were observed in the dosing regimen of acetaminophen across the studies. There is hardly any data available for a relatively higher dose of intravenous acetaminophen (15 mg/kg/dose every 6 hours) in the preterm population. We present here the results of a prospective study with this dose of intravenous acetaminophen for treating PDA in critically ill preterm neonates. METHODS: Preterm neonates (≤37 weeks of gestational age) with haemodynamically significant PDA were enrolled. Intravenous acetaminophen at 15 mg/kg/dose every 6 hours was administered. Echocardiographic monitoring, liver and renal function tests were carried out. Standard definitions were adhered for defining acute kidney injury (AKI) and hepatotoxicity. RESULTS: Fifty-five neonates were recruited. Following the first dose, less than half had their serum acetaminophen concentrations in the therapeutic range. Extreme preterm neonates were less likely to have a sustained therapeutic acetaminophen concentration after the first dose. Following multiple doses and at steady state, 97.2% and 98.8% respectively were in the therapeutic range. Forty-three (78.2%) neonates had successful closure of the ductus arteriosus of which 22 were extreme preterm, 17 were very preterm and 4 were late preterm neonates; and considering their birthweights, 21 were extremely low, 16 were very low and 6 were low birthweight categories. Ten neonates had elevated alanine aminotransferase levels with three in the low-to-moderate risk of hepatotoxicity category. Eight neonates had altered renal function tests indicating AKI. WHAT IS NEW AND CONCLUSION: Intravenous acetaminophen at 15 mg/kg/dose every 6 hours was efficacious in 78.2% of the preterm neonates with PDA. We observed a lower incidence of hepatotoxicity, and AKI in the study population. No association was observed between the serum acetaminophen concentrations and PDA closure.

Is fat-free mass-based gentamicin dosing regimen preferable than whole-body weight in neonates?

Importance: Body fluid dynamics and renal maturation status vary during the neonatal period. We hypothesized that differences in peak and trough gentamicin concentrations could be expected. Objective: To predict the peak and trough gentamicin concentrations in critically ill neonates and to predict the changes in the predicted peak plasma concentrations of gentamicin following fat-free mass dosing. Methods: Critically ill neonates that received gentamicin and have gentamicin concentration measured were recruited. Fat mass was estimated using skinfold thicknesses. Changes in the peak plasma concentrations (Cmax) using whole-body weight (estimated using the current dosing regimen) and predicted concentrations following the fat-free mass-based dosing were the outcome measures. Results: Eighty-nine critically ill neonates were recruited. Sub-therapeutic Cmax was estimated using the current dosing regimen in 32.6%, and 22.5% neonates following the first and second doses of gentamicin. Preterm neonates had significantly higher fat mass compared to term neonates. All except one had Cmax above 12 µg/ml after the first dose and all had after the second gentamicin dose following the predicted fat-free mass-based gentamicin dosing. The recommended doses are as follows: extreme preterm: 7.95 mg/kg every 48 h; very preterm: 7.30 mg/kg every 36-48 h; late preterm: 5.90 mg/kg every 36-48 h; and term neonates at 5.10 mg/kg every 24 h. Interpretation: Fat-free mass dosing may be considered for obtaining optimal therapeutic effects in the neonatal population.

Gentamicin in Neonates with Hemodynamically Significant Patent Ductus Arteriosus.

Background: Gentamicin has been shown to cause vasodilation in preclinical studies. Hemodynamically significant patent ductus arteriosus (hsPDA) is a commonly observed congenital heart disorder in preterm neonates. Concomitant gentamicin theoretically shall delay the closure/result in nonclosure of ductus arteriosus (DA). Similarly, hsPDA can alter the pharmacokinetics of gentamicin and so trough gentamicin concentrations. We carried out the present study to evaluate the association between gentamicin use and closure of hsPDA (treated with acetaminophen) as well as the effect of hsPDA on trough concentrations. Methods: This study was a prospective, observational study that included 60 neonates diagnosed with hsPDA by echocardiography and 102 neonates without hsPDA. Demographic details, size of DA as per echocardiography at the end of treatment with acetaminophen, gentamicin-dosing regimen, and trough concentrations were collected. Standard definitions were adhered in classifying the gestational age, birth weights, and size of DA. The numerical values are reported in median (range). Results: Neonates with hsPDA had significantly lower daily doses of gentamicin [4.5 (2.5-10), 7 (3.2-13) mg; P < 0.001] but longer duration of therapy [8 (3-14), 5 (3-7) days; P < 0.001] than those without hsPDA in very preterm neonates. No significant differences were observed in the trough concentrations of gentamicin between the groups. No association was observed between gentamicin use and closure of DA. However, those with successful closure of DA received gentamicin for a longer duration [6 (3-10), 4 (3-14) days; P < 0.05] that was independent of acetaminophen duration and had received higher cumulative doses of gentamicin. Conclusion: In conclusion, we observed a significantly longer duration of gentamicin therapy in neonates with hsPDA compared to those without hsPDA. No significant differences were observed in the rates of closure of DA with concomitant gentamicin administration and gentamicin trough concentrations.

Evaluation of Genetic Polymorphisms of the Antioxidant Enzymes and Biomarkers of Oxidative Stress in Preterm Neonates With Respiratory Distress Syndrome Receiving External Surfactant.

Background: Preterm neonates, particularly extremely preterm, are susceptible to respiratory distress syndrome (RDS) due to surfactant deficiency. Single nucleotide polymorphisms (SNPs) in the antioxidant enzymes influence the balance between antioxidant and oxidative stress molecules. Objectives: To ascertain the role of SNPs of antioxidant enzymes and oxidative stress biomarkers in preterm neonates with RDS. Design: Observational, cross-sectional study. Methods: Preterm neonates diagnosed with RDS receiving external surfactant within 24 hours were considered as the cases and those without RDS were the control group. Umbilical cord blood and peripheral blood samples before administering surfactant (day 1), and on days 2 and 3 were collected. Plasma malondialdehyde, 8-hydroxy-2-deoxy guanosine (8-OH-dG), advanced oxidation protein products (AOPP), total antioxidant capacity (TAC), visfatin, reduced glutathione, and chaperonin 60 were evaluated using enzyme-linked immunosorbent assay. SNPs in manganese superoxide dismutase (MnSOD), copper/zinc superoxide dismutase (Cu/Zn SOD), glutathione peroxidase (GPX1 and GPX3), catalase (CAT), glutathione S-transferase (GSTP1) were evaluated using real-time polymerase-chain-reaction. The receiver-operating characteristics curve was used for predicting the accuracy of biomarkers using the area under the curve (AUC) and 95% confidence intervals (95% CI). Results: GSTP1, MnSOD, and eNOS (rs1799983) SNPs were observed to significantly influence the oxidative biomarker concentrations in the entire study population. SNPs in GSTP1, MnSOD, and eNOS (rs1799983) were significantly associated with differences in oxidative stress biomarkers. MnSOD (rs4880) significantly increased the risk of pulmonary complications in neonates with RDS. DNA damage product (8-OH-dG) concentrations before surfactant administration has the best predictive accuracy (AUC: 0.8; 95% CI: 0.7-1; P = .001) for pulmonary complications with a cut-off value of 5008.8 pg/mL. TAC concentrations are significantly greater on day 2 and day 3 amongst neonates receiving surfactant compared to the control group. AOPP in the umbilical cord blood was observed to significantly predict the severity of RDS (AUC: 0.8; 95% CI: 0.6-1; P = .01) with an optimal cut-off value of 88.78 µmol/L. Conclusion: We observed that SNPs in eNOS and MnSOD significantly influence the production of oxidative stress biomarkers in preterm neonates. Baseline 8-OH-dG concentrations best predict the risk of pulmonary complications and AOPP concentrations in the umbilical cord blood predict the risk of RDS severity.

Off-label drug use and the risk of medication errors in critically ill neonates: A conceptual pilot study.

BACKGROUND: Off-label drug (OLD) use is common in neonates. OBJECTIVE: There is a dearth of information associating the OLD use and the risk of medication errors in critically ill neonates. Hence, the present study was carried out. METHODS: Drug prescriptions in neonates admitted to the intensive care unit of a tertiary care hospital between September 2018 and June 2019 were evaluated. Details on their demographics, reason for admission in intensive care unit, drug-related information and serum creatinine were extracted. United States Food and Drug Administration approved drug labels were compared. World Health Organization (WHO) anatomy, therapeutic and chemical (ATC) classification was used for drug categorization. We assessed the risk of medication errors in the adult population using a validated tool: medication risk score (MERIS). RESULTS: One hundred and seventy-one neonates with 2394 prescriptions were included in this study. Seventy one percent of the neonates in the present study received at least one OLD/unlicensed prescription item. A trend in increased numbers of OLD/unlicensed drug use in more premature and lower birth weight neonates were observed. Medication risk score was significantly higher in neonates receiving OLD/unlicensed drugs compared to those with only labelled drugs. Very and extreme pre-term (along with very low and extremely low birth weight) neonates were at higher risk of medication errors compared to others. Presence of OLD/unlicensed prescribed items is associated with a potentially increased risk of medication errors by an odds ratio of 20.4 compared to labelled drugs. CONCLUSION: Significant proportions of critically ill neonates received at least one OLD/unlicensed drug and such use was associated with potentially increased risk of medication errors.

Drug utilisation in adult, paediatric and neonatal intensive care units, with an emphasis on systemic antimicrobials.

INTRODUCTION: Critically ill adults, children and neonates receive drugs that are often administered parenterally and in infusions. Considering patient illness severity, empirical broad-spectrum antimicrobials are commonly used. We conducted the present study to evaluate the drug use in this population, with a special focus on antimicrobials. MATERIAL AND METHODS: A prospective cross-sectional study was implemented in adult, paediatric and neonatal intensive care units. Various prescribing and supplemental indicators were used for drug comparisons. The World Health Organisation's list of essential drugs, the national drug formulary and critically important antimicrobial drugs were assessed. Proportions and median (range) were used to represent categorical and numerical values. RESULTS: Four hundred and ninety-six critically ill patients were enrolled in the study, with 5,636 prescribed drugs used for 31,993 patient-days. Critically ill adults received significantly more drugs compared to children and the neonatal population (11 [8-16], 9 [6-17] and 5 [3-12] respectively). Critically ill neonates received significantly fewer of the drugs listed in the national formulary compared to older children and adults (94.1% [10.1], 92.4% [32.4] and 80.1% [20.4]). Critically ill neonates received fewer antimicrobials (82% compared to 91.3% in adults and 98% in children). Furthermore, critically ill adults received more broad-spectrum antimicrobials compared to neonates. Prolonged empirical antimicrobial use was observed more in critically ill children (52%) compared to adults (29.8%). A large majority of the antimicrobials were critically important for 87.7%, 83.9% and 86.5% of patients in the adult, paediatric and neonatal intensive care units. CONCLUSIONS: We observed significant differences in terms of drug classes predominantly used in various age groups of critically ill patients, particularly regarding the nature and type of antimicrobial drugs and the duration of antimicrobial therapy.

Population pharmacokinetic-pharmacodynamic modeling of acetaminophen in preterm neonates with hemodynamically significant patent ductus arteriosus.

BACKGROUND: Pharmacokinetics (PK) of intravenous acetaminophen has not been assessed in preterm neonates with hemodynamically significant patent ductus arteriosus (PDA). Moreover, there is a lack of data evaluating the association between PK and pharmacodynamics (PD) of acetaminophen in hemodynamically significant PDA. Hence, we performed a population PK-PD modeling of acetaminophen in preterm neonates with hemodynamically significant PDA. METHODS: A prospective, observational study was carried out in preterm neonates with hemodynamically significant PDA receiving intravenous acetaminophen (15 mg/kg six hourly) for maximum of nine days. The diameter of the ductus arteriosus was measured using General Electric Vivid 7® (echocardiography) and was the PD measure. The PK-PD modeling was performed using Monolix 2019R2. We performed Monte Carlo (MC) simulations to determine the probability of ductus arteriosus closure from first to the ninth day of acetaminophen treatment. RESULTS: Fifty-five neonates were recruited. A one-compartment model with first-order elimination described well the PK of acetaminophen. Clearance (CL) and volume of distribution (Vd) for typical neonate weighing 0.98 kg was 0.0452 L/h and 1.18 L, respectively. A combination of an Imax model with effect compartment and an exponential disease progression model described well the PD of acetaminophen. The average baseline diameter of the ductus arteriosus (E0) was 2.53 mm while IC50 was 0.477 µg/mL. The disease progression rate constant (Kprog) and effect compartment transfer rate constant (ke0) were 0.00425 h-1 and 0.000103 h-1, respectively. MC simulations of the current dosing regimen revealed a probability of 73.7% ductus arteriosus closure compared to 83.8% with 20 mg/kg six hourly dose. CONCLUSION: The PK-PD model developed can be used for dosing acetaminophen in premature neonates with hemodynamically significant PDA. Intravenous dose of 20 mg/kg intravenously every six hours is likely to provide a better therapeutic effect than the existing dosing regimen.

Possible effects of excipients used in the parenteral drugs administered in critically ill adults, children, and neonates.

BACKGROUND: Critically ill patients receiving parenteral drugs are at an increased risk of exposure to various excipients administered simultaneously and at increased amounts. Hence, we carried out the present study. RESEARCH DESIGN AND METHODS: Patients admitted in the adult, pediatric, and neonatal intensive care units were recruited following their consent. Details on their demographics, diagnoses, and drugs administered and the excipients were collected. RESULTS: Almost all the critically ill patients received drugs containing at least one excipient. Significant numbers of critically ill neonates received at least one of either known to be harmful or potentially harmful excipients. Critically ill neonates had significantly greater daily exposure of macrogol than children and adults; and benzyl alcohol (v/v) and propyl paraben compared to adults. Critically ill neonates and children had greater exposure to benzyl alcohol (w/v), methyl paraben, sodium metabisulfite than adults did. Benzyl alcohol exposure was likely to be several-fold high in critically ill patients. Exposures to benzyl alcohol and propylene glycol were possibly linked to increased risk of mortality particularly in neonates. CONCLUSION: Critically ill neonates and children are likely to receive a significantly greater quantity of harmful excipients than critically ill adults. Benzyl alcohol and propylene glycol exposure are likely to be associated with increased risk of mortality in critically ill.