Abstract: Extracorporeal membrane oxygenation (ECMO) is a lifesaving support technology for potentially reversible neonatal cardiac and/or respiratory failure. As the survival and the overall outcome of patients rely on the treatment and reversal of the underlying disease, effective and preferentially evidence-based pharmacotherapy is crucial to target recovery. Currently limited data exist to support the clinicians in their every-day intensive care prescribing practice with the contemporary ECMO technology. Indeed, drug dosing to optimize pharmacotherapy during neonatal ECMO is a major challenge. The impact of the maturational changes of the organ function on both pharmacokinetics (PK) and pharmacodynamics (PD) has been widely established over the last decades. Next to the developmental pharmacology, additional non-maturational factors have been recognized as key-determinants of PK/PD variability. The dynamically changing state of critical illness during the ECMO course impairs the achievement of optimal drug exposure, as a result of single or multi-organ failure, capillary leak, altered protein binding, and sometimes a hyperdynamic state, with a variable effect on both the volume of distribution (Vd) and the clearance (Cl) of drugs. Extracorporeal membrane oxygenation introduces further PK/PD perturbation due to drug sequestration and hemodilution, thus increasing the Vd and clearance (sequestration). Drug disposition depends on the characteristics of the compounds (hydrophilic vs. lipophilic, protein binding), patients (age, comorbidities, surgery, co-medications, genetic variations), and circuits (roller vs. centrifugal-based systems; silicone vs. hollow-fiber oxygenators; renal replacement therapy). Based on the potential combination of the above-mentioned drug PK/PD determinants, an integrated approach in clinical drug prescription is pivotal to limit the risks of over- and under-dosing. The understanding of the dose-exposure-response relationship in critically-ill neonates on ECMO will enable the optimization of dosing strategies to ensure safety and efficacy for the individual patient. Next to in vitro and clinical PK data collection, physiologically-based pharmacokinetic modeling (PBPK) are emerging as alternative approaches to provide bedside dosing guidance. This article provides an overview of the available evidence in the field of neonatal pharmacology during ECMO. We will identify the main determinants of altered PK and PD, elaborate on evidence-based recommendations on pharmacotherapy and highlight areas for further research.

Abstract: Proteins interact with small molecules to modulate several important cellular functions. Many acute diseases were cured by small molecule binding in the active site of protein either by inhibition or activation. Currently, there are several docking programs to estimate the binding position and the binding orientation of protein-ligand complex. Many scoring functions were developed to estimate the binding strength and predict the effective protein-ligand binding. While the accuracy of current scoring function is limited by several aspects, the solvent effect, entropy effect, and multibody effect are largely ignored in traditional machine learning methods. In this paper, we proposed a new deep neural network-based model named DeepBindRG to predict the binding affinity of protein-ligand complex, which learns all the effects, binding mode, and specificity implicitly by learning protein-ligand interface contact information from a large protein-ligand dataset. During the initial data processing step, the critical interface information was preserved to make sure the input is suitable for the proposed deep learning model. While validating our model on three independent datasets, DeepBindRG achieves root mean squared error (RMSE) value of pKa (-logKd or -logKi) about 1.6-1.8 and R value around 0.5-0.6, which is better than the autodock vina whose RMSE value is about 2.2-2.4 and R value is 0.42-0.57. We also explored the detailed reasons for the performance of DeepBindRG, especially for several failed cases by vina. Furthermore, DeepBindRG performed better for four challenging datasets from DUD.E database with no experimental protein-ligand complexes. The better performance of DeepBindRG than autodock vina in predicting protein-ligand binding affinity indicates that deep learning approach can greatly help with the drug discovery process. We also compare the performance of DeepBindRG with a 4D based deep learning method "pafnucy", the advantage and limitation of both methods have provided clues for improving the deep learning based protein-ligand prediction model in the future.

Abstract: Traditional Chinese medicine (TCM) has a longstanding history and has gained widespread clinical applications. San Cao Decoction (SCD) is an experience prescription first formulated by Prof. Duzhou Liu. We previously demonstrated its antihypertensive effects; however, to systematically explain the underlying mechanisms of action, we employed a systems pharmacology approach for pharmacokinetic screening and target prediction by constructing protein-protein interaction networks of hypertension-related and putative SCD-related targets, and Database for Annotation, Visualization, and Integrated Discovery enrichment analysis. We identified 123 active compounds in SCD and 116 hypertension-related targets. Furthermore, the enrichment analysis of the drug-target network showed that SCD acts in a multidimensional manner to regulate PI3K-Akt-endothelial nitric oxide synthase signaling to maintain blood pressure. Our results highlighted the molecular mechanisms of antihypertensive actions of medicinal herbs at a systematic level.

Abstract: The juvenile conventional pig has been suggested as a preclinical animal model to evaluate pharmacokinetic (PK), pharmacodynamic (PD), and safety parameters in children. However, a lot of developmental changes in pig physiology still need to be unraveled. While the in vitro ontogeny of pig biotransformation enzymes is getting more attention in literature, the in vivo developmental changes have not yet been investigated. Therefore, the aim of the current study was to evaluate the biotransformation of ibuprofen (IBU) in conventional pigs aged 1 week, 4 weeks, 8 weeks, and 6-7 months after a single intravenous and oral administration of 5 mg/kg body weight (BW) of IBU, using a PK approach in a crossover design for each age group. An ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was developed and validated to determine 2-hydroxyibuprofen (2OH-IBU), carboxyibuprofen (COOH-IBU), and ibuprofen glucuronide (IBU-GlcA) in pig plasma. All three metabolites could be quantified in plasma and the following PK parameters were determined: C max, T max, AUC0-->6h, area under plasma concentration-time curve (AUC) ratio between parent drug and metabolite, and the absolute oral bioavailability of the parent drug IBU. The plasma concentrations of the metabolites were always lower than those of IBU. The bioavailability was high, indicating limited pre-systemic biotransformation. The AUC ratio of 2OH-IBU and COOH-IBU/IBU showed a significant increase at 4 weeks of age compared to the 1-week-old and 6- to 7-month-old pigs. Interestingly, the IBU-GlcA/IBU AUC ratio did not change with age. The present study demonstrated that the main metabolites of IBU in human are also present in growing pigs. The oxidative phase I metabolism of IBU in growing conventional pigs did change with age. In contrast, age did not seem to affect the glucuronidation capacity of IBU in conventional pigs, although more studies with other substrate drugs are needed to confirm this.

Abstract: Drug response variations amongst different individuals/populations are influenced by several factors including allele frequency differences of single nucleotide polymorphisms (SNPs) that functionally affect drug-response genes. Here, we aim to identify drugs that potentially exhibit population differences in response using SNP data mining and analytics. Ninety-one pairwise-comparisons of >22,000,000 SNPs from the 1000 Genomes Project, across 14 different populations, were performed to identify 'population-differentiated' SNPs (pdSNPs). Potentially-functional pdSNPs (pf-pdSNPs) were then selected, mapped into genes, and integrated with drug-gene databases to identify 'population-differentiated' drugs enriched with genes carrying pf-pdSNPs. 1191 clinically-approved drugs were found to be significantly enriched (Z > 2.58) with genes carrying SNPs that were differentiated in one or more population-pair comparisons. Thirteen drugs were found to be enriched with such differentiated genes across all 91 population-pairs. Notably, 82% of drugs, which were previously reported in the literature to exhibit population differences in response were also found by this method to contain a significant enrichment of population specific differentiated SNPs. Furthermore, drugs with genetic testing labels, or those suspected to cause adverse reactions, contained a significantly larger number (P < 0.01) of population-pairs with enriched pf-pdSNPs compared with those without these labels. This pioneering effort at harnessing big-data pharmacogenomics to identify 'population differentiated' drugs could help to facilitate data-driven decision-making for a more personalized medicine.

Abstract: BACKGROUND: Essential medicines lists and related policies are intended to meet the priority health needs of populations and their implementation is associated with more appropriate use of medicines. The World Health Organization (WHO) recommends that countries carefully select the medicines to be included in their national essential medicines lists. Lists that are used to prioritize access to important treatments should not include medicines that have been withdrawn elsewhere because of an unfavourable benefit-to-harm balance; however, countries still list and use medicines that have been withdrawn worldwide. The objective of this study was to determine whether the national essential medicines lists of 137 countries include medicines that have been withdrawn in other countries. METHODS AND FINDINGS: We performed an audit of national essential medicines lists for medicines that had been withdrawn. Medicines withdrawn from worldwide markets between 1953 and 2014 were identified using a systematic review of published literature and regulatory documents. The reviewers used sources including the WHO's database of drugs, PubMed, and the websites of regulatory agencies to obtain information regarding adverse effects associated with the medicines, the year of first withdrawal, markets of withdrawal, and the level of evidence supporting each withdrawal. We recorded the number of countries with a withdrawn medicine included in their national medicines list, the number of withdrawn medicines included in each nation's list, and the number of national essential medicines including each withdrawn medicine. 97 medicines were withdrawn in at least one country but still included in one more national essential medicines list. Of 137 countries with a national essential medicines list, 136 lists included at least one withdrawn medicine, with 54% of the lists containing 5 or fewer withdrawn medicines, and 27% including 10 or more withdrawn medicines. 11 medicines were withdrawn worldwide but still included on at least one national essential medicines list. Countries with longer essential medicines lists had more withdrawn medicines included in their lists. CONCLUSIONS: This study found that withdrawn medicines are included in all but one national essential medicines list, representing a need for more stringent processes for selecting and removing medicines on these lists. Countries may wish to apply special scrutiny to medicines withdrawn in other nations when selecting medicines to include on their lists.

Abstract: Combinatorial drug therapy can improve the therapeutic effect and reduce the corresponding adverse events. In silico strategies to classify synergistic vs. antagonistic drug pairs is more efficient than experimental strategies. However, most of the developed methods have been applied only to cancer therapies. In this study, we introduce a novel method, XGBoost, based on five features of drugs and biomolecular networks of their targets, to classify synergistic vs. antagonistic drug combinations from different drug categories. We found that XGBoost outperformed other classifiers in both stratified fivefold cross-validation (CV) and independent validation. For example, XGBoost achieved higher predictive accuracy than other models (0.86, 0.78, 0.78, and 0.83 for XGBoost, logistic regression, naive Bayesian, and random forest, respectively) for an independent validation set. We also found that the five-feature XGBoost model is much more effective at predicting combinatorial therapies that have synergistic effects than those with antagonistic effects. The five-feature XGBoost model was also validated on TCGA data with accuracy of 0.79 among the 61 tested drug pairs, which is comparable to that of DeepSynergy. Among the 14 main anatomical/pharmacological groups classified according to WHO Anatomic Therapeutic Class, for drugs belonging to five groups, their prediction accuracy was significantly increased (odds ratio < 1) or reduced (odds ratio > 1) (Fisher's exact test, p < 0.05). This study concludes that our five-feature XGBoost model has significant benefits for classifying synergistic vs. antagonistic drug combinations.

Abstract: The discovery of new pharmaceutical drugs is one of the preeminent tasks-scientifically, economically, and socially-in biomedical research. Advances in informatics and computational biology have increased productivity at many stages of the drug discovery pipeline. Nevertheless, drug discovery has slowed, largely due to the reliance on small molecules as the primary source of novel hypotheses. Natural products (such as plant metabolites, animal toxins, and immunological components) comprise a vast and diverse source of bioactive compounds, some of which are supported by thousands of years of traditional medicine, and are largely disjoint from the set of small molecules used commonly for discovery. However, natural products possess unique characteristics that distinguish them from traditional small molecule drug candidates, requiring new methods and approaches for assessing their therapeutic potential. In this review, we investigate a number of state-of-the-art techniques in bioinformatics, cheminformatics, and knowledge engineering for data-driven drug discovery from natural products. We focus on methods that aim to bridge the gap between traditional small-molecule drug candidates and different classes of natural products. We also explore the current informatics knowledge gaps and other barriers that need to be overcome to fully leverage these compounds for drug discovery. Finally, we conclude with a "road map" of research priorities that seeks to realize this goal.

Abstract: Leishmaniasis is a neglected tropical disease caused by parasites of the genus Leishmania (NTD) endemic in 98 countries. Although some drugs are available, current treatments deal with issues such as toxicity, low efficacy, and emergence of resistance. Therefore, there is an urgent need to identify new targets for the development of new antileishmanial drugs. Protein kinases (PKs), which play an essential role in many biological processes, have become potential drug targets for many parasitic diseases. A refined bioinformatics pipeline was applied in order to define and compare the kinomes of L. infantum and L. braziliensis, species that cause cutaneous and visceral manifestations of leishmaniasis in the Americas, the latter being potentially fatal if untreated. Respectively, 224 and 221 PKs were identified in L. infantum and L. braziliensis overall. Almost all unclassified eukaryotic PKs were assigned to six of nine major kinase groups and, consequently, most have been classified into family and subfamily. Furthermore, revealing the kinomes for both Leishmania species allowed for the prioritization of potential drug targets that could be explored for discovering new drugs against leishmaniasis. Finally, we used a drug repurposing approach and prioritized seven approved drugs and investigational compounds to be experimentally tested against Leishmania. Trametinib and NMS-1286937 inhibited the growth of L. infantum and L. braziliensis promastigotes and amastigotes and therefore might be good candidates for the drug repurposing pipeline.