Abstract: Social media has been identified as a promising potential source of information for pharmacovigilance. The adoption of social media data has been hindered by the massive and noisy nature of the data. Initial attempts to use social media data have relied on exact text matches to drugs of interest, and therefore suffer from the gap between formal drug lexicons and the informal nature of social media. The Reddit comment archive represents an ideal corpus for bridging this gap. We trained a word embedding model, RedMed, to facilitate the identification and retrieval of health entities from Reddit data. We compare the performance of our model trained on a consumer-generated corpus against publicly available models trained on expert-generated corpora. Our automated classification pipeline achieves an accuracy of 0.88 and a specificity of >0.9 across four different term classes. Of all drug mentions, an average of 79% (+/-0.5%) were exact matches to a generic or trademark drug name, 14% (+/-0.5%) were misspellings, 6.4% (+/-0.3%) were synonyms, and 0.13% (+/-0.05%) were pill marks. We find that our system captures an additional 20% of mentions; these would have been missed by approaches that rely solely on exact string matches. We provide a lexicon of misspellings and synonyms for 2978 drugs and a word embedding model trained on a health-oriented subset of Reddit.

Abstract: This paper presents a new multi-residue method for the quantification of more than 142 anthropogenic compounds of emerging concern (CECs) in various environmental matrices. These CECs are from a wide range of major classes including pharmaceuticals, household, industrial and agricultural. This method utilises ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) for analysis of five matrices (three liquid and two solid) from wastewater treatment processes and the surrounding environment. Relative recoveries were predominantly between 80 and 120%; however, due to the complexity of the matrices used in this work, not all compounds were recovered in all matrices, from 138/142 analytes in surface water to 96/142 analytes in digested solids. Method quantification limits (MQLs) ranged from 0.004 ng L(-1) (bisoprolol in surface water) to 3118 ng L(-1) (creatinine in wastewater treatment work (WwTW) influent). The overall method accuracy was 107.0%, and precision was 13.4%. To test its performance, the method was applied to the range of environmental matrices at WwTWs in South West England. Overall, this method was found to be suitable for application in catchment-based exposure-driven studies, as, of the total number of analytes quantifiable in each matrix, 61% on average was found to be above their corresponding MQL. The results confirm the need for analysing both the liquid and solid compartments within a WwTW to prevent under-reporting of concentrations.

Abstract: The aim of the present study was to evaluate the potential network of arsenic trioxide (ATO) target genes in pancreatic cancer. The DrugBank, STITCH, cBioPortal, Kaplan-Meier plotter and Oncomine websites were used to analyze the association of ATO and its target genes with pancreatic cancer. Initially, 19 ATO target genes were identified, along with their associated protein-protein interaction networks and Kyoto Encyclopedia of Genes and Genomes pathways. ATO was found to be associated with multiple types of cancer, and the most common solid cancer was pancreatic cancer. A total of 6 ATO target genes (namely AKT1, CCND1, CDKN2A, IKBKB, MAPK1 and MAPK3) were found to be associated with pancreatic cancer. Next, the mutation information of the 6 ATO target genes in pancreatic cancer was collected. A total of 20 ATO interacting genes were identified, which were mainly involved in hepatitis B, prostate cancer, pathways in cancer, glioma and chronic myeloid leukemia. Finally, the genes CCND1 and MAPK1 were detected to be prognostic factors in patients with pancreatic cancer. In conclusion, bioinformatics analysis may help elucidate the molecular mechanisms underlying the involvement of ATO in pancreatic cancer, enabling more effective treatment of this disease.

Abstract: PURPOSE: Lenalidomide is used widely in B-cell malignancies for its immunomodulatory activity. It is primarily eliminated via the kidneys, with a significant proportion of renal elimination attributed to active processes. Lenalidomide is a weak substrate of P-glycoprotein (P-gp), though it is unclear whether P-gp is solely responsible for lenalidomide transport. This study aimed to determine whether the current knowledge of lenalidomide was sufficient to describe the pharmacokinetics of lenalidomide in multiple tissues. METHODS: A physiologically based pharmacokinetic model was developed using the Open Systems Pharmacology Suite to explore the pharmacokinetics of lenalidomide in a variety of tissues. Data were available for mice dosed intravenously at 0.5, 1.5, 5, and 10 mg/kg, with concentrations measured in plasma, brain, heart, kidney, liver, lung, muscle, and spleen. P-gp expression and activity were sourced from the literature. RESULTS: The model predictions in plasma, liver, and lung were representative of the observed data (median prediction error 13%, - 10%, and 30%, respectively, with 90% confidence intervals including zero), while other tissue predictions showed sufficient similarity to the observed data. Contrary to the data, model predictions for the brain showed no drug reaching brain tissue when P-gp was expressed at the blood-brain barrier. The data were better described by basolateral transporters at the intracellular wall. Local sensitivity analysis showed that transporter activity was the most sensitive parameter in these models for exposure. CONCLUSION: As P-gp transport at the blood-brain barrier did not explain the observed brain concentrations alone, there may be other transporters involved in lenalidomide disposition.

Abstract: Background: The cancer molecular targeted therapy has achieved unprecedented progress in the past decade and is thought to be the most promising direction for cancer treatment in future. As the fast growing of the clinical trials of targeted anticancer agents for different cancer types, it is critical to collect and integrate such information to guide clinical practice. Methods: We constructed the Cancer Molecular Targeted Therapy database (CMTTdb) to store and retrieve molecular targeted therapy data about randomized clinical trials (RCTs) of targeted agents and also accompanied targets, biomarkers, targeted cancer subtypes, etc. Results: Different with some existing resources, CMTTdb particularly focuses on clinical application of the trails. Design of the trails, such as treatment modalities (monotherapy or combination with other therapies), as well as results on clinical efficacy parameters, adverse events are also collected. In this current version, CMTTdb contains data for 1,088 clinical trials which cover 165 agents, 80 targets, 15 cancer types (95 molecular subtypes and 56 histological or cytological subtypes) from public literatures. This database is freely available at http://www.biosino.org/CMTTdb. A user-friendly web interface was designed so that these data can be easily retrieved. Conclusions: CMTTdb will be a valuable source for providing access to information of clinical trials on the rapidly growing number of novel targeted agent and be useful in guiding oncologists for the optimization of the therapy strategy for cancer treatment.

Abstract: Amfepramone (AFP) is an appetite-suppressant drug used in the treatment of obesity. Nonetheless, studies on interindividual pharmacokinetic variability and its association with genetic variants are limited. We employed a pharmacokinetic and pharmacogenetic approach to determine possible metabolic phenotypes of AFP and identify genetic markers that could affect the pharmacokinetic variability in a Mexican population. A controlled, randomized, crossover, single-blind, two-treatment, two-period, and two sequence clinical study of AFP (a single 75 mg dose) was conducted in 36 healthy Mexican volunteers who fulfilled the study requirements. Amfepramone plasma levels were measured using high-performance liquid chromatography mass spectrometry. Genotyping was performed using real-time PCR with TaqMan probes. Four AFP metabolizer phenotypes were found in our population: slow, normal, intermediate, and fast. Additionally, two gene polymorphisms, ABCB1-rs1045642 and CYP3A4-rs2242480, had a significant effect on AFP pharmacokinetics (P < 0.05) and were the predictor factors in a log-linear regression model. The ABCB1 and CYP3A4 gene polymorphisms were associated with a fast metabolizer phenotype. These results suggest that metabolism of AFP in the Mexican population is variable. In addition, the genetic variants ABCB1-rs1045642 and CYP3A4-rs2242480 may partially explain the AFP pharmacokinetic variability.

Abstract: Interactions between proteins and small molecules are critical for biological functions. These interactions often occur in small cavities within protein structures, known as ligand-binding pockets. Understanding the physicochemical qualities of binding pockets is essential to improve not only our basic knowledge of biological systems, but also drug development procedures. In order to quantify similarities among pockets in terms of their geometries and chemical properties, either bound ligands can be compared to one another or binding sites can be matched directly. Both perspectives routinely take advantage of computational methods including various techniques to represent and compare small molecules as well as local protein structures. In this review, we survey 12 tools widely used to match pockets. These methods are divided into five categories based on the algorithm implemented to construct binding-site alignments. In addition to the comprehensive analysis of their algorithms, test sets and the performance of each method are described. We also discuss general pharmacological applications of computational pocket matching in drug repurposing, polypharmacology and side effects. Reflecting on the importance of these techniques in drug discovery, in the end, we elaborate on the development of more accurate meta-predictors, the incorporation of protein flexibility and the integration of powerful artificial intelligence technologies such as deep learning.

Abstract: The BIOPEP-UWM database of bioactive peptides (formerly BIOPEP) has recently become a popular tool in the research on bioactive peptides, especially on these derived from foods and being constituents of diets that prevent development of chronic diseases. The database is continuously updated and modified. The addition of new peptides and the introduction of new information about the existing ones (e.g., chemical codes and references to other databases) is in progress. New opportunities include the possibility of annotating peptides containing D-enantiomers of amino acids, batch processing option, converting amino acid sequences into SMILES code, new quantitative parameters characterizing the presence of bioactive fragments in protein sequences, and finding proteinases that release particular peptides.

Abstract: The causes of a disease and its therapies are not only related to genotypes, but also associated with other factors, including phenotypes, environmental exposures, drugs and chemical molecules. Distinguishing disease-related factors from many neutral factors is critical as well as difficult. Over the past two decades, bioinformaticians have developed many computational resources to integrate the omics data and discover associations among these factors. However, researchers and clinicians are experiencing difficulties in choosing appropriate resources from hundreds of relevant databases and software tools. Here, in order to assist the researchers and clinicians, we systematically review the public computational resources of human diseases related to genotypes, phenotypes, environment factors, drugs and chemical exposures. We briefly describe the development history of these computational resources, followed by the details of the relevant databases and software tools. We finally conclude with a discussion of current challenges and future opportunities as well as prospects on this topic.

Abstract: Drug repurposing offers a promising alternative to dramatically shorten the process of traditional de novo development of a drug. These efforts leverage the fact that a single molecule can act on multiple targets and could be beneficial to indications where the additional targets are relevant. Hence, extensive research efforts have been directed toward developing drug based computational approaches. However, many drug based approaches are known to incur low successful rates, due to incomplete modeling of drug-target interactions. There are also many technical limitations to transform theoretical computational models into practical use. Drug based approaches may, thus, still face challenges for drug repurposing task. Upon this challenge, we developed a consensus inverse docking (CID) workflow, which has a ~ 10% enhancement in success rate compared with current best method. Besides, an easily accessible web server named auto in silico consensus inverse docking (ACID) was designed based on this workflow (http://chemyang.ccnu.edu.cn/ccb/server/ACID).