A novel graph mining approach to predict and evaluate food-drug interactions.
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ABSTRACT:
SUBMITTER: Rahman MM
PROVIDER: S-EPMC8776972 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Motivation:Finding computationally drug-target interactions (DTIs) is a convenient strategy to identify new DTIs at low cost with reasonable accuracy. However, the current DTI prediction methods suffer the high false positive prediction rate. Results:We developed DDR, a novel method that improves the DTI prediction accuracy. DDR is based on the use of a heterogeneous graph that contains known DTIs with multiple similarities between drugs and multiple similarities between target proteins. DDR applies non-linear similarity fusion method to combine different similarities. Before fusion, DDR performs a pre-processing step where a subset of similarities is selected in a heuristic process to obtain an optimized combination of similarities. Then, DDR applies a random forest model using different graph-based features extracted from the DTI heterogeneous graph. Using 5-repeats of 10-fold cross-validation, three testing setups, and the weighted average of area under the precision-recall curve (AUPR) scores, we show that DDR significantly reduces the AUPR score error relative to the next best start-of-the-art method for predicting DTIs by 34% when the drugs are new, by 23% when targets are new and by 34% when the drugs and the targets are known but not all DTIs between them are not known. Using independent sources of evidence, we verify as correct 22 out of the top 25 DDR novel predictions. This suggests that DDR can be used as an efficient method to identify correct DTIs. Availability and implementation:The data and code are provided at https://bitbucket.org/RSO24/ddr/. Contact:vladimir.bajic@kaust.edu.sa. Supplementary information:Supplementary data are available at Bioinformatics online.
| S-EPMC5998943 | biostudies-literature
Project description:MotivationDrug-food interactions (DFIs) occur when some constituents of food affect the bioaccessibility or efficacy of the drug by involving in drug pharmacodynamic and/or pharmacokinetic processes. Many computational methods have achieved remarkable results in link prediction tasks between biological entities, which show the potential of computational methods in discovering novel DFIs. However, there are few computational approaches that pay attention to DFI identification. This is mainly due to the lack of DFI data. In addition, food is generally made up of a variety of chemical substances. The complexity of food makes it difficult to generate accurate feature representations for food. Therefore, it is urgent to develop effective computational approaches for learning the food feature representation and predicting DFIs.ResultsIn this article, we first collect DFI data from DrugBank and PubMed, respectively, to construct two datasets, named DrugBank-DFI and PubMed-DFI. Based on these two datasets, two DFI networks are constructed. Then, we propose a novel end-to-end graph embedding-based method named DFinder to identify DFIs. DFinder combines node attribute features and topological structure features to learn the representations of drugs and food constituents. In topology space, we adopt a simplified graph convolution network-based method to learn the topological structure features. In feature space, we use a deep neural network to extract attribute features from the original node attributes. The evaluation results indicate that DFinder performs better than other baseline methods.Availability and implementationThe source code is available at https://github.com/23AIBox/23AIBox-DFinder.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC9828147 | biostudies-literature
Project description:BACKGROUND:The INhibitor of Growth (ING) family of type II tumor suppressors (ING1-ING5) is involved in many cellular processes such as cell aging, apoptosis, DNA repair and tumorigenesis. To expand our understanding of the proteins with which the ING proteins interact, we designed a method that did not depend upon large-scale proteomics-based methods, since they may fail to highlight transient or relatively weak interactions. Here we test a cross-species (yeast, fly, and human) bioinformatics-based approach to identify potential human ING-interacting proteins with higher probability and accuracy than approaches based on screens in a single species. RESULTS:We confirm the validity of this screen and show that ING1 interacts specifically with three of the three proteins tested; p38MAPK, MEKK4 and RAD50. These novel ING-interacting proteins further link ING proteins to cell stress and DNA damage signaling, providing previously unknown upstream links to DNA damage response pathways in which ING1 participates. The bioinformatics approach we describe can be used to create an interaction prediction list for any human proteins with yeast homolog(s). CONCLUSION:None of the validated interactions were predicted by the conventional protein-protein interaction tools we tested. Validation of our approach by traditional laboratory techniques shows that we can extract value from the voluminous weak interaction data already elucidated in yeast and fly databases. We therefore propose that the weak (low signal to noise ratio) data from large-scale interaction datasets are currently underutilized.
| S-EPMC2565686 | biostudies-literature
Project description:In silico prediction of drug-target interactions is a critical phase in the sustainable drug development process, especially when the research focus is to capitalize on the repositioning of existing drugs. However, developing such computational methods is not an easy task, but is much needed, as current methods that predict potential drug-target interactions suffer from high false-positive rates. Here we introduce DTiGEMS+, a computational method that predicts Drug-Target interactions using Graph Embedding, graph Mining, and Similarity-based techniques. DTiGEMS+?combines similarity-based as well as feature-based approaches, and models the identification of novel drug-target interactions as a link prediction problem in a heterogeneous network. DTiGEMS+?constructs the heterogeneous network by augmenting the known drug-target interactions graph with two other complementary graphs namely: drug-drug similarity, target-target similarity. DTiGEMS+?combines different computational techniques to provide the final drug target prediction, these techniques include graph embeddings, graph mining, and machine learning. DTiGEMS+?integrates multiple drug-drug similarities and target-target similarities into the final heterogeneous graph construction after applying a similarity selection procedure as well as a similarity fusion algorithm. Using four benchmark datasets, we show DTiGEMS+?substantially improves prediction performance compared to other state-of-the-art in silico methods developed to predict of drug-target interactions by achieving the highest average AUPR across all datasets (0.92), which reduces the error rate by 33.3% relative to the second-best performing model in the state-of-the-art methods comparison.
| S-EPMC7325230 | biostudies-literature
Project description:Developing ontologies to account for the complexity of biological systems requires the time intensive collaboration of many participants with expertise in various fields. While each participant may contribute to construct a list of terms for ontology development, no objective methods have been developed to evaluate how relevant each of these terms is to the intended domain. We have developed a computational method based on a hypergeometric enrichment test to evaluate the relevance of such terms to the intended domain. The proposed method uses the PubMed literature database to evaluate whether each potential term for ontology development is overrepresented in the abstracts that discuss the particular domain. This evaluation provides an objective approach to assess terms and prioritize them for ontology development.
| S-EPMC3153945 | biostudies-literature
Project description:Protein-RNA interactions play important roles in the biological systems. Searching for regular patterns in the Protein-RNA binding interfaces is important for understanding how protein and RNA recognize each other and bind to form a complex. Herein, we present a graph-mining method for discovering biological patterns in the protein-RNA interfaces. We represented known protein-RNA interfaces using graphs and then discovered graph patterns enriched in the interfaces. Comparison of the discovered graph patterns with UniProt annotations showed that the graph patterns had a significant overlap with residue sites that had been proven crucial for the RNA binding by experimental methods. Using 200 patterns as input features, a support vector machine method was able to classify protein surface patches into RNA-binding sites and non-RNA-binding sites with 84.0% accuracy and 88.9% precision. We built a simple scoring function that calculated the total number of the graph patterns that occurred in a protein-RNA interface. That scoring function was able to discriminate near-native protein-RNA complexes from docking decoys with a performance comparable with that of a state-of-the-art complex scoring function. Our work also revealed possible patterns that might be important for binding affinity.
| S-EPMC5220573 | biostudies-literature
Project description:BackgroundDrug discovery is the process through which potential new medicines are identified. High-throughput screening and computer-aided drug discovery/design are the two main drug discovery methods for now, which have successfully discovered a series of drugs. However, development of new drugs is still an extremely time-consuming and expensive process. Biomedical literature contains important clues for the identification of potential treatments. It could support experts in biomedicine on their way towards new discoveries.MethodsHere, we propose a biomedical knowledge graph-based drug discovery method called SemaTyP, which discovers candidate drugs for diseases by mining published biomedical literature. We first construct a biomedical knowledge graph with the relations extracted from biomedical abstracts, then a logistic regression model is trained by learning the semantic types of paths of known drug therapies' existing in the biomedical knowledge graph, finally the learned model is used to discover drug therapies for new diseases.ResultsThe experimental results show that our method could not only effectively discover new drug therapies for new diseases, but also could provide the potential mechanism of action of the candidate drugs.ConclusionsIn this paper we propose a novel knowledge graph based literature mining method for drug discovery. It could be a supplementary method for current drug discovery methods.
| S-EPMC5975655 | biostudies-literature
Project description:Motivation:A heterogeneous network topology possessing abundant interactions between biomedical entities has yet to be utilized in similarity-based methods for predicting drug-target associations based on the array of varying features of drugs and their targets. Deep learning reveals features of vertices of a large network that can be adapted in accommodating the similarity-based solutions to provide a flexible method of drug-target prediction. Results:We propose a similarity-based drug-target prediction method that enhances existing association discovery methods by using a topology-based similarity measure. DeepWalk, a deep learning method, is adopted in this study to calculate the similarities within Linked Tripartite Network (LTN), a heterogeneous network generated from biomedical linked datasets. This proposed method shows promising results for drug-target association prediction: 98.96% AUC ROC score with a 10-fold cross-validation and 99.25% AUC ROC score with a Monte Carlo cross-validation with LTN. By utilizing DeepWalk, we demonstrate that: (i) this method outperforms other existing topology-based similarity computation methods, (ii) the performance is better for tripartite than with bipartite networks and (iii) the measure of similarity using network topology outperforms the ones derived from chemical structure (drugs) or genomic sequence (targets). Our proposed methodology proves to be capable of providing a promising solution for drug-target prediction based on topological similarity with a heterogeneous network, and may be readily re-purposed and adapted in the existing of similarity-based methodologies. Availability and Implementation:The proposed method has been developed in JAVA and it is available, along with the data at the following URL: https://github.com/zongnansu1982/drug-target-prediction . Contact:nazong@ucsd.edu. Supplementary information:Supplementary data are available at Bioinformatics online.
| S-EPMC5860112 | biostudies-literature
Project description:BackgroundAccurate estimation of conception is critical in the assessment of the effects of drugs used during pregnancy or to prevent pregnancy. In a novel application, we studied the effectiveness of oral contraceptives (OCs), where misclassification of conception relative to OC exposure may obscure effect estimates.MethodsWe studied OC failure, in a large claims database, among women who used antiepileptic drugs with metabolizing enzyme-inducing properties (carbamazepine or oxcarbazepine), which reduce OC's effectiveness or enzyme-neutral properties (lamotrigine or levetiracetam), with no expected impact on OC effectiveness. We compared conception rates in women 12-48 years of age concomitantly using OCs and enzyme-inducing drugs with rates in concomitant users of OCs and enzyme-neutral drugs. We measured conception with a validated algorithm that estimates gestational age based on pregnancy endpoints. We estimated relative and attributable risk using generalized estimating equation models after standardized mortality ratio weighting.ResultsWe identified 89,777 concomitant use episodes with adjusted contraceptive failure rates of 1.6 (95% confidence interval (CI) = 1.4, 1.8) per 100 person-years among users of enzyme-neutral drugs and 18,964 episodes with a rate of 2.3 (1.9, 2.8) among users of enzyme-inducing drugs. The relative risk of conception for enzyme-inducing group was 1.4 (1.1, 1.8), and the rate difference was 0.7 (0.2, 1.2).ConclusionsOCs in combination with antiepileptic drugs that interact with metabolic enzymes were associated with increased contraceptive failure rates. Measurement of conception in claims data had adequate accuracy to uncover a strong drug-drug interaction, offering promise for broader application in comparative effectiveness studies on hormonal contraceptives to inform clinical and regulatory decisionmaking.
| S-EPMC7850590 | biostudies-literature
Project description:Most small molecule drugs interact with unintended, often unknown, biological targets and these off-target interactions may lead to both preclinical and clinical toxic events. Undesired off-target interactions are often not detected using current drug discovery assays, such as experimental polypharmacological screens. Thus, improvement in the early identification of off-target interactions represents an opportunity to reduce safety-related attrition rates during preclinical and clinical development. In order to better identify potential off-target interactions that could be linked to predictable safety issues, a novel computational approach to predict safety-relevant interactions currently not covered was designed and evaluated. These analyses, termed Off-Target Safety Assessment (OTSA), cover more than 7,000 targets (~35% of the proteome) and > 2,46,704 preclinical and clinical alerts (as of January 20, 2019). The approach described herein exploits a highly curated training set of >1 million compounds (tracking >20 million compound-structure activity relationship/SAR data points) with known in vitro activities derived from patents, journals, and publicly available databases. This computational process was used to predict both the primary and secondary pharmacological activities for a selection of 857 diverse small molecule drugs for which extensive secondary pharmacology data are readily available (456 discontinued and 401 FDA approved). The OTSA process predicted a total of 7,990 interactions for these 857 molecules. Of these, 3,923 and 4,067 possible high-scoring interactions were predicted for the discontinued and approved drugs, respectively, translating to an average of 9.3 interactions per drug. The OTSA process correctly identified the known pharmacological targets for >70% of these drugs, but also predicted a significant number of off-targets that may provide additional insight into observed in vivo effects. About 51.5% (2,025) and 22% (900) of these predicted high-scoring interactions have not previously been reported for the discontinued and approved drugs, respectively, and these may have a potential for repurposing efforts. Moreover, for both drug categories, higher promiscuity was observed for compounds with a MW range of 300 to 500, TPSA of ~200, and clogP ≥7. This computation also revealed significantly lower promiscuity (i.e., number of confirmed off-targets) for compounds with MW > 700 and MW<200 for both categories. In addition, 15 internal small molecules with known off-target interactions were evaluated. For these compounds, the OTSA framework not only captured about 56.8% of in vitro confirmed off-target interactions, but also identified the right pharmacological targets for 14 compounds as one of the top scoring targets. In conclusion, the OTSA process demonstrates good predictive performance characteristics and represents an additional tool with utility during the lead optimization stage of the drug discovery process. Additionally, the computed physiochemical properties such as clogP (i.e., lipophilicity), molecular weight, pKa and logS (i.e., solubility) were found to be statistically different between the approved and discontinued drugs, but the internal compounds were close to the approved drugs space in most part.
| S-EPMC7931946 | biostudies-literature