Potential risk of drug-drug interactions with hormonal contraceptives and antiretrovirals: prevalence in women living with HIV.
ABSTRACT: Background:Family planning services are vital for women living with HIV (WLH); however, the use of concomitant antiretroviral therapy (ART) and hormonal contraceptives (HCs) may pose challenges due to the risk of potential drug-drug interactions (DDIs). The objectives of this study were to assess ART and HC use among WLH and quantify the frequency of potential DDIs between ART and HCs. Methods:This was a retrospective, observational, cohort study of WLH aged 18-55 years, prescribed ART, with at least one clinic visit from January 1, 2010 to April 30, 2014. Potential DDIs between HCs and ART were assessed using the University of Liverpool HIV Drug Interactions website (www.hiv-druginteractions.org) and categorized as 'weak potential interaction,' 'potential interaction,' or 'do not co-administer.' Results:Overall, a contraceptive method was reported in 167 (54%) of the 309 women included in the study. Of those using contraception, 73 (43.7%) reported using HCs, which was most frequently a progestin intrauterine device (n=43), progestin injection (n=17), or combination oral contraceptive pills (n=9). Out of a total of 449 ART regimens, a potential DDI was identified in 21 of 115 (18.3%) ART-HC combinations from 19 women using ART and HCs. Atazanavir/ritonavir was the most common potentially interacting ART (10, 47.6%); for HCs, these were combination oral contraceptive pills (16, 76.2%) and progestin implants (2, 9.5%). Conclusion:In this cohort, one-quarter of WLH on ART-HCs had a potential DDI. Future studies should investigate the impact of DDIs on unintended pregnancies, the side effects of DDIs, and the effects of HC DDIs on ART concentrations.
Project description:BACKGROUND:Drug-drug interactions (DDIs) are a major concern in patients' medication. It's unfeasible to identify all potential DDIs using experimental methods which are time-consuming and expensive. Computational methods provide an effective strategy, however, facing challenges due to the lack of experimentally verified negative samples. RESULTS:To address this problem, we propose a novel positive-unlabeled learning method named DDI-PULearn for large-scale drug-drug-interaction predictions. DDI-PULearn first generates seeds of reliable negatives via OCSVM (one-class support vector machine) under a high-recall constraint and via the cosine-similarity based KNN (k-nearest neighbors) as well. Then trained with all the labeled positives (i.e., the validated DDIs) and the generated seed negatives, DDI-PULearn employs an iterative SVM to identify a set of entire reliable negatives from the unlabeled samples (i.e., the unobserved DDIs). Following that, DDI-PULearn represents all the labeled positives and the identified negatives as vectors of abundant drug properties by a similarity-based method. Finally, DDI-PULearn transforms these vectors into a lower-dimensional space via PCA (principal component analysis) and utilizes the compressed vectors as input for binary classifications. The performance of DDI-PULearn is evaluated on simulative prediction for 149,878 possible interactions between 548 drugs, comparing with two baseline methods and five state-of-the-art methods. Related experiment results show that the proposed method for the representation of DDIs characterizes them accurately. DDI-PULearn achieves superior performance owing to the identified reliable negatives, outperforming all other methods significantly. In addition, the predicted novel DDIs suggest that DDI-PULearn is capable to identify novel DDIs. CONCLUSIONS:The results demonstrate that positive-unlabeled learning paves a new way to tackle the problem caused by the lack of experimentally verified negatives in the computational prediction of DDIs.
Project description:Detecting drug-drug interactions (DDI) is important because information on DDIs can help prevent adverse effects from drug combinations. Since there are many new DDI-related papers published in the biomedical domain, manually extracting DDI information from the literature is a laborious task. However, text mining can be used to find DDIs in the biomedical literature. Among the recently developed neural networks, we use a Recursive Neural Network to improve the performance of DDI extraction. Our recursive neural network model uses a position feature, a subtree containment feature, and an ensemble method to improve the performance of DDI extraction. Compared with the state-of-the-art models, the DDI detection and type classifiers of our model performed 4.4% and 2.8% better, respectively, on the DDIExtraction Challenge'13 test data. We also validated our model on the PK DDI corpus that consists of two types of DDIs data: in vivo DDI and in vitro DDI. Compared with the existing model, our detection classifier performed 2.3% and 6.7% better on in vivo and in vitro data respectively. The results of our validation demonstrate that our model can automatically extract DDIs better than existing models.
Project description:Drug⁻drug interactions (DDIs) are a leading cause of morbidity and mortality. New tools are needed to improve identification and treatment of DDIs. We conducted a randomized controlled trial to assess the clinical utility of a new test to identify DDIs and improve their management. Primary care physicians (PCPs) cared for simulated patients presenting with DDI symptoms from commonly prescribed medications and other ingestants. All physicians, in either control or one of two intervention groups, cared for six patients over two rounds of assessment. Intervention physicians were educated on the DDI test and given access to these test reports when caring for their patients in the second round. At baseline, we saw no significant differences in making the DDI diagnosis (p = 0.071) or DDI-related treatment (p = 0.640) between control and intervention arms. By round two, providers who accessed the DDI test performed significantly better in making the DDI diagnosis (+41.6%) and performing DDI-specific treatment (+12.2%) than in the previous round, and were 9.8 and 20.4 times more likely to diagnose and identify the DDI (p < 0.001 for all). The introduction of a definitive DDI test significantly increased identification, appropriate management, and counseling of DDIs among PCPs, which has the potential to improve clinical care.
Project description:Drug-drug interactions (DDIs) may cause serious side-effects that draw great attention from both academia and industry. Since some DDIs are mediated by unexpected drug-human protein interactions, it is reasonable to analyze the chemical-protein interactome (CPI) profiles of the drugs to predict their DDIs. Here we introduce the DDI-CPI server, which can make real-time DDI predictions based only on molecular structure. When the user submits a molecule, the server will dock user's molecule across 611 human proteins, generating a CPI profile that can be used as a feature vector for the pre-constructed prediction model. It can suggest potential DDIs between the user's molecule and our library of 2515 drug molecules. In cross-validation and independent validation, the server achieved an AUC greater than 0.85. Additionally, by investigating the CPI profiles of predicted DDI, users can explore the PK/PD proteins that might be involved in a particular DDI. A 3D visualization of the drug-protein interaction will be provided as well. The DDI-CPI is freely accessible at http://cpi.bio-x.cn/ddi/.
Project description:When one drug influences the level or activity of another drug this is known as a drug-drug interaction (DDI). Knowledge of such interactions is crucial for patient safety. However, the volume and content of published biomedical literature on drug interactions is expanding rapidly, making it increasingly difficult for DDIs database curators to detect and collate DDIs information manually. In this paper, we propose a single kernel-based approach to extract DDIs from biomedical literature. This novel kernel-based approach can effectively make full use of syntactic structural information of the dependency graph. In particular, our approach can efficiently represent both single subgraph topological information and the relation of two subgraphs in the dependency graph. Experimental evaluations showed that our single kernel-based approach can achieve state-of-the-art performance on the publicly available DDI corpus without exploiting multiple kernels or additional domain resources.
Project description:Despite their high potential for drug-drug interactions (DDI), clinical DDI studies of antiretroviral drugs (ARVs) are often lacking, because the full range of potential interactions cannot feasibly or pragmatically be studied, with some high-risk DDI studies also being ethically difficult to undertake. Thus, a robust method to screen and to predict the likelihood of DDIs is required. We developed a method to predict DDIs based on two parameters: the degree of metabolism by specific enzymes, such as CYP3A, and the strength of an inhibitor or inducer. These parameters were derived from existing studies utilizing paradigm substrates, inducers, and inhibitors of CYP3A to assess the predictive performance of this method by verifying predicted magnitudes of changes in drug exposure against clinical DDI studies involving ARVs. The derived parameters were consistent with the FDA classification of sensitive CYP3A substrates and the strength of CYP3A inhibitors and inducers. Characterized DDI magnitudes (n = 68) between ARVs and comedications were successfully quantified, meaning 53%, 85%, and 98% of the predictions were within 1.25-fold (0.80 to 1.25), 1.5-fold (0.66 to 1.48), and 2-fold (0.66 to 1.94) of the observed clinical data. In addition, the method identifies CYP3A substrates likely to be highly or, conversely, minimally impacted by CYP3A inhibitors or inducers, thus categorizing the magnitude of DDIs. The developed effective and robust method has the potential to support a more rational identification of dose adjustment to overcome DDIs, being particularly relevant in an HIV setting, given the treatment's complexity, high DDI risk, and limited guidance on the management of DDIs.
Project description:Adverse events resulting from drug-drug interactions (DDI) pose a serious health issue. The ability to automatically extract DDIs described in the biomedical literature could further efforts for ongoing pharmacovigilance. Most of neural networks-based methods typically focus on sentence sequence to identify these DDIs, however the shortest dependency path (SDP) between the two entities contains valuable syntactic and semantic information. Effectively exploiting such information may improve DDI extraction.In this article, we present a hierarchical recurrent neural networks (RNNs)-based method to integrate the SDP and sentence sequence for DDI extraction task. Firstly, the sentence sequence is divided into three subsequences. Then, the bottom RNNs model is employed to learn the feature representation of the subsequences and SDP, and the top RNNs model is employed to learn the feature representation of both sentence sequence and SDP. Furthermore, we introduce the embedding attention mechanism to identify and enhance keywords for the DDI extraction task. We evaluate our approach using the DDI extraction 2013 corpus. Our method is competitive or superior in performance as compared with other state-of-the-art methods. Experimental results show that the sentence sequence and SDP are complementary to each other. Integrating the sentence sequence with SDP can effectively improve the DDI extraction performance.The experimental data is available at https://github.com/zhangyijia1979/hierarchical-RNNs-model-for-DDIemail@example.com or firstname.lastname@example.org.Supplementary data are available at Bioinformatics online.
Project description:BACKGROUND:Because drug-drug interactions (DDIs) may cause adverse drug reactions or contribute to complex-disease treatments, it is important to identify DDIs before multiple-drug medications are prescribed. As the alternative of high-cost experimental identifications, computational approaches provide a much cheaper screening for potential DDIs on a large scale manner. Nevertheless, most of them only predict whether or not one drug interacts with another, but neglect their enhancive (positive) and depressive (negative) changes of pharmacological effects. Moreover, these comprehensive DDIs do not occur at random, but exhibit a weakly balanced relationship (a structural property when considering the DDI network), which would help understand how high-order DDIs work. RESULTS:This work exploits the intrinsically structural relationship to solve two tasks, including drug community detection as well as comprehensive DDI prediction in the cold-start scenario. Accordingly, we first design a balance regularized semi-nonnegative matrix factorization (BRSNMF) to partition the drugs into communities. Then, to predict enhancive and degressive DDIs in the cold-start scenario, we develop a BRSNMF-based predictive approach, which technically leverages drug-binding proteins (DBP) as features to associate new drugs (having no known DDI) with other drugs (having known DDIs). Our experiments demonstrate that BRSNMF can generate the drug communities, which exhibit more reasonable sizes, the property of weak balance as well as pharmacological significances. Moreover, they demonstrate the superiority of DBP features and the inspiring ability of the BRSNMF-based predictive approach on comprehensive DDI prediction with 94% accuracy among top-50 predicted enhancive and 86% accuracy among bottom-50 predicted degressive DDIs. CONCLUSIONS:Owing to the regularization of the weak balance property of the comprehensive DDI network into semi-nonnegative matrix factorization, our proposed BRSNMF is able to not only generate better drug communities but also provide an inspiring comprehensive DDI prediction in the cold-start scenario.
Project description:Drug-drug interaction (DDI) is a change in the effect of a drug when patient takes another drug. Characterizing DDIs is extremely important to avoid potential adverse drug reactions. We represent DDIs as a complex network in which nodes refer to drugs and links refer to their potential interactions. Recently, the problem of link prediction has attracted much consideration in scientific community. We represent the process of link prediction as a binary classification task on networks of potential DDIs. We use link prediction techniques for predicting unknown interactions between drugs in five arbitrary chosen large-scale DDI databases, namely DrugBank, KEGG, NDF-RT, SemMedDB, and Twosides. We estimated the performance of link prediction using a series of experiments on DDI networks. We performed link prediction using unsupervised and supervised approach including classification tree, k-nearest neighbors, support vector machine, random forest, and gradient boosting machine classifiers based on topological and semantic similarity features. Supervised approach clearly outperforms unsupervised approach. The Twosides network gained the best prediction performance regarding the area under the precision-recall curve (0.93 for both random forests and gradient boosting machine). The applied methodology can be used as a tool to help researchers to identify potential DDIs. The supervised link prediction approach proved to be promising for potential DDIs prediction and may facilitate the identification of potential DDIs in clinical research.
Project description:Identifying drug-drug interaction (DDI) is an important topic for the development of safe pharmaceutical drugs and for the optimization of multidrug regimens for complex diseases such as cancer and HIV. There have been about 150,000 publications on DDIs in PubMed, which is a great resource for DDI studies. In this paper, we introduced an automatic computational method for the systematic analysis of the mechanism of DDIs using MeSH (Medical Subject Headings) terms from PubMed literature. MeSH term is a controlled vocabulary thesaurus developed by the National Library of Medicine for indexing and annotating articles. Our method can effectively identify DDI-relevant MeSH terms such as drugs, proteins and phenomena with high accuracy. The connections among these MeSH terms were investigated by using co-occurrence heatmaps and social network analysis. Our approach can be used to visualize relationships of DDI terms, which has the potential to help users better understand DDIs. As the volume of PubMed records increases, our method for automatic analysis of DDIs from the PubMed database will become more accurate.