Dataset Information

In vitro and in silico prediction of antibacterial interaction between essential oils via graph embedding approach.

ABSTRACT: Essential oils contain a variety of volatile metabolites, and are expected to be utilized in wide fields such as antimicrobials, insect repellents and herbicides. However, it is difficult to foresee the effect of oil combinations because hundreds of compounds can be involved in synergistic and antagonistic interactions. In this research, it was developed and evaluated a machine learning method to classify types of (synergistic/antagonistic/no) antibacterial interaction between essential oils. Graph embedding was employed to capture structural features of the interaction network from literature data, and was found to improve in silico predicting performances to classify synergistic interactions. Furthermore, in vitro antibacterial assay against a standard strain of Staphylococcus aureus revealed that four essential oil pairs (Origanum compactum-Trachyspermum ammi, Cymbopogon citratus-Thujopsis dolabrata, Cinnamomum verum-Cymbopogon citratus and Trachyspermum ammi-Zingiber officinale) exhibited synergistic interaction as predicted. These results indicate that graph embedding approach can efficiently find synergistic interactions between antibacterial essential oils.

SUBMITTER: Yabuuchi H

PROVIDER: S-EPMC10622510 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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In vitro and in silico prediction of antibacterial interaction between essential oils via graph embedding approach.

Yabuuchi Hiroaki H Hayashi Kazuhito K Shigemoto Akihiko A Fujiwara Makiko M Nomura Yuhei Y Nakashima Mayumi M Ogusu Takeshi T Mori Megumi M Tokumoto Shin-Ichi SI Miyai Kazuyuki K

Scientific reports 20231102 1

Essential oils contain a variety of volatile metabolites, and are expected to be utilized in wide fields such as antimicrobials, insect repellents and herbicides. However, it is difficult to foresee the effect of oil combinations because hundreds of compounds can be involved in synergistic and antagonistic interactions. In this research, it was developed and evaluated a machine learning method to classify types of (synergistic/antagonistic/no) antibacterial interaction between essential oils. Gr ...[more]

PMID: 37919469

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Project description:BackgroundThe pharmaceutical field faces a significant challenge in validating drug target interactions (DTIs) due to the time and cost involved, leading to only a fraction being experimentally verified. To expedite drug discovery, accurate computational methods are essential for predicting potential interactions. Recently, machine learning techniques, particularly graph-based methods, have gained prominence. These methods utilize networks of drugs and targets, employing knowledge graph embedding (KGE) to represent structured information from knowledge graphs in a continuous vector space. This phenomenon highlights the growing inclination to utilize graph topologies as a means to improve the precision of predicting DTIs, hence addressing the pressing requirement for effective computational methodologies in the field of drug discovery.ResultsThe present study presents a novel approach called DTIOG for the prediction of DTIs. The methodology employed in this study involves the utilization of a KGE strategy, together with the incorporation of contextual information obtained from protein sequences. More specifically, the study makes use of Protein Bidirectional Encoder Representations from Transformers (ProtBERT) for this purpose. DTIOG utilizes a two-step process to compute embedding vectors using KGE techniques. Additionally, it employs ProtBERT to determine target-target similarity. Different similarity measures, such as Cosine similarity or Euclidean distance, are utilized in the prediction procedure. In addition to the contextual embedding, the proposed unique approach incorporates local representations obtained from the Simplified Molecular Input Line Entry Specification (SMILES) of drugs and the amino acid sequences of protein targets.ConclusionsThe effectiveness of the proposed approach was assessed through extensive experimentation on datasets pertaining to Enzymes, Ion Channels, and G-protein-coupled Receptors. The remarkable efficacy of DTIOG was showcased through the utilization of diverse similarity measures in order to calculate the similarities between drugs and targets. The combination of these factors, along with the incorporation of various classifiers, enabled the model to outperform existing algorithms in its ability to predict DTIs. The consistent observation of this advantage across all datasets underlines the robustness and accuracy of DTIOG in the domain of DTIs. Additionally, our case study suggests that the DTIOG can serve as a valuable tool for discovering new DTIs.

Project description:BackgroundCurrent approaches to identifying drug-drug interactions (DDIs), include safety studies during drug development and post-marketing surveillance after approval, offer important opportunities to identify potential safety issues, but are unable to provide complete set of all possible DDIs. Thus, the drug discovery researchers and healthcare professionals might not be fully aware of potentially dangerous DDIs. Predicting potential drug-drug interaction helps reduce unanticipated drug interactions and drug development costs and optimizes the drug design process. Methods for prediction of DDIs have the tendency to report high accuracy but still have little impact on translational research due to systematic biases induced by networked/paired data. In this work, we aimed to present realistic evaluation settings to predict DDIs using knowledge graph embeddings. We propose a simple disjoint cross-validation scheme to evaluate drug-drug interaction predictions for the scenarios where the drugs have no known DDIs.ResultsWe designed different evaluation settings to accurately assess the performance for predicting DDIs. The settings for disjoint cross-validation produced lower performance scores, as expected, but still were good at predicting the drug interactions. We have applied Logistic Regression, Naive Bayes and Random Forest on DrugBank knowledge graph with the 10-fold traditional cross validation using RDF2Vec, TransE and TransD. RDF2Vec with Skip-Gram generally surpasses other embedding methods. We also tested RDF2Vec on various drug knowledge graphs such as DrugBank, PharmGKB and KEGG to predict unknown drug-drug interactions. The performance was not enhanced significantly when an integrated knowledge graph including these three datasets was used.ConclusionWe showed that the knowledge embeddings are powerful predictors and comparable to current state-of-the-art methods for inferring new DDIs. We addressed the evaluation biases by introducing drug-wise and pairwise disjoint test classes. Although the performance scores for drug-wise and pairwise disjoint seem to be low, the results can be considered to be realistic in predicting the interactions for drugs with limited interaction information.

Dataset Information

In vitro and in silico prediction of antibacterial interaction between essential oils via graph embedding approach.

Publications

In vitro and in silico prediction of antibacterial interaction between essential oils via graph embedding approach.

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