Predicting drug-target binding affinity through molecule representation block based on multi-head attention and skip connection

Predicting potential microbe-disease associations based on dual branch graph convolutional network

Studying the association between microbes and diseases not only aids in the prevention and diagnosis of diseases, but also provides crucial theoretical support for new drug development and personalized treatment. Due to the time-consuming and costly nature of laboratory-based biological tests to confirm the relationship between microbes and diseases, there is an urgent need for innovative computational frameworks to anticipate new associations between microbes and diseases. Here, we propose a novel computational approach based on a dual branch graph convolutional network (GCN) module, abbreviated as DBGCNMDA, for identifying microbe-disease associations. First, DBGCNMDA calculates the similarity matrix of diseases and microbes by integrating functional similarity and Gaussian association spectrum kernel (GAPK) similarity. Then, semantic information from different biological networks is extracted by two GCN modules from different perspectives. Finally, the scores of microbe-disease associations are predicted based on the extracted features. The main innovation of this method lies in the use of two types of information for microbe/disease similarity assessment. Additionally, we extend the disease nodes to address the issue of insufficient features due to low data dimensionality. We optimize the connectivity between the homogeneous entities using random walk with restart (RWR), and then use the optimized similarity matrix as the initial feature matrix. In terms of network understanding, we design a dual branch GCN module, namely GlobalGCN and LocalGCN, to fine-tune node representations by introducing side information, including homologous neighbour nodes. We evaluate the accuracy of the DBGCNMDA model using five-fold cross-validation (5-fold-CV) technique. The results show that the area under the receiver operating characteristic curve (AUC) and area under the precision versus recall curve (AUPR) of the DBGCNMDA model in the 5-fold-CV are 0.9559 and 0.9630, respectively. The results from the case studies using published experimental data confirm a significant number of predicted associations, indicating that DBGCNMDA is an effective tool for predicting potential microbe-disease associations.

FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe

Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure prediction. Here we propose FoldPAthreader, a protein folding pathway prediction method that uses a novel folding force field model by exploring the intrinsic relationship between protein evolution and folding from the known protein universe. Further, the folding force field is used to guide Monte Carlo conformational sampling, driving the protein chain fold into its native state by exploring potential intermediates. On 30 example targets, FoldPAthreader successfully predicts 70% of the proteins whose folding pathway is consistent with biological experimental data.

DCGAN-DTA: Predicting drug-target binding affinity with deep convolutional generative adversarial networks

BACKGROUND

In recent years, there has been a growing interest in utilizing computational approaches to predict drug-target binding affinity, aiming to expedite the early drug discovery process. To address the limitations of experimental methods, such as cost and time, several machine learning-based techniques have been developed. However, these methods encounter certain challenges, including the limited availability of training data, reliance on human intervention for feature selection and engineering, and a lack of validation approaches for robust evaluation in real-life applications.

RESULTS

To mitigate these limitations, in this study, we propose a method for drug-target binding affinity prediction based on deep convolutional generative adversarial networks. Additionally, we conducted a series of validation experiments and implemented adversarial control experiments using straw models. These experiments serve to demonstrate the robustness and efficacy of our predictive models. We conducted a comprehensive evaluation of our method by comparing it to baselines and state-of-the-art methods. Two recently updated datasets, namely the BindingDB and PDBBind, were used for this purpose. Our findings indicate that our method outperforms the alternative methods in terms of three performance measures when using warm-start data splitting settings. Moreover, when considering physiochemical-based cold-start data splitting settings, our method demonstrates superior predictive performance, particularly in terms of the concordance index.

CONCLUSION

The results of our study affirm the practical value of our method and its superiority over alternative approaches in predicting drug-target binding affinity across multiple validation sets. This highlights the potential of our approach in accelerating drug repurposing efforts, facilitating novel drug discovery, and ultimately enhancing disease treatment. The data and source code for this study were deposited in the GitHub repository, https://github.com/mojtabaze7/DCGAN-DTA . Furthermore, the web server for our method is accessible at https://dcgan.shinyapps.io/bindingaffinity/ .

HyperPCM: Robust Task-Conditioned Modeling of Drug-Target Interactions

A central problem in drug discovery is to identify the interactions between drug-like compounds and protein targets. Over the past few decades, various quantitative structure-activity relationship (QSAR) and proteo-chemometric (PCM) approaches have been developed to model and predict these interactions. While QSAR approaches solely utilize representations of the drug compound, PCM methods incorporate both representations of the protein target and the drug compound, enabling them to achieve above-chance predictive accuracy on previously unseen protein targets. Both QSAR and PCM approaches have recently been improved by machine learning and deep neural networks, that allow the development of drug-target interaction prediction models from measurement data. However, deep neural networks typically require large amounts of training data and cannot robustly adapt to new tasks, such as predicting interaction for unseen protein targets at inference time. In this work, we propose to use HyperNetworks to efficiently transfer information between tasks during inference and thus to accurately predict drug-target interactions on unseen protein targets. Our HyperPCM method reaches state-of-the-art performance compared to previous methods on multiple well-known benchmarks, including Davis, DUD-E, and a ChEMBL derived data set, and particularly excels at zero-shot inference involving unseen protein targets. Our method, as well as reproducible data preparation, is available at https://github.com/ml-jku/hyper-dti.

A comprehensive review of the recent advances on predicting drug-target affinity based on deep learning

Accurate calculation of drug-target affinity (DTA) is crucial for various applications in the pharmaceutical industry, including drug screening, design, and repurposing. However, traditional machine learning methods for calculating DTA often lack accuracy, posing a significant challenge in accurately predicting DTA. Fortunately, deep learning has emerged as a promising approach in computational biology, leading to the development of various deep learning-based methods for DTA prediction. To support researchers in developing novel and highly precision methods, we have provided a comprehensive review of recent advances in predicting DTA using deep learning. We firstly conducted a statistical analysis of commonly used public datasets, providing essential information and introducing the used fields of these datasets. We further explored the common representations of sequences and structures of drugs and targets. These analyses served as the foundation for constructing DTA prediction methods based on deep learning. Next, we focused on explaining how deep learning models, such as Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), Transformer, and Graph Neural Networks (GNNs), were effectively employed in specific DTA prediction methods. We highlighted the unique advantages and applications of these models in the context of DTA prediction. Finally, we conducted a performance analysis of multiple state-of-the-art methods for predicting DTA based on deep learning. The comprehensive review aimed to help researchers understand the shortcomings and advantages of existing methods, and further develop high-precision DTA prediction tool to promote the development of drug discovery.

HRGCNLDA: Forecasting of lncRNA-disease association based on hierarchical refinement graph convolutional neural network

Long non-coding RNA (lncRNA) is considered to be a crucial regulator involved in various human biological processes, including the regulation of tumor immune checkpoint proteins. It has great potential as both a cancer biomolecular biomarker and therapeutic target. Nevertheless, conventional biological experimental techniques are both resource-intensive and laborious, making it essential to develop an accurate and efficient computational method to facilitate the discovery of potential links between lncRNAs and diseases. In this study, we proposed HRGCNLDA, a computational approach utilizing hierarchical refinement of graph convolutional neural networks for forecasting lncRNA-disease potential associations. This approach effectively addresses the over-smoothing problem that arises from stacking multiple layers of graph convolutional neural networks. Specifically, HRGCNLDA enhances the layer representation during message propagation and node updates, thereby amplifying the contribution of hidden layers that resemble the ego layer while reducing discrepancies. The results of the experiments showed that HRGCNLDA achieved the highest AUC-ROC (area under the receiver operating characteristic curve, AUC for short) and AUC-PR (area under the precision versus recall curve, AUPR for short) values compared to other methods. Finally, to further demonstrate the reliability and efficacy of our approach, we performed case studies on the case of three prevalent human diseases, namely, breast cancer, lung cancer and gastric cancer.

Drug-target affinity prediction with extended graph learning-convolutional networks

BACKGROUND

High-performance computing plays a pivotal role in computer-aided drug design, a field that holds significant promise in pharmaceutical research. The prediction of drug-target affinity (DTA) is a crucial stage in this process, potentially accelerating drug development through rapid and extensive preliminary compound screening, while also minimizing resource utilization and costs. Recently, the incorporation of deep learning into DTA prediction and the enhancement of its accuracy have emerged as key areas of interest in the research community. Drugs and targets can be characterized through various methods, including structure-based, sequence-based, and graph-based representations. Despite the progress in structure and sequence-based techniques, they tend to provide limited feature information. Conversely, graph-based approaches have risen to prominence, attracting considerable attention for their comprehensive data representation capabilities. Recent studies have focused on constructing protein and drug molecular graphs using sequences and SMILES, subsequently deriving representations through graph neural networks. However, these graph-based approaches are limited by the use of a fixed adjacent matrix of protein and drug molecular graphs for graph convolution. This limitation restricts the learning of comprehensive feature representations from intricate compound and protein structures, consequently impeding the full potential of graph-based feature representation in DTA prediction. This, in turn, significantly impacts the models' generalization capabilities in the complex realm of drug discovery.

RESULTS

To tackle these challenges, we introduce GLCN-DTA, a model specifically designed for proficiency in DTA tasks. GLCN-DTA innovatively integrates a graph learning module into the existing graph architecture. This module is designed to learn a soft adjacent matrix, which effectively and efficiently refines the contextual structure of protein and drug molecular graphs. This advancement allows for learning richer structural information from protein and drug molecular graphs via graph convolution, specifically tailored for DTA tasks, compared to the conventional fixed adjacent matrix approach. A series of experiments have been conducted to validate the efficacy of the proposed GLCN-DTA method across diverse scenarios. The results demonstrate that GLCN-DTA possesses advantages in terms of robustness and high accuracy.

CONCLUSIONS

The proposed GLCN-DTA model enhances DTA prediction performance by introducing a novel framework that synergizes graph learning operations with graph convolution operations, thereby achieving richer representations. GLCN-DTA does not distinguish between different protein classifications, including structurally ordered and intrinsically disordered proteins, focusing instead on improving feature representation. Therefore, its applicability scope may be more effective in scenarios involving structurally ordered proteins, while potentially being limited in contexts with intrinsically disordered proteins.

CCL-DTI: contributing the contrastive loss in drug-target interaction prediction

BACKGROUND

The Drug-Target Interaction (DTI) prediction uses a drug molecule and a protein sequence as inputs to predict the binding affinity value. In recent years, deep learning-based models have gotten more attention. These methods have two modules: the feature extraction module and the task prediction module. In most deep learning-based approaches, a simple task prediction loss (i.e., categorical cross entropy for the classification task and mean squared error for the regression task) is used to learn the model. In machine learning, contrastive-based loss functions are developed to learn more discriminative feature space. In a deep learning-based model, extracting more discriminative feature space leads to performance improvement for the task prediction module.

RESULTS

In this paper, we have used multimodal knowledge as input and proposed an attention-based fusion technique to combine this knowledge. Also, we investigate how utilizing contrastive loss function along the task prediction loss could help the approach to learn a more powerful model. Four contrastive loss functions are considered: (1) max-margin contrastive loss function, (2) triplet loss function, (3) Multi-class N-pair Loss Objective, and (4) NT-Xent loss function. The proposed model is evaluated using four well-known datasets: Wang et al. dataset, Luo's dataset, Davis, and KIBA datasets.

CONCLUSIONS

Accordingly, after reviewing the state-of-the-art methods, we developed a multimodal feature extraction network by combining protein sequences and drug molecules, along with protein-protein interaction networks and drug-drug interaction networks. The results show it performs significantly better than the comparable state-of-the-art approaches.

scGIR: deciphering cellular heterogeneity via gene ranking in single-cell weighted gene correlation networks

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cellular heterogeneity through high-throughput analysis of individual cells. Nevertheless, challenges arise from prevalent sequencing dropout events and noise effects, impacting subsequent analyses. Here, we introduce a novel algorithm, Single-cell Gene Importance Ranking (scGIR), which utilizes a single-cell gene correlation network to evaluate gene importance. The algorithm transforms single-cell sequencing data into a robust gene correlation network through statistical independence, with correlation edges weighted by gene expression levels. We then constructed a random walk model on the resulting weighted gene correlation network to rank the importance of genes. Our analysis of gene importance using PageRank algorithm across nine authentic scRNA-seq datasets indicates that scGIR can effectively surmount technical noise, enabling the identification of cell types and inference of developmental trajectories. We demonstrated that the edges of gene correlation, weighted by expression, play a critical role in enhancing the algorithm's performance. Our findings emphasize that scGIR outperforms in enhancing the clustering of cell subtypes, reverse identifying differentially expressed marker genes, and uncovering genes with potential differential importance. Overall, we proposed a promising method capable of extracting more information from single-cell RNA sequencing datasets, potentially shedding new lights on cellular processes and disease mechanisms.

Recent Advances and Challenges in Protein Structure Prediction

Artificial intelligence has made significant advances in the field of protein structure prediction in recent years. In particular, DeepMind's end-to-end model, AlphaFold2, has demonstrated the capability to predict three-dimensional structures of numerous unknown proteins with accuracy levels comparable to those of experimental methods. This breakthrough has opened up new possibilities for understanding protein structure and function as well as accelerating drug discovery and other applications in the field of biology and medicine. Despite the remarkable achievements of artificial intelligence in the field, there are still some challenges and limitations. In this Review, we discuss the recent progress and some of the challenges in protein structure prediction. These challenges include predicting multidomain protein structures, protein complex structures, multiple conformational states of proteins, and protein folding pathways. Furthermore, we highlight directions in which further improvements can be conducted.

Fusing Sequence and Structural Knowledge by Heterogeneous Models to Accurately and Interpretively Predict Drug-Target Affinity

Drug-target affinity (DTA) prediction is crucial for understanding molecular interactions and aiding drug discovery and development. While various computational methods have been proposed for DTA prediction, their predictive accuracy remains limited, failing to delve into the structural nuances of interactions. With increasingly accurate and accessible structure prediction of targets, we developed a novel deep learning model, named S2DTA, to accurately predict DTA by fusing sequence features of drug SMILES, targets, and pockets and their corresponding graph structural features using heterogeneous models based on graph and semantic networks. Experimental findings underscored that complex feature representations imparted negligible enhancements to the model's performance. However, the integration of heterogeneous models demonstrably bolstered predictive accuracy. In comparison to three state-of-the-art methodologies, such as DeepDTA, GraphDTA, and DeepDTAF, S2DTA's performance became more evident. It exhibited a 25.2% reduction in mean absolute error (MAE) and a 20.1% decrease in root mean square error (RMSE). Additionally, S2DTA showed some improvements in other crucial metrics, including Pearson Correlation Coefficient (PCC), Spearman, Concordance Index (CI), and R2, with these metrics experiencing increases of 19.6%, 17.5%, 8.1%, and 49.4%, respectively. Finally, we conducted an interpretability analysis on the effectiveness of S2DTA by bidirectional self-attention mechanism. The analysis results supported that S2DTA was an effective and accurate tool for predicting DTA.

Multi-dimensional search for drug-target interaction prediction by preserving the consistency of attention distribution

Predicting drug-target interaction (DTI) is a crucial step in the process of drug repurposing and new drug development. Although the attention mechanism has been widely used to capture the interactions between drugs and targets, it mainly uses the Simplified Molecular Input Line Entry System (SMILES) and two-dimensional (2D) molecular graph features of drugs. In this paper, we propose a neural network model called MdDTI for DTI prediction. The model searches for binding sites that may interact with the target from the multiple dimensions of drug structure, namely the 2D substructures and the three-dimensional (3D) spatial structure. For the 2D substructures, we have developed a novel substructure decomposition strategy based on drug molecular graphs and compared its performance with the SMILES-based decomposition method. For the 3D spatial structure of drugs, we constructed spatial feature representation matrices for drugs based on the Cartesian coordinates of heavy atoms (without hydrogen atoms) in each drug. Finally, to ensure the search results of the model are consistent across multiple dimensions, we construct a consistency loss function. We evaluate MdDTI on four drug-target interaction datasets and three independent compound-protein affinity test sets. The results indicate that our model surpasses a series of state-of-the-art models. Case studies demonstrate that our model is capable of capturing the potential binding regions between drugs and targets, and it shows efficacy in drug repurposing. Our code is available at https://github.com/lhhu1999/MdDTI.

Attention is all you need: utilizing attention in AI-enabled drug discovery

Recently, attention mechanism and derived models have gained significant traction in drug development due to their outstanding performance and interpretability in handling complex data structures. This review offers an in-depth exploration of the principles underlying attention-based models and their advantages in drug discovery. We further elaborate on their applications in various aspects of drug development, from molecular screening and target binding to property prediction and molecule generation. Finally, we discuss the current challenges faced in the application of attention mechanisms and Artificial Intelligence technologies, including data quality, model interpretability and computational resource constraints, along with future directions for research. Given the accelerating pace of technological advancement, we believe that attention-based models will have an increasingly prominent role in future drug discovery. We anticipate that these models will usher in revolutionary breakthroughs in the pharmaceutical domain, significantly accelerating the pace of drug development.

GPCNDTA: Prediction of drug-target binding affinity through cross-attention networks augmented with graph features and pharmacophores

Drug-target affinity prediction is a challenging task in drug discovery. The latest computational models have limitations in mining edge information in molecule graphs, accessing to knowledge in pharmacophores, integrating multimodal data of the same biomolecule and realizing effective interactions between two different biomolecules. To solve these problems, we proposed a method called Graph features and Pharmacophores augmented Cross-attention Networks based Drug-Target binding Affinity prediction (GPCNDTA). First, we utilized the GNN module, the linear projection unit and self-attention layer to correspondingly extract features of drugs and proteins. Second, we devised intramolecular and intermolecular cross-attention to respectively fuse and interact features of drugs and proteins. Finally, the linear projection unit was applied to gain final features of drugs and proteins, and the Multi-Layer Perceptron was employed to predict drug-target binding affinity. Three major innovations of GPCNDTA are as follows: (i) developing the residual CensNet and the residual EW-GCN to correspondingly extract features of drug and protein graphs, (ii) regarding pharmacophores as a new type of priors to heighten drug-target affinity prediction performance, and (iii) devising intramolecular and intermolecular cross-attention, in which the intramolecular cross-attention realizes the effective fusion of different modal data related to the same biomolecule, and the intermolecular cross-attention fulfills the information interaction between two different biomolecules in attention space. The test results on five benchmark datasets imply that GPCNDTA achieves the best performance compared with state-of-the-art computational models. Besides, relying on ablation experiments, we proved effectiveness of GNN modules, pharmacophores and two cross-attention strategies in improving the prediction accuracy, stability and reliability of GPCNDA. In case studies, we applied GPCNDTA to predict binding affinities between 3C-like proteinase and 185 drugs, and observed that most binding affinities predicted by GPCNDTA are close to corresponding experimental measurements.

E2EDA: Protein Domain Assembly Based on End-to-End Deep Learning

With the development of deep learning, almost all single-domain proteins can be predicted at experimental resolution. However, the structure prediction of multi-domain proteins remains a challenge. Achieving end-to-end protein domain assembly and further improving the accuracy of the full-chain modeling by accurately predicting inter-domain orientation while improving the assembly efficiency will provide significant insights into structure-based drug discovery. In this work, we propose an End-to-End Domain Assembly method based on deep learning, named E2EDA. We first develop RMNet, an EfficientNetV2-based deep learning model that fuses multiple features using an attention mechanism to predict inter-domain rigid motion. Then, the predicted rigid motions are transformed into inter-domain spatial transformations to directly assemble the full-chain model. Finally, the scoring strategy RMscore is designed to select the best model from multiple assembled models. The experimental results show that the average TM-score of the model assembled by E2EDA on the benchmark set (282) is 0.827, which is better than those of other domain assembly methods SADA (0.792) and DEMO (0.730). Meanwhile, on our constructed multi-domain data set from AlphaFold DB, the model reassembled by E2EDA is 7.0% higher in TM-score compared to the full-chain model predicted by AlphaFold2, indicating that E2EDA can capture more accurate inter-domain orientations to improve the quality of the model predicted by AlphaFold2. Furthermore, compared to SADA and AlphaFold2, E2EDA reduced the average runtime on the benchmark by 64.7% and 19.2%, respectively, indicating that E2EDA can significantly improve assembly efficiency through an end-to-end approach. The online server is available at http://zhanglab-bioinf.com/E2EDA.

Machine learning-based model for accurate identification of druggable proteins using light extreme gradient boosting

The identification of druggable proteins (DPs) is significant for the development of new drugs, personalized medicine, understanding of disease mechanisms, drug repurposing, and economic benefits. By identifying new druggable targets, researchers can develop new therapies for a range of diseases, leading to better patient outcomes. Identification of DPs by machine learning strategies is more efficient and cost-effective than conventional methods. In this study, a computational predictor, namely Drug-LXGB, is introduced to enhance the identification of DPs. Features are discovered by composition, transition, and distribution (CTD), composition of K-spaced amino acid pair (CKSAAP), pseudo-position-specific scoring matrix (PsePSSM), and a novel descriptor, called multi-block pseudo amino acid composition (MB-PseAAC). The dimensions of CTD, CKSAAP, PsePSSM, and MB-PseAAC are integrated and utilized the sequential forward selection as feature selection algorithm. The best characteristics are provided by random forest, extreme gradient boosting, and light eXtreme gradient boosting (LXGB). The predictive analysis of these learning methods is measured via 10-fold cross-validation. The LXGB-based model secures the highest results than other existing predictors. Our novel protocol will perform an active role in designing novel drugs and would be fruitful to explore the potential target. This study will help better to capture a more universal view of a potential target.Communicated by Ramaswamy H. Sarma.

PTBGRP: predicting phage-bacteria interactions with graph representation learning on microbial heterogeneous information network

Identifying the potential bacteriophages (phage) candidate to treat bacterial infections plays an essential role in the research of human pathogens. Computational approaches are recognized as a valid way to predict bacteria and target phages. However, most of the current methods only utilize lower-order biological information without considering the higher-order connectivity patterns, which helps to improve the predictive accuracy. Therefore, we developed a novel microbial heterogeneous interaction network (MHIN)-based model called PTBGRP to predict new phages for bacterial hosts. Specifically, PTBGRP first constructs an MHIN by integrating phage-bacteria interaction (PBI) and six bacteria-bacteria interaction networks with their biological attributes. Then, different representation learning methods are deployed to extract higher-level biological features and lower-level topological features from MHIN. Finally, PTBGRP employs a deep neural network as the classifier to predict unknown PBI pairs based on the fused biological information. Experiment results demonstrated that PTBGRP achieves the best performance on the corresponding ESKAPE pathogens and PBI dataset when compared with state-of-art methods. In addition, case studies of Klebsiella pneumoniae and Staphylococcus aureus further indicate that the consideration of rich heterogeneous information enables PTBGRP to accurately predict PBI from a more comprehensive perspective. The webserver of the PTBGRP predictor is freely available at http://120.77.11.78/PTBGRP/.

Deciphering ligand-receptor-mediated intercellular communication based on ensemble deep learning and the joint scoring strategy from single-cell transcriptomic data

BACKGROUND

Cell-cell communication in a tumor microenvironment is vital to tumorigenesis, tumor progression and therapy. Intercellular communication inference helps understand molecular mechanisms of tumor growth, progression and metastasis.

METHODS

Focusing on ligand-receptor co-expressions, in this study, we developed an ensemble deep learning framework, CellComNet, to decipher ligand-receptor-mediated cell-cell communication from single-cell transcriptomic data. First, credible LRIs are captured by integrating data arrangement, feature extraction, dimension reduction, and LRI classification based on an ensemble of heterogeneous Newton boosting machine and deep neural network. Next, known and identified LRIs are screened based on single-cell RNA sequencing (scRNA-seq) data in certain tissues. Finally, cell-cell communication is inferred by incorporating scRNA-seq data, the screened LRIs, a joint scoring strategy that combines expression thresholding and expression product of ligands and receptors.

RESULTS

The proposed CellComNet framework was compared with four competing protein-protein interaction prediction models (PIPR, XGBoost, DNNXGB, and OR-RCNN) and obtained the best AUCs and AUPRs on four LRI datasets, elucidating the optimal LRI classification ability. CellComNet was further applied to analyze intercellular communication in human melanoma and head and neck squamous cell carcinoma (HNSCC) tissues. The results demonstrate that cancer-associated fibroblasts highly communicate with melanoma cells and endothelial cells strong communicate with HNSCC cells.

CONCLUSIONS

The proposed CellComNet framework efficiently identified credible LRIs and significantly improved cell-cell communication inference performance. We anticipate that CellComNet can contribute to anticancer drug design and tumor-targeted therapy.

AADB: A Manually Collected Database for Combinations of Antibiotics With Adjuvants

Antimicrobial resistance is a global public health concern. The lack of innovations in antibiotic development has led to renewed interest in antibiotic adjuvants. However, there is no database to collect antibiotic adjuvants. Herein, we build a comprehensive database named Antibiotic Adjuvant DataBase (AADB) by manually collecting relevant literature. Specifically, AADB includes 3,035 combinations of antibiotics with adjuvants, covering 83 antibiotics, 226 adjuvants, and 325 bacterial strains. AADB provides user-friendly interfaces for searching and downloading. Users can easily obtain these datasets for further analysis. In addition, we also collected related datasets (e.g., chemogenomic and metabolomic data) and proposed a computational strategy to dissect these datasets. As a test case, we identified 10 candidates for minocycline, and 6 of 10 candidates are the known adjuvants that synergize with minocycline to inhibit the growth of E. coli BW25113. We hope that AADB can help users to identify effective antibiotic adjuvants. AADB is freely available at http://www.acdb.plus/AADB.

MOKPE: drug-target interaction prediction via manifold optimization based kernel preserving embedding

BACKGROUND

In many applications of bioinformatics, data stem from distinct heterogeneous sources. One of the well-known examples is the identification of drug-target interactions (DTIs), which is of significant importance in drug discovery. In this paper, we propose a novel framework, manifold optimization based kernel preserving embedding (MOKPE), to efficiently solve the problem of modeling heterogeneous data. Our model projects heterogeneous drug and target data into a unified embedding space by preserving drug-target interactions and drug-drug, target-target similarities simultaneously.

RESULTS

We performed ten replications of ten-fold cross validation on four different drug-target interaction network data sets for predicting DTIs for previously unseen drugs. The classification evaluation metrics showed better or comparable performance compared to previous similarity-based state-of-the-art methods. We also evaluated MOKPE on predicting unknown DTIs of a given network. Our implementation of the proposed algorithm in R together with the scripts that replicate the reported experiments is publicly available at https://github.com/ocbinatli/mokpe .

SAELGMDA: Identifying human microbe-disease associations based on sparse autoencoder and LightGBM

Introduction

Identification of complex associations between diseases and microbes is important to understand the pathogenesis of diseases and design therapeutic strategies. Biomedical experiment-based Microbe-Disease Association (MDA) detection methods are expensive, time-consuming, and laborious.

Methods

Here, we developed a computational method called SAELGMDA for potential MDA prediction. First, microbe similarity and disease similarity are computed by integrating their functional similarity and Gaussian interaction profile kernel similarity. Second, one microbe-disease pair is presented as a feature vector by combining the microbe and disease similarity matrices. Next, the obtained feature vectors are mapped to a low-dimensional space based on a Sparse AutoEncoder. Finally, unknown microbe-disease pairs are classified based on Light Gradient boosting machine.

Results

The proposed SAELGMDA method was compared with four state-of-the-art MDA methods (MNNMDA, GATMDA, NTSHMDA, and LRLSHMDA) under five-fold cross validations on diseases, microbes, and microbe-disease pairs on the HMDAD and Disbiome databases. The results show that SAELGMDA computed the best accuracy, Matthews correlation coefficient, AUC, and AUPR under the majority of conditions, outperforming the other four MDA prediction models. In particular, SAELGMDA obtained the best AUCs of 0.8358 and 0.9301 under cross validation on diseases, 0.9838 and 0.9293 under cross validation on microbes, and 0.9857 and 0.9358 under cross validation on microbe-disease pairs on the HMDAD and Disbiome databases. Colorectal cancer, inflammatory bowel disease, and lung cancer are diseases that severely threat human health. We used the proposed SAELGMDA method to find possible microbes for the three diseases. The results demonstrate that there are potential associations between Clostridium coccoides and colorectal cancer and one between Sphingomonadaceae and inflammatory bowel disease. In addition, Veillonella may associate with autism. The inferred MDAs need further validation.

Conclusion

We anticipate that the proposed SAELGMDA method contributes to the identification of new MDAs.