Prediction Of Drug Combinations Research Articles

A weighted Bayesian integration method for predicting drug combination using heterogeneous data

BackgroundIn the management of complex diseases, the strategic adoption of combination therapy has gained considerable prominence. Combination therapy not only holds the potential to enhance treatment efficacy but also to alleviate the side effects caused by excessive use of a single drug. Presently, the exploration of combination therapy encounters significant challenges due to the vast spectrum of potential drug combinations, necessitating the development of efficient screening strategies.MethodsIn this study, we propose a prediction scoring method that integrates heterogeneous data using a weighted Bayesian method for drug combination prediction. Heterogeneous data refers to different types of data related to drugs, such as chemical, pharmacological, and target profiles. By constructing a multiplex drug similarity network, we formulate new features for drug pairs and propose a novel Bayesian-based integration scheme with the introduction of weights to integrate information from various sources. This method yields support strength scores for drug combinations to assess their potential effectiveness.ResultsUpon comprehensive comparison with other methods, our method shows superior performance across multiple metrics, including the Area Under the Receiver Operating Characteristic Curve, accuracy, precision, and recall. Furthermore, literature validation shows that many top-ranked drug combinations based on the support strength score, such as goserelin and letrozole, have been experimentally or clinically validated for their effectiveness.ConclusionsOur findings have significant clinical and practical implications. This new method enhances the performance of drug combination predictions, enabling effective pre-screening for trials and, thereby, benefiting clinical treatments. Future research should focus on developing new methods for application in various scenarios and for integrating diverse data sources.

Predicting Effective Drug Combinations for Cancer Treatment Using a Graph-Based Approach

Drug combination therapy, involving the use of two or more drugs, has been widely employed to treat complex diseases such as cancer. It enhances therapeutic efficacy, reduces drug resistance, and minimizes side effects. However, traditional methods to identify effective drug combinations are time-consuming, costly, and less efficient than computational methods. Therefore, developing computational approaches to predict drug combinations has become increasingly important.In this paper, we developed the Random Walk with Restart for Drug Combination (RWRDC) model to predict effective drug combinations for cancer therapy. The RWRDC model offers a quantitative mathematical method for predicting the potential effective drug combinations. Cross-validation results indicate that the RWRDC model outperforms other predictive models, particularly in breast, colorectal, and lung cancer predictions across various performance metrics. We have theoretically proven the convergence of its algorithm and provided an explanation for the algorithm's rationality. A targeted case study on breast cancer further highlights the capability of RWRDC to identify effective drug combinations. These findings highlight our model as a novel and effective tool for discovering potential effective drug combinations, offering new possibilities in therapy. Additionally, the graph-based framework of RWRDC holds potential for predicting drug combinations in other complex diseases, expanding its utility in the medical field.

MMFSyn: A Multimodal Deep Learning Model for Predicting Anticancer Synergistic Drug Combination Effect.

Combination therapy aims to synergistically enhance efficacy or reduce toxic side effects and has widely been used in clinical practice. However, with the rapid increase in the types of drug combinations, identifying the synergistic relationships between drugs remains a highly challenging task. This paper proposes a novel deep learning model MMFSyn based on multimodal drug data combined with cell line features. Firstly, to ensure the full expression of drug molecular features, multiple modalities of drugs, including Morgan fingerprints, atom sequences, molecular diagrams, and atomic point cloud data, are extracted using SMILES. Secondly, for different modal data, a Bi-LSTM, gMLP, multi-head attention mechanism, and multi-scale GCNs are comprehensively applied to extract the drug feature. Then, it selects appropriate omics features from gene expression and mutation omics data of cancer cell lines to construct cancer cell line features. Finally, these features are combined to predict the synergistic anti-cancer drug combination effect. The experimental results verify that MMFSyn has significant advantages in performance compared to other popular methods, with a root mean square error of 13.33 and a Pearson correlation coefficient of 0.81, which indicates that MMFSyn can better capture the complex relationship between multimodal drug combinations and omics data, thereby improving the synergistic drug combination prediction.

PiscesCSM: prediction of anticancer synergistic drug combinations

While drug combination therapies are of great importance, particularly in cancer treatment, identifying novel synergistic drug combinations has been a challenging venture. Computational methods have emerged in this context as a promising tool for prioritizing drug combinations for further evaluation, though they have presented limited performance, utility, and interpretability. Here, we propose a novel predictive tool, piscesCSM, that leverages graph-based representations to model small molecule chemical structures to accurately predict drug combinations with favourable anticancer synergistic effects against one or multiple cancer cell lines. Leveraging these insights, we developed a general supervised machine learning model to guide the prediction of anticancer synergistic drug combinations in over 30 cell lines. It achieved an area under the receiver operating characteristic curve (AUROC) of up to 0.89 on independent non-redundant blind tests, outperforming state-of-the-art approaches on both large-scale oncology screening data and an independent test set generated by AstraZeneca (with more than a 16% improvement in predictive accuracy). Moreover, by exploring the interpretability of our approach, we found that simple physicochemical properties and graph-based signatures are predictive of chemotherapy synergism. To provide a simple and integrated platform to rapidly screen potential candidate pairs with favourable synergistic anticancer effects, we made piscesCSM freely available online at https://biosig.lab.uq.edu.au/piscescsm/ as a web server and API. We believe that our predictive tool will provide a valuable resource for optimizing and augmenting combinatorial screening libraries to identify effective and safe synergistic anticancer drug combinations.Scientific contributionThis work proposes piscesCSM, a machine-learning-based framework that relies on well-established graph-based representations of small molecules to identify and provide better predictive accuracy of syngenetic drug combinations. Our model, piscesCSM, shows that combining physiochemical properties with graph-based signatures can outperform current architectures on classification prediction tasks. Furthermore, implementing our tool as a web server offers a user-friendly platform for researchers to screen for potential synergistic drug combinations with favorable anticancer effects against one or multiple cancer cell lines.

Insight into Mantle Cell Lymphoma Pathobiology, Diagnosis, and Treatment Using Network-Based and Drug-Repurposing Approaches.

Mantle cell lymphoma (MCL) is a rare, incurable, and aggressive B-cell non-Hodgkin lymphoma (NHL). Early MCL diagnosis and treatment is critical and puzzling due to inter/intra-tumoral heterogeneity and limited understanding of the underlying molecular mechanisms. We developed and applied a multifaceted analysis of selected publicly available transcriptomic data of well-defined MCL stages, integrating network-based methods for pathway enrichment analysis, co-expression module alignment, drug repurposing, and prediction of effective drug combinations. We demonstrate the "butterfly effect" emerging from a small set of initially differentially expressed genes, rapidly expanding into numerous deregulated cellular processes, signaling pathways, and core machineries as MCL becomes aggressive. We explore pathogenicity-related signaling circuits by detecting common co-expression modules in MCL stages, pointing out, among others, the role of VEGFA and SPARC proteins in MCL progression and recommend further study of precise drug combinations. Our findings highlight the benefit that can be leveraged by such an approach for better understanding pathobiology and identifying high-priority novel diagnostic and prognostic biomarkers, drug targets, and efficacious combination therapies against MCL that should be further validated for their clinical impact.

Prediction of cancer drug combinations based on multidrug learning and cancer expression information injection

Compared with patients with common diseases, cancer patients usually have a more fragile cellular microenvironment and more complex or varied complications. Therefore, to meet treatment needs while also keeping the body in a state of balance between resistance and protection, there is an urgent need for the large-scale accurate identification of effective cancer drug combinations. Inspired by many approaches to drug molecule representation learning and cancer-related gene recognition, we propose a feature fusion model in this paper. The model can combine the molecular representation of drugs with the representation of target genes containing cancer information. It is a means to infuse specific disease information into drugs to guide drug combination prediction for specific cancers. Experimental results show that our method has achieved outstanding results in terms of predictive performance across seven common cancers, such as colorectal adenocarcinoma. For instance, in the case of osteosarcoma, the model achieved an AUROC of 0.9246. Additionally, excellent results were obtained in terms of running time and model complexity. New pairs of effective drug combinations can be mined for each of them, and out-of-sample predictions can be verified against relevant databases. This demonstrates that the feature fusion model can make full and convenient use of the existing advanced feature extraction technology and effectively promote the realization of precision therapy. In addition, we integrated a cancer drug combination dataset constructed from anticancer drugs. All entries in this dataset are standardized and uniformly identified, containing a wealth of information for the search of experts in related fields.

TRLS-04. EARLY INSIGHTS FROM PNOC027: PERSONALIZED TREATMENT APPROACHES BASED ON REAL-TIME DRUG SCREENING AND GENOMIC TESTING IN PEDIATRIC AND ADOLESCENT PATIENTS WITH RECURRENT MEDULLOBLASTOMA

Abstract BACKGROUND PNOC027, a clinical trial conducted by the Pediatric Neuro-Oncology Consortium (PNOC), explores a precision medicine strategy with up to four FDA-approved agents integrating real-time drug screening with whole exome DNA and RNA sequencing to guide personalized treatment approaches for children and young adults with relapsed medulloblastoma. METHODS Freshly isolated tumor cells from patients undergo high-throughput drug screening, evaluating responses to 232 clinically available compounds over 72 hours. In vitro drug responses are integrated with tumor genomic and transcriptomic data to predict drug combinations for each patient. Drugs are prioritized based on blood-brain barrier permeability, patient age, prior treatments, and other co-morbidities. Correlative studies include the collection of blood to assess circulating tumor DNA (ctDNA) before surgery and during treatment. Health-related quality of life (HRQOL) assessments will also be collected during therapy. RESULTS To date, nine patients have been enrolled. Eight of these have successfully completed real time drug screening with a median turnaround of 7 days from sample receipt. One patient was excluded due to ineligible (non-medulloblastoma) pathology after enrollment. Seven of these had whole exome sequencing, and six had RNA sequencing. Tumor board recommendations were rendered within 21 business days from the date of surgery. Among the diverse drug classes evaluated, histone deacetylase (HDAC) inhibitors, proteasome inhibitors, anthracyclines, DNA crosslinkers, and kinase inhibitors showed the most robust in vitro responses. Six patients received the recommended regimens, experiencing tolerable (grade 1/2) toxicities. Two patients succumbed to disease prior to therapy initiation, three exhibited disease progression while on therapy, and three remain on therapy. CONCLUSION PNOC027 demonstrates preliminary feasibility of real-time drug screening combined with DNA/RNA sequencing to inform targeted therapy selection in clinically relevant timeframes and with potential for disease response.

Accurate prediction of drug combination risk levels based on relational graph convolutional network and multi-head attention

BackgroundAccurately identifying the risk level of drug combinations is of great significance in investigating the mechanisms of combination medication and adverse reactions. Most existing methods can only predict whether there is an interaction between two drugs, but cannot directly determine their accurate risk level.MethodsIn this study, we propose a multi-class drug combination risk prediction model named AERGCN-DDI, utilizing a relational graph convolutional network with a multi-head attention mechanism. Drug-drug interaction events with varying risk levels are modeled as a heterogeneous information graph. Attribute features of drug nodes and links are learned based on compound chemical structure information. Finally, the AERGCN-DDI model is proposed to predict drug combination risk level based on heterogenous graph neural network and multi-head attention modules.ResultsTo evaluate the effectiveness of the proposed method, five-fold cross-validation and ablation study were conducted. Furthermore, we compared its predictive performance with baseline models and other state-of-the-art methods on two benchmark datasets. Empirical studies demonstrated the superior performances of AERGCN-DDI.ConclusionsAERGCN-DDI emerges as a valuable tool for predicting the risk levels of drug combinations, thereby aiding in clinical medication decision-making, mitigating severe drug side effects, and enhancing patient clinical prognosis.

Deep learning for predicting synergistic drug combinations: State‐of‐the‐arts and future directions

AbstractCombination therapy has emerged as an efficacy strategy for treating complex diseases. Its potential to overcome drug resistance and minimize toxicity makes it highly desirable. However, the vast number of potential drug pairs presents a significant challenge, rendering exhaustive clinical testing impractical. In recent years, deep learning‐based methods have emerged as promising tools for predicting synergistic drug combinations. This review aims to provide a comprehensive overview of applying diverse deep‐learning architectures for drug combination prediction. This review commences by elucidating the quantitative measures employed to assess drug combination synergy. Subsequently, we delve into the various deep‐learning methods currently employed for drug combination prediction. Finally, the review concludes by outlining the key challenges facing deep learning approaches and proposes potential challenges for future research.

MMSyn: A New Multimodal Deep Learning Framework for Enhanced Prediction of Synergistic Drug Combinations.

Combination therapy is a promising strategy for the successful treatment of cancer. The large number of possible combinations, however, mean that it is laborious and expensive to screen for synergistic drug combinations in vitro. Nevertheless, because of the availability of high-throughput screening data and advances in computational techniques, deep learning (DL) can be a useful tool for the prediction of synergistic drug combinations. In this study, we proposed a multimodal DL framework, MMSyn, for the prediction of synergistic drug combinations. First, features embedded in the drug molecules were extracted: structure, fingerprint, and string encoding. Then, gene expression data, DNA copy number, and pathway activity were used to describe cancer cell lines. Finally, these processed features were integrated using an attention mechanism and an interaction module and then input into a multilayer perceptron to predict drug synergy. Experimental results showed that our method outperformed five state-of-the-art DL methods and three traditional machine learning models for drug combination prediction. We verified that MMSyn achieved superior performance in stratified cross-validation settings using both the drug combination and cell line data. Moreover, we performed a set of ablation experiments to illustrate the effectiveness of each component and the efficacy of our model. In addition, our visual representation and case studies further confirmed the effectiveness of our model. All results showed that MMSyn can be used as a powerful tool for the prediction of synergistic drug combinations.

Metabolic models predict fotemustine and the combination of eflornithine/rifamycin and adapalene/cannabidiol for the treatment of gliomas.

Gliomas are the most common type of malignant brain tumors, with glioblastoma multiforme (GBM) having a median survival of 15months due to drug resistance and relapse. The treatment of gliomas relies on surgery, radiotherapy and chemotherapy. Only 12 anti-brain tumor chemotherapies (AntiBCs), mostly alkylating agents, have been approved so far. Glioma subtype-specific metabolic models were reconstructed to simulate metabolite exchanges, in silico knockouts and the prediction of drug and drug combinations for all three subtypes. The simulations were confronted with literature, high-throughput screenings (HTSs), xenograft and clinical trial data to validate the workflow and further prioritize the drug candidates. The three subtype models accurately displayed different degrees of dependencies toward glutamine and glutamate. Furthermore, 33 single drugs, mainly antimetabolites and TXNRD1-inhibitors, as well as 17 drug combinations were predicted as potential candidates for gliomas. Half of these drug candidates have been previously tested in HTSs. Half of the tested drug candidates reduce proliferation in cell lines and two-thirds in xenografts. Most combinations were predicted to be efficient for all three glioma types. However, eflornithine/rifamycin and cannabidiol/adapalene were predicted specifically for GBM and low-grade glioma, respectively. Most drug candidates had comparable efficiency in preclinical tests, cerebrospinal fluid bioavailability and mode-of-action to AntiBCs. However, fotemustine and valganciclovir alone and eflornithine and celecoxib in combination with AntiBCs improved the survival compared to AntiBCs in two-arms, phase I/II and higher glioma clinical trials. Our work highlights the potential of metabolic modeling in advancing glioma drug discovery, which accurately predicted metabolic vulnerabilities, repurposable drugs and combinations for the glioma subtypes.

A review on graph neural networks for predicting synergistic drug combinations

Combinational therapies with synergistic effects provide a powerful treatment strategy for tackling complex diseases, particularly malignancies. Discovering these synergistic combinations, often involving various compounds and structures, necessitates exploring a vast array of compound pairings. However, practical constraints such as cost, feasibility, and complexity hinder exhaustive in vivo and in vitro experimentation. In recent years, machine learning methods have made significant inroads in pharmacology. Among these, Graph Neural Networks (GNNs) have gained increasing attention in drug discovery due to their ability to represent complex molecular structures as networks, capture vital structural information, and seamlessly handle diverse data types. This review aims to provide a comprehensive overview of various GNN models developed for predicting effective drug combinations, examining the limitations and strengths of different models, and comparing their predictive performance. Additionally, we discuss the datasets used for drug synergism prediction and the extraction of drug-related information as predictive features. By summarizing the state-of-the-art GNN-driven drug combination prediction, this review aims to offer valuable insights into the promising field of computational pharmacotherapy.

Predicting drug synergy using a network propagation inspired machine learning framework.

Combination therapy is a promising strategy for cancers, increasing therapeutic options and reducing drug resistance. Yet, systematic identification of efficacious drug combinations is limited by the combinatorial explosion caused by a large number of possible drug pairs and diseases. At present, machine learning techniques have been widely applied to predict drug combinations, but most studies rely on the response of drug combinations to specific cell lines and are not entirely satisfactory in terms of mechanism interpretability and model scalability. Here, we proposed a novel network propagation-based machine learning framework to predict synergistic drug combinations. Based on the topological information of a comprehensive drug-drug association network, we innovatively introduced an affinity score between drug pairs as one of the features to train machine learning models. We applied network-based strategy to evaluate their therapeutic potential to different cancer types. Finally, we identified 17 specific-, 21 general- and 40 broad-spectrum antitumor drug combinations, in which 69% drug combinations were validated by vitro cellular experiments, 83% drug combinations were validated by literature reports and 100% drug combinations were validated by biological function analyses. By quantifying the network relationships between drug targets and cancer-related driver genes in the human protein-protein interactome, we show the existence of four distinct patterns of drug-drug-disease relationships. We also revealed that 32 biological pathways were correlated with the synergistic mechanism of broad-spectrum antitumor drug combinations. Overall, our model offers a powerful scalable screening framework for cancer treatments.

Deep Drug Synergy Prediction Network Using Modified Triangular Mutation-Based Differential Evolution.

Drug combination therapy is crucial in cancer treatment, but accurately predicting drug synergy remains a challenge due to the complexity of drug combinations. Machine learning and deep learning models have shown promise in drug combination prediction, but they suffer from issues such as gradient vanishing, overfitting, and parameter tuning. To address these problems, the deep drug synergy prediction network, named as EDNet is proposed that leverages a modified triangular mutation-based differential evolution algorithm. This algorithm evolves the initial connection weights and architecture-related attributes of the deep bidirectional mixture density network, improving its performance and addressing the aforementioned issues. EDNet automatically extracts relevant features and provides conditional probability distributions of output attributes. The performance of EDNet is evaluated over two well-known drug synergy datasets, NCI-ALMANAC and deep-synergy. The results demonstrate that EDNet outperforms the competing models. EDNet facilitates efficient drug interactions, enhancing the overall effectiveness of drug combinations for improved cancer treatment outcomes.

Network-based prediction of anti-cancer drug combinations.

Drug combinations have emerged as a promising therapeutic approach in cancer treatment, aimed at overcoming drug resistance and improving the efficacy of monotherapy regimens. However, identifying effective drug combinations has traditionally been time-consuming and often dependent on chance discoveries. Therefore, there is an urgent need to explore alternative strategies to support experimental research. In this study, we propose network-based prediction models to identify potential drug combinations for 11 types of cancer. Our approach involves extracting 55,299 associations from literature and constructing human protein interactomes for each cancer type. To predict drug combinations, we measure the proximity of drug-drug relationships within the network and employ a correlation clustering framework to detect functional communities. Finally, we identify 61,754 drug combinations. Furthermore, we analyze the network configurations specific to different cancer types and identify 30 key genes and 21 pathways. The performance of these models is subsequently assessed through in vitro assays, which exhibit a significant level of agreement. These findings represent a valuable contribution to the development of network-based drug combination design strategies, presenting potential solutions to overcome drug resistance and enhance cancer treatment outcomes.

MDNNSyn: A Multi-Modal Deep Learning Framework for Drug Synergy Prediction.

Synergistic drug combination prediction tasks based on the computational models have been widely studied and applied in the cancer field. However, most of models only consider the interactions between drug pairs and specific cell lines, without taking into account the multiple biological relationships of drug-drug and cell line-cell line that also largely affect synergistic mechanisms. To this end, here we propose a multi-modal deep learning framework, termed MDNNSyn, which adequately applies multi-source information and trains multi-modal features to infer potential synergistic drug combinations. MDNNSyn extracts topology modality features by implementing the multi-layer hypergraph neural network on drug synergy hypergraph and constructs semantic modality features through similarity strategy. A multi-modal fusion network layer with gated neural network is then employed for synergy score prediction. MDNNSyn is compared to five classic and state-of-the-art prediction methods on DrugCombDB and Oncology-Screen datasets. The model achieves area under the curve (AUC) scores of 0.8682 and 0.9013 on two datasets, an improvement of 3.70% and 2.71% over the second-best model. Case study indicates that MDNNSyn is capable of detecting potential synergistic drug combinations.

Predicting anticancer synergistic drug combinations based on multi-task learning

BackgroundThe discovery of anticancer drug combinations is a crucial work of anticancer treatment. In recent years, pre-screening drug combinations with synergistic effects in a large-scale search space adopting computational methods, especially deep learning methods, is increasingly popular with researchers. Although achievements have been made to predict anticancer synergistic drug combinations based on deep learning, the application of multi-task learning in this field is relatively rare. The successful practice of multi-task learning in various fields shows that it can effectively learn multiple tasks jointly and improve the performance of all the tasks.MethodsIn this paper, we propose MTLSynergy which is based on multi-task learning and deep neural networks to predict synergistic anticancer drug combinations. It simultaneously learns two crucial prediction tasks in anticancer treatment, which are synergy prediction of drug combinations and sensitivity prediction of monotherapy. And MTLSynergy integrates the classification and regression of prediction tasks into the same model. Moreover, autoencoders are employed to reduce the dimensions of input features.ResultsCompared with the previous methods listed in this paper, MTLSynergy achieves the lowest mean square error of 216.47 and the highest Pearson correlation coefficient of 0.76 on the drug synergy prediction task. On the corresponding classification task, the area under the receiver operator characteristics curve and the area under the precision–recall curve are 0.90 and 0.62, respectively, which are equivalent to the comparison methods. Through the ablation study, we verify that multi-task learning and autoencoder both have a positive effect on prediction performance. In addition, the prediction results of MTLSynergy in many cases are also consistent with previous studies.ConclusionOur study suggests that multi-task learning is significantly beneficial for both drug synergy prediction and monotherapy sensitivity prediction when combining these two tasks into one model. The ability of MTLSynergy to discover new anticancer synergistic drug combinations noteworthily outperforms other state-of-the-art methods. MTLSynergy promises to be a powerful tool to pre-screen anticancer synergistic drug combinations.

Computational Approach Based on Independent Drug Action Identifies Clinically Relevant Combinations for Acute Myeloid Leukemia

Background Acute myeloid leukemia (AML) is clinically and genetically heterogenous due to complex co-mutation landscape. Combination therapy has shown effectiveness in overcoming tumor heterogeneity and acquired resistance across multiple cancers including AML. However, the discovery of novel combinations has traditionally relied on cell line-based measurements that often fail clinically due to inter- and intra-tumor heterogeneity of patients. To address this challenge of finding clinically relevant combination therapy for AML, we applied the independent drug action (IDA) principle (Palmer & Sorger, 2017) to computationally predict drug combinations using ex vivo monotherapy responses measured in primary AML patient specimens (n > 1000). Methods We utilized the ex vivo drug sensitivity testing (DST) of primary AML samples from three studies; 1. FPMTB (Malani et al. 2021), 164 patient responses to 515 single agents; 2. Beat-AML (Tyner et al. 2018), 579 patient responses to 166 single agents; 3. Oregon Health & Science University (OSHU), 596 patient responses to 51 single agents and 170 2-drug combinations (Figure 1A). To summarize the multiparametric dose-response relationship into a single metric, drug sensitivity score (DSS) (Yadav et al. 2014) was calculated from the dose-response cell viability data of the samples using the BREEZE pipeline (Potdar et al. 2020) to derive monotherapy efficacy. We modified IDACombo package (Ling & Huang, 2020) to predict the mean combination DSS of every pairwise combination. IDAComboscore was calculated for each predicted combination to determine if it is more efficacious than its constituent monotherapies. The top hits from predicted combinations were selected by filtering for combinations with mean DSS in the top 10 th percentile, and positive IDAComboscore. These combinations were then ranked in descending order of IDAComboscore. For validation, Spearman correlation was applied to compare the predicted DSS against ex vivo DST-derived DSS of 170 combinations from the OSHU dataset. Results By applying IDA-based prediction on FPMTB and Beat-AML datasets, we identified that the mean combination DSS exceeded monotherapy DSS (p < 2.2x10 -6, Wilcoxon rank-sum test), suggesting that the predicted combination would outperform monotherapy. After accounting for monotherapies that displayed pan-toxicity across healthy samples and primary AML samples (mean DSS > 95 th percentile), we found venetoclax as the top combination partner of the top 100 most effective predicted combinations (FPMTB, n = 33; Beat-AML, n = 35). We further interrogated the makeup of venetoclax-based combinations and found kinase inhibitors (PI3Ki, MEKi, mTORi), and epigenetic modifiers (BETi, HDACi) as common partners. A total of 8 (FPMTB) and 18 (Beat-AML) out of these 100 combinations were made of FDA-approved drugs (both partners). Next, we investigated the robustness of the predictions across 2 datasets, and we found 1767 overlapping combinations with a strong correlation between their predicted mean DSS (Spearman ρ = 0.74, p < 2.2x10 -6). We finally validated the performance of IDA predictions using ex vivo DST data of 170 unique combinations from 596 primary AML samples. We found that the predicted DSS values of the 170 combinations strongly correlated with the actual ex vivo DST-derived combination DSS (Spearman ρ = 0.76, p < 2.2x10 -6, Figure 1B). Using 75 th percentile of DSS distribution as effective combination cutoff, the approach showed an accuracy of 84.7%. We then asked if disease status of patients affected prediction accuracy and found that IDA approach successfully predicted effective combinations for patients at diagnosis as well as at relapse (diagnosis ρ = 0.74 vs relapse ρ = 0.73). Conclusion We have computationally identified and validated clinically actionable drug combinations for AML using ex vivo monotherapy responses from >1000 tumor specimens based on IDA principle. Irrespective of pharmacological interaction, IDA-based combinations are more efficacious than single drugs in AML primary tumors. Our approach enables the major advantage of identifying effective combinations for the entire patient population as an alternative to personalized combinations. Further associations with genetic makeup and transcriptomics signature can be leveraged to identify suitable combinations.

Review of Predicting Synergistic Drug Combinations.

The prediction of drug combinations is of great clinical significance. In many diseases, such as high blood pressure, diabetes, and stomach ulcers, the simultaneous use of two or more drugs has shown clear efficacy. It has greatly reduced the progression of drug resistance. This review presents the latest applications of methods for predicting the effects of drug combinations and the bioactivity databases commonly used in drug combination prediction. These studies have played a significant role in developing precision therapy. We first describe the concept of synergy. we study various publicly available databases for drug combination prediction tasks. Next, we introduce five algorithms applied to drug combinatorial prediction, which include traditional machine learning methods, deep learning methods, mathematical methods, systems biology methods and search algorithms. In the end, we sum up the difficulties encountered in prediction models.

EDST: a decision stump based ensemble algorithm for synergistic drug combination prediction

IntroductionThere are countless possibilities for drug combinations, which makes it expensive and time-consuming to rely solely on clinical trials to determine the effects of each possible drug combination. In order to screen out the most effective drug combinations more quickly, scholars began to apply machine learning to drug combination prediction. However, most of them are of low interpretability. Consequently, even though they can sometimes produce high prediction accuracy, experts in the medical and biological fields can still not fully rely on their judgments because of the lack of knowledge about the decision-making process.Related workDecision trees and their ensemble algorithms are considered to be suitable methods for pharmaceutical applications due to their excellent performance and good interpretability. We review existing decision trees or decision tree ensemble algorithms in the medical field and point out their shortcomings.MethodThis study proposes a decision stump (DS)-based solution to extract interpretable knowledge from data sets. In this method, a set of DSs is first generated to selectively form a decision tree (DST). Different from the traditional decision tree, our algorithm not only enables a partial exchange of information between base classifiers by introducing a stump exchange method but also uses a modified Gini index to evaluate stump performance so that the generation of each node is evaluated by a global view to maintain high generalization ability. Furthermore, these trees are combined to construct an ensemble of DST (EDST).ExperimentThe two-drug combination data sets are collected from two cell lines with three classes (additive, antagonistic and synergistic effects) to test our method. Experimental results show that both our DST and EDST perform better than other methods. Besides, the rules generated by our methods are more compact and more accurate than other rule-based algorithms. Finally, we also analyze the extracted knowledge by the model in the field of bioinformatics.ConclusionThe novel decision tree ensemble model can effectively predict the effect of drug combination datasets and easily obtain the decision-making process.