DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations

The identification of physical interactions between drug candidate compounds and target biomolecules is an important process in drug discovery. Since conventional screening procedures are expensive and time consuming, computational approaches are employed to provide aid by automatically predicting n...

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Bibliographic Details
Published in:Chemical science (Cambridge) 2020-03, Vol.11 (9), p.2531-2557
Main Authors: Rifaioglu, Ahmet Sureyya, Nalbat, Esra, Atalay, Volkan, Martin, Maria Jesus, Cetin-Atalay, Rengul, Do an, Tunca
Format: Article
Language:English
Subjects:
Artificial neural networks
Biomolecules
Datasets
Molecular docking
Neural networks
Optimization
Phosphorylation
Prediction models
Proteins
Representations
Screening
Source code
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Summary:The identification of physical interactions between drug candidate compounds and target biomolecules is an important process in drug discovery. Since conventional screening procedures are expensive and time consuming, computational approaches are employed to provide aid by automatically predicting novel drug-target interactions (DTIs). In this study, we propose a large-scale DTI prediction system, DEEPScreen, for early stage drug discovery, using deep convolutional neural networks. One of the main advantages of DEEPScreen is employing readily available 2-D structural representations of compounds at the input level instead of conventional descriptors that display limited performance. DEEPScreen learns complex features inherently from the 2-D representations, thus producing highly accurate predictions. The DEEPScreen system was trained for 704 target proteins (using curated bioactivity data) and finalized with rigorous hyper-parameter optimization tests. We compared the performance of DEEPScreen against the state-of-the-art on multiple benchmark datasets to indicate the effectiveness of the proposed approach and verified selected novel predictions through molecular docking analysis and literature-based validation. Finally, JAK proteins that were predicted by DEEPScreen as new targets of a well-known drug cladribine were experimentally demonstrated in vitro on cancer cells through STAT3 phosphorylation, which is the downstream effector protein. The DEEPScreen system can be exploited in the fields of drug discovery and repurposing for in silico screening of the chemogenomic space, to provide novel DTIs which can be experimentally pursued. The source code, trained "ready-to-use" prediction models, all datasets and the results of this study are available at https://github.com/cansyl/DEEPscreen . The DEEPScreen system is composed of 704 target protein specific prediction models, each independently trained using experimental bioactivity measurements against many drug candidate small molecules, and optimized according to the binding properties of the target proteins.
ISSN:2041-6520
2041-6539
DOI:10.1039/c9sc03414e