Machine learning and deep learning strategies in drug repositioning

2021 ◽  
Vol 16 ◽  
Author(s):  
Fei Wang ◽  
Yulian Ding ◽  
Xiujuan Lei ◽  
Bo Liao ◽  
Fang-Xiang Wu
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Drug Discovery ◽  
Learning Strategies ◽  
Drug Repositioning ◽  
Multiple Data ◽  
Great Performance ◽  
Disease Associations ◽  
Traditional Drug ◽  
Future Work

: Drug repositioning is to find novel usages for existing drugs. It plays an important role in drug discovery, especially in the pre-clinical stages. Compared with the traditional drug discovery approaches, computational approaches can save time and reduce cost significantly. Since drug repositioning relies on existing drug-, disease-, and target-centric data, many machine learning (ML) approaches have been proposed to identify useful information from multiple data resources. Deep learning (DL) is a subset of ML and appears in drug repositioning much later than basic ML. Nevertheless, DL methods have shown great performance in predicting potential drugs in many studies. In this article, we review the commonly used basic ML and DL approaches in drug repositioning. Firstly, the related databases are introduced, while all of them are publicly available for researchers. Two types of pre-processing steps, calculating similarities and constructing networks based on those data, are discussed. Secondly, the basic ML and DL strategies are illustrated separately. Thirdly, we review the latest studies about the applications of basic ML and DL in identifying potential drugs through three paths: drug-disease associations, drug-drug interactions, and drug-target interactions. Finally, we discuss the limitations in current studies and suggest several directions of future work to address those limitations.

Data augmentation and transfer learning strategies for reaction prediction in low chemical data regimes

2021 ◽  
Author(s):  
Yun Zhang ◽  
Ling Wang ◽  
Xinqiao Wang ◽  
Chengyun Zhang ◽  
Jiamin Ge ◽  
...  
Keyword(s):  
Organic Chemistry ◽  
Deep Learning ◽  
Drug Discovery ◽  
Research And Development ◽  
Learning Strategies ◽  
Transfer Learning ◽  
Chemical Reactions ◽  
Data Augmentation ◽  
Learning Method ◽  
Reaction Prediction

An effective and rapid deep learning method to predict chemical reactions contributes to the research and development of organic chemistry and drug discovery.

scholarly journals Prioritizing Small Molecule as Candidates for Drug Repositioning using Machine Learning

2018 ◽  
Author(s):  
Khader Shameer ◽  
Kipp W. Johnson ◽  
Benjamin S. Glicksberg ◽  
Rachel Hodos ◽  
Ben Readhead ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Small Molecule ◽  
Chemical Space ◽  
Drug Repositioning ◽  
Chemical Properties ◽  
Support Vector ◽  
Feature Engineering ◽  
Connectivity Map ◽  
Molecular Features

ABSTRACTDrug repositioning, i.e. identifying new uses for existing drugs and research compounds, is a cost-effective drug discovery strategy that is continuing to grow in popularity. Prioritizing and identifying drugs capable of being repositioned may improve the productivity and success rate of the drug discovery cycle, especially if the drug has already proven to be safe in humans. In previous work, we have shown that drugs that have been successfully repositioned have different chemical properties than those that have not. Hence, there is an opportunity to use machine learning to prioritize drug-like molecules as candidates for future repositioning studies. We have developed a feature engineering and machine learning that leverages data from publicly available drug discovery resources: RepurposeDB and DrugBank. ChemVec is the chemoinformatics-based feature engineering strategy designed to compile molecular features representing the chemical space of all drug molecules in the study. ChemVec was trained through a variety of supervised classification algorithms (Naïve Bayes, Random Forest, Support Vector Machines and an ensemble model combining the three algorithms). Models were created using various combinations of datasets as Connectivity Map based model, DrugBank Approved compounds based model, and DrugBank full set of compounds; of which RandomForest trained using Connectivity Map based data performed the best (AUC=0.674). Briefly, our study represents a novel approach to evaluate a small molecule for drug repositioning opportunity and may further improve discovery of pleiotropic drugs, or those to treat multiple indications.

scholarly journals Developing a machine learning model to identify protein–protein interaction hotspots to facilitate drug discovery

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10381
Author(s):  
Rohit Nandakumar ◽  
Valentin Dinu
Keyword(s):  
Machine Learning ◽  
Amino Acid ◽  
Drug Discovery ◽  
Structural Information ◽  
Learning Model ◽  
Protein Protein Interaction ◽  
Drug Molecules ◽  
Machine Learning Model ◽  
Disease Associations ◽  
History Of

Throughout the history of drug discovery, an enzymatic-based approach for identifying new drug molecules has been primarily utilized. Recently, protein–protein interfaces that can be disrupted to identify small molecules that could be viable targets for certain diseases, such as cancer and the human immunodeficiency virus, have been identified. Existing studies computationally identify hotspots on these interfaces, with most models attaining accuracies of ~70%. Many studies do not effectively integrate information relating to amino acid chains and other structural information relating to the complex. Herein, (1) a machine learning model has been created and (2) its ability to integrate multiple features, such as those associated with amino-acid chains, has been evaluated to enhance the ability to predict protein–protein interface hotspots. Virtual drug screening analysis of a set of hotspots determined on the EphB2-ephrinB2 complex has also been performed. The predictive capabilities of this model offer an AUROC of 0.842, sensitivity/recall of 0.833, and specificity of 0.850. Virtual screening of a set of hotspots identified by the machine learning model developed in this study has identified potential medications to treat diseases caused by the overexpression of the EphB2-ephrinB2 complex, including prostate, gastric, colorectal and melanoma cancers which are linked to EphB2 mutations. The efficacy of this model has been demonstrated through its successful ability to predict drug-disease associations previously identified in literature, including cimetidine, idarubicin, pralatrexate for these conditions. In addition, nadolol, a beta blocker, has also been identified in this study to bind to the EphB2-ephrinB2 complex, and the possibility of this drug treating multiple cancers is still relatively unexplored.

scholarly journals Machine Learning Methods in Drug Discovery

Molecules ◽  
2020 ◽  
Vol 25 (22) ◽  
pp. 5277
Author(s):  
Lauv Patel ◽  
Tripti Shukla ◽  
Xiuzhen Huang ◽  
David W. Ussery ◽  
Shanzhi Wang
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Drug Discovery ◽  
High Throughput Screening ◽  
Drug Targets ◽  
Learning Algorithms ◽  
Machine Learning Techniques ◽  
Online Information ◽  
Drug Candidates ◽  
Novel Drug

The advancements of information technology and related processing techniques have created a fertile base for progress in many scientific fields and industries. In the fields of drug discovery and development, machine learning techniques have been used for the development of novel drug candidates. The methods for designing drug targets and novel drug discovery now routinely combine machine learning and deep learning algorithms to enhance the efficiency, efficacy, and quality of developed outputs. The generation and incorporation of big data, through technologies such as high-throughput screening and high through-put computational analysis of databases used for both lead and target discovery, has increased the reliability of the machine learning and deep learning incorporated techniques. The use of these virtual screening and encompassing online information has also been highlighted in developing lead synthesis pathways. In this review, machine learning and deep learning algorithms utilized in drug discovery and associated techniques will be discussed. The applications that produce promising results and methods will be reviewed.

scholarly journals Proposed Improvements for Automated Chemical Safety Evaluations Using In-Silico Techniques

2020 ◽  
Author(s):  
Bryan Jordan
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Chemical Space ◽  
Machine Learning Techniques ◽  
Training Dataset ◽  
Generative Adversarial Networks ◽  
Chemical Safety ◽  
Adversarial Networks ◽  
Wide Range ◽  
Traditional Drug

The vastness of chemical-space constrains traditional drug-discovery methods to the organic laws that are guiding the chemistry involved in filtering through candidates. Leveraging computing with machine-learning to intelligently generate compounds that meet a wide range of objectives can bring significant gains in time and effort needed to filter through a broad range of candidates. This paper details how the use of Generative-Adversarial-Networks, novel machine learning techniques to format the training dataset and the use of quantum computing offer new ways to expedite drug-discovery.

scholarly journals Intrusion Detection in IoT Networks Using Deep Learning Algorithm

Information ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 279 ◽  
Author(s):  
Bambang Susilo ◽  
Riri Fitri Sari
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Learning Strategies ◽  
Learning Algorithm ◽  
Human Life ◽  
Denial Of Service ◽  
The Internet ◽  
Dos Attacks ◽  
Deep Learning Algorithm ◽  
Iot Devices

The internet has become an inseparable part of human life, and the number of devices connected to the internet is increasing sharply. In particular, Internet of Things (IoT) devices have become a part of everyday human life. However, some challenges are increasing, and their solutions are not well defined. More and more challenges related to technology security concerning the IoT are arising. Many methods have been developed to secure IoT networks, but many more can still be developed. One proposed way to improve IoT security is to use machine learning. This research discusses several machine-learning and deep-learning strategies, as well as standard datasets for improving the security performance of the IoT. We developed an algorithm for detecting denial-of-service (DoS) attacks using a deep-learning algorithm. This research used the Python programming language with packages such as scikit-learn, Tensorflow, and Seaborn. We found that a deep-learning model could increase accuracy so that the mitigation of attacks that occur on an IoT network is as effective as possible.

Current Advances and Limitations of Deep Learning in Anticancer Drug Sensitivity Prediction

2020 ◽  
Vol 20 (21) ◽  
pp. 1858-1867
Author(s):  
Xian Tan ◽  
Yang Yu ◽  
Kaiwen Duan ◽  
Jingbo Zhang ◽  
Pingping Sun ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Drug Discovery ◽  
Anticancer Drug ◽  
Drug Screening ◽  
Drug Sensitivity ◽  
Data Sources ◽  
Advantages And Disadvantages ◽  
Computational Performance ◽  
Drug Sensitivity Prediction

Anticancer drug screening can accelerate drug discovery to save the lives of cancer patients, but cancer heterogeneity makes this screening challenging. The prediction of anticancer drug sensitivity is useful for anticancer drug development and the identification of biomarkers of drug sensitivity. Deep learning, as a branch of machine learning, is an important aspect of in silico research. Its outstanding computational performance means that it has been used for many biomedical purposes, such as medical image interpretation, biological sequence analysis, and drug discovery. Several studies have predicted anticancer drug sensitivity based on deep learning algorithms. The field of deep learning has made progress regarding model performance and multi-omics data integration. However, deep learning is limited by the number of studies performed and data sources available, so it is not perfect as a pre-clinical approach for use in the anticancer drug screening process. Improving the performance of deep learning models is a pressing issue for researchers. In this review, we introduce the research of anticancer drug sensitivity prediction and the use of deep learning in this research area. To provide a reference for future research, we also review some common data sources and machine learning methods. Lastly, we discuss the advantages and disadvantages of deep learning, as well as the limitations and future perspectives regarding this approach.

Precision Psychiatry: Machine learning as a tool to find new pharmacological targets

2021 ◽  
Vol 21 ◽  
Author(s):  
João Rema ◽  
Filipa Novais ◽  
Diogo Telles-Correia
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Drug Repositioning ◽  
Biological Data ◽  
New Drugs ◽  
Current Evidence ◽  
Multiple Drug ◽  
Pharmacological Targets ◽  
New Findings ◽  
Treatment Research

: There is an increasing amount of data arising from neurobehavioral sciences and medical records that cannot be adequately analyzed by traditional research methods. New drugs develop at a slow rate and seem unsatisfactory for the majority of neurobehavioral disorders. Machine learning (ML) techniques, instead, can incorporate psychopathological, computational, cognitive, and neurobiological underpinning knowledge leading to a refinement of detection, diagnosis, prognosis, treatment, research, and support. Machine and deep learning methods are currently used to accelerate the process of discovering new pharmacological targets and drugs. Objective: The present work reviews current evidence regarding the contribution of machine learning to the discovery of new drug targets. Methods: Scientific articles from PubMed, SCOPUS, EMBASE, and Web of Science Core Collection published until May 2021 were included in this review. Results : The most significant areas of research are schizophrenia, depression and anxiety, Alzheimer´s disease, and substance use disorders. ML techniques have pinpointed target gene candidates and pathways, new molecular substances, and several biomarkers regarding psychiatric disorders. Drug repositioning studies using ML have identified multiple drug candidates as promising therapeutic agents. Conclusion: Next-generation ML techniques and subsequent deep learning may power new findings regarding the discovery of new pharmacological agents by bridging the gap between biological data and chemical drug information.

scholarly journals The assessment of efficient representation of drug features using deep learning for drug repositioning

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mahroo Moridi ◽  
Marzieh Ghadirinia ◽  
Ali Sharifi-Zarchi ◽  
Fatemeh Zare-Mirakabad
Keyword(s):  
Deep Learning ◽  
Linear Models ◽  
De Novo ◽  
Drug Repositioning ◽  
Linear Method ◽  
Cost Effective ◽  
Biological Data ◽  
Non Linear ◽  
Disease Associations ◽  
Efficient Representation

Abstract Background De novo drug discovery is a time-consuming and expensive process. Nowadays, drug repositioning is utilized as a common strategy to discover a new drug indication for existing drugs. This strategy is mostly used in cases with a limited number of candidate pairs of drugs and diseases. In other words, they are not scalable to a large number of drugs and diseases. Most of the in-silico methods mainly focus on linear approaches while non-linear models are still scarce for new indication predictions. Therefore, applying non-linear computational approaches can offer an opportunity to predict possible drug repositioning candidates. Results In this study, we present a non-linear method for drug repositioning. We extract four drug features and two disease features to find the semantic relations between drugs and diseases. We utilize deep learning to extract an efficient representation for each feature. These representations reduce the dimension and heterogeneity of biological data. Then, we assess the performance of different combinations of drug features to introduce a pipeline for drug repositioning. In the available database, there are different numbers of known drug-disease associations corresponding to each combination of drug features. Our assessment shows that as the numbers of drug features increase, the numbers of available drugs decrease. Thus, the proposed method with large numbers of drug features is as accurate as small numbers. Conclusion Our pipeline predicts new indications for existing drugs systematically, in a more cost-effective way and shorter timeline. We assess the pipeline to discover the potential drug-disease associations based on cross-validation experiments and some clinical trial studies.

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