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Curr Pharm Des. 2018 Jun 7. doi: 10.2174/1381612824666180607124038. [Epub ahead of print]

Machine Learning-based Virtual Screening and Its Applications to Alzheimer's Drug Discovery: A Review.

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1
Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129. United States.

Abstract

BACKGROUND:

Virtual Screening (VS) has emerged as an important tool in the drug development process, as it conducts efficient in silico searches over millions of compounds, ultimately increasing yields of potential drug leads. As a subset of Artificial Intelligence (AI), Machine Learning (ML) is a powerful way of conducting VS for drug leads. ML for VS generally involves assembling a filtered training set of compounds, comprised of known actives and inactives. After training the model, it is validated and, if sufficiently accurate, used on previously unseen databases to screen for novel compounds with desired drug target binding activity.

OBJECTIVE:

The study aims to review ML-based methods used for VS and applications to Alzheimer's disease (AD) drug discovery.

METHODS:

To update the current knowledge on ML for VS, we review thorough backgrounds, explanations, and VS applications of the following ML techniques: Naïve Bayes (NB), k-Nearest Neighbors (kNN), Support Vector Machines (SVM), Random Forests (RF), and Artificial Neural Networks (ANN).

RESULTS:

All techniques have found success in VS, but the future of VS is likely to lean more heavily toward the use of neural networks - and more specifically, Convolutional Neural Networks (CNN), which are a subset of ANN that utilize convolution. We additionally conceptualize a work flow for conducting ML-based VS for potential therapeutics of for AD, a complex neurodegenerative disease with no known cure and prevention. This both serves as an example of how to apply the concepts introduced earlier in the review and as a potential workflow for future implementation.

CONCLUSION:

Different ML techniques are powerful tools for VS, and they have advantages and disadvantages albeit. ML-based VS can be applied to AD drug development.

KEYWORDS:

Alzheimer’s Disease. ; Artificial Intelligence; Artificial Neural Networks; Convolutional Neural Networks; Drug Discovery; Machine Learning; Naïve Bayes; Random Forests; Support Vector Machines; Virtual Screening; k-Nearest Neighbors

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