Machine-learning technique, QSAR and molecular dynamics for hERG–drug interactions

Abstract

One of the most well-known anti-targets defining medication cardiotoxicity is the voltage-dependent hERG K + channel, which is well-known for its crucial involvement in cardiac action potential repolarization. Torsades de Pointes, QT prolongation, and sudden death are all caused by hERG (the human Ether-à-go-go-Related Gene) inhibition. There is great interest in creating predictive computational (in silico) tools to identify and weed out potential hERG blockers early in the drug discovery process because testing for hERG liability and the traditional experimental screening are complicated, expensive and time-consuming. This study used 2D descriptors of a large curated dataset of 6766 compounds and machine learning approaches to build robust descriptor-based QSAR and predictive classification models for KCNH2 liability. Decision Tree, Random Forest, Logistic Regression, Ada Boosting, kNN, SVM, Naïve Bayes, neural network and stochastic gradient classification classifier algorithms were used to build classification models. If a compound’s IC₅₀ value was between 10 μM and less, it was classified as a blocker (hERG-positive), and if it was more, it was classified as a non-blocker (hERG-negative). Matthew’s correlation coefficient formula and F1score were applied to compare and track the developed models’ performance. Molecular docking and dynamics studies were performed to understand the cardiotoxicity relating to the hERG–gene. The hERG residues interacting after 100 ns are LEU:697, THR:708, PHE:656, HIS:674, HIS:703, TRP:705 and ASN:709 and the hERG–ligand-16 complex trajectory showed stable behaviour with lesser fluctuations in the entire simulation of 200 ns.

Communicated by Ramaswamy H. Sarma

Keywords:

• hERG
• CORALSEA software
• machine-learning techniques
• QSAR
• molecular docking
• molecular dynamics

Disclosure statement

All the authors declare that there is no conflict of interest.

Correction Statement

This article has been corrected with minor changes. These changes do not impact the academic content of the article.

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Funding

The author(s) reported there is no funding associated with the work featured in this article.