Applications of molecular dynamics simulations in drug discovery

S AlRawashdeh, KH Barakat - Computational Drug Discovery and Design, 2023 - Springer
In the current drug development process, molecular dynamics (MD) simulations have proven
to be very useful. This chapter provides an overview of the current applications of MD …

Structure-based prediction of hERG-related cardiotoxicity: A benchmark study

TM Creanza, P Delre, N Ancona, G Lentini… - Journal of Chemical …, 2021 - ACS Publications
Drug-induced blockade of the human ether-à-go-go-related gene (hERG) channel is today
considered the main cause of cardiotoxicity in postmarketing surveillance. Hence, several …

Graph theory-based simulation tools for protein structure networks

KF Kantelis, V Asteriou… - … Modelling Practice and …, 2022 - Elsevier
Abstract Analysis of interactions in biological systems is at the core of almost every
biological study. Being a principal tool, graph theory as a mathematical formalism, aims to …

Drug-target interactions prediction based on network topology feature representation embedded deep forest

M Lian, X Wang, W Du - Neurocomputing, 2023 - Elsevier
Identifying drug-target interactions (DTIs) is instructive in drug design and disease treatment.
Existing studies typically used the properties of nodes (drug chemical structure and protein …

Towards the design of active pharmaceutical ingredients mineralizing readily in the environment

N Puhlmann, R Mols, O Olsson, JC Slootweg… - Green …, 2021 - pubs.rsc.org
Active pharmaceutical ingredients (APIs), their metabolites, and transformation products
(TPs) occur globally in the environment. They pose a risk to both environmental and human …

Structural modeling of hERG channel–drug interactions using Rosetta

AM Emigh Cortez, KR DeMarco, K Furutani… - Frontiers in …, 2023 - frontiersin.org
The human ether-a-go-go-related gene (hERG) not only encodes a potassium-selective
voltage-gated ion channel essential for normal electrical activity in the heart but is also a …

Assessing hERG1 blockade from Bayesian machine-learning-optimized site identification by ligand competitive saturation simulations

M Mousaei, M Kudaibergenova… - Journal of chemical …, 2020 - ACS Publications
Drug-induced cardiotoxicity is a potentially lethal and yet one of the most common side
effects with the drugs in clinical use. Most of the drug-induced cardiotoxicity is associated …

TSSF-hERG: A machine-learning-based hERG potassium channel-specific scoring function for chemical cardiotoxicity prediction

J Meng, L Zhang, L Wang, S Li, D Xie, Y Zhang, H Liu - Toxicology, 2021 - Elsevier
The human ether-à-go-go-related gene (hERG) encodes the Kv11. 1 voltage-gated
potassium ion (K+) channel that conducts the rapidly activating delayed rectifier current (I Kr) …

Synthesis of 1, 3, 5-triphenyl-1, 2, 4-triazole derivatives and their neuroprotection by anti-oxidative stress and anti-inflammation and protecting BBB

Y Wang, R Su, J Chen, X Liu, J Luo, Y Lao… - European Journal of …, 2023 - Elsevier
Acute ischemic stroke (AIS) is a serious cardiovascular and cerebrovascular disease;
Oxidative stress and neuroinflammation are important factors which destroy blood-brain …

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

NR Das, T Sharma, AA Toropov… - Journal of …, 2023 - Taylor & Francis
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 …