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 …

Fludarabine, a potential DNA-dependent RNA polymerase inhibitor, as a prospective drug against monkeypox virus: A computational approach

HN Altayb - Pharmaceuticals, 2022 - mdpi.com
Monkeypox is a zoonotic contagious disease that has recently re-emerged in different
countries worldwide. Due to the lack of an effective treatment that eliminates the virus, there …

A hybrid structure-based machine learning approach for predicting kinase inhibition by small molecules

C Liu, P Kutchukian, ND Nguyen… - Journal of Chemical …, 2023 - ACS Publications
Kinases have been the focus of drug discovery programs for three decades leading to over
70 therapeutic kinase inhibitors and biophysical affinity measurements for over 130,000 …

Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states

J Zeng, Y Tao, TJ Giese, DM York - The Journal of chemical physics, 2023 - pubs.aip.org
Modern semiempirical electronic structure methods have considerable promise in drug
discovery as universal “force fields” that can reliably model biological and drug-like …

Developing an implicit solvation machine learning model for molecular simulations of ionic media

A Coste, E Slejko, J Zavadlav… - Journal of chemical …, 2023 - ACS Publications
Molecular dynamics (MD) simulations of biophysical systems require accurate modeling of
their native environment, ie, aqueous ionic solution, as it critically impacts the structure and …

Systematic computational strategies for identifying protein targets and lead discovery

A Kataria, A Srivastava, DD Singh, S Haque… - RSC Medicinal …, 2024 - pubs.rsc.org
Computational algorithms and tools have retrenched the drug discovery and development
timeline. The applicability of computational approaches has gained immense relevance …

Discovery of Nonretinoid Inhibitors of CRBP1: Structural and Dynamic Insights for Ligand-Binding Mechanisms

J Plau, CE Morgan, Y Fedorov, S Banerjee… - ACS Chemical …, 2023 - ACS Publications
The dysregulation of retinoid metabolism has been linked to prevalent ocular diseases
including age-related macular degeneration and Stargardt disease. Modulating retinoid …

Phytochemical Analysis and Evaluation of Antioxidant and Antimicrobial Properties of Essential Oils and Seed Extracts of Anethum graveolens from Southern …

N Hadi, A Drioiche, EM Bouchra, S Baammi… - Pharmaceuticals, 2024 - mdpi.com
Anethum graveolens is an aromatic plant traditionally used as an antispasmodic and
carminative. The objective of this study is to analyze the chemical composition of the …

Structure-based virtual screening and molecular dynamics studies to explore potential natural inhibitors against 3C protease of foot-and-mouth disease virus

S Sahoo, HK Lee, D Shin - Frontiers in Veterinary Science, 2024 - frontiersin.org
Foot-and-mouth disease (FMD) is a highly infectious animal disease caused by foot-and-
mouth disease virus (FMDV) and primarily infects cloven-hoofed animals such as cattle …

Design of ionic liquids containing glucose and choline as drug carriers, finding the link between QM and MD studies

S Kalhor, A Fattahi - Scientific Reports, 2022 - nature.com
Designing drug delivery systems for therapeutic compounds whose receptors are located in
the cytosol of cells is challenging as a bilayer cell membrane is negatively charged. The …