Molecular dynamics simulations in drug discovery and pharmaceutical development

OMH Salo-Ahen, I Alanko, R Bhadane, AMJJ Bonvin… - Processes, 2020 - mdpi.com
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

[HTML][HTML] The current understanding of KRAS protein structure and dynamics

T Pantsar - Computational and structural biotechnology journal, 2020 - Elsevier
One of the most common drivers in human cancer is the mutant KRAS protein. Not so long
ago KRAS was considered as an undruggable oncoprotein. After a long struggle, however …

Molecular dynamics simulation for mechanism elucidation of food processing and safety: State of the art

G Chen, K Huang, M Miao, B Feng… - … reviews in food …, 2019 - Wiley Online Library
Molecular dynamics (MD) simulation is a useful technique to study the interaction between
molecules and how they are affected by various processes and processing conditions. This …

Structural insights into understudied human cytochrome P450 enzymes

D Machalz, S Pach, M Bermudez, M Bureik… - Drug discovery today, 2021 - Elsevier
Human cytochrome P450 (CYP) enzymes are widely known for their pivotal role in the
metabolism of drugs and other xenobiotics as well as of endogenous chemicals. In addition …

Fentanyl family at the mu-opioid receptor: uniform assessment of binding and computational analysis

PFJ Lipiński, P Kosson, J Matalińska, P Roszkowski… - Molecules, 2019 - mdpi.com
Interactions of 21 fentanyl derivatives with μ-opioid receptor (μOR) were studied using
experimental and theoretical methods. Their binding to μOR was assessed with radioligand …

Strategies for the discovery of biased GPCR ligands

M Bermudez, TN Nguyen, C Omieczynski… - Drug Discovery …, 2019 - Elsevier
Highlights•Biased GPCR modulators provide various therapeutic benefits.•The number of
newly identified biased ligands is constantly increasing.•Understanding underlying receptor …

A molecular modeling approach to identify novel inhibitors of the major facilitator superfamily of efflux pump transporters

SG Zárate, P Morales, K Świderek, VM Bolanos-Garcia… - Antibiotics, 2019 - mdpi.com
Multidrug efflux systems play a prominent role in medicine, as they are important
contributors to bacterial antibiotic resistance. NorA is an efflux pump transporter from the …

Molecular dynamics simulations: principles, methods, and applications in protein conformational dynamics

AK Padhi, M Janežič, KYJ Zhang - Advances in protein molecular and …, 2022 - Elsevier
Molecular dynamics (MD) is a powerful computational technique that allows us to simulate
the interactions of atoms and molecules of a system over a specific period of time through …

Truly target-focused pharmacophore modeling: a novel tool for mapping intermolecular surfaces

J Mortier, P Dhakal, A Volkamer - Molecules, 2018 - mdpi.com
Pharmacophore models are an accurate and minimal tridimensional abstraction of
intermolecular interactions between chemical structures, usually derived from a group of …

GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models

P Miszta, P Pasznik, J Jakowiecki, A Sztyler… - Nucleic acids …, 2018 - academic.oup.com
Due to the involvement of G protein-coupled receptors (GPCRs) in most of the physiological
and pathological processes in humans they have been attracting a lot of attention from …