From structure to the dynamic regulation of a molecular switch: A journey over 3 decades

SS Taylor, J Wu, JGH Bruystens, JC Del Rio… - Journal of Biological …, 2021 - ASBMB
structural information. For regulation of kinase activity, we focus on the cAMP-binding protein
kinase … , NMR, and millisecond molecular dynamics simulations is opening a new world for …

Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases

J Gizzio, A Thakur, A Haldane, RM Levy - Elife, 2022 - elifesciences.org
… to guide absolute binding free- energy molecular dynamics simulations of 74 protein- ligand
… ∆Greorg and ∆EPotts identified in this study reveals that the conformational landscape has a …

Complete reconstruction of dasatinib unbinding pathway from c-Src kinase by supervised molecular dynamics simulation method; assessing efficiency and …

F Sohraby, M Javaheri Moghadam… - … and Dynamics, 2022 - Taylor & Francis
simulation, the SuMD, into account in a case study, revealing the unbinding pathway of the
anticancer drug dasatinib from its target protein, the c-SRC kinase… kinetic and thermodynamic

Binding analysis using accelerated molecular dynamics simulations and future perspectives

S Pawnikar, A Bhattarai, J Wang… - … and Applications in …, 2022 - Taylor & Francis
… , thermodynamics and kinetics of biomolecular recognition. … successfully captured to the Src
protein kinase, Citation13 the β 1 … This study reveals a novel allosteric site that is expected to …

Design of novel anti-cancer drugs targeting TRKs inhibitors based 3D QSAR, molecular docking and molecular dynamics simulation

M Er-Rajy, M El Fadili, S Mujwar… - … and Dynamics, 2023 - Taylor & Francis
kinase (PLKs) and pyrazol inhibitors was performed using 3D-QSAR modeling, molecular
docking, and MD simulations … or yellow shows a positive contribution to the biological activity, …

[PDF][PDF] Discovery of Inhibitors Targeting p38γ and PLK1 Using Combined Virtual Screening, Molecular Dynamics Simulations and Biological Evaluation

Z Cheng - 2024 - researchbank.swinburne.edu.au
… The serine/threonine kinases p38y and PLK1 promote … The previous quantitative structure
activity relationship models were … The most promising compound revealed higher activity than …

Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer

SM Ajjarapu, A Tiwari, G Taj, DB Singh, S Singh… - BMC Pharmacology and …, 2021 - Springer
… This investigation revealed the … molecular docking and molecular dynamics simulation
studies on taxifolin targeting W80R mutant protein of protein kinase B/serine- threonine kinase/…

Molecular dynamics simulations and biochemical characterization of Pf14-3-3 and PfCDPK1 interaction towards its role in growth of human malaria parasite

R Jain, P Dey, S Gupta, S Pati… - Biochemical …, 2020 - portlandpress.com
revealed strong resemblance with it's counterparts from other living organisms, with overall
folds forming a clamp like structure… in regulating PfCDPK1 activity, we tested kinase activity of …

Molecular dynamic study of SARS-CoV-2 with various S protein mutations and their effect on thermodynamic properties

M Abdalla, WA Eltayb, AA El-Arabey, K Singh… - Computers in Biology …, 2022 - Elsevier
… on S protein stability and solubility through molecular dynamic (MD) simulation in a 100 ns
(ns) … Our results revealed that the SASA of all variants dramatically decreased during the …

Investigating the ibrutinib resistance mechanism of L528W mutation on Brutonʼs tyrosine kinase via molecular dynamics simulations

B Xu, L Liang, Y Jiang, Z Zhao - … of Molecular Graphics and Modelling, 2024 - Elsevier
… Impact: Molecular dynamics simulations reveal that L528W … that predicts the thermodynamic
stability changes caused by … domains that participate in kinase activity. Orange represents …