The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering

BZ Zsidó, B Bayarsaikhan, R Börzsei, V Szél… - International Journal of …, 2023 - mdpi.com
Water is a key actor of various processes of nature and, therefore, molecular engineering
has to take the structural and energetic consequences of hydration into account. While the …

Uncovering water effects in protein–ligand recognition: importance in the second hydration shell and binding kinetics

W Chen, H He, J Wang, J Wang… - Physical Chemistry …, 2023 - pubs.rsc.org
Developing a ligand with high affinity for a specific protein target is essential for drug design,
and water molecules are well known to play a key role in protein–drug recognition …

tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking

DJ Hsu, RB Davidson, A Sedova… - Journal of Chemical …, 2023 - ACS Publications
A critical step in structure-based drug discovery is predicting whether and how a candidate
molecule binds to a model of a therapeutic target. However, substantial protein side chain …

Elucidation of a Thermodynamical Feature Attributed to Substrate Binding to the Prokaryotic H+/Oligopeptide Cotransporter YdgR with Calorimetric Analysis: The …

A Omori, S Sasaki, T Kikukawa, K Shimono… - Biochemistry, 2023 - ACS Publications
Here, we have elucidated the substrate recognition mechanism by a prokaryotic
H+/oligopeptide cotransporter, YdgR, using isothermal titration calorimetry. Under acidic …

WaterKit: thermodynamic profiling of protein hydration sites

J Eberhardt, S Forli - Journal of Chemical Theory and …, 2023 - ACS Publications
Water desolvation is one of the key components of the free energy of binding of small
molecules to their receptors. Thus, understanding the energetic balance of solvation and …

Virtual structure-based docking and molecular dynamics of FDA-approved drugs for the identification of potential IKKB inhibitors possessing dopaminergic activity in …

PC Gurram, S Satarker, A Nassar, J Mudgal… - Chemical Papers, 2023 - Springer
In Alzheimer's disease (AD), neuroinflammation is detrimental in causing
neurodegeneration. In the central nervous system, inhibitor of nuclear factor kappa B kinase …