Insights into protein–ligand interactions: mechanisms, models, and methods

X Du, Y Li, YL Xia, SM Ai, J Liang, P Sang… - International journal of …, 2016 - mdpi.com
Molecular recognition, which is the process of biological macromolecules interacting with
each other or various small molecules with a high specificity and affinity to form a specific …

Applying thermodynamic profiling in lead finding and optimization

G Klebe - Nature Reviews Drug Discovery, 2015 - nature.com
Small-molecule drug discovery involves the optimization of various physicochemical
properties of a ligand, particularly its binding affinity for its target receptor (or receptors). In …

Dynamic activation of an allosteric regulatory protein

SR Tzeng, CG Kalodimos - Nature, 2009 - nature.com
Allosteric regulation is used as a very efficient mechanism to control protein activity in most
biological processes, including signal transduction, metabolism, catalysis and gene …

The thermodynamics of protein–ligand interaction and solvation: insights for ligand design

TSG Olsson, MA Williams, WR Pitt… - Journal of molecular …, 2008 - Elsevier
Isothermal titration calorimetry is able to provide accurate information on the thermodynamic
contributions of enthalpy and entropy changes to free energies of binding. The …

Interplay between conformational entropy and solvation entropy in protein–ligand binding

ML Verteramo, O Stenstrom, MM Ignjatovic… - Journal of the …, 2019 - ACS Publications
Understanding the driving forces underlying molecular recognition is of fundamental
importance in chemistry and biology. The challenge is to unravel the binding …

Functional aspects of protein flexibility

K Teilum, JG Olsen, BB Kragelund - Cellular and Molecular Life Sciences, 2009 - Springer
Proteins are dynamic entities, and they possess an inherent flexibility that allows them to
function through molecular interactions within the cell, among cells and even between …

Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3

C Diehl, O Engstrom, T Delaine… - Journal of the …, 2010 - ACS Publications
Rational drug design is predicated on knowledge of the three-dimensional structure of the
protein− ligand complex and the thermodynamics of ligand binding. Despite the …

Monosaccharide derivatives with low‐nanomolar lectin affinity and high selectivity based on combined Fluorine–Amide, Phenyl–Arginine, Sulfur–π, and halogen bond …

FR Zetterberg, K Peterson, RE Johnsson… - …, 2018 - Wiley Online Library
The design of small and high‐affinity lectin inhibitors remains a major challenge because
the natural ligand binding sites of lectin are often shallow and have polar character. Herein …

Fundamentals of molecular modeling in drug design

MK Tripathi, S Ahmad, R Tyagi, V Dahiya… - Computer Aided Drug …, 2022 - Elsevier
The advent of high-performance computing has increased the role of computer application
as a tool for in silico experiments in all research areas, including drug discovery. This …

[HTML][HTML] Thermodynamics of ligand-protein interactions: implications for molecular design

AK Bronowska - … -Interaction Studies-Solids, Liquids and Gases, 2011 - intechopen.com
Biologically relevant macromolecules, such as proteins, do not operate as static, isolated
entities. On the contrary, they are involved in numerous interactions with other species, such …