Thermodynamics and kinetics of drug-target binding by molecular simulation
S Decherchi, A Cavalli - Chemical Reviews, 2020 - ACS Publications
Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
Predicting biomolecular binding kinetics: A review
Biomolecular binding kinetics including the association (k on) and dissociation (k off) rates
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …
[HTML][HTML] Trends in oral small-molecule drug discovery and product development based on product launches before and after the Rule of Five
S Stegemann, C Moreton, S Svanbäck, K Box… - Drug Discovery …, 2023 - Elsevier
Highlights•Orally delivered drug products gradually continue to exceed the Rule-of-five on
Molecular Weight and clogP.•New predictive descriptors and tools, advanced chemistry and …
Molecular Weight and clogP.•New predictive descriptors and tools, advanced chemistry and …
New approaches for computing ligand–receptor binding kinetics
Highlights•Many new approaches to computing biomolecular binding kinetics developed
recently.•Enhanced sampling simulation methods permit long-time binding kinetics to be …
recently.•Enhanced sampling simulation methods permit long-time binding kinetics to be …
Machine learning analysis of τRAMD trajectories to decipher molecular determinants of drug-target residence times
Drug-target residence times can impact drug efficacy and safety, and are therefore
increasingly being considered during lead optimization. For this purpose, computational …
increasingly being considered during lead optimization. For this purpose, computational …
Computational study of protein-ligand unbinding for enzyme engineering
SM Marques, D Bednar, J Damborsky - Frontiers in chemistry, 2019 - frontiersin.org
The computational prediction of unbinding rate constants is presently an emerging topic in
drug design. However, the importance of predicting kinetic rates is not restricted to …
drug design. However, the importance of predicting kinetic rates is not restricted to …
Harnessing big data for systems pharmacology
Systems pharmacology aims to holistically understand mechanisms of drug actions to
support drug discovery and clinical practice. Systems pharmacology modeling (SPM) is data …
support drug discovery and clinical practice. Systems pharmacology modeling (SPM) is data …
The prediction of protein–ligand unbinding for modern drug discovery
Q Zhang, N Zhao, X Meng, F Yu, X Yao… - Expert Opinion on Drug …, 2022 - Taylor & Francis
Introduction Drug–target thermodynamic and kinetic information have perennially important
roles in drug design. The prediction of protein–ligand unbinding, which can provide …
roles in drug design. The prediction of protein–ligand unbinding, which can provide …
Quantitative ranking of ligand binding kinetics with a multiscale milestoning simulation approach
Efficient prediction and ranking of small molecule binders by their kinetic (k on and k off) and
thermodynamic (Δ G) properties can be a valuable metric for drug lead optimization, as …
thermodynamic (Δ G) properties can be a valuable metric for drug lead optimization, as …
Baseline model for predicting protein–ligand unbinding kinetics through machine learning
N Amangeldiuly, D Karlov… - Journal of Chemical …, 2020 - ACS Publications
Derivation of structure–kinetics relationships can help rational design and development of
new small-molecule drug candidates with desired residence times. Efforts are now being …
new small-molecule drug candidates with desired residence times. Efforts are now being …