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 …

Predicting biomolecular binding kinetics: A review

J Wang, HN Do, K Koirala, Y Miao - Journal of Chemical Theory …, 2023 - ACS Publications
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 …

[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 …

New approaches for computing ligand–receptor binding kinetics

NJ Bruce, GK Ganotra, DB Kokh, SK Sadiq… - Current opinion in …, 2018 - Elsevier
Highlights•Many new approaches to computing biomolecular binding kinetics developed
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

DB Kokh, T Kaufmann, B Kister… - Frontiers in molecular …, 2019 - frontiersin.org
Drug-target residence times can impact drug efficacy and safety, and are therefore
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 …

Harnessing big data for systems pharmacology

L Xie, EJ Draizen, PE Bourne - Annual review of pharmacology …, 2017 - annualreviews.org
Systems pharmacology aims to holistically understand mechanisms of drug actions to
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 …

Quantitative ranking of ligand binding kinetics with a multiscale milestoning simulation approach

BR Jagger, CT Lee, RE Amaro - The journal of physical chemistry …, 2018 - ACS Publications
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 …

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 …