ArticleJournal of molecular recognition : JMR2014
Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics.
Article in Journal of molecular recognition : JMR, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed, 28 citations in OpenAlex.
- Triamcinolone Acetonide Produced by Bacillus velezensis YEBBR6 Exerts Antagonistic Activity Against Fusarium oxysporum f. sp. Cubense: A Computational Analysis.Molecular biotechnology · 2026Article
- A Glucose-Responsive CeO₂@GOx Nanozyme Embedded in Chitosan/PVA Hydrogel for Accelerated Diabetic Wound Healing: from Molecular Simulations toNanotheranostics · 2026Article
- Pathway Specific Unbinding Free Energy Profiles of Ritonavir Dissociation from HIV-1 Protease.Biochemistry · 2025Article
- Network-based analysis and experimental validation of identified natural compounds from Yinchen Wuling San for acute myeloid leukemia.Frontiers in pharmacology · 2025Article
- Unraveling the Molecular Mechanism of Recognition of Selected Next-Generation Antirheumatoid Arthritis Inhibitors by Janus Kinase 1.ACS omega · 2022Article
- Ritonavir and xk263 Binding-Unbinding with HIV-1 Protease: Pathways, Energy and Comparison.Life (Basel, Switzerland) · 2022Article
- Tetrahydrocurcumin Has Similar Anti-Amyloid Properties as Curcumin: In Vitro Comparative Structure-Activity Studies.Antioxidants (Basel, Switzerland) · 2021Article
- Brownian Dynamics Simulations of Biological Molecules.Trends in chemistry · 2019Article
- Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways.Biophysical journal · 2018Article
- Ligand Binding Pathways and Conformational Transitions of the HIV Protease.Biochemistry · 2018Article
- Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition.Journal of chemical theory and computation · 2018Article
- Mechanism of the Association Pathways for a Pair of Fast and Slow Binding Ligands of HIV-1 Protease.Biochemistry · 2017Article
- Understanding ligand-receptor non-covalent binding kinetics using molecular modeling.Frontiers in bioscience (Landmark edition) · 2017Review
- Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools.Catalysts (Basel, Switzerland) · 2016Article
- Revealing origin of decrease in potency of darunavir and amprenavir against HIV-2 relative to HIV-1 protease by molecular dynamics simulations.Scientific reports · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Revealing the processes of ligand-protein associations deepens our understanding of molecular recognition and binding kinetics. Hydrogen bonds (H-bonds) play a crucial role in optimizing ligand-protein interactions and ligand specificity. In addition to the formation of stable H-bonds in the final bound state, the formation of transient H-bonds during binding processes contributes binding kinetics that define a ligand as a fast or slow binder, which also affects drug action. However, the effect of forming the transient H-bonds on the kinetic properties is little understood. Guided by results from coarse-grained Brownian dynamics simulations, we used classical molecular dynamics simulations in an implicit solvent model and accelerated molecular dynamics simulations in explicit waters to show that the position and distribution of the H-bond donor or acceptor of a drug result in switching intermolecular and intramolecular H-bond pairs during ligand recognition processes. We studied two major types of HIV-1 protease ligands: a fast binder, xk263, and a slow binder, ritonavir. The slow association rate in ritonavir can be attributed to increased flexibility of ritonavir, which yields multistep transitions and stepwise entering patterns and the formation and breaking of complex H-bond pairs during the binding process. This model suggests the importance of conversions of spatiotemporal H-bonds during the association of ligands and proteins, which helps in designing inhibitors with preferred binding kinetics.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.