ArticleJournal of chemical theory and computation2013
Variational Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Cucurbit[7]uril|
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 11 citations in OpenAlex.
- Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding.Journal of chemical theory and computation · 2021Article
- Testing inhomogeneous solvation theory in structure-based ligand discovery.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- "Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins.The journal of physical chemistry. B · 2017Article
- Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations.The Journal of chemical physics · 2016Article
- LS-VISM: A software package for analysis of biomolecular solvation.Journal of computational chemistry · 2015Article
- Limitations and extensions of the lock-and-key principle: differences between gas state, solution and solid state structures.International journal of molecular sciences · 2015Review
- Variational Implicit Solvation with Poisson-Boltzmann Theory.Journal of chemical theory and computation · 2014Article
- STABILITY OF A CYLINDRICAL SOLUTE-SOLVENT INTERFACE: EFFECT OF GEOMETRY, ELECTROSTATICS, AND HYDRODYNAMICS.SIAM journal on applied mathematicsArticle
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
The synthetic host cucurbit[7]uril (CB[7]) binds aromatic guests or metal complexes with ultrahigh affinity compared with that typically displayed in protein-ligand binding. Due to its small size, CB[7] serves as an ideal receptor-ligand system for developing computational methods for molecular recognition. Here, we apply the recently developed variational implicit-solvent model (VISM), numerically evaluated by the level-set method, to study hydration effects in the high-affinity binding of the B2 bicyclo[2.2.2]octane derivative to CB[7]. For the unbound host, we find that the host cavity favors the hydrated state over the dry state due to electrostatic effects. For the guest binding, we find reasonable agreement to experimental binding affinities. Dissection of the individual VISM free-energy contributions shows that the major driving forces are water-mediated hydrophobic interactions and the intrinsic (vacuum) host-guest van der Waals interactions. These findings are in line with recent experiments and molecular dynamics simulations with explicit solvent. It is expected that the level-set VISM, with further refinement on the electrostatic descriptions, can efficiently predict molecular binding and recognition in a wide range of future applications.
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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.