Octa-acid (OA) and tetra- endo -methyl octa-acid (TEMOA) are deep cavity cavitands that readily form multimeric complexes with hydrophobic guests, like n -alkanes, in aqueous solution. Experimentally, OA displays a monotonic progression from monomeric to dimeric complexes with n -alkanes of increasing length, while TEMOA exhibits a non-monotonic progression from monomeric, to dimeric, to monomeric, to dimeric complexes over the same range of guest sizes. Previously we have conducted simulations demonstrating this curious behavior arises from the methyl units ringing TEMOA's portal to its hydrophobic pocket barring the possibility for two alkane chains to simultaneously bridge between two hosts in a dimer. Here we expand our prior simulation study to consider the partially methylated hosts mono- endo -methyl octa-acid, 1,3-di- endo -methyl octa-acid, and tri- endo -methyl octa-acid to examine the emergence of non-monotonic assembly behavior. Our simulations demonstrate a systematic progression of non-monotonic assembly with increasing portal methylation. This behavior is traced to the progressive destabilization of 2 : 2 complexes (two hosts assembled with two guests) rather than stabilizing other potential host/guest complexes that could be formed.
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Proximal charge effects on guest binding to a non-polar pocket
Science still does not have the ability to accurately predict the affinity that ligands have for proteins. In an attempt to address this, the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) series of blind predictive challenges is a community-wide exercise aimed at advancing computational techniques as standard predictive tools in rational drug design. In each cycle, a range of biologically relevant systems of different levels of complexity are selected to test the latest modeling methods. As part of this on-going exercise, and as a step towards understanding the important factors in context dependent guest binding, we challenged the computational community to determine the affinity of a series of negatively and positively charged guests to two constitutionally isomeric cavitand hosts: octa-acid 1 , and exo -octa acid 2 . Our affinity determinations, combined with molecular dynamics simulations, reveal asymmetries in affinities between host–guest pairs that cannot alone be explained by simple coulombic interactions, but also point to the importance of host–water interactions. Our work reveals the key facets of molecular recognition in water, emphasizes where improvements need to be made in modelling, and shed light on the complex problem of ligand-protein binding in the aqueous realm.
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- Award ID(s):
- 1805167
- PAR ID:
- 10157675
- Date Published:
- Journal Name:
- Chemical Science
- Volume:
- 11
- Issue:
- 14
- ISSN:
- 2041-6520
- Page Range / eLocation ID:
- 3656 to 3663
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Hydrophobic interactions drive the binding of nonpolar ligands to the oily pockets of proteins and supramolecular species in aqueous solution. As such, the wetting of host pockets is expected to play a critical role in determining the thermodynamics of guest binding. Here we use molecular simulations to examine the impact of pressure on the wetting and dewetting of the nonpolar pockets of a series of deep-cavity cavitands in water. The portals to the cavitand pockets are functionalized with both nonpolar (methyl) and polar (hydroxyl) groups oriented pointing either upward or inward toward the pocket. We find wetting of the pocket is favored by the hydroxyl groups and dewetting is favored by the methyl groups. The distribution of waters in the pocket is found to exhibit a two-state-like equilibrium between wet and dry states with a free energy barrier between the two states. Moreover, we demonstrate that the pocket hydration of the cavitands can be collapsed onto a unified adsorption isotherm by assuming the effective pressures within each cavitand pocket differ by a shift pressure that depends on the chemical identity and number of functional groups placed about the portal. These observations support the development of a twostate capillary evaporation model that accurately describes the equilibrium between states and naturally gives rise to the effective shift pressures observed from simulation. This work demonstrates that the hydration of host pockets can be tuned following simple design rules that in turn are expected to impact the thermodynamics of guest complexation.more » « less
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Abstract Cooperativity plays a critical role in self‐assembly and molecular recognition. A rigid aromatic oligoamide macrocycle with a cyclodirectional backbone binds with DABCO‐based cationic guests in a 2 : 1 ratio in high affinities (
K total≈1013 M−2) in the highly polar DMF. The host–guest binding also exhibits exceptionally strong positive cooperativity quantified by interaction factors α that are among the largest for synthetic host–guest systems. The unusually strong positive cooperativity, revealed by isothermal titration calorimetry (ITC) and fully corroborated by mass spectrometry, NMR and computational studies, is driven by guest‐induced stacking of the macrocycles and stabilization from the alkyl end chains of the guests, interactions that appear upon binding the second macrocycle. With its tight binding driven by extraordinary positive cooperativity, this host–guest system provides a tunable platform for studying molecular interactions and for constructing stable supramolecular assemblies. -
The presence of pharmaceuticals as microcontaminants in the environment has become a particular concern given the growing increase in water reuse and recycling to promote global sustainability of this resource. Pharmaceuticals can often undergo reversible interactions with soluble dissolved organic material such as humic acid, which may be an important factor in determining the bioavailability and effects of these compounds in the environment. In this study, high-performance affinity microcolumns containing non-covalently entrapped and immobilized humic acid are used to examine the binding strength and interactions of this agent for tetracycline, carbamazepine, ciprofloxacin, and norfloxacin, all common pharmaceutical microcontaminants known to bind humic acid. The binding constants, as measured with Aldrich humic acid, have good agreement with values reported in the literature. In addition, the effects of temperature, ionic strength, and pH on these interactions are examined with the humic acid microcolumns. This technique made it possible to determine the relative importance of electrostatic interactions vs non-polar interactions or hydrogen bonding on these binding processes. This study illustrates how affinity microcolumns can be used to screen and uniformly quantify binding by pharmaceuticals with humic acid, as well as to study the mechanisms of these interactions, with this information often being acquired in minutes and with small amounts of binding agent (~0.3 mg per microcolumn, which could be used over 200-300 experiments). Use of entrapment and affinity microcolumns can support similar research for a wide range of other microcontaminants with humic acid or alternative binding agents found in water and the environment.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/C9SC06268H
