Triptycene walled glycoluril trimer: synthesis and recognition properties

Ndendjio, Sandra Zebaze; Liu, Wenjin; Yvanez, Nicolas; Meng, Zihui; Zavalij, Peter Y.; Isaacs, Lyle

doi:10.1039/c9nj05336k

Cited by 17 publications

(32 citation statements)

References 57 publications

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“…No significant self-association is observed for this host. 96 All of the 16 guest molecules for the host in the blinded dataset of the SAMPL7 challenge are simulated. The structures of the hosts and guests are obtained from the online server of the SAMPL7 challenge.…”

Section: Methodology and Computational Detailsmentioning

confidence: 99%

“…1. The protonation states of the guests are adjusted to match the experimental reference, 96 and a summary of the net charges of the host and guests and the experimental binding affinities are given in Table S1. As in the host-guest and protein-ligand binding cases, the corrected semi-empirical charges and the restrained electrostatic potential (RESP) charges often give similar results, here we only use the AM1-BCC 103 charge scheme.…”

Section: Methodology and Computational Detailsmentioning

confidence: 99%

“…Therefore, they serve as nice candidates for calibrating computational approaches. 93,[96][97][98] Due to the similarity between host-guest systems and protein-ligand complexes, similar free energy methods are employed to investigate the host-guest binding. For instance, equilibrium free energy methods such as umbrella sampling and the double decoupling method were used to calculate the binding free energies in the SAMPL6 host-guest cases.…”

Section: Introductionmentioning

confidence: 99%

“…100 In the newest 7 th SAMPL challenge (SAMPL7), a new TrimerTrip host is synthesized and the thermodynamic parameters of the host-guest binding systems are measured. 96 No binding pose is provided by the server of SAMPL7, 102 which indicates that the binding-pose prediction is also a challenge in the current case. Therefore, in this work, we employed the same spherical-coordinate-biased strategy to explore the space of binding poses and calculate the binding affinities of the TrimerTrip-guest systems.…”

Section: Introductionmentioning

confidence: 99%

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SAMPL7 TrimerTrip Host-Guest Binding Poses and Binding Affinities from Spherical-Coordinates-Biased Simulations

Sun¹

2020

Preprint

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Host-guest binding remains a major challenge in modern computational modelling. The newest 7<sup>th</sup> statistical assessment of the modeling of proteins and ligands (SAMPL) challenge contains a new series of host-guest systems. The TrimerTrip host binds to 16 structurally diverse guests. Previously, we have successfully employed the spherical coordinates as the collective variables coupled with the enhanced sampling technique metadynamics to enhance the sampling of the binding/unbinding event, search for possible binding poses and predict the binding affinities in all three host-guest binding cases of the 6<sup>th</sup> SAMPL challenge. In this work, we employed the same protocol to investigate the TrimerTrip host in the SAMPL7 challenge. As no binding pose is provided by the SAMPL7 host, our simulations initiate from randomly selected configurations and are proceeded long enough to obtain converged free energy estimates and search for possible binding poses. The predicted binding affinities are in good agreement with the experimental reference, and the obtained binding poses serve as a nice starting point for end-point or alchemical free energy calculations.

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Section: Methodology and Computational Detailsmentioning

confidence: 99%

Section: Methodology and Computational Detailsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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SAMPL7 TrimerTrip Host-Guest Binding Poses and Binding Affinities from Spherical-Coordinates-Biased Simulations

Sun¹

2020

Preprint

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“…Previously SAMPL challenges have included a variety of host-guest systems, but the majority of SAMPL hosts have been in the cucurbituril [58] and Gibb deep cavity cavitand (often "OctaAcid") families [59] thanks to the contributions of Lyle Isaacs and Bruce Gibb's labs. There have been several analogs of these two families since host-guest systems first appeared in SAMPL3.…”

Section: Previous Sampl Host-guest Challenges Used Similar Hostsmentioning

confidence: 99%

SAMPL7 Host-Guest Challenge Overview: Assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations

Amezcua¹,

Khoury²,

Mobley

2020

Preprint

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The SAMPL challenges focus on testing and driving progress of computational methods to help guide pharmaceutical drug discovery. However, assessment of methods for predicting binding affinities is often hampered by computational challenges such as conformational sampling, protonation state uncertainties, variation in test sets selected, and even lack of high quality experimental data. SAMPL blind challenges have thus frequently included a component focusing on host-guest binding, which removes some of these challenges while still focusing on molecular recognition. Here, we report on the results of the SAMPL7 blind prediction challenge for host-guest affinity prediction. In this study, we focused on three different host-guest categories -- a familiar deep cavity cavitand series which has been featured in several prior challenges (where we examine binding of a series of guests to two hosts), a new series of cyclodextrin derivatives which are monofunctionalized around the rim to add amino acid-like functionality (where we examine binding of a two guests to a series of hosts), and binding of a series of guests to a new acyclic TrimerTrip host which is related to previous cucurbituril hosts. Many predictions used methods based on molecular simulations, and overall success was mixed, though several methods stood out. As in SAMPL6, we find that one strategy for achieving reasonable accuracy here was to make empirical corrections to binding predictions based on previous data for host categories which have been studied well before, though this can be of limited value when new systems are included. Additionally, we found that methods using the AMOEBA polarizable force field had considerable success for the two host categories in which they participated. The new TrimerTrip system was also found to introduce some sampling problems, because multiple conformations may be relevant to binding and interconvert only slowly. Overall, results in this challenge tentatively suggest that further investigation of polarizable force fields for these challenges may be warranted.

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Acyclic Cucurbit[n]uril Receptors Function as Solid State Sequestrants for Organic Micropollutants

Perera,

Shaurya,

Baptiste

et al. 2024

Angewandte Chemie

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The accumulation of organic micropollutants (OMP) in aquatic systems is a major societal problem that can be addressed by approaches including nanofiltration, flocculation, reverse osmosis and adsorptive methods using insoluble materials (e.g. activated carbon, MOFs, nanocomposites). More recently, polymeric versions of supramolecular hosts (e.g. cyclodextrins, calixarenes, pillararenes) have been investigated as OMP sequestrants. Herein, we report our study of the use of water insoluble dimethylcatechol walled acyclic cucurbit[n]uril (CB[n]) hosts as solid state sequestrants for a panel of five OMPs. A series of hosts (H1 – H4) were synthesized by reaction of glycoluril oligomer (monomer – tetramer) with 3,6‐dimethylcatechol and fully characterized by spectroscopic means and x‐ray crystallography. The solid hosts sequester OMPs from water with removal efficiencies exceeding 90% in some cases. The removal efficiencies of the new hosts parallel the known molecular recognition properties of analogous water soluble acyclic CB[n]. OMP uptake by solid host occurs rapidly (≈120 seconds). Head‐to‐head comparison with CB[6] in batch‐mode separation and DARCO activated carbon in flow‐through separation mode show that tetramer derived host (H4) performs very well under identical conditions. The work establishes insoluble acyclic CB[n]‐type receptors as a promising new platform for OMP sequestration.

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Triptycene walled glycoluril trimer: synthesis and recognition properties

Abstract: The synthesis, characterization, and molecular recognition properties of 1 toward organic ammonium ions in water is reported.

Cited by 17 publications

References 57 publications

SAMPL7 TrimerTrip Host-Guest Binding Poses and Binding Affinities from Spherical-Coordinates-Biased Simulations

SAMPL7 TrimerTrip Host-Guest Binding Poses and Binding Affinities from Spherical-Coordinates-Biased Simulations

SAMPL7 Host-Guest Challenge Overview: Assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations

Acyclic Cucurbit[n]uril Receptors Function as Solid State Sequestrants for Organic Micropollutants

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