We apply the Alchemical Transfer Method (ATM) and a bespoke fixed partial charge force field to the SAMPL9 bCD host-guest binding free energy prediction challenge that comprises a combination of complexes formed between five phenothiazine guests and two cyclodextrin hosts. Multiple chemical forms, competing binding poses, and computational modeling challenges pose significant obstacles to obtaining reliable computational predictions for these systems. The phenothiazine guests exist in solution as racemic mixtures of enantiomers related by nitrogen inversions that bind the hosts in various binding poses, each requiring an individual free energy analysis. Due to the large size of the guests and the conformational reorganization of the hosts, which prevent a direct absolute binding free energy route, binding free energies are obtained by a series of absolute and relative binding alchemical steps for each chemical species in each binding pose. Metadynamics-accelerated conformational sampling was found to be necessary to address the poor convergence of some numerical estimates affected by conformational trapping. Despite these challenges, our blinded predictions quantitatively reproduced the experimental affinities for the beta-cyclodextrin host and, to a lesser extent, those with a methylated derivative. The work illustrates the challenges of obtaining reliable free energy data in in-silico drug design for even seemingly simple systems and introduces some of the technologies available to tackle them.
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Synthetic β-Cyclodextrin Dimers for Squaraine Binding: Effect of Host Architecture on Photophysical Properties, Aggregate Formation and Chemical Reactivity: Synthetic β-Cyclodextrin Dimers for Squaraine Binding: Effect of Host Architecture on Photophysical Properties, Aggregate Formation and Chemical React
- NSF-PAR ID:
- 10077573
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- European Journal of Organic Chemistry
- Volume:
- 2018
- Issue:
- 17
- ISSN:
- 1434-193X
- Page Range / eLocation ID:
- 1964 to 1974
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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