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SAMPL7 Challenge Overview: Assessing the Reliability of Polarizable and Non-Polarizable Methods for Host-Guest Binding Free Energy Calculations

preprint
submitted on 05.08.2020 and posted on 07.08.2020 by Martin Amezcua, David Mobley
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.

Funding

Advancing predictive physical modeling through focused development of model systems to drive new modeling innovations

National Institute of General Medical Sciences

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History

Email Address of Submitting Author

dmobley@uci.edu

Institution

University of California, Irvine

Country

United States

ORCID For Submitting Author

0000-0002-1083-5533

Declaration of Conflict of Interest

David Mobley serves on the advisory board of OpenEye Scientific Software and is an Open Science Fellow with Silicon Therapeutics.

Licence

Exports