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SAMPL7: Host–guest binding prediction by molecular dynamics and quantum mechanics

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Abstract

Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges provide routes to compare chemical quantities determined using computational chemistry approaches to experimental measurements that are shared after the competition. For this effort, several computational methods have been used to calculate the binding energies of Octa Acid (OA) and exo-Octa Acid (exoOA) host–guest systems for SAMPL7. The initial poses for molecular dynamics (MD) were generated by molecular docking. Binding free energy calculations were performed using molecular mechanics combined with Poisson–Boltzmann or generalized Born surface area solvation (MMPBSA/MMGBSA) approaches. The factors that affect the utility of the MMPBSA/MMGBSA approaches including solvation, partial charge, and solute entropy models were also analyzed. In addition to MD calculations, quantum mechanics (QM) calculations were performed using several different density functional theory (DFT) approaches. From SAMPL6 results, B3PW91-D3 was found to overestimate binding energies though it was effective for geometry optimizations, so it was considered for the DFT geometry optimizations in the current study, with single-point energy calculations carried out with B2PLYP-D3 with double-, triple-, and quadruple-ζ level basis sets. Accounting for dispersion effects, and solvation models was deemed essential for the predictions. MMGBSA and MMPBSA correlated better to experiment when used in conjunction with an empirical/linear correction.

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Acknowledgements

We gratefully acknowledge support from the University of North Texas Academic Computing Services for the use of the UNT Research Clusters and Institute for Cyber-Enabled Research (iCER) at Michigan State University. Computational resources were provided via the NSF Major Research Instrumentation program supported by the National Science Foundation under Grant No. CHE-1531468.

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Authors and Affiliations

  1. Department of Chemistry, Michigan State University, East Lansing, MI, 48864, USA

    Yiğitcan Eken, Nuno M. S. Almeida, Cong Wang & Angela K. Wilson

  2. Department of Chemistry, University of North Texas, Denton, TX, 76201, USA

    Angela K. Wilson

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  1. Yiğitcan Eken
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Correspondence to Angela K. Wilson.

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Eken, Y., Almeida, N.M.S., Wang, C. et al. SAMPL7: Host–guest binding prediction by molecular dynamics and quantum mechanics. J Comput Aided Mol Des 35, 63–77 (2021). https://doi.org/10.1007/s10822-020-00357-3

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