Configurational Preferences of Arylamide α‑Helix Mimetics via Alchemical Free Energy Calculations of Relative Binding Affinities

We use molecular docking and free energy calculations
to estimate
the relative free energy of binding of six arylamide compounds designed
to inhibit the hDM2–p53 interaction. We show
that using docking methods to predict or rank the binding affinity
of a series of arylamide inhibitors of the hDM2–p53
interaction is problematic. However, using free energy calculations,
we show that we can achieve levels of accuracy that can guide the
development of novel arylamide compounds. We perform alchemical free
energy calculations using the Desmond molecular dynamics package with
the same arylamide inhibitors of the hDM2–p53
system and illustrate the challenges of performing accurate free energy
calculations for realistic systems. To our knowledge, these are the
first calculations for inhibitors of the hDM2 system
that employ a full treatment of statistical mechanics including explicit
water representation and full protein flexibility. We show that mutating
three functional groups in a single transformation can be more efficient
than mutating the groups one by one if proper intermediates are used.
We also show that Hamiltonian exchanges can improve the efficiency
of the calculation compared to standard alchemical methods, with a
novel use of the phase space overlap to monitor sampling extent. We
show that, despite sampling limitations, this approach can achieve
levels of accuracy sufficient to bias further inhibitor modification
toward binding, and identifies antiparallel configurations as stable
or more stable than the parallel configurations that are typically
considered.