Peptide Drug Design Using Alchemical Free Energy Calculation: An Application and Validation on Agonists of Ghrelin Receptor

With recent large-scale applications and validations,
the relative binding free energy (RBFE) calculated using alchemical
free energy methods has been proven to be an accurate measure to probe
the binding of small-molecule drug candidates. On the other hand,
given the flexibility of peptides, it is of great interest to find
out whether sufficient sampling could be achieved within the typical
time scale of such calculation, and a similar level of accuracy could
be reached for peptide drugs. However, the systematic evaluation of
such calculations on protein–peptide systems has been less
reported. Most reported studies of peptides were restricted to a limited
number of data points or lacking experimental support. To demonstrate
the applicability of the alchemical free energy method for protein–peptide
systems in a typical real-world drug discovery project, we report
an application of the thermodynamic integration (TI) method to the
RBFE calculation of ghrelin receptor and its peptide agonists. Along
with the calculation, the synthesis and in vitro EC50 activity
of relamorelin and 17 new peptide derivatives were also reported.
A cost-effective criterion to determine the data collection time was
proposed for peptides in the TI simulation. The average of three TI
repeats yielded a mean absolute error of 0.98 kcal/mol and Pearson’s
correlation coefficient (R) of 0.77 against the experimental
free energy derived from the in vitro EC50 activity, showing
good repeatability of the proposed method and a slightly better agreement
than the results obtained from the arbitrary time frames up to 20
ns. Although it is limited by having one target and a deduced binding
pose, we hope that this study can add some insights into alchemical
free energy calculation of protein–peptide systems, providing
theoretical assistance to the development of peptide drugs.