The computational modeling of peptide inhibitors to target protein-protein binding interfaces is growing in interest as these are often too large, too shallow, and too feature-less for conventional small molecule compounds. Here, we present a rare successful application of an alchemical binding free energy method for the calculation of converged absolute binding free energies of a series of protein-peptide complexes. Specifically, we report the binding free energies of a series of cyclic peptides derived from the LEDGF/p75 protein to the integrase receptor of the HIV1 virus. The simulations recapitulate the effect of mutations relative to the wild-type binding motif of LEDGF/p75, providing structural, energetic and dynamical interpretations of the observed trends. The equilibration and convergence of the calculations are carefully analyzed. Convergence is aided by the adoption of a single-decoupling alchemical approach with implicit solvation, which circumvents the convergence difficulties of conventional double-decoupling protocols. We hereby present the single-decoupling methodology and critically evaluate its advantages and limitations. We also discuss some of the challenges and potential pitfalls of binding free energy calculations for complex molecular systems which have generally limited their applicability to the quantitative study of protein-peptide binding equilibria.

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We present a parametrized analytic statistical model of the thermodynamics of alchemical molecular binding within the solvent potential of mean force formalism. The model describes the free energy profiles of linear single-decoupling alchemical binding free energy calculations accurately. The parameters of the model, which are physically motivated, are derived by maximum likelihood inference from data obtained from alchemical molecular simulations. The validity of the model has been assessed on a set of host–guest complexes. The model faithfully reproduces both the binding free energy profiles and the probability densities of the perturbation energy as a function of the alchemical progress parameter. The model offers a rationalization for the characteristic shape of binding free energy profiles. The parameters obtained from the model are potentially useful descriptors of the association equilibrium of molecular complexes. Potential applications of the model for the classification of molecular complexes and the design of alchemical molecular simulations are envisioned.