Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange Simulations

Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes

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.

Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations

We present a new release (6.0β) of the ORAC program [Marsili et al. J. Comput. Chem. 2010, 31, 1106-1116] with a hybrid OpenMP/MPI (open multiprocessing message passing interface) multilevel parallelism tailored for generalized ensemble (GE) and fast switching double annihilation (FS-DAM) nonequilibrium technology aimed at evaluating the binding free energy in drug-receptor system on high performance computing platforms. The production of the GE or FS-DAM trajectories is handled using a weak scaling parallel approach on the MPI level only, while a strong scaling force decomposition scheme is implemented for intranode computations with shared memory access at the OpenMP level. The efficiency, simplicity, and inherent parallel nature of the ORAC implementation of the FS-DAM algorithm, project the code as a possible effective tool for a second generation high throughput virtual screening in drug discovery and design. The code, along with documentation, testing, and ancillary tools, is distributed under the provisions of the General Public License and can be freely downloaded at www.chim.unifi.it/orac .

II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands

The fast switch double annihilation method (FS-DAM) provides an effective mean to the compute the binding free energies in drug-receptor systems. Here we present an application to the FK506-related ligands of the FKBP12 protein.

I. Dissociation free energies of drug–receptor systems via non-equilibrium alchemical simulations: a theoretical framework

In this contribution I critically discuss the alchemical approach for evaluating binding free energies in drug–receptor systems, placing this methodology into the broader context of non-equilibrium thermodynamics.