Abstract
Recent improvements to the free energy perturbation (FEP) calculations, especially FEP+ , established their utility for pharmaceutical lead optimization. Herein, we propose a modified version of the FEP/REST (i.e., replica exchange with solute tempering) sampling protocol, based on detail studies on several targets by probing a large number of perturbations with different sampling schemes. Improved FEP+ binding affinity predictions for regular flexible-loop motions and considerable structural changes can be obtained by extending the prior to REST (pre-REST) sampling time from 0.24 ns/λ to 5 ns/λ and 2 × 10 ns/λ, respectively. With this new protocol, much more precise ∆∆G values of the individual perturbations, including the sign of the transformations and decreased error were obtained. We extended the REST simulations from 5 ns to 8 ns to achieve reasonable free energy convergence. Implementing REST to the entire ligand as opposed to solely the perturbed region, and also some important flexible protein residues (pREST region) in the ligand binding domain (LBD) has considerably improved the FEP+ results in most of the studied cases. Preliminary molecular dynamics (MD) runs were useful for establishing the correct binding mode of the compounds and thus precise alignment for FEP+ . Our improved protocol may further increase the FEP+ accuracy.
Highlights
free energy perturbation (FEP) remains insufficient in several aspects and requires improvement
Our sampling protocol can be divided into two sub-protocols which are useful in different cases: (1) the 5-ns pre-REST and 8-ns REST simulation protocol typically provides reasonable results when either an X-ray structure is available or there are no significant structural rearrangements, whereas (2) the 2 × 10-ns pre-REST sampling per lambda is more suitable for systems in which there are significant structural changes
Based on the obtained results it can be concluded that for more significant protein structural changes the longer sampling time is a better option and our results showed that the optimal time is 2 × 10 ns pre-REST and 8 ns REST runs
Summary
Detection of the most likely ligand binding mode, the presence of multiple stable binding conformations, insufficient equilibration, and determining an adequate sampling time (especially when significant protein side chain and backbone residue flexibility is possible) are the most critical aspects of FEP, and have been recently reviewed in detail[8]. These problems can be at least partially resolved by execution of reasonably long (≈100–300 ns) preliminary MD simulations, such an approach is often underutilized in applied simulations[8,9,10]. We have developed our FEP+ modified protocol based on one ligand-protein system and tested it on four different protein systems
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