Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design

Challenges of docking in large, flexible and promiscuous binding sites

After decades of work, the correct determination of the binding mode of a small molecule into a target protein is still a challenging problem, whose difficulty depends on: (i) the sizes of the binding site and the ligand; (ii) the flexibility of both interacting partners, and (iii) the differential solvation of bound and unbound partners. We have evaluated the performance of standard rigid(receptor)/flexible(ligand) docking approaches with respect to last-generation fully flexible docking methods to obtain reasonable poses in a very challenging case: soluble Epoxide Hydrolase (sEH), a flexible protein showing different binding sites. We found that full description of the flexibility of both protein and ligand and accurate description of solvation leads to significant improvement in the ability of docking to reproduce well known binding modes, and at the same time capture the intrinsic binding promiscuity of the protein.

Molecular dynamics simulations: advances and applications

Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.

CSAR Benchmark of Flexible MedusaDock in Affinity Prediction and Nativelike Binding Pose Selection

While molecular docking with both ligand and receptor flexibilities can help capture conformational changes upon binding, correct ranking of nativelike binding poses and accurate estimation of binding affinities remains a major challenge. In addition to the commonly used scoring approach with intermolecular interaction energies, we included the contribution of intramolecular energies changes upon binding in our flexible docking method, MedusaDock. In CSAR 2013-2014 binding prediction benchmark exercises, the new scoring function MScomplex was found to better recapitulate experimental binding affinities and correctly identify ligand-binding sequences from decoy receptors. Our further analysis with the DUD data sets indicates significant improvement of virtual screening enrichment using the new scoring function when compared to the previous intermolecular energy based scoring method. Our postanalysis also suggests a new approach to select nativelike poses in the clustering-based pose ranking approach by MedusaDock. Since the calculation of intramolecular energy changes and clustering-based pose ranking and selection are not MedusaDock specific, we expect a broad application in force-field based estimation of binding affinities and pose ranking using flexible ligand-receptor docking.

Improvements, trends, and new ideas in molecular docking: 2012-2013 in review

Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher-level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods.

SEABED: Small molEcule activity scanner weB servicE baseD

Motivation: The SEABED web server integrates a variety of docking and QSAR techniques in a user-friendly environment. SEABED goes beyond the basic docking and QSAR web tools and implements extended functionalities like receptor preparation, library editing, flexible ensemble docking, hybrid docking/QSAR experiments or virtual screening on protein mutants. SEABED is not a monolithic workflow tool but Software as a Service platform.

Availability and implementation: SEABED is a free web server available athttp://www.bsc.es/SEABED. No registration is required.

Contact:ramon.goni@bsc.es

Supplementary information:Supplementary data are available atBioinformatics online.

A theoretical view of protein dynamics

Proteins are fascinating supramolecular structures, which are able to recognize ligands transforming binding information into chemical signals. They can transfer information across the cell, can catalyse complex chemical reactions, and are able to transform energy into work with much more efficiency than any human engine. The unique abilities of proteins are tightly coupled with their dynamic properties, which are coded in a complex way in the sequence and carefully refined by evolution. Despite its importance, our experimental knowledge of protein dynamics is still rather limited, and mostly derived from theoretical calculations. I will review here, in a systematic way, the current state-of-the-art theoretical approaches to the study of protein dynamics, emphasizing the most recent advances, examples of use and the expected lines of development in the near future.

Molecular dynamics of class A β-lactamases-effects of substrate binding

The effects of substrate binding on class A β-lactamase dynamics were studied using molecular dynamics simulations of two model enzymes; 40 100-ns trajectories of the free and substrate-bound forms of TEM-1 (with benzylpenicillin) and PSE-4 (with carbenicillin) were recorded (totaling 4.0 μs). Substrates were parameterized with the CHARMM General Force Field. In both enzymes, the Ω loop exhibits a marked flexibility increase upon substrate binding, supporting the hypothesis of substrate gating. However, specific interactions that are formed or broken in the Ω loop upon binding differ between the two enzymes: dynamics are conserved, but not specific interactions. Substrate binding also has a global structuring effect on TEM-1, but not on PSE-4. Changes in TEM-1's normal modes show long-range effects of substrate binding on enzyme dynamics. Hydrogen bonds observed in the active site are mostly preserved upon substrate binding, and new, transient interactions are also formed. Agreement between NMR relaxation parameters and our theoretical results highlights the dynamic duality of class A β-lactamases: enzymes that are highly structured on the ps-ns timescale, with important flexibility on the μs-ms timescale in regions such as the Ω loop.