Flexible ligand docking to multiple receptor conformations: a practical alternative

State of the art docking algorithms predict an incorrect binding pose for about 50–70% of all ligands when only a single fixed receptor conformation is considered. In many more cases, lack of receptor flexibility results in meaningless ligand binding scores, even when the correct pose is obtained. Incorporating conformational rearrangements of the receptor binding pocket into predictions of both ligand binding pose and binding score is crucial for improving structure-based drug design and virtual ligand screening methodologies. However, direct modeling of protein binding site flexibility remains challenging because of the large conformational space that must be sampled, and difficulties remain in constructing a suitably accurate energy function. Here we show that using multiple fixed receptor conformations, either experimentally determined by crystallography or NMR, or computationally generated, is a practical shortcut that may improve docking calculations. In several cases, such an approach has led to experimentally validated predictions.

Introduction

Molecular docking is playing an increasingly important role in lead discovery and design. Nevertheless, the docking field is still far from the goal of accurately and reliably predicting complex structures for arbitrary ligand–receptor pairs. It has long been recognized that a simplistic rigid ‘lock-and-key’ model of ligand–receptor interaction is inadequate and incorporation of ligand and receptor flexibility is required for accurate docking. While ligand flexibility has been addressed by a variety of algorithms, receptor flexibility remains a formidable challenge.

Several approaches to incorporate receptor flexibility in ligand docking were previously reviewed by Teodoro and Kavraki [1^••]. They propose a classification of methods that spans five categories: (a) ‘soft’ receptors that limit penalties because of steric clashes, (b) selection of a few critical degrees of freedom in the binding site, (c) use of multiple receptor structures, (d) use of modified molecular simulation methods, and (e) use of collective degrees of freedom as a new basis of representation for protein flexibility. In this review, we focus on using static multiple receptor conformations, either experimental or computationally generated.

Direct modeling of protein movements associated with binding site flexibility represents a significant problem because of the dual challenge of high dimensionality of the conformational space and of the complexity of energy function. A typical ligand binding site for a drug-like molecule consists of ten to twenty amino acid side-chains, which may mean dozens of potentially rotatable torsions. This number can easily be several times larger than the number of degrees of freedom for the ligand (typically 6–12). Considering the backbone movements may dramatically worsen the situation since, in contrast to relatively independent side-chains, each backbone movement affects multiple side-chains. Thus, fully flexible receptor/ligand docking simulation may involve sampling of an order of magnitude higher number of degrees of freedom than typical rigid-receptor/flexible ligand simulations routinely used in current structure-based virtual screening and ligand design projects. Apart from being computationally demanding, this expansion of sampling imposes high requirements on the energy function that must be able to discriminate a small number of low energy structures that are actually realized in nature from the vast number of hypothetical conformations generated by the sampling procedures. Taken to the limit, ligand docking into the flexible receptor essentially becomes the protein folding problem in the presence of ligand. Therefore, practical approaches to receptor flexibility incorporation into docking simulations must restrict radically the subspace of the full protein conformational space that they actually search.

Limiting flexibility to side-chains makes the problem much more tractable, and an exhaustive search of the binding site side-chain conformations, similar to what has been done in protein docking [2], is possible for smaller ligands [3, 4]. As an alternative to exhaustive search, a ‘minimal rotation hypothesis’ was proposed by Zavodsky and Kuhn [5^•]. Their docking algorithm, SLIDE, attempts to resolve ligand–receptor steric clashes by a minimal number of side-chain rotations, with the cost of side-chain movement evaluated as a product of the rotation angle and the number of atoms moved.

Depending on the specific system, side-chain flexibility alone may or may not be sufficient for adequate modeling. For example, conformational variability in the HIV protease binding site is apparently well described in terms of movements of several side-chains and a water molecule [6]. On the contrary, many kinases exhibit loop rearrangements as well as large-scale mutual movement of the two ‘lobes’ delimiting the active site [7]. Diversity in ligand binding mechanisms and the frequent unpredictability of receptor movement types makes the use of pre-determined (by experimental or computational means) multiple receptor conformations (MRC) an attractive practical alternative.