Polyphony: superposition independent methods for ensemble-based drug discovery.

William R Pitt,Rinaldo W Montalvão,Tom L Blundell

doi:10.1186/1471-2105-15-324

Abstract

BackgroundStructure-based drug design is an iterative process, following cycles of structural biology, computer-aided design, synthetic chemistry and bioassay. In favorable circumstances, this process can lead to the structures of hundreds of protein-ligand crystal structures. In addition, molecular dynamics simulations are increasingly being used to further explore the conformational landscape of these complexes. Currently, methods capable of the analysis of ensembles of crystal structures and MD trajectories are limited and usually rely upon least squares superposition of coordinates.ResultsNovel methodologies are described for the analysis of multiple structures of a protein. Statistical approaches that rely upon residue equivalence, but not superposition, are developed. Tasks that can be performed include the identification of hinge regions, allosteric conformational changes and transient binding sites. The approaches are tested on crystal structures of CDK2 and other CMGC protein kinases and a simulation of p38α. Known interaction - conformational change relationships are highlighted but also new ones are revealed. A transient but druggable allosteric pocket in CDK2 is predicted to occur under the CMGC insert. Furthermore, an evolutionarily-conserved conformational link from the location of this pocket, via the αEF-αF loop, to phosphorylation sites on the activation loop is discovered.ConclusionsNew methodologies are described and validated for the superimposition independent conformational analysis of large collections of structures or simulation snapshots of the same protein. The methodologies are encoded in a Python package called Polyphony, which is released as open source to accompany this paper [http://wrpitt.bitbucket.org/polyphony/].

Highlights

Structure-based drug design is an iterative process, following cycles of structural biology, computer-aided design, synthetic chemistry and bioassay
X-ray crystal structures are the basis of the majority of structure-based drug design (SBDD) projects, and drug companies often amass hundreds of crystal structures of the same protein with different ligands bound over the course of a drug discovery project
The initial emphasis of Polyphony is on the analysis of structures from X-ray crystallography but it can be used on Nuclear magnetic resonance (NMR) structures and snapshots along the trajectories of protein simulations

Summary

Introduction

Structure-based drug design is an iterative process, following cycles of structural biology, computer-aided design, synthetic chemistry and bioassay. In favorable circumstances, this process can lead to the structures of hundreds of protein-ligand crystal structures. Researchers carrying out structure-based drug design (SBDD) are constantly looking to improve the modelling of protein conformational change and its relationship to ligand binding. Changes in protein conformation, when experimentally observed, can lead to the discovery of highly prized cryptic binding sites [4] and allosteric pockets [5,6]. Single sets of structure coordinates can be used to generate ensembles using conformational sampling techniques [11] or simulations [12]. We would like to distinguish this approach from more traditional (single) SBDD by the coining the expression “ensemble-based drug discovery” (EBDD)

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Conclusion