Mapping small molecule binding data to structural domains

Felix A Kruger,Raghd Rostom,John P Overington

doi:10.1186/1471-2105-13-s17-s11

Felix A Kruger, Raghd Rostom + Show 1 more

Open Access

https://doi.org/10.1186/1471-2105-13-s17-s11

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Journal: BMC Bioinformatics	Publication Date: Dec 1, 2012
Citations: 50	License type: CC BY 2.0

Affiliation: European Bioinformatics Institute

Abstract

BackgroundLarge-scale bioactivity/SAR Open Data has recently become available, and this has allowed new analyses and approaches to be developed to help address the productivity and translational gaps of current drug discovery. One of the current limitations of these data is the relative sparsity of reported interactions per protein target, and complexities in establishing clear relationships between bioactivity and targets using bioinformatics tools. We detail in this paper the indexing of targets by the structural domains that bind (or are likely to bind) the ligand within a full-length protein. Specifically, we present a simple heuristic to map small molecule binding to Pfam domains. This profiling can be applied to all proteins within a genome to give some indications of the potential pharmacological modulation and regulation of all proteins.ResultsIn this implementation of our heuristic, ligand binding to protein targets from the ChEMBL database was mapped to structural domains as defined by profiles contained within the Pfam-A database. Our mapping suggests that the majority of assay targets within the current version of the ChEMBL database bind ligands through a small number of highly prevalent domains, and conversely the majority of Pfam domains sampled by our data play no currently established role in ligand binding. Validation studies, carried out firstly against Uniprot entries with expert binding-site annotation and secondly against entries in the wwPDB repository of crystallographic protein structures, demonstrate that our simple heuristic maps ligand binding to the correct domain in about 90 percent of all assessed cases. Using the mappings obtained with our heuristic, we have assembled ligand sets associated with each Pfam domain.ConclusionsSmall molecule binding has been mapped to Pfam-A domains of protein targets in the ChEMBL bioactivity database. The result of this mapping is an enriched annotation of small molecule bioactivity data and a grouping of activity classes following the Pfam-A specifications of protein domains. This is valuable for data-focused approaches in drug discovery, for example when extrapolating potential targets of a small molecule with known activity against one or few targets, or in the assessment of a potential target for drug discovery or screening studies.

Highlights

IntroductionResearch in the field of drug discovery is increasingly driven by the data mining of large-scale pharmacological, screening, patent, literature and other bioactivity data
Large-scale bioactivity/SAR Open Data has recently become available, and this has allowed new analyses and approaches to be developed to help address the productivity and translational gaps of current drug discovery
51 percent of all proteins from the interaction data set were found to contain more than one Pfam domain

Summary

Introduction

Research in the field of drug discovery is increasingly driven by the data mining of large-scale pharmacological, screening, patent, literature and other bioactivity data Such approaches have led to interesting concepts that challenge historical dogma - for example the view that many small molecules and drugs exert their effect through interactions with multiple rather than a single target [1]. Previous studies have statistically associated small molecule binding to protein domains [13] and direct mapping has been applied to ligands in crystallographic structures [14] We extrapolate these mappings to pharmacologically relevant interactions described in the CHEMBL database

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