A platform for target prediction of phenotypic screening hit molecules.
J Mol Graph Model 2019;
95:107485. [PMID:
31836397 PMCID:
PMC6983931 DOI:
10.1016/j.jmgm.2019.107485]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 09/25/2019] [Accepted: 10/21/2019] [Indexed: 01/09/2023]
Abstract
Many drug discovery programmes, particularly for infectious diseases, are conducted phenotypically. Identifying the targets of phenotypic screening hits experimentally can be complex, time-consuming, and expensive. However, it would be valuable to know what the molecular target(s) is, as knowledge of the binding pose of the hit molecule in the binding site can facilitate the compound optimisation. Furthermore, knowing the target would allow de-prioritisation of less attractive chemical series or molecular targets. To generate target-hypotheses for phenotypic active compounds, an in silico platform was developed that utilises both ligand and protein-structure information to generate a ranked set of predicted molecular targets. As a result of the web-based workflow the user obtains a set of 3D structures of the predicted targets with the active molecule bound. The platform was exemplified using Mycobacterium tuberculosis, the causative organism of tuberculosis. In a test that we performed, the platform was able to predict the targets of 60% of compounds investigated, where there was some similarity to a ligand in the protein database.
An algorithm to predict the molecular target(s) of phenotypic hits against TB.
Uses information based on the ligand and protein structure.
Allow visualisation of proposed binding pose.
Web interface developed.
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