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Molecules 2018, 23(2), 353; https://doi.org/10.3390/molecules23020353

VSpipe, an Integrated Resource for Virtual Screening and Hit Selection: Applications to Protein Tyrosine Phospahatase Inhibition

1
School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
2
School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
3
Insight Centre for Data Analytics, NUIG, Galway H91, Ireland
*
Author to whom correspondence should be addressed.
Received: 20 December 2017 / Revised: 2 February 2018 / Accepted: 4 February 2018 / Published: 7 February 2018
(This article belongs to the Special Issue Protein-Tyrosine Phosphatase Inhibitors)
Full-Text   |   PDF [3333 KB, uploaded 9 February 2018]   |  

Abstract

The use of computational tools for virtual screening provides a cost-efficient approach to select starting points for drug development. We have developed VSpipe, a user-friendly semi-automated pipeline for structure-based virtual screening. VSpipe uses the existing tools AutoDock and OpenBabel together with software developed in-house, to create an end-to-end virtual screening workflow ranging from the preparation of receptor and ligands to the visualisation of results. VSpipe is efficient and flexible, allowing the users to make choices at different steps, and it is amenable to use in both local and cluster mode. We have validated VSpipe using the human protein tyrosine phosphatase PTP1B as a case study. Using a combination of blind and targeted docking VSpipe identified both new and known functional ligand binding sites. Assessment of different binding clusters using the ligand efficiency plots created by VSpipe, defined a drug-like chemical space for development of PTP1B inhibitors with potential applications to other PTPs. In this study, we show that VSpipe can be deployed to identify and compare different modes of inhibition thus guiding the selection of initial hits for drug discovery. View Full-Text
Keywords: computational screening; virtual screening (VS); protein tyrosine phosphatase (PTP); ligand efficiency indices (LEIs); drug discovery computational screening; virtual screening (VS); protein tyrosine phosphatase (PTP); ligand efficiency indices (LEIs); drug discovery
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary materials

  • Supplementary File 1:

    PDF-Document (PDF, 1698 KB)

  • Externally hosted supplementary file 1
    Link: https://github.com/sabifo4/VSpipe
    Description: The Linux version of VSpipe-local mode and documentation are available at https://github.com/sabifo4/VSpipe. The VSpipe-cluster mode is available upon request.
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Álvarez-Carretero, S.; Pavlopoulou, N.; Adams, J.; Gilsenan, J.; Tabernero, L. VSpipe, an Integrated Resource for Virtual Screening and Hit Selection: Applications to Protein Tyrosine Phospahatase Inhibition. Molecules 2018, 23, 353.

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