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A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening
Negative image-based (NIB) screening is a rigid molecular docking methodology that can also be employed in docking rescoring. During the NIB screening, a negative image is generated based on the target protein’s ligand-binding cavity by inverting its shape and electrostatics. The resulting NIB model...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6600450/ https://www.ncbi.nlm.nih.gov/pubmed/31174295 http://dx.doi.org/10.3390/ijms20112779 |
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author | Ahinko, Mira Kurkinen, Sami T. Niinivehmas, Sanna P. Pentikäinen, Olli T. Postila, Pekka A. |
author_facet | Ahinko, Mira Kurkinen, Sami T. Niinivehmas, Sanna P. Pentikäinen, Olli T. Postila, Pekka A. |
author_sort | Ahinko, Mira |
collection | PubMed |
description | Negative image-based (NIB) screening is a rigid molecular docking methodology that can also be employed in docking rescoring. During the NIB screening, a negative image is generated based on the target protein’s ligand-binding cavity by inverting its shape and electrostatics. The resulting NIB model is a drug-like entity or pseudo-ligand that is compared directly against ligand 3D conformers, as is done with a template compound in the ligand-based screening. This cavity-based rigid docking has been demonstrated to work with genuine drug targets in both benchmark testing and drug candidate/lead discovery. Firstly, the study explores in-depth the applicability of different ligand 3D conformer generation software for acquiring the best NIB screening results using cyclooxygenase-2 (COX-2) as the example system. Secondly, the entire NIB workflow from the protein structure preparation, model build-up, and ligand conformer generation to the similarity comparison is performed for COX-2. Accordingly, hands-on instructions are provided on how to employ the NIB methodology from start to finish, both with the rigid docking and docking rescoring using noncommercial software. The practical aspects of the NIB methodology, especially the effect of ligand conformers, are discussed thoroughly, thus, making the methodology accessible for new users. |
format | Online Article Text |
id | pubmed-6600450 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-66004502019-07-16 A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening Ahinko, Mira Kurkinen, Sami T. Niinivehmas, Sanna P. Pentikäinen, Olli T. Postila, Pekka A. Int J Mol Sci Article Negative image-based (NIB) screening is a rigid molecular docking methodology that can also be employed in docking rescoring. During the NIB screening, a negative image is generated based on the target protein’s ligand-binding cavity by inverting its shape and electrostatics. The resulting NIB model is a drug-like entity or pseudo-ligand that is compared directly against ligand 3D conformers, as is done with a template compound in the ligand-based screening. This cavity-based rigid docking has been demonstrated to work with genuine drug targets in both benchmark testing and drug candidate/lead discovery. Firstly, the study explores in-depth the applicability of different ligand 3D conformer generation software for acquiring the best NIB screening results using cyclooxygenase-2 (COX-2) as the example system. Secondly, the entire NIB workflow from the protein structure preparation, model build-up, and ligand conformer generation to the similarity comparison is performed for COX-2. Accordingly, hands-on instructions are provided on how to employ the NIB methodology from start to finish, both with the rigid docking and docking rescoring using noncommercial software. The practical aspects of the NIB methodology, especially the effect of ligand conformers, are discussed thoroughly, thus, making the methodology accessible for new users. MDPI 2019-06-06 /pmc/articles/PMC6600450/ /pubmed/31174295 http://dx.doi.org/10.3390/ijms20112779 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Ahinko, Mira Kurkinen, Sami T. Niinivehmas, Sanna P. Pentikäinen, Olli T. Postila, Pekka A. A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening |
title | A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening |
title_full | A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening |
title_fullStr | A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening |
title_full_unstemmed | A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening |
title_short | A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening |
title_sort | practical perspective: the effect of ligand conformers on the negative image-based screening |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6600450/ https://www.ncbi.nlm.nih.gov/pubmed/31174295 http://dx.doi.org/10.3390/ijms20112779 |
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