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In this issue of tips and tricks we will demonstrate using tutorial movies how quickly scaffold cores can be replaced with our scaffold replacement tool ReCore and show its fragment merging/linking capabilities. Here we will show you how easy it is to use ReCore to propose scaffolds and demonstrate to you that in minutes, interesting and chemically diverse scaffolds for your existing molecules or competitor compounds can be produced.
Hopefully you'll try it yourself, we encourage you to obtain your 2 weeks free copy of ReCore and replicate the online tutorial movies with some example files provided below and within the ReCore download. Please note that the results obtained with the current version of ReCore may be slightly altered as the fragment library used has been updated since the online movies were recorded.
To obtain a more thorough guide to ReCore's capabilities please do contact us or simply go to the drop down menu in the ReCore GUI and click on the entry. There you'll find detailed information on how ReCore can also be used on the command line.
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| ReCore basics |
The first tutorial movie portrays the basic concept of ReCore.
- You can use the to load the Cox-2 inhibitor Etoricoxib.
- Select your scaffold by clicking on two of the molecule's bonds (exit vectors) in the 3D view after pressing the button in the wizard.
- Then by simply clicking in the wizard your chemically diverse solutions will appear within seconds for you to scroll through... it's as simple as that!
Have a go yourselves!
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| ReCore – using 3 bonds and pharmacophore constraints |
The second movie elaborates on the basic functionality of ReCore.
- In this example 3 bonds are used to select the scaffold instead of 2 and the search is performed on a peptide using the file 1ppm_min.mol.
- This can be found in the query_examples directory with your download.
- Furthermore, using the peptide in 1ppm the pharmacophore constraints features are demonstrated.
Take a look at how this works.
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| ReCore – fragment merging exercise |
The third movie demonstrates how ReCore can be used in fragment merging/linking.
- Here a thought experiment is shown, consider having run a fragment based crystallographic screen with three different resulting hits, or having 3 known binders.
- In our case here, we have taken 3 different ligand fragments corresponding to 3 different ligands, occupying 3 different pockets of the drug target 'BACE'.
- In such a situation ReCore can be used to propose a scaffold which could merge/link these fragments together.
- Using these files follow the demo.
Now you can start merging and linking your fragment hits today.
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If you have any difficulties following the movies, would like more information on ReCore or a personal online demonstration please do feel free to contact us.
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