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In this issue of tips & tricks we will demonstrate how our scaffold replacement tool ReCore can be used for fragment-growing type of applications. The scenario we describe here is quite typical in the lead optimization phase of a project. Assume that you have a known binder in the context of a binding site (see figure below, Thrombin as found in PDB-code 1dwd). Now you want to replace a side-chain, poking into a certain sub-pocket by something more promising.
Note that you can either load a Protein from PDB, prepare it in the ReCore-GUI, or prepare it externally and load it from mol2. The required functions are found under the main menue items and .
So far you know ReCore as a scaffold replacement tool, requiring at least 2 bonds that connect the 'core' to the side-chains. However, if you
- tick the checkbox (labeled: Use One-Bond-Only Mode) in Step 2 of the ReCore-widget
- select one of the pharmacophore-types found on your known binder (preferably donor or acceptor)
- klick in the 3D-view on one of a pharmacophore-features of this type
then these simple steps define a query on the basis of just one bond. A click on the in the widget (in fact any ) in order to obtain a brief help text about what needs to be done.
Now coming back to our application scenario, we have the known binder with a side-chain that should be optimized. Obviously you would select the bond pointing into the sub-pocket of interest and at least one other 'directed' pharmacophore feature, as the basis of your query. You will usually get a highly diverse set of hits as shown in the next figure.
Now it is up to you to trim down the result-set to the most promising side-chains for your task at hand. For example you usually want to constrain the 'permissible space' by introducing exclusion volumes as follows:
- Open the tab of the optional step 3 in the ReCore-widget.
- Select the type of constraint as .
- Click in the 3D-view on any visible object to place an exclusion sphere. Note that if you click on multiple objects in the 3D-view, ReCore will automatically calculate the center of mass of these objects and place the sphere there.
You may also move the sphere around by altering the x-, y-, z-coordinates in the widget as well as change the radius of the sphere.
- Once you are satisfied with the position, click on . This puts the sphere constraint in the table and changes the color of the sphere in the 3D-view.
In our application example we simply clicked on some of the atoms of the previously generated ReCore-solutions, which were protruding far out from the original side-chain. However, you may also switch on the view of the protein (tick the corresponding check-box in the ) and click on protein-atoms to place those spheres.
Needless to say that, as with the standard scaffold-replacement task, you can further constrain your result-list by adding more pharmacophore-constrains. Once you have produced a number of interesting solutions, you can highlight multiple solutions using the usual 'Shift'-click / 'Crtl'-click selection in the table. A 'right'-click then gives you access to a context-menu, which allows you to save the highlighted solution to disk for further processing.
Hopefully you'll try it yourself, we encourage you to obtain your 2 weeks free copy of ReCore and replicate the above and/or the online tutorial movies. Some example files are also provided within the ReCore download-package.
To obtain a more thorough guide to ReCore's capabilities please do contact us. We are happy to provide you with a personal online demonstration.
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