using FlexX-Pharm with interaction constraints
Ever since its first release in 2002, FlexX-Pharm has been the most popular add-on module to FlexX. One more reason to tell our users a little more about the directional pharm constraints in order to get the most out of this powerful tool.
FlexX-Pharm works with receptor-based pharmacophores. This means that the constraints are built on the receptor side rather than the ligand side. There are two types of constraints: spatial constraints (regarding a specific location in the active site) and interaction constraints which we will have a closer look at here. FlexX knows a number of different types of interactions: h_acc of carboxylic acids, phenyl_center, amides exhibit a strong directionality defined on the basis of one or two so-called interaction surfaces (see Fig 1).
Defining constraints for interaction partners with two interaction surfaces requires special attention. Here you need to provide the so-called surface identifier (either 0 or 1) in order to tell FlexX-Pharm which one to use.
Altogether the user has to provide the surface identifier together with the constraint type, residue name, residue identifier, atom name, and the priority. Only then will FlexX-Pharm use the correct constraint.
There are two ways to define the constraint for the constraints file:
- You can use FlexV (which has a Pharm-GUI built-in) to describe your pharmacophore pattern and write it to a file:
- Load your ligand and receptor into FlexX, draw them, change to the pharm menu and type PICKPH. This command will bring up the FlexV-Pharm dialog automatically (assuming you have specified FlexV as your default viewer in config.dat). You will see the receptor active site and the ligand molecule.
- Select the type of interactions you would like to see. As an example, we use phenyl_center here (see Fig 2).
- Pick the half-sphere pointing in the right direction. There are two for this type of interaction, a sphere 0 and a sphere 1. In our example figure (ligand and receptor from PDB code 1ivf), phenyl_center '0' for the TRP178 which is facing downwards would be the correct one, since it can build a favorable interaction with the methyl group C11 of the ligand. Click on this half-sphere and it will be listed in the FlexV-Pharm Control Constraints Set. You can see that in the last column, under surface ID, a 0 is listed.
- Once your are done defining, click 'Write Pharm' to save your constraints to a file, define a name that has the extension .phm or .bat, save and load this file into FlexX-Pharm in order to use your constraints.
- You can also specify the constraints by hand, writing the constraints file yourself. But you should know exactly what you are doing. A good idea is to re-dock a ligand which is known to form this particular interaction. If FlexX-Pharm is unable to find the position and fulfill the constraint, we suggest you to triple-check the definition!!! As shown in our example, it is much easier to define it with the FlexV-Pharm GUI, as the specification of the correct sphere is unambiguous.
This is what the content of the pharmacophore file we specified in the example would look like:
|essential _CE3 TRP _ 178 phenyl_center 0||<— Interaction Surface ID|
|@partial 0 0|
Note that there is another keyword in the definition 'essential'. It means that this constraint must be fulfilled for every generated docking-pose. Besides essential there is 'optional' and also the ability to define logical expressions based on the individual constraints. You can find a detailed explanation in the FlexX user guide on page 147.