Setup your Fragment Linking generator with 3D structural parameters

Thank you for answering our questionnaire! Based on your answers, we have provided our team's recommendations to help you properly set up Makya for your project. 

Your answers

1. I want to modify the center of my molecule, keeping the external branches fixed
2. I want to explore and discover new molecules with important modifications, including new groups, functions, and scaffolds.
3. Yes, I have structural information.

Given the requirements of your project, we recommend setting up a Fragment Linking generator coupled with 3D structural parameters.

 

1. Selection of the generator 

The Fragment Linking generator can be used for generating compounds by proposing new linkers and/or scaffolds between two building blocks and their reaction centers. It is purely chemistry-driven so a good understanding of organic chemistry is required. By defining the exit vectors (where the chemistry will take place), the generator will search for commercial building blocks which can react in such a position. 

For example, given a couple of building blocks: A and B and their reaction centers (exit vectors) -NH2 and -Br respectively, the fragment linking generator will propose novel compounds by attaching new scaffolds at those centers while keeping the rest of the building blocks intact.

2. Makya 3D structure-based parameters

Makya 3D structure-based parameters allow you to use embedded docking to guide molecule generation inside Makya. The generated molecules are docked inside the target protein binding pocket, and optimized with respect to the Docking Score, and to the Contact Score, a proprietary score that rewards the presence of key interactions. 

 

3. Step by Step setup

Step 1: set up your 3D structure-based parameters

• Prepare the input files:
  • The protein file, in PDB format and without ligand, should be prepared as it would be for any docking software (more information here).
  • The reference ligand file, in SDF format, should be prepared by adding the hydrogens and protonating the reference ligand at pH=7.4 in the target binding pocket.
• To add your 3D structure-based parameters, simply follow the steps described in the documentation: Set-up of 3D Structure-Based Parameters. 

Step 2: set up your Fragment Linking generator with 3D

A description of the Fragment Linking generator and of the setting-up steps is provided in the documentation: Fragment Linking generator. You can also find examples in our use-cases: for example, Scaffold Hopping with the Fragment Linking generator.

• Create a new Fragment Linking generator in the Generators tab of your project. The generator set-up page appears. 
• In the Exit Vectors tab, enter the two external branches of your reference molecule. 
  • The fragments should not contain any charged atoms, as protonation is performed directly inside Makya. They should not be chiral either.
  • It is important to input fragments that are suitable building blocks for chemical synthesis (for example, brominated or chlorinated fragments, or molecules with an OH to form an ester), as the Fragment Linking generator is a chemistry-based generator trained on chemical reactions. 
• After having entered your fragments, select the exit vectors by clicking on Set and inputting the atoms ID. 
  • Make sure to select all the atoms that will be involved in the reaction.
• In the 3D Structure based tab, select the 3D structure configuration that you set up in step 1.
  • If you wish to parameter an anchor, click on the Anchor tab. 
    • The anchor is a subunit of the reference molecule used as a starting point for 3D alignment. 
    • It has to be present in all the generated molecules for the 3D alignment to be done and the 3D scores to be calculated (this can be done by using substructure constraints, for example). 
    • The anchor should contain a minimum of 5 heavy atoms, and should not be too long (max 20 heavy atoms) as it can cause computation issues. 
    • Just like the starting fragments, it should not contain any charged atoms or be chiral, even if the reference ligand is. 
  • Enter the anchor you wish to use. You can enter the SMILES for one of your branches, for example; or a substructure constraint specified in the Products tab. This will ensure that all your generated molecules contain the anchor.

These are the minimal steps needed to fit the requirements of your project. If you want to add more constraints on the generation, you can do so during the set-up of your generator. For example, you can add substructure constraints (forcing or preventing the presence of specific substructures) either on the building blocks that will be chosen as the new molecular cores, or directly on the generated molecules. The first option will drastically accelerate the generation by reducing the size of the catalog of building blocks explored by the algorithm: thus, we recommend using it whenever appropriate. The second option can allow you to exclude patented scaffolds.

Step 3: run the generator and analyze your results

• To run your generator, go back to the Generation tab and click on Run.
• You can see the first generated molecules while the generation is still running. Check that there is no error in your set-up and that the generated molecules look conform to the requirements of your problem.

Once you have enough molecules, you can use the Parallel Coordinates to filter the molecules based on scores such as the Docking or Contact Scores. For more information on the visualization, analysis and export of your results, check the documentation: Visualisation and Analysis of Generated Molecules.

For any questions, contact your Application scientist.