Skip to content

Macrocyclic Linker Design User Guide

1: Introduction to the Algorithm

Macrocycles have been used successfully on most pharmaceutical target classes. Macrocycles are more conformationally restricted than their acyclic analogues, which potentially can impart higher target binding and selectivity and improved oral bioavailability. Therefore, there are more applications in medicinal chemistry which utilized macrocyclization as an alternative way to improve binding activity and ADMET properties.

Tencent’s macrocycles generative algorithm will design the linkers from the reference acyclic molecule at the two given linking positions.

2: Start to Use

2.1 Upload molecule and get 3D conformer

iDrug provides two methods of inputting data, including inputting SMILES, and uploading SDF file with 3D conformation.

  • Input SMILES

    Select the "Input your SMILES" check box, then enter one SMILES in the text box, or click the "DRAW" icon at the end of the text box to pop up the molecular editor, in which you can draw the molecular structure and click "Confirm" to convert it to SMILES which will be displayed in the text box.

    Click the "Get 3D conformation" button, then iDrug will generate 10 3D conformers for this molecule, which will be displayed below. After selecting a suitable 3D conformer as the reference conformation of this molecule, you can click the "Next" button to enter the next step.



  • Upload SDF file with 3D conformation

    Select the "Upload SDF file with 3D conformation" check box, then click the "Click to upload" button to upload an SDF file, and click "Get 3D conformation" button to display the conformer in this file below. Select this conformer and then click the "Next" button to enter the next step.

    There can only be one molecular conformer in the uploaded SDF file, which must be 3D conformation, and do not support protonation.


2.2 Indicate linker positions

Click on the molecular image on the right to indicate linker-connecting positions by selecting two hydrogen atoms. After successful indication, the effect picture will be displayed on the left.

The positions marked with * in the left image are the linker-connecting positions for generated linkers.


2.3 Set filters

Users can set the length range of the generated linkers, which is limited between 3-10.

Users can also choose whether to allow linkers with ring systems.


2.4 Submit task

After completing the above steps, click the "Submit" button to submit the task. If "Your task has been created successfully!" is displayed, the submission is successful.

If the task is completed successfully, the user's registered mailbox will receive the notification of task completion. Usually, the calculation time of a task takes several hours.

In order to allocate the limited resources reasonably, we limit the user's task quota. Hover the mouse over the "Submit" button or the "Next" button to see the restriction and usage. The "Submit" button and the "Next" button will be disabled when quota is insufficient.


3. Query the Result of Your Task

3.1 Query history

Users can view the "Recent History" below, which only displays the last 10 history records, or click the "all history" to see all history records.

Users can "Check" completed tasks (marked in green).

Users can "Delete" completed or failed or pending tasks. Tasks in running status can not be deleted.

Click the drop-down arrow next to "Status" to filter according to the task running status.


3.2 Query results

Click the "Check" button on the history records to view the task results.

The result interface displays:

  • Linker-connecting positions of linkers in the input molecule, which help users to confirm the input information of the task.

  • Filtering results by properties.

  • Molecule cards, which show the predicted similarity scores of the generated molecules.


  • Click one molecule card to view the molecular attributes and ADMET attributes (predicted values) of this molecule.


3.3 Download results

In the result interface, click "Export CSV" and select the attributes to be retained to download all results.

Click one molecule card to view the attributes of this molecule, and then click "Export CSV" to download result of this molecule.