How to Use the Bispecific Module in PKSim: Step-by-Step Demo & Instructions

Learn how to use the bispecific module in PKSim, including renaming molecules, handling reactions, and building simulations for bispecific drugs targeting PD-1 and TNF. Follow this step-by-step guide for efficient model extension and quality checks.

December 19, 2025 By Wilbert de Witte

In this guide, we'll learn how to use the bispecific extension module in a PKSim model to add features such as trimer formation, target turnover, internalization, recycling, and degradation for each target and complex.

We'll focus on the process of renaming and removing molecules and reactions to ensure the module works correctly with your base model. This will help you prepare your model for simulation and quality checks.

Let's get started

Okay. Here is a quick demo and instructions on how to use the bispecific module we created. The expected starting point for this extension module is a bispecific PKsim model, which already includes most of the relevant molecules.

Step #1: Click on "‣bispec" — Click on "‣bispec"

Step #2: Click on "▸ery" — Click on "▸ery"

We have a bispecific drug that binds to two different targets. In this case, we made it PD-1 and TNF. We have the complex formation in the base model, but that's all.

We need to include trimer formation, as well as the turnover of all targets: internalization, recycling, and degradation for each target and each complex.

That is what we do with the extension module here.

We have a molecule building block that needs to be renamed.

Step #5: Double-click on "Molecules" — Double-click on "Molecules"

It's important to note that only the "rename and remove" actions need to be completed. The others are mainly for your convenience, as well as for proper transparency and documentation. I will now demonstrate renaming this using only the rename and remove options. This approach makes the process shorter.

We need to pay attention because all these molecules are also in the base module. One molecule here is named after a reaction. This is simply a way to rename a reaction and its pathway for a parameter.

Step #7: Click on "- Target2-- RENAME AND REMOVE" — Click on "- Target2-- RENAME AND REMOVE"

Step #8: Click on "- Target1 Complex internalized" — Click on "- Target1 Complex internalized"

Drug target one complex needs to be renamed to bispec PD1 complex.

Step #9: Right-click on "Target1 Complex - RENAME" — Right-click on "Target1 Complex - RENAME"

Step #10: Click on "..." — Click on "..."

We can do that here.

Step #11: Click on "Drug Target1 Complex" — Click on "Drug Target1 Complex"

We automatically receive a request if everything needs to be renamed, which is the case here.

I will double-check that the name and spelling match exactly with the molecule's name. Yeah.

Step #14: Click on "Drug - Target1 -- RENAME AND REMOVE" — Click on "Drug - Target1 -- RENAME AND REMOVE"

This is the other reaction. There are actually two reactions here.

Step #15: Right-click on "Bispec - PD1-- Complex" — Right-click on "Bispec - PD1-- Complex"

Step #16: Click on "..." — Click on "..."

Step #17: Drag "Drug Target1 -- RENAME AND REMOVE" — Drag "Drug Target1 -- RENAME AND REMOVE"

So should be "bispec PD1", followed by a double dash, and nothing else.

This issue occurs regularly. The problem is that we cannot rename it to... We cannot rename this reaction or molecule to the name of a reaction because MOBI recognizes that a reaction with that name already exists. It assumes this is not what we want and does not allow the change. We need to open a new MOBI file and rename it there. Okay.

Step #19: Click on "Cancel" — Click on "Cancel"

We open a new MOBI file and import the module.

Step #20: Right-click here — Right-click here

Step #21: Right-click here — Right-click here

First, we need to state that this is an amount-based reactions model. Only then can we load the module.

Step #23: Click on "File" — Click on "File"

Step #24: Click on "Amount Based Reactions" — Click on "Amount Based Reactions"

Step #25: Right-click on "Modules" — Right-click on "Modules"

Step #26: Click on "Load Modules..." — Click on "Load Modules..."

The module is now loaded. We can repeat the same process.

Step #27: Click on "Molecules" — Click on "Molecules"

Step #29: Double-click on "Molecules" — Double-click on "Molecules"

Step #30: Click on "Drug - Target1 Complex -RENAME AND REMOVE-" — Click on "Drug - Target1 Complex -RENAME AND REMOVE-"

This is a bispecific PD1 complex.

Step #31: Right-click on "Drug - Target1 Complex -RENAME AND REMOVE-" — Right-click on "Drug - Target1 Complex -RENAME AND REMOVE-"

Step #32: Click on "Rename" — Click on "Rename"

You can check your other Moby file to confirm if this is what you need.

Okay.

Step #36: Right-click on "Drug - Target1 -- RENAME AND REMOVE" — Right-click on "Drug - Target1 -- RENAME AND REMOVE"

This, again, is for the reaction.

Step #37: Click on "..." — Click on "..."

Step #38: Drag "Drug - Target1 - RENAME AND REMOVE" — Drag "Drug - Target1 - RENAME AND REMOVE"

If you do it correctly, you will see that it also finds some paths that will be renamed with it.

If you do not see this pop-up, you have not entered the name correctly.

Step #43: Click on "Drug - Target2 Complex -RENAME AND REMOVE-" — Click on "Drug - Target2 Complex -RENAME AND REMOVE-"

Okay.

Step #44: Right-click on "- Target2 Complex internalized -RENAME-" — Right-click on "- Target2 Complex internalized -RENAME-"

Step #45: Click on "..." — Click on "..."

This is now the TNF target.

Step #46: Click on "Drug - Target" — Click on "Drug - Target"

Step #48: Click on "Bispec - TNF Complex -RENAME AND REMOVE-" — Click on "Bispec - TNF Complex -RENAME AND REMOVE-"

Step #49: Select Drag "TNF-- Complex" — Select Drag "TNF-- Complex"

There we go.

repeat this for all molecules with -RENAME AND REMOVE- and remove them all after renaming

Now, all the other molecules here did not need to be renamed or removed.

That is why they do not need to be renamed, since there is nothing they need to match. These are all new molecules, such as the trimer or any internalized target and drug target complexes. Okay. Now we have the module with the new name for our base module. We can save this as a PKML file.

Step #52: Right-click on "bispecific" — Right-click on "bispecific"

Step #53: Click on " Save As PKML ..." — Click on " Save As PKML ..."

Now, we can return to our original file and load the PKML module.

Step #54: Right-click on "Modules" — Right-click on "Modules"

Step #55: Click on "Load Module" — Click on "Load Module"

Step #56: Click on "Double target and complex turnover with recycling" — Click on "Double target and complex turnover with recycling"

Step #57: Click on "Open" — Click on "Open"

Step #58: Click on "A module named ' bispecific binding and recycling ' already exists . Please enter a new name" — Click on "A module named ' bispecific binding and recycling ' already exists . Please enter a new name"

Alright. Now we can build a simulation using these modules.

Step #62: Right-click on "Simulations" — Right-click on "Simulations"

Step #63: Click on "Create Simulation ..." — Click on "Create Simulation ..."

Step #65: Click on "Add" — Click on "Add"

Step #66: Click on "binding and recycling renamed" — Click on "binding and recycling renamed"

Step #67: Click on "recycling renamed" — Click on "recycling renamed"

Step #68: Click on "Add" — Click on "Add"

Step #71: Click on "Next" — Click on "Next"

Step #74: Click on "Results" — Click on "Results"

Okay. That seems to work. We do not receive any errors. We can run a simulation and perform all the quality checks we need.

We now have a working model, which means we also have a functioning module. Here, you can quickly check if all the reactions you added to the module appear in this list.

How to Use the Bispecific Module in PKSim: Step-by-Step Demo & Instructions

Learn how to use the bispecific module in PKSim, including renaming molecules, handling reactions, and building simulations for bispecific drugs targeting PD-1 and TNF. Follow this step-by-step guide for efficient model extension and quality checks.

December 19, 2025 By Wilbert de Witte

Let's get started

We have a bispecific drug that binds to two different targets. In this case, we made it PD-1 and TNF. We have the complex formation in the base model, but that's all.

We need to include trimer formation, as well as the turnover of all targets: internalization, recycling, and degradation for each target and each complex.

That is what we do with the extension module here.

We have a molecule building block that needs to be renamed.

Drug target one complex needs to be renamed to bispec PD1 complex.

We can do that here.

We automatically receive a request if everything needs to be renamed, which is the case here.

I will double-check that the name and spelling match exactly with the molecule's name. Yeah.

This is the other reaction. There are actually two reactions here.

So should be "bispec PD1", followed by a double dash, and nothing else.

We open a new MOBI file and import the module.

First, we need to state that this is an amount-based reactions model. Only then can we load the module.

The module is now loaded. We can repeat the same process.

This is a bispecific PD1 complex.

You can check your other Moby file to confirm if this is what you need.

Okay.

This, again, is for the reaction.

If you do it correctly, you will see that it also finds some paths that will be renamed with it.

If you do not see this pop-up, you have not entered the name correctly.

Okay.

This is now the TNF target.

There we go.

repeat this for all molecules with -RENAME AND REMOVE- and remove them all after renaming

Now, all the other molecules here did not need to be renamed or removed.

Now, we can return to our original file and load the PKML module.

Alright. Now we can build a simulation using these modules.

Okay. That seems to work. We do not receive any errors. We can run a simulation and perform all the quality checks we need.

We now have a working model, which means we also have a functioning module. Here, you can quickly check if all the reactions you added to the module appear in this list.