BioDMET Quick Start Guide. Biodistribution Simulation

BioDMET Quick Start Guide Biodistribution Simulation 1

Contents Introduction 3 Welcome to BioDMET 5 Applications Getting Started 7 System Requirements 8 The BioDMET Website 9 User Registration 10 Install and Run BioDMET 12 The BioDMET Interface Perform a Simulation: Biodistribution Tutorial 15 Task 1: Calculate the Biodistribution of Linezolid in the Mouse 16 Preparation 17 Calculation Wizard Setup 23 Running the Calculation 24 Exporting Simulation Results 25 Analyzing the Results Modifying the Model 28 Task 2: Add an Injection 30 Task 3: Change the Injected Dose 31 Task 4: Change the Sampling Times Validating the Model 32 Task 5: Add Sampling Measurement Finishing Notes 34 Database Provided with BioDMET 2

Introduction: Welcome to BioDMET Introduction BioDMET is physiologically-based pharmacokinetic (PBPK) modeling and simulation tool that has been developed in the Computational Biology and Biostatistics Laboratory at GE Global Research. The tool uses ordinary differential equations to represent at the macro scale the circulation of body fluids through organs and tissues, and at the molecular scale the biological transport mechanisms and biotransformations within cells and their organelles. Each major organ in the body is modeled, accounting for the circulation flows of arterial and venous blood and lymph. Each organ is composed of one or more tissues which are made up of cell types, spaces and cell types containing spaces. 3

Introduction: Welcome to BioDMET (Cont.) Introduction GE s mechanistic PBPK tool has been used to model the biodistribution of molecules in mice, rats, and humans including specifics on age, gender and body mass index. The sizes of the modeled molecules have ranged from small molecules (<1 kda) to medium peptides (1 to 60 kda) to large proteins (>60 kda) and nano-particles. Passive vesicular transport and passive membrane permeability is calculated and accounted for in the model. Receptors, carrier mediated transporters, and biotransformation reactions can also be used in the current version of the tool by specifying enzyme concentrations, sub-cellular locations, and substrate kinetic rates. 4

Introduction: Applications Introduction Imaging This tool has been under development for over three years in parallel with its practical application to GE Healthcare programs focused on the development of molecular imaging agents in oncology, neurology, cardiology, diabetes, and inflammation. GE Healthcare s molecular imaging programs have provided rich datasets of compounds measured in multiple tissues over time thus providing a unique environment to develop and test mechanistic PBPK models. 5

Introduction: Applications Introduction Drug Discovery and Development Currently, the tool is being extended for the Transformational Medical Technologies Initiative (TMTI) supported by a contract awarded by the Defense Threat Reduction Agency (DTRA), a division of the U.S. Department of Defense. The PBPK tool is being adapted to computationally model the impact of bacterial, viral and other infectious agents on the human body. The modified tool simulates the effect of new antibiotic or antiviral drug therapies in response to a specific threat. In addition, a database is being generated with the PBPK parameters required to accurately represent the physiological changes in a critically ill patient suffering from burns, trauma, or recent surgery to help evaluate the effectiveness of the drug therapy under the various conditions it might be administered. 6

Getting Started: System Requirements BioDMET should run on any platform that supports Java and web browsing. However, it has only been tested thoroughly on Windows using Internet Explorer. Java BioDMET requires version 1.6 (or newer) of the Java Runtime Environment (JRE) installed on your computer. (Note: this is also known as version 6 of Java.) To check if you have the latest version of Java follow this link. If the resulting web page says you have "Version 6" installed, then you have the right environment to run the BioDMET application. Otherwise, to get the latest version of Java go to: http://www.java.com/en/download/. Click on the "Free Java Download" button in order to begin the download and installation process. Model Files The other requirement to run the BioDMET application is a set of host and agent model files, prebuilt model components used to run a simulation. When you first run BioDMET, the files have to be downloaded to a local user directory. We recommend creating a subdirectory named biodmet off of your user account. This will then contain a data directory with the following subdirectories: agents models - Contains a set of agent model files that can be used with the application. - Contains a set of host/species model files that can be used with the application. pathogens - Contains a set of pathogen model files that can be used with the application. validation - Contains a set of files used internally to validate the application. To limit the size and time of the download, only a fraction of the existing model files will be downloaded to your computer at this step. All available model files can be downloaded from the Downloads section of our web site. 7

Getting Started: The BioDMET Website http://pdsl.research.ge.com/biodmet/ This site will let you download, install and run the latest version of BioDMET. 8

Getting Started: User registration Why is it needed: To monitor usage To allow sending update notices to users What it does: Creates a cookie on user s computer Allows the user to run BioDMET 9

Getting Started: Install and Run BioDMET 1. First, select Run BioDMET from the left side menu of the BioDMET website. 2. Next, click on the Launch the BioDMET application icon 3. A series of windows will pop up as the application starts. It might take several minutes to download application the first time. Please wait patiently. Even if you see no status bar or hourglass, progress is being made. 10

Getting Started: Install and Run BioDMET (Cont.) 5. The BioDMET application reads and writes files from/to your computer's local file system. To enable that functionality, the Java library files used to bundle the application must be digitally signed. For the beta version we are using a signature key that we generated ourselves, versus using one generated by a third party (such as Verisign) who can authenticate our identity. This is why you are getting the warning message that the signature cannot be independently verified. Please click on the Run button in the popup window. 6. Create a BioDMET data directory If you are running BioDMET the first time, you need to download the model data files. Click on OK. When prompted, select the directory in which you wish to create a biodmet folder. In Windows this will be something like: C:\Documents and Settings\account_name\biodmet (account_name is the user account you use to log into your computer). In Linux, your home account would be something like: /home/account_name/ 7. The files will be extracted into a subdirectory named data in your newly created biodmet directory. The data directory will contain the following subdirectories: agents models pathogens validation 8. Application is launched, the BioDMET interface opens. 9. After the first run, most of the steps are skipped and starting the program is simpler and faster. 11

Getting Started: The BioDMET Interface To get a quick visual of what the various interface elements provide, open the existing BioDMET model of a healthy human male: File > Open > human_male_40yr_71kg_healthy.xml found in your biodmet/data/models directory. Menu & Icon Bars Tabs Property Window Model Tree View Information Window 12

Getting Started: The BioDMET Interface Elements The host is a hierarchical construct of systems, tissues and spaces represented as green, yellow, purple, and blue boxes. A model is made up of Animal models, Elements, Administration information, and specifications on Sampling times, entities, locations and measurements. Animals are made up of organ systems made up of tissues, which contain spaces with different cell types. Cells are made up of spaces representing the cellular compartments such as cytosol, nucleus, etc. The structure of any element of the construct can be expanded or collapsed by double clicking on it. A single click on an element (system, tissue, space) will bring up its properties in the upper right property window Hierarchical System Connections The following connection types are represented as lines between elements in BioDMET: Surface: blue Flow:red Injection of a drug/agent: pink Element insertion: green Connections and the Spaces/elements coupled by them and associated properties Tip: Window Panes are Adjustable 13

Getting Started: The BioDMET Interface Connections between spaces and elements of the PBPK model Connections (Cont.) Spaces are connected by surfaces (blue lines) and/or pipes (red lines). Surfaces usually represent membranes, while the pipes represent flow of material from one space into the other. The connections of a space can be visualized by clicking on that space. Injections are a third type of connection between the administered drug/agent and a specific space in the host. The connections are shown as dashed lines when one partner from a connection is within a collapsed (hidden) compartment. Clicking on a dashed line will expand these collapsed compartments. To see the properties of a connection, single click on it. The paths to the elements connected by each connection are shown in the lower right Connections window of the GUI (Click on the Connections tab) 14

Perform a Simulation: Biodistribution Tutorial 1 Task 1: Calculate the Biodistribution of Linezolid in the Mouse This tutorial will demonstrate how to compute the concentration of the antibiotic linezolid in the various tissues of a healthy mouse model with BioDMET. It will show you how to selectively export the calculated concentrations in the tissues of interest into a data file that can be used by plotting software. After running the calculation, you will compare the computed concentrations at different time points to experimental data published in the literature. The host We will create the PBPK model of a healthy female mouse by modifying the weight and gender of the existing male mouse model. The drug We inject 80mg/kg of the drug linezolid into the mouse intravenously at time 0 and monitor its concentration for the following 24 hours. Assuming BioDMET is installed (see Pg.11) Lets get started with the tutorial 15

Perform a Simulation: Preparation 1 Tutorial Inputs: a. The model of the healthy mouse b. Drug chemical structure and physico-chemical properties. If you have access to the software Marvin from ChemAxon, you will need only the chemical structure. Otherwise you will have to compute the molecular weight and logp/logd of the agent with another tool or, in case of a known compound, look them up in a small molecule database such as PubChem: http://pubchem.ncbi.nlm.nih.gov/. The hydrodynamic radius, diffusion coefficient, and membrane permeability of the molecule are calculated by BioDmet based on the previously specified properties. a. Drug parameters: Percent plasma protein binding Rate of metabolism in liver microsomes if the drug is metabolized by the liver μ μ μ ( ) Tutorial Output: a. Concentration of the drug in various tissues/compartments of the body as a function of time. 16

Perform a Simulation: Calculation Wizard Setup 1 Start the program: a. Go to: http://pdsl.research.ge.com/biodmet/ click on the run button. b. After accepting the certificate, this will open the BioDMET application: BioDMET web site Running the application 1. Starting the wizard: a. A wizard will walk you through the setup of the simulation. To start the wizard, from the top menu bar, select Simulation > New Biodistribution Simulation. This wizard screen will open: b. Click Next. 2. Specify the simulation name: a. Name: Linezolid biodistribution in mouse Description: Tutorial run Entering a description is optional, and the model can be saved after the setup is completed. b. Click Next. BioDMET Wizard Opening Page BioDMET Wizard Specify a Name 17

Perform a Simulation: Calculation Wizard Setup 1 3. Select the host: a. Click on Create New Host Model b. Host/Species: Mouse c. Gender: Female d. Body Mass (Grams): 22 The program will derive all the host physiological parameters necessary for a PBPK calculation from the existing mouse model. You can also browse for and select other existing or user-created host model files. a. Click Next. 4. Select the drug to administer: Here we will select the existing agent xml file of linezolid which we generated with Marvin (ChemAxon). a. Click on Load existing drug property file and browse for linezolid.xml in your biodmet/data/agents directory. If you want to use another drug, you can rename and modify the properties of this agent through the wizard and save the resulting agent/drug profile from BioDmet into a new agent file. The drug properties can come from another program that calculates physicochemical properties from the chemical structure or from the literature. b. Click Next. Loading the Model Selecting the drug You can also import existing host models by clicking here Browsing for linezolid.xml 18

Perform a Simulation: Calculation Wizard Setup 1 5. Specify the drug properties: a. Drug/Agent Name: linezolid b. Description: antibiotic (optional) c. Application type: select Therapeutic d. Select by clicking on the button next to the appropriate answer Is the drug/agent radioactive? YES NO Is the drug/agent metabolized by the liver? YES NO Does the drug/agent bind to plasma proteins? YES NO Can the drug/agent be ionized? YES NO Is there an enzyme target? YES NO e. Click Next. 6. Specify the drug properties (cont d): a. These values will be prefilled in, but you may change them, for example if you are administering a different drug/agent. Default values: Drug/Agent Name: linezolid Molecular Weight (Daltons): 337.346 Hydrodynamic Diameter (nanometers): 1.023 nm Plasma Protein Binding: 31.0 % Liver Microsome Clearance Rate (ml/min/mg protein): 2.5E-3 b. Click Next. 7. Enter the drug LogP/LogD: a. No need to modify the LogP value unless administering a different agent. A table for the logd values at different ph-s appears only if the drug/agent can be ionized. Default logp value for linezolid: 0.637 b. Click Next. Drug Properties Drug Properties (Cont.) Drug LogP/LogD 19

Perform a Simulation: Calculation Wizard Setup 1 8. Select the administration method: a. These values will be prefilled in, but you may change them, for example if you are administering a different drug/agent or administering multiple doses Default values: Drug/Agent Name: linezolid Method: Injection intravenous Number of administrations: 1 b. Click Next. 9. Specify the drug dosage: a. These values will be prefilled, change only the drug dosage to 80. Default values: Drug/Agent Name: linezolid Method: Injection intravenous Number of Administrations: 1 Dosage Units: milligrams per kilogram bodymass Start time (minutes): 0.0 Total time (minutes): 0.1 Dosage: 80 Hit Enter after entering a new value. Lines can be added to or deleted from the table for multiple administrations with the Add and Delete buttons on the right. b. Click Next. Administration Method Drug Dosage 20

Perform a Simulation: Calculation Wizard Setup 1 10. Specify the sampling times: a. The default sampling times cover 0-24 hours, with denser sampling at the beginning. The default sampling times can be changed. Individual sampling times can be added one at a time by clicking on the Add Sampling Time button. Existing times can be deleted by selecting them and click on Delete Selected Times. The Number of Samples is updated automatically after each addition or deletion. Multiple sampling times can be added using the Add Linear or the Add Non-Linear buttons. You can specify the number of samples and the sampling intervals in the pop-up dialog boxes. b. Click Next. Add Linear Sampling Sampling Times Add Non-Linear Sampling 21

Perform a Simulation: Calculation Wizard Setup 1 11. Review simulation setup: If something has been omitted or mistaken, this is the time to go back and correct it. Entered information does not get lost by going back to previous steps. You can start the simulation in the next step by clicking the checkbox next to Do you want to run the simulation right away? and clicking Finish. For now, let s just finish the setup, examine the model you set up and then start the calculation from the BioDmet GUI later. Review Simulation Setup a. Click Finish. The Simulation Setup is Complete! Back to the BioDMET GUI: The wizard window will close and the BioDMET program will now contain all of the information on the host and agent you ve just specified in the previous steps. Now would be a good time to save your work. Click on the Save As button on the top toolbar. Name and save your file to a folder of your choice (The BioDMET folder or My Documents are good places). 22

Perform a Simulation: Run the Calculation 1 Run the calculation: a. To run the calculation, click the Run button from the top toolbar. A status window will appear during the several minutes the calculation takes to run. Calculation status window BioDMET Main Screen with details of the mouse model and the administered drug linezolid after the setup BioDMET Main Screen with the calculated linazolid concentration in the plasma following the calculation 23

Perform a Simulation: Export Simulation Results 1 Simulation data & exporting: The numerical concentration-time values of the drug can be exported into an Excel worksheet for customized plotting, further analysis, or saving. Transferring the data into Excel is not absolutely necessary because BioDMET will create the plots. To save the simulation data, select File > Export Simulation Results. The data export window will appear. a. Select the spaces or sampling locations of interest: Locations > Lung b. Click on the Add Location button at the bottom of the tissue/space hierarchy panel c. Select the Entity you want to monitor: linezolid. This is the total (bound + unbound) drug concentration. You could select to save the free drug concentration as well. d. Select the Concentration Unit: Microgram per ml e. Select the Time Units: Hours f. Select the file Format: Tab-delimited. The other alternative is Comma-delimited. g. Select two more locations: Plasma and Muscle h. To save the data in a file, click on Export to File and type in a file name: linezolid_distrib_in_mouse.txt i. Browse to select the location for the file: biodmet/data/output It is a good idea to create a new output folder under your biodmet/data directory) Alternatively, you could just copy the selected data in the specified format to the clipboard and paste it into an Excel worksheet. j. Click Open, then OK to save the file and get back to BioDMET. 24

Perform a Simulation: Analyze the Results 1 Results are shown as concentration-time plots in the right lower window of the GUI. If part of the plot is not visible, you can resize the entire window or move the dotted sliding bars separating the three panels of the GUI window as indicated by the red arrows. You can: Select a Location to monitor the average agent concentration in one or multiple tissues (e.g. liver or brain). Double click on green Locations button at the lower end of the left panel then left-click on one of the blue location boxes. Select a Space by clicking on one of the dark blue Space boxes in the left window to monitor the concentration in the individual spaces (e.g. the endosome of an alveolar macrophage located in the interstitial space of the lung). The title above the plot specifies the location or space for which the concentration is shown. Configure the plot axes by clicking on the x-y Axis button. Select from several different units both for the concentration and the time Switch between linear and logarithmic scale. Space selection for concentration monitoring Customize plot axes Concentration-time plot - Monitoring the agent concentration in a specific location or space *Remember that the window panes are adjustable 25

Perform a Simulation: Analyze the Results (cont.) 1 To compare the concentration of a drug in multiple tissues, right click on the location, then select Add to plot. You can monitor either the free or the total concentration of the drug (if the drug binds to plasma proteins or to a receptor) by making the appropriate selection by clicking on either linezolid or free linezolid under Entities. Concentration-time plot Plotting drug and pathogen concentrations simultaneously Customize plot display, zoom in/out of plot data, copy plots to the clipboard, and save plots to a file by right-clicking on the plot and selecting the appropriate command from the pop-up window. 26

Perform a Simulation: Analyze the Results (cont.) 1 BioDMET also computes a set of frequently used pharmacokinetic properties of the drug: 27

Modifying the Model 2 Once the model is defined, the user can start asking what if? type questions to examine the effect of various dosing regimens or initial bacterial loads, experiment with different antibiotic types, etc. These modifications can be done directly through the user interface and the modified models can be saved for future calculations. Task 2: Add an injection There are usually multiple ways to modify an existing model in BioDMET. To add a second injection 6 hours after the first one, select one of the following options: Option 1 From the top menu bar, select Administer > Add injection Option 2 Alternatively, you can right-click on the Administer button and select Add injection. Default values: Name: Injection_2 Method: Injection intravenous Molecule: linezolid Amount: 80 Amount units: Milligrams per kilogram body mass Start time (minutes): 360 Total time (minutes): 0.1 b. Click OK. Tip: At this point, you can only select another injection of the same drug that is already present in the model. As more drugs are added to your model, they become selectable. 1 2 28

Modifying the Model 2 Task 2: Add an injection (Cont.) Now that you have modified your model, you must run the simulation to update the results. From the top icon bar, click Run Status Window Updated Results 29

Modifying the Model 3 Task 3: Change the Injected Dose a. Click on Injection_2 in the model tree view b. Click in the field with the number next to the Dosage field in the property window; delete the existing number and type in the new dose, and hit Enter. c. Click Run. b a Modifying the Administered Dose 30

Modifying the Model 4 Task 4: Change the Sampling Times If using the default non-linear sampling, you will notice that the sampling for the added injections is not exactly the same as for the original injection on the time-concentration curves. You can easily modify this by adding new sampling times or deleting existing ones. a. Click on the Times icon under Sampling in the model tree view. The sampling times will appear in the property window and the Edit Sampling Times icon from the top of the GUI becomes activated. b. Click on the Edit Sampling Times icon, and add or delete sampling times in minutes, one per line, in the window that opens up. c. Click OK. d. Click Run. Modifying the Sampling Times 31

Validating the Model 5 Task 5: Add Sampling Measurement The best way to visually compare the predicted time-concentration data to existing experimental results is to show them on the same plot. This can be achieved by exporting the simulation output for the desired tissues/spaces (see page 25) and using a plotting software such as Excel or Origin. For a quick assessment, the BioDMET GUI provides the capability to add the experimental data to the time-concentration plots. To add experimental data to your plot in BioDMET: a. Select Sampling > Add Sampling Measurement b. Select location to monitor from the dialog box: Plasma c. Click OK d. In the Measurements table that appears in the upper right panel, input the number of sampling times: 4 e. This will add four lines to the table where you can input the experimental data taken from the paper of Andes and colleagues (Figure 1, Antimicrobial Agents and Chemotherapy 46(11): 3484-3489, 2002) obtained after administering 80 mg/kg linezolid intravenously to mice: f. For the total number of Moles Administered enter: 5.22E-6 32

Validating the Model 5 Task 5: Add Sampling Measurement (Cont.) As you enter the values in the table, you will notice blue symbols appearing on your plot corresponding to the experimental measurements. Since data was measured only during the first three hours after administration, zoom in to this part of the plot. Change the time units to hours. This is what you should see: Experimental data Measurement appeared under Sampling Plot with measured and calculated data zoomed in to show the first four hours Comparison to experimental data 33

Finishing Notes: Database Provided with BioDMET The human and animal models as well as the agent/drug property files can be used as they are, they can be customized or simply serve as examples to develop new models and property files. The entire database can be downloaded from the BioDMET web site (under Downloads and Validation): http://pdsl.research.ge.com/biodmet/ The following items are provided with BioDMET: A number of different organism/healthy hosts: human, monkey, rat, guinea pig, mouse A set of pathogen model files with phases, typical symptoms and tissue bacterial loads Agent/drug properties: xml files with physico-chemical properties or a number of drugs/agents Validation set: experimental concentration-time values for a number of drugs/agents and the corresponding calculated values 34