GastroPlus-
`
`user manual
`
`November 2006 – Version 5.2
`
`Better decisions through better science
`
`simulationsp/us,inc.
`42505 10th Street West, Lancaster, California 93534-7059
`Telephone: 661-723-7723 or 888-266-9294 (toll-free U.S. and Canada)
`FAX: 661-723-5524
`E-mail: info@simulations-plus.com Web site: www.simulations-plus.com
`(AMEX :SLP)
`
`Apotex v. Cellgene - IPR2023-00512
`Petitioner Apotex Exhibit 1027-0001
`
`

`

`ii
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`Apotex v. Cellgene - IPR2023-005 12
`Petitioner Apotex Exhibit 1027-0002
`
`Apotex v. Cellgene - IPR2023-00512
`Petitioner Apotex Exhibit 1027-0002
`
`

`

`Warranty Exclusion
`
`Simulations Plus, Inc. makes no representations or warranties, expressed or
`implied, concerning the use of the information contained in this document, its
`accuracy, or results that may be obtained from its use, and makes no expressed or
`implied warranties of merchantability or fitness for a particular purpose.
`Simulations Plus, Inc. shall not be liable for any damages or losses of any type
`arising from its use. Final determination of the suitability of this information, for
`the use contemplated by the Buyer, is the sole responsibility of the Buyer, and
`Simulations Plus, Inc. shall have no responsibility in connection with such
`suitability. All information contained in this document is provided "As Is".
`Simulations Plus, Inc. makes no legal warranties, implied or otherwise, as to the
`credibility or accuracy of any information provided.
`
`© Copyright 1998-2006 Simulations Plus, Inc.
`
`All rights reserved. No part of this manual may be reproduced, stored in any retrieval system, or
`transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or
`otherwise, without prior written permission from Simulations Plus, Inc.
`
`Printed in the United States of America.
`
`GastroPlus™, ClassPharmerTM, DDDPlus™, MembranePlus™, QMPRPlus™, ADMET
`Predictor™, QMPRchitect™, and ADMET Modeler™ are trademarks of Simulations Plus, Inc.
`Windows®, Windows NT™, Microsoft® Excel™, and Microsoft® Access™ are trademarks or
`registered trademarks of Microsoft Corporation. Pentium® is a registered trademark of Intel
`Corporation. ISIS/Base™ and ISIS/Draw™ are trademarks of MDL Information Systems, Inc.
`
`iii
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`Apotex v. Cellgene - IPR2023-00512
`Petitioner Apotex Exhibit 1027-0003
`
`

`

`iv
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`Apotex v. Cellgene - IPR2023-005 12
`Petitioner Apotex Exhibit 1027-0004
`
`Apotex v. Cellgene - IPR2023-00512
`Petitioner Apotex Exhibit 1027-0004
`
`

`

`TABLE OF CONTENTS
`TABLE OF CONTENTS .......................................................................................................... v
`1.0 Introduction and program overview............................................................................ 2
`1.1 What is GastroPlus? ............................................................................................................ 2
`1.2 How GastroPlus can be used in drug discovery................................................................ 4
`1.2.1 Predicting percent absorbed ............................................................................................ 5
`1.2.2 Parameter Sensitivity Analysis (PSA)............................................................................. 5
`1.2.3 General model building................................................................................................... 6
`1.3 How GastroPlus can be used in drug development .......................................................... 6
`1.3.1 Drug-specific model building.......................................................................................... 6
`1.3.2 Dosage formulation evaluation and design ..................................................................... 7
`1.3.3 Controlled release evaluation and design........................................................................ 7
`1.3.4 Pharmacokinetic studies.................................................................................................. 7
`1.3.5 Parameter Sensitivity Analysis........................................................................................ 8
`1.3.6 Virtual Trials ................................................................................................................... 8
`1.3.7 Drug metabolism and nonlinear dose-PK response ........................................................ 8
`1.3.8 Pharmacodynamic simulations........................................................................................ 9
`2.0 Installing GastroPlus ................................................................................................. 10
`2.1 System requirements ......................................................................................................... 10
`2.2 Installing GastroPlus on your computer.......................................................................... 10
`2.3 Standalone installation ...................................................................................................... 10
`2.4 Authorizing GastroPlus on your computer ..................................................................... 10
`2.5 Network installation .......................................................................................................... 11
`2.6 User log ............................................................................................................................... 12
`2.7 Other versions .................................................................................................................... 13
`2.7.1 Demonstration Version ................................................................................................. 13
`3.0 Running GastroPlus simulations .............................................................................. 14
`3.1 Simulation inputs ............................................................................................................... 14
`3.1.1 Creating a new database................................................................................................ 15
`3.1.2 Opening a database ....................................................................................................... 15
`3.1.3 Compound tab ............................................................................................................... 15
`3.1.3.1 Selected Compound section ...................................................................................... 15
`3.1.3.2 Drug Information box................................................................................................ 20
`3.1.3.3 Formulation variables................................................................................................ 20
`3.1.3.4 Effective Permeability section................................................................................... 25
`3.1.3.5 Nondimensional biopharmaceutical characterization numbers................................. 27
`3.1.3.6 Setting database defaults ........................................................................................... 28
`3.1.4 Physiology tab............................................................................................................... 28
`3.1.5 Pharmacokinetics tab..................................................................................................... 32
`3.1.6 Simulation tab ............................................................................................................... 37
`3.1.7 Graph tab....................................................................................................................... 39
`3.1.8 Menu bar ....................................................................................................................... 40
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`v
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`Apotex v. Cellgene - IPR2023-00512
`Petitioner Apotex Exhibit 1027-0005
`
`

`

`3.1.8.1 File............................................................................................................................. 40
`3.1.8.2 Edit ............................................................................................................................ 50
`3.1.8.3 Database .................................................................................................................... 51
`3.1.8.4 Simulation Setup ....................................................................................................... 55
`3.1.8.5 Controlled Release .................................................................................................... 59
`3.1.8.6 Modules (optional) .................................................................................................... 62
`3.1.8.7 Help ........................................................................................................................... 62
`3.2 Running simulations.......................................................................................................... 63
`3.2.1 Single Simulation mode ................................................................................................ 63
`3.2.1.1 Single Simulation Input............................................................................................. 65
`3.2.1.2 Single Simulation Output .......................................................................................... 65
`3.2.1.3 Gastrointestinal tract graphical display ..................................................................... 66
`3.2.2 Batch Simulation mode ................................................................................................. 66
`3.2.2.1 Batch Mode Input...................................................................................................... 68
`3.2.2.2 Batch Mode Display Output...................................................................................... 68
`3.2.2.3 Batch Mode Output File............................................................................................ 68
`3.2.3 Virtual Trial mode......................................................................................................... 68
`3.2.3.1 Virtual Trial Mode Input ........................................................................................... 73
`3.2.3.2 Virtual Trial Mode Output ........................................................................................ 73
`3.2.3.3 Virtual Trial panel ..................................................................................................... 74
`3.2.3.4 Parameter distribution functions ............................................................................... 76
`3.2.3.5 Virtual Trial Parameters file menu............................................................................ 77
`3.2.4 Parameter Sensitivity Analysis mode............................................................................ 78
`3.3 Graph tab ........................................................................................................................... 80
`3.3.1 New Plot Window in Single Simulation Mode............................................................. 84
`3.3.1.1 – Select Curves.......................................................................................................... 85
`4.0 Simulation model description .................................................................................... 88
`4.1 Original Compartmental Absorption and Transit (CAT) model.................................. 88
`4.2 Advanced CAT (ACAT) model......................................................................................... 90
`4.2.1 Numerical integration.................................................................................................... 91
`4.2.2 Release .......................................................................................................................... 92
`4.2.3 Solubility and dissolution.............................................................................................. 92
`4.2.4 Lumenal degradation..................................................................................................... 97
`4.2.5 Absorption..................................................................................................................... 98
`4.2.5.1 Effective permeability and absorption rate coefficient ............................................. 98
`4.2.5.2 Absorption Scale Factor (ASF) models in GastroPlus.............................................. 99
`4.2.6 Compartmental Pharmacokinetics............................................................................... 104
`4.2.6.1 Enterohepatic Circulation (EHC) ............................................................................ 105
`4.2.7
`Saturable processes in the gut and in the liver....................................................... 106
`4.2.7.1 Saturable liver metabolism...................................................................................... 106
`4.2.7.2 Saturable gut metabolism ........................................................................................ 108
`4.2.7.3 Saturable carrier-mediated transport ....................................................................... 109
`4.2.8 Pharmacodynamic simulations.................................................................................... 110
`4.2.8.1 Introduction ............................................................................................................. 110
`4.2.8.2 Direct response models ........................................................................................... 110
`4.2.8.3 Indirect models........................................................................................................ 112
`4.2.9 Physiologically-based Pharmacokinetics (PBPK)....................................................... 116
`4.2.9.1 Introduction ............................................................................................................. 116
`4.2.9.2 Perfusion-limited tissues ......................................................................................... 117
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`vi
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`Apotex v. Cellgene - IPR2023-00512
`Petitioner Apotex Exhibit 1027-0006
`
`

`

`4.2.9.3 Permeability-limited tissues .................................................................................... 118
`4.2.9.4 Enterohepatic Circulation (EHC) in PBPK ............................................................. 120
`4.2.9.5 Calculation of tissue:plasma partition coefficients.................................................. 121
`4.2.9.6 Population Estimates for Age-Related Physiology (PEAR) ................................... 124
`5.0 GastroPlus Tutorial .............................................................................................. 126
`5.1 Introduction...................................................................................................................... 126
`5.2 Overview of GastroPlus................................................................................................... 127
`5.3 Common simulations that can be run with GastroPlus (no optional modules).......... 128
`5.3.1 Predict the fraction absorbed of a drug using in vitro properties ................................ 129
`5.3.2 Predict the fraction absorbed for a new compound..................................................... 130
`5.3.3 Predict Fa using in vivo data in other species and in vitro data................................... 130
`5.3.4 Ionization effects in GastroPlus .................................................................................. 132
`5.3.5 Support files ................................................................................................................ 134
`5.3.6 Screening a database of compounds for fraction absorbed and ranking them by order.
`.............................................................................................................................................. 139
`5.3.7 Running a Parameter Sensitivity Analysis .................................................................. 140
`5.3.8 Running a Virtual Trial ............................................................................................... 142
`5.3.9 Controlled release........................................................................................................ 144
`5.3.10 Enterohepatic circulation........................................................................................... 147
`5.4 Additional modules with GastroPlus ............................................................................. 149
`5.4.1 Optimization................................................................................................................ 149
`5.4.2 PKPlus™..................................................................................................................... 151
`5.4.3 Metabolism and Transporter Module.......................................................................... 152
`5.4.4 PDPlus™ – Pharmacodynamics Example .................................................................. 154
`5.4.5 PBPKPlus™ – Physiologically Based Pharmacokinetics Module.............................. 155
`APPENDIX A: Glossary............................................................................................... 158
`APPENDIX B: References ........................................................................................... 164
`APPENDIX C: Import ASCII Data ............................................................................. 170
`TABLE: DrugDataTable-GastDemo.xls............................................................................. 170
`TABLE: AcidBaseTable-GastDemo.xls ............................................................................. 172
`TABLE: EnzymesTable-GastDemo.xls .............................................................................. 173
`TABLE: TransporterTable-GastDemo.xls .......................................................................... 173
`TABLE: PharmacodynamicsTable-GastDemo.xls.............................................................. 173
`TABLE: PBPKParamsTable-GastDemo.xls ....................................................................... 174
`TABLE: Formats for support data files............................................................................... 175
`Steps to create a new GastroPlus database by importing ASCII text files....................... 179
`APPENDIX D: Optimization Module ........................................................................... 182
`D.1 What is the Optimization Module? ............................................................................... 182
`D.2 Unlocking the Optimization Module............................................................................. 182
`D.3 What can I do with the Optimization Module?............................................................ 182
`D.4 The Objective function ................................................................................................... 183
`D.5 Running optimizations.................................................................................................... 183
`Build your database:............................................................................................................. 183
`Select “Modules (optional)” from the menu bar: ................................................................. 184
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`vii
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`Apotex v. Cellgene - IPR2023-00512
`Petitioner Apotex Exhibit 1027-0007
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`

`

`Select “Optimization”: ......................................................................................................... 184
`Select “Select Parameters and Objective Function”: ........................................................... 184
`Select parameters to be optimized:....................................................................................... 185
`Select “Next”:....................................................................................................................... 185
`Observation Weights:.......................................................................................................... 188
`Select “Next”:....................................................................................................................... 189
`Simulation tab: ..................................................................................................................... 191
`Click on the Optimize button ............................................................................................... 191
`Akaike Information Criterion and Schwarz Criterion......................................................... 194
`D6. Are there any tricks to using optimization? ................................................................. 195
`APPENDIX E: In Vitro – In Vivo Correlation Module............................................... 196
`E.1 What is the In Vitro – In Vivo Correlation Module?................................................... 196
`E.2 Unlocking the In Vitro – In Vivo Correlation Module ................................................ 197
`E.3 What can I do with the In Vitro – In Vivo Correlation Module? ............................... 197
`APPENDIX F: PKPlus™ Module ................................................................................ 200
`F.1 What is the PKPlus™ Module? ..................................................................................... 200
`F.2 Unlocking the PKPlus™ Module ................................................................................... 200
`F.3 What can I do with the PKPlus™ Module?.................................................................. 201
`F.4 Main Menu items............................................................................................................. 201
`F.4.1 File .............................................................................................................................. 202
`F.4.1.1 Load .ipd file........................................................................................................... 202
`F.4.1.2 Save PKPlus™ output as ASCII text ...................................................................... 202
`F.4.1.3 View/Edit ASCII text file........................................................................................ 203
`F.4.1.4 Export...................................................................................................................... 203
`F.4.1.5 Exit.......................................................................................................................... 203
`F.4.2 Model Options ............................................................................................................ 203
`F.4.2.1 – 1 Linear kinetics solution..................................................................................... 203
`F.4.2.2 - 2 Nonlinear kinetics solution ................................................................................ 203
`F.4.2.2 – 3 Fixed Vd (Dose/C0) for 1-compt bolus dose..................................................... 203
`F.4.2.3 – 4 Find Vd for 1-compt bolus dose......................................................................... 204
`F.4.3 Search Method ............................................................................................................ 204
`F.4.3.1 – 1 Hooke & Jeeves Pattern Search ........................................................................ 204
`F.4.3.2 – 2 Nelder-Mead Simplex ....................................................................................... 204
`F.4.4 Objective Function Weighting.................................................................................... 205
`F.5 Input IV Dose, Infusion Time, Body Weight ................................................................ 206
`F.6 Plot Model selector and Plot Type selector ................................................................... 206
`F.7 Solve for Compartment selector..................................................................................... 207
`F.8 Solve/Stop button............................................................................................................. 207
`F.9 Output window ................................................................................................................ 207
`APPENDIX G: Metabolism and Transporter Module ................................................ 208
`G.1 What is the Metabolism and Transporter Module? .................................................... 208
`G.2 Unlocking the Metabolism and Transporter Module.................................................. 208
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`Apotex v. Cellgene - IPR2023-00512
`Petitioner Apotex Exhibit 1027-0008
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`G.3 What can I do with the Metabolism and Transporter Module? ................................ 209
`G.4 Enzymes table.................................................................................................................. 209
`G.5 Transporters table .......................................................................................................... 211
`G.6 Metabolism and Transporter Module Units Converter.............................................. 211
`APPENDIX H: PDPlus Module.................................................................................... 216
`H.1 What is the PDPlus Module? ......................................................................................... 216
`H.2 Unlocking the PDPlus Module....................................................................................... 216
`H.3 What can I do with the PDPlus Module? ..................................................................... 217
`H.4 Pharmacodynamics table ............................................................................................... 218
`APPENDIX I: PBPKPlus™ Module ............................................................................ 220
`I.1 What is the PBPKPlus Module? ..................................................................................... 220
`I.2 Unlocking the PBPKPlus Module................................................................................... 220
`I.3 What can I do with the PBPKPlus Module?.................................................................. 220
`I.4 PBPK Table and PBPK Editor ....................................................................................... 221
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`Apotex v. Cellgene - IPR2023-00512
`Petitioner Apotex Exhibit 1027-0009
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`

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`1
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`Apotex v. Cellgene - IPR2023-005 12
`Petitioner Apotex Exhibit 1027-0010
`
`Apotex v. Cellgene - IPR2023-00512
`Petitioner Apotex Exhibit 1027-0010
`
`

`

`1.0 Introduction and program overview
`
`This manual is divided into five major sections and a number of appendices. This section
`provides a basic description of GastroPlus™ and suggests some ways it can be used in drug
`discovery and development. Installation instructions and system requirements are presented in
`Section 2. Section 3 provides instructions on setting up and running the program. Section 4
`describes the mathematical models used in the program. Section 5 provides a Tutorial with a
`number of examples to help you learn how to use GastroPlus in your work. The appendices
`provide a glossary, reference list, instructions for importing ASCII data, and descriptions of the
`six optional modules available at the time of this writing: In vitro – In vivo Correlation,
`Optimization, Metabolism and Transporter, PKPlus™, PDPlus™, and PBPKPlus™.
`
`~ GastroPlus{TM) : ~idazolam-PD\Midazolam-PD-2 .mdb
`Eile
`!;_dit
`!)_atabase
`:limulation Setup Controlled !ielease Modules (Opt[onal)
`
`tielp
`Simulation
`.!;_ompound
`PharmacQkinetics
`Ph~siology
`.!araph
`Selected Compo!!_nd - -~ . - - - - - - - - - - - - - - - - - - - - - - - - -
`~
`--, SI Trans Time (h) = 3.239
`Mean Abs Time (h) = 0.474
`P8PK 15GFJ ~ .:.J Longest Diss. Time (h) is@ pH 6.8 = 0.276 hours
`~
`Max Abs Dose (S+)= 3.936E+4 mg.
`Max Abs Dose (lit)= 2.428E+1 mg.
`................................... Support Files ..................................... .
`P8PK 15GFJ.opd
`P8PK 15GFJ.efd
`
`Current= 1; Total= 4
`
`l'.J~IBJ
`
`Dosage jlR: Solution
`Form:
`
`C I
`
`1/
`
`F
`
`Molecular Formula: I C18H13CIFN3
`Molecular l/leight(g/mol): I 325. 78
`logP (neutral): fT7 @pH: r,
`I
`p.!S.a Table
`I
`I
`
`Tran.sporter Table
`
`Enzyme Table
`
`~ Effective Permeability- -
`....:J
`Initial Dose (mg): J15
`Source: ) Human
`Subsequent Doses, mg: JO
`Dosing Interval, h: JO
`Dose volume (ml): )200
`pH for Reference Solubility: fTJ
`Solubility (mg/ml @pH=7.3): I 0.0103
`Mean Precipitation time (sec): rs-
`Diff. Coeff. (cm'2/s x 10'5): j 0.856 I Absorption No . • 6.83
`Drug Particle Density (g/ml): fu ·
`I I Dissolution No. • 11. 751
`Particle Radius= 1
`
`Peff (cm/s x 10'4):
`
`3.5
`
`Convert from User Data
`
`Simulation Peff x10'4 = 3.5
`
`1.1 What is GastroPlus?
`GastroPlus is an advanced technology computer program that simulates gastrointestinal
`absorption, pharmacokinetics, and optionally, pharmacodynamic effects, for drugs dosed orally
`and/or intravenously in humans and animals.
`
`The fraction absorbed in GastroPlus is defined as the net fraction of the dose that is absorbed
`across the apical membrane and into the epithelial cells in the gastrointestinal tract. Note that this
`does not necessarily mean that the drug crossed the basolateral membrane of the epithelial cells to
`
`2
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`Apotex v. Cellgene - IPR2023-00512
`Petitioner Apotex Exhibit 1027-0011
`
`

`

`reach the blood of the mesentary and then on to the portal vein – only that it left the lumen and
`went into the cells lining the gut wall. For drugs that undergo metabolism in the gut enterocytes,
`the amount of drug that reaches the portal vein will be less than the amount that was absorbed. In
`addition, some drug may be left in the enterocytes at the end of a simulation.
`
`Based on Fick’s First Law, the GastroPlus simulation allows exsorption (secretion from
`enterocytes to lumen) as well as absorption from lumen to enterocytes. Therefore, the fraction
`absorbed is calculated as the net absorption – exsorption causes a reduction in fraction absorbed
`unless the secreted drug is later completely reabsorbed before the end of the simulation.
`
`Enterohepatic circulation can also be simulated, and when it is, the fraction absorbed reported by
`GastroPlus may exceed 100%, because some of the dose may be absorbed more than once.
`
`A one-, two-, or three-compartment pharmacokinetic model allows prediction of plasma
`concentration (Cp)-time profiles with appropriate additional inputs, accounting for the interactions
`between absorption and pharmacokinetics seen with some drugs. The physiologically based
`pharmacokinetics (PBPK) model in the optional PBPKPlus™ module allows for prediction of
`drug distribution in various tissues as well as clearance profiles specific for given tissues. With
`the optional PDPlus™ Module, multiple pharmacodynamic effects can be fitted and predicted as
`well. Pharmacodynamic models can be based on drug concentrations in individual tissues (rather
`than central compartment plasma) through the combined use of PBPKPlus and PDPlus.
`
`Six optional modules are available to extend the capabilities of GastroPlus™ beyond the basic
`absorption and pharmacokinetic simulation. Optional modules currently available include:
`
`• Optimization Module
`•
`In Vitro – In Vivo Correlation Module
`• Metabolism and Transporter Module
`• PKPlus™ - Intravenous (iv) Pharmacokinetics Module
`• PDPlus™ - Pharmacodynamics Module
`• PBPKPlus™ - Physiologically Based Pharmacokinetics Module
`
`The simulation consists of the numerical integration of differential equations that coordinate a set
`of well-characterized physical phenomena that occur and interact as a result of drug transport,
`dissolution/precipitation, lumenal degradation, absorption/exsorption, excretion, gut metabolism,
`distribution, hepatic metabolism, enterohepatic circulation, renal clearance, and other clearance
`mechanisms.
`
`The mathematical model for the absorption/pharmacokinetic simulation (which is described in
`detail in Section 4) accounts for:
`
`• Physicochemical properties of the compound under study: lipophilicity, pKa’s,
`solubility, diffusion coefficient, and effective permeability.
`• The pH dependence of solubility, permeability, and dissolution/precipitation, including
`dissolution rates for different particle sizes when a particle size distribution is specified
`• Formulation variables for both immediate release and controlled release dosage forms.
`•
`Intravenous (iv) bolus and infusion dosage forms.
`• Mixed multiple doses – combining any combination of iv and peroral (PO) doses of
`arbitrary amounts at arbitrary times, and changing from fasted to fed states (or vice versa)
`at any time
`
`3
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`Apotex v. Cellgene - IPR2023-00512
`Petitioner Apotex Exhibit 1027-0012
`
`

`

`• Physiological variables: pH’s, transit