Entering the era of computationally driven drug development

Abstract Historically, failure rates in drug development are high; increased sophistication and investment throughout the process has shifted the reasons for attrition, but the overall success rates have remained stubbornly and consistently low. Only 8% of new entities entering clinical testing gain regulatory approval, indicating that significant obstacles still exist for efficient therapeutic development. The continued high failure rate can be partially attributed to the inability to link drug exposure with the magnitude of observed safety and efficacy-related pharmacodynamic (PD) responses; frequently, this is a result of nonclinical models exhibiting poor prediction of human outcomes across a wide range of disease conditions, resulting in faulty evaluation of drug toxicology and efficacy. However, the increasing quality and standardization of experimental methods in preclinical stages of testing has created valuable data sets within companies that can be leveraged to further improve the efficiency and accuracy of preclinical prediction for both pharmacokinetics (PK) and PD. Models of Quantitative structure–activity relationships (QSAR), physiologically based pharmacokinetics (PBPK), and PK/PD relationships have also improved efficiency. Founded on a core understanding of biochemistry and physiological interactions of xenobiotics, these in silico methods have the potential to increase the probability of compound success in clinical trials. Integration of traditional computational methods with machine-learning approaches and existing internal pharma databases stands to make a fundamental impact on the speed and accuracy of predictions during the process of drug development and approval.

[1]  Alicia Rodríguez-Gascón,et al.  Applications of the pharmacokinetic/pharmacodynamic (PK/PD) analysis of antimicrobial agents. , 2015, Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy.

[2]  Lawrence X. Yu,et al.  Utility of Physiologically Based Absorption Modeling in Implementing Quality by Design in Drug Development , 2011, The AAPS Journal.

[3]  D J Rance,et al.  The prediction of human pharmacokinetic parameters from preclinical and in vitro metabolism data. , 1997, The Journal of pharmacology and experimental therapeutics.

[4]  Gerald M. Maggiora,et al.  On Outliers and Activity Cliffs-Why QSAR Often Disappoints , 2006, J. Chem. Inf. Model..

[5]  D. Howells,et al.  Can Animal Models of Disease Reliably Inform Human Studies? , 2010, PLoS medicine.

[6]  Sean Ekins,et al.  Predicting Mouse Liver Microsomal Stability with “Pruned” Machine Learning Models and Public Data , 2015, Pharmaceutical Research.

[7]  B. Ploeger,et al.  Mechanism-based pharmacokinetic-pharmacodynamic (PK-PD) modeling in translational drug research. , 2008, Trends in pharmacological sciences.

[8]  Xiaomei Zhuang,et al.  PBPK modeling and simulation in drug research and development , 2016, Acta pharmaceutica Sinica. B.

[9]  W J Jusko,et al.  Pharmacodynamics of chemotherapeutic effects: dose-time-response relationships for phase-nonspecific agents. , 1971, Journal of pharmaceutical sciences.

[10]  Stefan Willmann,et al.  Using Bayesian-PBPK modeling for assessment of inter-individual variability and subgroup stratification , 2013, In Silico Pharmacology.

[11]  U. Boelsterli Animal models of human disease in drug safety assessment. , 2003, The Journal of toxicological sciences.

[12]  William J. Jusko,et al.  A pharmacodynamic model for cell-cycle-specific chemotherapeutic agents , 1973, Journal of Pharmacokinetics and Biopharmaceutics.

[13]  G Levy,et al.  Mechanism‐based pharmacodynamic modeling , 1994, Clinical pharmacology and therapeutics.

[14]  Aman P. Singh,et al.  Application of a PK-PD Modeling and Simulation-Based Strategy for Clinical Translation of Antibody-Drug Conjugates: a Case Study with Trastuzumab Emtansine (T-DM1) , 2017, The AAPS Journal.

[15]  Benjamin Wu,et al.  The application of mechanism-based PK/PD modeling in pharmacodynamic-based dose selection of muM17, a surrogate monoclonal antibody for efalizumab. , 2006, Journal of pharmaceutical sciences.

[16]  Tae Hwan Kim,et al.  Model-based drug development: application of modeling and simulation in drug development , 2017, Journal of Pharmaceutical Investigation.

[17]  W R Gillespie,et al.  Noncompartmental Versus Compartmental Modelling in Clinical Pharmacokinetics , 1991, Clinical pharmacokinetics.

[18]  M. Bracken Why animal studies are often poor predictors of human reactions to exposure , 2009, Journal of the Royal Society of Medicine.

[19]  D. Monroe,et al.  A mouse bleeding model to study oral anticoagulants. , 2014, Thrombosis research.

[20]  L Aarons,et al.  Physiologically based pharmacokinetic modelling: a sound mechanistic basis is needed. , 2005, British journal of clinical pharmacology.

[21]  R. M. Owen,et al.  An analysis of the attrition of drug candidates from four major pharmaceutical companies , 2015, Nature Reviews Drug Discovery.

[22]  Erik Butterworth,et al.  Compartmental modeling in the analysis of biological systems. , 2012, Methods in molecular biology.

[23]  L B Sheiner,et al.  Kinetics of pharmacologic response. , 1982, Pharmacology & therapeutics.

[24]  D. Sprous,et al.  QSAR in the pharmaceutical research setting: QSAR models for broad, large problems. , 2010, Current topics in medicinal chemistry.

[25]  Sean Ekins,et al.  Opportunities and challenges using artificial intelligence in ADME/Tox , 2019, Nature Materials.

[26]  Robert P. Sheridan,et al.  Time-Split Cross-Validation as a Method for Estimating the Goodness of Prospective Prediction , 2013, J. Chem. Inf. Model..

[27]  N. Holford Clinical Pharmacokinetics and Pharmacodynamics of Warfarin , 1986, Clinical pharmacokinetics.

[28]  R. W. Hansen,et al.  Journal of Health Economics , 2016 .

[29]  A. Collins,et al.  A systematic review of the validity of patient derived xenograft (PDX) models: the implications for translational research and personalised medicine , 2018, PeerJ.

[30]  William J Jusko,et al.  Moving from basic toward systems pharmacodynamic models. , 2013, Journal of pharmaceutical sciences.

[31]  Kyungsoo Park,et al.  A Review of Modeling Approaches to Predict Drug Response in Clinical Oncology , 2016, Yonsei medical journal.

[32]  J. Meng,et al.  Investigation into the pharmacokinetic–pharmacodynamic model of Zingiberis Rhizoma / Zingiberis Rhizoma Carbonisata and contribution to their therapeutic material basis using artificial neural networks , 2017 .

[33]  V. Cristini,et al.  Nonlinear simulation of tumor necrosis, neo-vascularization and tissue invasion via an adaptive finite-element/level-set method , 2005, Bulletin of mathematical biology.

[34]  J. Dressman,et al.  Application of the relationship between pharmacokinetics and pharmacodynamics in drug development and therapeutic equivalence: a PEARRL review , 2019, The Journal of pharmacy and pharmacology.

[35]  D. Kaufman,et al.  Population Pharmacokinetics of Fluconazole in Young Infants , 2008, Antimicrobial Agents and Chemotherapy.

[36]  Lars M. Blank,et al.  Integration of genome-scale metabolic networks into whole-body PBPK models shows phenotype-specific cases of drug-induced metabolic perturbation , 2018, npj Systems Biology and Applications.

[37]  Espen A. Sjoberg Logical fallacies in animal model research , 2017, Behavioral and Brain Functions.

[38]  Jarrod Bailey,et al.  Non-human Primates in Neuroscience Research: The Case against its Scientific Necessity , 2016, Alternatives to laboratory animals : ATLA.

[39]  T. Shike,et al.  Animal models. , 2001, Contributions to nephrology.

[40]  P. Gerk,et al.  Inhibition of glucuronidation and oxidative metabolism of buprenorphine using GRAS compounds or dietary constituents/supplements: in vitro proof of concept , 2017, Biopharmaceutics & drug disposition.

[41]  Hui C. Ko,et al.  Convergence of direct and indirect pharmacodynamic response models , 1995, Journal of Pharmacokinetics and Biopharmaceutics.

[42]  K. Yoshida,et al.  Impact of Physiologically Based Pharmacokinetic Models on Regulatory Reviews and Product Labels: Frequent Utilization in the Field of Oncology , 2017, Clinical pharmacology and therapeutics.

[43]  Scott D. Kahn,et al.  Current Status of Methods for Defining the Applicability Domain of (Quantitative) Structure-Activity Relationships , 2005, Alternatives to laboratory animals : ATLA.

[44]  Stephen B Duffull,et al.  Understanding the time course of pharmacological effect: a PKPD approach. , 2011, British journal of clinical pharmacology.

[45]  L B Sheiner,et al.  Simultaneous modeling of pharmacokinetics and pharmacodynamics: application to d-tubocurarine. , 1980, Clinical pharmacology and therapeutics.

[46]  Varun Garg,et al.  Comparison of four basic models of indirect pharmacodynamic responses , 1993, Journal of Pharmacokinetics and Biopharmaceutics.

[47]  Carl Petersson,et al.  In Silico Absorption, Distribution, Metabolism, Excretion, and Pharmacokinetics (ADME-PK): Utility and Best Practices. An Industry Perspective from the International Consortium for Innovation through Quality in Pharmaceutical Development. , 2017, Journal of medicinal chemistry.

[48]  V. Sinha,et al.  PDUFA VI: It Is Time to Unleash the Full Potential of Model‐Informed Drug Development , 2018, CPT: pharmacometrics & systems pharmacology.

[49]  Rajiv Mahajan,et al.  Food and drug administration’s critical path initiative and innovations in drug development paradigm: Challenges, progress, and controversies , 2010, Journal of pharmacy & bioallied sciences.

[50]  Michael Hay,et al.  Clinical development success rates for investigational drugs , 2014, Nature Biotechnology.

[51]  Alexander Golbraikh,et al.  Predictive QSAR modeling: Methods and applications in drug discovery and chemical risk assessment , 2012 .

[52]  W. Craig,et al.  In Vivo Pharmacodynamic Activity of Daptomycin , 2004, Antimicrobial Agents and Chemotherapy.

[53]  Franco Lombardo,et al.  A hybrid mixture discriminant analysis-random forest computational model for the prediction of volume of distribution of drugs in human. , 2006, Journal of medicinal chemistry.

[54]  L Kuepfer,et al.  Applied Concepts in PBPK Modeling: How to Build a PBPK/PD Model , 2016, CPT: pharmacometrics & systems pharmacology.

[55]  Jin Y. Jin,et al.  Physiologically Based Pharmacokinetic Modeling as a Tool to Predict Drug Interactions for Antibody-Drug Conjugates , 2014, Clinical Pharmacokinetics.

[56]  Lisa E. Wagar,et al.  Advanced model systems and tools for basic and translational human immunology , 2018, Genome Medicine.

[57]  S. Batra,et al.  Concise Review: Current Status of Three‐Dimensional Organoids as Preclinical Models , 2018, Stem cells.

[58]  Weihsueh A. Chiu,et al.  Applying a Global Sensitivity Analysis Workflow to Improve the Computational Efficiencies in Physiologically-Based Pharmacokinetic Modeling , 2018, Front. Pharmacol..

[59]  W J Jusko,et al.  Precursor-dependent indirect pharmacodynamic response model for tolerance and rebound phenomena. , 1998, Journal of pharmaceutical sciences.

[60]  Rafael Gozalbes,et al.  QSAR-based solubility model for drug-like compounds. , 2010, Bioorganic & medicinal chemistry.

[61]  R. Ransohoff All (animal) models (of neurodegeneration) are wrong. Are they also useful? , 2018, The Journal of experimental medicine.

[62]  M O Karlsson,et al.  A turnover model of irreversible inhibition of gastric acid secretion by omeprazole in the dog. , 2000, The Journal of pharmacology and experimental therapeutics.

[63]  P. Toutain,et al.  Benazeprilat disposition and effect in dogs revisited with a pharmacokinetic/pharmacodynamic modeling approach. , 2000, The Journal of pharmacology and experimental therapeutics.

[64]  M. Danhof,et al.  Mechanism‐based PK/PD Modeling of the Respiratory Depressant Effect of Buprenorphine and Fentanyl in Healthy Volunteers , 2007, Clinical pharmacology and therapeutics.

[65]  Alexander Golbraikh,et al.  Predictive QSAR modeling workflow, model applicability domains, and virtual screening. , 2007, Current pharmaceutical design.

[66]  J. Venitz,et al.  Use of generally recognized as safe or dietary compounds to inhibit buprenorphine metabolism: potential to improve buprenorphine oral bioavailability , 2019, Biopharmaceutics & drug disposition.

[67]  William J Jusko,et al.  Diversity of mechanism-based pharmacodynamic models. , 2003, Drug metabolism and disposition: the biological fate of chemicals.

[68]  Lucia Marucci,et al.  Mathematical Models of Organoid Cultures , 2019, Front. Genet..

[69]  P. Hunter,et al.  Bioinformatics, multiscale modeling and the IUPS Physiome Project , 2008, Briefings Bioinform..

[70]  Vittorio Cristini,et al.  Multiscale cancer modeling. , 2010, Annual review of biomedical engineering.

[71]  Yuan Chen,et al.  Physiologically Based Pharmacokinetic Modeling to Predict Drug-Drug Interactions Involving Inhibitory Metabolite: A Case Study of Amiodarone , 2015, Drug Metabolism and Disposition.

[72]  Jingjing Yu,et al.  Physiologically Based Pharmacokinetic (PBPK) Modeling and Simulation Approaches: A Systematic Review of Published Models, Applications, and Model Verification , 2015, Drug Metabolism and Disposition.

[73]  J. Wagner,et al.  Kinetics of pharmacologic response. I. Proposed relationships between response and drug concentration in the intact animal and man. , 1968, Journal of theoretical biology.

[74]  D. Andes,et al.  Animal models in the pharmacokinetic/pharmacodynamic evaluation of antimicrobial agents. , 2016, Bioorganic & medicinal chemistry.

[75]  P. Pound,et al.  Is it possible to overcome issues of external validity in preclinical animal research? Why most animal models are bound to fail , 2018, Journal of Translational Medicine.

[76]  Johan Gabrielsson,et al.  Non-compartmental analysis. , 2012, Methods in molecular biology.

[77]  D. Gailani,et al.  Murine models in the evaluation of heparan sulfate-based anticoagulants. , 2015, Methods in molecular biology.

[78]  W J Jusko,et al.  Transit compartments versus gamma distribution function to model signal transduction processes in pharmacodynamics. , 1998, Journal of pharmaceutical sciences.

[79]  Hans Clevers,et al.  Cancer modeling meets human organoid technology , 2019, Science.

[80]  Alexander Tropsha,et al.  Best Practices for QSAR Model Development, Validation, and Exploitation , 2010, Molecular informatics.

[81]  J. Dearden,et al.  QSAR modeling: where have you been? Where are you going to? , 2014, Journal of medicinal chemistry.

[82]  Peng Li,et al.  Current status and perspectives of patient-derived xenograft models in cancer research , 2017, Journal of Hematology & Oncology.