ABSTRACT
Since the Open Source Initiative laid the foundation for the open source software environment in 1998, the popularity of free and open source software has been steadily increasing. Model-informed drug discovery and development (MID3), a key component of pharmaceutical research and development, heavily makes use of computational models which can be developed using various software including the Open Systems Pharmacology (OSP) software (PK-Sim/MoBi), a free and open source software tool for physiologically based pharmacokinetic (PBPK) modeling. In this study, we aimed to investigate the impact, application areas, and reach of the OSP software as well as the relationships and collaboration patterns between organizations having published OSP-related articles between 2017 and 2023. Therefore, we conducted a bibliometric analysis of OSP-related publications and a social network analysis of the organizations with which authors of OSP-related publications were affiliated. On several levels, we found evidence for a significant growth in the size of the OSP community as well as its visibility in the MID3 community since OSP's establishment in 2017. Specifically, the annual publication rate of PubMed-indexed PBPK-related articles using the OSP software outpaced that of PBPK-related articles using any software. Our bibliometric analysis and network analysis demonstrated that the expansion of the OSP community was predominantly driven by new authors and organizations without prior connections to the community involving the generation of research clusters de novo and an overall diversification of the network. These findings suggest an ongoing evolution of the OSP community toward a more segmented, diverse, and inclusive network.
Subject(s)
Bibliometrics , Models, Biological , Social Network Analysis , Humans , Software , Pharmacokinetics , Drug Discovery/methodsABSTRACT
Accurate prediction of a new compound's pharmacokinetic (PK) profile is pivotal for the success of drug discovery programs. An initial assessment of PK in preclinical species and humans is typically performed through allometric scaling and mathematical modeling. These methods use parameters estimated from in vitro or in vivo experiments, which although helpful for an initial estimation, require extensive animal experiments. Furthermore, mathematical models are limited by the mechanistic underpinning of the drugs' absorption, distribution, metabolism, and elimination (ADME) which are largely unknown in the early stages of drug discovery. In this work, we propose a novel methodology in which concentration versus time profile of small molecules in rats is directly predicted by machine learning (ML) using structure-driven molecular properties as input and thus mitigating the need for animal experimentation. The proposed framework initially predicts ADME properties based on molecular structure and then uses them as input to a ML model to predict the PK profile. For the compounds tested, our results demonstrate that PK profiles can be adequately predicted using the proposed algorithm, especially for compounds with Tanimoto score greater than 0.5, the average mean absolute percentage error between predicted PK profile and observed PK profile data was found to be less than 150%. The suggested framework aims to facilitate PK predictions and thus support molecular screening and design earlier in the drug discovery process.
Subject(s)
Drug Discovery , Machine Learning , Animals , Rats , Drug Discovery/methods , Pharmaceutical Preparations/metabolism , Pharmaceutical Preparations/chemistry , Humans , Models, Biological , Algorithms , Molecular Structure , Pharmacokinetics , Small Molecule Libraries/pharmacokineticsABSTRACT
Tusamitamab ravtansine is an antibody-drug conjugate (ADC) composed of a humanized monoclonal antibody (IgG1) and DM4 payload. Even if DM4 and its main metabolite methyl-DM4 (Me-DM4) circulate at low concentrations after ADC administration, their potential as perpetrators of cytochrome P450 mediated drug-drug interaction was assessed. In vitro studies in human hepatocytes indicated that Me-DM4 elicited a clear concentration-dependent down regulation of cytochrome P450 enzymes (CYP3A4, 1A2, and 2B6). Because DM4 was unstable under the incubation conditions studied, the in vitro constants could not be determined for this entity. Thus, to predict the clinical relevance of this observed downregulation, an in vitro-in vivo extrapolation (IVIVE) pharmacokinetic (PK) based approach was developed. To mitigate model prediction errors and because of their similar inhibitory effect on tubulin polymerization, the same downregulation constants were used for DM4 and Me-DM4. This approach describes the time course of decreasing CYP3A4, 1A2, and 2B6 enzyme amounts as a function of circulating concentrations of DM4 and Me-DM4 predicted from a population PK model. The developed IVIVE-PK model showed that the highest CYP abundance decrease was observed for CYP3A4, with a transient reduction of < 10% from baseline. The impact on midazolam exposure, as probe substrate of CYP3A, was then simulated based on a physiologically-based PK static method. The maximal CYP3A4 abundance reduction was associated with a predicted midazolam area under the curve (AUC) ratio of 1.14. To conclude, the observed in vitro downregulation of CYPs by Me-DM4 is not expected to have relevant clinical impact.
Subject(s)
Antibodies , Cytochrome P-450 CYP3A , Midazolam , Humans , Cytochrome P-450 CYP3A/metabolism , Down-Regulation , Midazolam/pharmacokinetics , Cytochrome P-450 Enzyme System/metabolism , Drug InteractionsABSTRACT
The antiarrhythmic agent quinidine is a potent inhibitor of cytochrome P450 (CYP) 2D6 and P-glycoprotein (P-gp) and is therefore recommended for use in clinical drug-drug interaction (DDI) studies. However, as quinidine is also a substrate of CYP3A4 and P-gp, it is susceptible to DDIs involving these proteins. Physiologically-based pharmacokinetic (PBPK) modeling can help to mechanistically assess the absorption, distribution, metabolism, and excretion processes of a drug and has proven its usefulness in predicting even complex interaction scenarios. The objectives of the presented work were to develop a PBPK model of quinidine and to integrate the model into a comprehensive drug-drug(-gene) interaction (DD(G)I) network with a diverse set of CYP3A4 and P-gp perpetrators as well as CYP2D6 and P-gp victims. The quinidine parent-metabolite model including 3-hydroxyquinidine was developed using pharmacokinetic profiles from clinical studies after intravenous and oral administration covering a broad dosing range (0.1-600 mg). The model covers efflux transport via P-gp and metabolic transformation to either 3-hydroxyquinidine or unspecified metabolites via CYP3A4. The 3-hydroxyquinidine model includes further metabolism by CYP3A4 as well as an unspecific hepatic clearance. Model performance was assessed graphically and quantitatively with greater than 90% of predicted pharmacokinetic parameters within two-fold of corresponding observed values. The model was successfully used to simulate various DD(G)I scenarios with greater than 90% of predicted DD(G)I pharmacokinetic parameter ratios within two-fold prediction success limits. The presented network will be provided to the research community and can be extended to include further perpetrators, victims, and targets, to support investigations of DD(G)Is.
Subject(s)
Cytochrome P-450 CYP2D6 , Cytochrome P-450 CYP3A , Humans , Cytochrome P-450 CYP2D6/genetics , Cytochrome P-450 CYP2D6/metabolism , Cytochrome P-450 CYP3A/genetics , Cytochrome P-450 CYP3A/metabolism , Quinidine , ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics , Drug Interactions , Models, Biological , Cytochrome P-450 CYP3A Inhibitors/pharmacokineticsABSTRACT
The immunosuppressant and narrow therapeutic index drug tacrolimus is metabolized mainly via cytochrome P450 (CYP) 3A4 and CYP3A5. For its pharmacokinetics (PK), high inter- and intra-individual variability can be observed. Underlying causes include the effect of food intake on tacrolimus absorption as well as genetic polymorphism in the CYP3A5 gene. Furthermore, tacrolimus is highly susceptible to drug-drug interactions, acting as a victim drug when coadministered with CYP3A perpetrators. This work describes the development of a whole-body physiologically based pharmacokinetic model for tacrolimus as well as its application for investigation and prediction of (i) the impact of food intake on tacrolimus PK (food-drug interactions [FDIs]) and (ii) drug-drug(-gene) interactions (DD[G]Is) involving the CYP3A perpetrator drugs voriconazole, itraconazole, and rifampicin. The model was built in PK-Sim® Version 10 using a total of 37 whole blood concentration-time profiles of tacrolimus (training and test) compiled from 911 healthy individuals covering the administration of tacrolimus as intravenous infusions as well as immediate-release and extended-release capsules. Metabolism was incorporated via CYP3A4 and CYP3A5, with varying activities implemented for different CYP3A5 genotypes and study populations. The good predictive model performance is demonstrated for the examined food effect studies with 6/6 predicted FDI area under the curve determined between first and last concentration measurements (AUClast ) and 6/6 predicted FDI maximum whole blood concentration (Cmax ) ratios within twofold of the respective observed ratios. In addition, 7/7 predicted DD(G)I AUClast and 6/7 predicted DD(G)I Cmax ratios were within twofold of their observed values. Potential applications of the final model include model-informed drug discovery and development or the support of model-informed precision dosing.
Subject(s)
Cytochrome P-450 CYP3A , Tacrolimus , Humans , Cytochrome P-450 CYP3A/genetics , Cytochrome P-450 CYP3A/metabolism , Pharmaceutical Preparations , Immunosuppressive Agents , Drug Interactions , GenotypeABSTRACT
The development of novel candidate molecules for tuberculosis remains challenging, as drug distribution into the target tissue is not fully characterised in preclinical models of infection. Often antitubercular human dose selection is derived from pharmacokinetic data in plasma. Here, we explore whether whole-body physiologically-based pharmacokinetic (PBPK) modelling enables the prediction of lung exposure to anti-tubercular drugs in humans. Whole-body PBPK models were developed for rifampicin, isoniazid, pyrazinamide, and ethambutol using plasma data in mice as basis for the prediction of lung exposure. Model parameters were subsequently used to extrapolate disposition properties from mouse and determine lung:plasma ratio in humans. Model predictions were compared to biopsy data from patients. Predictions were deemed adequate if they fell within two-fold range of the observations. The concentration vs time profiles in lung were adequately predicted in mice. Isoniazid and pyrazinamide lung exposures were predicted to be comparable to plasma levels, whereas ethambutol lung exposure was predicted to be higher than in plasma. Lung:plasma ratio in humans could be reasonably predicted from preclinical data, but was highly dependent on the distribution model. This analysis showed that plasma pharmacokinetics may be used in conjunction with PBPK modelling to derive lung tissue exposure in mice and humans during early lead optimisation phase. However, the impact of uncertainty in predicted tissue exposure due to distribution should be always investigated through a sensitivity analysis when only plasma data is available. Despite these limitations, insight into lung tissue distribution represents a critical step for the dose rationale in tuberculosis patients.
Subject(s)
Ethambutol , Tuberculosis , Animals , Antitubercular Agents/pharmacokinetics , Ethambutol/pharmacokinetics , Humans , Isoniazid , Lung , Mice , Pyrazinamide , Tuberculosis/drug therapyABSTRACT
Whole-body physiologically based pharmacokinetic (WB-PBPK) models have become an important tool in drug development, as they enable characterization of pharmacokinetic profiles across different organs based on physiological (systems-specific) and physicochemical (drug-specific) properties. However, it remains unclear which data are needed for accurate predictions when applying the approach to novel candidate molecules progressing into the clinic. In this work, as case study, we investigated the predictive performance of WB-PBPK models both for prospective and retrospective evaluation of the pharmacokinetics of ethambutol, considering scenarios that reflect different stages of development, including settings in which the data are limited to in vitro experiments, in vivo preclinical data, and when some clinical data are available. Overall, the accuracy of PBPK model-predicted systemic and tissue exposure was heavily dependant on prior knowledge about the eliminating organs. Whilst these findings may be specific to ethambutol, the challenges and potential limitations identified here may be relevant to a variety of drugs, raising questions about (1) the minimum requirements for prospective use of WB-PBPK models during the characterization of drug disposition and (2) implication of uncertainty for dose selection in humans.
Subject(s)
Antitubercular Agents/pharmacokinetics , Drug Development , Ethambutol/pharmacokinetics , Models, Biological , Antitubercular Agents/blood , Antitubercular Agents/urine , Ethambutol/blood , Ethambutol/urine , HumansSubject(s)
Pharmacology, Clinical/methods , Access to Information , Computer Simulation , Humans , Systems BiologyABSTRACT
BACKGROUND: Physiologically-based pharmacokinetic (PBPK) modeling has received growing interest as a useful tool for the assessment of drug pharmacokinetics by continuous knowledge integration. OBJECTIVE: The objective of this study was to build a ciprofloxacin PBPK model for intravenous and oral dosing based on a comprehensive literature review, and evaluate the predictive performance towards pediatric and geriatric patients. METHODS: The aim of this report was to establish confidence in simulations of the ciprofloxacin PBPK model along the development process to facilitate reliable predictions outside of the tested adult age range towards the extremes of ages. Therefore, mean data of 69 published clinical trials were identified and integrated into the model building, simulation and verification process. The predictive performance on both ends of the age scale was assessed using individual data of 258 subjects observed in own clinical trials. RESULTS: Ciprofloxacin model verification demonstrated no concentration-related bias and accurate simulations for the adult age range, with only 4.8% of the mean observed data points for intravenous administration and 12.1% for oral administration being outside the simulated twofold range. Predictions towards the extremes of ages for the area under the plasma concentration-time curve (AUC) and the maximum plasma concentration (Cmax) over the entire span of life revealed a reliable estimation, with only two pediatric AUC observations outside the 90% prediction interval. CONCLUSION: Overall, this ciprofloxacin PBPK modeling approach demonstrated the predictive power of a thoroughly informed middle-out approach towards age groups of interest to potentially support the decision-making process.
Subject(s)
Anti-Bacterial Agents/administration & dosage , Ciprofloxacin/administration & dosage , Models, Biological , Administration, Intravenous , Administration, Oral , Adolescent , Adult , Age Factors , Aged , Aged, 80 and over , Anti-Bacterial Agents/pharmacokinetics , Area Under Curve , Child , Child, Preschool , Ciprofloxacin/pharmacokinetics , Computer Simulation , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Reproducibility of Results , Young AdultABSTRACT
The environmental fates of pharmaceuticals and the effects of crop protection products on non-target species are subjects that are undergoing intense review. Since measuring the concentrations and effects of xenobiotics on all affected species under all conceivable scenarios is not feasible, standard laboratory animals such as rabbits are tested, and the observed adverse effects are translated to focal species for environmental risk assessments. In that respect, mathematical modelling is becoming increasingly important for evaluating the consequences of pesticides in untested scenarios. In particular, physiologically based pharmacokinetic/toxicokinetic (PBPK/TK) modelling is a well-established methodology used to predict tissue concentrations based on the absorption, distribution, metabolism and excretion of drugs and toxicants. In the present work, a rabbit PBPK/TK model is developed and evaluated with data available from the literature. The model predictions include scenarios of both intravenous (i.v.) and oral (p.o.) administration of small and large compounds. The presented rabbit PBPK/TK model predicts the pharmacokinetics (Cmax, AUC) of the tested compounds with an average 1.7-fold error. This result indicates a good predictive capacity of the model, which enables its use for risk assessment modelling and simulations.
Subject(s)
Models, Biological , Pharmacokinetics , Toxicokinetics , Algorithms , Animals , Area Under Curve , Computer Simulation , Inulin/pharmacokinetics , Inulin/toxicity , Rabbits , Reproducibility of Results , WorkflowABSTRACT
Diseases and toxins may lead to death of active liver tissue, resulting in a loss of total clearance capacity at the whole-body level. However, it remains difficult to study, whether the loss of metabolizing tissue is sufficient to explain loss of metabolic capacity of the liver or whether the surviving tissue undergoes an adaptive response to compensate the loss. To understand the cellular impact of toxic liver damage in an in vivo situation, we here used physiologically-based pharmacokinetic modelling to investigate pharmacokinetics of a specifically designed drug cocktail at three different sampling sites of the body in healthy mice and mice treated with carbon tetrachloride (CCl4). Liver zonation was explicitly quantified in the models through immunostaining of cytochrome P450s enzymes. Comparative analyses between the simulated decrease in clearance capacity and the experimentally measured loss in tissue volume indicated that CCl4-induced impairment of metabolic functions goes beyond the mere loss of metabolically active tissue. The here established integrative modelling strategy hence provides mechanistic insights into functional consequences of toxic liver damage in an in vivo situation, which would not have been accessible by conventional methods.
Subject(s)
Carbon Tetrachloride/toxicity , Chemical and Drug Induced Liver Injury/pathology , Liver/pathology , Pharmaceutical Preparations/metabolism , Animals , Chemical and Drug Induced Liver Injury/etiology , Chemical and Drug Induced Liver Injury/metabolism , Drug Design , Liver/drug effects , Male , Mice , Mice, Inbred C57BL , Tissue DistributionABSTRACT
INTRODUCTION: Thanks to recent advances in biotechnology, the use of peptides and proteins as drugs has become a concrete clinical reality, and consequently an interesting challenge has emerged for non-parenteral drug delivery. Leuprolide is a synthetic nonapeptide agonist to the luteinizing hormone-releasing hormone (LH-RH) receptor with principal clinical applications for prostate cancer. Although a large number of formulations available, they mainly consist in depot subcutaneous injections or implantable devices. Both of these routes of administration present multiple limitations considering the large clinical applications of this active substance. AREA COVERED: The objective of this review is to critically discuss the formulations currently available on the market for leuprolide optimization and to consider how drug delivery plays an important role in improving the bioavailability of this compound. EXPERT OPINION: Due to its physicochemical properties and its economical market, leuprolide is an interesting candidate for drug delivery to improve the efficacy of existing treatments, dose adjustments, and patient compliance and safety.
Subject(s)
Genital Diseases, Female/drug therapy , Leuprolide/administration & dosage , Prostatic Neoplasms/drug therapy , Administration, Cutaneous , Administration, Intranasal , Administration, Oral , Administration, Sublingual , Amino Acid Sequence , Antineoplastic Agents, Hormonal/administration & dosage , Antineoplastic Agents, Hormonal/chemistry , Breast Neoplasms/drug therapy , Chemistry, Pharmaceutical , Endometriosis/drug therapy , Female , Gonadotropin-Releasing Hormone/agonists , Humans , Infusions, Parenteral , Injections, Subcutaneous , Leuprolide/chemistry , Male , Puberty, Precocious/drug therapy , Receptors, LHRH/agonistsABSTRACT
The oral route is probably the preferred method for drug administration, owing to simplicity and positive safety aspects. Despite these advantages, this route of administration presents limitations relating to difficult absorption for some molecules, such as peptides, proteins and nucleic acids. Numerous approaches have been proposed to circumvent this drawback and improve the absorption of these active substances, but today, these approaches are often inefficient. Therefore, the use of patches for oral delivery was proposed, realized by using traditional techniques or microfabrication procedures. This review will focus on the rationale underlying the development of these dosage forms, critically discussing their performance and potential.