Bayesian PBPK modeling using R/Stan/Torsten and Julia/SciML/Turing.Jl.

Physiologically-based pharmacokinetic (PBPK) models are mechanistic models that are built based on an investigator's prior knowledge of the in vivo system of interest. Bayesian inference incorporates an investigator's prior knowledge of parameters while using the data to update this knowledge. As such, Bayesian tools are well-suited to infer PBPK model parameters using the strong prior knowledge available while quantifying the uncertainty on these parameters. This tutorial demonstrates a full population Bayesian PBPK analysis framework using R/Stan/Torsten and Julia/SciML/Turing.jl.

A Quantitative Modeling and Simulation Framework to Support Candidate and Dose Selection of Anti-SARS-CoV-2 Monoclonal Antibodies to Advance Bamlanivimab Into a First-in-Human Clinical Trial.

Neutralizing monoclonal antibodies (mAb), novel therapeutics for the treatment of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), have been urgently researched from the start of the pandemic. The selection of the optimal mAb candidate and therapeutic dose were expedited using open-access in silico models. The maximally effective therapeutic mAb dose was determined through two approaches; both expanded on innovative, open-science initiatives. A physiologically-based pharmacokinetic (PBPK) model, incorporating physicochemical properties predictive of mAb clearance and tissue distribution, was used to estimate mAb exposure that maintained concentrations above 90% inhibitory concentration of in vitro neutralization in lung tissue for up to 4 weeks in 90% of patients. To achieve fastest viral clearance following onset of symptoms, a longitudinal SARS-CoV-2 viral dynamic model was applied to estimate viral clearance as a function of drug concentration and dose. The PBPK model-based approach suggested that a clinical dose between 175 and 500 mg of bamlanivimab would maintain target mAb concentrations in the lung tissue over 28 days in 90% of patients. The viral dynamic model suggested a 700 mg dose would achieve maximum viral elimination. Taken together, the first-in-human trial (NCT04411628) conservatively proceeded with a starting therapeutic dose of 700 mg and escalated to higher doses to evaluate the upper limit of safety and tolerability. Availability of open-access codes and application of novel in silico model-based approaches supported the selection of bamlanivimab and identified the lowest dose evaluated in this study that was expected to result in the maximum therapeutic effect before the first-in-human clinical trial.

Brexpiprazole Pharmacokinetics in CYP2D6 Poor Metabolizers: Using Physiologically Based Pharmacokinetic Modeling to Optimize Time to Effective Concentrations.

Brexpiprazole is an oral antipsychotic agent indicated for use in patients with schizophrenia, or as adjunctive treatment for major depressive disorder. As cytochrome P450 (CYP) 2D6 contributes significantly to brexpiprazole metabolism, there is a label-recommended 50% reduction in dose among patients with the CYP2D6 poor metabolizer phenotype. This study uses a whole-body physiologically based pharmacokinetic (PBPK) model to compare the pharmacokinetics of brexpiprazole in patients known to be extensive metabolizers (EMs) and poor metabolizers (PMs). A PBPK model was constructed, verified, and validated against brexpiprazole clinical data, and simulations of 500 subjects were performed to establish the median time to effective concentrations in EMs and PMs. The PBPK simulations captured brexpiprazole PK well and demonstrated significant differences in the time to effective concentrations between EMs and PMs according to the label-recommended titration. Additionally, these simulations suggest that CYP2D6 PMs consistently achieve lower minimum concentrations during the dosing interval than CYP2D6 EMs. Simulations using an alternative dosing strategy of twice-daily dosing (as opposed to once daily) in PMs during the first week of brexpiprazole dosing yielded more consistent plasma concentrations between EMs and PMs, without exceeding the area under the plasma concentration-time curve observed in the EMs. Taken together, the results of these PBPK simulations suggest that product labeling for brexpiprazole titration in CYP2D6 PMs likely overcompensates for the decreased clearance seen in this population. We propose an alternative dosing strategy that decreases the time to effective concentrations and recommend a reevaluation of steady-state PK in this population to potentially allow for higher daily doses in CYP2D6 PMs.

Impact of Obesity on Brexpiprazole Pharmacokinetics: Proposal for Improved Initiation of Treatment.

Brexpiprazole is an oral antipsychotic agent indicated for use in patients with schizophrenia or as adjunctive treatment for major depressive disorder. As obesity (body mass index ≥35 kg/m2 ) has the potential to affect drug pharmacokinetics and is a common comorbidity of both schizophrenia and major depressive disorder, it is important to understand changes in brexpiprazole disposition in this population. This study uses a whole-body physiologically based pharmacokinetic model to compare the pharmacokinetics of brexpiprazole in obese and normal-weight (body mass index 18-25 kg/m2 ) individuals known to be cytochrome P450 2D6 extensive metabolizers (EMs) and poor metabolizers (PMs). The physiologically based pharmacokinetic simulations demonstrated significant differences in the time to effective concentrations between obese and normal-weight individuals within metabolizer groups according to the label-recommended titration. Simulations using an alternative dosing strategy of 1 week of twice-daily dosing in obese EMs or 2 weeks of twice-daily dosing in obese poor metabolizers, followed by a return to once-daily dosing, yielded more consistent plasma concentrations between normal-weight and obese patients without exceeding the area under the plasma concentration-time curve observed in the normal-weight EMs. These alternative dosing strategies reduce the time to effective concentrations in obese patients and may improve clinical response to brexpiprazole.

A Model-Informed Drug Development (MIDD) Approach for a Low Dose of Empagliflozin in Patients with Type 1 Diabetes.

In clinical trials, sodium-glucose co-transporter (SGLT) inhibitor use as adjunct to insulin therapy in type 1 diabetes (T1D) provides glucometabolic benefits while diabetic ketoacidosis risk is increased. The SGLT2 inhibitor empagliflozin was evaluated in two phase III trials: EASE-2 and EASE-3. A low, 2.5-mg dose was included in EASE-3 only. As the efficacy of higher empagliflozin doses (i.e., 10 and 25 mg) in T1D has been established in EASE-2 and EASE-3, a modeling and simulation approach was used to generate additional supportive evidence on efficacy for the 2.5-mg dose. We present the methodology behind the development and validation of two modeling and simulation frameworks: M-EASE-1, a semi-mechanistic model integrating information on insulin, glucose, and glycated hemoglobin; and M-EASE-2, a descriptive model informed by prior information. Both models were developed independently of data from EASE-3. Simulations based on these models assessed efficacy in untested clinical trial scenarios. In this manner, the models provide supportive evidence for efficacy of low-dose empagliflozin 2.5 mg in patients with T1D, illustrating how pharmacometric analyses can support efficacy assessments in the context of limited data.

Quantification of the Impact of Partition Coefficient Prediction Methods on Physiologically Based Pharmacokinetic Model Output Using a Standardized Tissue Composition.

Tissue:plasma partition coefficients are key parameters in physiologically based pharmacokinetic (PBPK) models, yet the coefficients are challenging to measure in vivo. Several mechanistic-based equations have been developed to predict partition coefficients using tissue composition information and the compound's physicochemical properties, but it is not clear which, if any, of the methods is most appropriate under given circumstances. Complicating the evaluation, each prediction method was developed, and is typically employed, using a different set of tissue composition information, thereby making a controlled comparison impossible. This study proposed a standardized tissue composition for humans that can be used as a common input for each of the five frequently used prediction methods. These methods were implemented in R and were used to predict partition coefficients for 11 drugs, classified as strong bases, weak bases, acids, neutrals, and zwitterions. PBPK models developed in R (mrgsolve) for each drug and each set of partition coefficient predictions were compared with respective observed plasma concentration data. Percent root mean square error and half-life percent error were used to evaluate the accuracy of the PBPK model predictions using each partition coefficient method as summarized by strong bases, weak bases, acids, neutrals, and zwitterions characterization. The analysis indicated that no partition coefficient method consistently yielded the most accurate PBPK model predictions. As such, PBPK model predictions using all partition coefficient methods should be considered during drug development. SIGNIFICANCE STATEMENT: Several mechanistic-based methods exist to predict tissue:plasma partition coefficients critical to PBPK modeling. Controlled comparisons are confounded by the use of different tissue composition values for each method; a standardized tissue composition was proposed. Resulting assessments indicated that no method was consistently superior; therefore, sensitivity of PBPK predictions to each method may be warranted prior to model optimization.

Low-dose empagliflozin as adjunct-to-insulin therapy in type 1 diabetes: A valid modelling and simulation analysis to confirm efficacy.

AIM: To confirm the observed reduction in HbA1c for the 2.5 mg dose in EASE-3 by modelling and simulation analyses. MATERIALS AND METHODS: Independent of data from EASE-3 that tested 2.5 mg, we simulated the effect of a 2.5 mg dose through patient-level, exposure-response modelling in the EASE-2 clinical study. A primary semi-mechanistic model evaluated efficacy considering clinical insulin dose adjustments made after treatment initiation that potentially limited HbA1c reductions. The model was informed by pharmacokinetic, insulin dose, mean daily glucose and HbA1c data, and was verified by comparing the simulations with the observed HbA1c change in EASE-3. One of two empagliflozin phase 3 trials in type 1 diabetes (EASE-3 but not EASE-2) included a lower 2.5 mg dose. A placebo-corrected HbA1c reduction of 0.28% was demonstrated without the increased risk of diabetic ketoacidosis observed at higher doses (10 mg and 25 mg). Since only one trial included the lower dose, we aimed to confirm the observed reduction in HbA1c for the 2.5 mg dose by modelling and simulation analyses. RESULTS: The simulated 26-week mean HbA1c change was -0.41% without insulin dose adjustment and -0.29% at 26 weeks with insulin dose adjustment. A simplified (descriptive) model excluding insulin dose and mean daily glucose confirmed the -0.29% HbA1c change that would have been observed had the EASE-2 population received a 2.5 mg dose for 26/52 weeks. CONCLUSIONS: The HbA1c benefit of low-dose empagliflozin directly observed in the EASE-3 trial was confirmed by two modelling and simulation approaches.

Quantitative Systems Pharmacology and Physiologically-Based Pharmacokinetic Modeling With mrgsolve: A Hands-On Tutorial.

mrgsolve is an open-source R package available on the Comprehensive R Archive Network. It combines R and C++ coding for simulation from hierarchical, ordinary differential equation-based models. Its efficient simulation engine and integration into a parallelizable, R-based workflow makes mrgsolve a convenient tool both for simple and complex models and thus is ideal for physiologically-based pharmacokinetic (PBPK) and quantitative systems pharmacology (QSP) model. This tutorial will first introduce the basics of the mrgsolve simulation workflow, including model specification, the introduction of interventions (dosing events) into the simulation, and simulated results postprocessing. An applied simulation example is then presented using a PBPK model for voriconazole, including a model validation step against adult and pediatric data sets. A final simulation example is then presented using a previously published QSP model for mitogen-activated protein kinase signaling in colorectal cancer, illustrating population simulation of different combination therapies.

Single-molecule localization microscopy as nonlinear inverse problem.

We present a statistical framework to model the spatial distribution of molecules based on a single-molecule localization microscopy (SMLM) dataset. The latter consists of a collection of spatial coordinates and their associated uncertainties. We describe iterative parameter-estimation algorithms based on this framework, as well as a sampling algorithm to numerically evaluate the complete posterior distribution. We demonstrate that the inverse computation can be viewed as a type of image restoration process similar to the classical image deconvolution methods, except that it is performed on SMLM images. We further discuss an application of our statistical framework in the task of particle fusion using SMLM data. We show that the fusion algorithm based on our model outperforms the current state-of-the-art in terms of both accuracy and computational cost.

Optimal Drift Correction for Superresolution Localization Microscopy with Bayesian Inference.

Single-molecule-localization-based superresolution microscopy requires accurate sample drift correction to achieve good results. Common approaches for drift compensation include using fiducial markers and direct drift estimation by image correlation. The former increases the experimental complexity and the latter estimates drift at a reduced temporal resolution. Here, we present, to our knowledge, a new approach for drift correction based on the Bayesian statistical framework. The technique has the advantage of being able to calculate the drifts for every image frame of the data set directly from the single-molecule coordinates. We present the theoretical foundation of the algorithm and an implementation that achieves significantly higher accuracy than image-correlation-based estimations.