Fast screening of covariates in population models empowered by machine learning.

One of the objectives of Pharmacometry (PMX) population modeling is the identification of significant and clinically relevant relationships between parameters and covariates. Here, we demonstrate how this complex selection task could benefit from supervised learning algorithms using importance scores. We compare various classical methods with three machine learning (ML) methods applied to NONMEM empirical Bayes estimates: random forest, neural networks (NNs), and support vector regression (SVR). The performance of the ML models is assessed using receiver operating characteristic (ROC) curves. The F1 score, which measures test accuracy, is used to compare ML and PMX approaches. Methods are applied to different scenarios of covariate influence based on simulated pharmacokinetics data. ML achieved similar or better F1 scores than stepwise covariate modeling (SCM) and conditional sampling for stepwise approach based on correlation tests (COSSAC). Correlations between covariates and the number of false covariates does not affect the performance of any method, but effect size has an impact. Methods are not equivalent with respect to computational speed; SCM is 30 and 100-times slower than NN and SVR, respectively. The results are validated in an additional scenario involving 100 covariates. Taken together, the results indicate that ML methods can greatly increase the efficiency of population covariate model building in the case of large datasets or complex models that require long run-times. This can provide fast initial covariate screening, which can be followed by more conventional PMX approaches to assess the clinical relevance of selected covariates and build the final model.

Translational pharmacokinetic-pharmacodynamic modeling of preclinical and clinical data of the oral MET inhibitor tepotinib to determine the recommended phase II dose.

Tepotinib is a highly selective and potent MET inhibitor in development for the treatment of patients with solid tumors. Given the favorable tolerability and safety profiles up to the maximum tested dose in the first-in-human (FIH) trial, an efficacy-driven translational modeling approach was proposed to establish the recommended phase II dose (RP2D). To study the in vivo pharmacokinetics (PKs)/target inhibition/tumor growth inhibition relationship, a subcutaneous KP-4 pancreatic cell-line xenograft model in mice with sensitivity to MET pathway inhibition was selected as a surrogate tumor model. Further clinical PK and target inhibition data (derived from predose and postdose paired tumor biopsies) from a FIH study were integrated with the longitudinal PKs and target inhibition profiles from the mouse xenograft study to establish a translational PK/pharmacodynamic (PD) model. Preclinical data showed that tumor regression with tepotinib treatment in KP-4 xenograft tumors corresponded to 95% target inhibition. We therefore concluded that a PD criterion of sustained, near-to-complete (>95%) phospho-MET inhibition in tumors should be targeted for tepotinib to be effective. Simulations of dose-dependent target inhibition profiles in human tumors that exceeded the PD threshold in more than 90% of patients established an RP2D of tepotinib 500 mg once daily. This translational mathematical modeling approach supports an efficacy-driven rationale for tepotinib phase II dose selection of 500 mg once daily. Tepotinib at this dose has obtained regulatory approval for the treatment of patients with non-small cell lung cancer harboring MET exon 14 skipping.

Semimechanistic Clearance Models of Oncology Biotherapeutics and Impact of Study Design: Cetuximab as a Case Study.

This study aimed to explore the currently competing and new semimechanistic clearance models for monoclonal antibodies and the impact of clearance model misspecification on exposure metrics under different study designs exemplified for cetuximab. Six clearance models were investigated under four different study designs (sampling density and single/multiple-dose levels) using a rich data set from two cetuximab clinical trials (226 patients with metastatic colorectal cancer) and using the nonlinear mixed-effects modeling approach. A two-compartment model with parallel Michaelis-Menten and time-decreasing linear clearance adequately described the data, the latter being related to post-treatment response. With respect to bias in exposure metrics, the simplified time-varying linear clearance (CL) model was the best alternative. Time-variance of the linear CL component should be considered for biotherapeutics if response impacts pharmacokinetics. Rich sampling at steady-state was crucial for unbiased estimation of Michaelis-Menten elimination in case of the reference (parallel Michaelis-Menten and time-varying linear CL) model.