skip to main content


Title: Prediction of Optimal Drug Schedules for Controlling Autophagy
Abstract

The effects of molecularly targeted drug perturbations on cellular activities and fates are difficult to predict using intuition alone because of the complex behaviors of cellular regulatory networks. An approach to overcoming this problem is to develop mathematical models for predicting drug effects. Such an approach beckons for co-development of computational methods for extracting insights useful for guiding therapy selection and optimizing drug scheduling. Here, we present and evaluate a generalizable strategy for identifying drug dosing schedules that minimize the amount of drug needed to achieve sustained suppression or elevation of an important cellular activity/process, the recycling of cytoplasmic contents through (macro)autophagy. Therapeutic targeting of autophagy is currently being evaluated in diverse clinical trials but without the benefit of a control engineering perspective. Using a nonlinear ordinary differential equation (ODE) model that accounts for activating and inhibiting influences among protein and lipid kinases that regulate autophagy (MTORC1, ULK1, AMPK and VPS34) and methods guaranteed to find locally optimal control strategies, we find optimal drug dosing schedules (open-loop controllers) for each of six classes of drugs and drug pairs. Our approach is generalizable to designing monotherapy and multi therapy drug schedules that affect different cell signaling networks of interest.

 
more » « less
NSF-PAR ID:
10153364
Author(s) / Creator(s):
; ; ; ; ;
Publisher / Repository:
Nature Publishing Group
Date Published:
Journal Name:
Scientific Reports
Volume:
9
Issue:
1
ISSN:
2045-2322
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    The objective of this study was to describe the pharmacokinetics (PK) of intravenous phenobarbital in neonates and infants on extracorporeal membrane oxygenation (ECMO) and to provide dosing recommendations in this population. We performed a retrospective single‐center PK study of phenobarbital in neonates and infants on ECMO between January 1, 2014, and December 31, 2018. We developed a population PK model using nonlinear mixed‐effects modeling, performed simulations using the final PK parameters, and determined optimal dosing based on attainment of peak and trough concentrations between 20 and 40 mg/L. We included 35 subjects with a median (range) age and weight of 14 days (1–154 days) and 3.4 kg (1.6–8.1 kg), respectively. A total of 194 samples were included in the analysis. Five children (14%) contributing 30 samples (16%) were supported by continuous venovenous hemodiafiltration (CVVHDF). A 1‐compartment model best described the data. Typical clearance and volume of distribution for a 3.4–kg infant were 0.038 L/h and 3.83 L, respectively. Clearance increased with age and CVVHDF. Although on ECMO, phenobarbital clearance in children on CVVHDF was 6‐fold higher than clearance in children without CVVHDF. In typical subjects, a loading dose of 30 mg/kg/dose followed by maintenance doses of 6–7 mg/kg/day administered as divided doses every 12 hours reached goal concentrations. Age did not impact dosing recommendations. However, higher doses were needed in children on CVVHDF. We strongly recommend therapeutic drug monitoring in children on renal replacement therapy (excluding slow continuous ultrafiltration) while on ECMO.

     
    more » « less
  2. Abstract

    Designing multi‐drug regimens often involves target‐ and synergy prediction‐based drug selection, and subsequent dose escalation to achieve the maximum tolerated dose (MTD) of each drug. This approach may improve efficacy, but not the optimal efficacy and often substantially increases toxicity. Drug interactions depend on many pathways in the omics networks and further complicate the design process. The virtually infinite drug–dose parameter space cannot be reconciled using conventional approaches, which are largely based on prediction. This barrier at least partially accounts for the low response rates that are observed with conventional mono‐ and combinatorial chemotherapy. A combination of nonstandard therapies for colorectal cancer (AGCH: adriamycin, gemcitabine, cisplatin, and herceptin) at ¼ MTD is used to treat the rats, the tumor response rates varied in a wide range. Some of the tumor response rates are close to that of control group. This work harnesses an artificial intelligence (AI) platform that is mechanism free and can dynamically optimize combinatorial therapy in rats. The individually optimized AGCH regimen reveal starkly different drug–dose parameters, which can converge each rat toward the same and low tumor response rate. Importantly, this AI‐based drug–dose optimization technology is an actionable platform, which can achieve N‐of‐1 therapy.

     
    more » « less
  3. Abstract

    Type 2 diabetes is exploding globally. Despite numerous treatment options, nearly half of type 2 diabetics are unsuccessful at properly managing the disease, primarily due to a lack of patient compliance, driven by adverse side effects as well as complicated and frequent dosing schedules. Improving the delivery of type 2 diabetes drugs has the potential to increase patient compliance and thus, greatly enhance health outcomes and quality of life. This review focuses on molecular and materials engineering strategies that have been implemented to improve the delivery of peptide drugs to treat type 2 diabetes. Peptide drugs benefit from high potency and specificity but suffer from instability and short half‐lives that limit their utility as therapeutics and pose a significant delivery challenge. Several approaches have been developed to improve the availability and efficacy of antidiabetic peptides and proteins in vivo. These methods are reviewed herein and include devices, which sustain the release of peptides in long term, and molecular engineering strategies, which prolong circulation time and slow the release of therapeutic peptides. By optimizing the delivery of these peptides and proteins using these approaches, long‐term glucose control can be achieved in type 2 diabetes patients.

     
    more » « less
  4. Abstract

    With the growing number of single-cell datasets collected under more complex experimental conditions, there is an opportunity to leverage single-cell variability to reveal deeper insights into how cells respond to perturbations. Many existing approaches rely on discretizing the data into clusters for differential gene expression (DGE), effectively ironing out any information unveiled by the single-cell variability across cell-types. In addition, DGE often assumes a statistical distribution that, if erroneous, can lead to false positive differentially expressed genes. Here, we present Cellograph: a semi-supervised framework that uses graph neural networks to quantify the effects of perturbations at single-cell granularity. Cellograph not only measures how prototypical cells are of each condition but also learns a latent space that is amenable to interpretable data visualization and clustering. The learned gene weight matrix from training reveals pertinent genes driving the differences between conditions. We demonstrate the utility of our approach on publicly-available datasets including cancer drug therapy, stem cell reprogramming, and organoid differentiation. Cellograph outperforms existing methods for quantifying the effects of experimental perturbations and offers a novel framework to analyze single-cell data using deep learning.

     
    more » « less
  5. Abstract

    Efficient and economical delivery of pharmaceuticals to patients is critical for effective therapy. Here we describe a multiorgan (lung, liver, and breast cancer) microphysiological system (“Body‐on‐a‐Chip”) designed to mimic both inhalation therapy and/or intravenous therapy using curcumin as a model drug. This system is “pumpless” and self‐contained using a rocker platform for fluid (blood surrogate) bidirectional recirculation. Our lung chamber is constructed to maintain an air‐liquid interface and contained a “breathable” component that was designed to mimic breathing by simulating gas exchange, contraction and expansion of the “lung” using a reciprocating pump. Three cell lines were used: A549 for the lung, HepG2 C3A for the liver, and MDA MB231 for breast cancer. All cell lines were maintained with high viability (>85%) in the device for at least 48 hr. Curcumin is used to treat breast cancer and this allowed us to compare inhalation delivery versus intravenous delivery of the drug in terms of effectiveness and potentially toxicity. Inhalation therapy could be potentially applied at home by the patient while intravenous therapy would need to be applied in a clinical setting. Inhalation therapy would be more economical and allow more frequent dosing with a potentially lower level of drug. For 24 hr exposure to 2.5 and 25 µM curcumin in the flow device the effect on lung and liver viability was small to insignificant, while there was a significant decrease in viability of the breast cancer (to 69% at 2.5 µM and 51% at 25 µM). Intravenous delivery also selectively decreased breast cancer viability (to 88% at 2.5 µM and 79% at 25 µM) but was less effective than inhalation therapy. The response in the static device controls was significantly reduced from that with recirculation demonstrating the effect of flow. These results demonstrate for the first time the feasibility of constructing a multiorgan microphysiological system with recirculating flow that incorporates a “breathable” lung module that maintains an air‐liquid interface.

     
    more » « less