Exercise PK-27 - Target Mediated Drug Disposition

2021-09-06

Background

  • Structural model - Target Mediated Drug Disposition Model (TMDD)

  • Route of administration - IV-Bolus

  • Dosage Regimen - 1.5, 5, 15, 45 mg/kg administered after complete washout

  • Number of Subjects - 4

pK27

Learning Outcome

  • To fit a full TMDD model with data from only ligand, ligand and target, target and ligand-target complex

  • Write a differential equation for a full TMDD model

Objective

  • The objective of this exercise is to simulate from a TMDD model

Libraries

Call the "necessary" libraries to get started

using Random
using Pumas
using PumasUtilities
using CairoMakie

Model

pk_27           = @model begin
  @metadata begin
    desc        = "Target Mediated Drug Disposition Model"
    timeu       = u"hr"
  end

  @param begin
    "Clearance of central compartment (L/kg/hr)"
    tvcl        ∈ RealDomain(lower=0)
    "Second oder on rate of ligand (L/mg/hr)"
    tvkon       ∈ RealDomain(lower=0)
    "First order off rate of ligand (1/hr)"
    tvkoff      ∈ RealDomain(lower=0)
    "Volume of Peripheral Compartment (L/kg)"
    tvvp        ∈ RealDomain(lower=0)
    "Inter-compartmental clearance (L/kg/hr)"
    tvq         ∈ RealDomain(lower=0)
    "Zero order receptor synthesis process (mg/L/hr)"
    tvkin       ∈ RealDomain(lower=0)
    "First order receptor degenration process (1/hr)"
    tvkout      ∈ RealDomain(lower=0)
    "First order elimination of complex (1/hr)"
    tvkerl      ∈ RealDomain(lower=0)
    "Volume of Central Compartment (L/kg)"
    tvvc        ∈ RealDomain(lower=0)
    Ω           ∈ PDiagDomain(9)
    "Proportional RUV - Plasma"
    σ²_prop_cp  ∈ RealDomain(lower=0)
    "Proportional RUV - Receptor"
    σ²_prop_rec ∈ RealDomain(lower=0)
    "Proportional RUV - Complex"
    σ²_prop_com ∈ RealDomain(lower=0)
  end

  @random begin
    η           ~ MvNormal(Ω)
  end

  @pre begin
    Cl          = tvcl * exp(η[1])
    Kon         = tvkon * exp(η[2])
    Koff        = tvkoff * exp(η[3])
    Vp          = tvvp * exp(η[4])
    Q           = tvq * exp(η[5])
    Kin         = tvkin * exp(η[6])
    Kout        = tvkout * exp(η[7])
    Kerl        = tvkerl * exp(η[8])
    Vc          = tvvc * exp(η[9])
  end

  @dosecontrol begin
    Vc_          = tvvc * exp(η[9])
    bioav       = (Central = 1/Vc_,)
  end

  @init begin
    Receptor    = Kin/Kout
  end

  @dynamics begin
    Central'    = -(Cl/Vc)*Central - (Q/Vc)*Central + (Q/Vp)*Peripheral - Kon*Receptor*Central + Koff*Complex
    Peripheral' = (Q/Vc)*Central - (Q/Vp)*Peripheral
    Receptor'   = Kin - Kout*Receptor - Kon*Receptor*Central + Koff*Complex
    Complex'    = Kon*Receptor*Central - Koff*Complex - Kerl*Complex
  end

  @derived begin
    cp          = @. Central
    """
    Observed Concentration - Plasma (mg/L)
    """
    dv_cp       = @. Normal(cp, sqrt(cp^2*σ²_prop_cp))
    rec         = @. Receptor
    """
    Observed Concentration - Receptor (mg/L)
    """
    dv_rec      = @. Normal(rec, sqrt(rec^2*σ²_prop_rec))
    com         = @. Complex
    """
    Observed Concentration - Complex (mg/L)
    """
    dv_com      = @. Normal(com, sqrt(com^2*σ²_prop_com))
  end
end

PumasModel
  Parameters: tvcl, tvkon, tvkoff, tvvp, tvq, tvkin, tvkout, tvkerl, tvvc, 
Ω, σ²_prop_cp, σ²_prop_rec, σ²_prop_com
  Random effects: η
  Covariates: 
  Dynamical variables: Central, Peripheral, Receptor, Complex
  Derived: cp, dv_cp, rec, dv_rec, com, dv_com
  Observed: cp, dv_cp, rec, dv_rec, com, dv_com

Parameters

The parameters are as given below. tv represents the typical value for parameters.

  • $Cl$ - Clearance of central compartment (L/kg/hr)

  • $Kon$ - Second oder on rate of ligand (L/mg/hr)

  • $Koff$ - First order off rate of ligand (1/hr)

  • $Vp$ - Volume of Peripheral Compartment (L/kg)

  • $Q$ - Inter-compartmental clearance (L/kg/hr)

  • $Kin$ - Zero order receptor synthesis process (mg/L/hr)

  • $Kout$ - First order receptor degeneration process (1/hr)

  • $Kerl$ - First order elimination of complex (1/hr)

  • $Vc$ - Volume of Central Compartment (L/kg)

param = ( tvcl        = 0.001,
          tvkon       = 0.096,
          tvkoff      = 0.001,
          tvvp        = 0.100,
          tvq         = 0.003,
          tvkin       = 0.11,
          tvkout      = 0.0089,
          tvkerl      = 0.003,
          tvvc        = 0.05,
          Ω           = Diagonal([0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0]),
          σ²_prop_cp  = 0.02,
          σ²_prop_rec = 0.012,
          σ²_prop_com = 0.015)

(tvcl = 0.001, tvkon = 0.096, tvkoff = 0.001, tvvp = 0.1, tvq = 0.003, tvki
n = 0.11, tvkout = 0.0089, tvkerl = 0.003, tvvc = 0.05, Ω = [0.0 0.0 … 0.0 
0.0; 0.0 0.0 … 0.0 0.0; … ; 0.0 0.0 … 0.0 0.0; 0.0 0.0 … 0.0 0.0], σ²_prop_
cp = 0.02, σ²_prop_rec = 0.012, σ²_prop_com = 0.015)

Dosage Regimen

  • Single dose of 1.5 mg/kg was administered as IV-Bolus at time=0

  • Single dose of 5 mg/kg was administered as IV-Bolus at time=0

  • Single dose of 15 mg/kg was administered as IV-Bolus at time=0

  • Single dose of 45 mg/kg was administered as IV-Bolus at time=0

dose = [1.5, 5, 15, 45]
ids  = ["1.5 mg/kg", "5 mg/kg", "15 mg/kg", "45 mg/kg"]
dose_ind(x) = DosageRegimen(dose[x], time = 0, cmt = 1)

pop4_sub = map(i -> Subject(id = ids[i], events = dose_ind(i), 
                            observations = (cp = nothing, rec = nothing, com = nothing)), 
                            1:length(ids))

Population
  Subjects: 4
  Observations: cp, rec, com

Simulation

Random.seed!(123)
sim_pop4 = simobs(pk_27, pop4_sub, param, obstimes = 0.1:1:500)

Visualization

figure = Figure(; fontsize = 12)
a1, p1 = sim_plot(figure[1,1], pk_27, sim_pop4, 
        observations = :cp, 
        color = :redsblues,
        linewidth = 4,
        axis = (title = "Ligand", 
                xlabel = "Time (hr)", 
                ylabel = "PK27 Concentrations (mg/L)",
                xticks = 0:100:500, yscale = log10))


a2, p2 = sim_plot(figure[1,2], pk_27, sim_pop4, 
        observations = :rec, 
        color = :redsblues,
        linewidth = 4,
        axis = (title = "Receptor", 
                xlabel = "Time (hr)", 
                ylabel = "PK27 Concentrations (mg/L)",
                xticks = 0:100:500, yscale = log10))

a3, p3 = sim_plot(figure[2,1], pk_27, sim_pop4, 
        observations = :com, 
        color = :redsblues,
        linewidth = 4,
        axis = (title = "Complex", 
                xlabel = "Time (hr)", 
                ylabel = "PK27 Concentrations (mg/L)",
                xticks = 0:100:500, yscale = log10))
Legend(figure[2, 2], a3, "Doses", tellwidth = false, framevisible = false)
figure

Published from pk27.jmd using Weave.jl v0.10.8 on 2021-09-06.