Structural model - IV infusion - Two compartment Model
Route of administration - Rapid intravenous infusion of recombinant human superoxide dismutase (r-hSOD)
Dosage Regimen - 20mg/kg IV rapid infusion for 15 seconds in two categories of rats
Number of Subjects - 1 normal rate, 1 clamped (nephrectomized) rat
In this model, collection of plasma concentration data of parent drug and concentration of parent and metabolite in urine, will help you to derive/ estimate the parameters: Clearance, Volume of Distribution, Km, Vmax.
To note that clearance and volume of central compartment are reduced in clamed rats, as removal of the kidneys increased the effective half life from 10mins in normal rats to 90mins in nephrectomized rats.
The time to steady state might differ 9-fold between the two groups.
Importance of kidneys in the elimination of r-hSOD and the impact of kidney disease/nephrectomy in the overall kinetics of the drug.
In this tutorial, you will learn how to construct a simple two compartment model with 2 set of parameters corresponding to normal and clamped rats.
call the "necessary" libraries to get started
using Pumas using Plots using CSV using StatsPlots using Random
In this two compartmental model, we administer dose on Central compartment.
pk_52 = @model begin @param begin tvcl ∈ RealDomain(lower=0) tvvc ∈ RealDomain(lower=0) tvvp ∈ RealDomain(lower=0) tvcld ∈ RealDomain(lower=0) Ω ∈ PDiagDomain(4) σ²_prop ∈ RealDomain(lower=0) end @random begin η ~ MvNormal(Ω) end @pre begin Cl = tvcl * exp(η) Vc = tvvc * exp(η) Vp = tvvp * exp(η) Cld = tvcld * exp(η) end @dynamics begin Central' = -(Cl/Vc)*Central - (Cld/Vc)*Central + (Cld/Vp) * Peripheral Peripheral' = (Cld/Vc)*Central - (Cld/Vp)*Peripheral end @derived begin cp = @. Central/Vc dv ~ @. Normal(cp,sqrt(cp^2*σ²_prop)) end end
PumasModel Parameters: tvcl, tvvc, tvvp, tvcld, Ω, σ²_prop Random effects: η Covariates: Dynamical variables: Central, Peripheral Derived: cp, dv Observed: cp, dv
Parameters are provided for the simulation as below.
tv represents the typical value for parameters.
tvcl - Clearance (mL/min/kg)
tvvc - Volume of Central Compartment (ml/min/kg)
tvvp - Volume of Peripheral CompartmentRenal (ml/min/kg)
tq - Intercompartmental Clearance (ml/min/kg)
Ω - Between Subject Variability
σ - Residual errors
param1 = (tvcl = 3.0, tvvc = 31, tvvp = 15, tvcld = 0.12, Ω = Diagonal([0.0,0.0,0.0,0.0]), σ²_prop = 0.04) param2 = (tvcl = 0.22, tvvc = 16, tvvp = 13, tvcld = 0.09, Ω = Diagonal([0.0,0.0,0.0,0.0]), σ²_prop = 0.04) param = vcat(param1, param2)
A dose of 20 mg/kg to a single rat of
2 categories (normal and clamped)
ev1 = DosageRegimen(20000,cmt=1) sub1 = Subject(id=1, events=ev1, covariates=(Rat="Normal_Rat",)) sub2 = Subject(id=2, events=ev1, covariates=(Rat="Clamped_Rat",)) pop2_sub = [sub1,sub2]
Population Subjects: 2 Covariates: Rat
Simulate the plasma concentration after IV infusion
Random.seed!(123) sim_pop2_sub = map(((subject, param),) -> simobs(pk_52, subject, param, obstimes=0:0.1:500), zip(pop2_sub, param)) df = DataFrame(sim_pop2_sub)
Use the dataframe for plotting
cp - Predicted concentration
dv - Observed concentration
df1 = filter(x -> x.id == "1", df) df2 = filter(x -> x.id == "2", df) df_dv = filter(x-> x.time in [0.2,2.1,4.9,9.5,14.7,29,60,119,239,480],df) @df df1 plot(:time, :cp, yaxis=:log, title="Simulated impact of disease on r-hSOD kinetics", label= "Pred - Normal Rats", xlabel= "Time (mins)", ylabel="Concentration (ug/mL)", color=[:blue], linewidth=3, xlims=(-1,500), xticks=[0,50,100,150,200,250,300,350,400,450,500], yticks=[0.01,0.1,1,10,100,1000,10000], ylims=(0.01,10000)) @df df2 plot!(:time, :cp,linewidth=3, label= "Pred - Clamped Rats", color=[:red]) @df df_dv scatter!(:time, :dv, label = "Obs - Conc")