ubiquity/inst/ubinc/systems/system-tmdd.txt at master · john-harrold/ubiquity · GitHub

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# Units:
#
#   mass          [=] nmoles
#   volume        [=] L
#   concentration [=] nM
#   time          [=] hours
#
#   Target Turnover
#   ---------------
#
#   If the target has a half-life specified in hours we
#   calculate the internalization rate in the following way:
#
#          log(2)
#   kint = --------
#          thalf_hr
#
#   Drug Properties
#   ---------------
#   Population values for a mAb taken from Dirks and Meibohm (2010)
#


# #-------------#
# # Parameters  #
# #-------------#
#
#   name         value  lower  upper    units       editable grouping
#                       bound  bound
<P> CL           0.0129   eps    inf      L/hr      yes      System
<P> Q            0.79     eps    inf      L/hr      yes      System
<P> Vt           2.8      eps    inf      L         yes      System
<P> Vp           3.1      eps    inf      L         yes      System
<P> thalf_hr     0.5      eps    inf      hr        yes      Target
<P> Tp_IC        1.0      eps    inf      nM        yes      Target
<P> Tp_MW       30        eps    inf      KDA       yes      Drug
<P> kon          0.1      eps    inf      1/nM-hr   yes      Drug
<P> KD           0.1      eps    inf      nM        yes      Drug
<P> D_MW       150        eps    inf      KDA       yes      Drug

<PSET:default> TMDD: Membrane bound target

<As> ktp  = Q/Vt
<As> kpt  = Q/Vp
<As> kel  = CL/Vp

<As> koff = kon*KD
<As> kint = SIMINT_LOGN[2.0]/thalf_hr
<As> ksyn = Tp_IC*kint*Vp

# #--------------------#
# # Dosing information #
# #--------------------#
#
#  Dosing times in   weeks ==> days
#  dosing magnitude in mpk ==> nM
#
#  Basis: 70 kg human
#         mAb with MW of 150 KDA
#
#    mg          1e6 ng     1nmoles         1          467  nmoles
#  X -- x 70kg x ------- x ------------ x ------ = X * ------------
#    kg          1 mg       150,000 ng    Vp (L)        Vp(L)
#
#
#
# Bolus Events
# times/events  state   values        scale      units
  <B:times>;              [  0  ];     24*7 ;       weeks
  <B:events>;      Cp ;   [ 30  ];    467/Vp;       mpk

# Initial conditions
# define the non-zero initial conditions
<I> Tp   = Tp_IC


#---------------------------------------------------------------------------#
# You can representent the system in many ways. Two methods are shown here. #
# The first is a set of ODEs and the second is by specifying the underlying #
# processes.                                                                #
#                                                                           #
# Select one or the other by commenting out the undesired method.           #
#                                                                           #
#---------------------------------------------------------------------------#

#---------------------------------------------------------------------------#
# Represetning the system simply as ODEs
# <ODE:Ct>  Cp*kpt*Vp/Vt - Ct*ktp
# <ODE:Cp> -Cp*kpt       + Ct*ktp*Vt/Vp -  kel*Cp   + koff*CpTp - kon*Cp*Tp
# <ODE:Tp>               + ksyn/Vp      - kint*Tp   + koff*CpTp - kon*Cp*Tp
# <ODE:CpTp>                            - kint*CpTp - koff*CpTp + kon*Cp*Tp
#---------------------------------------------------------------------------#


#---------------------------------------------------------------------------#
# Represetning the system simply as processes
# tissue distribution
Ct; Vt; ktp <C> Cp; Vp; kpt

# equilibrium
Cp + Tp <=kon:koff=> CpTp

# Turnover
 ksyn/Vp <S:Tp>   kint*Tp
         <S:Cp>    kel*Cp
         <S:CpTp> kint*CpTp
#---------------------------------------------------------------------------#

# #----------#
# # Outputs  #
# #----------#
# Outputs that begin with QC will not be displayed in the GUI
#
# Convert ng/ml to nM
#
#    ng   1000 ml        nmoles
#  X -- x ------- x --------------- = X/MW (KDA)
#    ml    1L       MW (KDA)*1000 ng
#
# Convert from nM to ng/ml:
#
# X nM  ===> X*MW(KDA) ng/ml
#
<O> Cp_Total = Cp + CpTp
<O> Coverage = 1- Tp/Tp_IC

# free drug in ng/ml
<O> Cp_free_ng_ml = Cp*D_MW


#---------#
# Options #
#---------#

# specify different time scales
<TS:hours> 1.0
<TS:days>  1.0/24.0
<TS:weeks> 1.0/24.0/7.0

# output times
<OPT:output_times> SIMINT_SEQ[0][2*7*24][10]
# default time scale
<OPT:TS>  weeks