armitage_eval: Evaluate the updated Armitage model

Description

Evaluate the Armitage model for chemical distributon in vitro. Takes input as data table or vectors of values. Outputs a data table. Updates over the model published in Armitage et al. (2014) include binding to plastic walls and lipid and protein compartments in cells.

Usage

armitage_eval(
  chem.cas = NULL,
  chem.name = NULL,
  dtxsid = NULL,
  casrn.vector = NA_character_,
  nomconc.vector = 1,
  this.well_number = 384,
  this.FBSf = NA_real_,
  tcdata = NA,
  this.sarea = NA_real_,
  this.v_total = NA_real_,
  this.v_working = NA_real_,
  this.cell_yield = NA_real_,
  this.Tsys = 37,
  this.Tref = 298.15,
  this.option.kbsa2 = FALSE,
  this.option.swat2 = FALSE,
  this.pseudooct = 0.01,
  this.memblip = 0.04,
  this.nlom = 0.2,
  this.P_nlom = 0.035,
  this.P_dom = 0.05,
  this.P_cells = 1,
  this.csalt = 0.15,
  this.celldensity = 1,
  this.cellmass = 3,
  this.f_oc = 1,
  this.conc_ser_alb = 24,
  this.conc_ser_lip = 1.9,
  this.Vdom = 0,
  this.pH = 7,
  restrict.ion.partitioning = FALSE
)

Value

Param	Description	Units
casrn	Chemical Abstracts Service Registry Number	character
nomconc	Nominal Concentration	uM=umol/L
well_number	Number of wells in plate (used to set default surface area)	unitless
sarea	Surface area of well	m^2
v_total	Total volume of well	uL
v_working	Filled volume of well	uL
cell_yield	Number of cells	cells
gkow	The log10 octanol to water (PC) (logP)	log10 unitless ratio
logHenry	The log10 Henry's law constant '	log10 unitless ratio
gswat	The log10 water solubility (logWSol)	log10 mg/L
MP	The chemical compound melting point	degrees Kelvin
MW	The chemical compound molecular weight	g/mol
gkaw	The air to water PC	unitless ratio
dsm
duow
duaw
dumw
gkmw	log10
gkcw	The log10 cell/tissue to water PC	log10 unitless ratio
gkbsa	The log10 bovine serum albumin to water partitiion coefficient	unitless
gkpl	log10
ksalt	Setschenow constant	L/mol
Tsys	System temperature	degrees C
Tref	Reference temperature	degrees K
option.kbsa2	Use alternative bovine-serum-albumin partitioning model	logical
option.swat2	Use alternative water solubility correction	logical
FBSf	Fraction fetal bovine serum	unitless
pseudooct	Pseudo-octanol cell storage lipid content
memblip	Membrane lipid content of cells
nlom	Structural protein content of cells
P_nlom	Proportionality constant to octanol structural protein	unitless
P_dom	Proportionality constant to dissolved organic material (DOM)	unitless
P_cells	Proportionality constant to octanol storage lipid	unitless
csalt	Ionic strength of buffer	M=mol/L
celldensity	Cell density	kg/L, g/mL
cellmass	Mass per cell	ng/cell
f_oc
cellwat
Tcor
Vm	Volume of media	L
Vwell	Volume of medium (aqueous phase only)	L
Vair	Volume of head space	L
Vcells	Volume of cells/tissue	L
Valb	Volume of serum albumin	L
Vslip	Volume of serum lipids	L
Vdom	Volume of dissolved organic matter	L
F_ratio
gs1.GSE
s1.GSE
gss.GSE
ss.GSE
kmw
kow	The octanol to water PC (i.e., 10^gkow)	unitless
kaw	The air to water PC (i.e., 10^gkaw)	unitless
swat	The water solubility (i.e., 10^gswat)	mg/L
kpl
kcw	The cell/tissue to water PC (i.e., 10^gkcw)	unitless
kbsa	The bovine serum albumin to water PC	unitless
swat_L
soct_L
scell_L
cinit	Initial concentration	uM=umol/L
mtot	Total micromoles	umol
cwat	Total concentration in water	uM=umol/L
cwat_s	Dissolved concentration in water	uM=umol/L
csat	Is the solution saturated (1/0)	logical
activity
cair	Concentration in head space	uM=umol/L
calb	Concentration in serum albumin	uM=umol/L
cslip	Concentration in serum lipids	uM=umol/L
cdom	Concentration in dissolved organic matter	uM=umol/L
ccells	Concentration in cells	uM=umol/L
cplastic	Concentration in plastic	uM=umol/m^2
mwat_s	Mass dissolved in water	umols
mair	Mass in air/head space	umols
mbsa	Mass bound to bovine serum albumin	umols
mslip	Mass bound to serum lipids	umols
mdom	Mass bound to dissolved organic matter	umols
mcells	Mass in cells	umols
mplastic	Mass bond to plastic	umols
mprecip	Mass precipitated out of solution	umols
xwat_s	Fraction dissolved in water	fraction
xair	Fraction in the air	fraction
xbsa	Fraction bound to bovine serum albumin	fraction
xslip	Fraction bound to serum lipids	fraction
xdom	Fraction bound to dissolved organic matter	fraction
xcells	Fraction within cells	fraction
xplastic	Fraction bound to plastic	fraction
xprecip	Fraction precipitated out of solution	fraction
eta_free	Effective availability ratio	fraction
cfree.invitro	Free concentration in the in vitro media (use for Honda1 and Honda2)	fraction

Arguments

chem.cas: A single or vector of Chemical Abstracts Service Registry Number(s) (CAS-RN) of desired chemical(s).
chem.name: A single or vector of name(s)) of desired chemical(s).
dtxsid: A single or vector ofEPA's DSSTox Structure ID(s) (https://comptox.epa.gov/dashboard)
casrn.vector: A deprecated argument specifying a single or vector of Chemical Abstracts Service Registry Number(s) (CAS-RN) of desired chemical(s).
nomconc.vector: For vector or single value, micromolar (uM = umol/L) nominal concentration (e.g. AC50 value)
this.well_number: For single value, plate format default is 384, used if is.na(tcdata)==TRUE. This value chooses default surface area settings for armitage_estimate_sarea based on the number of plates per well.
this.FBSf: Fraction fetal bovine serum, must be entered by user.
tcdata: A data.table with casrn, nomconc, MP, gkow, gkaw, gswat, sarea, v_total, v_working. Otherwise supply single values to this.params (e.g., this.sarea, this.v_total, etc.). Chemical parameters are taken from chem.physical_and_invitro.data.
this.sarea: Surface area per well (m^2)
this.v_total: Total volume per well (uL)
this.v_working: Working volume per well (uL)
this.cell_yield: Number of cells per well
this.Tsys: System temperature (degrees C)
this.Tref: Reference temperature (degrees K)
this.option.kbsa2: Use alternative bovine-serum-albumin partitioning model
this.option.swat2: Use alternative water solubility correction
this.pseudooct: Pseudo-octanol cell storage lipid content
this.memblip: Membrane lipid content of cells
this.nlom: Structural protein content of cells
this.P_nlom: Proportionality constant to octanol structural protein
this.P_dom: Proportionality constant to dissolve organic material
this.P_cells: Proportionality constant to octanol storage lipid
this.csalt: Ionic strength of buffer (M = mol/L)
this.celldensity: Cell density kg/L, g/mL
this.cellmass: Mass per cell, ng/cell
this.f_oc: Everything assumed to be like proteins
this.conc_ser_alb: Mass concentration of albumin in serum (g/L)
this.conc_ser_lip: Mass concentration of lipids in serum (g/L)
this.Vdom: 0 ml, the volume of dissolved organic matter (DOM)
this.pH: 7.0, pH of cell culture
restrict.ion.partitioning: FALSE, Should we restrict the chemical available to partition to only the neutral fraction?

Author

Greg Honda

References

Armitage, J. M.; Wania, F.; Arnot, J. A. Environ. Sci. Technol. 2014, 48, 9770-9779. https://doi.org/10.1021/es501955g

honda2019usinghttk

Examples

Run this code


library(httk)

# Check to see if we have info on the chemical:
"80-05-7" %in% get_cheminfo()

#We do:
temp <- armitage_eval(casrn.vector = c("80-05-7", "81-81-2"), this.FBSf = 0.1,
this.well_number = 384, nomconc = 10)
print(temp$cfree.invitro)

# Check to see if we have info on the chemical:
"793-24-8" %in% get_cheminfo()

# Since we don't have any info, let's look up phys-chem from dashboard:
cheminfo <- data.frame(
  Compound="6-PPD",
  CASRN="793-24-8",
  DTXSID="DTXSID9025114",
  logP=4.27, 
  logHenry=log10(7.69e-8),
  logWSol=log10(1.58e-4),
  MP=	99.4,
  MW=268.404
  )
  
# Add the information to HTTK's database:
chem.physical_and_invitro.data <- add_chemtable(
 cheminfo,
 current.table=chem.physical_and_invitro.data,
 data.list=list(
 Compound="Compound",
 CAS="CASRN",
  DTXSID="DTXSID",
  MW="MW",
  logP="logP",
  logHenry="logHenry",
  logWSol="logWSol",
  MP="MP"),
  species="Human",
  reference="CompTox Dashboard 31921")

# Run the Armitage et al. (2014) model:
out <- armitage_eval(
  casrn.vector = "793-24-8", 
  this.FBSf = 0.1,
  this.well_number = 384, 
  nomconc = 10)
  
print(out)

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