# Kinetic fitting of irreversible inhibition in a case of large Ki
# Remaining activity = 100 x exp (-kobs*t)
# kobs = kinact*[I] / (Ki + [I])
# Created by S. Fushinobu (2020.11.18)

# Edit the parameters below
expdecay.df <- read.csv("/Users/fushi/Documents/R/Irrinh-large-Ki-R-data.csv")
Mtitle <- "Irreversible Inhibition"  # main title of the plot
Inhname <- "Inhibitor"
Inhunit <- "mM"
Timeunit <- "min"
kobsinit <- 0.1              # initial values for fitting
#kinactinit <- 1 
#Kiinit <- 2.0

ncurve <- ncol(expdecay.df) -1
kobsvec <- c()
Inhvec <- c()

#plot blank
plot(0,0, pch="", xlim=c(0,max(expdecay.df[,1], na.rm=TRUE)),ylim=c(0,100), main=paste(Mtitle,"exponential decay to get kobs"),xlab=paste(Inhname,Inhunit),ylab="Remaining Activity (%)")

# write legends
labels <- paste(colnames(expdecay.df)[-1],Inhunit)
legend("topright", legend = labels, pch=c(1:length(labels)), lty=c(1:length(labels)), bg="white")

for (i in 1:ncurve){
ithdata.df <- expdecay.df[,1]
ithdata.df <- cbind(ithdata.df,expdecay.df[i+1])
colnames(ithdata.df) <- c("time","rem_act")
ithdata.df <- subset(ithdata.df, rem_act != "NA")
points(ithdata.df$time,ithdata.df$rem_act, pch=i)
expdecay.nls <- nls(rem_act ~ 100*exp(-(kobs*time)), data=ithdata.df, start=list(kobs=kobsinit))
summary(expdecay.nls)$parameters
kobs <- unname(coef(expdecay.nls)["kobs"])
kobsvec[i] <- kobs
Inhvec[i] <- substr(colnames(expdecay.df)[i+1],2,nchar(colnames(expdecay.df)[i+1])+1)
curve(100*exp(-kobs*x),0,max(ithdata.df$time),add=TRUE,lty=i)
mtext(paste(colnames(expdecay.df)[i+1],": kobs = ",signif(kobs,digits=3),"±",signif(summary(expdecay.nls)$parameters[1,2],digits=3),Timeunit,"(-1)"),side=1,line=-i,adj=0)
}

Inhkobs.df <- data.frame(conc=as.numeric(Inhvec),kobs=kobsvec)

# generate a replot (Inh - kobs) with kobs data
dev.new()
plot(Inhkobs.df$conc,Inhkobs.df$kobs,xlim=c(0,max(Inhkobs.df$conc)),ylim=c(0,max(Inhkobs.df$kobs)),main=paste(Mtitle," ([",Inhname,"]-kobs)",sep=""),xlab=paste("[",Inhname,"] (",Inhunit,")",sep=""),ylab=paste("kobs (1/",Timeunit,")",sep=""))

# Estimate Kinact/Ki by linear fit
Linearfit.lm <- lm(kobs ~ conc - 1,Inhkobs.df)
abline(Linearfit.lm)
mtext(paste("Kinact/Ki = ",signif(unname(coef(Linearfit.lm)["conc"]),digits=3),Timeunit,"(-1)",Inhunit,"(-1)"),side=1,line=-1,adj=1)