Computational identification of potential modulators of heme-regulated inhibitor (HRI) for pharmacological intervention against sickle cell disease

Authors

Afolabi Owoloye^1,2,3 Samuel Olubode⁴ Funmilayo Ligali^1,2,5 Adewale Ogunleye⁶ Adesola Musa² Oluwagbemiga Aina² Taiwo Idowu² Kolapo Oyebola^1,2

1. Centre for Genomic Research in Biomedicine (CeGRIB), College of Basic and Applied Sciences, Mountain Top University, Ibafo, Nigeria. 2. Nigerian Institute of Medical Research, Lagos, Nigeria. 3. Parasitology and Bioinformatics Unit, Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria. 4. Department of Biochemistry, Adekunle Ajasin University Akungba, Ondo State, Nigeria. 5. Department of Biochemistry, Faculty of Basic Medical Science, University of Lagos, Lagos, Nigeria. 6. Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany.

Usage

import library

library(ggplot2)
library(ggrepel)
library(readxl)

read data

Cannabiscitrin <- read_excel("Can_P_RMSF.xlsx")
Epigallocatechin <- read_excel('Epi_P_RMSF.xlsx')
Kaempferol <- read_excel('Kaemp_P_RMSF.xlsx')
Myricetin <- read_excel('Myri_P_RMSF.xlsx')
Tiliroside <- read_excel('Til_P_RMSF.xlsx')

create a .pdf out

pdf(file = 'Supplementary.pdf',useDingbats = F, paper = 'a4r', width = 40, height = 40)

make a plot for cannabiscitrin complex

ggplot(data = Cannabiscitrin, aes(label = ResName, y= Backbone, x=CA))+
  geom_line(color='darkorchid', lwd=0.4)+
  geom_point(data = subset(Cannabiscitrin, LigandContact == 'Yes'), size=0.5, color='black')+
  geom_text_repel(data = subset(Cannabiscitrin, LigandContact == 'Yes'), aes(label=ResName), size=3, color='maroon2')+
  ggtitle("Amino acid residues forming contact with cannabiscitrin") +
  xlab("C alpha") + ylab("Backbone") +
  theme_bw()+
  theme(axis.text.x = element_text(color="Black"),
        axis.text.y = element_text(color="Black"),
        plot.title = element_text(color="black", size=14, face="bold.italic"),
        axis.title.x = element_text(color="black", size=12, face="bold"),
        axis.title.y = element_text(color="black", size=12, face="bold"))+
  scale_x_continuous(breaks = seq(5, 30, by = 5))+
  scale_y_continuous(breaks = seq(5, 30, by = 5))+
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())

make a plot epigallocatechin gallate complex

ggplot(data = Epigallocatechin, aes(label = ResName, y= Backbone, x=CA))+
  geom_line(color='blue', lwd=0.4)+
  geom_point(data = subset(Epigallocatechin, LigandContact == 'Yes'), size=0.5, color='black')+
  geom_text_repel(data = subset(Epigallocatechin, LigandContact == 'Yes'), aes(label=ResName), size=3, color='maroon2')+
  ggtitle("Amino acid residues forming contact with epigallocatechin gallate") +
  xlab("C alpha") + ylab("Backbone") +
  theme_bw()+
  theme(axis.text.x = element_text(color="Black"),
        axis.text.y = element_text(color="Black"),
        plot.title = element_text(color="black", size=14, face="bold.italic"),
        axis.title.x = element_text(color="black", size=12, face="bold"),
        axis.title.y = element_text(color="black", size=12, face="bold"))+
  scale_x_continuous(breaks = seq(1, 6, by = 1))+
  scale_y_continuous(breaks = seq(1, 6, by = 1))+
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())

make a plot for Kaempferol-3-(2G-glucosylrutinoside) complex

ggplot(data = Kaempferol, aes(label = ResName, y= Backbone, x=CA))+
  geom_line(color='red', lwd=0.4)+
  geom_point(data = subset(Kaempferol, LigandContact == 'Yes'), size=0.5, color='black')+
  geom_text_repel(data = subset(Kaempferol, LigandContact == 'Yes'), aes(label=ResName), size=3, color='maroon2')+
  ggtitle("Amino acid residues forming contact with Kaempferol-3-(2G-glucosylrutinoside)" +
  xlab("C alpha") + ylab("Backbone") +
  theme_bw()+
  theme(axis.text.x = element_text(color="Black"),
        axis.text.y = element_text(color="Black"),
        plot.title = element_text(color="black", size=14, face="bold.italic"),
        axis.title.x = element_text(color="black", size=12, face="bold"),
        axis.title.y = element_text(color="black", size=12, face="bold"))+
  scale_x_continuous(breaks = seq(1, 10, by = 1))+
  scale_y_continuous(breaks = seq(1, 10, by = 1))+
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())

make a plot for myricetin complex

ggplot(data = Myricetin, aes(label = ResName, y= Backbone, x=CA))+
  geom_line(color='springgreen3', lwd=0.4)+
  geom_point(data = subset(Myricetin, LigandContact == 'Yes'), size=0.5, color='black')+
  geom_text_repel(data = subset(Myricetin, LigandContact == 'Yes'), aes(label=ResName), size=3, color='maroon2')+
  ggtitle("Amino acid residues forming contact with Myricetin") +
  xlab("C alpha") + ylab("Backbone") +
  theme_bw()+
  theme(axis.text.x = element_text(color="Black"),
        axis.text.y = element_text(color="Black"),
        plot.title = element_text(color="black", size=14, face="bold.italic"),
        axis.title.x = element_text(color="black", size=12, face="bold"),
        axis.title.y = element_text(color="black", size=12, face="bold"))+
  scale_x_continuous(breaks = seq(0.5, 2, by = 0.5))+
  scale_y_continuous(breaks = seq(0.5, 2, by = 0.5))+
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())

make a plot for tiliroside complex

ggplot(data = Tiliroside, aes(label = ResName, y= Backbone, x=CA))+
  geom_line(color='orange2', lwd=0.4)+
  geom_point(data = subset(Tiliroside, LigandContact == 'Yes'), size=0.5, color='black')+
  geom_text_repel(data = subset(Tiliroside, LigandContact == 'Yes'), aes(label=ResName), size=3, color='maroon2')+
  ggtitle("Amino acid residues forming contact with tiliroside") +
  xlab("C alpha") + ylab("Backbone") +
  theme_bw()+
  theme(axis.text.x = element_text(color="Black"),
        axis.text.y = element_text(color="Black"),
        plot.title = element_text(color="black", size=14, face="bold.italic"),
        axis.title.x = element_text(color="black", size=12, face="bold"),
        axis.title.y = element_text(color="black", size=12, face="bold"))+
  scale_x_continuous(breaks = seq(2, 10, by = 2))+
  scale_y_continuous(breaks = seq(2, 10, by = 2))+
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())

quit and save .pdf file

dev.off()

Scrip contributors

Afolabi Owoloye Adewale Ogunleye Samuel Olubode Kolapo Oyebola

Check out our handle for more publications

CeGRIB