Metabolomics in Drug Discovery

Assoc. Prof. Dr. Alfi Khatib

Department of Pharmaceutical Chemistry
Faculty of Pharmacy
International Islamic University Malaysia
Kuantan, Pahang, Malaysia
alfikhatib@iium.edu.my
What is metabolomics?

• Metabolomics: comprehensive analysis of the

whole metabolome under a given set of
conditions (Fiehn et al., 2000)
• Focuses on small molecules or low molecular
weight chemicals (<1500 Da) involved in
metabolisms network.
Scopus statistics on metabolomics
Some applications of metabolomics in
pharmaceutical industries
1. Analysis of known bioactive compounds and
screening of metabolites in the extracts prior
to isolation of unknown bioactive
compounds.
2. Analytical tool in quality control of
pharmaceutical products based on the
fingerprint of their metabolites.
3. Comprehensive bioactivity and toxicity
evaluation of the pharmaceutical products.
 Plant samples
(different quality)

Chemical Profiling/Fingerprinting Bioactivity test (in vitro and in vivo)

NMR, LC-MS, GC-MS, FT-IR, TLC

Biochemical Profiling
NMR, LC-MS

Multivariate Data Analysis

Mode of
Multivariate Data Analysis Identification of biomarkers
action

Identification of A valid calibration model to

bioactive compounds predict quality of the plant
samples
Multivariate Data Analysis

Institute of Bioscience
What is Multivariate Data Analysis?
• Extracting information from data with multiple
variables by using all the variables
simultaneously

Institute of Bioscience
Institute of Bioscience
 Each signal/peak is
one variable , K is
number of variable

Each sample
(biofluid, plant,
tissue, trial, time
points, etc) is one
observation, N is
number of
observation
Institute of Bioscience
 Projection
• All variables form new axes in dimensional
spaces
• One point is one observation (sample) in
multidimensional space
• Project points onto a plane

Institute of Bioscience
Application 1. Analysis of
bioactive compounds in
pharmaceutical product
• Lee, S. Y., Mediani, A., Khatib, A., Ismail, I. S., Zawawi, N., Abas, F.
Comparison of partial least squares and random forests for evaluating
relationship between phenolics and bioactivities of Neptunia oleracea.
Journal of the Science of Food and Agriculture. DOI: 10.1002/jsfa.8462
(2017).
• Lawal, U., Leong, S. W., Shaari, K., Ismail, I. S., Khatib, A., Abas, F. α-
Glucosidase Inhibitory and Antioxidant Activities of Different Ipomoea
aquatica Cultivars and LC–MS/MS Profiling of the Active Cultivar. Journal
of Food Biochemistry 41, Article number e12303 (2017).

• Lee, S. Y., Abas, F., Khatib, A., Ismail, I. S., Shaari, K., Zawawi, N.
Metabolite profiling of Neptunia oleracea and correlation with antioxidant
and α-glucosidase inhibitory activities using 1H NMR-based metabolomics.
Phytochemistry Letters 16, 23–33 (2016).

• Khoo, L. W., Mediani, A., Zolkeflee, N. K. Z., Leong, S. W., Ismail, I. S.,
Khatib, A., Shaari, K, Abas, F. Phytochemical diversity of Clinacanthus
nutans extracts and their bioactivity correlations elucidated by NMR based
metabolomics. Phytochemistry Letters 14, 123-133 (2015).
 Daun belalai gajah
(Clinacanthus nutans)
10= proline, 12= triptophan, 13= valine, 15=formic acid, 16=fumaric acid,
18=adenine, 25=clinacoside A, 30= isooreintin, 37= quercetin, 39=
quercetin 3-O-arabinofuranoside, 40= rutin, 41=chlorogenic acid
 Application 2. FT-IR based
fingerprinting for QC of herbal
products
• Khatib, A., Perumal, V., Ahmed, Q. U., Uzir, B. F., Abas, F., Murugesu, S.
Characterization of antioxidant activity of Momordica charantia fruit by
infrared based fingerprinting. Analytical Letters.
doi.org/10.1080/00032719.2016.1261877 (2017).

• Easmin, S., Sarker, M. Z. I., Ghafoor, K., Ferdosh, S., Jaffri, J., Ali, M.
E., Mirhosseini, H., Al-Juhaimi, F. Y., Perumal, V., Khatib, A. Rapid
investigation of α-glucosidase inhibitory activity of Phaleria macrocarpa
extracts using FTIR-ATR based fingerprinting. Journal of Food and Drug
Analysis 25, 306-315 (2017).

• Sharif, K. M., Rahman, M. M., Azmir, J., Khatib, A., Hadijah, S.,
Mohamed, A., Sahena, F., Zaidul, I. S. M.. Orthogonal Partial Least
Squares Model for Rapid Prediction of Antioxidant Activity of Pereskia
bleo by Fourier Transform Infrared Spectroscopy. Analytical Letters 47,
2061-2071 (2014).
A. Effect of location on quality of a herb
PCA score plot of ethanol 20% extracts of Phaleria macrocarpa
originated from different location in Malaysia (A= Melaka, B= Negeri
Sembilan, C= Selangor, D= Pahang) using PC 1 vs PC 3. PC1 and PC3
explained 98.5% and 0.5% of total variation, respectively. Area inside
the Hotelling’s T2 tolerance ellipse corresponds to 95% confidence
B. Prediction of bioactivity

FT-IR Αlpha-glucosidase
inhibitory test
 1.2

0.8
Actual activity

y = 0.997x + 0.0016
0.6
R² = 0.9971

0.4

0.2

0
0 0.2 0.4 0.6 0.8 1 1.2
Predicted activity
Shops Actual IC50 value Predicted IC50 value Differences (%)
(µg/mL) (µg/mL)
1 83.69 ± 1.20 C2 92.43 ± 1.50 B1 10.59 ± 2.74 A
2 103.47 ± 2.48 AB1 99.44 ± 1.38 B1 -3.71 ±1.90 B
3 97.37 ± 1.67 AB1 99.53 ± 3.60 B1 2.22 ± 3.11 AB
4 92.08 ± 6.50 BC1 92.19 ± 2.19 B1 2.08 ± 5.70 AB
5 96.98 ± 2.46 AB1 94.87 1.87 B1 -2.01 ± 2.04 AB
6 105.71 ± 1.68 A1 108.72 ± 2.12 A1 2.86 ± 1.34 AB
7 93.48 ± 1.37 ABC1 92.98 ± 0.72 B1 -0.46 ± 1.28 AB
8 100.82 ± 0.94 AB1 98.65 ± 1.25 B1 -2.09 ± 1.74 AB
9 97.4 ± 2.53 AB1 96.36 ± 1.09 B1 -0.64 ± 3.40 AB
10 97.61 ± 0.81 AB1 96.72 ± 0.87 B1 -0.88 ± 1.19 AB
C. Optimization of processing parameter

Response surface and contour plots for interaction effects of

temperature, air velocity and drying time on alpha-glucosidase inhibitry
activty of a medicinal herb
Application 3. Comprehensive
evaluation of bioactivity and
toxicity study
• Pariyani, R., Ismail, I. S., Azama, A., Khatib, A., Abas, F., Shaari, K., Hamza, H.
Urinary metabolic profiling of cisplatin nephrotoxicity andnephroprotective effects
of Orthosiphon stamineus leaves elucidated by1H NMR spectrsocopy. Journal of
Pharmaceutical and Biomedical Analysis 135, 20-30 (2017).

• Azam, A. A., Pariyani, R., Ismail, I. S., Ismail, A., Khatib, A., Abas, F., Shaari, H.
Urinary metabolomics study on the protective role of Orthosiphon stamineus in
Streptozotocin induced diabetes mellitus in rats via 1H NMR spectroscopy. BMC
Complementary and Alternative Medicine 17, 278 (2017).

• Jambocus, N. G. S., Ismail, A., Khatib, A., Mahomoodally, F., Saari, N., Mumtaz,
M. W., Hamid, A. A. Morinda citrifolia L. leaf extract prevent weight gain in
Sprague-Dawley rats fed a high fat diet. Food and Nutrition Research 61, 1338919
(2017).

• Mediani, A., Abas, F., Maulidiani, M., Khatib, A., Tan, C. P., Ismail, I. S., Shaari, K.,
Ismail, A., Lajis, N. H. Metabolic and biochemical changes in streptozotocin induced
obese-diabetic rats treated with Phyllanthus niruri extract. Journal of
Pharmaceutical and Biomedical Analysis 128, 302-312 (2016).
UPLC-ESI-QTOF/MS chromatogram of zebrafish extract
 Conclusion
• Metabolomics open the possibility to fasten
the identification of novel bio- and chemical
markers.
• Validated calibration model can be used to
predict the bioactivity of new set of herbal
extract.
• Toxicity of samples can be detected earlier
using metabolomics approach.
Faculty of Pharmacy IIUM Kuantan
and lets collaborate