Report shows how to find polypharmacologic compounds in Pathway Studio 12.0 using data from Reaxys Medicinal Chemistry

1. Drug repositioning for Hepatocellular
carcinoma
Prepared by Anton Yuryev, Ph.D., Elsevier Professional Services, on February 25th
2017
Disclaimer: Data in Pathway Studio and Reaxys Medicinal Chemistry is regular updated by Elsevier.
Therefore the reproduction of workflow described in this report may produce additional results that will
be different from the results presented in this report.
Contents
Selection of drug targets using “Hepatocellular Carcinoma Overview”.......................................................1
Figure 1: Location of “Hepatocellular Carcinoma Overview” pathway in Pathway Studio ..................2
Figure 2: “Hepatocellular Carcinoma Overview” pathway in Pathway Studio.....................................3
Table 1: List of targets from “Hepatocellular Carcinoma Overview” considered in this project..........3
Identification of polypharmacologic compounds for hepatocellular carcinoma using Reaxys Medicinal
Chemistry (RMC)...........................................................................................................................................4
Figure 3: Screenshot of Reaxys Medicinal Chemistry search interface showing query for all targets
names in Table 1 ...................................................................................................................................4
Figure 4: Reaxys Screenshot showing progressive filtering for polypharmacologic compounds
repositioned for hepatocellular carcinoma ..........................................................................................5
Identification of compounds tested against Hepatocellular Carcinoma using Pathway Studio...........5
Figure 5: 122 RMC compounds from Table 2 found in Pathway Studio, 52 of them have links to
“Hepatocellular Carcinoma” disease entity..........................................................................................5
Table 2: List of unique polypharmacologic compounds from RMC found for “Hepatocellular
Carcinoma Overview” and their relations to Hepatocellular Carcinoma in Pathway Studio. ..............6
Conclusion...................................................................................................... Error! Bookmark not defined.
Appendix A. Bioactivities for polypharmacologic compounds inhibiting multiple targets in
“Hepatocellular Carcinoma Overview”.......................................................... Error! Bookmark not defined.
Selection of drug targets using “Hepatocellular Carcinoma Overview”
“Hepatocellular Carcinoma Overview” disease pathway model is available in Pathway Studio Curated
Pathways “Disease Collections” in “Hepatocellular Carcinoma” folder (see screenshot below).

2. Figure 1: Location of “Hepatocellular Carcinoma Overview” pathway in Pathway Studio
Targets for Hepatocellular Carcinoma disease can be selected by visual inspection of “Hepatocellular
Carcinoma Overview” disease pathway and by reading pathway description available in its “Properties”.
The screenshot below shows “Hepatocellular Carcinoma Overview” as it is available in Pathway Studio.
Proteins with red-highlight are up-regulated in disease; proteins with blue highlight are down-regulated
in disease; proteins shown by white shapes and red border have mutations genetically linked to disease.
The detailed description of curated pathways is available in Pathway Studio Help.
The proteins shown by blue contour on Figure 2 were selected as drug targets. The following criteria for
target selection were used:
1) Targets must be druggable proteins, i.e. have 3D structure suitable for designing drugs. The
following classes of proteins are considered druggable:
a. Proteins that bind small molecules: kinases, metabolic enzymes, GPCRs, phosphatases,
protein modification enzymes, protein channels, proteases, ubiquitin-ligases
b. Secreted and extracellular portions of transmembrane proteins. They can bind antibody
drugs that are unable penetrate a cell for inhibition of intracellular proteins.
2) Targets must be major regulators in disease pathway. The major regulators in “Hepatocellular
Carcinoma Overview” are hormones and their receptors that control different stages of
oncological transformation and cancer growth.

3. Figure 2: “Hepatocellular Carcinoma Overview” pathway in Pathway Studio
From pathway analysis point of view the best drugs must inhibit multiple targets in disease pathway.
The approach for designing multi-target drugs against specific pathway is called polypharmacology.
Antibody drugs target protein hormones that are typically not druggable by small molecular weight
inhibitors. However, antibody drugs have high target selectivity and are not suitable for
polypharmacology. Therefore we chose receptors and proteins directly modifying the receptors in
“Hepatocellular Carcinoma Overview” for drug targeting. List of targets considered for
polypharmacologic repositioning is shown in Table 1 below.
Table 1: List of targets from “Hepatocellular Carcinoma Overview” considered in this project
Connectivity – number of relations in Pathway Studio database, indicates how much information is
available about the target in scientific literature.
Name Connectivity Description
LRP5 647 low density lipoprotein receptor-related protein 5
FZD7 269 frizzled family receptor 7
LRP6 745 low density lipoprotein receptor-related protein 6
FLT1 2218 fms-related tyrosine kinase 1
ERBB2 4372 erb-b2 receptor tyrosine kinase 2
ERBB3 1116 kinase inactive
FLT4 892 fms-related tyrosine kinase 4
ERBB4 1044 v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian)

4. KDR 3649 kinase insert domain receptor
MET 2937 met proto-oncogene (hepatocyte growth factor receptor)
PDGFRA 1417 platelet-derived growth factor receptor, alpha polypeptide
PDGFRB 1684 platelet-derived growth factor receptor, beta polypeptide
EGFR 8416 epidermal growth factor receptor
IGF1R 3244 insulin-like growth factor 1 receptor
NOTCH1 5272 notch 1
TGFBR1 1727 transforming growth factor, beta receptor 1
ADAM17 2014 ADAM metallopeptidase domain 17
-secretase 1470 Gamma-secretase complex cleaving NOTCH1receptor for signaling
Identification of polypharmacologic compounds for hepatocellular
carcinoma using Reaxys Medicinal Chemistry (RMC)
Figure 3: Screenshot of Reaxys Medicinal Chemistry search interface showing query for all
targets names in Table 1
Search for 18 targets from Table 1 in RMC yielded 461,151 bioactivities for 174,851 compounds. In
order to select most potent inhibitors that have high-affinity towards proteins in “Hepatocellular
Carcinoma Overview”, we filtered only compounds with pX>6. The filtering yielded 83,076 bioactivities
for 42,632 compounds. In order to find drugs that passed the first phase of clinical trials, i.e. compounds
that were found safe for humans we filtered only for compounds with highest clinical phase: II, III,
marketed, discontinued on II, discontinued on III. This filtering criterion yielded 2,232 bioactivities for
210 substances.

5. Figure 4: Reaxys Screenshot showing progressive filtering for polypharmacologic
compounds repositioned for hepatocellular carcinoma
Found bioactivities were exported into Microsoft Excel file using Export menu command in Reaxys with
“Hit data only” menu option. Using functions in Excel we further selected 515 unique compound-target
bioactivities with best pX. The complete list of 515 bioactivities is shown in Appendix A.
Identification of compounds tested against Hepatocellular Carcinoma using Pathway Studio
We were able to find 122 out of 215 RMC compounds in Pathway Studio by importing either Reaxys ID
or compounds names using Import->Import Entity list menu option in Pathway Studio. To find which
compounds were already tested against Hepatocellular Carcinoma we copied all compounds into new
pathway together with “Hepatocellular Carcinoma” disease entity. We then selected “Hepatocellular
Carcinoma” disease entity and used Add->Relations between Selected and Unselected menu option to
find compounds shown to inhibit “Hepatocellular Carcinoma” in various disease models or in patients.
Figure 5: 122 RMC compounds from Table 2 found in Pathway Studio, 52 of them have links
to “Hepatocellular Carcinoma” disease entity.

6. Table 2: List of unique polypharmacologic compounds from RMC found for “Hepatocellular
Carcinoma Overview” and their relations to Hepatocellular Carcinoma in Pathway Studio.
MedScan ID – compound identifier in Pathway Studio database; Reaxys ID - compound identifier in
Reaxys; # Targets – number of targets inhibited by compound in “Hepatocellular Carcinoma Overview”;
Relation to Hepatocellular Carcinoma– type of relation between compound and Hepatocellular
Carcinoma disease entity in Pathway Studio; # References – number of references supporting relation
between compound and Hepatocellular Carcinoma in Pathway Studio;
Reaxys ID Compound MedScan ID Relation to Hepatocellular
Carcinoma
# References # Targets
6674025 staurosporine 1206148 Regulation 7 10
9161676 vandetanib 1175784 Regulation 3 9
11404252 cediranib 1287940 ClinicalTrial 2 9
11404252 cediranib 1287940 Regulation 2 9
11326138 AEE788 1023004 Regulation 2 9
…….
…….
…….
Table shows partial data. To obtain the complete list of all polypharmacologic compounds the
workflow has to repeated in Pathway Studio 12.0