This shows a workflow on how one can use pharmaceutical patents in a curated manner in order to enhance analysis quality for Drug Discovery

1. BioVariance Research Services
Pathway-based Pharma portfolio analyses
Josef Scheiber, PhD
www.biovariance.com

2. BioVariance - Overview
Two distinct offerings rooted in the same data:
• “Medical value content”-as-a-Service for Healthcare
• making sense of genomic & other data IN CONTEXT as
service offering
Bio-Variance
BaVarians ;)

3. Overview
• Background
• Analysis approach
• Example
• Outlook

4. Background
• Patents hold a significant amount of recent,
highly relevant information
• Question to answer: What targets do my
competitors publish patents for? What indication
are they working on for a particular target?
• How can I use this for my efforts?
• We aim for testable hypotheses that are well-
supported by data from scientific databases and
the literature

5. Recent competitor patents provide
plenty of relevant knowledge
Competitor project
Patent
own project

6. Leveraging competitor information for
better drug understanding
Primary target of
competitor compound
Indication: Z
Consequence:
Primary target of own compound
Should we also look into Indication Z?
Indication: Y
Treating a disease/symptom

7. General workflow
Standard identifiers for basic content
TARGET NAME
Big Pharma A ABBREVIATION
UniProt ID
Patents published MODE OF ACTION
in 2011 Manual curation INDICATIONS
TYPE OF DRUG
MOLECULES
CHEMICAL NATURE OF
DRUG MOLECULE

8. General workflow
Big Pharma A Big Pharma B
Patents published Patents published
in 2011 compare in 2011
Machine-readable description of patent content

9. Statistics of targets in patents
• Pharma A 41 unique ID Targets, 7 of them with several patent
• Pharma B 36 unique ID Targets, 16 of them with several patents
• 6 Targets where both have patents (Q9UBL9; P04150; P30559;
P07550; P10275; Q9Y5N1)
35 30
A 6 B
Pharma A (2010) Pharma B (2011)
Total patents published (for specified year) 83 103
Relevant patents 75 76

10. Comparison of indications
on target-level
Opportunity?
Treatment of inflammation related condition (e.g. asthma,
rheumatoid arthritis, dermatitis, inflammatory bowel disease,
transplant rejection, multiple sclerosis, chronic uveitis, or chronic
obstructive pulmonary disease); mitigating bone loss associated with
Treatment of inflammation and/or allergic conditions., Treatment of
P04150 inflammatory and/or allergic conditions. prednisolone treatment., Treatment of inflammation related condition
(e.g. asthma, rheumatoid arthritis, dermatitis, inflammatory bowel
disease, transplant rejection, multiple sclerosis, chronic uveitis, or
chronic obstructive pulmonary disease); mitigating bone loss
associated with prednisolone treatment.
Treatment of pulmonary disorders, e.g. chronic obstructive
Treatment of premature labor, congestive heart failure, depression,
pulmonary disease (COPD) and asthma., Treatment and prophylaxis of
inflammatory and allergic skin diseases, psoriasis, proliferative skin
diseases associated with reversible airways obstruction such as
diseases, glaucoma and in conditions where there is an advantage in
asthma, chronic obstructive pulmonary diseases (COPD) (e.g. chronic
lowering gastric acidity, particularly in gastric and peptic ulceration,
and wheezy bronchitis, emphysema), respiratory tract infection and
chronic bronchitis and emphysema., Treatment of premature labor,
P07550 upper respiratory tract disease (e.g. rhinitis, including seasonal and congestive heart failure, depression, inflammatory and allergic skin
allergic rhinitis), premature labour, depression, congestive heart
diseases, psoriasis, proliferative skin diseases, glaucoma and in
failure, skin diseases (e.g. inflammatory, allergic, psoriatic, and
conditions where there is an advantage in lowering gastric acidity,
proliferative skin diseases), conditions where lowering peptic acidity
particularly in gastric and peptic ulceration, chronic bronchitis and
is desirable (e.g. peptic and gastric ulceration) and muscle wasting
emphysema.
disease.

11. Mapping into biological Pathways
(here: Nature Pathway Interaction Database)
Automated mapping of target
identifiers into biological
Target list pathways, each target can be a
T1 Pathway A member of several pathways
(exemplified with T2), thereby
T2 one can link annotations from
competitor patents (like
T3 indication) to the pathways of
own projects
Also a combined visualization is
possible
Pathway B

12. Mapping into biological Pathways
(here: Nature Pathway Interaction Database)
• Pharma A: 41 unique IDs map into 116 Pathways, 64 of them with several
targets (40% of pathways worked on covered by competitor)
• Pharma B: 36 unique ID Targets map into 77 Pathways, 32 of these with
several targets (61% of pathways worked on covered by competitor)
• 47 Pathways where both have patents (see next slide for example)
69 30
A 47 B

13. Comparison of indications on pathway level
(in total 47 matching pathways)
Pathway Indication Patent Company A Indication Patent Company B
Treatment of rheumatoid arthritis, osteoarthritis, meningitis,
ischemic and hemorrhagic stroke, neurotrauma/closed head
injury, stroke, endotoxemia and/or toxic shock syndrome,
other acute or chronic inflammatory disease states such as
angiopoietinreceptor_pathway the inflammatory reaction induced by endotoxin or Treatment of cancer.
inflammatory bowel disease, tuberculosis, atherosclerosis,
muscle degeneration, multiple sclerosis, cachexia, bone
resorption, psoriatic arthritis, Reiter's syndrome, gout,
traumatic arthritis, rubella arthritis and acute synovitis.
Opportunity?
Treatment of inflammatory disorders, autoimmune disorders (e.g., lupus), skin-
inflammatory disorders, intestinal inflammatory disorders, asthma and atopic
disorders, and transplant graft rejection, neurological disorders or complications
due to stroke or head injury, benign or malignant neoplastic disease, carcinomas
and adenocarcinoma and proliferative disorders., Treatment of inflammation
related condition (e.g. asthma, rheumatoid arthritis, dermatitis, inflammatory
bowel disease, transplant rejection, multiple sclerosis, chronic uveitis, or chronic
obstructive pulmonary disease); mitigating bone loss associated with
ap1_pathway Treatment of inflammation and/or allergic conditions., prednisolone treatment., Treatment of inflammatory disorders, autoimmune
disorders (e.g., lupus), skin-inflammatory disorders, intestinal inflammatory
disorders, asthma and atopic disorders, and transplant graft rejection,
neurological disorders or complications due to stroke or head injury, benign or
malignant neoplastic disease, carcinomas and adenocarcinoma and proliferative
disorders., Treatment of inflammation related condition (e.g. asthma, rheumatoid
arthritis, dermatitis, inflammatory bowel disease, transplant rejection, multiple
sclerosis, chronic uveitis, or chronic obstructive pulmonary disease); mitigating
bone loss associated with prednisolone treatment.

14. Outlook
The right drug for the right patient
at the right time & right dose is only possible
if you have the right knowledge within the right context
right in place
We will further work on this!

15. Thank you for your attention!
josef.scheiber@biovariance.com
Phone: +49 – 89 – 189 6582 – 80
Garmischer Str. 4/V
80339 Munich / Germany