BioVariance Research Services

Pathway-based Pharma portfolio analyses

Josef Scheiber, PhD
www.biovariance.com

BioVariance - Overview
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Overview
Background Analysis approach Example Outlook

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 wellsupported by data from scientific databases and the literature

Recent competitor patents provide plenty of relevant knowledge

Competitor project
Patent

own project

Leveraging competitor information for better drug understanding

Primary target of competitor compound

Indication: Z

Primary target of own compound

Consequence: Indication: Y Should we also look into Indication Z?

Treating a disease/symptom

General workflow
Standard identifiers for basic content

Big Pharma A
Patents published in 2011
Manual curation

TARGET NAME ABBREVIATION

UniProt ID
MODE OF ACTION INDICATIONS TYPE OF DRUG MOLECULES CHEMICAL NATURE OF DRUG MOLECULE

General workflow

Big Pharma A
Patents published in 2011
compare

Big Pharma B
Patents published in 2011

Machine-readable description of patent content

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 6

A
Total patents published (for specified year) Relevant patents

B
Pharma A (2010) 83 75 Pharma B (2011) 103 76

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 prednisolone treatment., Treatment of inflammation related condition P04150 inflammatory and/or allergic conditions. (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.

Mapping into biological Pathways

(here: Nature Pathway Interaction Database)

Target list
T1 T2 T3

Pathway A

Automated mapping of target identifiers into biological pathways, each target can be a member of several pathways (exemplified with T2), thereby one can link annotations from competitor patents (like indication) to the pathways of own projects Also a combined visualization is possible

Pathway B

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
47

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 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.

angiopoietinreceptor_pathway

Opportunity?
Treatment of inflammatory disorders, autoimmune disorders (e.g., lupus), skininflammatory 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., 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.

ap1_pathway

Treatment of inflammation and/or allergic conditions.,

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!

Thank you for your attention!

josef.scheiber@biovariance.com Phone: +49 89 189 6582 80 Garmischer Str. 4/V 80339 Munich / Germany