Biomedical Patents In The Postgenomic Era: Proprietary Drug Targets And Therapies

Biomedical Patents In The Postgenomic Era: Proprietary Drug Targets And Therapies

Publisher:	D&MD Publications Inc
Year of publication:	2005
Type of publication:	Management report
Publisher's reference (if any):	D&MD9149
Author(s):	Sreten Bogdanovic and Beata Langlands
Approximate page count:	130
Price when published:	$4,950
Remarks: Page numbers, where given, refer to the draft manuscript (which may differ from the published version). The copyright in this report is owned by the publisher, to whom any requests for copies should be addressed. The price shown is for a single copy of the print version. Multiple copies and electronic copies usually have different prices.
BIOMEDICAL PATENTS IN THE POSTGENOMIC ERA Proprietary drug targets and therapies TABLE OF CONTENTS CHAPTER 1 TRENDS IN POSTGENOMIC BIOTECHNOLOGY 1.1 Biomedical innovation in the postgenomic era 1.2 The role of patents in the biomedical industry 1.3 Post-genomic technologies 1.3.1 Functional genomics 1.3.2 Pharmacogenomics 1.3.3 Transcriptomics 1.3.4 Proteomics 1.3.5 Glycomics 1.3.6 Metabolomics 1.3.7 Other omics 1.4 Established and emerging therapies 1.4.1 Small molecules 1.4.2 Protein-based biotherapies 1.4.3 Nucleic acid-based biotherapies 1.4.3.1 Gene therapy 1.4.3.2 Antisense including RNA interference 1.5 Molecular diagnostics CHAPTER 2 PATENT LAW, PROCEDURES AND BIOMEDICAL INVENTIONS 2.1 What is a patent? 2.1.1 Patents confer an exclusionary right 2.1.2 Patents do not confer ownership of products 2.1.3 Patents and property rights 2.1.4 Patents and monopolies 2.1.5 Consideration for grant 2.2 Patents require international co-operation 2.2.1 The Paris Convention 2.2.2 The European Patent Convention 2.2.3 GATT-TRIPs 2.2.4 Recent developments 2.3 Patents are time-limited 2.4 What can be patented? 2.4.1 Novelty 2.4.2 The Inventive Step 2.4.3 Effect of unpublished prior applications 2.4.4 Industrial application 2.5 Exceptions to patentability 2.6 US utility patents 2.6.1 Patent costs 2.6.2 The patent document 2.6.3 Inventors and assignees 2.6.4 "First-to-invent" 2.6.5 Provisional applications 2.6.6 The American Inventors Protection Act 2.6.7 Novelty requirement 2.6.8 Non-obviousness requirement 2.6.9 Recent growth in patenting 2.7 Grace periods 2.8 Post-issue challenges to patent validity 2.8.1 EPO opposition procedure 2.8.2 US reexamination procedures 2.8.2.1 Proposals for post-grant review 2.9 Patenting chemical compounds 2.10 Patenting pharmaceuticals 2.10.1 Overview 2.10.2 First pharmaceutical use 2.10.3 Second pharmaceutical use 2.10.4 Other aspects of pharmaceutical patenting 2.11 Patenting natural products 2.12 Patenting microbiological inventions 2.13 Patent infringement 2.13.1 Overview 2.13.2 Remedies for infringement 2.13.3 Patent litigation in the US 2.13.3.1 Litigation costs 2.13.3.2 Doctrine of equivalents 2.13.3.3 Research use of an invention 2.13.4 Patent litigation in Europe CHAPTER 3 PATENTING OF GENES AND PROTEINS 3.1 Introduction 3.2 Patenting of genes 3.2.1 Background on genes 3.2.2 The drive towards patenting 3.2.3 Protection afforded by patent law 3.2.4 Growth in DNA-related patenting 3.3 Patenting of proteins 3.3.1 Background on proteins 3.3.2 Structural initiatives 3.3.3 The drive towards patenting 3.3.4 Protection afforded by patent law 3.4 Regulatory developments relevant to genes 3.4.1 Tightening patentability requirements 3.4.2 Areas of controversy 3.4.2.1 Patenting of ESTs 3.4.2.2 Patenting DNA sequence variations 3.5 Regulatory developments relevant to proteins 3.5.1 Patenting of 3-D structures 3.5.2 Areas of controversy 3.5.2.1 Computational prediction of function 3.5.2.2 Broadly interpreted patents 3.6 Patent claims and risk of litigation 3.7 Solutions to the patent thicket problem 3.8 Issues raised by exclusive licensing CHAPTER 4 ANALYSIS OF US PATENTS 1990-2005 4.1 Patent activity survey: aims and methodology 4.2 Overview of therapy areas 4.2.1 Cancer 4.2.2 CNS therapy 4.2.3 Metabolism/Cardiology 4.2.4 Infection/Immunology 4.3 Patent activity in major drug target classes 4.3.1 GPCRs 4.3.2 Enzymes 4.3.2.1 Kinases 4.3.2.2 Phosphatases 4.3.2.3 Proteases 4.3.2.4 ATPases and ABC transporters 4.3.2.5 Monamine oxidases 4.3.2.6 Glycoenzymes 4.3.3 Ion channels 4.3.4 Nuclear receptors 4.3.5 Cytokines and chemokines 4.4 Patent activity in gene therapy 4.5 Patent activity in RNA interference 4.6 Patent activity in pharmacogenomics 4.7 Summary of patent activity survey 4.8 Analysis of patents by filing and publication year 4.9 Analysis of patent maintenance 4.10 Analysis of patents by US classification CHAPTER 5 PATENT COMPETITIVE INTELLIGENCE 5.1 Mining patents for competitive intelligence 5.2 Patent searching 5.2.1 Internet-based patent resources 5.2.3 Computational patent mapping 5.3 Indicators of patent quality 5.3.1 Patent citations weights 5.3.2 Length of life and spatial weights 5.3.3 Composite index of patent quality 5.4 Competitive analysis of Biopatents survey 5.4.1 Most prolific assignees 5.4.2 Most frequently cited patents CHAPTER 6 TRENDS AND OPPORTUNITIES 6.1 The postgenomic tide of patents has risen 6.2 Expanding the universe of drug targets 6.3 Using patenting trends to guide strategies 6.4 Utilizing the trade secret system 6.5 Recognizing importance of target patents 6.6 Anticipating investors' concerns 6.7 Developing litigation awareness EXECUTIVE SUMMARY A knowledge of patenting trends can be used to guide commercial strategies, informing decisions relating to exploitation of new drug targets, therapies, or technologies. It can help companies anticipate new markets and market opportunities. Patent-awareness is therefore essential for everyone in the biomedical industry, including company executives developing internal R&D efforts, seeking investment or planning collaborative/licensing ventures. It is also essential for those investing capital in the industry. In the postgenomic era, intellectual property protection is critical. In the second chapter of this report, which begins with an introduction to postgenomic biotechnology in chapter 1, we review and assess the protection afforded by patent law, legal patentability requirements, and key regulatory developments worldwide. We also report on procedures which enable challenges to patent validity, remedies for infringement, and litigation. The focus in the report is on US utility patents, but efforts have been made to highlight key differences between US, Europe and other patent jurisdictions. The spotlight is then turned on genes and proteins, patents on which are the products of the postgenomic revolution. In the third chapter of this report we discuss the value of patenting genes and proteins, significant recent regulatory developments, areas of controversy, litigation risks, and other hotly debated issues. Patent protection for genes and proteins is crucial for biotech companies to justify the R&D and commercialization costs associated with genomic discoveries. Genes and proteins can be patented as compositions-of-matter and processes, but recently a new type of patent, research tool, has emerged. Patents can provide an early warning of new product launches. Since the early 1990s, new sequences have provided a new route to drug discovery, which was seized upon by biotechnology and pharmaceutical companies. Our survey of postgenomic patents ("Biopatents"), described in chapter 4 of this report, provides advance indication that in another 10 years or so drugs directed at novel genomic targets should reach advanced clinical trials. Since the development of diagnostics is faster, diagnostic products are likely to reach the market first. Effective patent surveillance needs to consider the whole patent landscape, as well as a patent's direct competitors, in order to discover potential threats, emerging therapeutic applications and new pharmacological approaches. In the postgenomic era, the landscape can be delineated into areas occupied by druggable protein superfamilies. In order to address the needs of industry or investment strategists, the Biopatents survey focused on druggable superfamilies of particular interest to the drug industry: G-protein coupled receptors; enzymes (kinases, phosphatases, proteases, ATPases, ABC Transporters, monoamine oxidases, glycosidases, glycosyltransferases); ion channels; nuclear receptors; and cytokines. To locate postgenomic patents, searches were performed using Thompson Delphion, a subscription-based patent database. Searches were also performed for three important postgenomic technologies: gene therapy, RNAi, and pharmacogenomics. Overall, the Biopatents survey produced 9,972 unique patents and created a snapshot of US patenting activity covering a large sector of the postgenomic drug industry over the period 1990-2005. Analysis of the data revealed features characteristic of particular druggable classes, for example with respect to types of patents claimed, therapeutic and/or diagnostic applications claimed, annual rates of growth, maturity indicators, and maintainance record. Patents are particularly well placed to provide a window onto the activities of key competitors. By becoming familiar with the competitors' patents and products companies can also develop essential litigation awarenes. In chapter 5 of this report we discuss approaches and resources which can be applied to mining patents for competitive intelligence, as well as measurements of patent quality, such as patent citations and other weightings. We apply these principles to reveal the most prolific assignees and the most influential patents in the Biopatents survey.

Publisher:

D&MD Publications Inc

Year of publication:

2005

Type of publication:

Management report

Publisher's reference (if any):

D&MD9149

Author(s):

Sreten Bogdanovic and Beata Langlands

Approximate page count:

130

Price when published:

$4,950

Remarks:

Page numbers, where given, refer to the draft manuscript (which may differ from the published version).
The copyright in this report is owned by the publisher, to whom any requests for copies should be addressed.
The price shown is for a single copy of the print version. Multiple copies and electronic copies usually have different prices.

                    BIOMEDICAL PATENTS IN THE POSTGENOMIC ERA
                      Proprietary drug targets and therapies

                                 TABLE OF CONTENTS

         CHAPTER 1  TRENDS IN POSTGENOMIC BIOTECHNOLOGY

          1.1 Biomedical innovation in the postgenomic era
          1.2 The role of patents in the biomedical industry
          1.3 Post-genomic technologies
             1.3.1 Functional genomics
             1.3.2 Pharmacogenomics
             1.3.3 Transcriptomics
             1.3.4 Proteomics
             1.3.5 Glycomics
             1.3.6 Metabolomics
             1.3.7 Other omics
          1.4 Established and emerging therapies
             1.4.1 Small molecules
             1.4.2 Protein-based biotherapies
             1.4.3 Nucleic acid-based biotherapies
               1.4.3.1 Gene therapy
               1.4.3.2 Antisense including RNA interference
          1.5 Molecular diagnostics

         CHAPTER 2  PATENT LAW, PROCEDURES AND BIOMEDICAL INVENTIONS

          2.1 What is a patent?
             2.1.1 Patents confer an exclusionary right
             2.1.2 Patents do not confer ownership of products
             2.1.3 Patents and property rights
             2.1.4 Patents and monopolies
             2.1.5 Consideration for grant
          2.2 Patents require international co-operation
             2.2.1 The Paris Convention
             2.2.2 The European Patent Convention
             2.2.3 GATT-TRIPs
             2.2.4 Recent developments
          2.3 Patents are time-limited
          2.4 What can be patented?
             2.4.1 Novelty
             2.4.2 The Inventive Step
             2.4.3 Effect of unpublished prior applications
             2.4.4 Industrial application
          2.5 Exceptions to patentability
          2.6 US utility patents
             2.6.1 Patent costs
             2.6.2 The patent document
             2.6.3 Inventors and assignees
             2.6.4 "First-to-invent"
             2.6.5 Provisional applications
             2.6.6 The American Inventors Protection Act
             2.6.7 Novelty requirement
             2.6.8 Non-obviousness requirement
             2.6.9 Recent growth in patenting
          2.7 Grace periods
          2.8 Post-issue challenges to patent validity
             2.8.1 EPO opposition procedure
             2.8.2 US reexamination procedures
               2.8.2.1 Proposals for post-grant review
          2.9 Patenting chemical compounds
          2.10 Patenting pharmaceuticals
             2.10.1 Overview
             2.10.2 First pharmaceutical use
             2.10.3 Second pharmaceutical use
             2.10.4 Other aspects of pharmaceutical patenting
          2.11 Patenting natural products
          2.12 Patenting microbiological inventions
          2.13 Patent infringement
             2.13.1 Overview
             2.13.2 Remedies for infringement
             2.13.3 Patent litigation in the US
               2.13.3.1 Litigation costs
               2.13.3.2 Doctrine of equivalents
               2.13.3.3 Research use of an invention
             2.13.4 Patent litigation in Europe

         CHAPTER 3  PATENTING OF GENES AND PROTEINS

          3.1 Introduction
          3.2 Patenting of genes
             3.2.1 Background on genes
             3.2.2 The drive towards patenting
             3.2.3 Protection afforded by patent law
             3.2.4 Growth in DNA-related patenting
          3.3 Patenting of proteins
             3.3.1 Background on proteins
             3.3.2 Structural initiatives
             3.3.3 The drive towards patenting
             3.3.4 Protection afforded by patent law
          3.4 Regulatory developments relevant to genes
             3.4.1 Tightening patentability requirements
             3.4.2 Areas of controversy
               3.4.2.1 Patenting of ESTs
               3.4.2.2 Patenting DNA sequence variations
          3.5 Regulatory developments relevant to proteins
             3.5.1 Patenting of 3-D structures
             3.5.2 Areas of controversy
               3.5.2.1 Computational prediction of function
               3.5.2.2 Broadly interpreted patents
          3.6 Patent claims and risk of litigation
          3.7 Solutions to the patent thicket problem
          3.8 Issues raised by exclusive licensing

         CHAPTER 4  ANALYSIS OF US PATENTS 1990-2005

          4.1 Patent activity survey: aims and methodology
          4.2 Overview of therapy areas
             4.2.1 Cancer
             4.2.2 CNS therapy
             4.2.3 Metabolism/Cardiology
             4.2.4 Infection/Immunology
          4.3 Patent activity in major drug target classes
             4.3.1 GPCRs
             4.3.2 Enzymes
               4.3.2.1 Kinases
               4.3.2.2 Phosphatases
               4.3.2.3 Proteases
               4.3.2.4 ATPases and ABC transporters
               4.3.2.5 Monamine oxidases
               4.3.2.6 Glycoenzymes
             4.3.3 Ion channels
             4.3.4 Nuclear receptors
             4.3.5 Cytokines and chemokines
          4.4 Patent activity in gene therapy
          4.5 Patent activity in RNA interference
          4.6 Patent activity in pharmacogenomics
          4.7 Summary of patent activity survey
          4.8 Analysis of patents by filing and publication year
          4.9 Analysis of patent maintenance
          4.10 Analysis of patents by US classification

         CHAPTER 5  PATENT COMPETITIVE INTELLIGENCE

          5.1 Mining patents for competitive intelligence
          5.2 Patent searching
             5.2.1 Internet-based patent resources
             5.2.3 Computational patent mapping
          5.3 Indicators of patent quality
             5.3.1 Patent citations weights
             5.3.2 Length of life and spatial weights
             5.3.3 Composite index of patent quality
          5.4 Competitive analysis of Biopatents survey
             5.4.1 Most prolific assignees
             5.4.2 Most frequently cited patents

         CHAPTER 6  TRENDS AND OPPORTUNITIES

          6.1 The postgenomic tide of patents has risen
          6.2 Expanding the universe of drug targets
          6.3 Using patenting trends to guide strategies
          6.4 Utilizing the trade secret system
          6.5 Recognizing importance of target patents
          6.6 Anticipating investors' concerns
          6.7 Developing litigation awareness

EXECUTIVE SUMMARY
A knowledge of patenting trends can be used to guide commercial strategies, informing decisions relating to exploitation of new drug targets, therapies, or technologies. It can help companies anticipate new markets and market opportunities. Patent-awareness is therefore essential for everyone in the biomedical industry, including company executives developing internal R&D efforts, seeking investment or planning collaborative/licensing ventures. It is also essential for those investing capital in the industry.
In the postgenomic era, intellectual property protection is critical. In the second chapter of this report, which begins with an introduction to postgenomic biotechnology in chapter 1, we review and assess the protection afforded by patent law, legal patentability requirements, and key regulatory developments worldwide. We also report on procedures which enable challenges to patent validity, remedies for infringement, and litigation. The focus in the report is on US utility patents, but efforts have been made to highlight key differences between US, Europe and other patent jurisdictions.
The spotlight is then turned on genes and proteins, patents on which are the products of the postgenomic revolution. In the third chapter of this report we discuss the value of patenting genes and proteins, significant recent regulatory developments, areas of controversy, litigation risks, and other hotly debated issues. Patent protection for genes and proteins is crucial for biotech companies to justify the R&D and commercialization costs associated with genomic discoveries. Genes and proteins can be patented as compositions-of-matter and processes, but recently a new type of patent, research tool, has emerged.
Patents can provide an early warning of new product launches. Since the early 1990s, new sequences have provided a new route to drug discovery, which was seized upon by biotechnology and pharmaceutical companies. Our survey of postgenomic patents ("Biopatents"), described in chapter 4 of this report, provides advance indication that in another 10 years or so drugs directed at novel genomic targets should reach advanced clinical trials. Since the development of diagnostics is faster, diagnostic products are likely to reach the market first.
Effective patent surveillance needs to consider the whole patent landscape, as well as a patent's direct competitors, in order to discover potential threats, emerging therapeutic applications and new pharmacological approaches. In the postgenomic era, the landscape can be delineated into areas occupied by druggable protein superfamilies. In order to address the needs of industry or investment strategists, the Biopatents survey focused on druggable superfamilies of particular interest to the drug industry: G-protein coupled receptors; enzymes (kinases, phosphatases, proteases, ATPases, ABC Transporters, monoamine oxidases, glycosidases, glycosyltransferases); ion channels; nuclear receptors; and cytokines. To locate postgenomic patents, searches were performed using Thompson Delphion, a subscription-based patent database. Searches were also performed for three important postgenomic technologies: gene therapy, RNAi, and pharmacogenomics.
Overall, the Biopatents survey produced 9,972 unique patents and created a snapshot of US patenting activity covering a large sector of the postgenomic drug industry over the period 1990-2005. Analysis of the data revealed features characteristic of particular druggable classes, for example with respect to types of patents claimed, therapeutic and/or diagnostic applications claimed, annual rates of growth, maturity indicators, and maintainance record.
Patents are particularly well placed to provide a window onto the activities of key competitors. By becoming familiar with the competitors' patents and products companies can also develop essential litigation awarenes. In chapter 5 of this report we discuss approaches and resources which can be applied to mining patents for competitive intelligence, as well as measurements of patent quality, such as patent citations and other weightings. We apply these principles to reveal the most prolific assignees and the most influential patents in the Biopatents survey.