synthetic biology and ip
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CRIBIQ event on Synthetic BiologySynthetic Biology: an IP perspective
Serge Lapointe, Ph.D.Partner, Patent Agent
February 29, 2012
2
Introduction
• Synthetic biology is a new area which intersects with biotechnology, computer and engineering
• Broad range of potential applications:
• Environment: clean up tasks, detection of pollutants
• New source of energy:hydrogen, cellulosic ethanol
• Medical: delivery vehicles,drug factories
• Food: preservatives,reconstructed plants
• Etc.
3
Introduction
• More ambitious than modifying components of living cells to achieve a desired functionality
• “extreme genetic engineering” or “genetic engineering on steroids
• Ultimate objective is to use “synthetic” raw material to create novel biological systemsand to create programmablemicroorganisms from scratch
• “There is no technical barrier tosynthesizing plants and animals,it will happen as soon asanyone pays for it.”
--Drew Endy, MIT
4
Presentation Plan
• Patenting activity in this emerging field
• Patent requirements applicable to synthetic biology
• Freedom to operate issues
5
Patenting Activity in Syn Bio
Number of Synthetic Biology-related Patents*
0
20
40
60
80
100
120
140
160
1982-1986 1987-1991 1992-1996 1997-2001 2002-2006 2006-2011
* Presence of key words such as “synthetic biology”, “synthetic gene”, ”synthetic genome”
“synthetic organism”, “synthetic cell” in the Title, Abstract or Claims.
6
Patenting Activity in Syn Bio
19Developing biobased alternatives to petroleum-based products using
a combination of synthetic biology and chemistry.
Engelwood
CO, USA
Gevo
www.gevo.com
700One of the pioneer in the field of industrial biotechnology. Now part
of Dupont. Develops and manufactures a wide range of industrial
enzymes, including for generation of biofuels.
Rochester
NY, USA
Genencor
www.genencor.com
20Develops genetic diagnostic assays based on artificial base paring.Madison
WI, USA
EraGen Biosciences
www.eragen.com
153Employs directed evolution to produce customized biocatalysts for
drug and biofuel production.
Redwood city
CA, USA
Codexis
www.codexis.com
35Developing synthetic microbes to produce pharmaceuticals, fine
chemicals, nutraceuticals, vitamins, flavors and biofuels
Emeryville
CA, USA
Amyris Biotechnologies
www.amyrisbiotech.com
81Develops biopharmaceuticals utilizing artificial amino acidsLa Jolla
CA, USA
Ambrx
www.ambrx.com
Nb of Patent FamiliesSyn Bio Business AreaLocationAssignee
7
Patenting Activity in Syn Bio
133Created from the merger of Diversa and Celunol in 2007.
Developing specialty enzymes products for the production of
cellulosic ethanol
San Diego
CA, USA
Verenium
www.verenium.com
27Designing metabolic pathways for the production of
biochemicals and next generation biofuels
La Jolla
CA, USA
Synthetic Genomics
www.syntheticgenomics.com
81Produce engineered “zinc finger” proteins for controlling gene
expression
Richmond
CA, USA
Sangamo Biosciences
www.sangamo.com
26Developing microbes to convert agricultural feedstock into
cellulosic ethanol
Waltham
MA, USA
Mascoma
www.mascoma.com
18Designs microbial factories for the production of biofuels and
sustainable biochemicals
S. San Francisco
CA, USA
LS9
www.ls9.com
52Developing synthetic biology platform with applications in
human therapeutics, protein production, industrial products,
agricultural biotech and animal sciences
Blacksburg
VA, USA
Intrexon
www.dna.com
Nb of Patent FamiliesSyn Bio Business AreaLocationAssignee
8
Patent Requirements
• Patentable subject matter
• Novelty
• Nonobviousness
• Utility
• Description
9
Patent Requirements
Subject matter eligibility
• U.S. law:
• “…any new and useful process, machine, manufacture or
composition of matter, or any new and useful improvement
thereof…” (Emphasis added)
• Isolated genetic material (DNA, RNA, genes, vectors, etc), proteins, compositions, methods of making, methods of use, etc. are patentable subject matter
• Genetically engineered microorganism and multicellular organism have been patentable for 30 years in the US
• “anything under the sun that is made by man”
• Diamond v. Chakrabarty (U.S. Supreme Court, 1980)
10
Patent Requirements
Patentable Subject Matter
• Innovative concepts to be patented can be summarized by:
• Parts
• Pathways
• Genomes
• Systems
11
Patent Requirements
Patentable Subject Matter
Parts
• A single “part” such as a gene or enzyme to perform a particular function
• Goal is to reduce biological systems to their modular and additive parts that can be assembled (engineered) to perform new functions
• Example: BioBricks™
• BioBricks registry of parts at: http://partsregistry.org
• Patent Claims:
• nucleic acid sequences for primers, probes, ribosome binding
site, transcription factors, regulatory proteins
• constructs, cassettes, vectors
• method of amplification or ligation, etc.
12
Patent Requirements
Patentable Subject Matter
Sangamo Biosciences• U.S Public company founded in 1995
(Nasdaq: SGMO)
• Sangamo is developing engineered transcriptionfactors for the regulation and modification of genes
• Its technology platform is based upon the engineering of a naturally occurring class of DNA transcription factors referred to as zinc finger DNA-binding proteins, or ZFPs
• Owns more than 80 patent families, including several broad patent on foundational technologies
• U.S. patent 7,951,925 issued May 31, 2011
“ 1. A protein comprising an engineered zing finger protein DNA-binding
domain, wherein the DNA-binding domain comprises four zinc finger
recognition regions ordered F1 to F4 from N-terminus to C-terminus, and
wherein F1, F3, and F4 comprise the following amino acid sequences: …”
13
Patent Requirements
Patentable Subject Matter
Pathways
• Several “parts” working together to perform an overall process
• Goal is to develop organisms which can serve as “chemical
factories” on a commercial scale
• Examples:
• production of cellulosic ethanol
• production of pharmaceutical compounds
• degradation of waste products
• Patent Claims:
• unique combination of genes, enzymes or recombinant organisms
• genetically modified host cells comprising a heterologous nucleic
acid
• methods of making or producing the chemical product
14
Patent Requirements
Patentable Subject Matter
Amyris Biotechnologies• Public company founded in 2003 (Nasdaq: AMRS)
• Started in 2004 a project to produce copious quantities
of synthetic artemisinin (an antimalarial drug) in E. coli
• Now focuses on genetically engineered yeast that contains
synthetic DNA to break down sugarcane to produce isoprenoids
which are then converted to biofuels
• 27 patent families
• U.S. patent 7,659,097 granted February 2010“ 1. A method for producing isoprenoid comprising:
(a) obtaining a plurality of bacterial or fungal host cells that comprises a heterologous nucleic acid encoding one or more enzymes of a mevalolate pathway for making isopentenyl pyrophosphate,…wherein said mevalolate pathway comprises (1) an enzyme that condenses acetoacetyl-CoA with acetyl-CoA to form HMG-CoA; (ii) en enzyme that converts …; (iii) an enzyme that phosphorylates …; (iv) an enzyme that converts…; v) an enzyme that converts …; and
(b) culturing the bacterial or fungal host cells in a medium …”
15
Patent requirements
Patentable Subject Matter
Genomes• Designing, modifying, reconstructing and synthesizing entire
genomes
• Goal is to fully synthesize a genome and insert it into a “biological shell”, resulting into a fully engineered organism with new functions
• Examples:
• complete chemical synthesis of a viral genome
• creating bacteria with a genome that was produced in yeast
• minimal genome (Synthetic Genomics’)
• Patent Claims:
• synthetic cells and host cells comprising a heterologous nucleic acid
• methods of synthesis, replication and transplantation of large DNA
molecules
• new set of genes and proteins
• products produced by these synthetic organisms
16
Patent Requirements
Patentable Subject Matter
Synthetic Genomics• Co-founded in 2005 by J. Craig Venter
• Venter’s previous company, Celera Genomics,
was in the race to sequence the human genome
• Currently working to produce biofuels on an industrial scale
• Received funding from ExxonMobil and BP
• 27 patent families
• May 2007: publication of U.S. application 20070122826 (filed Oct. 12, 2006)
• Describes a minimally operative genome of the bacterium Mycoplasma
genitalium
• 351 genes believed to be essential for the survival of the bacterium
• Rejected patent application still under examination
“ A plurality of bacterial genes, comprising isolated nucleic acid molecules, wherein each
molecule encodes one of at least 351 proteins, but no more than 450 proteins, wherein:
(i) the at least 351 proteins are required for growth and replication of a free-living bacterial
organism under axenic conditions in a rich bacterial medium; and
(ii) the at least 351 proteins perform at least the functions of the genes set forth in Table 3.”
17
Patent Requirements
Patentable Subject Matter
Systems• Goals are to:
• engineer an organism as a genetic biosensor or computer
• combine engineered organisms with existing computer or electronic systems for performing new functions
• Examples:
• programming bacterial to take photographs (Nature, 438: 441-442 (2005))
• synthetic multicellular system programmed for pattern formation that may be useful for detection of environmental pollutants (Nature, 433: 1130-34 (2005))
• Patent Claims:
• synthetic cells; methods of making these cells
• computer and electronic systems having biological components
• methods of use
18
Patent Requirements
Patentable Subject Matter
US 6,774,222
• Issued: August 10, 2004
• Title: MOLECULAR COMPUTING ELEMENTS, GATES AND
FLIP-FLOPS
• Assignee: U.S. government (Department of Health)
• Claims:
“ 51. A method of storing information, said method comprising the step of:
binding a nucleic acid binding protein to a first protein binding site on a
nucleic acid, …”
“64. A method of transforming binary information, said method
comprising the steps of:
(i) binding a nucleic acid binding protein to an input protein binding
site on a first nucleic acid; and (ii) determining whether or not a
nucleic acid binding protein can bind to an output protein binding site
on a second nucleic acid; ...”.
19
Patent Requirements
Patentable Subject Matter
Human beings are excluded
• Only non naturally occurring, nonhuman multicellular living organisms are patentable
• Patent will be rejected if thebroadest reasonableinterpretation of the claimedinvention encompasses ahuman being
20
Patent Requirements
Utility
Invention must provide some identifiable benefits
• EP: industrial applicability
• US: utility must be specific, credibleand substantial
• Moral utility issues?
• invention should not be frivolous or
injurious to the well-being, good policy
or sound morals of society
• rarely invoked but in the case of
synthetic biology innovations,
possibility of failing this test
21
Patent Requirements
Novelty and Nonobviousness
• Novelty
• invention must not have been previously publicly disclosed
anywhere in the world before the filing of the patent application
• Nonobviousness
• not a modification that would be considered trivial to someone
skilled in the art
• Patentability will revolves around the differences in view of:
• known molecular biology methods, existing tools, etc.
• the naturally occurring products on which the synthetic ones
are based
22
Patent Requirements
Description and Enablement
• Need a complete disclosure of the invention such that the person skilled in the art:
(1) Can unambiguously identify what has been invented; and
(2) Is enabled to practice the invention
• Written description:
• Invention must be adequately described in the patent
application such that one skilled in the art would recognize
Applicant was in possession of the claimed invention at the
time of filing
• Various considerations:• actual reduction to practice
• disclosure
• identifying characteristics (complete vs. partial structure)
• predictability
• etc.
23
Patent Requirements
Description and Enablement
Enablement
• Claimed invention must be enabled so that any person skilled in the art can make and use the invention without undue experimentation
• Various factors
• breadth of the claims
• nature of the invention
• state of the art
• level of predictability
• amount of guidance provided by the inventor
• etc.
24
Patent Requirements
Description and Enablement
Challenges
• File early to be first
• Actual reduction to practice
• Sufficient number of examples
• Foresee and describe possible alternatives
• Acceptable scope of protection
25
Freedom to Operate Issues
• Innovations in this field will require the use of many elements or methods for which patents exist
• nucleic acid sequences, promoters, genes, etc.
• constructs, cassettes, vectors, plasmids, etc.
• genetically modified host cells
• methods of amplification, ligation,replication and transplantation ofDNA molecules
• etc.
• “Patent thickets” and Stacking royalties
• “Hold-up” patents?
• Critical to make appropriate search in
order to assess the patent landscapebefore and during the R&D project
26
Freedom to Operate Issues
• Open source as an alternative?
• BioBricks Foundationwww.biobrick.org
• registry of more than 18 000 fundamental building blocks or
“BioBrick™” parts of synthetic biology (partsregistry.org)
• the BioBrick™ parts are freely
available for open innovation
• Biological Innovation for OpenSociety (BIOS) www.bios.net
• this group owns a few key patent
gene transfer technologies
• force licensees to make patented
improvements to these enabling
technologies available to others
27
Conclusions
• Synthetic biology is not a new idea but has recently been expanded to include whole genomes and organisms
• Patentability generally not an issue
• long recognized patentable subject matter
• advisable not to wait and be early in the game to obtain broad claims
• Challenging infringements issues
• possible that many licenses will be required for the various patented pieces and methods
• essential to search for existing patents and pending patent applications and monitor competitors’ activities
28
Questions
Thank you!
Serge Lapointe, Ph.D.
Partner, Patent Agent514-397-5219
slapointe@fasken.com
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