patenting compounds, compositions, and methods for viral...

Patenting Compounds, Compositions, and

Methods for Viral Infections: Patent Eligibility

Considerations and Challenges

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WEDNESDAY, OCTOBER 7, 2020

Presenting a live 90-minute webinar with interactive Q&A

Gaby L. Longsworth, Ph.D., Director, Sterne Kessler Goldstein Fox, Washington, D.C.

Robert Greene Sterne, Founding Director, Sterne Kessler Goldstein Fox, Washington, D.C.

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Technical Minds. Legal Muscle.

Patenting Compounds,

Compositions, and Methods

for Viral Infections

Gaby L. Longsworth, Ph.D.

Robert Greene Sterne

October 7, 2020

confidential © Sterne, Kessler, Goldstein & Fox P.L.L.C. 2020 66

• Covid-19 is the 3rd major global outbreak of a coronavirus in the past 20 years

− SARS ~8000 infected, 774 killed

− MERS ~2500 infected, 858 killed since April 2012

− Covid-19 > 35 million infected, ~ 1 million dead (as of 10/5)

Critical Issues Surrounding Covid-19

Region Infected

Source: WHO Coronavirus Disease (COVID-19) Dashboard


• Many other prior viral outbreaks:

− Ebola, Swine flu (H1N1), Bird flu (H5N1)

• Increased awareness of the IP issues surrounding patenting antiviral

research & preserving exclusive marketing rights for companies developing

products, diagnostic assays and kits, and treatments for viral infections


1. Ebola virus – Source: WebMD

2. H1N1 – Source: CDC.gov

3. H5N1 – source: CDC.gov

Ebola H1N1H5N1


• Investor interest in funding vaccines ebbs and flows with the

rise and fall of pandemics

− SARS appeared in 2003, then disappeared within a year

− In 2016, scientists ready to test a newly developed SARS vaccine in

healthy humans

− Investors not interested to fund testing in clinic and project went

dormant

• SARS and MERS should have triggered major federal and

private investments to develop treatments and vaccines in

anticipation of future global viral outbreaks



• Current funding of medical research tends to be market-driven

and reactive, rather than proactive

• Typically, it takes between 5 and 15 years to bring a vaccine to

market

− lengthy process of testing on animals, expensive clinical trials on

humans, and regulatory approvals

− New vaccines cost anywhere from US$400 million to US$2 billion from

initial research to commercial production

− Revenues from vaccine sales have remained relatively constant as

most vaccinations are only performed once in a lifetime

R&D and Market Drivers


1. Viral mechanisms

2. Subject matter eligibility for compound, composition, and method of use

claims

3. Global best practices

We will review these and other key issues:

• What are the critical patentability issues when preparing compound or composition

patents?

• How have the courts treated medical diagnostics claims?

• What strategies should counsel employ to increase the likelihood of getting patent

protection for compounds, composition, or method of use claims for viral infections?

Outline of today’s webinar

Viral Mechanisms and Patent

Strategies


• Compared to bacteria, viruses have different

mechanisms and machinery to survive and replicate in a

host

• Bacteria can reproduce on their own, whereas viruses

must insert their genetic material into a host's cells to

reproduce

• The virus hijacks the host cell's machinery to reproduce

and fill the cell with viral particles

• Viral particles then either bud off or cause the cell to

rupture, and the virus spreads to other cells

Science Photo Library/

Alamy Stock Photo

http://servingnature.blogspot.com/2013/03/virology.html

The bad about viruses…..and viral infections


• Viruses have developed many Machiavellian

strategies to evade host immune responses

• High rate of genetic change exhibited by

viruses creates a moving target

• Combating viruses with vaccines and

antiviral drugs is a constant challenge

− Antibiotics are ineffective

− Vaccines to prevent (the first line of defense)

− Antivirals to treat

The bad about viruses…..and viral infections

(Cont’d)

Image Credit: Konstantin Faraktinov/Shutterstock.com


• Small molecule inhibitors typically arise out of a structure-based

design of the viral target

• Steps in virus life cycle can

be targeted

• This approach involves a

detailed knowledge of viral

action and lifecycle

• Different types of viruses:

− DNA or RNA (ds, ss, retro)

Small Molecule Antivirals

ChemistryViews.org


https://www.clinicaloptions.com/

Preventing viral adhesion to

host cells (inhibitors of

host-cell receptors)

Inhibiting hemagglutinin

induced membrane fusion

Accelerating capsid assembly

• Targeting viral DNA-packaging motors

• Inhibiting viral RNA processing/packaging

(targeting viral polymerase complex)

Disrupting viral assembly

(nucleoprotein)

Enhancing intracellular

innate immunity

• Inhibiting viral escape from

endosome (protease inhibitors)

Preventing the release of

viral particles (blocking

neuraminidase)

Preventing viral reproduction

(blocking integrase or reverse

transcriptase)

Blocking ion-channels


Oseltamivir (TAMIFLU) Remdesivir


• Protease inhibitors: atazanavir (REYATAZ), darunavir

(PREZISTA), fosamprenavir (LEXIVA), indinavir (CRIXIVAN),

lopinavir/ritonavir (KALETRA), nelfinavir (VIRACEPT), ritonavir

(NORVIR), and saquinavir (INVIRASE).

• Prevent release of viral particles by blocking neuraminidase on

surface of flu viruses: baloxavir marboxil (XOFLUZA), zanamivir

(RELENZA), and oseltamivir (TAMIFLU)

• Reverse transcriptase inhibitor: doravirine (PIFELTRO)

Examples of small molecule antivirals (HIV):


• Compound claims (chemical entity, solvates, crystal forms)

• Methods of treatment

− Target – “ A method of treating HIV, comprising administering X”

− Dosing – “comprising administering at least about 250 mg of X”

− Regimen – “at least about 250 mg of X at least once about every 2 days”

• Process claims (e.g., methods of making/manufacture)

• Formulation claims (drug, excipient, salts, stabilizers, etc.)

Types of patent claims obtained


• Patents to novel small molecule antivirals are generally readily

granted at the IP5

• Second uses of known small molecules can be more difficult

− “cytokine storm” in some Covid-19 patients

• Viruses are rarely fully “cured” and many require prolonged

treatment to keep virus levels dormant

• Continued R&D (and subsequent patent filings) likely as viruses

mutate and patients are identified that are less responsive to

existing antiviral therapies

Small Molecules


Brand Name Viral Target Patent and Representative Claim

Prezista

(darunavir)

HIV protease U.S. Patent No. 8,518,987; Title: Pseudopolymorphic forms of a

HIV protease inhibitor

1. An ethanolate solvate of the compound (3R,3aS,6aR)-

hexahydrofuro[2,3-b]furan- 3-yl(1S,2R)-3-[[(4-

aminophenyl)sulfonyl](isobutyl)amino]-1-benzyl-2-

hydroxypropylcarbamate, in which the ratio of compound to

ethanol is about 1:1.

U.S. Patent No. 10,000,504 (Child of ‘987, above)

1. A process for preparing a pseudopolymorph of the

compound (3R,3aS,6aR)-hexahydrofuro . . . comprising

combining (3R,3aS,6aR)-hexahydrofuro . . . with an organic

solvent, water, or a mixture of water and a water miscible

organic solvent, and inducing crystallization.

Exemplary Small Molecule Antiviral Drugs and

Relevant Patent Claims



Vosevi

(voxilaprevir)

Hepatitis C,

inhibits viral

replication

U.S. Patent No. 8,735,372; Title: Nucleoside phosphoramidate

prodrugs

1. A method of treating a human infected by hepatitis C virus,

comprising administering to the subject an effective amount of

an NS5a inhibitor and an effective amount of a compound

represented by the following formula [ ].

Exemplary Patent Claims (Cont’d)



Xofluza

(baloxavir

marboxil)

Influenza A/B

endonuclease

U.S. Patent No. 8,927,710; Title: Substituted polycyclic

carbamoylpyridone derivative

1. A CAP dependent endonuclease inhibitor compound

represented by formula (I), a pharmaceutically acceptable salt, or

a solvate thereof [ ].




Sitavig

(acyclovir)

Herpes labialis

DNA

polymerase

U.S. Patent No. 8,592,434; Title: Mucoadhesive buccal tablets

for the treatment of orofacial herpes

1. A method for treating orofacial herpes comprising

administering to a patient suffering from orofacial herpes only

a single dose of a prolonged release mucoadhesive buccal

tablet comprising:

50 to 200 mg of acyclovir,

1 to 75% by weight of a diluent,

1 to 10% by weight of an alkali metal

alkylsulfate, to 5% by weight of a

binding agent,

5 to 80% by weight of natural milk proteins, and

5% to 80% by weight of at least one hydrophilic polymer that

provides a sustained release of acyclovir.




TPOXX

(tecovirimat)

Smallpox

(variola virus),

blocks viral

particle release

U.S. Patent No. 8,802,714; Title: Compounds, compositions

and methods for treatment and prevention of orthopoxvirus

infections and associated diseases

1. A method of treating or preventing an infection caused by

an orthopox virus in a living host having or susceptible to said

infection, said method comprising administering to said living

host a therapeutically effective amount of a mixture of

compounds comprising: (a) N-[(3aR,4R,4aR,5aS,6S,6aS)-

3,3a,4,4a,5,5a,6,6a- octahydro-1,3-dioxo-4,6-ethenocycloprop

[f]isoindol-2(1H)-yl]-4-(trifluoromethyl)- benzamide; and (b) N-

[(3aR,4S,4aS,5aR,6R,6aS)-3,3a,4,4a,5,5a,6,6a-octahydro-

1,3- dioxo-4,6-ethenocycloprop [f]isoindol-2(1H)-yl]-4-

(trifluoromethyl)-benzamide, or a pharmaceutically acceptable

salt thereof.



• Vaccines are a preemptive first line of defense

• Vaccines stimulate the immune system to produce antibodies

that may remain in the body for long periods of time

• Because of such long-term

“immune memory,” a rapid

immune response typically

results upon subsequent

exposure to the virus

REMAINS/ISTOCKPHOTO

Vaccines


• Development typically takes years (5-15 years)

− More difficult and expensive to manufacture and test in human

clinical trials than small molecule antiviral drugs

▪ US$400 million to US$2 billion

− Requires negative result—wait to see if a subject catches the

virus

− “Human Challenge” studies are controversial (vaccinate then

intentionally expose to the virus)

• Vital research for creating new viral treatments to

guarantee continued global human health

Vaccines


Attempts to Accelerate Time to Market

• Starting trials before

completing extensive

academic and pre-clinical

research

• Combining/overlapping

Phases of the clinical trials

• Ramping up production

before final approval

• Unpredictable

NEW YORK

TIMES


Vaccine IP

• Vaccine IP is complex:

− Many companies trying to achieve the same goal (especially for Covid)

− Can be highly collaborative

▪ Good for furthering research & development

▪ Complicates patent rights

− Political and public relations considerations

▪ Does a patent holder want to appear to be blocking vaccine development and/or

distribution?

− Multiple aspects can be patented

▪ Freedom to Operate considerations


− Nucleic acids

− amino acid

sequences

− viral vectors

− attenuated strains

− formulations

− culturing methods

− manufacturing methods

− methods of use

− Kits

− Packaging

− devices for vaccine

administration

Vaccine IP

• Various levels of patents

Nature

World Health Organization


Claims obtainable directed to:

• “A stable vaccine, comprising . . .”

• “A multivalent immunogenic composition . . .”

• “A live attenuated viral strain . . .”

• “A method of making a virus-like particle . . .”

• “A method of vaccinating a patient or inducing an immune

response in a subject in need thereof . . .”

Vaccine IP


Exemplary Patent Claims in the Vaccine Space

Brand Name Viral Target Exemplary Patent Claim

INFANRIX Diphtheria

and tetanus

toxoids and

acellular

pertussis

U.S. Patent No. 9,233,151; Title: Vaccine composition

1. A multivalent immunogenic composition comprising the

following components:

(a) killed whole-cell Bordetella pertussis,

(b) tetanus toxoid,

(c) diphtheria toxoid,

(d) Hepatitis B surface antigen,

(e) a conjugate of a carrier protein and the capsular

polysaccharide of Haemophilus influenzae type

B and

(f) one or more conjugates of a carrier protein and

the capsular polysaccharide of a bacterium

selected from the group consisting of Neisseria

meningitidis type A and N. meningitidis type C.



(Cont’d)


BIOTHRAX Bacillus

anthrax

U.S. Patent No. 8,778,359; Title: Stable anthrax vaccine

formulations

1. A stable vaccine for stimulating an immune response to

a Bacillus anthracis protective antigen comprising:

(a) a purified B. anthracis protective antigen protein;

(b) an alanine formulation buffer; and

(c) a pharmaceutically acceptable adjuvant.



(Cont’d)


DENGVAXIA Dengue

disease

U.S. Patent No. 9,169,298; Title: Dengue serotype 1 attenuated

strain

1. A live attenuated dengue-1 virus strain which comprises an

RNA sequence having the sequence of SEQ ID NO: 3

wherein said RNA sequence comprises uridines in place of

the deoxythymidines in SEQ ID NO: 3, wherein at least

nucleotides at positions 5962 and 7947 of the RNA

sequence are mutated with reference to SEQ ID NO: 3,

with the proviso that the following nucleotides of the RNA

sequence are not mutated: 1323, 1541, 1543, 1545,

1567,1608, 2363, 2695, 2782, 5063, 6048, 6806, 7330, and

9445.



(Cont’d)


GARDASIL 9 Human

papillomavirus

U.S. Patent No. 7,476,389; Title; Papillomavirus vaccines

1. A method of making a papillomavirus virus-like particle, which

method comprises: constructing a recombinant DNA molecule

that contains a sequence encoding

a papillomavirus L1 protein;

transfecting a host cell with the recombinant DNA molecule;

expressing papillomavirus L1 protein in the host cell;

and

obtaining papillomavirus virus-like particles from the

transfected host cell; wherein the papillomavirus is not

HPV 16.



(Cont’d)


PROQUAD Measles,

mumps,

rubella, and

varicella

virus

U.S. Patent No. 10,350,289; Title: Methods of immunization with

varicella zoster virus antigen

1. A method of vaccinating a patient against varicella zoster

virus (VZV) infection or reactivation of latent VZV infection

comprising injecting an effective amount of a live attenuated

VZV vaccine to the epidermis or the dermis of the patient's skin

at a depth of between 100 and 700 microns from the surface of

the skin, wherein the live attenuated VZV vaccine is liquid and

comprises a live attenuated VZV strain, and wherein the VZV

vaccine is injected with an intradermal delivery device

comprising one or more hollow needles for penetrating the skin,

wherein the device is adapted for shallow intradermal delivery

of the VZV vaccine.



(Cont’d)


IMOVAX Rabies U.S. Patent No. 9,750,800; Title: Method for purifying the rabies

virus

1. A vaccine comprising purified and inactivated rabies virus,

wherein the amount of residual DNA measured by quantitative

PCR and the amount of total protein present in one effective

dose of vaccine or in one dose of vaccine which contains 2.5 IU

as measured according to the European Pharmacopeia

monograph number 0216, are, respectively, less than 20 pg and

less than 40 μg.



(Cont’d)


JYNNEOS Smallpox and

monkey pox

U.S. Patent No. 9,707,291; Title: Single high dose of MVA

induces a protective immune response in neonates and

infants

1. A method for inducing a protective immune response against

a poxvirus in a human neonate or infant of less than 6 months

of age comprising administering a dose of at least 108 50%

tissue culture infectious dose (TCID50) of a modified vaccinia

virus Ankara (MVA) to a human neonate, wherein the

administration induces protective T- and B-cell responses

against a poxvirus in the human neonate prior to 6 months of

age in the absence of a second administration of the MVA.



(Cont’d)


RECOMBIVAX

HB

Hepatitis B U.S. Patent No. 6,544,757; Title: Synthesis of human virus

antigens by yeast

1. A DNA transfer vector comprising a yeast replication origin, a

yeast promoter fragment and, in correct orientation with said

promoter fragment, a DNA segment coding for the S-protein of

Hepatitis B virus.



(Cont’d)


n/a SARS U.S. Patent No. 10,130,701; Title: Coronavirus

1. A live, attenuated coronavirus comprising a variant replicase

gene encoding polyproteins comprising a mutation in one or

both of non-structural protein(s) nsp-10 and nsp-14, wherein

the variant replicase gene encodes a protein comprising an

amino acid mutation of Pro to Leu at the position corresponding

to position 85 of SEQ ID NO: 6, and/or wherein the variant

replicase gene encodes a protein comprising an amino acid

mutation of Val to Leu at the position corresponding to position

393 of SEQ ID NO: 7.



(Cont’d)


n/a H5N1 avian

influenza

U.S. Patent No. 9,283,198; Title: Materials and methods for

treating viral infections

1. A method for treating a subject infected with H5N1 strain of

avian influenza, wherein said method comprises diagnosing a

subject as being infected with the H5N1 strain of avian

influenza; and administering to the subject an effective amount

of a salt of cysteamine.


• Various aspects of vaccine product and development are

patentable

− Though PR reasons may discourage enforcement, freedom to operate

supports building a strong patent portfolio around vaccines

− Patents protection enhances potential outside funding, strengthens

negotiating power with potential collaborators/licensees, and helps

establish a company as a lead player in vaccine development

− Consider your potential infringer

▪ Target your competitor selling a vaccine, consider the label

▪ Not the doctor delivering the vaccine

Vaccine IP – Takeaways

Subject Matter Eligibility

Considerations in the USPTO


Novel compounds are patent eligible - do not exist in

nature (also crystal forms, hydrates, and solvates)

Novel Methods of Use, generally easily obtained

A new use for an old compound is typically patentable

assuming the use is novel and nonobvious

Small Molecules


Newly discovered, wild-type strain of a virus are not patentable

A genetically modified viral strain that differs structurally from the

wild-type virus is patentable

A vaccine composition comprising a live attenuated virus are

generally considered patentable subject matter –

− a live attenuated virus has different structural and functional characteristics

than what occurs in nature

Virus-like particles and viruses obtained by recombinant DNA

technology are also patentable

Vaccines

PHOTO: KINDPNG


Claims directed to a vaccine composition comprising an antigenic

peptide and a pharmaceutically acceptable carrier, such as water,

are not patent eligible because each component is a product of

nature


peptide and a novel pharmaceutically-acceptable carrier would be

patent eligible


peptide and a specific adjuvant would be patent eligible

Vaccines

Diagnostics in the USPTO


• Claims to methods of diagnosing in the U.S. are difficult to

obtain

− Keeps the cost of diagnostics down

− But, the Covid-19 outbreak has highlighted the lack of investment and

development of diagnostics

− Complicated patent issues and uncertainty could play a role in this lack

of corporate/government investment in diagnostics

Diagnostics – Patent Eligibility


• In vitro diagnostic methods, i.e., using a biological sample

isolated from a patient, are generally not patent eligible

− A method “for detecting a paternally inherited nucleic acid” (Ariosa)

− A method “for performing a prenatal diagnosis” (Ariosa)

Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015)

• Application of diagnostic results such as method of treatment

claims eligible (Vanda)

• Method of preparation, which involves a diagnostic, eligible

(Illumina)

Diagnostics – Patent Eligibility


Vanda Pharma Inc. v. West-Ward Pharma Int’l Ltd (Fed. Cir. 2018)

• A method for treating a patient with iloperidone, wherein the patient is suffering from

schizophrenia, the method comprising the steps of:

− determining whether the patient is a CYP2D6 poor metabolizer by:

▪ obtaining or having obtained a biological sample from the patient; and

▪ performing or having performed a genotyping assay on the biological sample to determine if the patient has a

CYP2D6 poor metabolizer genotype; and

− if the patient has a CYP2D6 poor metabolizer genotype, then internally administering

iloperidone to the patient in an amount of 12 mg/day or less, and

− if the patient does not have a CYP2D6 poor metabolizer genotype, then internally

administering iloperidone to the patient in an amount that is greater than 12 mg/day, up to 24

mg/day,

− wherein a risk of QTc prolongation for a patient having a CYP2D6 poor metabolizer genotype

is lower following the internal administration of 12 mg/day or less than it would be if the

iloperidone were administered in an amount of greater than 12 mg/day, up to 24 mg/day.

Diagnostics – Vanda


Illumina, Inc. v. Ariosa Diagnostics, Inc. (Fed. Cir. 2020)

• A method comprising:

(a) extracting DNA comprising maternal and fetal DNA fragments from a substantially cell-free

sample of blood plasma or blood serum of a pregnant human female;

(b) producing a fraction of the DNA extracted in (a) by:

(i) size discrimination of extracellular circulatory fetal and maternal DNA fragments, and

(ii) selectively removing the DNA fragments greater than approximately 300 base pairs,

wherein the DNA fraction after (b) comprises extracellular circulatory fetal and maternal DNA

fragments of approximately 300 base pairs and less and a plurality of genetic loci of the

extracellular circulatory fetal and maternal DNA fragments; and

(c) analyzing DNA fragments in the fraction of DNA produced in (b).

• “This is not a diagnostic case. And it is not a method of treatment case. It is a method of

preparation case.”

Diagnostics – Illumina


Diagnostics – USPTO Guidance

• To claim a diagnostic method,

you need “significantly more”

than just the diagnostic,

unpatentable, aspect:

− A method of treating a target

population, identified using a

particular diagnostic method

− A novel way of preparing a

sample, which can be part of a

diagnostic method

USPTO


• The law around patent eligible subject matter in the US is likely

still developing

− Include different claims to diagnostic methods to anticipate potential

tightening or loosening of restrictions

• The laws are different outside the US

− Language that may be allowable can vary by country (e.g., Europe,

South Korea, Israel, and various Asian countries)

Diagnostics – Drafting Considerations

Ongoing Effort Against

Covid-19


• Global Alliance for Vaccines and

Immunization (GAVI)

• UNICEF

• World Health Organization

• Biomedical Advanced Research

and Development Authority

(BARDA) (US DHHS)

• National Institute of Allergy and

Infectious Diseases (NIAID) (US

NIH)

• Coalition for Epidemic

Preparedness Innovations (CEPI)

A Global Effort

(New York Times – as of September 29, 2020)


• Altimmune

• BioNTech and Pfizer

• CytoDyn

• Gilead Sciences

• GlaxoSmithKline

• Heat Biologics

• Inovio Pharmaceuticals

• Johnson & Johnson

A Global Effort



• Moderna

• Novavax

• Regeneron

Pharmaceuticals

• Sanofi

• Roche

• Takeda Pharmaceutical

• Vaxart

• Vir Biotechnology

A Global Effort


Global Best Practices


• Critical Issues:

1. Testing

2. Starting/Raw Materials

3. Financing

4. Incentives for the Private Sector

5. Clinical Trials and Federal Approval

6. Supply Chain

7. Dependence on Foreign

Manufacturing

8. Allocation

9. Efficacy

10. Future Mutation and/or Resurgence

What have we learned from this Pandemic?


• For-profit pharmaceutical companies are “for-profit,” but crisis prevention

means being in front of a disease before it reaches pandemic proportions

• Governments and nonprofits must take the lead in funding proactive

vaccine research and development

• It is up to governments and the private sector around the world to step up

vaccine supplies, research, and development

• We ought to be better prepared to handle future viral outbreaks as the

disastrous effects on security, the economy, and commerce are currently

on full display with COVID-19

What have we learned from this Pandemic?


Contact

Robert Greene Sterne

[email protected]

+1 (202) 772 8555

Gaby L. Longsworth, Ph.D.

[email protected]

+1 (202) 772 8824
mailto:[email protected]:[email protected]

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