Patent: 10,787,671

Summary for Patent: 10,787,671

Title:	Method for production of recombinant Erwinia asparaginase
Abstract:	Provided herein are methods of production of recombinant Erwinia asparaginase. Methods herein produce asparaginase having high expression levels in the periplasm or the cytoplasm of the host cell having activity comparable to commercially available asparaginase preparations.
Inventor(s):	Coleman; Russell J. (San Diego, CA), Bruck; Torben (Lakeside, CA)
Assignee:	Pfenex Inc. (San Diego, CA)
Application Number:	16/163,382
Patent Claims:	see list of patent claims

Patent 10,787,671 (US) claims for cytoplasmic vs periplasmic recombinant type II asparaginase: scope, likely indefiniteness/enablement issues, and how competing estates can design around

What is US Patent 10,787,671 claiming about recombinant type II asparaginase production (crisantaspase) in Pseudomonadales?

US 10,787,671 claims US production methods for recombinant type II asparaginase where the active protein is expressed in Pseudomonadales host cells from an expression construct encoding a nucleic acid that is at least 85% homologous to SEQ ID NO: 1 (and/or the nucleic acid is at least 85% homologous to SEQ ID NO: 2). The claims then narrow to soluble yield windows and, depending on claim number, to the subcellular localization (cytoplasm or periplasm), plus several route-dependent and host-engineering features.

Core claim architecture

The independent claim set is effectively split into two “lanes”:

• Cytoplasm lane (claims 1–10, 24–28): recombinant type II asparaginase expressed in the cytoplasm; soluble yield about 20%–40% TCP.
• Periplasm lane (claims 11–23, 27, 29): recombinant type II asparaginase expressed in the periplasm; soluble yield about 20%–40% TCP (with an additional dependent yield range in claim 12 measured as g/L).

Both lanes share the same nucleic-acid identity hooks (85% homology to the listed SEQs), the same host genus constraints (Pseudomonadales), and similar engineering dependences (asparaginase deficiency; protease deficiency; folding modulator overexpression).

How broad are the nucleic-acid identity limits (85% homology) in US 10,787,671 claims?

The claims use a percent homology standard tied to SEQ ID NO: 1 (and, in other dependent claim language, SEQ ID NO: 2) rather than a strict sequence. That creates two practical consequences:

1. Claim coverage expands beyond exact sequences. An accused product method can still read on the claim if the nucleic acid is at least 85% homologous.
2. Enforcement is fact-intensive at claim-construction time. “Homologous to SEQ ID NO” typically invites disputes over (i) alignment method, (ii) where gaps count, (iii) whether homology is at nucleotide level, coding sequence level, or includes non-coding changes, and (iv) whether the homologous construct functionally expresses the enzyme as claimed.

Likely construction pressure points

• 85% is not “minor variation.” For coding regions, 15% divergence can be enough to alter codon usage, silent mutations, signal peptides, linkers, and regulatory elements, but it can also cross the line into substantial amino-acid changes depending on where substitutions land.
• Dependent claims tether to “amino acid sequence as set forth in SEQ ID NO: 1” (claims 6 and 16), which narrows to an exact or effectively exact protein sequence if SEQ ID NO: 1 is indeed an amino-acid listing in the patent.

Do the cytoplasmic and periplasmic localization limitations materially narrow infringement risk?

Yes. Subcellular location is often the easiest technical discriminator for process design.

• Claim 1 lane: “expressing … in the cytoplasm” and soluble yield 20%–40% TCP.
• Claim 11 lane: “expressing … in the periplasm” with the same soluble yield 20%–40% TCP.

A party can lower exposure by swapping localization:

• If they express in cytoplasm and avoid periplasm targeting, they reduce risk to periplasm-specific dependent claims.
• If they express in periplasm and avoid cytoplasmic expression, they reduce risk to cytoplasm-specific dependent claims.

But the independent claims likely still require the right localization per claim lane. A single method will not simultaneously meet both lanes unless constructs drive both localization patterns.

What is the yield threshold in TCP and how does it constrain “process-only” infringement theories?

Yield is a numerical limitation that can defeat “uses the same gene” arguments.

• Base yield limitation (both lanes via claim 1 and claim 11): recombinant type II asparaginase is produced in soluble form at about 20% to about 40% total cell protein (TCP).
• Additional quantitative dependent range:
  • Cytoplasm: about 10 g/L to about 25 g/L (claim 2).
  • Periplasm: about 5 g/L to about 30 g/L (claim 12).

Practical implications for validity and infringement

• Infringement needs process data. To prove infringement, the patentee typically needs comparable assays and documentation of soluble fractions and TCP accounting.
• “About” creates tolerance arguments. Defendants can argue that results outside the window, measurement technique differences, or batch variability avoid literal scope.

What do the dependent claims on activity measurements add (claims 3, 13, 22, 23)?

Claims 3 and 13 add an activity assay measuring soluble recombinant type II asparaginase activity.

Claims 22 and 23 add a comparative element: measured activity is comparable to a control type II asparaginase using the same activity assay.

This can strengthen enforcement by providing a functional benchmark, but it also introduces ambiguity:

• “Comparable” is not a defined numeric acceptance range in the claim text you provided.
• Different assay formats, units, incubation conditions, temperature, and substrate choices can change apparent activity.

Which product is singled out: Erwinia chrysanthemi L-asparaginase type II (crisantaspase)?

Dependent claims 4 and 14 specify that the recombinant type II asparaginase is Erwinia chrysanthemi L-asparaginase type II (crisantaspase).

This narrows the claimed subject matter to a specific type of type II asparaginase, even if upstream claims cover generic “type II asparaginase.”

If a competitor’s protein is a type II asparaginase variant that is not this specific crisantaspase sequence, the dependent claims may not read, but independent claim scope still depends on how “type II asparaginase” is interpreted in the patent record.

What host-engineering constraints are required (asparaginase deficiency, protease deficiency, folding modulators)?

The claims combine expression with host genetic modifications that affect degradation and folding.

Asparaginase deficiency (claims 8–9, 18–19)

• Host cell deficient in one or more native asparaginases.
• Deficiency can include type I and/or type II asparaginase.

This is process-restrictive. A generic strategy of expressing an exogenous asparaginase in an otherwise wild-type background may avoid some dependent claim coverage.

Protease deficiency and folding modulators (claims 10, 25–26)

• Claim 10 includes host deficiency in one or more proteases and/or overexpression of one or more folding modulators.
• Claim 26 enumerates specific proteases and variants:
  • HslUV, PrtB, Prc, DegP, AprA, Lon, La, DegP1, DegP2
  • plus overexpression DegP S219A

This is a strong narrowing cluster. Unless an accused host is engineered with comparable protease/folding modifications, dependent claims 10/25/26 are harder to assert.

How do secretion leaders and periplasm targeting shape claim validity and design-around options?

Claim 20 requires an expression construct with a secretion leader directing transfer to the periplasm.

Claim 21 lists secretion leaders:

• FlgI, Ibps31A, PbpA20V, DsbC, 8484, 5193

This matters in two ways:

1. Periplasm targeting provides a clear technical “fingerprint.” Competitors can choose alternative signal peptides not in the list to try to avoid dependent claim 21 coverage.
2. But claim 20 may still capture other secretion leaders if it does not require the listed set.

In other words, to avoid periplasm-dependent claims, a party can:

• avoid periplasm localization entirely (switch to cytoplasm), or
• keep periplasm localization but argue their secretion leader does not satisfy the claim 21 list (and only depends on whether claim 20 still reads).

Does US 10,787,671 cover half-life extension or is it limited to “producing” methods?

Claims 24 and 27 state the recombinant type II asparaginase is modified to increase half-life in patients.

That phrase can be interpreted as:

• engineered protein variants (amino-acid changes, PEGylation, Fc fusion analogs, or albumin-binding domains), or
• formulation-driven “half-life” effects, though the claim text you provided ties modification to the recombinant asparaginase itself.

Because the method claims are production methods, half-life modification still links to what is expressed and produced. Process defendants will need to match the modification conceptually and structurally to the claims.

Is the use in acute lymphoblastic leukemia an additional constraint or a weak one?

Claims 28 and 29 state use of the produced recombinant type II asparaginase in treatment of patients with acute lymphoblastic leukemia (ALL).

For method-of-use coverage, the clinical indication is a common narrowing element but often less restrictive than it appears because:

• the therapeutic protein is already known in the category for ALL treatment, and
• the patent may be expected to rely on the specificity of “produced” recombinant crisantaspase matching the prior production limitations.

If an infringing production method exists, indication claims usually track whether the marketed or used product is the same protein.

What are the strongest claim elements for the patentee to enforce?

Based strictly on your claim text, enforcement leverage concentrates in these elements:

1. Subcellular localization: cytoplasm vs periplasm.
2. Identity-by-homology: nucleic acid at least 85% homologous to SEQ ID NO: 1 and/or SEQ ID NO: 2.
3. Soluble yield windows: 20%–40% TCP soluble fraction.
4. Host engineering (dependent): asparaginase deficiency; protease deficiency; folding modulator overexpression.
5. Signal peptide list (dependent): secretion leaders enumerated for periplasm targeting.
6. Protein identity (dependent): amino acid sequence set forth in SEQ ID NO: 1 (claims 6/16).
7. Half-life-modified recombinant (dependent): modification to increase half-life in patients.
8. Indication (dependent): acute lymphoblastic leukemia.

What are the most credible design-around strategies based on the claim set?

From a competitor’s perspective, design-around should target at least one of the major limiting parameters:

1) Switch subcellular localization

• Express in cytoplasm to avoid periplasm-lane dependent claims, or vice versa.

2) Break the yield limitation

• Aim for soluble fraction outside ~20%–~40% TCP and/or g/L targets outside claim 2 (cytoplasm) and claim 12 (periplasm).

3) Avoid the homology threshold

• Use a nucleic acid construct with <85% homology to the cited SEQs, while still producing functional type II asparaginase.
• Alternatively, use a protein variant that changes enough sequence identity so that “amino acid sequence as set forth” dependent claims do not match.

4) Avoid host genotype constraints

• Use a host that is not deficient in specific proteases (or not engineered with DegP S219A) so dependent claim coverage fails.

5) Use non-listed secretion leaders (for periplasm targeting)

• If periplasm expression is needed, avoid the exact set in claim 21 and rely on the absence of claim 21 coverage while assessing whether claim 20 still applies.

How strong is the patent estate around production of crisantaspase specifically?

The claim set you provided is internally coherent around:

• production in specific localization compartments,
• homology-defined nucleic acids,
• soluble yield windows, and
• host engineering patterns commonly used to reduce proteolysis and improve folding.

However, the practical strength depends on the breadth and support of the specification, the definiteness of assay/yield accounting definitions, and the exactness of SEQ ID mapping (DNA vs protein). Those details are not in your excerpt. Based on the claim text alone, strength is highest where dependent claims force more specific matches (amino acid SEQ ID; secretion leader list; protease list; DegP S219A).

What could make claims vulnerable in US litigation (based on claim text alone)?

The claim text itself suggests a few litigation themes:

Ambiguity around “about” and TCP accounting

Yield windows use “about,” and “total cell protein” can be interpreted with different sampling and quantification methods. That is a frequent dispute driver.

Functional comparability language (“comparable activity”)

Comparability without a defined numeric metric invites argument that infringement proof cannot be made reliably.

Homology disputes

Homology-based infringement often turns into:

• alignment algorithm questions,
• whether percent homology is assessed for nucleotides vs translated coding sequences,
• and what constitutes the “sequence” (vector-added elements, linkers, codon optimization segments).

These are not automatic invalidity grounds, but they are common litigation battlegrounds affecting both infringement and validity narratives.

Key takeaways

• US 10,787,671 is a process patent aimed at recombinant type II asparaginase (including crisantaspase) made in Pseudomonadales host cells using nucleic acids that are ≥85% homologous to specified SEQs.
• The claims hinge on where the enzyme is expressed (cytoplasm vs periplasm) and on a soluble yield window (~20%–~40% TCP), with additional g/L ranges in dependent claims.
• Dependent claims stack additional host and construct limitations: asparaginase and protease deficiencies, folding modulator overexpression, and enumerated periplasm secretion leaders.
• The most direct design-arounds are to change localization, shift yield, alter sequence identity below 85% homology, or avoid the specific host engineering and signal peptide subsets.

FAQs

1. What does “85% homologous to SEQ ID NO: 1” mean for designing around nucleic-acid claims?
2. Can a cytoplasmic expression process avoid periplasmic dependent claims in US 10,787,671?
3. How do “about 20%–40% TCP soluble” and g/L windows affect infringement proof for asparaginase manufacturing?
4. Do protease knockouts like HslUV and DegP S219A matter only for dependent claims or also for independent coverage?
5. How do secretion leaders (FlgI, Ibps31A, PbpA20V, DsbC, 8484, 5193) change the periplasm claim’s design-around landscape?

References

1. United States Patent 10,787,671. (n.d.). Method for producing recombinant type II asparaginase in Pseudomonadales host cells.

Details for Patent 10,787,671

Applicant	Tradename	Biologic Ingredient	Dosage Form	BLA	Approval Date	Patent No.	Expiredate
Recordati Rare Diseases, Inc.	ELSPAR	asparaginase	For Injection	101063	January 10, 1978	10,787,671	2038-10-17
Jazz Pharmaceuticals, Inc.	ERWINAZE	asparaginase erwinia chrysanthemi	For Injection	125359	November 18, 2011	10,787,671	2038-10-17
Jazz Pharmaceuticals Ireland Limited	RYLAZE	asparaginase erwinia chrysanthemi (recombinant)-rywn	Injection	761179	June 30, 2021	10,787,671	2038-10-17

International Patent Family for US Patent 10,787,671

Country	Patent Number	Estimated Expiration
Australia	2018354067
China	111278852
European Patent Office	3700921
Japan	2021500896
Japan	2023123512
Singapore	11202002943P
United States of America	11377661