Patenting Antisense Oligonucleotides and Methods Robert A. Schwartzman, Ph.D. Acting Supervisory Patent Examiner Art Unit 1636

Antisense Art Unit Art Unit 1635 John LeGuyader, SPE Created October 1996 Art Unit 1636 George Elliott, Ph.D. SPE On fellowship at the National Academy of Sciences

Mechanism of Antisense

Antisense Technologies Antisense Oligonucleotides (Oligos) Catalytic Nucleic Acids: Ribozymes and Dnazymes Triplex Pnas and Other Nonstandard Nucleic Acids Aptamers Decoys Nucleic Acid Modifications Oligo-based Gene Regulation and Gene Therapy

Issued U. S. Patents Classified in 536/24 Issued U.S. Patents Classified in 536/24.5 – Nucleic Acid Expression Inhibitors (as of July 17, 2001) Data obtained using USPTO WEST subclass search for all issued patents citing 536/24.5 - Nucleic Acid Expression Inhibitor

Case Law Antisense-Specific: Enzo Biochem Inc. v. Calgene Inc., 52 USPQ2d 1129 (Fed. Cir. 1999) Enablement - antisense highly unpredictable Decision is based on patents with effective filing dates of at least 1989 and the technology at that time Decision does not necessarily determine the outcome for examination of antisense patent applications recently filed because current knowledge and level of skill in the art is high (antisense has progressed as a technology since 1989)

Gene Walk

Antisense Oligonucleotide Claims Consider a Broad Claim To: An antisense oligonucleotide that inhibits expression of a nucleic acid encoding protein X.

Utility Requirement Utility generally not an issue for antisense. If no function for target nucleic acid (protein or regulatory) is shown or was known: antisense would likely lack utility also raises enablement (how to use) and possibly written description issues probe function alone for target not sufficient to provide utility for antisense, but may be for purposes other than claiming antisense.

Written Description Requirement Written description generally not an issue for broad claims to antisense oligos inhibiting expression of a nucleic acid encoding a protein. May lack written description if the claim reads on targeting many different nucleic acids. Analysis turns on what is shown in the specification and what was known about the various versions of the gene at the time of filing. Provide evidence that antisense targets identified in one gene correlate with targets in other versions of the gene.

Enablement Requirement Probability of finding functional antisense oligonucleotide to a target gene is high. Predictability of any single antisense oligonucleotide being effective is low Claim to specific antisense oligonucleotide may require evidence of function The current state of predictability for antisense may support a broad claim to antisense oligonucleotides But this may also raise prior art issues depending on what was known at the time of filing

Pharmaceutical and Method Claims Consider Broad Claims To: A pharmaceutical composition comprising an antisense oligonucleotide that inhibits expression of a nucleic acid encoding protein X. A method of treating a disease comprising administering an antisense oligonucleotide that inhibits expression of a nucleic acid encoding protein X.

Enablement Analysis for In Vivo Method Claims Describe scope of the claimed invention Cite known unpredictability in the art via journal articles Indicate amount of guidance in the specification Indicate presence or absence of working examples Identify additional experimentation that would be required

Enablement Requirement Commonly Cited References Used by Examiners to Support Unpredictability in Antisense: Crooke, S.T. “Basic principles of antisense therapeutics”, Chapter 1, pages 1-50, Handbook of Experimental Pharmacology, Vol. 131, “Antisense Research and Application”, Ed.Cooke, S.T., Springer-Verlag, New York, 1998. Crooke, S.T. “Progress in antisense technology: the end of the beginning”, Methods in Enzymology, Vol. 313, pages 3-45, 2000. Agrawal et al. “Antisense therapeutics: is it as simple as complementary base recognition?”, Molecular Medicine Today, Vol. 6, Pages 72-81, February 2000. Jen et al. “Suppression of gene expression by targeted disruption of messenger RNA: available options and current strategies”, Stem Cells, Vol. 18, pages 307-319, 2000. Sun et al. “Catalytic nucleic acids”, Pharmacological Reviews, Vol. 52, Pages 325-347, 2000.

Enablement Requirement Commonly Cited Unpredictable Factors for Antisense: Predicting target accessibility Target folding/structure Antisense/target protein interactions Lack of correlation between in vitro and in vivo Efficient delivery to cells and cell targeting for specific disorders Oligo affinity/stability in vivo * Predicting target accessibility. - Screening for best sites still required in most cases for in vivo. * Efficient delivery to cells and cell targeting for specific diseases/conditions. - Adequate intracellular levels of ODNs in view of poor transit across cell membranes. - Immunologic effects from unmethylated G-C sequences and modified ODNs. - Toxicity effects from high concentrations and/or ODN modifications. * ODN Affinity/Stability in vivo - Intracellular ODN breakdown by nucleases. - Largely overcome by chemical modifications of sugar, base and backbone which retain the RNase-H activation. * In vitro (cell culture) results are generally not considered predictive and/or representative of successful in vivo delivery and/or treating disorders. * Evidence should be provided that an animal model is art recognized, especially for human applicability.

Enablement Requirement Modulation of target In vitro (cell culture) results generally  in vivo success Animal model shown may not be art recognized Human data is not ordinarily required by the examiner for in vivo claims But may be the only evidence to enable treatment claims Disorder dependent issue

Obviousness Expect an obviousness rejection against broad antisense claims to known genes if the prior art suggested inhibiting the gene by antisense or other means and the gene sequence was known. The current knowledge and level of skill in the art is high such that one of ordinary skill in the art would expect at least one effective antisense against every known gene (e.g. a full-length antisense), absent evidence to the contrary. Narrow claims to specific antisense oligos may be free of the art, since there may be no motivation to modify the prior art to achieve the specific antisense sequence claimed.

Recommendations Claim functional antisense oligos by specific sequence if you have evidence of activity. List Results of “Gene Walk” Showing activity of each oligo “Gene walk” data may provide representative number of species for broad breadth/scope for a generic claim, but there is no magic number If you can’t claim antisense because of 112 issues, try claiming probes.

Recommendations Provide claims commensurate in scope with the disclosure of the specification Consider the scope of the target nucleic acid. Consider the scope of disease/disorder being treated. Consider the scope of route of administration. Consider the scope of vector delivery system.

Recommendations Provide objective evidence that in vitro results are representative of in vivo applicability. Respond to examiner-cited unpredictable factors with objective evidence to the contrary. Expert opinions are more favorably viewed when supported using objective evidence. Provide objective evidence that a particular animal model is generally accepted as representative of disease or methods of treating, particularly for humans.

Recommendations Objective Evidence Case law Journal articles Experimental data Comparisons commensurate with the disclosure as filed.

QUESTIONS? John LeGuyader Robert Schwartzman SPE - Art Unit 1635 (703) 308-0447 john.leguyader@uspto.gov Robert Schwartzman Acting SPE - Art Unit 1636 (703) 308-7307 robert.schwartzman@uspto.gov

Patenting Antisense Oligonucleotides and Methods Robert A. Schwartzman, Ph.D. Acting Supervisory Patent Examiner Art Unit 1636