PTAB

IPR2014-00398

3D Matrix Ltd v. MenICON Co Ltd

Log In
Key Events
Petition
petition

1. Case Identification

2. Patent Overview

  • Title: Self-Assembling Peptides
  • Brief Description: The ’032 patent discloses self-assembling peptides comprising alternating polar and nonpolar amino acids that form a beta-sheet structure. The purported invention is a peptide of 12-32 amino acids that has a net charge of -3 to -2 or +2 to +3 in a neutral pH environment, which allegedly provides advantages over prior art peptides with a neutral net charge.

3. Grounds for Unpatentability

Ground 1: Anticipation over Dado - Claims 1-8 are anticipated by Dado under 35 U.S.C. §102(b).

  • Prior Art Relied Upon: Dado (G.P. Dado and S.H. Gellman, J. Am. Chem. Soc. 1993, 115, 12609-12610).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner argued that Dado disclosed a specific peptide ("Peptide 1°") that meets every limitation of claim 1. This peptide consists of 18 amino acid residues (within the claimed 12-32 range), comprises both acidic (glutamic acid) and basic (lysine) residues, and has a calculated net charge of +2 at neutral pH (within the claimed +2 to +3 range). Dado taught that this peptide forms a stable beta-sheet in an aqueous solution, and its amphipathic structure would form distinct polar and nonpolar faces upon self-assembly, as required by the claim.
    • Key Aspects: Although Dado did not explicitly state the pH for beta-sheet formation, Petitioner contended that a person of ordinary skill in the art (POSITA), informed by the extensive literature on similar peptides, would understand that Peptide 1° inherently self-assembles at a neutral pH. Petitioner asserted that this inherent disclosure anticipates claim 1 and that dependent claims 2-8 are also anticipated as they recite features (e.g., specific amino acids, peptide length) also present in Dado's Peptide 1°.

Ground 2: Obviousness over Zhang II, Yokoi, and Aggelli - Claims 1-8 are obvious over Zhang II in view of Yokoi and Aggelli under 35 U.S.C. §103(a).

  • Prior Art Relied Upon: Zhang II (Patent 5,670,483), Yokoi (Yokoi et al., Proc. Natl. Acad. Sci. USA 2005, 102:8414-8419), and Aggelli (WO 2004/007532).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner asserted that Zhang II disclosed self-assembling peptides (e.g., EAK16) with all the structural features of claim 1 except for the specific non-zero net charge. Zhang II’s EAK16 is a 16-residue peptide with alternating polar and nonpolar amino acids that forms a stable beta-sheet at neutral pH, but it is "fully complementary," meaning it has an equal number of acidic and basic residues and thus a net charge of zero.
    • Motivation to Combine: A POSITA would combine the teachings because the only difference between Zhang II’s disclosed peptides and the claimed invention was the net charge. Zhang II taught that peptides with mismatched or non-ionic pairs could still form stable membranes, suggesting that perfect charge complementarity was not required. Aggelli further provided a reason to create a non-zero charge by disclosing a self-assembling peptide with similar properties that had a net charge of -2.
    • Expectation of Success: A POSITA would have had a reasonable expectation of success in modifying Zhang II's EAK16 peptide—for example, by replacing two charged residues with neutral ones—to achieve a net charge of +2 or -2, expecting the resulting peptide to retain its ability to self-assemble and form a beta-sheet structure. Yokoi, co-authored by the ’032 patent's inventors, reinforced that such peptides form stable scaffolds at neutral pH.

Ground 3: Anticipation/Obviousness over Mira - Claims 1-8 are anticipated or rendered obvious by Mira in view of Zhang I under 35 U.S.C. §§102(b) and 103(a).

  • Prior Art Relied Upon: Mira (Mira et al., BMC Structural Biology 2004, 4:7) and Zhang I (Zhang et al., Proc. Natl. Acad. Sci. USA 1993, 99:3334-3338).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner argued that Mira disclosed a "peptide-1" that met all limitations of claim 1. Mira's peptide is 20 amino acids long, contains six acidic and four basic residues resulting in a net charge of -2 at neutral pH, and its CD spectrum confirmed a beta-sheet structure. Mira also explicitly taught that the peptide arranges into an amphipathic conformation with a hydrophobic face.
    • Motivation to Combine: The only potential discrepancy was that Mira’s peptide contained threonine residues on its hydrophobic face, whereas the ’032 patent listed threonine as a polar amino acid. Petitioner argued this was not a true difference, citing Zhang I, which taught that for self-assembling peptides, threonine is functionally hydrophobic and can be used in lieu of nonpolar residues like alanine. Under this technically-informed interpretation, Mira was anticipatory. Alternatively, if threonine were considered polar, it would have been obvious for a POSITA to substitute Mira’s threonine residues with known nonpolar amino acids (like alanine) to enhance the hydrophobicity of that face, with a clear expectation of forming an even more stable beta-sheet structure.

4. Relief Requested

  • Petitioner requested institution of an inter partes review and cancellation of all challenged claims, 1-8, of the ’032 patent as unpatentable.