PTAB

IPR2017-01598

Nuevolution AS v. Chemgene Holding ApS

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Key Events
Petition
petition

1. Case Identification

2. Patent Overview

  • Title: DNA-Encoded Synthesis Methods for Chemical Libraries
  • Brief Description: The ’381 patent discloses methods for preparing and screening large chemical libraries. The alleged invention combines two known techniques: a "Stage 1" involving split-and-mix synthesis to create a diverse population of "carrier molecules" (bi-functional molecules with a chemical fragment and an oligonucleotide identifier), and a "Stage 2" involving templated synthesis where these carriers are used to generate new encoded library members.

3. Grounds for Unpatentability

Ground 1: Anticipation over WO ’008 - Claims 1-2, 4-5, 7-9, 16, 18-22, 27, 29-30, 32-33, 35-36, 38-39, and 46 are anticipated by WO ’008.

  • Prior Art Relied Upon: Pedersen (International Publication No. WO 02/103008).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner argued that WO ’008 discloses all steps of the claimed methods for synthesizing DNA-encoded libraries. Specifically, WO ’008 teaches the creation of bi-functional "building blocks" (the claimed "carriers"), each comprising a molecule fragment linked to an oligonucleotide identifier. Petitioner asserted that Example 108 of WO '008 shows these carriers being prepared in twelve different reaction wells, which are then combined to form an admixture. This admixture is subsequently contacted with a DNA template containing specific coding regions that hybridize to the carrier identifiers, bringing the molecule fragments into proximity to facilitate a template-directed chemical reaction. This process was argued to anticipate every limitation of independent claims 1 and 5.
    • Key Aspects: Petitioner emphasized that WO ’008's explicit examples of preparing diverse carriers in separate wells, admixing them, and using codon-specific hybridization to templates for reaction directly map to the patent's core claims, leaving nothing for the patent to invent.

Ground 2: Anticipation over WO ’994 - Claims 1-2, 4-5, 7-9, 16, 18-23, 27, 29-30, 32-33, 35-36, 38-39, 45, and 46 are anticipated by WO ’994.

  • Prior Art Relied Upon: Gouliaev (International Publication No. WO 2004/056994).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner contended that WO ’994 describes a library synthesis method using multiple carriers and multiple templates that fully anticipates the challenged claims. The reference discloses "CCPNs" (Complementary Connector Polynucleotides), which are functionally equivalent to the ’381 patent’s bi-functional carriers, as they comprise a molecule fragment (substituent) and an oligonucleotide identifier (descriptor). Petitioner argued that WO '994 teaches preparing these CCPNs in different wells, combining them into a "pool" (an admixture), and contacting them with a "pool" of "CPNs" (templates). This disclosed process of carrier synthesis, admixing, and templated reaction was alleged to meet every limitation of independent claims 1 and 5, including the "region limitation" where the template hybridizes to a specific identifier region that identifies the fragment.

Ground 3: Obviousness over WO ’929 and WO ’767 - Claims 42 and 43 are obvious over WO ’929 in view of WO ’767.

  • Prior Art Relied Upon: Franch (International Publication No. WO 2004/024929) and Liu (International Publication No. WO 2004/016767).

  • Core Argument for this Ground:

    • Prior Art Mapping: Petitioner argued that claims 42 and 43, which require that the templates themselves be generated by a "split and mix procedure" involving the ligation of codon DNA duplexes, were obvious. WO '929 teaches template-encoded library synthesis but does not explicitly detail a split-and-mix method for creating the template library itself. WO '767 was introduced as teaching an efficient "split-pool" technique to synthesize a large variety of templates, including through the double-stranded ligation of codon duplexes using T4 DNA ligase.
    • Motivation to Combine: A POSITA seeking to create large and diverse chemical libraries—a primary goal in the field—would be motivated to combine WO '767's efficient method for template library generation with the synthesis methods taught in WO '929. This combination would allow for the creation of more complex and diverse template pools for use in the known synthesis reactions.
    • Expectation of Success: Petitioner asserted a POSITA would have a high expectation of success, as this combination merely applies a known technique (split-and-mix template generation) to improve a known process (template-encoded library synthesis) to achieve the predictable result of a larger, more diverse library.

  • Additional Grounds: Petitioner asserted additional anticipation and obviousness challenges. These grounds were based on WO ’627, WO ’825, and a combination of WO ’825 and WO ’008, relying on similar arguments that these references teach the fundamental steps of preparing bi-functional carriers and subsequently using them in templated synthesis reactions.

4. Key Claim Construction Positions

  • "Template": Petitioner argued that the term "template" should be construed not merely as an entity that binds a carrier molecule, but as one that also promotes a chemical reaction by bringing reactive groups into proximity. This construction was based on the specification's exclusive use of the term in the context of "templated synthesis" and affirmative statements made by the patentee during prosecution. This construction is critical to Petitioner's arguments, as it allows prior art that functionally directs a reaction via hybridization to be considered as teaching a "template," even if the reference does not use that specific term.

5. Relief Requested

  • Petitioner requests institution of an inter partes review and cancellation of claims 1-2, 4-5, 7-9, 16, 18-23, 27-30, 32-33, 35-36, 38-43, 45-46 of Patent 8,168,381 as unpatentable.