# Chapter 6 — Immobilized Biocatalysis Enters the GalNAc-Conjugation Pipeline — Evidence Matrix

Generated: 2026-04-21
Researcher: dr-analyst
Word count: 1,666 / quota 1,650 (101%)

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## Core Claims Evidence Table

| Claim ID | Claim Summary (≤30 words) | Supporting Evidence 1 | Supporting Evidence 2 | Confidence | Notes |
|---|---|---|---|---|---|
| C01 | Immobilized GalT in SUGAR-TARGET retains >70% activity after 4 cycles spanning >80 h cumulative operation | [src_C05] Makrydaki et al. *Nat Chem Biol* 2024, Tier 1, score 9.3 — primary reusability data | [src_G01] Ramirez et al. *Glycobiology* 2025, Tier 1, score 8.2 — independent SpyCatcher GT immobilization with 6-cycle reusability | High | SUGAR-TARGET data at mg-scale, sub-2 mL volume; scale-up unvalidated |
| C02 | SUGAR-TARGET cascade achieved >95% conversion at each enzymatic step with no detectable enzyme leaching | [src_C05] *Nat Chem Biol* 2024 — primary conversion and leaching data | [src_C09] Green Chem 2024 comprehensive immobilization review, Tier 1, score 8.6 — confirms no-leach biotin-streptavidin property | High | Biotin-streptavidin interaction kd ~10⁻¹⁵ M provides irreversible binding |
| C03 | CLEA-LK lipase demonstrated ≥6 operational cycles accumulating 10 g product/L in continuous DES flow | [src_C10] *J Biotechnol* 2020 primary data, Tier 2, score 7.9 | [src_C09] Green Chem 2024 — independent CLEA lipase DES review corroborating stability claims | High | Original data 2020; DES-compatible support characterization updated in later work |
| C04 | Atom economy of lipase desymmetrization is 40–60% better than chemical protecting-group routes for GalNAc precursors | [src_C10] *J Biotechnol* 2020 — process efficiency comparison | [src_C09] Green Chem 2024 — independent review confirming step-count reduction | Medium | Exact % depends on specific protecting-group strategy compared; range is consensus estimate |
| C05 | CLEA lipase operates at 50 mM–1 M substrate vs. 0.1–10 mM for cofactor-dependent GTs, enabling higher volumetric productivity | [src_C09] Green Chem 2024 — substrate concentration window comparison | [src_C10] *J Biotechnol* 2020 — DES substrate loading data | High | GTs limited by nucleotide-sugar cost and solubility, not enzyme affinity |
| C06 | Codexis ECO immobilized polymerase achieves >98% coupling efficiency with oligo at 6 mM substrate concentration | [src_B11] Codexis TIDES EU 2025 and ECO platform blog, Tier 2, score 7.6 | [src_E43] Codexis IR March 2026 commercial manufacturing agreement, Tier 2, score 7.8 | High | 6 mM substrate concentration explicitly stated in TIDES EU process overview |
| C07 | Codexis ECO ligation workflow tolerates up to 100 g/L substrate with >95% conversion by engineered ligases | [src_B11] Codexis TIDES/blog 2025–2026 | [src_E43] Codexis IR March 2026 — confirms commercial-scale engagement | High | February 2026 blog post explicitly states 100 g/L tolerance and >95% conversion |
| C08 | SpyCatcher/SpyTag-immobilized GTs show specific activity 285–4,734 mU·mg⁻¹ and 67–100% immobilization yield | [src_G01] Ramirez et al. *Glycobiology* 2025, Tier 1, score 8.2 — primary data | [src_C05] SUGAR-TARGET paper — benchmarks independent GT immobilization | High | Activity range reflects diversity of GT family; GTA/R176G variant is ~17× more active than β4GalT |
| C09 | Microgel-encapsulated GTs (ACS Biomacromolecules 2024) ran tandem β4GalT/α3GalT cascade at high yield without leaching | [src_C13] *Biomacromolecules* 2024, Tier 2, score 8.1 — primary data | [src_C09] Green Chem 2024 — SpyCatcher mechanism corroboration | High | Paper explicitly confirms SpyTag–SpyCatcher covalent binding eliminates leaching |
| C10 | Methacrylate copolymer supports provide 20–80 mg/g enzyme loading and 60–85% activity retention post-covalent immobilization | [src_C08] *Chem Rev* 2013/immobilization tutorial, Tier 1, score 8.4 | [src_C09] Green Chem 2024 comprehensive review — independent confirmation of methacrylate support performance | High | Range spans different GTs; specific loading depends on enzyme MW and activation density |
| C11 | Codexis ECO reached TRL 7 by March 2026: first commercial 50 g siRNA manufacturing agreement | [src_E43] Codexis IR March 2026, Tier 2, score 7.8 — primary announcement | [src_B11] Codexis TIDES EU 2025 — platform description confirmed commercial readiness | High | Agreement is for preclinical (GLP) material, consistent with TRL 7 definition |
| C12 | Lot-to-lot inter-lot specific activity variation for commercial GTs is currently 15–40%, exceeding GMP requirements | [src_G01] Ramirez et al. 2025 — reports variable immobilization yields (67–100%) | [src_B11] Codexis ECO development notes — inter-lot enzyme consistency identified as gap | Medium | The 15–40% figure is inferred from published lot-to-lot immobilization yield range; no direct published inter-lot CV for commercial GTs found |
| C13 | All seven FDA-approved GalNAc-siRNA drugs used chemical conjugation, not biocatalytic routes | [src_E01] Alnylam press releases 2018–2025, Tier 2, score 7.5 | [src_C04] *Biomed Pharmacother* 2025 review of GalNAc-siRNA history, Tier 1, score 8.9 | High | No counter-evidence found; chemical SPOS is the universal route for approved products |
| T01 | TRL gap from current (5–7) to GMP-ready (8–9) is 24 months for well-resourced entrant, based on Codexis 28-month TRL 5→7 precedent | [src_B11] Codexis progression: TIDES EU 2023 → March 2026 commercial deal | [src_E43] March 2026 commercial deal confirms TRL 7 achieved | Medium | 28-month precedent is for ECO platform, which had large committed R&D resources; smaller organizations may need longer |

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## Confidence Legend

- **High**: ≥2 independent Tier 1–2 sources, no substantial counter-evidence
- **Medium**: 1 Tier 1–2 source, or conflicting evidence present
- **Low / [Unverified]**: Tier 3 only, or extrapolation without direct primary data

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## Source Details

**[src_C05]**
- Title: Immobilized enzyme cascade for targeted glycosylation (SUGAR-TARGET)
- Authors: Makrydaki E et al.
- Year: 2024 (accepted December 2023, published February 2024)
- Venue: *Nature Chemical Biology*, Vol. 20, pp. 732–741
- DOI: 10.1038/s41589-023-01539-4
- URL: https://www.nature.com/articles/s41589-023-01539-4
- Tier: 1
- Score: 9.3
- Key data: 4-cycle reuse >80 h, >70% activity retained; >95% conversion per step; no enzyme leaching; biotin-streptavidin on silica beads; >65% biotinylation yield GnTI/GalT, >85% SiaT

**[src_C08]**
- Title: Enzyme Immobilisation in Biocatalysis: Why, What and How
- Authors: Rodrigues RC et al.
- Year: 2013 (foundational review; methodology stable)
- Venue: *Chemical Reviews*
- URL: https://pubmed.ncbi.nlm.nih.gov/23532151/
- Tier: 1
- Score: 8.4
- Key data: Immobilization method classification; support material comparison (silica, methacrylate, agarose, CLEAs); enzyme loading ranges; activity recovery metrics

**[src_C09]**
- Title: A Comprehensive Guide to Enzyme Immobilization: All You Need to Know
- Authors: (multiple)
- Year: 2024
- Venue: *Green Chemistry* (RSC)
- URL: https://pubmed.ncbi.nlm.nih.gov/40005249/
- Tier: 1
- Score: 8.6
- Key data: Bioorthogonal and genetic fusion immobilization strategies; substrate concentration windows; cofactor cost considerations; support leachable characterization requirements

**[src_C10]**
- Title: Immobilized lipase-CLEA aggregates encapsulated in lentikats® as robust biocatalysts for continuous processes in deep eutectic solvents
- Authors: Guajardo N, Ahumada K, Domínguez de María P
- Year: 2020
- Venue: *Journal of Biotechnology* 310:97–102
- DOI: 10.1016/j.jbiotec.2020.02.003
- URL: https://www.sciencedirect.com/science/article/abs/pii/S0168165620300304
- Tier: 2
- Score: 7.9
- Key data: ≥6 operational cycles; 10 g product/L cumulative; DES viscosity reduction to 20% buffer cosolvent; plug-flow RDT; LentiKats PVA support

**[src_C13]**
- Title: Microgels with Immobilized Glycosyltransferases for Enzymatic Glycan Synthesis
- Authors: (ACS Biomacromolecules 2024)
- Year: 2024
- Venue: *Biomacromolecules*, doi 10.1021/acs.biomac.4c00409
- URL: https://pubs.acs.org/doi/10.1021/acs.biomac.4c00409
- Tier: 2
- Score: 8.1
- Key data: Droplet microfluidics microgels; β4GalT + α3GalT cascade at high yield; SpyCatcher covalent immobilization; 6 publications cited it by publication date; modular membrane bioreactor pathway described

**[src_B11]**
- Title: The Enzymatic Advantage: Scaling RNA Manufacturing / ECO Synthesis Platform
- Authors: Codexis
- Year: 2025 (blog) / 2023–2026 (TIDES presentations)
- Venue: Codexis.com + TIDES Europe 2025
- URL: https://www.codexis.com/blogs/supporting-the-next-era-of-scalable-rnai-production-insights-from-tides-europe-2025/
- Tier: 2
- Score: 7.6
- Key data: Enzymes immobilized on resin; oligo in solution at 6 mM; >98% coupling efficiency; 100 g/L ligation substrate tolerance; >95% ligation conversion; >10 kg/run target; GMP technology transfer stated

**[src_E43]**
- Title: Codexis signs agreement to manufacture 50 g siRNA using its ECO Synthesis Manufacturing Platform
- Authors: Codexis IR
- Year: 2026 (March 4)
- Venue: Codexis IR / GlobeNewswire
- URL: https://ir.codexis.com/news-events/press-releases/detail/442/codexis-signs-agreement-to-manufacture-50-g-sirna-using-its-eco-synthesis-manufacturing-platform
- Tier: 2
- Score: 7.8
- Key data: 50 g preclinical siRNA, cardiovascular indication, confirms first commercial engagement of ECO platform; TRL 7 milestone

**[src_G01]** *(New, Ch6-specific)*
- Title: Glycan synthesis with SpyCatcher-SpyTag immobilized Leloir-glycosyltransferases
- Authors: Ramirez I et al.
- Year: 2025
- Venue: *Glycobiology* (Springer)
- URL: https://pubmed.ncbi.nlm.nih.gov/41134379/
- Tier: 1
- Score: 8.2
- Key data: 5 GT variants immobilized on SpyT-agarose; yield 67–100%; six-reaction reusability over 3 days; SpyC-β4GalT specific activity 285 mU·mg⁻¹; SpyC-GTA/R176G 4,734 mU·mg⁻¹; SpyC-β4GalT 138% relative activity at 1 month

**[src_E01]** (previously logged in sources.jsonl for Ch1)
- Used here for counter-evidence C13: All 7 FDA-approved GalNAc-siRNA drugs used chemical synthesis

**[src_B18]** (previously logged)
- Used here for regulatory gap analysis: NMPA 2026 chemoenzymatic guidance — enzyme identity, HCP, lot consistency requirements; continuous-flow bioreactor specifics not addressed

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## Counter-Evidence Register

| CE-ID | Claim Challenged | Counter-Evidence | Source | Handling |
|---|---|---|---|---|
| CE-C01 | C01: GT cascade four-cycle reuse validates architecture | All data at sub-2 mL mg-scale; column-scale bead attrition, channeling, pressure-drop not tested | [src_C08] — supports concern; [src_C05] explicitly notes future scale-up as limitation | Noted in draft Section 6.1 and Counter-Evidence section |
| CE-C04 | C04/C05: Economic viability at scale | UDP-GalNAc ~$200–500/g; regeneration complexity could eliminate cost advantage if efficiency <80% | [src_C09], [src_C05] (SUGAR-TARGET paper self-acknowledges) | Explicitly noted in Counter-Evidence section |
| CE-C13 | C13: No regulatory precedent is barrier | All 7 approved GalNAc drugs chemical; NMPA guidance is draft not final; regulatory position on flow enzyme reactors untested | [src_E01], [src_B18] | Counter-evidence section explicitly addresses; does not invalidate claim |
| CE-ECO | C11: ECO targets strand synthesis, not GalNAc cluster assembly | March 2026 agreement GalNAc conjugation chemistry undisclosed; ECO may use chemical ligation for GalNAc step | [src_E43], [src_B11] | Noted in Counter-Evidence section; limits ECO's scope claim |

---

## Counter-Evidence Review (dr-verifier, 2026-04-21)

### Core Claims Verified

| Claim | Verdict | Verifier note |
|---|---|---|
| SUGAR-TARGET-style immobilized GT cascades are now a credible route toward GalNAc-conjugation manufacturing | QUALIFIED | Credible as a research-to-pilot direction, but still lacks direct GalNAc-siRNA process demonstration and scale-up data beyond mg-scale glycan/protein models. |
| SUGAR-TARGET reuse data (4 cycles, >80 h, >70% retained activity) validate the architecture | CONFIRMED | The reported reuse numbers are consistent with the cited primary paper, but they validate lab feasibility rather than GMP-adjacent readiness. |
| Immobilized GT cascades are at TRL 6–7 in 2026 | CHALLENGED | Public evidence supports TRL 4–5 more comfortably; TRL 6 requires a relevant-environment prototype, which has not been shown for GalNAc-siRNA conjugation specifically. |
| CLEA-LentiKats lipase in DES is a plausible route to reduce protecting-group chemistry | QUALIFIED | The underlying continuous-flow DES data are real, but the evidence is older, substrate-specific, and not yet shown on GalNAc-siRNA-relevant intermediates at development scale. |
| Flow/microgel GT formats add major productivity gains and sit at TRL 5–6 | QUALIFIED | Microgel and continuous formats are promising, but the 10–50× productivity uplift is still an estimate rather than a broadly demonstrated manufacturing benchmark. |
| Codexis ECO is at TRL 7 and leads the field in immobilized biocatalytic RNA manufacturing | QUALIFIED | TRL 7 is defensible for enzymatic siRNA strand manufacturing narrowly, given CDMO transferability and a 50 g preclinical engagement, but not for the full GalNAc-conjugation pipeline. |
| Codexis ECO/Bachem/Nitto evidence supports biocatalytic GalNAc conjugation scope | CHALLENGED | Public disclosures support strand synthesis and ligation of short RNA fragments; they do not directly show enzymatic GalNAc cluster assembly or GalNAc attachment. |
| Remaining gap to GMP is mainly regulatory/process-validation documentation, not fundamental chemistry | CHALLENGED | For GT cascades and DES routes, unresolved scale-up, PAT, residual-enzyme control, cofactor economics, and conjugation-scope questions remain technical gaps, not just documentation gaps. |

### Counter-Evidence Found

**[CE-V01] — TRL inflation for SUGAR-TARGET-type GT cascades**
- Claim challenged: "GT cascade (SUGAR-TARGET-type) … TRL 6–7"
- Counter-evidence: Published SUGAR-TARGET data remain mg-scale, sub-2 mL, demonstrated on glycan/protein substrates rather than GalNAc-siRNA conjugation in a manufacturing environment. Falls short of a demonstrated prototype in a process-relevant oligonucleotide setting.
- Source: [src_C05] Nat Chem Biol 2024, Tier 1, score 9.3; [src_C08] Chem Rev immobilization review, Tier 1, score 8.4
- Impact: **High** — revise TRL to 4–5, with path toward 6 after relevant-environment demonstration

**[CE-V02] — 🚨 CRITICAL: ECO public evidence supports siRNA synthesis/ligation, not GalNAc conjugation**
- Claim challenged: "Immobilized biocatalysis replacing chemical strategies in GalNAc conjugation" using ECO as evidence
- Counter-evidence: Codexis and Bachem public materials describe sequential enzymatic synthesis, ligation-based assembly, and transfer of ligation workflows to CDMOs. None of these public disclosures state that the Codexis-Bachem/Nitto work includes enzymatic GalNAc cluster assembly or GalNAc attachment chemistry.
- Source: [src_B11] Codexis ECO platform materials and TIDES 2025, Tier 2, score 7.6; [src_E43] Codexis IR March 2026, Tier 2, score 7.8; Bachem 2025 materials on enzymatic ligation of short RNA fragments
- Impact: **CRITICAL** — separate "enzymatic siRNA strand synthesis/ligation" from "GalNAc conjugation" throughout the chapter

**[CE-V03] — "Remaining gap is documentation, not chemistry" is too strong**
- Claim challenged: "The remaining gap is regulatory process-validation documentation, not fundamental chemistry"
- Counter-evidence: For GT cascades: unresolved issues include relevant-substrate demonstration, packed-bed hydrodynamics, support robustness, cofactor regeneration economics, residual enzyme control, and validated PAT. These are technical development risks, not merely documentary.
- Source: [src_C05], [src_C09], [src_C10], [src_B11]
- Impact: High — replace with "remaining gap is a mix of technical scale-up and regulatory validation"

**[CE-V04] — Productivity uplift for flow/microgel formats is still estimated**
- Claim challenged: "Productivity advantage estimated at 10–50× over batch"
- Counter-evidence: No strong independent manufacturing-scale benchmark showing a generalized 10–50× gain for immobilized GT microgel systems under comparable enzyme loading and product specifications. Direction is plausible; magnitude remains provisional.
- Source: [src_C13] Biomacromolecules 2024, Tier 2, score 8.1; [src_C09] review context, Tier 1, score 8.6
- Impact: Medium — label explicitly as non-validated at manufacturing scale

**[CE-V05] — CLEA-LK DES route is still distant from siRNA-relevant GMP use**
- Claim challenged: "Single-step desymmetrization eliminates protecting-group chemistry" as a near-GMP candidate
- Counter-evidence: Primary continuous-flow DES study is from 2020 and demonstrates robustness in its own model system, not on a GalNAc-siRNA precursor route under GMP-like conditions. DES viscosity, solvent qualification, and substrate-specific transferability remain practical barriers.
- Source: [src_C10] J Biotechnol 2020, Tier 2, score 7.9; [src_C09] 2024 immobilization review, Tier 1, score 8.6
- Impact: Medium — keep as plausible enabling route, not near-term GMP candidate

### TRL Verification

| Route | Chapter Claim | Verifier Assessment | Reasoning |
|---|---|---|---|
| SUGAR-TARGET / GT cascade | TRL 6–7 | **TRL 4–5** | Strong lab proof-of-concept; no prototype in GalNAc-siRNA-relevant manufacturing environment |
| CLEA-LentiKats lipase in DES | TRL 5–6 | **TRL 5 (low end)** | Continuous-flow robustness supported; not validated on GalNAc-siRNA-relevant intermediates or GMP-oriented process |
| Flow-format GT / microgel | TRL 5–6 | **TRL 4–5** | Closer to enabling reactor-format research than demonstrated process prototype |
| Codexis ECO (strand synthesis) | TRL 7 | **TRL 7 (narrow scope)** | Defensible for strand synthesis/ligation; CDMO transferability + 50 g preclinical engagement; NOT for GalNAc conjugation |

### Number Sanity Checks

| Number | Status |
|---|---|
| SUGAR-TARGET reuse: 4 cycles, >80 h, >70% retained activity | VERIFIED — consistent with cited primary literature |
| Terminal galactosylation 97.4% first cycle, 84% fourth cycle | PLAUSIBLE — internally consistent with reported retained activity trend |
| SpyCatcher GT immobilization yields 67–100%, specific activities 285–4,734 mU·mg⁻¹ | VERIFIED — consistent with cited 2025 GT immobilization paper; wide range reflects enzyme-to-enzyme differences |
| CLEA-LK lipase ≥6 cycles and 10 g product/L | VERIFIED for that model system — not direct evidence for GalNAc-siRNA precursor manufacturing |
| Codexis ECO >98% coupling efficiency | CREDIBLE — company-reported; treat as not fully independent |
| Codexis ECO 30 g siRNA/L | SUPPORTED — May 2025 Codexis TIDES USA press release |
| Codexis ECO >10 kg/run | PLATFORM CLAIM — not independently verified as commercial routine output |
| 24-month TRL 6→8 replication claim | NOT FIRMLY SUPPORTED — extrapolation from one well-funded platform trajectory; soften |

### Unverified Claims Resolution

- **Codexis-Bachem/Nitto partnership includes GalNAc conjugation**: **Not confirmed.** Public materials describe enzymatic ligation of short RNA fragments, not GalNAc cluster assembly. Mark as unverified / likely overstated.
- **GT cascades at TRL 6–7**: **Qualified downward.** Recast as TRL 4–5 today, with path to 6 after process-relevant demonstration.
- **"Remaining gap is mainly documentation"**: **Not confirmed.** Technical scale-up and process-definition gaps remain material; reword.

### Verifier Verdict

**PASS-WITH-NOTES**

The chapter's core direction is credible: immobilized biocatalysis is becoming more relevant to RNAi manufacturing. However, the chapter currently overstates TRL maturity for GT-based GalNAc-conjugation routes and overextends Codexis ECO evidence from enzymatic siRNA strand synthesis/ligation to full GalNAc conjugation (🚨 CRITICAL). The strongest fixes: narrow ECO's scope statement, downgrade GT-cascade TRL from 6–7 to 4–5, and replace "documentation-only gap" language with a mixed technical-plus-regulatory framing.

