Archive · 2026 · September 2026

Daily digest — 2026-09-17

2026-09-17

Today: eight papers on E3 ligase structures, BBB-penetrant PROTACs, a WBP4 glue, ADC linkers, AI screening, oligonucleotide SAR, a DUBTAC platform, and an hCES2A probe — plus Vera's Phase 3 win, GSK's $750M deal, Encoded's $275M raise, and Merck layoffs.

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Medicinal Chemistry

7 articles

Structural Study Reveals How CTLH-MKLN1 Ligase Recognizes Multiple Degron Types

  • Cryo-EM structures of the CTLH-MKLN1 E3 ligase, bound to three distinct substrate proteins, map how this receptor engages its targets.
  • MKLN1 uses its discoidin and Kelch domains together, contacting substrates at multiple points rather than one binding surface.
  • MKLN1 recognizes copies of itself via discoidin-Kelch pairing between dimers, competing with binding of other substrates.
  • For ZMYND19 and adaptor-bound UNG2, C-terminal arginine residues insert into MKLN1's Kelch channel, marking MKLN1 as an arginine/C-degron receptor.
  • A separate adaptor positions UNG2's acetylated N-terminus in an internal tunnel, revealing a distinct acetyl-N-terminal degron pathway.
  • The findings broaden known E3 ligase substrate-recognition mechanisms, relevant to targeted protein degradation strategies beyond CRBN and VHL.
💡 Points

Three degron classes, one receptor — that's the headline for degrader hunters tired of CRBN/VHL. The Kelch channel reading C-terminal Arg is the most druggable-looking piece: Kelch domains (think KEAP1) have a track record of taking small, polar ligands into narrow grooves, so a compact peptidomimetic anchor there feels plausible. The acetyl-N-degron tunnel is murkier — adaptor-dependent, no small molecule has touched an acetyl-N-degron pocket yet, so that's fragment-screening territory, not a near-term glue. Biggest catch: MKLN1 self-dimerizes through the same discoidin-Kelch interface, meaning any exploiting ligand has to outcompete an endogenous, high-avidity PPI — selectivity and target engagement won't be trivial. Pure structural biology here, no chemical matter yet, but a legitimate new hub to diversify the E3 ligase toolbox beyond the same two receptors everyone's already crowded into.

Multimodal substrate recruitment enables CTLH-MKLN1 E3 ligase to target N-, C-, and internal degrons ↗

BBB-Crossing PROTAC Macrocycles Selectively Degrade DAPK1 in Aging Alzheimer's Brains

  • BmTACs — a new class of brain-penetrant degrader molecules — fuse a macrocyclic peptide shuttle to a PROTAC-type small-molecule module.
  • The peptide shuttle exploits a transcytosis route across brain blood vessels that becomes more active with age, enabling efficient blood-brain-barrier crossing and neuronal delivery.
  • A chemical cage on the degrader's VHL-recruiting ligand keeps it silent until it meets the high-oxidative-stress conditions found in Alzheimer's-affected tissue, limiting activity elsewhere in the brain.
  • Once activated, the compound selectively degrades an activated, disease-linked form of the kinase DAPK1.
  • In aged Alzheimer's-model mice, systemic treatment reduced activated DAPK1, lessened amyloid-beta and tau pathology, and improved cognitive function, demonstrating an aging-adapted strategy for brain-targeted protein degradation.
💡 Points

The caged VHL ligand is the clever bit — redox-triggered decaging means the warhead sits as a prodrug until it hits oxidative-stress tissue, which could finally address the peripheral-toxicity problem that's dogged systemic PROTAC dosing. I want the counter-screen though: how much decaging leaks in non-lesion CNS tissue over chronic dosing, and does 'activated DAPK1' selectivity hold in human proteoform or is that mouse-conformer-specific? The macrocyclic peptide-small molecule hybrid is a brutal synthesis — SPPS, macrocyclization, PROTAC conjugation, yield bleeding at every step — this is proof-of-concept, not a scalable series. Exploiting age-upregulated transcytosis instead of fixed RMT receptors (transferrin, insulin) is the real advance over TfR-shuttle degraders; the open question is whether that route is druggable across disease stages, not just aged models.

Blood-Brain Barrier-Permeable Macrocyclic Chimeras (BmTACs) for Targeted Protein Degradation in the Aging Brain ↗

Modular H-Phosphonate Platform Opens New Route to Backbone-Modified Oligonucleotides

  • Oligonucleotide backbone chemistry gets a new modular entry point: an H-phosphonate diester dinucleotide 'blockmer' platform that builds backbone-modified oligonucleotides through standard solid-phase synthesis.
  • The method exploits the ambiphilic reactivity of H-phosphonate diesters, allowing diverse phosphate backbone modifications to be installed without air- or moisture-sensitive P(III) reagents or hazardous chemicals.
  • Accessible backbone modifications span a wide range, from simple alkyl substitutions to sulfonamide-linked phosphate analogs, well beyond conventional phosphorothioate-type chemistries.
  • Because the dinucleotide blockmers are compatible with existing solid-phase assembly workflows, they can be combined and positioned flexibly within a single oligonucleotide sequence.
  • The platform is designed to enable systematic backbone structure-activity relationship studies in oligonucleotide drug discovery, providing a scalable and robust route for rapid analog generation.
💡 Points

H-phosphonate diesters as bench-stable P(III) surrogates is the headline: no more babysitting moisture-sensitive phosphitylating reagents under inert atmosphere just to install a novel backbone linkage. Backbone modification has been the stubborn bottleneck in oligo SAR — everyone can vary the sugar or the base, but stepping outside phosphorothioate/phosphorodiester space usually means bespoke phosphoramidite synthesis for every single analog. Pre-made dinucleotide blockmers flip that: build a small library of linkage types once, then mix-and-match them like ordinary phosphoramidites on standard solid-phase cycles, placing modifications at any position in the sequence. For a team running iterative backbone SAR, that's the difference between a multi-week custom-monomer detour and a same-week analog set. Real question is whether coupling efficiencies and diastereomer control hold up across the full modification set, not just the showcase examples.

Versatile H-Phosphonate Platform for Backbone-Modified Dinucleotide Blockmers Enabling Oligonucleotide SAR ↗

Bifunctional Pyridine Linker Enables Sequential, Stable Bioconjugation for ADCs and Peptides

  • A programmable, bifunctional pyridine scaffold bearing a thianthrenium leaving group and a fluorine handle enables two sequential, chemoselective coupling reactions — first with alkylamines, then with cysteine thiols.
  • The resulting aryl-cysteine linkage is non-chiral and stable, addressing limitations of existing bioconjugation approaches that often yield reversible linkages or stereochemical mixtures.
  • Both coupling steps show high functional-group tolerance and chemoselectivity, making the chemistry compatible with complex peptides and proteins.
  • The platform was applied to late-stage peptide diversification and stapling, as well as site-selective protein functionalization.
  • Researchers also used the method to build an analog of the HER2-targeting antibody-drug conjugate MRG002 with a tunable drug-to-antibody ratio, reporting improved payload retention in serum relative to conventional linkage chemistry.
💡 Points

Maleimide-cysteine chemistry's dirty secret is retro-Michael instability — payload leaches back into circulation, and DAR isn't as fixed as the spec sheet claims. This bifunctional pyridine/thianthrenium scaffold attacks that head-on: the resulting aryl-thioether is non-chiral and hydrolytically stable, so no diastereomer mixtures and no slow linker exchange with serum thiols. Sequential chemoselectivity — amine coupling first, cysteine second, off one handle — is a real practical upgrade for installing orthogonal payloads/tags, not just another NHS-ester variant. What earns my attention is that they didn't stop at peptide-stapling demos: a tunable-DAR HER2 ADC analog of MRG002 with improved serum payload retention versus conventional linkage is the kind of proof point that actually moves a methodology from academic curiosity toward something worth piloting. Thianthrenium reagent scale-up and cost will decide if it ever displaces maleimide on a GMP line.

Modular Assembly of Bioconjugates Enabled by a Pyridine-Based Chemoselective Sequential Conjugation Platform ↗

New Functional Screen Identifies Noninhibitory USP7 Ligand Enabling DUBTAC-Based CFTR Stabilization

  • Ligands that bind deubiquitinating enzymes (DUBs) without blocking their catalytic activity are notoriously hard to find — a new on-bead, proximity-driven functional screening platform is designed to identify them.
  • Such noninhibitory DUB ligands are essential for building DUBTACs (deubiquitinase-targeting chimeras), bifunctional molecules that stabilize target proteins by recruiting DUBs to strip ubiquitin marks, the inverse of degrader-based targeted protein degradation.
  • That rarity has made noninhibitory DUB ligands the central bottleneck in DUBTAC development.
  • Using the platform, the team discovered a previously unreported noninhibitory ligand for the deubiquitinase USP7.
  • Conjugating this USP7 ligand to a CFTR-binding moiety produced a DUBTAC lead, WJ045, which stabilized cellular CFTR protein levels.
  • The results demonstrate the platform's utility for discovering DUB-recruiting ligands and advancing targeted protein stabilization, with relevance to cystic fibrosis biology.
💡 Points

A noninhibitory DUB ligand is a harder ask than it sounds - you need a binder that occupies USP7 without touching the catalytic cleft, so a standard activity-inhibition screen is the wrong tool entirely. That's what makes the on-bead, proximity-driven functional assay the real story here: it's a hit-finding method, not just a molecule, and if it generalizes across other DUBs it addresses the actual bottleneck in this space. DUBTACs have quietly been the underdeveloped mirror image of degrader chemistry for years - everyone chasing PROTACs, almost nobody with tractable DUB recruiters in hand. WJ045 stabilizing CFTR is a nice proof point tying this to real biology, though it's a single cellular readout so far - want to see USP-family selectivity and whether the platform yields a second, unrelated ligand.

A Proximity-Driven Functional Screening Platform for the Discovery of Noninhibitory USP7 Ligand Enabling Targeted Protein Stabilization ↗

New Molecular Glue Degrader Targets WBP4, Debuts wTAG Degron-Tag Platform

  • WBP4, a spliceosome-associated scaffold protein long considered undruggable, now has a first-in-class molecular glue degrader: dWBP4-1, which selectively eliminates it.
  • The compound works through the CRBN E3 ligase, engaging WBP4 via a canonical G-loop interface to trigger rapid, highly potent degradation.
  • Proteome-wide profiling showed the degrader was highly selective, with minimal off-target effects on gene expression or splicing patterns.
  • The team pinpointed a compact 41-amino-acid region of WBP4 sufficient to serve as a degradation tag, naming the resulting chemical-genetic system "wTAG."
  • When attached to other proteins of interest, wTAG enabled clean, dose-dependent degradation without the "hook effect" that limits many degrader tools, expanding its potential as a general research platform.
💡 Points

WBP4 is a spliceosome scaffold with no ligandable pocket — this isn't a kinase-with-a-degron-tail story, it's proof CRBN can be steered onto a genuinely undruggable surface via a G-loop contact. That binding hypothesis is worth stealing for other scaffold targets sitting in my own tractability triage pile. The selectivity data is the real flex: clean proteome-wide profile AND minimal splicing perturbation, exactly where glues usually get you in trouble (neosubstrate promiscuity, cryptic RBM39-style splicing hits). Getting both together is rare. wTAG might matter more than the degrader itself — a 41-residue portable degron with no hook effect is a cleaner dTAG-class tool, and I'd rather have that in my assay toolbox than another single-target lead.

Selective and Potent First-in-Class CRBN-Dependent Molecular Glue Degraders of WW Domain-Binding Protein 4 ↗

ER-Targeted NIR Probe Enables High-Throughput Discovery of hCES2A Inhibitors

  • PA-HDCI, a near-infrared fluorogenic probe built on the HDCI fluorophore scaffold, localizes to the endoplasmic reticulum and reports on human carboxylesterase 2A (hCES2A) activity in living cells and animals.
  • The probe combines a large Stokes shift, high metabolic stability, and reliable ER targeting, enabling in situ, real-time imaging of hCES2A function across multiple biological systems.
  • Using PA-HDCI in a high-throughput screening assay, the team identified compound A4, a highly potent covalent inhibitor of hCES2A.
  • hCES2A is the intestinal enzyme that converts the chemotherapy drug irinotecan into its toxic active metabolite, driving irinotecan-induced intestinal toxicity (IIT).
  • In tumor-bearing mouse models, A4 showed a favorable safety profile and reduced irinotecan-associated intestinal toxicity while therapeutic efficacy was maintained.
  • Together, the work delivers both a new imaging tool and a validated drug-discovery platform for hCES2A-targeted therapeutics.
💡 Points

Solid probe engineering, not just a screening reagent: coaxing ER-selective localization and a large Stokes shift out of the HDCI scaffold gives clean signal separation in situ — photophysics that holds up in cells, not just a cuvette. The real value-add is methodological. A mechanistic imaging tool doubling as an HTS readout turns hCES2A activity into a screenable phenotype in living systems, closing the usual gap between biochemical assays and cellular reality. Target-wise, nothing novel here — hCES2A is a known off-target liability that bioactivates irinotecan into its gut-toxic metabolite, so this is a 'fix the side effect' play, not a new mechanism. A4 is an HTS-derived covalent hit with encouraging mouse data, but still needs the standard covalent-hit workup: reactivity profiling, esterase-family selectivity, and SAR.

An ER-Targeting Near-Infrared Fluorogenic Probe for In Situ hCES2A Functional Imaging and Inhibitor Discovery ↗

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Computational & AI

1 article

AI Screening Pipeline Flags Repositioned CASP4 Inhibitor Candidates for Alzheimer's

  • CASP4, an inflammatory caspase linked to Alzheimer's disease, is the target of a new computational drug-repositioning pipeline built to screen DrugBank compounds for potential inhibitors.
  • The workflow combined docking-based prioritization with ChemBERTa language-model embeddings and physicochemical descriptors to train machine-learning classifiers.
  • A Random Forest classifier and regressor were used to identify likely active compounds and rank them by predicted potency.
  • Downstream cheminformatics, PK-PD evaluation, and molecular docking narrowed the pool to five repositioning candidates.
  • Molecular dynamics simulations and MM/PBSA free-energy analysis were then applied to assess binding stability, identifying two compounds (DB05316 and DB00519) with predicted binding compared favorably to the reference drug donepezil.
  • The authors present the pipeline as a general strategy for prioritizing repurposed compounds against novel drug targets.
💡 Points

A five-stage funnel — docking, ChemBERTa embeddings, Random Forest, then MD/MM-PBSA — down to two compounds looks disciplined, but each stage has its own error rate, and stacking filters doesn't guarantee the errors cancel out. MM/PBSA rescoring of structurally unrelated ligands is notoriously unreliable for absolute ranking; chain enough filters and you can end up polishing false positives rather than eliminating them. Where this actually sits in the AI hit-finding wave: not novel chemistry, but faster triage of known-compound space, which is a real and growing niche. The genuine advantage is DrugBank sourcing — DB05316 and DB00519 already carry ADMET, safety, and formulation data, so there's no synthesis or fresh tox package standing between candidate and IND-enabling work. None of that substitutes for a binding assay. Until CASP4 activity is confirmed biochemically, this is a ranked hypothesis list, not a hit.

AI Accelerated Chemical Screening Integrates ChemBERTa to Identify Repositionable CASP4 Inhibitors via MD Simulations and MM/PBSA Analysis ↗

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Industry News

4 articles

GSK Licenses Trispecific T-Cell Engager from Chimagen for Multiple Myeloma in Deal Worth Up to $750M

  • GSK has agreed to license a preclinical trispecific T-cell engager (TCE) from China-based Chimagen Biosciences for the treatment of multiple myeloma.
  • The agreement includes an upfront payment plus development and commercial milestones, with total potential deal value of up to $750 million.
  • Unlike currently approved bispecific TCEs in myeloma, the candidate binds T cells while simultaneously engaging two validated tumor-associated antigens, a design intended to improve efficacy and tolerability.
  • The program remains preclinical; GSK expects the asset to enter Phase I trials in 2027.
  • This is GSK's second licensing deal with Chimagen, following a 2024 agreement worth up to $850 million for a separate TCE targeting B-cell-mediated autoimmune disease.
💡 Points

Preclinical asset, real money: up to $750M for a molecule years from human data is a differentiation bet, not a de-risking buy — GSK is wagering the third binding arm clears a bar that Tecvayli, Talvey, and Elrexfio already set. Trispecific design is the pitch, but myeloma TCEs are now a crowded field; incremental antigen coverage has to translate into durability or safety gains, not just a cleaner mechanism story. Second Chimagen deal in under two years (after the $850M autoimmune TCE in 2024) turns a one-off license into a platform relationship — GSK is treating this China-based biotech's engineering as a recurring pipeline source, echoing the broader Western-pharma pivot to China for early oncology assets. Phase I isn't until 2027, so this is a multi-year credibility test for GSK's TCE bet across both oncology and autoimmune.

GSK strikes deal for Chimagen's T cell engager for blood cancer ↗

Vera's Trutakna Hits All Endpoints in Final Phase 3 IgA Nephropathy Trial

  • Vera Therapeutics announced that TRUTAKNA (atacicept-vymj) met all prespecified endpoints in the final efficacy analysis of the Phase 3 ORIGIN 3 trial in adults with primary IgA nephropathy at risk of disease progression.
  • Over 52 weeks, TRUTAKNA stabilized kidney function (eGFR), while patients on placebo continued to decline.
  • Through 104 weeks, the drug substantially reduced composite kidney disease progression events, including dialysis, transplant, and death, compared with placebo.
  • Secondary measures also improved, including proteinuria, galactose-deficient IgA1, and hematuria, with a safety profile comparable to placebo.
  • TRUTAKNA already holds accelerated FDA approval for IgA nephropathy, and Vera plans to file a supplemental BLA in the fourth quarter of 2026 seeking full approval, alongside early positive commercial uptake since launch.
💡 Points

Confirmatory data this clean removes the single biggest overhang on TRUTAKNA's commercial story: accelerated approvals routinely get pulled or delayed when post-marketing trials disappoint, and Vera now walks into its Q4 sBLA filing with full-approval leverage rather than hope. That matters in a field crowding fast — Travere's Filspari, Calliditas/Otsuka's Tarpeyo, Novartis's Fabhalta, and Otsuka's sibeprenlimab are all fighting for the same nephrologists. Atacicept's dual APRIL/BAFF mechanism gives Vera a real differentiation story on upstream disease modification, not just symptom control, which should support pricing and payer positioning as uptake scales. For a company Vera's size, a de-risked full approval also reshapes M&A calculus — this is now a cleaner acquisition target for a larger nephrology or immunology player looking to buy share rather than build it.

Vera kidney drug Trutakna shows strong final results in Phase 3 trial ↗

Encoded Therapeutics Raises $275M Series F for Dravet Syndrome Gene Therapy

  • Encoded Therapeutics closed a $275 million Series F financing round, co-led by GV and an undisclosed healthcare investor, with participation from ARCH Venture Partners, Braidwell, Farallon, Illumina Ventures, Invus, Janus Henderson, Matrix Capital, RTW Investments, SoftBank Vision Fund 2, Venrock and others.
  • Proceeds will fund pivotal and age-expansion studies of ETX101, an AAV9-delivered gene-regulation therapy designed to restore SCN1A gene expression in children with SCN1A-positive Dravet syndrome, a severe and treatment-resistant form of pediatric epilepsy.
  • Interim data from the Phase 1/2 POLARIS trial, presented at the European Epilepsy Congress, showed encouraging reductions in seizure frequency and gains on developmental measures among treated children.
  • The financing will also support manufacturing scale-up and advancement of a second pipeline program, ETX301, targeting post-amputation neuroma pain, toward an IND filing in 2027.
💡 Points

Two hundred seventy-five million is a lot of private capital for a single indication, and it's flowing into gene regulation, not editing or replacement — investors betting that tunable, reversible expression control beats permanent genomic rewrites for a pediatric CNS target. The POLARIS interim data give Encoded first-mover clinical standing in SCN1A-directed Dravet therapy, ahead of gene-replacement and antisense rivals still in earlier stages. The size and syndicate here — GV, ARCH, SoftBank Vision Fund 2 — also reads as a financing-market tell: late-stage private mega-rounds are absorbing capital that might otherwise chase an IPO, a sign the window stays selectively closed. Earmarking part of the raise for ETX301, an unrelated pain asset, is a platform bet — diversification that could dilute focus on the pivotal Dravet push.

Encoded closes $275M Series F for Dravet syndrome drug ↗

Merck Cuts 54 More Jobs at NJ Headquarters Amid Cost-Cutting Push

  • Merck & Co. filed a WARN notice announcing plans to cut approximately 54 jobs at its Rahway, New Jersey headquarters, with the reductions taking effect in two phases on December 11, 2026 and January 4, 2027.
  • The cuts add to a string of 2026 workforce reductions at the Rahway site, including an earlier round of roughly 88 positions eliminated in September, bringing New Jersey job losses this year to more than 140.
  • The move is part of Merck's broader multiyear restructuring, launched in 2025, aimed at cutting roughly $3 billion in annual costs by the end of 2027.
  • Merck has framed the cost-cutting as preparation for the eventual loss of patent exclusivity on Keytruda, its top-selling cancer immunotherapy, while continuing to invest in newer pipeline programs.
💡 Points

Fifty-four jobs at Rahway barely moves the needle against a $3 billion, ~6,000-role restructuring — but the drip-feed pattern is the real story. This is at least the second Rahway tranche in 2026 alone, part of a rolling cadence that keeps each WARN filing small enough to avoid a single damaging headline, even as the cumulative New Jersey total quietly tops 140 for the year. That looks like a deliberate IR strategy: stagger the pain, let every notice read as routine. Underneath sits the actual driver — Keytruda's 2028 patent cliff, the largest LOE event in oncology, pushing Merck to reshape its cost base years ahead of the revenue hit rather than scrambling once exclusivity lapses. Expect more of these incremental announcements through 2027.

Fierce Biotech Layoff Tracker 2026: Merck trims more NJ jobs ↗