Synthetic chemistry & methods
12 articles
Longer semi-rigid linkers drive VHL-based HDAC6 degraders with antileukemic activity
- A solid-phase route enabled systematic variation of VHL ligand, exit vector and linker in vorinostat-derived HDAC6 PROTACs.
- Longer, semi-rigid linkers gave the best degradation; the lead compounds degraded HDAC6 preferentially in MM.1S and MV4-11 cells.
- A matched non-degrading control with similar HDAC inhibition was clearly less antiproliferative, pointing to degradation itself as the driver.
The non-degrading control with matched enzyme inhibition is the kind of experiment that separates degradation from plain inhibition, and it favors the PROTAC. Preferential, not exclusive, HDAC6 selectivity from a vorinostat-like warhead is the weak point; a more isoform-selective ligand might sharpen it.
Direct-to-Biology Screening Yields a GRP78 Inhibitor That Spares Other HSP70 Isoforms
- Isoform selectivity within the highly conserved HSP70 family is notoriously hard; the team targeted the peptide-binding pocket of GRP78's substrate-binding domain.
- A direct-to-biology workflow, testing crude library reactions without purification, pointed to compound 12.
- It engages GRP78 in biochemical, biophysical and cellular thermal shift assays, is selective over other tested HSP70s, and perturbs unfolded protein response signaling with selective killing of A549 cells.
Going after the substrate pocket rather than the ATP site is the sensible way to buy HSP70 selectivity, and D2B makes iterating on it cheap. The cell-line-selective killing is the part I'd treat cautiously: it could reflect UPR dependence or something off-target. Orthogonal engagement data like CETSA are encouraging; I'd want a close inactive analog next.
Development of Isoform-Selective GRP78 Inhibitors from a Direct-to-Biology Strategy ↗
New ACS Platform Streamlines Drug Discovery by Screening Crude Reaction Mixtures Directly
- A direct-to-biology (D2B) platform synthesizes candidate compounds at small scale and evaluates the crude reaction mixtures directly in biological assays, bypassing conventional purification.
- The approach couples miniaturized, automation-compatible chemistry with rapid biological readout to shorten the design-make-test cycle typical of early hit-finding and library exploration.
- Positioned within a broader wave of D2B methodology in medicinal chemistry, applicable to accelerating hit identification across diverse chemotypes.
Skipping purification is the real win—cuts days off the DMT cycle when you're triaging hundreds of analogs. But I want hard numbers on false-positive rates from residual catalyst/byproducts before trusting crude-mixture hits blind; great for rapid SAR triage, not for anything feeding a confirmatory dose-response.
Fluorine Tweaks to Lipid Nanoparticles Boost PROTAC Delivery Efficiency
- Researchers built ionizable lipid nanoparticles with fluorinated lipid tails to encapsulate and deliver a PROTAC degrader payload.
- Tuning the degree of fluorination altered nanoparticle physicochemical properties and redirected intracellular trafficking, promoting more efficient endosomal escape into the cytosol.
- Optimized fluorinated formulations achieved greater cytosolic PROTAC release and stronger target-protein degradation than non-fluorinated lipid controls.
Most LNP-delivered PROTAC payload never escapes the endosome — it gets trapped and degraded lysosomally, so tuning fluorine content on the lipid tail to boost cytosolic release is a smart lever, borrowed straight from siRNA-LNP playbooks. If this scaffold generalizes beyond whichever degrader they tested, it could rescue plenty of otherwise-undruggable bifunctional PROTACs too big or polar for oral dosing.
A Smarter Sugar Anchor Sharpens a Phage-Based Cancer Vaccine
- Chemists built fluorinated Tn-antigen mimics using a tyrosine-linked GalNAc (Tyr-GalNAc) instead of the natural serine/threonine attachment, then conjugated them to bacteriophage Qβ virus-like particles.
- Qβ is a multivalent carrier platform known for driving strong antibody responses to small carbohydrate tumor antigens.
- The fluorinated Tyr-GalNAc-Qβ conjugates showed potent antitumor activity in preclinical models, adding to evidence that targeted fluorination can boost carbohydrate-antigen vaccine immunogenicity.
Tn's Achilles' heel has always been the native GalNAc-α-O-Ser/Thr linkage: glycosidase-labile and a weak, self-like hapten that struggles to break B-cell tolerance. Rerouting to a Tyr-aryl glycoside dodges the enzymes evolved for O-Ser/Thr GalNAc, and fluorination looks like classic conformational/electronic tuning to sharpen epitope recognition. Neither move touches the target — it's synthetic hapten engineering, with Qβ's ~180-copy multivalent display doing the real work of forcing an antibody response.
Dynamic Chemical Library Yields Sub-Picomolar Thrombin Inhibitor
- Researchers applied dynamic combinatorial chemistry (DCC), a hit-finding method in which reversible chemical building blocks assemble and reassemble under target guidance, letting the biological target itself select its best-binding partners.
- A new platform uses short peptide nucleic acid (PNA) tags to template three-fragment combinations, generating a library of 125,000 possible trivalent assemblies screened against thrombin.
- Candidate complexes are isolated by size-exclusion filtration and identified by MALDI mass spectrometry, compressing an entire selection-and-readout cycle to under an hour.
- Thrombin favored combinations engaging its active site and both flanking exosites at once, and this trivalent binding mode underlies the exceptionally tight affinity.
- The winning assembly is a fully reversible inhibitor with sub-picomolar affinity, achieving near-stoichiometric inhibition of thrombin activity.
DCC keeps getting overshadowed by DEL and FBDD, but this is the kind of result that should change that — a sub-hour select-and-read cycle via PNA templating plus MALDI readout tackles the real bottleneck that's always killed DCC in practice: slow kinetics and painful analytics. What actually earns the affinity isn't luck, though — it's rational exploitation of thrombin's well-mapped exosite architecture, deliberately building a trivalent ligand that bridges the active site and both exosites simultaneously. That's textbook multivalency applied with real target knowledge. My immediate skepticism: a PNA-templated trivalent assembly hitting sub-picomolar affinity is almost certainly a big, charged, un-drug-like molecule — I'd want MW, PK, and oral bioavailability numbers before getting excited about anything beyond a tool compound or long-acting parenteral candidate. Still, as a proof of concept for DCC against other exosite-rich or multi-pocket targets, this is a template worth stealing.
Discovery of a Reversible Sub‐Picomolar Thrombin Inhibitor Using DCC ↗
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.
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.
Dynamic Combinatorial Chemistry Delivers a Reversible, Sub-Picomolar Trivalent Thrombin Inhibitor
- A PNA-templated dynamic combinatorial chemistry (DCC) platform assembles a three-fragment library (~125,000 possible combinations) using DNA/PNA hybridization handles for unbiased equilibration.
- Thrombin itself templates the library, selecting and amplifying the best-binding fragment combination; size-exclusion filtration coupled with MALDI mass spectrometry gives a full selection-to-readout cycle in under an hour.
- The selected trivalent assembly engages thrombin's active site plus both exosites simultaneously, driving exceptionally high (sub-picomolar-range) binding affinity and near-stoichiometric inhibition.
- Unlike covalent thrombin inhibitors, binding is fully reversible — pharmacologically relevant for an anticoagulant, where reversibility matters for managing bleeding risk.
- Demonstrates target-templated DCC as a rapid route to multivalent, exosite-spanning inhibitors, even against a well-studied target.
Sub-picomolar affinity out of a 125,000-member DCC library gets my attention immediately — that's an avidity effect, not a single tight pocket, and it's essentially bivalirudin's active-site/exosite-1 logic pushed one contact further to include exosite II as well. Exosite engagement should also buy real selectivity over trypsin-like serine proteases that don't share thrombin's exosite topology, though I'd want that confirmed head-to-head against fXa and trypsin. My hesitation is tractability: a DNA/PNA-templated trivalent assembly is a fantastic proof-of-concept and chemical tool, not yet a lead — that's a long way from oral. Against DOACs' one-pocket, small-molecule simplicity, this wins on affinity and reversibility but loses badly on drug-likeness; the real test is whether target-templated DCC can be steered toward a druggable combination, not just the tightest binder.
Discovery of a Reversible Sub-Picomolar Thrombin Inhibitor Using DCC ↗
A SuFEx Click Reaction Streamlines DNA-Encoded Macrocyclic Peptide Libraries
- DNA-encoded libraries (DELs) let researchers screen ultralarge collections of macrocyclic peptides to find hit compounds for drug discovery, but efficient on-DNA cyclization chemistry has remained a bottleneck.
- A new on-DNA macrocyclization method uses sulfur(VI) fluoride exchange (SuFEx), a fast, click-type reaction, to close peptide rings directly on DNA tags.
- The design embeds a phenol and an aryl sulfonyl fluoride within a single DNA-tagged peptide, positioning the two groups to react with each other intramolecularly.
- Simply dissolving the construct in basic aqueous buffer triggers rapid, high-conversion cyclization without added catalysts or harsh conditions.
- The method enables efficient, high-yielding synthesis of ultralarge DNA-encoded macrocyclic peptide libraries, expanding the chemical space available for DEL-based hit discovery.
On-DNA chemistry is where good click reactions go to die — CuAAC needs copper that chews up your barcode, most coupling chemistry leaves truncation side-products you chase off HPLC for weeks. SuFEx actually respects the constraints: no metal, no coupling reagent, just a phenol and an ArSO2F sitting in basic water reacting with each other. That's "click" chemistry finally earning its name in DEL work instead of just borrowing the marketing. High conversion with zero catalyst also means boring QC, in the best sense — fewer truncated/uncyclized side-populations polluting the pool means the hits you pull downstream are more likely real signal, not artifacts of your worst-yielding step. For macrocycles — the space between small molecules and biologics everyone wants but few can screen efficiently — a clean cyclization step is what lets you scale diversity without sacrificing quality. This is the unglamorous methods advance that keeps unlocking new DEL generations.
SuFEx Cyclization Enables DNA-Encoded Macrocyclic Peptide Libraries for Drug Discovery ↗
Siderophore 'Trojan Horse' Boosts Antibiotic Potency Against Resistant Klebsiella
- Chemists conjugated the beta-lactam antibiotic aztreonam to aerobactin, a bacterial iron-scavenging siderophore, exploiting bacteria's own iron-uptake machinery as a 'Trojan horse' to smuggle the drug inside cells.
- A modular synthetic route enabled controlled mono- and di-functionalization of aerobactin, with late-stage click-chemistry (CuAAC) attachment of payloads, providing a flexible platform applicable beyond this single conjugate.
- The lead monovalent conjugate was markedly more potent than aztreonam alone against a hypervirulent, clinically concerning Klebsiella pneumoniae strain, a substantial improvement over the parent antibiotic.
- Competition and iron-dependent activity studies confirmed delivery proceeds through the aerobactin iron-acquisition pathway, supporting genuine siderophore-mediated uptake rather than incidental potency gains.
- The results establish aerobactin as a viable scaffold for delivering antibacterial payloads against multidrug-resistant, hypervirulent Enterobacteriaceae.
Call this the cefiderocol playbook done cleaner. Aerobactin's a natural Fe(III) chelator with dedicated Klebsiella uptake receptors, so hijacking it to smuggle aztreonam past the outer membrane is exactly the kind of Trojan-horse logic that's already proven clinically viable — nice to see it extended to a hypervirulent strain, which is a genuinely scary unmet-need bug. What I like more, honestly, is the platform: modular mono-/di-functionalization plus late-stage CuAAC means this isn't a one-off heroic synthesis, it's a conjugation chassis I could point at other payloads. And they didn't just show a potency bump and wave hands — the competition/iron-dependence data actually nail down siderophore-pathway uptake, not some off-target membrane-permeabilization artifact. That's the control every conjugate paper should run but often skips.
Direct-to-Biology Approach Delivers a Selective GRP78 Inhibitor Probe
- GRP78 (BiP/HSPA5) is a chaperone in the highly conserved HSP70 family, making isoform-selective inhibitors difficult to design.
- Using a Direct-to-Biology (D2B) strategy — synthesizing and screening compounds without intermediate purification — researchers identified compound 12 as a selective GRP78 inhibitor.
- Compound 12 binds the peptide-binding pocket in GRP78's substrate-binding domain and is selective for GRP78 over other tested HSP70 isoforms.
- It potently and selectively kills A549 lung cancer cells while showing minimal activity in other tested lung cancer cell lines.
- Cellular thermal shift assay (CETSA) confirmed cellular target engagement, and compound 12 modulates GRP78-linked unfolded protein response (UPR) stress signaling.
- The authors present compound 12 as a chemical probe for studying GRP78 biology and a starting point for GRP78-targeted therapeutics.
Substrate-binding domain, not the ATPase pocket — that's the harder but more selective play, since most HSP70-family programs chase the nucleotide site and inherit its cross-reactivity problem. Getting selectivity for GRP78 over other HSP70 isoforms out of a peptide-binding groove is a real medicinal chemistry win; those pockets are shallow and promiscuous by design. What I'd want to see next: the SAR trail from D2B — crude-plate hits jumping straight to CETSA-confirmed engagement is fast, but I'd want a clean resynthesis and dose-response before trusting potency off unpurified reactions. Still, as a probe-grade starting point with A549-selective killing, compound 12 is a legitimate template for follow-on optimization, not another ATPase-site me-too.
Development of Isoform-Selective GRP78 Inhibitors from a Direct-to-Biology Strategy ↗
New Conjugate Chemistry Releases Payload on Target Binding, Bypassing Endocytosis
- Researchers introduce a binding-to-release (BTR) strategy that triggers drug-conjugate payload release directly upon target binding, rather than requiring receptor-mediated endocytosis.
- The approach uses a new bioconjugation reaction, phosphorus(V)-phenol exchange (PhoPEx) — inspired by SuFEx click chemistry — engineered so that chemistry within the binding pocket itself cleaves the drug free once the conjugate engages its target.
- Because only a minority of drug targets support efficient endocytosis, this binding-triggered release could extend conjugate-based therapies to otherwise poorly internalizing targets.
- The authors describe proof-of-concept work with a conjugate targeting fibroblast activation protein (FAP), evaluated from in vitro settings through patient-derived tissue specimens.
The clever bit is topological: you need a nucleophilic residue (Ser/Tyr/Lys) sitting close enough to the P(V) center once the conjugate is bound, so this only works when pocket geometry cooperates — not a universal fix, more a case-by-case design problem per target. SuFEx proved robust and bioorthogonal enough to become a real click-chemistry platform; whether PhoPEx's release kinetics and selectivity hold up outside FAP is the real open question — proof-of-concept in patient tissue is promising but still one target. What I like: it decouples release from endocytosis and lysosomal processing entirely, which is the actual bottleneck for most ADC-style approaches against non-internalizing or slowly-trafficking surface receptors (GPCRs, some ion channels, stromal markers like FAP itself). If the chemistry generalizes, it's a genuine expansion of addressable target space for conjugates, not just a linker tweak.
A binding-to-release strategy for targeted anticancer drug delivery ↗