Structure-based design
28 articles
Designing out a BRD4 liability from dual TLR7/8 antagonists for lupus
- Structure-based optimization of 2-(pyridin-2(1H)-one)indoles gave dual TLR7/8 antagonists with better permeability, less ion-channel activity and lower volume of distribution than the earlier series.
- Early pyridone leads unexpectedly suppressed immune-cell proliferation, which the team traced to a hypothesized BRD4 off-target.
- Optimizing away BRD4 binding removed the anti-proliferative effect while keeping potent inhibition of TLR7/8-driven IL-6 in human whole blood.
This is a tidy example of phenotype-led off-target triage: odd toxicity in cell panels, a mechanistic guess, then SAR that separates the two activities. Endosomal TLR7/8 antagonists need to be both cell-permeable and cleanly selective, and BRD4 is an easy trap for flat heteroaromatics. I would check the pyridone's binding mode in the TLR7/8 dimer interface before borrowing the fix for other scaffolds.
Crystal structures show how CNS-oriented EGFR TKIs gain potency, not just brain exposure
- Several EGFR TKIs redesigned for blood-brain barrier penetration were studied by X-ray crystallography and potency assays.
- The BBB-enhancing groups engage varied regions of the EGFR kinase domains, and biochemical and cellular potency generally improved.
- Salt-bridge-forming moieties combined with certain halogen substitutions worked best, pointing to a 'two-for-one' design logic.
CNS exposure and potency are usually traded off against each other, so a crystallographic case that the same polar or basic handle can buy both is useful. The salt-bridge-plus-halogen pairing is a concrete design rule I could try on my own kinase series. It does not address efflux or unbound brain concentrations, which still decide whether it works in a patient.
Structural Insights into Brain-Penetrant EGFR Tyrosine Kinase Inhibitors with Enhanced Potency ↗
A covalent ligand at cereblon's cryptic Cys287 locks the E3 ligase open and blocks IMiD-driven degradation
- Cysteine-directed chemoproteomic screening found covalent ligands for Cys287, an allosteric pocket far from the thalidomide-binding site.
- Lead VVD-105917 broadly blocks degradation of neosubstrates driven by IMiDs and CELMoDs.
- Cryo-EM shows it traps cereblon in its open, inactive state, and ligand order matters. A previously reported ligand at the same site promotes closure instead, so the pocket is 'sign-switchable'.
Every CRBN drug so far sits in one orthosteric pocket, so a covalent handle that controls the open/closed switch is a genuinely new knob. A pan-inhibitor is an excellent tool to dissect degrader mechanisms and rescue off-target degradation. A site that can push either way also means a degrader-enhancing ligand might be hiding in the same pocket. This is a preprint, so wait for review.
Allosteric covalent inhibition of cereblon through cryptic cysteine targeting ↗
Cryo-EM-guided pocket merging yields an oral allosteric SLC6A19 inhibitor
- Virtual screening against the allosteric pocket seen in the SLC6A19/cinromide cryo-EM structure gave a starting hit.
- A second, partially overlapping pocket from a further cryo-EM structure inspired merged analogues, leading to a potent, selective, orally bioavailable compound 20.
- Compound 20 was weaker on mouse than on non-human primate SLC6A19, yet oral dosing raised urinary amino acid excretion dose-dependently.
Membrane transporters rarely give such a clean example of structure-driven design: two cryo-EM pockets, one merged series, in vivo pharmacodynamics from a simple urinary readout. The mouse potency shift is the practical snag for efficacy models, so the primate retention is reassuring. Next I'd want to know the margin for amino acid depletion.
Co-crystal-guided HDAC6 inhibitors that reach the L2 loop and trigger autophagy in lung cancer cells
- Second-generation HDAC6 inhibitors were designed from X-ray structures of earlier compounds bound to the zebrafish HDAC6 catalytic domain.
- Co-crystal structures of two leads showed engagement of S531 in the L2 loop; cells showed raised acetylated tubulin without a clear histone acetylation change.
- One lead cut A549 viability in 2D and 3D culture through pro-autophagic signalling and also affected phase-separation behaviour.
Grabbing the L2 loop is the obvious handle for isoform selectivity: the CD2 pocket is conserved, the loop is not. Acetylated tubulin up and histones flat is the readout I want before believing a selectivity claim. I'd still ask for a broad HDAC panel and some PK before getting excited about the autophagy story.
Hybrid indazole–bicyclic pyrrole chemotype targets mutant-selective LRRK2
- Structure-guided hybridization of an indazole with an octahydrocyclopenta[c]pyrrole gave a new LRRK2 inhibitor chemotype for Parkinson's disease.
- Early piperidine-containing analogs were potent but barely distinguished wild-type from G2019S LRRK2.
- Swapping the piperidine for the fused bicyclic amine was the change introduced to widen that selectivity window.
A narrow wild-type/G2019S window is the usual reason LRRK2 leads stall, so a scaffold change that buys mutant bias is worth a look. I'd want to see whether that bias holds in cells at physiological ATP and what the bicyclic amine does to brain penetration and clearance.
Binding kinetics help isolate HDAC2-selective inhibitor KTT-1
- KTT-1 (compound 12) was identified as HDAC2-selective by evaluating both thermodynamics and kinetics of enzyme–inhibitor binding, rather than affinity alone.
- Crystallography of HDAC2 with the compound, plus quantum chemical calculations on model compounds, suggests its 2-furanyl group drives the selectivity.
- In cells it preferentially inhibited HDAC2 over the highly homologous HDAC1 and promoted neurite outgrowth; in stress-vulnerable mice it improved memory and depression-like behavior.
Screening on residence time rather than IC50 alone is how you get past the near-identical HDAC1/2 active sites, and a furanyl contact backed by both crystallography and QM is a clean, testable rationale. Cellular HDAC2-over-HDAC1 preference is rare, so I'd want it confirmed in neurons with real brain exposure.
DEL hit becomes brain-penetrant reversible MAGL inhibitor MAGLi 432
- A bicyclopiperazine hit from a DNA-encoded library was optimized by structure-guided design into compound 1.5 (MAGLi 432), a reversible MAGL inhibitor.
- The compound combines high potency, selectivity over other serine hydrolases and CNS drug-like properties, with a favorable oral half-life in rats.
- It inhibited MAGL in human brain homogenate and worked in mouse neuroinflammation models; the campaign was steered by a translational "Five-Star Matrix" framework.
Reversibility is the part I'd want here, since irreversible MAGL agents ran into CB1 desensitization on chronic dosing. A non-covalent DEL chemotype that already shows target engagement in human brain tissue is a good template, and I'd steal the habit of testing in human tissue early rather than at the end.
Pose prediction plateaus after about five crystal structures per scaffold
- Using 403 SARS-CoV-2 main protease structures from the open COVID Moonshot campaign, the authors asked how many new crystal structures are worth collecting.
- Similar reference ligands give the best pose prediction, and success plateaus at roughly five structures per Bemis-Murcko scaffold, exceeding 95% for the lead series.
This gives structural biology a concrete budget line: after about five structures per scaffold, the next soak buys little for pose prediction. Caveat: Mpro is a rigid, well-behaved pocket, so I'd not carry that number over to flexible kinases or induced-fit targets.
How Many Crystal Structures Do You Need to Trust Your Docking Results? ↗
Modeling-led design yields a pan-serotype dengue NS4B inhibitor candidate
- Comparative models of the structurally unresolved NS4B across all four dengue serotypes reveal a conserved transmembrane pocket that fits known resistance mutations.
- Docking of the JNJ-series inhibitors fed predictive field-based 3D-QSAR models, which were used to screen bioisosteres and in-house compounds.
- The top candidate, BNJ-495, was extremely potent against serotype 2 with a high selectivity index, and its conserved binding contacts suggest broad-spectrum activity.
A homology-model plus 3D-QSAR workflow that delivers a prospectively validated hit against a membrane protein with no structure is rare, and that is what makes this worth a look. Before I trust 'pan-serotype', I'd want to see the other three serotypes tested and whether the JNJ-series liabilities carried over.
Structure-Guided Design of a Subnanomolar Dengue Virus NS4B Inhibitor ↗
Structure-based medicinal chemistry yields potent pan-YTHDF m6A reader ligands
- YTHDF1, YTHDF2 and YTHDF3 read m6A-modified mRNA in the cytosol, and this preprint reports a protein structure-based medicinal chemistry campaign against them.
- The aim is ligands that bind all three paralogs, rather than one reader at a time.
- Only the abstract opening was accessible, so potency and cellular data are not covered here.
The YTH domains' aromatic cage is a tough, charged pocket, so any structure-guided progress on it is worth tracking. A pan-paralog ligand is a sensible choice, given the redundancy among the three readers. I'd want selectivity over YTHDC1/2 and evidence of cellular target engagement before calling this a probe.
First synthetic PAPP-A inhibitors dampen IGF-1 signaling in cells and in vivo
- PAPP-A is a secreted metalloproteinase that cleaves IGF-binding proteins to control local IGF signaling, offering an alternative to IGF-1R targeting.
- Inhibitors were built on an IGFBP-5-derived anchor sequence, with the scissile bond replaced by phosphinate or phosphonate groups, giving potent and selective compounds.
- Cryo-EM showed how they bind the active site, and they blocked IGFBP-4 and IGFBP-5 cleavage.
- They suppressed IGF-1 signaling in A549 cells, comparably to stanniocalcin-1, and inhibited Papp-aa-dependent signaling in vivo.
Swapping the scissile bond of an IGFBP-5 anchor sequence for a phosphinate or phosphonate is classic transition-state mimicry, and a cryo-EM pose would validate the zinc-binding hypothesis. Going after the protease rather than IGF-1R is smart for selectivity. I'd want Ki values against related metalloproteinases, and cell permeability and stability of these peptidic leads, before trusting the in vivo claim.
Entrance-channel design tames cytotoxicity of the JK-4b NNRTI lead
- JK-4b, a potent NNRTI active against wild-type and clinical HIV-1 variants, was shelved because of high cytotoxicity; the authors used it as a lead for new analogues.
- Structure-guided designs addressing the NNRTI entrance channel gave a series with lower cytotoxicity and improved selectivity.
- Lead compound 9n retained strong potency against common resistance mutants, including double mutants, at levels comparable to etravirine.
- 9n also showed minimal cytochrome P450 inhibition and good human liver microsome stability, supporting further development.
Rescuing a shelved lead is always more interesting than starting cold: JK-4b already had the potency and resistance coverage, so the real question was whether entrance-channel contacts could decouple that from its cytotoxicity. If 9n's profile holds up, that suggests the toxicity was scaffold-tunable, not baked into the pharmacophore. Matching etravirine on double mutants while staying clean on P450 and microsome stability is what I'd want to see before making more.
Structure-guided design yields selective wild-type KIT inhibitors that avoid class III RTK off-targets
- Close ATP-site similarity across class III receptor tyrosine kinases makes selective KIT inhibition hard; this work tackles it with structure-guided optimization.
- A triazolopyridine hinge binder gave a selective start, and a central linker change led to a reverse arylacetamide series with better potency and pharmacokinetics.
- A pyrazole linker and hinge-motif edits kept potency in human serum, while terminal aryl tuning reduced CYP time-dependent inhibition and sharpened kinome selectivity.
- Crystal structures showed that linker stereoelectronics near the gatekeeper can drive selectivity, yielding a lead suited to chronic therapy.
The linker, not the hinge binder, is what caught my eye: stereoelectronics near the gatekeeper apparently buy selectivity that ATP-site similarity across class III RTKs would otherwise deny. That is a handle worth stealing for other crowded kinase families. I also like that CYP time-dependent inhibition and human-serum potency were fixed in the same campaign, which reads like a lead meant for chronic dosing.
Aryl Sulfamates Get a Systematic SAR Look as Carbonic Anhydrase IX Binders
- Ortho- and meta-substituted aryl sulfamates were synthesized and profiled by thermal shift, enzyme inhibition and a live-cell competition assay against CA IX, the isozyme overexpressed in hypoxic solid tumors.
- The best compounds bound CA IX with very high affinity, and X-ray structures with several isozymes identified the groups driving affinity and selectivity.
- pH-dependent binding data indicate the deprotonated, negatively charged sulfamate nitrogen coordinates the active-site zinc.
CA inhibitors are dominated by sulfonamides, so a clean sulfamate SAR backed by crystal structures is useful chemotype diversification. Selectivity over the ubiquitous CA I and II is what sinks tumor-CA programs, and the co-crystals give a concrete handle on it. Live-cell competition data beat purely recombinant assays, but I'd want hypoxic-cell potency and physicochemical properties before calling these lead-like.
Structure-Affinity and Selectivity of Aryl-Sulfamates as Inhibitors of Carbonic Anhydrase IX ↗
Brain-Penetrant Covalent BChE Inhibitor Shows Procognitive Effects in Alzheimer's Model
- Researchers used structure-guided design to develop a covalent small-molecule inhibitor of human butyrylcholinesterase (BChE), an enzyme increasingly implicated in Alzheimer's disease progression.
- The lead compound was engineered for blood-brain barrier penetration, a key hurdle for centrally acting cholinesterase inhibitors.
- In vivo testing showed procognitive efficacy, supporting covalent BChE inhibition as a potential treatment approach for Alzheimer's disease.
BChE rising while AChE falls late in disease is finally moving the field past AChE-centric dogma. A covalent warhead in a serine hydrolase family full of close paralogs (AChE, esterases) needs hard selectivity data, not just potency. What actually differentiates this from rivastigmine-class reversible inhibitors is CNS penetration — brain exposure they never solved well.
AI Pocket-Based Design Yields a Potent STAT3 Inhibitor for Colorectal Cancer
- A pocket-conditioned, autoregressive generative AI model was used to design candidate molecules directly within the STAT3 binding pocket, rather than screening pre-existing compound libraries.
- This structure-based generative approach produced a potent small-molecule STAT3 inhibitor that advanced to biological evaluation.
- The inhibitor showed activity against colorectal cancer, where STAT3 hyperactivation is a recognized driver of tumor growth and survival.
STAT3's SH2 dimerization pocket is shallow and dynamic — the reason most inhibitor programs (niclosamide analogs, peptidomimetics) never reached clinic. Generating atoms directly inside that pocket geometry, rather than rescoring a static virtual library, is the real methodological jump here. Still, "potent" on paper means little until we see SH2 selectivity over STAT1/5 and a synthesizable route — that's where de novo hits usually stall.
Two-Stage Generation Dynamics Enable Training-Free AI Drug Design
- Bayesian flow networks design molecules for protein pockets by jointly generating atom types and 3D coordinates.
- The two channels behave differently: atom types shift abruptly at a defined point, while coordinates sharpen gradually, a pattern consistent across model variants.
- Timing refinement to these transition points yields a training-free method matching baseline docking performance on a standard benchmark, with no extra predictor needed.
What earns this a second look is the lack of per-target retraining — that's the step that kills most generative tools before they reach my bench, so a training-free trick timed to a phase transition is worth trying. But matching baseline docking, not beating it, is a floor, not a win — and CrossDocked2020 scores say nothing about synthesizability or real binding.
Hierarchical Phase Transitions in Bayesian Flow Networks Enable Training-Free Molecular Design ↗
Docking Showdown: Physics-Based, Co-Folding, and Hybrid Models Face Off
- Compares physics-based docking, deep-learning co-folding, and hybrid rescoring methods on how well they generalize to unfamiliar protein targets and chemical scaffolds.
- Builds on the recent Runs-n-Poses benchmark, which found that classical physics-based docking held an edge over several co-folding tools on truly novel targets.
- Assesses pose accuracy and ranking performance to offer practical guidance on choosing a docking strategy based on target novelty.
Physics-based docking still beating co-folding tools on genuinely novel targets is the finding I keep coming back to — these deep-learning models are pattern-matching PDB coverage, not solving folding physics, and it shows the moment a target has no close analog. Until a co-folding tool proves itself on a zero-analog case, I'm running both and trusting the classical scorer as the tiebreaker.
Multiparadigm Benchmark of Molecular Docking: From Physics to Co-Folding and Hybrid Models ↗
Structural Survey Reveals How Kinase Inhibitors Engage Conserved Catalytic Residues
- More than 300 X-ray cocrystal structures spanning diverse kinase-inhibitor complexes were analyzed to catalog recurring non-covalent contact patterns.
- The study highlights a set of conserved Lys, Asp, and Glu residues near the ATP pocket, dubbed "Catalytic Cluster Residues" (CCRs), that support catalysis and frequently contact bound inhibitors.
- Across most inhibitor chemotypes, these polar residues form non-covalent interactions rather than covalent bonds, making them broadly relevant handles for ligand design.
- Side-chain orientation of the CCRs tracks with the kinase's active or inactive conformational state, linking binding geometry to structural dynamics.
- The authors argue this conformation-coupled behavior can guide rational, structure-based inhibitor design aimed at improving potency and tuning selectivity across the kinome.
"Catalytic Cluster Residues" is new branding for something most kinase chemists already lean on informally — the Lys-Glu ion pair, DFG-Asp contacts. The real value here is systematizing it: 300+ structures gives a statistical backbone for deciding when to actually chase these polar contacts instead of hinge binding or a back-pocket selectivity vector. If CCR geometry really tracks active/inactive state, that's a usable lever — bias type-I vs type-II engagement via salt bridges and H-bonds instead of reaching for a covalent warhead, attractive when cysteine liabilities or covalent reversibility are a concern. I'm skeptical the conformational-coupling claim generalizes cleanly across the kinome, though — 300 structures sounds like a lot until you split it by subfamily, and PDB deposition bias means scaffolds like EGFR, ABL, and CDKs are almost certainly overrepresented relative to understudied kinases.
A Structural Perspective on Non-covalent Targeting of Conserved Polar Residues in Protein Kinases ↗
Large-Scale Virtual Screen Delivers Potent New TAAR1 Agonists for Schizophrenia
- TAAR1 is a G protein-coupled receptor pursued as a non-dopaminergic drug target for schizophrenia and antipsychotic therapy.
- A structure-based virtual screen docked about 65 million candidate molecules against an active-state model of TAAR1.
- Of 55 top-ranked hits tested experimentally, 14 showed genuine TAAR1 agonist activity, ranging from mid-nanomolar to micromolar potency.
- Hit optimization then yielded agonists with nanomolar potency, and cryo-EM structures confirmed the binding poses the docking had predicted.
- Three optimized agonists showed high brain exposure and potency described as exceeding that of ulotaront, a clinical-stage TAAR1 antipsychotic candidate.
- In mice, all three normalized amphetamine-induced disruption of pre-pulse inhibition, a schizophrenia-relevant behavioral measure, without causing catalepsy, a common antipsychotic side effect.
A 25% experimental hit rate (14/55) out of 65 million docked molecules is the number that jumps out — that's an unusually clean confirmation rate for an active-state GPCR model, and it's real validation for structure-based virtual screening on TAAR1, not just a docking-score exercise. Better still, cryo-EM backs up the predicted binding poses, so the model isn't just getting lucky on affinity. The pharmacology is the real prize: brain-penetrant, potency beating ulotaront, and no catalepsy in the PPI assay — that's the non-dopaminergic promise actually paying off, not just a slogan. Ulotaront is now the bar every TAAR1 agonist has to clear, and these three cleared it. Worth watching whether the SAR generalizes beyond these three chemotypes.
Structure based discovery of antipsychotic-like TAAR1 agonists ↗
Researchers Advance Quinoline CYP8B1 Inhibitor as Lead for Metabolic Disease
- CYP8B1 is a liver enzyme in the bile-acid synthesis pathway now being explored as a drug target for metabolic disorders such as nonalcoholic fatty liver disease and type 2 diabetes.
- The project started from compound 1, a CYP8B1 inhibitor identified by high-throughput screening, which broke down too quickly to be tested in live animals.
- Chemists used structure-based design and metabolite identification to learn how the molecule degraded, then ran DMPK-guided analog synthesis to explore structure-activity relationships.
- That work produced compound 9, a quinoline analog with markedly improved metabolic stability.
- In mice, compound 9 showed robust in vivo CYP8B1 inhibition, providing a validated lead for further optimization.
This is textbook DMPK-guided lead optimization done right: compound 1 degrades too fast for in vivo work, so instead of abandoning it, they identify the metabolite, figure out exactly where the molecule is falling apart, and redesign around that liability. That's the disciplined way to do hit-to-lead, and it's refreshing to see it laid out explicitly rather than glossed over. Landing on a quinoline is a plus for tractability — cheap chemistry, well-understood SAR space, easy to riff on for follow-up analogs. CYP8B1/bile-acid signaling is also a nice change of scenery from the overworked FXR and GLP-1 real estate in NAFLD/T2D. My one nagging question: going from compound 1 to a stable, in vivo-active compound 9 reads suspiciously clean for a single campaign — what substituent or ring modification actually killed the metabolic soft spot? That's the detail I'd want in the SAR table before believing this fully.
Chemists Engineer Isoform-Selective HDAC4/HDAC7 Probes to Dissect Th17 Inflammation
- HDAC4 and HDAC7 are class IIa histone deacetylases with limited tissue expression, making them attractive, more selective epigenetic drug targets than broadly expressed HDAC family members.
- Both enzymes help drive the transcriptional program behind Th17 cell differentiation, a pathway linked to inflammatory bowel disease and other Th17-associated inflammatory conditions.
- Chemists reworked the metal-binding and hydrophobic contact regions of TMP269, a known class IIa scaffold, to build a new series of HDAC4/7-directed analogs.
- Reporter-gene, binding, and docking studies uncovered distinct structural features that separately steer potency toward HDAC4 versus HDAC7.
- The work delivered isoform-selective, potent compounds usable as chemical probes to separately study HDAC4 and HDAC7 function, and as starting points for Th17-targeted therapeutics.
Class IIa HDACs are the pseudo-catalytic oddballs of the family — barely any intrinsic deacetylase activity, so their biology runs largely through protein contacts rather than a clean catalytic pocket, which is why generic HDAC pharmacophores rarely discriminate them well. Building off TMP269 instead of starting de novo is the pragmatic call: it's a validated class IIa binder, so tuning the metal-binding warhead plus the adjacent hydrophobic contacts is a much more tractable SAR exercise than blind discovery. Pulling HDAC4 vs HDAC7 selectivity out of that is the real win — these two are highly homologous, and clean separation is notoriously hard. Most clinical HDAC drugs are pan- or Class I-selective, so isoform-pure IIa probes are genuinely useful tool compounds for picking apart Th17 biology, well before anyone's thinking about a lead.
Kinase Inhibitor Reshapes Its Own Binding Pocket to Gain Selectivity
- Researchers led by Seidler and colleagues designed a small-molecule inhibitor of p38δ (p38 delta), a MAP kinase linked to cancer, and reported its binding mechanism in Angewandte Chemie International Edition.
- Structural analysis showed the inhibitor initially collided with a flexible loop lining the kinase's ATP-binding pocket, a clash that would normally be expected to weaken or block binding.
- Instead of being excluded, the inhibitor caused that loop to change conformation and fold around the molecule, producing an unusually tight, self-encapsulating fit within the remodeled pocket.
- The authors present this induced-fit, pocket-remodeling behavior as a previously undescribed route to kinase selectivity, distinct from conventional structure-based design, which treats the binding pocket as a fixed template the inhibitor must be shaped to match.
- The finding suggests that deliberately exploiting pocket flexibility, rather than avoiding steric clashes, could become a strategy for engineering selectivity in future kinase-targeted drug design.
The steric clash was the feature, not the bug — that's the part that makes me sit up. We're trained to treat the ATP pocket as a fixed template and design ligands to fit it; here the loop folded around the inhibitor and the "bad" collision became the selectivity handle. That inverts the whole lock-and-key mental model. Selectivity-wise, this is a genuinely new lever. Everyone's chasing hinge tweaks, DFG-out, or allosteric pockets — induced self-encapsulation is a different axis entirely, and worth stealing for other kinase programs. My skepticism: is this designable, or did they get lucky in one series and rationalize it after the crystal structure came back? Rational pocket-remodeling on demand would be huge; a one-off induced-fit anecdote is just a nice paper. Also worth noting: p38δ is far less drugged than p38α, so any new selectivity trick here has real headroom.
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.
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.
The Hidden Loop Guiding Malaria Invasion
- This is a perspective/analysis article, not a new experimental study, focused on Plasmodium falciparum apical membrane antigen 1 (PfAMA1) as an anti-malarial drug target.
- PfAMA1 binds rhoptry neck protein 2 (PfRON2) to form the moving junction that enables the malaria parasite to invade red blood cells, making this protein-protein interaction a key therapeutic target.
- Most structure-based inhibitor design has targeted the hydrophobic trough, a well-defined groove on PfAMA1 that accommodates the PfRON2 peptide.
- The authors highlight a domain 2 (D2) loop near the trough that shows cryptic, conformation-dependent dynamics rather than a fixed structure.
- They argue this loop flexibility, previously overlooked, meaningfully shapes how PfAMA1 recognizes PfRON2.
- The perspective calls for future anti-malarial drug design to incorporate D2 loop dynamics alongside the trough itself, rather than treating the binding site as static.
If I'd been designing against the trough alone, I'd have built a static pharmacophore off one co-crystal pose and wondered why my analogs kept losing potency in ways the model couldn't explain — that's the D2 loop talking. A cryptic, conformation-dependent element next to your primary pocket means the 'druggable groove' you're staring at in PyMOL isn't the whole binding event; you need ensemble docking or short MD runs to even see the states worth targeting, not another round of rigid-receptor SBDD. This is the same lesson from Bcl-2/Mcl-1 and MDM2-p53 campaigns — flexible loops or helices near a defined hot spot often carry the selectivity, not the anchor pocket. No new chemical matter here, but it's a real prompt to revisit our PfAMA1 series with loop-aware ensembles before writing off SAR gaps as noise.
Reversible-Work Metadynamics Delivers Fast Hit Triage — and Exposes a Memorization Blind Spot in AI Co-Folding
- Virtual screening often yields false positives from fast, approximate scoring functions, while accurate free-energy calculations to filter them remain too costly for routine high-throughput use.
- The authors introduce CTMD (c(t)-based metadynamics), which ranks binding stability using the nonequilibrium reversible-work estimator c(t) from short, independent metadynamics runs, without requiring converged binding free energies.
- Across diverse targets and chemotypes, CTMD shows robust early enrichment while staying fast, transferable, and largely tuning-free.
- Benchmarking AI co-folding, the authors find Boltz-2's enrichment tracks similarity to its training data and persists even after active-site modifications, pointing to memorization rather than true binding physics.
- CTMD is offered as an open-source middle ground between quick docking/co-folding and costly free-energy methods, cutting wasted discovery-campaign resources.
A triage tier between docking and full FEP is exactly what's been missing from my workflow. Standard docking scores are too noisy to prioritize synthesis, and running FEP on every virtual-screening hit is a non-starter for budget and turnaround — CTMD's short, independent metadynamics runs with the c(t) estimator could slot right into that gap and actually change which compounds we send to synthesis, without a cluster's worth of compute. Open-source and largely tuning-free means it's adoptable without a specialist babysitting it. The Boltz-2 finding is the one I'd flag to my team before anyone leans on AI co-folding for real decisions: enrichment tracking training-set similarity even after active-site mutation means it may be pattern-matching known chemotypes, not scoring genuine binding physics. That's a trap for exactly the novel scaffolds we're chasing.
Early-Enrichment Hit Discovery via Reversible-Work c(t) Estimation in Metadynamics (CTMD) ↗
Many Virtual Screening 'Improvements' May Not Be Real, Pre-Registered Study Finds
- The preprint asks a foundational methods question: given the size of a typical structure-based virtual screening benchmark, how large a difference in AUROC or enrichment between two protocols can actually be distinguished from statistical noise.
- Rather than assuming benchmark comparisons are inherently reliable, the authors first directly measure these resolution limits.
- They then pre-registered six candidate interventions to docking/scoring protocols and tested each against the measured resolution limits, rather than reporting post-hoc 'wins.'
- The pre-registration design is meant to guard against selective reporting, a known issue where small, benchmark-specific gains get presented as general improvements.
- This is a methodology/rigor study, not a new-inhibitor or target-specific paper; it addresses how virtual screening improvements should be evaluated.
- Practical implication: many published claims of improved virtual screening performance may fall within the noise floor of typical benchmarks, so hit-finding teams should treat single-benchmark improvement claims cautiously.
Every VS vendor pitch should have to clear this paper's bar. If a 'protocol improvement' can't beat the measured noise floor of AUROC/enrichment on a benchmark our size, it's not an improvement — it's a coin flip dressed up in a webinar slide. Six pre-registered interventions is a high bar; realistically most of us won't pre-register anything before a campaign, but I can at least ask collaborators to report effect sizes against a resolution limit, not just a headline AUROC bump. Sharpest implication for me: the co-folding hype (Boltz-2 and friends) needs the same treatment — if those models are just pattern-matching PDB-adjacent chemotypes, their 'wins' over classic docking/FEP on public benchmarks could be memorization, not generalization. I'm not swapping FEP for a black box on this evidence alone.