Journal of the American Chemical Society

Covalent chemistry coupled with activity-based protein profiling (ABPP) offers a versatile approach for small-molecule ligand discovery in native biological contexts. The covalent ligandability maps generated by ABPP that target cysteine have frequently leveraged the acrylamide as a reactive group due to its tempered electrophilicity and presence in many advanced tool compounds and therapeutics. More recently, alternative cysteine-directed reactive groups such as the butynamide have emerged as an additional source of covalent probes and drugs, but their global reactivity with the proteome remains largely unexplored. Here, we compare the ligandability maps of stereochemically defined acrylamide and butynamide compounds (stereoprobes) built from a common tryptoline core and find that the butynamides, despite exhibiting attenuated intrinsic and proteome-wide reactivity, preferentially engage a diverse set of proteins in human cancer cells. Among the butynamide-preferring proteins was C19orf54/ACTMAP, a cysteine protease required for the post-translational maturation of actin. We show that (1S, 3R)-tryptoline butynamides stereoselectively react with the catalytic nucleophile of ACTMAP, leading to accumulation of N-terminally unprocessed actin in cancer cells. Our findings support reactive group diversification as a strategy for expanding the ligandability of the human proteome and the butynamide, more specifically, as a differentiated cysteine-directed electrophile for chemical probe discovery.

Diacylglycerols (DAGs) are central intermediates in lipid metabolism and signaling, yet their trafficking and persistence within lipid droplets (LDs) remain incompletely understood due to the lack of chemically stable, DAG-mimetic imaging tools. Here, we report the development of a family of solvatochromic fluorescent lipid analogs, termed DONDI, designed to probe DAG-associated dynamics at LDs. These probes are based on a 1,8-naphthalimide scaffold conjugated to modified aminoglycerol backbones bearing oleoyl chains to mimic native glycerolipids. Biophysical characterization and atomistic molecular dynamics simulations revealed probe-specific membrane insertion and hydrogen-bonding behaviors consistent with distinct lipid-mimetic properties. Live-cell imaging in NIH 3T3 fibroblasts demonstrated that DONDI probes were efficiently internalized and selectively accumulated within lipid droplets. Structure-function analysis identified DONDI-5 as the closest mimic of 1,2-diacylglycerol, displaying rapid uptake, strong LD enrichment, and prolonged intracellular retention without detectable relocalization to other cellular membranes. These properties enabled sustained visualization of LD-associated DAG pools over extended time scales. Collectively, this work establishes DONDI-5 as a chemically stable DAG-mimetic probe and provides direct experimental support that DAGs can be transported to and transiently stored within lipid droplets without prior conversion to triacylglycerols.

Fluorine NMR is a powerful tool for probing biomolecular structure and dynamics, yet the performance of 19F probes is fundamentally constrained by rapid transverse relaxation driven by chemical shift anisotropy (CSA). Despite its central role, CSA has largely been treated as an immutable nuclear property rather than a chemically addressable design parameter. Here we demonstrate that the geometry of the CSA tensor - specifically its magnitude, symmetry, and orientation relative to the internuclear dipolar interaction - constitutes a decisive and engineerable determinant of relaxation behavior in coupled 19F-13C spin systems. Guided by electronic-structure calculations and Bloch-Redfield-Wangsness relaxation theory, we establish quantitative design rules that predict when CSA-dipolar interference can be exploited to suppress transverse relaxation. Implementation of these principles in a cysteine-reactive fluoropyrimidine scaffold yields a reporter that supports simultaneous 19F and 13C TROSY optimization, validated by solid-state MAS NMR and protein-based experiments. When incorporated into the 42 kDa maltose binding protein, the probe exhibits exceptionally slow 13C transverse relaxation (R2 {approx} 2-3 s-1) corresponding to linewidths of [~]2 Hz that persist even at apparent molecular weights exceeding 200 kDa. These results recast relaxation optimization as a chemically programmable problem and provide a general framework for the rational design of next-generation NMR probes tailored to large, dynamic, and heterogeneous biomolecular systems.

Cells utilize liquid-liquid phase separation to organize biochemical reactions within biomolecular condensates, which function as membraneless organelles. Although these assemblies are known to enhance reaction rates by concentrating reactants, the mechanisms beyond simple mass-action effects remain poorly understood. Here, we examined how the physicochemical microenvironment within condensates modulates reaction kinetics using spontaneous protein ligation as a model reaction, conducting a systematic analysis across various condensates, ranging from structured scaffolds (PRM-SH3 systems) to intrinsically disordered protein (IDP)-based scaffolds such as LAF, TAF, and FUS. We designed a FRET-based proximity-sensitive client probe to quantify increases in effective local concentration arising from excluded-volume effects. In parallel, we measured internal hydrophilicity and water activity, revealing them as additional key determinants of reaction acceleration. Together, the findings presented here elucidate how phase-separated compartments regulate biochemical reactions through the interplay of physical (effective concentration) and chemical (hydrophilicity and water activity) microenvironments and provide mechanistic insights for engineering condensates with tunable reactivity.

High-valent metal-nitrido species are powerful nitrogen-atom transfer intermediates but remain difficult to access and control due to intrinsic instability and bimolecular N-N coupling pathways. Herein, we report the first formation of a high-valent Mn(V)-nitrido complex within a de novo designed protein scaffold and demonstrate that a reactive precursor to this species can be catalytically intercepted for enantioselective aziridination. A Mn(V){equiv}N unit derived from an abiological diphenyl porphyrin is confined within a designed helical bundle protein, where the protein environment suppresses bimolecular decay and enables detailed spectroscopic characterization. Electron paramagnetic resonance, resonance Raman, and circular dichroism spectroscopies confirm formation of a low-spin Mn(V)-nitrido species that is stable for weeks at room temperature and exhibits minimal perturbation of the Mn{equiv}N unit upon modulation of the axial histidine ligand, while catalytic activity and stereochemical outcome are sensitive to its presence. Mechanistic studies identify monochloramine (NH2Cl) as the operative nitrogen-atom donor and support the involvement of a transient Mn-bound N-transfer intermediate en route to nitrido formation. Under catalytic conditions, this intermediate is inter-cepted to perform aziridination with TON {approx} 180 and an enantiomeric ratio of 65:35. Together, these results establish de novo protein design as a platform for stabilizing high-valent metal-nitrido species and harnessing their reactivity for nitrogen-atom transfer chemistry beyond the limits of natural metalloenzymes and small-molecule catalysts.

Summary paragraphThe central dogma of molecular biology describes how genetic information stored in nucleic acids guides the formation of structured proteins from a single molecular alphabet of twenty amino acids (C20)1,2. The extent to which C20 is uniquely capable of forming structural polymers remains a fundamental open question. Here we demonstrate that peptides built from other, "xeno" amino acid alphabets can adopt protein-like secondary structural motifs. Having designed two different xeno alphabets, with them we constructed both combinatorial random sequence libraries and specific, designed 25-mer sequences. We report sequence-dependent structural motifs that result according to circular dichroism, infrared spectroscopy and nuclear magnetic resonance interpreted by molecular dynamics simulations, supported by extensive quantum mechanical calculations. This evidence, including a solution-phase NMR-resolved helical motif, demonstrates that the potential for amino acids to form structure bearing sequences is not unique to lifes alphabet, and thereby reveals a previously unexplored sequence-structure space. Results inform the search for extraterrestrial life, lay foundations for incorporating novel synthetic functional groups and heteroatoms into structure-bearing alphabets, and provide the first truly independent data with which to test and improve all that has been learned about protein folding from the study of lifes 20 side chains.

Huntingtons disease (HD) is caused by expansion of a polyglutamine tract in the huntingtin (Htt) protein, leading to aggregation of the exon 1 fragment (HttEx1) into amyloid fibrils. HttEx1 forms one of the lowest-complexity amyloid cores known, its fibril core consists of a single amino acid, glutamine. With emerging therapies improving patients prospects by silencing expression of HTT, tools to monitor HttEx1 aggregation become essential for timely intervention and next-generation therapeutics. Here, we show that the peptide FibrilPaint1 selectively binds HttEx1Q44 fibrils without interacting with monomeric protein, allowing to measure and trace HttEx1 amyloid fibrils. Using the FibrilRuler assay, we tracked fibril formation from early species to larger clustered assemblies. The non-fluorescent variant, FibrilPaint20, was used to recruit the E3 ubiquitin ligase CHIP to HttEx1 fibrils, enabling site-specific ubiquitin tagging. However, unlike Tau fibrils, ubiquitinated HttEx1 fibrils resisted proteasomal degradation. This reveals a fundamental difference in how amyloids with extremely low-complexity cores respond to cellular clearance machinery. Together, our findings establish the FibrilPaint peptide family as a toolset for the detection and molecular targeting of amyloids, providing new opportunities to study protein aggregation and act as building blocks for future diagnostic and therapeutic strategies in neurodegenerative diseases. HighlightsO_LIFibrilPaint1 selectively binds HttEx1Q44 amyloid fibrils and allows monitoring of fibril growth using the hydrodynamic radius (FibrilRuler). C_LIO_LIFibrilPaint20 recruits the E3 ligase CHIP to Htt fibrils, enabling ubiquitination. C_LIO_LIDespite successful ubiquitination, Htt fibrils resist proteasomal degradation in vitro, highlighting structural barriers. C_LIO_LIFibrilPaint provides a scaffold for functional targeting of amyloids with diagnostic and therapeutic potential. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/695423v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@18acc7corg.highwire.dtl.DTLVardef@1771f3borg.highwire.dtl.DTLVardef@1a35e51org.highwire.dtl.DTLVardef@85270a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO The FibrilRuler Test: FibrilPaint enables measurement of Huntingtin fibril size during aggregation After a short lag-phase following removal of the protective MBP tag by Factor Xa, fibrillation proceeds rapidly. Subsequent fibril clustering further accelerates growth, leading to exponential increases in aggregate size. C_FIG

The chemical basis underlying the striking blue hue of live H. americanus, known as American lobster, are studied in evolutionary biology and in polyene physical chemistry. Carapace colouration is generated by the antioxidant astaxanthin bound within the carotenoprotein crustacyanin complexes. Here, we present the ex vivo structure of the most abundant -crustacyanin and {beta}-crustacyanin forms, determined respectively by cryo-electron microscopy and X-ray crystallography to a resolution of 2.75 [A]. Our structural analysis reveals -crustacyanin as an elongated arrangement of {beta}-crustacyanin heterodimers tethered by an heptatricopeptide repeat (HPR) protein. In vitro complex formation between the {beta}-crustacyanin unit with a synthetic heptatricopeptide reproduces the observed blue colour of -crustacyanin, identifying the HPR protein, in concert with crustacyanins, as contributor in tuning carapace colour. Overall, these results explain how nature adjusts the colour across the entire visible spectrum by exploiting the bathochromic shift of astaxanthin from its unbound red form ({lambda}max = 472 nm) firstly to the {beta}-crustacyanin violet bound form ({lambda}max = 591 nm), and then to the -crustacyanin bound blue form ({lambda}max = 631 nm).

Nicotinamide adenine dinucleotide (NAD+) is crucial for cellular functions including DNA repair and metabolism. Nicotinamide mononucleotide adenylyltransferase (NMNAT) enzymes catalyze the final step of NAD+ synthesis from NMN and ATP. There are three NMNAT isoforms: NMNAT1, NMNAT2, and NMNAT3, located in the nucleus, cytoplasm, and mitochondria, respectively. Nuclear NAD+ promotes disease progression in NAD+-dependent cancers, and it is hypothesized that targeting NMNAT1 with small-molecule inhibitors could be an effective therapeutic strategy. Here, we identify an NMNAT1 inhibitor from a bioactive compound screen and report its effects on NAD+ levels and the viability of NMNAT1-dependent cancer cell lines. The compound AMI-1 is a known inhibitor of Protein Arginine N-Methyltransferase 1, and we find that it also inhibits NMNAT1 with similar potency. Additionally, we determined a cryo-EM structure of NMNAT1 bound to AMI-1 and revealed its mechanism of inhibition. This provides proof of principle for inhibiting NMNAT1 to target NAD+ metabolism in dependent cancers, while also highlighting that caution is warranted when interpreting studies using AMI-1 as a PRMT1 inhibitor, given its effect on NAD+ through NMNAT1. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/716846v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@59933borg.highwire.dtl.DTLVardef@d1298borg.highwire.dtl.DTLVardef@1fe902dorg.highwire.dtl.DTLVardef@1abb3cc_HPS_FORMAT_FIGEXP M_FIG C_FIG

Polyketide biosynthesis relies on the conformational adaptability of type II polyketide synthases and accessory enzymes, which direct chain folding and regiospecific cyclization. The aromatase/cyclase TcmN from Streptomyces glaucescensis catalyzes the first two ring closures of tetracenomycin C. Still, the molecular basis by which conformational dynamics regulate substrate binding and product release remains unresolved. Understanding how conformational transitions control ligand recognition and prevent aggregation is crucial for deciphering the molecular bases of polyketide biosynthesis and for guiding engineering strategies to synthesize novel natural products. Here, we investigated how ligand interactions modulate the conformational equilibrium of TcmN and the mechanistic consequences for catalysis. Using NMR spectroscopy (STD, CSP, relaxation dispersion), calorimetry, molecular docking, and microsecond-scale molecular dynamics simulations, we mapped the conformational ensembles of apo TcmN and its complexes with naringenin (a substrate/product analogue) and intermediate 12 (INT12). Apo TcmN samples both open and closed conformations. Naringenin preferentially stabilizes the closed state, a conformation thought to protect hydrophobic residues from solvent exposure. In contrast, INT12 shifts the equilibrium toward the open state, characterized by an expanded cavity that permits substrate entry, product release, and accommodation of extended intermediates. Hydrogen-bond analysis highlighted conserved catalytic residues (R82, E34, Q110, T133) as key anchors for productive poses. These results establish that TcmN functions through a ligand-gated breathing mechanism, in which successive intermediates selectively tune the cavity volume and shape, balancing catalytic efficiency with protection against aggregation. Conformational adaptability emerges as a central determinant of aromatase/cyclase function, providing molecular insights relevant for polyketide biosynthetic engineering. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/708631v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@5646aorg.highwire.dtl.DTLVardef@39016org.highwire.dtl.DTLVardef@1e8c285org.highwire.dtl.DTLVardef@3aba20_HPS_FORMAT_FIGEXP M_FIG C_FIG

Molecular glue degraders represent a powerful modality for targeting proteins that are refractory to traditional inhibition. However, rational design principles for molecular glue degraders remain poorly defined. Previously, we reported a chemistry-centric strategy to identify covalent degradative handles that, when appended to established ligands, convert non-degradative inhibitors into molecular glue degraders by engaging permissive E3 ligases. This effort identified a fumarate-based electrophilic handle that covalently modified the E3 ligase RNF126, enabling degradation of multiple protein targets when transplanted across diverse ligands. Despite its conceptual impact, the high intrinsic reactivity and cytotoxicity of the fumarate handle limited its translational utility. Here, we report the development of an optimized and metabolically stabilized RNF126-targeting covalent handle incorporating a trans-cyclobutane linker that exhibits reduced glutathione reactivity and diminished cytotoxicity while retaining robust degradative activity. When appended to the BET bromodomain inhibitor JQ1, this optimized handle yielded a potent and selective BRD4 degrader whose activity was dependent on RNF126. Importantly, transplantation of this handle onto a previously non-inhibitory ligand targeting the androgen receptor (AR) and its truncation variant, AR-V7, enabled selective degradation of both AR and AR-V7 in androgen-independent prostate cancer cells, thereby robustly inhibiting AR transcriptional activity beyond the established AR antagonist enzalutamide. Collectively, these findings demonstrate an optimized RNF126-based covalent handle for the rational development of molecular glue degraders against transcriptional regulators, including undruggable variants such as AR-V7.

Conformational dynamics play a central role in enzyme function by controlling substrate access and productive binding. Yet mutations that beneficially modulate these properties are difficult to identify. Here, we used ultrahigh-throughput fluorescence-activated droplet sorting (FADS) with a bulky fluorogenic substrate derived from coumarin (COU-3) to impose steric selection pressure on the haloalkane dehalogenase LinB. Screening a focused library yielded five single substitutions located 11.5-15.5 [A] from the catalytic centre. Variant I138N showed a fourfold increase in catalytic efficiency toward COU-3 through reduced KM and increased kcat, associated with increased cap-domain flexibility and facilitated substrate entry. In contrast, variant P208S markedly reduced substrate inhibition and shifted specificity toward bulkier iodinated haloalkanes by reshaping its tunnel environment. Integrated kinetic and structural analyses revealed that screening with bulky substrates directs selection toward distal regions controlling substrate access and unproductive binding. These findings demonstrate that ultrahigh-throughput FADS can reveal dynamic mechanisms of enzyme adaptation that remain difficult to predict by rational design. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=183 SRC="FIGDIR/small/713925v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@782038org.highwire.dtl.DTLVardef@8b43f3org.highwire.dtl.DTLVardef@11a403eorg.highwire.dtl.DTLVardef@6fcaea_HPS_FORMAT_FIGEXP M_FIG C_FIG

P(V) electrophiles such as tabun, sarin, soman, and VX are notorious for their lethality and nefarious intent in chemical warfare. Consequently, these deadly agents have largely been abandoned except for fluorophosphonate tool compounds that were repurposed for activity-based protein profiling (ABPP). Stereogenic P(V) centers hold strong potential as enabling scaffolds for synthetic and medicinal chemistry due to their inherent chirality and favorable bioavailability but are limited principally by potent off-target toxicity. Herein, we developed phosphorus-azole exchange (PhAzE) chemistry for tuning reactivity of the stereogenic P(V) pharmacophore to increase selectivity and mitigate off-target activity in cells and animal models. We demonstrate ultrapotent (300 pM in cells, 1 mg kg-1 in mice), enantioselective, covalent inhibition of the serine hydrolases DPP8/9 with PhAzE ligand in cells and in vivo; no overt toxicity was detected in mice treated daily over the course of a week. These finding show the P(V) electrophile can potently and enantioselectively engage a target protein without a deadly outcome, charting a path towards broader adoption of these agents in laboratory and industry settings.

Direct solar-to-chemical conversion offers a compelling route to clean, dispatchable energy. Photosystem I (PSI), an evolutionarily optimized light-driven oxidoreductase central to oxygenic photosynthesis, can be repurposed for direct solar-fuel production by efficiently coupling its photochemistry to catalysts, thereby storing sunlight as chemical energy in the H-H bond of H2. One promising architecture integrates PSI with Pt nanoparticle (PtNP) catalysts to create photocatalytic PSI-PtNP biohybrids. Advancing these systems requires molecular-level insight into protein-nanoparticle interactions and the bio-nano electron transfer pathways that govern activity; however, progress has been constrained by limited structural data to guide rational design. Here, we present two molecular structures of active PSI-PtNP assemblies that (a) compare thermophilic and mesophilic PSI scaffolds and (b) probe how removal of the terminal [4Fe-4S] clusters and stromal subunits in PSI reshapes protein-nanoparticle interfaces and photocatalysis. Structural analyses and molecular dynamics simulations define the interface topology, electrostatics, and cofactor-to-nanoparticle distances, revealing key molecular features that control biohybrid formation and electron transfer efficiency. These data establish mechanistic links between scaffold composition, bio-nano interface geometry, and catalytic performance, yielding design principles for optimizing PSI-PtNP architectures. The resulting structure-function insights provide a blueprint for engineering PSI-based solar-fuels systems and, more broadly, inform the design of protein-nanomaterial interfaces for light-driven catalysis.

Histamine is a key signaling molecule in pathophysiology that can exhibit significant regulatory roles in diverse health and disease status. Besides the well-studied noncovalent interactions between histamine and its receptors, protein histaminylation is a recently discovered mode of action, through which histamine regulates cellular signaling pathways in a covalent-interaction manner. Histaminylation is an emerging protein post-translational modification, where an isopeptide bond is formed between the histamine primary amine and {gamma}-carboxyl group of glutamine through a transamidation reaction catalyzed by transglutaminase 2 (TGM2). However, due to the lack of efficient pan-specific antibodies targeting histaminylated glutamine, the histaminylation proteome in cells remains poorly explored. Here, we report the design and development of a novel N{tau}-propargylated histamine probe as well as its successful application in chemical proteomic profiling of the histaminylation proteome in cancer cells. Notably, new TGM2-catalyzed epigenetic marks on core histones, e.g., H2AXQ84 and Q104 histaminylation, have been identified from cancer cells and verified in this study.

Providing immediate access for functional proteins inside living cells would unlock unprecedented control over cellular processes; however, commonly used endocytic delivery suffers from endosomal trapping and degradation. One of the most powerful non-endosomal delivery methods uses cell surface anchored cell penetrating peptide (CPP)-additives that allow proteins to enter cells directly. Nevertheless, the underlying molecular mechanism involved in direct entry via crossing the cell membrane (protein translocation through the cell) and the major driving forces remain controversially discussed. Here, we provide a stepwise molecular picture on how CPP-additives enable uptake of protein cargoes through direct membrane translocation. CPP-additives accumulate on the cell surface in nucleation zones, locally hyperpolarizing the membrane, and induce transient water pores that allow selective CPP-protein entry without compromising membrane integrity. These fundamental mechanistic insights provide a firm basis for rationally optimizing delivery strategies using highly cationic CPPs, ultimately resulting in innovative and smart protein delivery strategies to advance therapeutic protein applications. Abstract Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/707441v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@14c1386org.highwire.dtl.DTLVardef@195f765org.highwire.dtl.DTLVardef@a52258org.highwire.dtl.DTLVardef@171dd7c_HPS_FORMAT_FIGEXP M_FIG C_FIG

Cyclopeptide alkaloids are an expanding class of plant peptide natural products defined by a macrocyclic ether-crosslink via a tyrosine-derived phenol. Classical cyclopeptide alkaloids are characterized by strained 13-to 15-membered cyclophanes and terminal modifications such as N-methylation and C-terminal styrylamine moieties. While synthetic access to many classical cyclopeptide alkaloids has been established, no biosynthetic route has been reported. Here, we elucidate the biosynthetic pathway of a 14-membered cyclopeptide alkaloid, lotusine A, from Chinese date tree (Ziziphus jujuba) which features peptide cyclization on a ribosomal precursor peptide by a split burpitide cyclase, non-heme-iron and 2-oxoglutarate-dependent oxidative decarboxylation affording the C-terminal hydroxystyrylamine, and SAM-dependent N-terminal -N,N-dimethylation. We apply discovered Z. jujuba enzymes in combination with a clubmoss cyclopeptide alkaloid cyclase for biosynthesis and diversification of analgesic adouetine X and anxiolytic sanjoinine A by combining in planta and in vitro reactions. Our work expands the biocatalytic repertoire of non-heme-iron- and 2-oxoglutarate-dependent enzymology to oxidative peptide decarboxylation and primes scaled metabolic engineering and chemoenzymatic synthesis of 14-membered cyclopeptide alkaloids with terminal posttranslational modifications.

Enzyme-activatable chemical tools, including fluorogenic probes and prodrugs, are essential in chemical biology and targeted therapeutics but remain challenging to access in structurally diverse forms because their synthesis is often bespoke and difficult to standardize. Here, we introduce synthesis based on covalent capture and release (SCCR) as a programmable chemical strategy that enables the modular assembly of protease-activatable molecules through specifically designed protecting-group logic. The SCCR framework establishes a standardized capture-elongation- release workflow that decouples molecular diversification from individual synthetic optimization, thereby enabling automated preparation of complex libraries. Using this chemistry, we generated a diverse set of fluorogenic probes and applied them to single-molecule enzyme activity analyses to identify candidate activity-based biomarkers of liver diseases. The generality of the SCCR strategy was further demonstrated by extending the same chemical logic to the preparation of antibody-drug conjugate (ADC) linkers, allowing systematic evaluation of plasma stability and cytotoxic potential. By establishing a programmable capture-release chemistry for the synthesis of enzyme-activatable molecules, this work provides a generalizable chemical foundation for the scalable and automated construction of functional small-molecule tools across biological and translational research.

Mutant KRAS is a potent oncogene, serving as a tumor driver in many solid human cancers. Current small-molecule inhibitors target the highly conserved G-domain, but to gain further mechanistic insight into the roles of different isoforms, we investigated the strategy of sterically shielding the unstructured hypervariable regions (HVRs). KRAS HVRs undergo a series of post-translational modifications that enable intracellular trafficking and membrane attachment. Previous attempts to drug KRAS by preventing its post-translational modification, based on inhibition of the involved prenylation enzymes have been largely unsuccessful. In this study, we explored the property of Designed Armadillo Repeat Proteins (dArmRPs) to specifically bind unstructured regions. We assembled a dArmRP to recognize the unstructured KRAS4B-HVR and developed it into a high-affinity binder by directed evolution. The resulting dArmRP recognizes the 14 C-terminal residues of unprocessed KRAS4B, thereby blocking the farnesyltransferase-binding epitope. This steric shielding disrupts KRAS4B post-translational modification and thereby significantly reduces its plasma membrane localization, while demonstrating complete selectivity over KRAS4A, NRAS, and HRAS. This work establishes the shielding of intrinsically disordered regions as a precise biochemical strategy to control protein function and provides an isoform-specific tool to dissect KRAS biology. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/712636v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@791ac4org.highwire.dtl.DTLVardef@cc4c91org.highwire.dtl.DTLVardef@b6c920org.highwire.dtl.DTLVardef@4e8a9c_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical representation of how the unstructured KRAS4B-HVR is occupied by a dArmRP, making it inaccessible for the FTase.

Therapeutic peptides combine high target specificity with potent biological activity.1 However, treatment success is often limited by rapid clearance and the need for frequent injections.2, 3 This challenge is particularly acute for therapeutic peptides used in obesity, where clinical benefit must be balanced against dose-dependent adverse effects. In nature, these constraints are overcome by storing hormones as reversible fibrils,4 but pharmacokinetic control is essential for widespread adoption of bio-inspired self-assembled depots for therapeutic peptides. Here, we show that tuneable pharmacokinetics can be achieved and modelled by mapping the fundamental chemical parameters of reversibly self-assembly in vitro. We demonstrate this approach for the amylin analogue pramlintide. Amylin analogues are under development for the next generation of diabetes and obesity treatments, with improved mechanism of action e.g. preserving lean body mass.5-8 Pramlintide is an approved drug with a well-established safety profile, however, it has a comparable half-life to native amylin.8-12 In a pilot study, we achieve in vitro-in vivo correlation, increasing the half-life of pramlintide 20-82-fold in rats, while controlling burst release. These findings demonstrate that the optimisation of pharmacokinetics can be decoupled from peptide engineering, establishing a generalisable framework for generating long-acting peptide formulations by emulating native storage mechanisms.