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ACS Central Science

American Chemical Society (ACS)

Preprints posted in the last 90 days, ranked by how well they match ACS Central Science's content profile, based on 66 papers previously published here. The average preprint has a 0.07% match score for this journal, so anything above that is already an above-average fit.

1
Harnessing TfR1 for Cross-Species Systemic Delivery of siRNAs to Deep Brain Regions Using Single-Domain Antibodies

JACQUOT, G.; DAVID, M.; PECQUEUX, B.; MECHIOUKHI, Y.; GIRARD, S.; GODARD, M.; VARINI, K.; BOURSERY, C.; FRAPOLLI, C.; ROUX, S.; BIGONNET, M.; BROUSSE, B.; AUGUSTIN, E.; GODEFROY, G.; FRAISIER, C.; SERRANO, B.; ROMETTE, A.; THOMAS, M.; MAZOUZI, K.; CALLEYA, B.; BEUZELIN, D.; FAUCON, A.; BAKLOUL, K.; DANGLA-PELISSIER, G.; LECORCHE, P.; ABOUDOU, S.; BENOIST, F.; MASSE, M.; FERRACCI, G.; TEMSAMANI, J.; KHRESTCHATISKY, M.

2026-05-22 pharmacology and toxicology 10.64898/2026.05.20.726486 medRxiv
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Despite their therapeutic potential across a wide range of central nervous system (CNS) disorders, nucleic acid-based therapeutics are limited by inefficient delivery to deep brain regions at clinically viable doses. Transferrin receptor 1 (TfR1) has emerged as an attractive target for receptor-mediated transcytosis across the blood-brain barrier (BBB), enabling systemic delivery of biologics such as lysosomal enzymes and monoclonal antibodies. In this study, we demonstrated the translational potential of recently described TfR1-targeting camelid-derived single-domain antibodies (VHHs) for CNS delivery of siRNAs. When conjugated 1:1 to different tool siRNAs, these VHHs promote rapid and robust intracellular uptake, resulting in potent RNAi activity at low nanomolar concentrations in neural cells. Systemic administration of VHH-siRNA conjugates in wild-type mice, hTfR1 transgenic-mice and non-human primates revealed a favourable pharmacokinetic profile characterized by rapid TfR-dependent distributional clearance and efficient functional uptake in deep brain structures. This translated into durable target knockdown of 50-80% at both mRNA and protein levels and with ED50 below 1 mg/kg siRNA. Collectively, these findings establish our TfR1 targeting VHHs as a fit-for-purpose platform for the systemic delivery of therapeutic oligonucleotides to deep brain structures at clinically relevant doses, opening new avenues for the treatment of diverse CNS disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/726486v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@13668eorg.highwire.dtl.DTLVardef@1b1feeeorg.highwire.dtl.DTLVardef@d7be2dorg.highwire.dtl.DTLVardef@6b221_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Next-generation genetically encoded biosensors for spatiotemporal intracellular pH monitoring, mapping, and profiling

Isom, D. G.; Taylor, S.; Colon, B.; Lee, K. D.; Arcuri, J.; Chandthakuri, S.

2026-05-21 biochemistry 10.64898/2026.05.19.726343 medRxiv
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Bioluminescence resonance energy transfer (BRET) systems are widely used for live-cell spectroscopy and biosensor engineering, yet the intrinsic pH sensitivity of commonly used BRET components has not been systematically examined. Here, we show that major BRET luciferase donors, fluorescent acceptors, and donor-acceptor assay pairs exhibit pronounced pH-dependent spectroscopic behavior across physiologically relevant conditions, identifying environmental pH responsiveness as a fundamental property of widely used BRET systems and a potential source of previously underappreciated assay artifacts. Leveraging these principles, we engineered ORION (ratiOmetRIc prOton seNsor), a genetically encoded ratiometric BRET pH sensor based on the NanoLuc-mVenus fusion. ORION exhibited strong brightness, an approximately 9-fold dynamic range, and robust responsiveness across a substantially broader pH range than that of existing genetically encoded sensors. Compared to pHluorin2, ORION maintained substantially improved quantitative performance at acidic pH values below 6.0. To demonstrate its utility in a biological application, we applied ORION across diverse cancer cell models and identified heterogeneous acid imprinting states, suggesting that tumor cells can retain persistent physiological memory of adaptation to acidic microenvironments even after prolonged ex vivo culture. Together, these findings establish pH responsiveness as a fundamental property of BRET systems and position ORION as a best-in-class platform for interrogating and quantifying pH regulation of biology in living systems.

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Steroid-based Tide Quencher 1 probes enable real-time mapping of novel non-canonical cholesterol sites on the M1 muscarinic receptor

Chetverikov, N.; Szanti-Pinter, E.; Jurica, J.; Vodolazhenko, M.; Budesinsky, M.; Zima, V.; Svoboda, M.; Dolejsi, E.; Janouskova-Randakova, A.; Urbankova, A.; Jakubik, J.; Kudova, E.

2026-04-01 pharmacology and toxicology 10.64898/2026.03.26.714567 medRxiv
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Steroid-based fluorescent-quencher probes now enable real-time, residue-level mapping of previously inaccessible cholesterol-binding sites on G-protein-coupled receptors. We designed Tide Quencher 1 (TQ1) conjugated steroids that target two distinct peripheral sites on the M1 muscarinic receptor. One near the extracellular N-terminus and another adjacent to the intracellular C-terminus. Using pregnanolone glutamate as a versatile scaffold, we synthesised a library of probes varying in C-3 linker length ({gamma}-aminobutyric acid vs. L-glutamic acid) and C-3/C-5 stereochemistry (3/3{beta}/5/5{beta}). Fluorescence-quenching assays with CFP-tagged receptors revealed that TQ1 probes consistently outperformed Dabcyl, delivering up to 40 % quenching within minutes and sub-micromolar EC50 values. The most potent N-terminal probe (35-PRG-Glu-TQ1 (5)) achieved 300 nM potency, while the best C-terminal probe (35{beta}-PRG-Glu-TQ1 (3)) reached 1 {micro}M potency with rapid association. Molecular docking and MD simulations identified key residues (K20, Q24, W405 at the N-site; K57, Y62, W150 at the C-site) mediating binding, a prediction confirmed by alanine-scan mutagenesis that markedly reduced quenching at the N-terminus and only modestly affected the C-terminus. Competition experiments with non-quenching analogues further validated probe specificity. Crucially, the pregnane core proved essential; alternative steroid backbones failed to generate robust quenching. This fluorescence-quenching platform overcomes the limitations of traditional radioligand assays, providing kinetic insight, high-throughput compatibility, and the ability to dissect lipid-GPCR interactions in native membranes. The approach is readily extensible to other GPCR families, opening new avenues for structure-guided drug discovery targeting allosteric cholesterol sites.

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UTag, a cysteine-free thermostable tagging system for tracking single mRNA translation live

Aguilera, L. U.; Chen, S.; Sears, R. M.; Yarbro, J.; DeRoo, J.; Ogg, H. A.; Geiss, B. J.; Stasevich, T. J.; Snow, C. D.; Zhao, N.

2026-05-07 biophysics 10.64898/2026.05.06.723082 medRxiv
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Spatiotemporal regulation of mRNA translation is central to gene expression. Over the past decade, translation has become directly observable in live cells at single-mRNA resolution by tagging nascent chains with tandem arrays of short epitope tags recognized by genetically encodable fluorescent intracellular antibodies (intrabodies). While this technology has revolutionized our understanding of translation regulation, the current toolbox of tagging systems remains limited. Here, we developed a novel and tight-binding intrabody against a short (11-amino acid) HIV protease epitope (named UTag). To ensure robust intracellular folding of the anti-UTag intrabody, we further engineered a cysteine-free variant that folds and functions independently of disulfide-bond formation, as validated by X-ray crystallography. The cysteine-free anti-UTag intrabody retains high binding affinity comparable to the parental intrabody while exhibiting significantly improved thermostability ([~]80 {degrees}C). Importantly, the cysteine-free UTag system enables real-time tracking of single-mRNA translation in live cells with performance on par with the parental UTag system as well as the established SunTag and ALFA-tag. Collectively, these results demonstrate that the newly developed UTag system expands the toolbox for live-cell translation tracking and provides complementary tools for multiplexed applications.

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A microscale platform for the comprehensive analysis of bacterial translation initiation

Vinogradova, D. S.; Kasatsky, P. S.; Spiridonova, Z. A.; Leyva, S.; Sanchez-Castro, A.; Penaranda, K.; Zegarra, V.; Soriano, P.; Paleskava, A.; Milon, P.; Konevega, A. L.

2026-04-24 biophysics 10.64898/2026.04.22.719552 medRxiv
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In prokaryotes translation initiation orchestrates protein synthesis through a network of dynamic interactions among the ribosome, mRNA, initiator tRNAfMet, and initiation factors (IFs). Traditional approaches that rely on radioactive labeling or surface immobilization are hindered by inherent safety risks and methodological constraints. We present a fluorescence-based analytical platform that integrates microscale thermophoresis (MST) to investigate translation initiation at the molecular level. Employing fluorescently labeled molecules including the initiator tRNAfMet, mRNA, and Ifs, enabled a detailed characterization of initiation complex assembly as it progresses from bimolecular to higher-order multicomponent states. To expand the fluorescent toolbox for translation studies we established a novel BODIPY-labeling protocol for 70S ribosomes and confirmed their conformational integrity using nano differential scanning fluorimetry (nanoDSF). Our microscale fluorescent system facilitates probing initiation at a variety of steps, since the role of magnesium ions and initiation factors upon 30S initiation complex formation. The same platform can be applied to investigate the effects of different compounds on translation initiation, as demonstrated for a number of antibiotics, aptamers, and antimicrobial peptides. Using this approach, we determined the antibiotic streptomycin dissociation constant for both 30S and 70S ribosomes, which proved identical at 0.3{+/-}0.1 M, and demonstrated the effect of the antimicrobial peptide rumicidin-1 on translation initiation. Offering a cost-effective and high-sensitivity alternative to conventional methods, this approach advances mechanistic understanding of prokaryotic translation and provides a versatile framework for the discovery of novel protein synthesis inhibitors.

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Uncovering Functional Distant Mutations by Ultra-High-Throughput Screening of Dehalogenases

Faldynova, H.; Kovar, D.; Jain, A.; Slanska, M.; Martinek, M.; Jakob, A.; Sulova, M.; Vasina, M.; Planas-Iglesias, J.; Marques, S.; Verma, N.; Vanacek, P.; Damborsky, D.; Badenhorst, C.; Buryska, T.; Chiu, F.; Majerova, M.; Kohutekova, T.; Kouba, P.; Sendlerova, N.; deMello, A.; Damborsky, J.; Sivic, J.; Bornscheuer, U.; Bednar, D.; Mazurenko, S.; Hernychova, L.; Marek, M.; Klan, P.; Stavrakis, S.; Prokop, Z.

2026-03-26 biochemistry 10.64898/2026.03.24.713925 medRxiv
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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

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Discovery and Development of First-in-Class Cereblon-Recruiting RIPK1 Degraders

Lu, D.; Yu, X.; Wang, J.

2026-04-14 pharmacology and toxicology 10.64898/2026.04.10.717852 medRxiv
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Receptor-interacting protein kinase 1 (RIPK1) is a critical regulator of programmed cell death and is implicated in various pathological conditions, particularly in mediating tumor resistance to immune checkpoint inhibitors (ICBs). In this study, we have pioneered the development of a novel cereblon (CRBN)-recruiting RIPK1 degrader, LD5095, through systematic optimization of linker and CRBN ligand portion. LD5095 demonstrates potent and selective RIPK1 degradation across cell lines, with rapid kinetics and sustained degradation over 72h post-washout. Functionally, RIPK1 degradation by LD5095 significantly sensitized Jurkat cells to TNF-induced apoptosis. Furthermore, LD5095 exhibited favorable pharmacokinetics, including metabolic stability and an extended half-life. Strikingly, in vivo, a single dose of LD5095 achieved durable RIPK1 degradation in xenograft tumors over 6 days. These findings underscore the potential of LD5095 as a chemical probe for studying RIPK1 biology and a promising candidate for cancer treatment.

8
Chemoproteomic Characterization of GPX4 Covalent Ligands and Targeted Degradation

Kadam, V. D.; Bai, G.; Mozes, C.; Guo, H.; Xue, Z.; Miao, Q.; Wang, J.; Li, M.; Li, F.; Nakada, D.; Tan, Z.; Zhang, X.; Teng, M.

2026-05-03 cancer biology 10.64898/2026.04.29.721679 medRxiv
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Despite intensive efforts, the ferroptosis gatekeeper glutathione peroxidase 4 (GPX4) remains difficult to selectively target due to stringent structural constraints surrounding its catalytic selenocysteine, which impose tight requirements on warhead reactivity and geometry. Here, leveraging a chemoproteomic approach, we characterize a potent and selective covalent GPX4 inhibitor featuring a pyrimidinylmethyl isourea warhead and define the chemical features underlying its proteome-wide selectivity. This chemotype enables tunable electrophile reactivity through steric and electronic modulation of leaving group ability, suggesting potential broader utility for targeting other recalcitrant proteins. Building on this scaffold, we further develop two selective GPX4 degraders - one CRBN-dependent and the other CRBN-independent - enabling complementary modulation of GPX4 through both inhibition and degradation. Together, these molecules expand the GPX4 chemical toolbox for more nuanced interrogation of GPX4 biology.

9
An Optimized RNF126-Targeting Covalent Handle for Molecular Glue Degraders

Modi, A.; Toriki, E. S.; Stieger, C. E.; Lau, E. A.; Song, C.; Chew, A.; Tsao, A.; Nishikawa, K.; McKenna, J.; Nomura, D. K.

2026-03-07 biochemistry 10.64898/2026.03.06.709959 medRxiv
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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.

10
HaloTag Ligand and HaloTag Protein engineering for a binary fluorescent turn-on probe

Gatin-Fraudet, B.; Pabst, U.; Olesen, C. H.; Baciu, B. C.; Birke, R.; Milles, S.; Broichhagen, J.

2026-05-15 synthetic biology 10.64898/2026.05.15.724826 medRxiv
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Protein labelling by covalent attachment of a specific substrate to a self-labelling protein tag has become a regular in the life sciences. Herein, we report the design of a two-component labelling system, comprised of a non-fluorescent difluorinated xanthene, called F2X, and a HaloTag mutant engineered for targeted reactivity towards F2X. Upon primary covalent locking of the ligand at the canonical aspartate residue, two proximal lysine residues located at the protein surface can undergo nucleophilic aromatic substitution with the F2X core, building a fluorescent rhodamine via triple-covalent fusion. We used a generalizable in silico pipeline for heuristic conformational sampling of covalent protein-ligand complexes to find suitable mutation sites, culminating in the curation of 7 double-lysine HaloTag mutants for targeted in vitro testing. Reaction with the best-performing mutant, HTPL161K_Q165K, is characterized by full protein mass spectrometry, fluorescence polarization fluorescence lifetime, and fluorescence anisotropy and rationalized by computational modelling. We showcase the system in single molecule microscopy, where obviation of post-labelling purification is a prime advantage when targeting recombinant proteins that may not be expressed in larger quantities, and employ F2X in living cells with reduced photobleaching. Lastly, a cell-impermeable version was obtained by means of sulfonation, exclusively targeting extracellularly exposed HTPKK fused to the neuromodulatory G protein-coupled receptor metabotropic glutamate receptor 2.

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Extreme Hydrophobicity of Cytotoxic Drugs Enables Design of Next Generation Antibody-Drug Conjugates Nanotherapeutics

Khyade, A.; Sharma, A.; Sandanaraj, B.

2026-05-04 pharmacology and toxicology 10.64898/2026.04.29.721383 medRxiv
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Antibody and protein-drug conjugates (XDCs) have emerged as promising cancer therapeutics, yet their clinical utility remains constrained by dose-limiting toxicities and narrow therapeutic windows. These safety challenges stem primarily from two factors: premature payload release during systemic circulation, and poor physicochemical properties inherent to the hydrophobic cytotoxic drugs they carry. Prior strategies attempted to address these limitations by appending water-soluble tags to reduce overall conjugate hydrophobicity, but achieved only modest improvements. As a result, the hydrophobic nature of cytotoxic payloads has remained a persistent obstacle in XDC development. Here, we report a fundamentally different chemical strategy that reframes this liability as a design opportunity. Rather than masking drug hydrophobicity, we exploit it as the driving force for self-assembly of facially amphiphilic protein-drug conjugates with programmable drug moieties (PDCs). In this architecture, the hydrophobic cytotoxic drug and the hydrophilic protein serve as the core and shell, respectively, spontaneously assembling into monodisperse, well-defined spherical protein nanotherapeutics of controlled size. This design principle transforms a longstanding physicochemical challenge into a functional engineering tool, enabling precise nanostructure formation without sacrificing potency. In vitro studies confirm that the resulting nanotherapeutics effectively kill cancer cells, establishing a strong foundation for further therapeutic development.

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Solid-Phase Synthesis of ProTide Fluorogenic Probes Enables Systematic Profiling of Carboxypeptidase Activity

Komatsu, T.; Minoda, M.; Uchida, T.; Hata, M.; Kanai, S.; Hiraide, H.; Kagami, Y.; Honda, K.; Urano, Y.

2026-03-12 biochemistry 10.64898/2026.03.10.710453 medRxiv
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Carboxypeptidases play diverse roles in physiological and pathological processes, yet comprehensive analysis of their activities in complex biological samples remains challenging. Here we report a solid-phase synthesis strategy for fluorogenic ProTide-based probes that enables systematic profiling of carboxypeptidase activities based on defined C-terminal amino acid motifs. By modular synthesis of dipeptide-fluorophore conjugates, we generated a focused probe set that revealed distinct substrate preferences among carboxypeptidases, including carboxypeptidase A and B family enzymes. Integration of these probes with a single-molecule enzyme activity assay allowed ultrasensitive detection of circulating carboxypeptidase activities in human blood samples. Application of this platform to clinical specimens demonstrated that specific carboxypeptidase activities are elevated in patients with pancreatic cancer compared with healthy controls, whereas closely related enzymes showed limited diagnostic value. These results establish a scalable chemical strategy for activity-based profiling of exopeptidases and highlight circulating carboxypeptidase activity as a functional enzymatic signature associated with pancreatic cancer.

13
A bio-orthogonal and covalent 5 kDa small protein tag

Pabst, U.; Rossius, J.; Olesen, C. H.; Birol, M.; Broichhagen, J.

2026-04-10 synthetic biology 10.64898/2026.04.10.717487 medRxiv
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Precise and minimally perturbative protein labelling remains a key challenge for studying biomolecular function in living systems. Here, a minimal way to specifically label proteins based on SNAP-tag and intein-mediated protein splicing reaction is introduced. Termed CLUSTER (for Chemical Label-Unfold-Splice Technology Enables Recombination), this chimeric platform supports efficient labelling across diverse targets in living cells by retaining a fluorescent, 5 kDa sized peptide on a fusion protein of interest after splicing. A bacterial screening workflow was developed to optimize the reaction efficiency and construct design. Quantitative characterization using fluorescence polarization provides mechanistic insight into labelling efficiency and dynamics, while molecular dynamics simulations elucidate its stability, grasping the intricate nature of protein behaviour upon covalent labelling. This bio-orthogonal labelling technology allows for a versatile and minimally invasive approach for protein labelling, providing a powerful tool to probe protein behavior in native cellular systems.

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Refined USP25/28 inhibitors with improved selectivity towards c-Myc driven squamous lung cancer cells

Pinto-Fernandez, A.; Heride, C.; Turnbull, A. P.; Krajewski, W. W.; Bell, C.; Pedroso, D.; Smith, V.; Mullee, L.; Varca, A.; Charlton, T.; Jones, D. T.; McAllister, T.; Fischer, R.; Guerrero, E. N.; Ebner, D.; Kawamura, A.; Kim, S.; Guerin, D.; Hammonds, T. R.; Kearns, J.; Jones, N.; Buhrlage, S. J.; Urbe, S.; Komander, D.; Clague, M.; Kessler, B. M.

2026-03-20 cancer biology 10.64898/2026.03.17.712179 medRxiv
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The ubiquitin specific protease 28 (USP28) is implicated in tumorigenesis by controlling the turnover of the oncogene c-MYC and the ubiquitin ligase FBW7. Here, we describe small molecule inhibitors of USP25 and USP28, leading to cancer cell cycle arrest and death. However, genetic deletion of USP25/28 does not replicate this effect. An integrated -omics approach revealed off-target effects for thienopyridine carboxamide compounds upon the translation apparatus. Chemoproteomics and CRISPR-GOF analyses suggested binding of the compound to a region near the ribosome complex polypeptide exit tunnel. Structural analysis of a USP28-inhibitor complex enabled the design of modified USP25/28 inhibitor molecules which minimized translation-related off-target effects. In distinction to earlier compounds, the optimized inhibitors were non-toxic to breast cancer cells yet retained potent anti-proliferative activity in squamous lung carcinoma cells, where USP28 is associated with disease progression. Together, our results demonstrate that refined USP25/28 inhibitors can selectively suppress tumor growth by targeting the TP63-FBW7-c-MYC signaling axis, offering a more precise therapeutic strategy for treating squamous lung cancers whilst minimizing undesired cytotoxicity.

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FLEX: A heparin-binding fusion partner engineered from fibroblast growth factor 1 to enhance protein expression, solubility and purity

Mistry, R.; Harris, J. A.; Byrne, D. P.; Morris, R.; Li, Y.; Theron, C. W.; Kaye, S. B.; Fernig, D. G.; Foulkes, D. M.

2026-03-18 biochemistry 10.64898/2026.03.17.712271 medRxiv
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Expression of aggregation-prone, unstable, or cytotoxic recombinant proteins remains a major bottleneck in both academic and industrial research. Although solubility-enhancing affinity tags can improve expression, they often compromise purification stringency, increase construct size, or require additional downstream processing. Here we report FLEX, a compact 15.5-kDa dual-function fusion tag engineered from human fibroblast growth factor-1 (FGF1) that integrates intrinsic protein-stabilising properties with high-affinity heparin binding. Structure-guided computational redesign of the FGF1 scaffold reduced exposed hydrophobic residues, removed flexible protease-susceptible regions, and expanded the electropositive surface while preserving the canonical heparin-binding interface. FLEX exhibits markedly improved thermal and chemical stability relative to wild-type FGF1 together with enhanced heparin affinity, enabling high-stringency washing and improved purity in a single affinity step. We demonstrate the broad utility of FLEX by expressing and purifying a panel of challenging proteins in Escherichia coli, including cytotoxic Pseudomonas aeruginosa virulence factors that are difficult to obtain in active form. Unexpectedly, FLEX also performed robustly in mammalian expression systems, where transiently expressed FLEX-tagged proteins were recovered at higher yield and purity than with gold standard Myc and Strep tags, including difficult targets such as Tribbles 3 (TRIB3). These findings establish FLEX as a versatile affinity-and-stabilisation tag that improves expression and purification across diverse systems, providing a practical new tool for structural, biochemical, and translational studies of otherwise intractable proteins.

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Mirror-image mRNA display uncovers isoform-selective D-peptide macrocycles targeting a cryptic KRAS pocket

Mitcheltree, M. J.; Boo, N.; Boyer, N.; Brown, Z. Z.; Chai, X.; Duggal, R.; Garrigou, M.; Hayes, R. P.; Johnston, J. M.; Josien, H.; Lacey, B.; Lim, S.; Lin, S.; Mayhood, T.; Ogawa, H.; Orth, P.; Reid, P. C.; Shigeta, R.; Soriano, A.; Tomiyama, T.; Venkatachalam, G.; Zhou, Y.; Bennett, D. J.; Partridge, A. W.; Biswas, K.

2026-05-22 cancer biology 10.64898/2026.05.20.726527 medRxiv
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Activating KRAS mutations drive millions of cancers diagnosed worldwide,1 yet for decades this oncoprotein was deemed "undruggable", reflecting the challenge of discovering molecules capable of perturbing its complex biological functions, and of translating these discoveries into effective cancer therapeutics.2 Recent advances propelled by innovative screening have identified diverse modalities that bind at or near the switch-II pocket (SII-P) of RAS proteins, including molecular glues,3 macrocyclic peptides,4 fragment-derived small molecules,5 and approved therapies that covalently target KRASG12C.6,7 Unfortunately, resistance to approved therapies has emerged,8,9 highlighting the need for molecules that engage new or underexploited binding sites on RAS oncoproteins with mechanisms complementary to established SII-P inhibitors.10,11 Here we show that mirror-image mRNA display12 enabled the discovery of all-D macrocyclic peptide ligands targeting a cryptic RAS back pocket (CRB-P).13 These ligands engage KRAS(OFF) and KRAS(ON) with equal affinity, exploit a single-residue difference among isoforms to bind KRAS selectively, and successfully inhibit oncogenic signaling in KRAS-mutant cells through a mechanism distinct from SII-P binders. Mirror-image screening directly afforded nanomolar peptide ligands stable toward cellular proteolysis and delivered probes targeting distinct epitopes not accessible by homochiral peptide-display methods. Together, these findings establish the CRB-P as a specifically druggable and mechanistically differentiated site on KRAS with potential for combination with emerging RAS-targeting therapies and substantiate mirror-image mRNA display as a strategy for discovering stable all-D macrocyclic peptides targeting previously inaccessible epitopes on challenging targets.

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Activated Caso₄-Induced Vacuolation As A Quantitative Platform For Phagocytosis-Driven Drug Screening

Goswami, V.; Faiz, A.; Dutt, G.; Kumar, A.; Bashir, S.; Gupta, A.; Das, S.; Joshi, A.; Das, S. K.

2026-03-13 cell biology 10.64898/2026.03.11.711143 medRxiv
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Cytoplasmic vacuolization is a fundamental process associated with phagocytosis, lysosomal acidification, and autophagy, yet robust in-vitro models for its quantification and pharmacological screening remainlimitedor insufficiently established. In this study, we demonstrate that thermally activated calcium sulfate (ACS) induces extensive vacuolation across mammalian cell lines including HeLa, RAW 264.7, 3T3-L1, and SH-SY5Y, thereby establishing a versatile platform to study vacuole biogenesis. To ensure reproducibility, particle heterogeneity was addressed using sedimentation-based fractionation, with homogeneous suspensions obtained at the 5th minute producing stable and consistent vacuole formation. Vacuolation was subsequently quantified by Neutral Red (NR) uptake, dose and time dependent response analyses confirmed direct correlation between ACS concentration and vacuole induction. The assay was validated with bafilomycin A1 (BFA1), a selective V-ATPase inhibitor, which served as a positive control and demonstrated concentration and time dependent inhibition of vacuole formation and acidification. Building on this framework, ten commercially available drugs were screened, revealing distinct profiles ranging from early cytotoxicity, strong vacuole inhibition to partial suppression or negligible effects. This dual capacity to discriminate between vacuole inhibition and cytotoxic responses highlights the utility of ACS-induced vacuolization as a sensitive and scalable in vitro platform. Collectively, our findings position this system as a tractable assay for mechanistic studies of vacuole biology and a functional screening tool for identifying modulators of lysosomal and phagocytic pathways relevant to infection, Lysosomal Disorders, and Phagocytotic dysfunction disorders. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/711143v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@e5b920org.highwire.dtl.DTLVardef@1dd1072org.highwire.dtl.DTLVardef@62ae59org.highwire.dtl.DTLVardef@a468bf_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Mapping the Modification Landscape of MHC-I Epitopes: A Framework for Immunogenic Peptidomimetic Antigen Design

Newkirk, S. E.; Kelly, J. J.; Hourn, N.; Bhandari, S.; Spencer, N.; Pires, M.

2026-03-10 immunology 10.64898/2026.03.06.710184 medRxiv
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Peptide-based cancer vaccines offer a promising strategy to target tumor-specific neoantigens, yet their clinical translation is restricted by poor metabolic stability, limited intracellular permeability, and stringent requirements for MHC-I binding and T cell receptor (TCR) recognition. Although peptidomimetic modifications have been widely explored to improve pharmacokinetics, their impact on antigen presentation and immune recognition remains poorly understood. Here, we systematically evaluate backbone N-methylation, peptoid substitution, and stereochemical inversion using the canonical MHC-I epitope from ovalalbumin (OVA), SIINFEKL. Through integrated assays measuring pMHC-I stability, T cell activation, cellular permeability, and serum stability, we demonstrate that tolerance to peptidomimetic modification is highly position-dependent. Specific N-methylated variants retained MHC binding and TCR engagement while exhibiting enhanced cytosolic accumulation, whereas peptoid and stereochemical substitutions were generally disruptive to TCR recognition and membrane permeability. Guided by these insights, we designed combinatorially modified peptides to probe the balance between immunogenicity and pharmacokinetic improvement, revealing that multiple modifications exert non-additive effects on immune recognition. Collectively, these findings establish design principles and provide a framework for balancing immune recognition with enhanced stability and permeability in peptidomimetic antigen design.

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Tuning the Structural Properties of a Single-Domain Antibody Scaffold for Improved Fibroblast Activation Protein Targeting

Ott, K.; Gallant, J.; Kwon, O.; Adeniyi, A.; Bednarz, B.; Barrett, K.; Rosenkrans, Z.; Mixdorf, J.; Engle, J.; Aluicio Sarduy, E.; Hernandez, R. T.; LeBeau, A.

2026-03-13 cancer biology 10.64898/2026.03.11.711127 medRxiv
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Fibroblast activation protein (FAP) is an attractive target for the development of cancer theranostics due to its selective expression on cancer-associated fibroblasts (CAFs). While a number of small-molecule FAP inhibitors (FAPIs) have been developed, few biologics have been investigated as FAP targeting vectors. Camelid-derived single-domain antibodies, or variable-heavy-heavy domains (VHHs), offer a compelling alternative, combining high affinity with versatile engineering options. In this study, we first identified a novel anti-FAP VHH, F7, from an affinity-matured camelid phage display library. To investigate how valency and molecular weight affected target engagement and in vivo properties, F7 was engineered into three formats: a monomer (F7), a tethered dimer (F7D), and an Fc-fusion protein (F7-Fc). All three were specific for FAP with the two bivalent constructs demonstrating picomolar affinity. Positron emission tomography imaging in FAP-positive xenograft models revealed distinct pharmacokinetic profiles across constructs with notable differences in tumor uptake and clearance. F7 had rapid uptake and clearance resulting in significantly higher tumor uptake than FAPI-46. Low molecular weight bivalent F7D demonstrated similar kinetics but was retained by the tumor resulting in a high tumor-to-blood ratio with secondary uptake limited to clearance organs. The largest construct, F7-Fc, resulted in the highest tumor uptake and allowed for longitudinal imaging. Absorbed dose calculations confirmed that tumors received significantly higher radiation doses compared to normal tissues. These findings demonstrate that tuning VHH scaffold size and valency can improve biodistribution and retention, establishing F7-based constructs as promising targeting vectors for FAP.

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Italia: A PARP-Directed Auger Electron-Emitting Agent for Targeted Radionuclide Therapy of Cancer

Unnikrishnan, S.; Rua, C.; Li, G.; Delgado Mayenco, N.; Hernandez Cano, L.; Bozan, G.; Patmanidis, I.; Simwaka, S.; Kurniawan, A.; Szymanski, W.; de Vries, E. F. J.; Elsinga, P. H.; Farinha Antunes, I.; Destro, G.; Cornelissen, B. T.

2026-03-17 cancer biology 10.64898/2026.03.13.711622 medRxiv
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Poly(ADP-ribose) polymerase 1 (PARP1) is a central mediator of DNA damage repair and an established therapeutic target in homologous recombination-deficient cancers. Radiolabelled PARP inhibitors provide a strategy to deliver cytotoxic radiation directly to tumour DNA by exploiting PARP overexpression and trapping at sites of DNA damage. Here, we describe the design, radiosynthesis, and in vitro evaluation of [123I]Italia, a talazoparib-derived Auger electron-emitting agent for PARP-targeted radionuclide therapy. Stereochemically pure [123I]Italia, (8S,9R)-5-fluoro-8-(4-(iodo-123I)phenyl)-9-(1-methyl-1H-1,2,4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one was synthesised in one step via copper-mediated iodo-deboronation, achieving activity yields >80% and molar activities >6.2 {+/-} 3.1 GBq/{micro}mol (n=8). UPLC analysis confirmed radiochemical purity >97%. Italia exhibited potent PARP1 inhibition (IC50 0.48 nM) and in silico predicted binding affinity comparable to talazoparib. In a panel of PARP-expressing cancer cell lines, [123I]Italia demonstrated highest uptake at 60 min, PARP-selective uptake, predominant nuclear localisation (up to 60% of added activity) and chromatin association consistent with PARP trapping (up to 15% of total activity recorded). Uptake was reduced more than 50-fold by addition of an excess of any PARP inhibitor (e.g. olaparib, talazoparib, and rucaparib) and in PARP1 knockout cells, confirming target specificity. Clonogenic assays showed a marked, added activity-dependent reduction in survival of PARP-expressing cells following a brief one-hour exposure, whereas PARP1-deficient cells were resistant. Collectively, these findings identify [123I]Italia as a promising PARP-targeted Auger electron-emitting theranostic candidate that warrants further in vivo evaluation.