Cell Chemical Biology

N-linked Fc galactosylation drives variability in therapeutic mAb quality, affecting complement-dependent cytotoxicity and ADCC. Current control strategies suffer from narrow ranges, productivity loss, or unwanted glycoforms. Here, we combine metabolic and cellular glycoengineering by feeding 2-deoxy-2-fluorogalactose (2FG) to CHO cells engineered for hypergalactosylation via COSMC knockout and {beta}4-galactosyltransferase overexpression (C /GT+), achieving broad, tuneable control of Fc {beta}4-galactosylation. In DP12 C-/GT+ cells, a split-feed regimen spanned a wide galactosylation range (95-46%) but generated substantial aglycosylated and Man5 glycoforms. The same regimen in a second host, VRC01 C-/GT+, gave only a narrow range, indicating 2FG dosing does not transfer directly across cell lines. Based on a proposed mechanism where 2FG is metabolised via the Leloir pathway into inhibitory fluorinated nucleotide-sugar intermediates, we developed a cell-normalised, multi-bolus feeding strategy that substantially broadened control in VRC01 C-/GT+ cells while suppressing aglycosylation and Man5 formation. In a fed-batch Ambr(R) 250 process, this strategy achieved comparable galactosylation reduction with roughly ten-fold less 2FG, showing that the fraction of mAb secreted after feeding is a key determinant of control strategy efficiency. Across the resulting glycoform range, Bio-Layer Interferometry identified Fc {beta}4-galactosylation as the strongest correlate of Fc{gamma}RIIIA (CD16a) binding affinity (R2 = 0.92). Together, these findings establish combined metabolic and cellular glycoengineering as a platform for controlling mAb galactosylation across a broad range, with potential to fine-tune downstream pharmacological activity.

Macrophages are critical regulators of inflammation and tissue homeostasis, yet aberrant macrophage activation contributes to a wide spectrum of inflammatory and malignant diseases. Therapeutic strategies that directly reduce macrophage numbers have shown promise, but macrophage survival pathways remain incompletely defined, limiting the development of targeted therapeutic strategies. Here, we establish a high-throughput screening platform to identify small molecule inhibitors that impair macrophage survival. Screening a library of more than 2,000 targeted compounds in a cell survival assay, combined with in silico and in vitro analysis of macrophage specificity, revealed the identification of three potent inhibitors: BIX-01294, GSK-J4, and Masitinib. All three compounds downregulated leukemia inhibitory factor receptor (LIFR), whose inhibition markedly reduced macrophage viability. In vivo, these inhibitors effectively depleted large peritoneal macrophages, ameliorated key symptoms of macrophage activation syndrome (MAS), and suppressed tumor growth in a syngeneic transplanted melanoma model as well as in an autochthonous lung cancer model. Together, these findings identify small molecule-mediated macrophage depletion as a promising therapeutic strategy and establish an experimental approach to uncover regulators of macrophage survival.

DNA mismatch repair (MMR) maintains genome stability but paradoxically drives expansion of pathogenic repeats responsible for trinucleotide repeat disorders. Attenuating repeat instability through targeted inhibition of MMR is therefore a therapeutic strategy of interest; however, progress is constrained by a lack of robust methods for defining and isolating MMR subpathways. We exploited features of prime editing to profile the effects of core MMR genes on thousands of programmed DNA mispairs in cells and resolved distinct MMR processes, including a noncanonical, loop-directed mechanism. Guided by these results, we built a set of scalable reporters that detect loss of separable MMR processes and screened ~72,000 small molecules for activity against MutS{beta}-directed MMR. This effort identified a novel series of MutS{beta} inhibitors that reduced (CAG)n expansion in a cell model. Altogether, this study establishes several methods for systematically interrogating MMR, with demonstrated capacity to identify inhibitors of therapeutic value.

Isocitrate dehydrogenase 1 (IDH1) catalyses the interconversion of isocitrate and -ketoglutarate and is overexpressed in several cancers, supporting tumour survival and treatment resistance. Inhibitors targeting the oncogenic mutant forms of IDH1 also inhibit the wild-type (WT) protein, but lose substantial potency due to greater competition with native substrates (isocitrate and Mg2+). We hypothesised that a covalent inhibitor may be more effective at overcoming the higher substrate affinity of wild-type IDH1. Here, a covalent fragment-based approach was used to develop IDH1-C269 selective inhibitors which prevent the key regulatory segment from forming an -helix required for catalytic competency. Following the identification of C269-selective fragments, we used X-ray crystallography to characterise IDH1-fragment bound complexes and guide structure-based design efforts. Inspired by the unexpected detection of bound isocitrate molecule in an X-ray crystal structure, fragment expansion yielded a series of compounds exploiting both an adjacent site and a unique water-mediated hydrogen bonding network. This series achieved strong potency (reaching IC50 = 47.5 nM, a 155-fold improvement in potency relative to the original fragment), retained activity in the presence of competing Mg2+, showed selectivity against IDH2 and reduced NADPH concentrations in a relevant PDAC cell model. Together, these findings present a mechanistic rationale for the covalent targeting of wild-type IDH1 and provide structurally validated inhibitors for further development.

Dysregulation of insulin-like growth factor (IGF) signaling contributes to diverse human diseases. Therapeutic strategies have largely targeted the IGF-1 receptor, but the complexity of the IGF system has limited their clinical efficacy. Pregnancy-associated plasma protein-A (PAPP-A) is a secreted metalloproteinase that regulates local IGF signaling through proteolytic cleavage of IGF-binding proteins (IGFBPs) and represents an attractive therapeutic target. Here, we report the first synthetic PAPP-A inhibitors designed to target the enzyme active site using an IGFBP-5-derived anchor sequence. Replacing the scissile bond with phosphinate or phosphonate moieties yielded potent and selective PAPP-A inhibitors. Cryo-electron microscopy revealed the molecular basis of inhibition and key active-site interactions. The compounds inhibited cleavage of IGFBP-4 and IGFBP-5, two physiological PAPP-A substrates. They suppressed IGF-1 signaling in A549 lung cancer cells, with efficacy comparable to the endogenous PAPP-A inhibitor stanniocalcin-1. They also inhibited Papp-aa-dependent IGF signaling and cell proliferation in wild-type and stc1a-/- mutant zebrafish in vivo in a dose-dependent manner. Together, these findings establish the first class of synthetic, selective PAPP-A inhibitors capable of modulating IGF signaling. They provide new chemical tools for studying and modulating pathological IGF signaling and offer new directions for developing PAPP-A-targeted therapeutic strategies.

Triple-negative breast cancer (TNBC) remains a major clinical challenge due to a lack of effective interventions and severe drug resistance. Disrupting tumor metabolism using nitric oxide (NO) donors to drive ferroptosis represents a promising therapeutic strategy. Here, we developed 3A72, a novel furan-coumarin-based NO donor with potent anti-TNBC efficacy. In vitro and in vivo studies demonstrated that 3A72 significantly suppresses TNBC cell proliferation and restricts xenograft tumor growth. Notably, its efficacy matches the first-line drug paclitaxel but with enhanced safety and reduced systemic toxicity. Mechanistically, 3A72 induces ferroptosis in triple negative breast cancer (TNBC) cells via a synergistic dual-pathway mechanism. Initially, 3A72 releases intracellular NO to trigger cytoplasmic calcium overload, followed by high-affinity binding to both inositol 1,4,5-trisphosphate receptor (IPR) and acyl-CoA synthetase long-chain family member 4 (ACSL4). Binding to IP3R provokes mitochondrial calcium overload and a massive burst of reactive oxygen species (ROS), while concurrent ACSL4 activation drives essential membrane phospholipid remodeling. Crucially, our transcriptomic and structural predictions reveal that while ACSL4 exhibits a broader distribution across organelle membranes, its functional association with IP3R spatially converges at the endoplasmic reticulum membranes associated with mitochondria (MAMs). This subcellular niche closely couples IPR-mediated ROS generation with ACSL4-driven lipid remodeling, accelerating lethal malondialdehyde (MDA) accumulation and triggering irreversible ferroptosis. Overall, these findings highlight the MAMs calcium-lipid metabolic hub as a promising structural scaffold for antitumor drug development.

Protein kinase CK2 (CK2), a ubiquitously expressed serine/threonine kinase, has emerged as a key host factor exploited by several viruses, including Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we investigate the role of CK2 subunits in SARS-CoV-2 replication and evaluate the antiviral potential and broad-spectrum anti-coronavirus activity of two CK2 inhibitors: the previously described ATP-competitive inhibitor CX-4945 and a newly developed, highly selective bivalent inhibitor, AB668. The siRNA-mediated knockdown of CK2 subunits significantly reduced SARS-CoV-2 replication, highlighting its essential role in the viral lifecycle. Co-immunoprecipitation assays revealed that the SARS-CoV-2 nucleoprotein interacts with CK2. Furthermore, bio-layer interferometry assays demonstrated that the nucleoprotein specifically binds to the tetrameric CK2 holoenzyme (CK22{beta}2) but not to individual CK2 or CK2{beta} subunits. Pharmacological inhibition of CK2 with AB668 exhibited potent antiviral activity, significantly reducing viral replication by targeting a pre-replicative or RNA-replicative step of the viral life cycle. Importantly, AB668 displayed broad-spectrum antiviral activity, effectively inhibiting both HCoV-OC43 ({beta}-CoV) and HCoV-229E (-CoV). In summary, our findings establish CK2 as a critical host factor for SARS-CoV-2 replication and identify AB668 as a promising candidate for broad-spectrum antiviral therapy. With its high selectivity, minimized off-target effects, and efficacy against multiple coronaviruses, AB668 represents a valuable chemobiological and therapeutic tool.

Therapeutic inhibition of the RAS/MAPK cascade, an oncogenic driver in over one-third of human cancers, has been limited by a core trade-off: effective pathway blockade in tumors versus dose-limiting toxicity in normal tissues. Although Type 1.5 RAF inhibitors successfully mitigated this trade-off in BRAF-monomer-driven tumors, an equivalent strategy has been lacking for RAF-dimer-driven cancers, including those with RAS mutations. Here, we characterize ELV-3111, a next-generation, potent, and selective Type 1 RAF inhibitor that overcomes this limitation via a distinct mechanism of action. ELV-3111 induces paradoxical MAPK hyperactivation in normal tissues by binding RAF and promoting the active conformation (priming) followed by rapid dissociation (fast off-rate), a biochemical feature that spares RAS-mutant tumors, where RAF is already primed. In these and other RAF dimer-driven tumor models, ELV-3111 achieves potent and selective MAPK and growth suppression. When combined with a MEK inhibitor, ELV-3111 enables complementary pharmacology: additive inhibition in tumors and compensatory effects in normal tissues. The combination produced durable regressions across RAS-mutant and BRAF-mutant models, including a RAS-mutant model refractory to current therapies, while maintaining favorable tolerability. Thus, we uncover a generalizable mechanism that enables Type 1 RAF inhibitor plus MEK inhibitor combinations to achieve tumor-selective MAPK suppression, with the potential to inform targeted therapy design.

Exploring the ability of metabolic enzymes to interact with diverse small molecules can provide insights into their ligand recognition and activity regulation. Glucose-6-phosphate isomerase (GPI) is an enzyme that catalyzes the second step of glycolysis, a critical node that links glucose metabolism to other cytosolic pathways, such as pentose phosphate and hexosamine biosynthetic pathways. Despite its importance in cellular metabolism, little is known about the broad ligandability of GPI. Here, we performed a structure-based virtual screening using molecular docking to identify new modulators predicted to engage with the human GPI active site. Enzyme kinetic and binding studies confirmed eleven compounds as active-site binders of GPI, exhibiting inhibitory activities and binding affinities in upper micromolar to sub-millimolar range. The binding of several ligands to GPI active site was further supported by X-ray crystallographic data. In addition, in vitro assays were performed to evaluate the modulatory effects of the GPI hits on cellular glycolysis and viability. The identified inhibitors included the mono-phosphorylated metabolite of ribavirin, which inhibited glycolytic flux and cell viability; two compounds with phosphate bioisosteres; and endogenous phosphate-containing metabolites from the pentose phosphate, hexosamine, nucleotide, and mevalonate pathways. Collectively, these findings expanded the repertoire of human GPI ligands and revealed previously unrecognized GPI-metabolite interactions that may contribute to modulation of glycolytic flux.

Cytokines can elicit potent antitumor immunity, but their clinical use is often limited by systemic immune activation and dose-limiting toxicity. Protease-responsive masking offers a way to improve selectivity by linking cytokine activity to disease-associated protease cleavage, but current approaches have faced several challenges. Here we describe a de novo protein design strategy for generating protease-activatable cytokine prodrugs that overcomes these challenges. We use this strategy to design and characterize cytokine prodrugs and well-behaved AND-gated split systems that require both target-dependent colocalization and proteolytic unmasking to generate active cytokines. In challenging syngeneic tumor models, our IL-21 prodrugs reduced treatment-associated toxicity while maintaining antitumor efficacy.

MAPK-activated protein kinase 2 (MAPKAPK2, MK2) is a downstream substrate of p38 MAPK that regulates inflammatory signaling and cytokine synthesis, making it an attractive therapeutic target. Although several crystal structures of MAPKAPK2 with ATP-competitive inhibitors have supported drug discovery, structural elucidation of selective non-ATP-competitive inhibitors has remained challenging. MK-25 is a non-ATP-competitive furan-2-carboxamide MAPKAPK2 inhibitor developed at Merck to overcome the selectivity and cellular-efficacy limitations of ATP-competitive chemotypes. Here, we show through isothermal titration calorimetry that MK-25 binds the activated MAPKAPK2, consistent with state-dependent allosteric binding. To determine the binding mode of MK-25, we solved a 2.8 A resolution crystal structure of an activated MAPKAPK2 construct in ternary complex with the ATP-site inhibitor PF-3644022 and a bromo-analogue of MK-25. The ligand occupies a pocket in the C-lobe overlapping the protein-substrate recognition region and formed through rearrangements of D and G helices and the activation segment. These interactions are consistent with the structure-activity relationships reported for the furan-2-carboxamide chemotype and identify a ligandable allosteric pocket that may facilitate future structure-guided design of selective, non-ATP-competitive MAPKAPK2 inhibitors.

Fatty acid synthase (FASN) is the sole enzyme capable of lipogenesis in cells and is upregulated in many cancers. Herein we report the discovery and development of SBP-5917 (78S), a novel, reversible, small-molecule probe which targets the thioesterase (TE) domain of FASN. SBP-5917 and other compounds in the series possess IC50 < 1 M and < 5 M for inhibiting recombinantly purified FASN-TE and cellular FASN respectively. Co-crystal structures of our inhibitors bound to the FASN-TE domain show that they are positioned in the substrate tunnel of the enzyme. Biochemical and biophysical analyses quantify the strength of compound binding and demonstrate their selectivity for FASN-TE. Preliminary pharmacokinetic studies indicate promising in vivo potency for many of the compounds in the series. SBP-5917 is the first structurally validated, reversible inhibitor of FASN-TE with demonstrated cellular target engagement and can serve as a chemical probe to investigate FASN as a therapeutic target.

Reactivation of telomerase confers immortality to approximately 90% of human tumors by enabling continuous elongation of the DNA at chromosome ends, or telomeres. The telomerase catalytic subunit TERT adds TTAGGG repeats using a portion of the telomerase RNA component hTR as a template. Because telomerase is inactive in most normal somatic cells, it remains an attractive therapeutic target; however, no telomerase inhibitor has yet demonstrated robust clinical efficacy with acceptable safety. Here we evaluate thiomorpholino oligonucleotides (TMOs) as a new class of antisense oligonucleotides targeting the template region of hTR. TMOs incorporate morpholino rings and phosphorothioate linkages, which enhance nuclease resistance, RNA binding and nuclear uptake. Two anti-hTR TMOs inhibited telomerase activity in vitro with an IC50 below 1 nM, whereas two control TMOs were at least 100-fold less active. HeLa cells treated with anti-hTR TMOs showed progressive telomere shortening, detectable after one week of treatment. Growth inhibition was observed after substantial telomere erosion, and both telomere length and proliferation recovered upon withdrawal of TMOs. These findings establish TMOs as a promising new chemistry for telomerase-targeted therapeutics.

In a previous screen for compounds that inhibit Plasmodium falciparum merozoite invasion of red blood cells, we identified the Medicines for Malaria Venture compound MMV006833. This compound inhibits PfSTART1, a protein implicated in the expansion of the nascent parasitophorous vacuole membrane following invasion, to accommodate the developing ring-stage parasite. Live-cell lattice light-sheet microscopy of invading merozoites revealed that mNeonGreen-tagged PfSTART1 is released from structures within the merozoite into the nascent parasitophorous vacuole approximately 109 seconds after invasion. Expansion microscopy of PfSTART1-HA merozoites further showed that these punctate PfSTART1-containing structures do not colocalise with known secretory organelles (rhoptries, micronemes and dense granules). Although analogues of MMV006833 are highly potent against P. falciparum, they were previously found to be ineffective against P. berghei parasites in the mouse malaria model. Here, we demonstrate that PbSTART1 is highly resistant to MMV006833 and its analogues when expressed in P. falciparum, indicating that structural differences between the orthologous proteins reduce inhibitor potency. The crystal structure of PfSTART1 in complex with WEHI-991 revealed the molecular basis for inhibition and provided a structural explanation for the reduced potency of this family of compounds against P. berghei. To sensitise P. berghei parasites to MMV006833 analogues, the parasites were engineered to express PfSTART1; however, these chimeric parasites remained insensitive to the compounds. This suggests that factors beyond target engagement, such as compound half-life or bioavailability, contribute to the lack of efficacy observed in the mouse malaria model.

Abstract Peptide lasso-grafting strategies enable the transfer of established pharmacophores into compact protein scaffolds but often require optimization to preserve target binding and biological activity. Here, we report Random in-vitro Protein single-Loop Engineering (RiPLE), an mRNA-display strategy for the direct discovery of engineered ubiquitin binders, termed U-bodies, from a library containing a fully randomized surface loop of variable length. Using receptor tyrosine kinase-like orphan receptor 1 (ROR1) as a model target, we generated U-bodies through RiPLE and compared them with lasso-grafted U-bodies derived from a previously identified ROR1-binding macrocyclic peptide. Both approaches yielded U-bodies bearing single-digit nanomolar affinity to ROR1; however, RiPLE converged on de novo binding sequences that were distinct from the parental peptide. Notably, most selected U-bodies exhibited strong selectivity for ROR1 over the closely related receptor ROR2, whereas the parental peptide bound both receptors with high affinity. Representative ROR1-binding U-bodies also inhibited wound closure in ROR1-expressing MDA-MB-231 cells without detectable cytotoxicity. Applying RiPLE to the heterotrimeric G-protein subunit (GS) similarly yielded high-affinity binders and revealed sequence convergence patterns distinct from lasso-grafting. Together, these results establish RiPLE as a powerful and complementary alternative to peptide-guided lasso-grafting, enabling de novo evolution of functional binding surfaces directly within their final protein scaffold.

Antisense oligonucleotides (ASOs) inducing exon-skipping during pre-mRNA splicing offer promising treatment for diseases such as Duchenne muscular dystrophy. Recently, dual-targeting ASOs that simultaneously bind two splicing regulatory sequences have been shown to improve exon-skipping efficiency. Current ASOs are designed to interact with target RNAs solely based on Watson-Crick base pairing. Here we report the development of dual-targeting three-dimensional bridge (3D-bridge) ASOs in which tertiary interactions are engineered to increase target-binding affinity and the number of target residues occupied. We designed a 3D-bridge ASO for skipping exon 44 of dystrophin mRNA and biochemically validated its enhanced binding affinity for the target RNA over a similar ASO with the tertiary interactions disrupted. We subsequently optimized the 3D-bridge ASO by varying its ends and ribose chemical modifications using patient-derived induced directly reprogrammed myotubes and identified an LNA/DNA mixmer as the most potent. We further demonstrate enhanced exon-skipping efficacy and potency of the 3D-bridge ASO compared to previously reported ASOs in myotubes differentiated from patient-derived primary myoblasts and MyoD-reprogrammed fibroblasts harboring mutations amenable to reframing through exon 44 skipping. In conclusion, the 3D-bridge ASO technology improves the current dual-targeting design, demonstrating the utility and power of structure-based ASO design methods.

The ability to map protein interactomes and organelle proteomes is foundational for achieving a molecular understanding of living cells. Proximity labeling (PL) provides a powerful strategy for this, but existing enzymes and photocatalysts are limited by their spatial resolution, reliance on biotin, and/or in vivo compatibility. Here we report FlexID, an engineered promiscuous ligase that catalyzes the rapid attachment of diverse small-molecule probes to proximal endogenous proteins. Critically, FlexID operates through a zero-radius, direct-contact mechanism, offering superior spatial precision compared to existing PL tools. We engineered FlexID by combining the strengths of sequence- and structure-trained computational models to enhance its catalytic activity and structural stability. Biophysical analysis revealed that specific conformational changes in FlexID improve its ability to recognize diverse target proteins while simultaneously preventing the premature release of the reactive intermediate. We demonstrate FlexID's versatility through in vivo proximity labeling, comprehensive organelle proteome mapping, and a high-throughput, fluorescence-based screen for molecular glues. Our work shows that computational methods can be harnessed to create mechanistically distinct PL enzymes and establishes FlexID as a flexible, high-resolution tool for mapping protein interactions and proteomes in living cells.

Many therapeutically relevant signaling pathways are sensed inside the cell, yet a modular synthetic biology platform for responding to intracellular signaling at the post-translational level is lacking. Signaling pathways control the nuclear localization and activity of native transcription factors via phosphorylation of nuclear localization/export or cytoplasmic anchor sequences. Here, we apply this concept to develop a platform of nucleocytoplasmic localization tags (NCtags) that control the nuclear translocation of a synthetic transcription factor (synTF) for transgene induction in engineered cells. We identify human-based synTF components that are basally cytoplasmic and induce transgenes under the control of NCtags with minimal background. We demonstrate the modular nature of this platform through transcriptional reporter induction in response to a calcium-inducible NFAT-derived NCtag, and development of novel NCtags responsive to hyperosmolarity, cAMP, or logical combinations of cAMP and calcium. Multiple factors in the tumor microenvironment elevate cAMP in T cells, leading to reduced function. We demonstrate that NCtag-synTF fusions expressed in T cells can respond to endogenous sources of cAMP or calcium in breast cancer spheroids to induce transgene expression. Our use of human components and an all-in-one lentiviral vector encoding the NCtag-synTF-transgene system establishes this as a novel platform for sense-and-response inside therapeutic cells.

Sphingolipids are bioactive lipids that regulate key signaling pathways both directly as ligands and through membrane re-organization. Ceramide sits at the center of this network and is considered pro-death in many contexts, making ceramide accumulation an attractive therapeutic strategy. Given the wide-ranging regulation of cellular responses this network exerts, better understanding ceramide metabolism may promote therapeutic efficacy of sphingolipid-based therapeutics. Ceramide glycosylation, catalyzed by glucosylceramide synthase (GCS; UGCG), is in turn widely regarded as a detoxification route thus limiting efficacy of ceramide- based therapeutics. Here we show the opposite. Delivery of short-chain C6-ceramide via a ceramide nanoliposome (CNL) induced organelle stress and cell death in chronic lymphocytic leukemia (CLL) via the accumulation of glycosphingolipids (GSLs), rather than through ceramide itself. Pharmacologic and genetic blockade of GCS protected B-cell leukemia, breast carcinoma, glioblastoma, lung adenocarcinoma, and non- malignant embryonic kidney cells from CNL-induced death. Conversely, exogenous C8-glucosylceramide was sufficient to kill cells that cannot degrade it. We show that GSL accumulation drives an ordered organelle response beginning with lysosomal deacidification, endoplasmic reticulum stress, followed by mitochondrial respiratory capacity decline, each attenuated by inhibition of GSL synthesis. These effects were accompanied by MLKL phosphorylation, increased activity of the stress sensor JNK and CHOP induction, with JNK inhibition partially protecting from death. These findings invert the prevailing view of ceramide glycosylation as a resistance mechanism and identify glycosphingolipid flux as a required effector arm of ceramide-directed therapy.

Massive library-based platforms enable rapid early hit discovery, yet subsequent hit resynthesis and validation remain major bottlenecks in drug discovery. This delay is amplified when optimizing hits, or elaborating structures towards more advanced modalities, such as chemical inducers of proximity (CIPs). Here, we report PROXINAUT, an end-to-end workflow integrating self-encoded library-based hit discovery with an automated parallel solid-phase synthesis platform to streamline hit discovery, validation, optimization, and degrader development. As a demonstration, screening a 176k-member benzimidazole library against BRD4 yielded six hit candidates, which were obtained via parallel automated synthesis and validated as submicromolar binders. The automation workflow empowered a rapid structure activity relationship exploration around the whole scaffold and resulted in a variant with six fold improved binding affinity. Next, we aimed to automatize the development of bifunctional degraders. Solid phase synthesis typically leaves a C-terminal amide as a synthetic artifact that can compromise druglike properties. We developed a strategy to repurpose this resin-attachment site, converting it into functional degrons featuring either FBXO31-targeting C-terminal amides or cereblon-binding cyclic imides. Operating without human intervention, our automated platform executes up to 16 synthetic steps across multiple parallel structures, enabling true de novo synthesis of full bifunctional scaffolds, where ligand, linker and E3 recruiter variations can all be explored within the same workflow. This resulted in cell-active BRD4 degraders with subnanomolar to nanomolar potency. Overall, we show how library selections can merge with multi-step parallel automation to convert hits directly into validated leads and advanced degrader modalities.