Biology subjects

Zheng, H.

Publications and source records attributed to Zheng, H..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Microglia are not required for normal postnatal brain development and cognitive function in the rat.

The development, maintenance and survival of microglia, the brains resident immune cells, requires signalling via the colony stimulating factor 1 receptor (CSF1R). In mice, the Fms intronic regulatory element (FIRE), a highly conserved super enhancer, is required for CSF1R expression in microglia and germ-line deletion of FIRE leads to microglial deficiency. We have generated Csf1r{Delta}FIRE/{Delta}FIRE (Fireko) rats using CRISPR/Cas9. Fireko rats are born at expected Mendelian frequency, grow normally and survive to adulthood. Like Fireko mice, they lack microglia and subpopulations of resident macrophages in kidney and heart, but retain the other brain associated macrophages and resident populations in the liver, spleen and lungs. In contrast to mutant mice, macrophages in the peritoneum are unaffected and CSF1R expression is not completely abolished in the blood. Aside from the loss of microglia-specific transcripts, the Fireko has no effect on expression of genes associated with neurons, oligodendrocytes or astrocytes in adult rats but is associated with detectable calcification in the thalamus. Despite the absence of microglia, we detected no significant differences in ethologically relevant behaviours compared to littermates. The results suggest that microglia are not essential for normal cognitive development. Fireko rats provide an alternative to mice as a model for human microglial deficiency and the functions of microglia in development and homeostasis in the brain.

immunology↗

bioRxiv2025

AI Identifies Broadly Neutralizing Antibodies from an IGHV1-69 Public Antibody Class Exerting Continued Selection Over SARS-CoV-2

R1-32-like public antibodies, characterized by shared IGHV1-69/IGLV1-40 usage, are elicited in more than 50% of individuals with COVID-19 and have been implicated in driving recurrent mutations at L452SARS2 and F490SARS2 within their convergent epitope in the SARS-CoV-2 spike receptor-binding domain. These mutations effectively mediate escape from non-affinity-matured R1-32-like antibodies with germline-like sequences. Here, we characterize four affinity-matured R1-32-like antibodies, C092, C807, BD56-104, and BD56-597, that tolerate L452SARS2 and F490SARS2 mutations. We show that this tolerance arises from residues introduced by somatic hypermutation at convergent positions across multiple CDR loops and surrounding regions, thereby creating additional contacts that reinforce epitope binding. An unusual N354SARS2 glycosylation site, which emerged in BA.2.86 and became fixed in its descendants, is linked to escape from affinity-matured R1-32-like antibodies, implying ongoing selection by this public antibody class. Using an AI model trained on integrated structural, neutralization, and binding data, we further identified ZL525, an ultrapotent R1-32-like antibody with pan-SARS-CoV-2 variant activity, including against the highly evasive KP.3 variant carrying the N354SARS2 glycosylation, and broad sarbecovirus cross-reactivity extending to SARS-CoV-1. Together, these findings show how affinity maturation enables public antibodies to adapt to viral antigenic drift, reveal their role in shaping SARS-CoV-2 antigenic evolution, and demonstrate the potential of AI-empowered strategies for discovering broadly neutralizing antibodies.

immunology↗

bioRxiv2025

AI recognizes convergent somatic hypermutation signatures to allow the discovery of variant-resilient broadly neutralizing antibodies

Elucidating the mechanisms by which broadly neutralizing antibodies (bnAbs) develop to confer durable immunity in humans is pivotal for the rational design of next-generation vaccines and therapeutics. VH3-53/3-66-encoded public antibodies are widely elicited in the population after the COVID-19 pandemic. Here, we isolated 15 VH3-53/3-66-encoded bnAbs from elite neutralizers who experienced sequential SARS-CoV-2 Omicron breakthrough infections. These bnAbs exhibit exceptional potency and breadth against circulating variants and, as members of a long-lived public antibody lineage, likely contribute to durable humoral protection. Genetic analysis of VH3-53/3-66-encoded bnAbs reveals a convergent somatic hypermutation pattern at seven positions in and around the CDR loops that emerges with repeated viral exposures and distinguishes them from non-bnAbs. Grafting these combined mutations onto clinically escaped antibodies broadens their breadth and restores neutralization activity. Structural analysis shows that these convergent mutations cooperatively remodel CDRs to bind and tolerate virus receptor-binding domain mutations. Using an AI-based antibody language model trained on data linking somatic hypermutations to binding affinity and neutralization, the model is able to identify mutational patterns predictive of breadth, enabling the discovery of a rare bnAb with protective activity against the latest variants from early-pandemic antibody repertoires. This demonstrates the feasibility of establishing an AI-empowered pipeline to identify mutation-tolerant bnAbs from early-pandemic antibody repertoires to fight fast-evolving newly introduced viruses.

immunology↗

bioRxiv2025

Astrocyte cell-surface proteomics identified CD44 as an OPN/SPP1 receptor regulating lipid metabolism and glial crosstalk in Alzheimer s disease

Abstract/SummaryThe development of {beta}-amyloid (A{beta}) pathology in Alzheimers disease (AD) is accompanied by profound changes in astrocytes and microglia. How these responses are orchestrated by cell surface proteins, key mediators of cell-cell communication, remain unclear. Using in situ astrocyte cell-surface proteome profiling in 5xFAD mice, we identified a set of dysregulated surface proteins induced by A{beta} pathology, including CD44. CD44 was selectively upregulated in plaque-adjacent astrocytes and interacted with osteopontin (OPN), encoded by the disease-associated microglia gene Spp1, to promote lipid accumulation, and this effect is {gamma}-secretase dependent. Astrocytic CD44 in turn regulated Spp1 expression and microglial activity. Conditional deletion of Cd44 in adult astrocytes of 5xFAD mice attenuated glial reactivity, reduced A{beta} pathology, and improved cognition. These findings define a plaque-proximal OPN-CD44 axis that controls astrocyte lipid metabolism and glial activity, positioning CD44 as a surface-accessible therapeutic target in AD.

neuroscience↗

bioRxiv2025

Peri-Head Distance Coding in the Mouse Brainstem

Perceiving object distance in peri-personal space is essential for guiding movement and avoiding danger. During active sensation, distance information is often anchored to the body via touch; yet how early somatosensory circuits extract distance information from tactile inputs remains unclear. Here, we investigate how second-order neurons in the mouse whisker brainstem encode peri-head distance. Using in vivo extracellular recordings in awake mice in a naturalistic wall-passing paradigm, we find brainstem neurons employ two distance-coding schemes: a "proximity" code, where firing increases monotonically as objects approach the face; and a "map" code, where neurons exhibit peak tuning at specific distances to collectively tile peri-head space. The map code outperforms proximity code in population decoding of distance. Perturbation experiments reveal multi-whisker integration and internuclear inhibition contribute to the generation of map-like tuning. These findings highlight a previously underappreciated computational role for brainstem circuits, where inhibition acts as a neural comparator to transform proximity-based sensory inputs into a map-like representation of peri-personal space.

neuroscience↗

bioRxiv2025

Spatial patterning of transcriptional and regulatory programs in the primate subcortex

Mammalian brain cell identity is shaped by intrinsic factors and external context. We present a spatially resolved transcriptomic and gene regulatory atlas of cell types across all subcortical regions in a primate, the common marmoset. Dense sampling and cross-species integration revealed spatially precise neuronal assemblies, including in complex midbrain and diencephalic structures. Chromatin accessibility and transcriptional identity are spatially tuned within and across subcortical structures; spatial gradients within hippocampal subfields are orchestrated by graded transcription factors acting through graded enhancers. The primate-expanded thalamic GABAergic population shares transcriptional and regulatory syntax with conserved midbrain populations, reflecting an evolutionary adaptation compared with rodents. Similar regional expression across cell types can arise by distinct regulatory architectures, as for telencephalic astrocytes and neurons. Conversely, distant cell types can share regulatory programs despite divergent identities: striatal GABAergic medium spiny neurons and telencephalic glutamatergic neurons share a postsynaptic regulatory program despite divergent lineage, region, and neurotransmitter identity.

neuroscience↗

bioRxiv2025

Integrating Millions of Years of Evolutionary Information into Protein Structure Models for Function Prediction

BackgroundUnderstanding life processes relies on accurate protein function prediction, fundamentally requiring the integration of evolutionary information encoded in sequences with spatial characteristics from 3D structures. Existing approaches often face limitations, however, by either over-relying on sequence, using simplified structural representations instead of fine-grained spatial details, or failing to capture the synergistic relationship between sequence and structure, compounded by challenges in acquiring annotated data. ResultsTo address these issues, we propose a novel contrast-aware pre-training framework, ESMSCOP. ESMSCOP leverages a state-of-the-art protein language model to harness evolutionary insights embedded in sequences, and introduces a new encoder to fuse topological and fine-grained spatial structural features. By employing a contrastive pre-training strategy with auxiliary supervision, ESMSCOP effectively bridges the sequence-structure gap, yielding rich and informative representations. ConclusionsExtensive experiments conducted on multiple benchmark datasets demonstrate that ESMSCOP achieves superior performance in protein function prediction tasks compared to existing methods. Furthermore, it shows strong performance even when utilizing relatively less pre-training data compared to some large-scale models.

bioinformatics↗

bioRxiv2025

Screening of Oyster Peptides for Anti-Muscle Atrophy Based on Machine Learning and Computer Simulation: Guided by Antioxidant Pathways

Muscle atrophy poses a serious threat to human health, with its primary pathogenic mechanisms closely linked to oxidative stress. This study focuses on the potential of oyster peptides in alleviating dexamethasone (DEX)-induced skeletal muscle atrophy and their underlying antioxidant mechanisms. Utilizing efficient integrated machine learning and computer simulation methods, a systematic screening of active peptides and mechanistic research was conducted. The results revealed that oyster peptides at concentrations of 25-50 g/mL significantly improved the decline in cell viability and myotube atrophy induced by DEX, while downregulating the expression of muscle atrophy markers Atrogin-1 and MuRF1. Through LC-MS/MS, 220 high-activity peptide sequences were identified. Following the replication and extension of the iAnOxPep integrated learning model, 15 potential antioxidant peptides were selected. Among them, the short peptide AWPGPQ demonstrated the strongest binding affinity with Keap1 and PPAR{gamma} targets. Molecular dynamics simulations confirmed its stability, suggesting that AWPGPQ may exert its dual effects--antioxidant and anti-muscle atrophy--by modulating the Keap1-Nrf2 and PPAR{gamma} signaling pathways. This study established a systematic and efficient strategy for screening natural active peptides, providing theoretical support and technical pathways for the discovery of multifunctional short peptide candidates, with significant theoretical value and application prospects.

molecular biology↗

bioRxiv2025

A systematic comparison of cooperation and coordination across behavioural, psychological, and neural scales

Cooperation and coordination are the two fundamental mechanisms for enhancing social welfare. However, the intrinsic differences between the dynamics of cooperation and coordination remain elusive, particularly from an interpretable perspective that bridges behavioural, psychological, and neural scales. Here, we compare and analyze cooperation and coordination within a unified framework by assigning participants to an adjustable public goods game for iterated real-time interactions. By integrating model-free behavioural patterns and psychological intentions, we show that individuals are driven by increased flexibility and are more susceptible to peer influence in decision-making under cooperation. While under coordination, it is easier to reach the group consensus, inspiring individuals to stick more closely to their existing behavioural patterns and the default social norms. Furthermore, although peer punishment can enhance reciprocal contributions in all scenarios, the detailed impact and the resultant adverse phenomena (anti-social punishment) in cooperation and coordination are different. Notably, behavioural motive differences are also reflected in the neural responses recorded via fNIRS, in which coordination is associated with activation of the rTPJ and more consistent inter-brain synchronization in the dmPFC, while there is a negative correlation between dmPFC-rTPJ connectivity and contributions under cooperation. In addition, rTPJ during the punishment phase is significantly activated compared with the investment phase. Our study systematically reveals the fundamental differences between cooperation and coordination at the multi-scale levels, which not only deepens the understanding of reciprocal behaviour in social groups, but also provides a foundation for designing targeted incentive mechanisms.

animal behavior and cognition↗

bioRxiv2025

A Druggable Tumor Suppressor and Leukemic Stem Cell Marker

Withdrawal StatementThe authors have withdrawn this preprint because the co-authors were not in agreement about posting the work in its current form. The authors request that this work not be cited. Please contact the corresponding author (Dr. Xunlei Kang, kangxu@health.missouri.edu) with questions.

cancer biology↗

bioRxiv2025

ProTDyn: a foundation Protein language model for Thermodynamics and Dynamics generation

AO_SCPLOWBSTRACTC_SCPLOWMolecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation protein language model that unifies conformational ensemble generation and multi-timescale dynamics modeling within a single framework. Unlike prior approaches that treat these tasks separately, ProTDyn allows flexible independent and identically distributed (i.i.d.) ensemble sampling and dynamic trajectory simulation. Across diverse protein systems, ProTDyn yields thermodynamically consistent ensembles, faithfully reproduces dynamical properties over multiple timescales, and generalizes to proteins beyond its training data. It offers a scalable and efficient alternative to conventional MD simulations. Code is available at: https://github.com/Harrydirk41/ProTDyn.

biochemistry↗

bioRxiv2025

Leveraging BRG1 Driven Ferroptosis Resistance to Overcome Treatment Resistance

Resistance to Brutons tyrosine kinase inhibitors (BTKi) remains a major therapeutic challenge in B-cell malignancies, limiting treatment durability. Here, we identify ferroptosis suppression as a central mechanism of BTKi resistance in mantle cell lymphoma (MCL). Aberrant BRG1 activity protects cells from BTKi-induced ferroptosis by restricting reactive oxygen species (ROS) and labile iron. Mechanistically, BRG1 promotes resistance through both BTK-dependent survival signaling and a BTK-independent transcriptional program. The latter is mediated by BRG1-driven induction of MEF2B, which upregulates NDUFA4L2 to inhibit mitochondrial respiration, thereby blocking mitochondria-dependent ferroptosis. Pharmacologic inhibition of BRG1 disrupts these programs, restoring ferroptotic sensitivity and synergizing with BTKi across resistant MCL models. Together, these findings establish BRG1 as a central regulator of therapy resistance and provide a rationale for co-targeting BRG1 and BTK as a therapeutic strategy for B-cell malignancies.

cancer biology↗

bioRxiv2025

Cellular and Molecular Architecture of Renin-Angiotensin System Signaling in the PVN Under Cardiometabolic Stress

The hypothalamic paraventricular nucleus (PVN) integrates neuroendocrine and autonomic signals that regulate blood pressure and metabolism. Although the renin- angiotensin system (RAS) is implicated in neurogenic hypertension and obesity, cell-type- specific expression and regulation of its components within the PVN remain poorly understood. Here, we employed single-nucleus RNA sequencing (snRNA-seq) to profile the transcriptomic landscape of the PVN in male mice under baseline conditions and in models of DOCA-salt-induced hypertension and high-fat diet (HFD)-induced obesity. We identified major PVN cell types, including neurons, astrocytes, precursor oligodendrocytes, oligodendrocytes, microglia and endothelial cells, and further resolved eight transcriptionally distinct neuronal subtypes. Expression of RAS-related genes was highly cell-type specific: Agt (angiotensinogen) was enriched in astrocytes, whereas Ace (angiotensin-converting enzyme), Atp6ap2 (also known as the (pro)renin receptor [PRR]), Agtr1a (angiotensin II type 1a receptor, aka AT1aR), Lnpep (leucyl/cystinyl aminopeptidase, aka angiotensin 4 receptor [AT4R]), and the Mas1 proto-oncogene were predominantly expressed in neurons. DOCA-salt treatment increased the proportion of GABAergic and vasopressin neurons and enhanced neuronal Agt and Atp6ap2 expression, while reducing astrocytic Agt, suggesting activation of a vasoconstrictive RAS axis. HFD exposure increased excitatory and stress-responsive neuronal subtypes (glutamatergic, vasopressin, corticotropin-releasing hormone) and upregulated Atp6ap2, Agtr1b, Lnpep, and Mas1 in vasopressin neurons, while downregulating multiple RAS genes in GABAergic neurons. These findings reveal dynamic, cell-type-specific remodeling of RAS signaling in the PVN in response to hypertensive and metabolic stress, providing a transcriptomic atlas of RAS expression in the PVN and identifying potential cellular targets for therapeutic strategies addressing cardiometabolic disorders.

genomics↗

bioRxiv2025

Netrin-1 promotes pancreatic tumorigenesis and innervation through NEO1.

Nerves have been shown to regulate cancer progression. However, a clear demonstration of a role for axon guidance molecules in pancreatic tumorigenesis, innervation, and metastasis has been lacking. Using murine KrasG12D-mutant pancreatic organoids, we screened axon guidance molecules by qRT-PCR, identified Ntn1 upregulation, and then verified its in vivo upregulation during pancreatic tumorigenesis in humans and mice. NTN1 and its receptor NEO1 were upregulated in epithelial cells by the Kras mutation and {beta}-adrenergic signaling, in part, through the MAPK pathway. Ex-vivo culture of celiac ganglia showed that NTN1 promoted the axonogenesis of sympathetic neurons through the nerve NEO1 receptor. In the Pdx1-Cre;LSL-KrasG12D/+ model, Ntn1 knockout decreased sympathetic innervation and the development of pancreatic intraepithelial neoplasia. Treatment of pancreatic tumor organoids with recombinant NTN1 enhanced cell growth, epithelial-mesenchymal transition (EMT), and cancer stemness with the upregulation of ZEB1 and SOX9 through NEO1-mediated activation of focal adhesion kinase (FAK). In Pdx1-Cre;LSL-KrasG12D/+;LSL-Trp53R172H/+mice, Ntn1 knockout reduced innervation, FAK phosphorylation, and the features of EMT and stemness to extend mouse survival. In a liver metastasis model of PDAC (pancreatic ductal adenocarcinoma), treatment with a NTN1-neutralizing antibody or tumoral knockdown of Neo1 reduced ZEB1 and SOX9 and decreased tumor progression. In contrast, Ntn1 overexpression promoted innervation and the progression of PDAC liver metastasis. These data suggest that the NTN1/NEO1 axis is a key regulator of PDAC progression, directly influencing cancer cell stemness and EMT, while indirectly promoting tumor growth through nerves. Inhibiting the NTN1/NEO1 axis could represent a potential therapeutic approach for PDAC. Statement of SignificanceNTN1 promotes pancreatic tumorigenesis and metastasis directly and indirectly through nerves, highlighting the importance of tumor cell-nerve crosstalk in cancer. NTN1 blockade could represent a promising strategy for treating PDAC liver metastasis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/666009v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@ca611corg.highwire.dtl.DTLVardef@ad9264org.highwire.dtl.DTLVardef@1661c00org.highwire.dtl.DTLVardef@b86798_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Interactome Analysis of the CC2D1A Scaffold Reveals Novel Neuronal Interactions and a Postsynaptic Role

Loss of the protein scaffold Coiled-coil and C2 domain containing 1A (CC2D1A) leads to intellectual disability (ID), autism spectrum disorder (ASD), and other neurodevelopmental presentations in humans. CC2D1A interactions have been studied in different cell lines proposing diverse roles in endolysosomal maturation and intracellular signaling, but the composition and functional mechanisms of the CC2D1A interactome remain poorly understood, especially in the brain. We performed comprehensive proteomic analyses to characterize CC2D1A binding partners, first comparing immunoprecipitations with three different anti-CC2D1A antibodies in HEK293 cells and then probing the mouse hippocampus. In HEK cells, Gene Ontology (GO) analysis revealed broad interaction networks in the nucleus, mitochondrion, and cytoplasmic vesicles sharing functions in organelle organization, vesicle mediated transport, and protein metabolism. These are unified by the best characterized CC2D1A interactor, the ESCRT III component CHMP4B, and define a pleiotropic role for CC2D1A in membrane trafficking and protein homeostasis. In the hippocampus, using stringent criteria and additional controls, including a Cc2d1a hypomorph mouse line, we identified 10 high-confidence interactors in addition to CHMP4B (TNIK, G3BP2, CEP135, MAPKAP1, SHFL, PPT1, PNKD, VAMP5, and PPP6R2) revealing roles for RNA regulation and synaptic function. The HEK studies had also pointed to CC2D1B, the only paralog of CC2D1A, as an interactor. We confirmed that not only the two proteins can bind in the brain, but also localize in different synaptic compartments, showing that CC2D1A is uniquely enriched in the post-synapse. This supports a unique function of CC2D1A in regulation of synaptic transmission that could explain the more severe cognitive deficits in humans and mice upon its loss. To our knowledge these findings provide the most comprehensive characterization of the CC2D1A interactome to date, elucidating novel, multifaceted, and dynamic cellular functions, providing potential implications for its role in neurodevelop-mental disorders.

molecular biology↗

bioRxiv2025

Modular striatal dynamics and reciprocal inhibition orchestrate skilled action sequencing

The basal ganglia, particularly the striatum, are critical for orchestrating skilled behavioral sequences, yet the precise mechanisms underlying this process remain unclear. Using high-resolution kinematic tracking and neural recordings in mice performing a water-reaching task, we found spatially distributed modules of striatal projection neurons whose activity corresponded to the generation of each element in the sequence--aiming, reaching, and drinking. They are activated sequentially and exhibit reciprocal inhibition, ensuring a strict serial order. Optogenetic activation of the direct pathway of the orofacial module promoted licking while suppressing reaching. Reaching could in turn suppress stimulation-evoked licking, revealing bidirectional inhibitory interactions. Our findings demonstrate that the striatums modular organization, coupled with lateral inhibition, sculpts the temporal progression of actions, providing a mechanistic framework for understanding how the basal ganglia coordinate complex behaviors.

neuroscience↗

bioRxiv2025

Ultra-wide-field, deep, adaptive two-photon microscopy

Observing the activity patterns of large neural populations throughout the brain is essential for understanding brain function. However, capturing neural interactions across widely distributed brain regions from both superficial and deep cortical layers remains challenging with existing microscopy technologies. Here, we introduce a state-of-the-art two-photon microscopy system, ULTRA, capable of single-cell resolution imaging across an ultra-large field of view (FOV) exceeding 50 mm{superscript 2}, enabling deep and very wide field in vivo imaging. To demonstrate its capabilities, we conducted a series of experiments under multiple imaging conditions, successfully visualizing brain structures and neuronal activities spanning a spatial range of over 7 mm from superficial layers to depths of up to 900 m, while covering a volume of 45.24 mm3 in the mouse brain. This versatile imaging platform overcomes traditional spatial constraints, providing a powerful tool for comprehensive exploration of neuronal circuitry over extensive spatial scales with cellular resolution.

neuroscience↗

bioRxiv2025

Beyond the G-Loop: CRBN Molecular Glues Potently Target VAV1 via a Novel SH3 RT-Loop Degron

This study reports the discovery and characterization of novel CRBN molecular glues that selectively induce the proteasomal degradation of the hematopoietic-specific signaling protein VAV1, a key target in hematological malignancies and autoimmune diseases. Utilizing unbiased global proteomics, we identified phenyl-glutarimide derivatives NGT-201-12, as effective VAV1 degraders, with its C-terminal SH3 domain (SH3-2) being crucial for this interaction. A significant finding is the elucidation of a non-canonical RT-loop degron (RDxS motif, residues 796-799) within VAV1 SH3-2, distinct from previously characterized G-loop degrons. This discovery, supported by advanced computational modeling using the physics- and AI-driven GluePlex workflow and validated by site-directed mutagenesis, highlights versatility of CRBN in recognizing diverse neosubstrate motifs. Furthermore, we demonstrate that applying Free Energy Perturbation (FEP+) calculations to these predicted ternary structures yields cooperativity metrics that correlate with experimental degradation potency, overcoming the limitations of standard molecular docking. This establishes a robust workflow where, once a ternary complex is predicted, even with initial weak binders, FEP+ can be utilized to prospectively rank analogs and optimize molecular glue potency. Additionally, we demonstrate that strategic chemical modifications, particularly conformational restriction via halogen substitution (e.g., NGT-201-18), markedly potentiate VAV1 degradation, a principle supported by density functional theory (DFT) calculations. Comprehensive structure-activity relationship (SAR) studies provided a roadmap for designing next-generation VAV1 degraders. Importantly, dose-response proteomics not only confirmed VAV1 as the primary target but also revealed LIMD1, possessing a canonical G-loop, as an off-target for some analogs, indicating a single molecular glue can engage disparate degron motifs. The identification of the VAV1 RT-loop degron prompted a proteome-wide search, revealing other SH3-containing proteins as potential targets or off-targets. In conclusion, this research unveils a novel non-canonical RT-loop degron in VAV1, demonstrates the utility of conformational restriction in enhancing degrader potency, and underscores the critical role of integrating global proteomics with advanced structural modeling and FEP calculations for understanding degrader potency and selectivity. These findings offer a promising therapeutic strategy for targeting VAV1 and significantly expand the landscape of CRBN neosubstrate recognition and the rational design of molecular glue degraders.

biochemistry↗