Biology subjects

Guo, H.

Publications and source records attributed to Guo, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Integrative analysis reveals extensive interactions among C2H2 zinc finger proteins at chromatin loop anchors

Cys2-His2 -zinc-finger proteins (C2H2-ZFPs) form the largest class of human transcription factors, yet their potential role (s) in higher-order genome organization has remained largely poorly defined. To date, only a small number of family members, e.g., CTCF and YY1, have been shown to function in chromatin organization. Here, we examined the global relationship between C2H2-ZFPs and long-range chromatin interactions (LRIs). By integrating ChIP-seq datasets for 216 C2H2-ZFPs and genome-wide maps of chromatin looping, we observe that more than 40% of the human C2H2-ZFPs are significantly enriched at LRI anchors. We found that depletion of a subset of such C2H2-ZFPs is associated with altered expression of genes linked by the LRIs they occupy. To investigate whether protein-protein interactions (PPIs) contribute to this pattern, we generated a large-scale interactome using affinity purification followed by mass spectrometry experiments, encompassing 345 C2H2-ZFPs, and LUMIER binary interaction assays for 204 C2H2-ZFPs. We identified 1,732 binary interactions, suggesting extensive connectivity among the C2H2-ZFP family members. Integrative analysis of PPI, ChIP-seq, and chromatin interaction datasets revealed that interacting C2H2-ZFP pairs are significantly co-enriched at LRIs and frequently localize to either the same or opposing loop anchors. Finally, by correlating ChIP-seq with cancer mutational datasets, we observe that DNA-binding sites of [~]35% of LRI-associated C2H2-ZFPs overlap somatic mutations in cancer genomes. Together, our results reveal a widespread network of C2H2-ZFP interactions associated with chromatin loop anchors, providing an important resource for elucidating mechanisms regulating chromatin organization.

genomics↗

bioRxiv2026

Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles

AO_SCPLOWBSTRACTC_SCPLOWGenerative models have recently advanced de novo protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce RigidSSL (Rigidity-Aware Self-Supervised Learning), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling. The code is available on this repository.

bioinformatics↗

bioRxiv2026

Isthmin-1 is a Key Regulator of Induced Pluripotent Stem Cell-Derived Cardiomyocytes Maturation through Activation of p53 Signaling

AimsHuman induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) exhibit an immature structural and metabolic phenotype that limits their utility for cardiac disease modeling and regenerative therapy. Although multiple extrinsic strategies have been proposed to enhance iPSC-CM maturation, intrinsic molecular regulators governing this process remain incompletely defined. This study aimed to identify and characterize a novel molecular factor that promotes cardiomyocyte maturation. Methods and ResultsCross-species transcriptomic analyses comparing adult versus fetal hearts and hypertrophic cardiomyopathy versus healthy myocardium identified Isthmin-1 (ISM1) as a conserved maturation-associated gene. In human iPSC-CMs, ISM1 overexpression enhanced sarcomere organization, mitochondrial oxidative phosphorylation, ATP production, and calcium-handling properties, whereas ISM1 knockdown impaired these maturation features. RNA sequencing revealed global transcriptional reprogramming toward an adult-like state, characterized by suppression of cell-cycle-related gene programs and activation of oxidative metabolic pathways. KEGG pathway enrichment, GSVA, and GSEA consistently identified p53 signaling as the most significantly activated pathway in ISM1-overexpressing iPSC-CMs. Mechanistically, ISM1 directly interacted with p53, enhanced its protein stability, promoted nuclear localization, and increased transcription of p53 downstream targets involved in metabolic remodeling and cell-cycle exit. Pharmacological inhibition of p53 abolished ISM1-induced structural and metabolic maturation, demonstrating that ISM1 promotes cardiomyocyte maturation in a p53-dependent manner. ConclusionsISM1 is a previously unrecognized molecular driver of cardiomyocyte maturation that promotes structural, metabolic, and functional maturation of iPSC-CMs through activation of p53-dependent transcriptional programs. These findings provide new mechanistic insight into cardiomyocyte maturation and identify ISM1 as a promising target for improving the maturity of stem cell-derived cardiomyocytes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/698535v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@15daca3org.highwire.dtl.DTLVardef@f1396dorg.highwire.dtl.DTLVardef@f13400org.highwire.dtl.DTLVardef@18d0b41_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

TMPO promotes cellular dissemination and metastasis in circulating tumor cells

Metastasis--the process by which cancer cells spread beyond the primary tumor to distant organs--accounts for the vast majority of cancer-related deaths. To elucidate mechanisms underlying dissemination and metastasis in prostate cancer, we have investigated circulating tumor cells (CTCs) obtained from genetically engineered mouse models (GEMMs). The phenotypic and molecular properties of the CTCs, and organoids derived from these CTCs, closely model the tumor and metastatic phenotypes of their parental GEMMs. Moreover, organoids derived from individual CTCs exhibit molecular and morphological heterogeneity that is associated with distinct metabolic states as well as differences in human prostate cancer outcome. Using computational systems analyses, we have identified TMPO, encoding the nuclear membrane protein lamina-associated polypeptide 2 (Lap2), as a key driver of this heterogeneity. TMPO activity is upregulated in advanced human prostate tumors, metastases, and CTCs, and is associated with adverse clinical outcome. Our findings indicate that TMPO promotes dissemination and metastasis in vivo by enhancing survival in conditions of metabolic stress, and reveal a novel mechanistic link between CTC heterogeneity, stress adaptation, and metastatic potential.

cell biology↗

bioRxiv2025

Methanotrophic acetogenesis drives a novel pathway of arsenic mobilization in reducing groundwaters

Geogenic arsenic (As) contamination in groundwater, widely used as drinking water, poses a global health risk, yet the microbial pathways linking electron donor oxidation to the reduction of As-bearing Fe(III) oxyhydroxides remain poorly understood. Here, we deployed Fe(III) (oxyhydr)oxide-coated pumice stones in high-As, high-methane groundwater in Cambodia for 270 days to capture planktonic metal-reducing microbial communities in-situ. These were used to inoculate anaerobic microcosms with methane or volatile fatty acids (VFAs) as electron donors over 200 days. Genome-resolved metagenomics revealed that methane oxidation via reverse methanogenesis led to acetate production, which in turn provided the primary electrons for Fe(III) and As(V) reduction in the microcosms, resulting in As(III) release. Our findings highlight an indirect coupling between methane oxidation and arsenic mobilization, with acetate as the key intermediate. This study offers new insights into the role of methane in subsurface biogeochemical cycling and its implications for arsenic contamination in groundwater systems. SynopsisThe study uses a novel in situ sampling procedure, coupled with metagenomic analysis, to identify anaerobic methane oxidation producing acetate, as a potentially important pathway to generate electron donors for microbial Fe(III) and As(V) reduction in aquifer sediments. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/696296v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@801222org.highwire.dtl.DTLVardef@268d01org.highwire.dtl.DTLVardef@f342e2org.highwire.dtl.DTLVardef@ac1f9d_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Nano-Sieve Enabled On Chip Concentration and Multiplexed Detection of Raman-Dye Labeled Nanocubes

To address persistent challenges in molecular detection--particularly signal variability, low analyte abundance, and poor spectral reproducibility--a portable bead-stacked nano-sieve platform was engineered to enable robust on-chip Raman signal amplification using silver nanocubes (AgNCs) functionalized with Raman-active thiolated ligands. The microdevice integrates deformable elastomeric channels with magnetic bead stacking to immobilize and concentrate AgNCs within confined nanoscopic junctions, thereby generating densely packed plasmonic hot-spot architectures that markedly enhance Surface-Enhanced Raman Scattering (SERS) efficiency. Time-resolved measurements revealed substantial increases in Raman intensity for both 4-mercaptobenzoic acid (4-MBA) and 4-aminothiophenol (4-ATP), outperforming corresponding off-chip assays and maintaining stable enhancement factors over a four-hour operational window. Furthermore, the platform successfully demonstrated multiplexed sensing capability: mixed-analyte experiments containing 4-MBA, 4-ATP, and cysteamine produced clearly distinguishable spectral fingerprints, even under serial dilution and dynamically pulsed sample delivery. Collectively, these results establish the bead-stacked nano-sieve as a versatile, label-free, and scalable diagnostic architecture capable of achieving high sensitivity and spectral fidelity under continuous-flow conditions. Our technology holds significant promise for real-time, non-invasive molecular surveillance, point-of-care diagnostics, and early disease monitoring in resource-limited or field-deployable settings.

bioengineering↗

bioRxiv2025

In vitro study of the growth, reproduction and pathogenicity responses of Fusarium oxysporum f. sp. zingiberi to autotoxins from ginger

Long-term monoculture of ginger triggers Fusarium wilt, a disease caused by Fusarium oxysporum f. sp. niveum (Foz). However, the role of autotoxins in promoting pathogen growth remains unclear. Four representative autotoxins, syringic acid, coumarin, ferulic acid and 7-Hydrooxycoumarin were selected to investigate their allelopathic effects on the growth, reproduction, and virulence-associated traits of Foz. The responses of Foz to these compounds exhibited notable variations, which may be attributed to the structural differences among the autotoxins. The autotoxic compounds differentially enhanced the key pathogenic traits of Foz. Syringic acid was the most effective stimulant of mycelial growth and cell wall-degrading enzymes activity, concurrently boosting mycotoxin production via upregulating FUB3 gene expression. Ferulic acid was the most potent promoter of sporulation and biomass accumulation, whereas 7-Hydroxycoumarin most effectively stimulated conidial germination. Notably, coumarin suppressed mycelial growth but strongly induced mycotoxin synthesis in Foz. These results provide mechanistic insights into how autotoxins in ginger monoculture systems promote Fusarium wilt.

microbiology↗

bioRxiv2025

The functional divergence of two ethylene receptor subfamilies that exhibit Ca2+-permeable channel activity

Ethylene is a gaseous plant hormone crucial for regulating plant growth, development, and stress adaptation, yet the molecular basis underlying ethylene receptor function remains elusive. Here, we show that subfamily I receptors constitute core ethylene-sensing module and function epistatically to subfamily II receptors. Notably, we discover that only subfamily I receptors possess Ca2+-permeable channel activity, which are indispensable for ethylene-induced cytosolic calcium influx. Overall, this work supports a mechanistic framework in which subfamily I receptors integrate ethylene sensing with Ca2+ influx, providing new insight into how plants translate hormonal cues into downstream signaling events.

plant biology↗

bioRxiv2025

A Reference Atlas of the Human Dorsal Root Ganglion

Somatosensory perception largely emerges from diverse peripheral sensory neurons whose cell bodies reside in dorsal root ganglia (DRG). Damage or dysfunction of DRG neurons is a major cause of chronic pain and sensory loss. In mice, deep single-cell transcriptomic profiling and genetically defined models have offered important clues into DRG function, but in humans, the cellular and molecular landscape of DRG neurons remains less understood. Here, we constructed a reference cell atlas of the human DRG by profiling transcriptomes of cells and nuclei from 126 donors sampled across cervical, thoracic, and lumbar DRGs. This atlas resolves 22 neuronal subtypes, including known and previously unrecognized subtypes linked to nociception, mechanosensation, thermosensation, and proprioception, as well as 10 types of non-neuronal cells. Cross-species integration, spatial transcriptomics, and microneurography enabled cell-type-specific comparisons of soma size and conduction velocity between species. Human DRG somata are larger across all cell types than their mouse counterparts, and the conduction velocities of human hair follicle innervating A-fibers are faster than in mice, suggesting a functional shift in rapid mechanical detection in humans. This integrated human DRG reference cell atlas provides a resource for exploring new molecular and physiological features of human DRG, which could help identify new strategies for treating chronic pain and other diseases of the peripheral nervous system.

neuroscience↗

bioRxiv2025

Atypical activation and molecular glue-like dimerization mechanism of an intrinsically-biased chemokine receptor

CXCR7, also known as atypical chemokine receptor 3 (ACKR3), is a naturally-biased, {beta}-arrestin-coupled seven transmembrane receptor (7TMR) that lacks productive coupling with heterotrimeric G-proteins. Despite a critical involvement in cancer metastasis, cardiovascular pathophysiology, and inflammatory disorders, the molecular basis of non-canonical activation and functional divergence of CXCR7 remains elusive. Here, we present a complete landscape of CXCR7 activation using a series of cryo-EM structures, and discover an atypical activation mechanism that is distinct from prototypical GPCRs. CXCR7 is maintained in a basal conformation by a unique tripartite ionic-lock involving TM5-TM6, in contrast to a broadly conserved TM3-TM6 ionic-lock in GPCRs, which is disrupted upon receptor activation. Importantly, activation of CXCR7 results in a constricted pocket and distinct surface topology on the intracellular side compared to prototypical GPCRs. Serendipitously, we capture novel dimeric arrangements of CXCR7 with an inter-protomer stitching by a native phospholipid serving as a molecular glue, and identify previously unanticipated extrahelical allosteric sites on the receptor. Surprisingly, in an intermediate state structure of CXCR7, the second extracellular loop (ECL2) displays a self-blocking conformation, in stark contrast to ECL2-mediated self-activating mechanism reported recently for some orphan GPCRs. Finally, we unequivocally establish CXCR7 as an atypical opioid receptor via a large peptide library screening and structure elucidation in complex with distinct opioid peptides imparting full receptor activation. In summary, our study elucidates an atypical mechanism of CXCR7 activation, and establishes it as an alternative, non-canonical opioid receptor target with potential for novel pain therapeutics.

biochemistry↗

bioRxiv2025

MemConverter: An Iterative Pipeline for Reprogramming Protein Localization in Membrane or Aqueous Solution

We propose a pipeline, MemConverter, for the conversion of soluble proteins to membrane proteins and vice versa, based on the prediction of membrane contact probability (MCP). By fine-tuning ProteinMPNN with a membrane protein dataset to create MemProtMPNN, and integrating it with iterative structure refinement using AlphaFold2, our approach enables precise reprogramming of protein surface properties. The pipeline utilizes MCP-guided sequence fusion to direct the evolution of protein sequences towards the desired membrane or soluble environments. During this process, selective residues are fixed to concentrate design efforts on regions requiring alteration. The pipeline demonstrates superior performance compared to existing methods, and molecular dynamics simulations validate that the designed proteins exhibit stable membrane integration or enhanced solubility, depending on the target localization. This pipeline introduces a novel computational tool for engineering proteins to be localized in membranes or aqueous solutions.

biophysics↗

bioRxiv2025

A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex

The genetic and spatial determinants of cell type diversity in human cerebral cortices remain poorly defined. Here, we present a population-level single-cell spatial transcriptomic atlas of human cortices from 71 donors across the lifespan. We identified 906 layer-specific genes showing conserved and divergent laminar expression patterns between humans and other species. Spatial analysis revealed neuronal vulnerability and glial activation during aging, together with a decline in the proportion of superficial SST neurons and their interactions with other cells. Disease-associated genes exhibited high cell-type and layer-specific expression, implicating the pathogenic role of spatially specific gene expression. Spatial cis-eQTL analysis identified regulatory variants linked to genes related to diseases like Tourette syndrome. Cross-species comparison demonstrated glial expansion in the human cortex, accompanied by enhanced neuron-glia communication via the neuregulin signaling. Together, we provide a comprehensive single-cell atlas of the human cortex that is essential for understanding aging, evolution, and disease pathogenesis.

neuroscience↗

bioRxiv2025

Unlocking biological insight from single-cell data with an interpretable dual-stream foundation model

Deep learning foundation models are revolutionizing single-cell biology, yet learning holistic and discriminative representations from complex, high-dimensional data remains a central challenge. Although Transformer-based single-cell language models have shown significant progress, they typically rely on a single input-encoding scheme, a practice that results in the loss of critical gene expression information and hinders the effective learning of global cellular representations. To address these challenges, we introduce scDMC, an innovative single-cell Dual-stream Masked Contrastive pre-training framework designed to synergistically optimize information fidelity at both the gene and cellular levels. Pre-trained on only 2 million cells far fewer than the datasets used by mainstream models, scDMC sets a new state-of-the-art in multiple benchmark tasks, including cell annotation, clustering, and data integration. More importantly, we demonstrate that scDMC can uncover functional gene modules, infer cell-type-specific regulatory networks in a data-driven manner, and exhibits a high degree of biological interpretability.

bioinformatics↗

bioRxiv2025

Large-Scale Neural Network Compensation Underlying Camouflaging in Trait Autism and Its Potential Mental Health Costs

Social camouflaging refers to strategies to hide or compensate for social difficulties, often at a significant mental health cost, and is particularly prevalent in autism. The large-scale neural network mechanisms underlying this adaptation remain poorly understood. This study aimed to identify these neural underpinnings and their link to other potential mental health issues. Using a dimensional approach, we recruited 110 healthy young adults who completed self-report questionnaires measuring autistic traits and camouflaging as well as depression and anxiety, and underwent resting-state fMRI scans. Using the 300-node Seitzman atlas encompassing 13 functional networks, we examined the interaction between camouflaging and autistic traits on brain network connectivity. Results showed that among individuals with higher autistic traits, greater camouflaging was associated with hyperconnectivities between the Default Mode (DMN) and Cingulo-Opercular Networks (CON), and within the CON. Crucially, DMN-CON hyperconnectivity mediated the relationship between camouflaging and potential mental health cost (i.e., depression and anxiety scores) but only in individuals with higher autistic traits. These findings reveal a specific neuro-compensatory mechanism underlying autistic camouflaging involving self-referential and executive control systems and provide a neurobiological explanation for its potential mental health burden, highlighting the need for societal changes that reduce the pressure for such adaptations. Lay AbstractSocial camouflaging refers to strategies autistic people often use to hide their social differences to better adapt to everyday social contexts. While it may help in the short term, this constant effort can be mentally exhausting and is often linked to severe anxiety and depression. However, little is known about how different brain networks work together to enable social camouflaging and might contribute to a greater risk of anxiety and depression. In this study, autistic traits were measured in 110 young healthy adults in addition to questionnaire-based measures of social camouflaging, anxiety, and depression. Additionally, brain activity was recorded using magnetic resonance imaging while they were resting and not doing any task. We found that, in people with higher autistic traits, social camouflaging was linked to stronger connections between the brain network involved in thinking about oneself (self-reflection; Default Mode Network) and the one in charge of maintaining goal-directed behavior (action control; Cingulo-Opercular Network), as well as stronger connections within the latter brain network. These stronger connections between the self-reflection network and action control network partly explained why camouflaging may be associated with higher levels of anxiety and depression. In short, autistic camouflaging seems to rely on a cognitively demanding neural compensatory process, which can take a toll on mental health. Understanding this underscores the importance of creating a more accepting society to support the well-being of autistic individuals.

neuroscience↗

bioRxiv2025

Uranium mining fuels evolution in deep groundwater microbiomes

Deep-biosphere microbes have been underpinning global biogeochemical cycles throughout Earth history, yet their evolutionary responses to long-term anthropogenic disturbance remain poorly understood. Neutral-pH in-situ leaching (ISL), the dominant uranium-mining strategy, imposes persistent radiochemical and redox stress offering rare natural experiments across decades for observing subsurface microbial evolution. Here, by exploiting metagenomics and metatranscriptomics in examining microbial responses through various mining stages, we show that neutral U ISL causes substantial changes in microbial communities spanning 2,294 strains accompanied by diversification and selection of active microbial species. These changes occurred during elevated dissolved uranium and radiological activity which correlated with a substantial transcriptional change in energy metabolism, and with an overexpression of specific genes for oxidative-stress defence and DNA-repair pathways. Increased nucleotide diversity in 101 out of 392 species clusters and nonsynonymous/synonymous polymorphism ratios greater than one in 139 species clusters were predominantly observed in metatranscriptomes with elevated radiation, highlighting positive selection of transcriptionally active populations. These findings demonstrate that neutral U ISL drives functional and genetic diversification of subsurface microbiomes, revealing a dynamic and evolutionarily responsive deep biosphere.

genomics↗

bioRxiv2025

Inactivating a β1 subunit of SnRK1 promotes broad-spectrum disease resistance in rice

Rice is a staple crop for over half of the worlds population, and its sustainable production is vital to ensure global food security. However, rice is highly susceptible to several devastating fungal diseases1, including blast disease caused by Magnaporthe oryzae, sheath blight by Rhizoctonia solani, false smut by Ustilaginoidea virens, brown spot by Bipolaris oryzae, bakanae by Fusarium fujikuroi, and head blight by F. graminearum. The mechanisms underlying the susceptibility of rice to these fungal diseases remain unclear. Here, we report that the {beta} subunit of SnRK1, SnRK1{beta}1A, confers broad-spectrum susceptibility to these fungal diseases. Our findings reveal that diverse rice fungal pathogens have convergently evolved an effector, Gas2, which interacts with SnRK1{beta}1A to prevent its ubiquitination-mediated degradation and promotes its nuclear translocation. While SnRK1{beta}1A is expressed at low levels in healthy plants, its expression is markedly induced upon fungal infections, facilitating susceptibility by inhibiting SnRK11, the subunit of SnRK1, whose overexpression has been shown to enhance broad-spectrum resistance in rice2. Notably, rice lines with disrupted SnRK1{beta}1A are resistant to multiple fungal diseases without compromising growth and yield in the field. Together, this study demonstrates that broad-spectrum disease resistance in crops can be achieved by disrupting inducible susceptibility genes whose encoded proteins are targeted by effectors conserved in multiple pathogens.

plant biology↗

bioRxiv2025

Identification of antibody-drug conjugate payloads which are substrates of ATP-binding cassette drug efflux transporters

AimAntibody-drug conjugates (ADCs) feature an antibody recognizing a specific protein joined to a potent toxic payload. Numerous antibody-drug conjugates have received FDA approval; however, clinical resistance arises. Resistance mechanisms include decreased expression or mutation of the antibody target, impaired payload release, or increased expression of ATP-binding cassette (ABC) efflux transporters associated with multidrug resistance. We therefore sought to characterize the interactions of ABC multidrug transporters with ADC payloads. MethodsWe performed a high-throughput screen with 27 common ADC payloads using cells lines expressing ABC transporters P-glycoprotein (P-gp, encoded by ABCB1) or ABCG2 (encoded by ABCG2). Confirmatory assays were also performed using cells transfected to express P-gp, ABCG2, or MRP1 (encoded by ABCC1). ResultsSeveral commonly used ADC payloads were substrates of P-gp, including calicheamicin gamma1, monomethyl auristatin E, DM1, and DM4. All the pyrrolobenzodiazepines tested--SJG136, SGD-1882, SG2057, and SG3199--were substrates of P-gp, ABCG2, and MRP1. The modified anthracyclines nemorubicin and its metabolite PNU-159682 were poorly transported by both ABCB1 and ABCG2 and displayed nanomolar to picomolar toxicity. Further, we found that the efficacy of the FDA-approved ADC mirvetuximab soravtansine, with DM4 as the toxic payload, was decreased in cell lines expressing P-gp. Duocarmycin DM and PNU-159682 were exquisitely toxic to a panel of 99 cancer cell lines of varying origins. ConclusionSeveral commonly used ADC payloads can be transported by ABC transporters, potentially leading to transporter-mediated drug resistance in patients. Future ADCs should be developed using payloads that are not ABC transporter substrates.

pharmacology and toxicology↗

bioRxiv2025

GenVS TBDB: An Open AI-Generated andVirtual Screened Small-Molecule Database for Tuberculosis Drug Discovery

Tuberculosis (TB) remains a leading global health threat, with over 10 million new cases and 1.25 million deaths reported in 2023. Current TB therapies rely on a limited drug repertoire and prolonged treatment courses that have changed little in four decades. Here, we present GenVS-TBDB, a target-aware AI-generated and virtual-screened small-molecule database, which expands the chemical space against Mycobacterium tuberculosis (M.tb) essential proteins. We first identified 460 probable small-molecule binding pockets across 377 essential M.tb proteins by integrating multiple sources. Then, by leveraging the target-aware molecule generative model, over 1.2 million novel small molecules tailored to these pockets were produced. The key physicochemical properties were computed for all compounds to ensure medicinal chemistry tractability. These compounds were also evaluated using molecular docking and anti-TB specific graph neural network model, yielding binding propensity ranking and whole-cell activity prioritization for each target. To substantiate the integrated AI-driven workflow for anti-TB discovery, 30 compounds were obtained, including 22 AI-designed molecules synthesized de novo and 8 commercially available analogs. In validation, 2 synthesized compounds demonstrated significant thermal stabilization of FtsZ, confirming target engagement. 6 compounds exhibited cellular inhibition below 50 {micro}M, the most potent at 12 {micro}M. Furthermore, GDI-11785 showed binding to the cell wall biosynthesis pathway with 35 {micro}M cellular activity, establishing a promising starting point for tuberculosis drug discovery. Our findings contribute a significant library of bioactive molecules which may hasten the preliminary phase of tuberculosis drug discovery. The GenVS-TBDB small library is publicly accessible and can be downloaded freely at https://datascience.ghddi.org/database/view.

pharmacology and toxicology↗