Biology subjects

Fan, H.

Publications and source records attributed to Fan, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Defining the Mycobacterium tuberculosis Pangenome and Suggestions for a New Composite Reference Sequence

Mycobacterium tuberculosis (Mtb) causes tuberculosis (TB), a global disease with diverse clinical and microbiological manifestations. Studies into the biological causes of this phenotypic diversity have been largely limited to a few reference strains. A pangenome approach is likely to provide new insights. Pangenomic tuberculosis studies have been limited the availability of only fragmented genome sequences and error-prone reference genomes. We used a de novo assembly pipeline that generates extremely complete and accurate whole genome sequences to generate 50 closed Mtb genomes across all seven major lineages. We identified 3,377 core gene clusters and 379 accessory clusters. Analysis showed multi-copy core clusters were largely due to gene fragmentation (76%), paralogs (12%), nearly identical gene duplications (4%), or combinations (8%). Sixteen hypervariable regions (HVRs) were identified, including novel paralogs and variable PE/PPE genes. We consolidated these findings into a Pangenome Gene Reference Resource (PGRR) for precision alignment. Our study demonstrates the closed nature of the Mtb pangenome, with most variation in accessory genes and HVRs. The PGRR provides a foundation for improved drug/vaccine target discovery and highlights the need to move beyond the commonly used H37Rv strain to study Mtb genetic and phenotypic diversity. IMPORTANCETuberculosis (TB), caused by Mycobacterium tuberculosis, affects millions globally. Genetic differences among Mtb strains have been difficult to resolve due to incomplete genome references. We sequenced and analyzed complete genomes of 50 Mtb strains from all lineages, identifying 16 hypervariable regions and 3,498 core gene clusters whose diversity mostly stemmed from gene fragmentation, paralog duplication and deletion events and differences in the PE/PPE gene family representation. These differences may explain many of the varied clinical manifestations of TB. We created Pangenome Gene Reference Resource to unify genetic data for precise comparison studies to aid in developing new drugs vaccines and other interventions against this disease.

microbiology↗

bioRxiv2025

Chronic kidney disease exacerbates hyperlipidemia and atherosclerosis via miR-148a-3p targeting SIK1/AMPKα1 in liver

BackgroundCardiovascular complications are the leading cause of death in patients with chronic kidney disease (CKD). As a major risk factor for atherosclerotic cardiovascular disease (ASCVD), hyperlipidemia is a common sequela of CKD, which is linked to increased lipid synthesis, impaired lipoprotein clearance, and maladapted reverse cholesterol transport. Because exosomes can transport miRNAs to modulate intercellular and tissue communication, we hypothesized that exosomal miRNAs can act as endocrine-like molecules to modulate the CKD-associated hyperlipidemia and ASCVD. MethodsSmall RNA-seq and qPCR were used to determine the differential plasma level of exosomal miR-148a-3p in ASCVD patients with and without CKD. RNA-seq and in silico analysis were used to establish the regulation of lipid metabolism via miR-148a-3p/salt-inducible kinase 1 (SIK1)/AMP-activated protein kinase alpha 1 subunit (AMPK1) in the liver. Inhibition of miR-148a-3p or overexpression of SIK1/AMPK1 in ApoE-/- mice with 5/6 nephrectomy was used to elucidate the role of the miR-148a-3p/SIK1/AMPK1 axis in CKD-related hyperlipidemia and atherosclerosis. ResultsThe plasma level of exosomal miR-148a-3p was significantly elevated in patients with ASCVD and CKD (ASCVD/CKD) and ApoE-/- mice with 5/6 nephrectomy. Via circulating exosomes, kidney-generated miR-148a-3p was delivered to the liver, where it targeted SIK1/AMPK1 transcripts, thereby upregulating SREBP2/PCSK9 and reciprocally downregulating LDLR. Levels of SIK1 and AMPK1 were decreased in hepatocytes transfected with miR-148a-3p or treated with plasma exosomes from ASCVD/CKD patients, with attendant SREBP2 activation and attenuated LDL-C binding. The decreased LDL-C binding was rectified by SIK1/AMPK1 or LNA-miR-148a-3p overexpression. LNA-miR-148a-3p or AAV8-SIK1/AMPK administration in 5/6 nephrectomy/ApoE-/- mice significantly ameliorated hyperlipidemia and atherosclerosis. ConclusionIn ASCVD/CKD patients and nephrectomy/ApoE-/- mice, kidney-originating miR-148a-3p targeted hepatic SIK1/AMPK1 mRNA. This exosome-mediated endocrine effect upregulated SREBP2/PCSK9 and reciprocally reduced LDLR level, which elevated plasma LDL-C level and exacerbated ASCVD. These findings underscore a kidney-liver-artery axis involved in cardiovascular-kidney-metabolic syndrome.

pathology↗

bioRxiv2025

Mitoxantrone Hydrochloride Targets APP and LRRK2 to Improve Neurodegeneration in Parkinson's Models

BackgroundParkinsons disease (PD) is the second common neurodegenerative disorder, driven by the loss of dopaminergic neurons and pathological -synuclein protein accumulation. Currently, there is no disease-modifying therapy that can halt PD progression. Our previous study uncovered a critical pathogenic feed-forward loop between amyloid precursor protein (APP) and leucine-rich repeat kinase 2 (LRRK2), in which the two proteins mutually enhance each others expression, ultimately leading to mitochondrial dysfunction and neurotoxicity. Targeting this vicious cycle represents a promising therapeutic strategy for PD. MethodsTo discover novel inhibitors targeting this axis, we performed high-throughput screening of an FDA-approved drug library using a fluorescence-based biosensor system. We identified Mitoxantrone hydrochloride (MH), an antineoplastic agent, as a lead compound that inhibits both APP and LRRK2 expression. Its efficacy was validated in cellular models, including patient induced pluripotent stem cell (iPSC)-derived dopaminergic neurons and human peripheral blood mononuclear cells (PBMCs). Motor behavioural and safety assessments were subsequently conducted in PD mouse models. ResultsWe demonstrated that MH suppresses both APP and LRRK2 expression in various cell types in a dosage-dependent manner. In addition, MH also inhibits phosphorylation of LRRK2 and its downstream substrate Rab10. We further showed MH inhibits LRRK2 activity through direct binding to its kinase domain. Critically, MH treatment rescued dopaminergic neuron loss and reversed motor deficits in both 6-Hydroxydopamine (6-OHDA)-induced and LRRK2G2019S genetic PD mouse models. Moreover, we found that oral administration of MH is therapeutically effective, providing superior neuroprotection and behavioral recovery without detectable cardiotoxicity or gastrointestinal damage. ConclusionsOur findings demonstrate MH as a compelling, repurposable therapeutic candidate capable of disrupting a core pathogenic mechanism in PD.

neuroscience↗

bioRxiv2025

Integrating Multi-Structure Covalent Docking with Machine Learning Consensus Scoring Enhances Virtual Screening of Human Acetylcholinesterase Inhibitors

Acetylcholinesterase (AChE) inhibition is a key mechanism in the treatment of neurodegenerative diseases and in counteracting toxic exposures to pesticides and nerve agents. However, virtual screening of AChE remains challenging due to the enzymes structural flexibility and the chemical diversity of its covalently binding inhibitors. In this study, we developed an in silico protocol that integrates multi-structure covalent docking and machine learning (ML) consensus scoring to improve the prediction of AChE inhibitors. We analyzed 65 ligand-bound (holo) human AChE crystal structures using hierarchical clustering to identify four representative conformations, along with one high-resolution apo structure, for multi-structure docking. A curated library of 412 organophosphate and carbamate inhibitors was then docked covalently and non-covalently into each receptor conformation. The resulting docking scores were evaluated against inhibitors experimental logIC50 values using Spearmans rank correlation coefficient (r). Covalent docking outperformed non-covalent docking (r values up to 0.54 vs 0.18), and our ML consensus model trained on the five structures covalent docking scores achieved the highest predictive accuracy (r = 0.70), surpassing all single-structure and conventional consensus baselines. Chemical cluster analysis revealed structure-activity trends based on ligand flexibility, polarity, and aromaticity. SHapley Additive exPlanations analysis highlighted the ML consensus models ability to flexibly distribute the influence each structures scores played on its predictions. It identified and exploited relationships based on its training dataset that would be difficult to anticipate through a manual analysis of individual structures docking performance metrics. This framework is broadly applicable to other covalently targeted proteins, offering a generalizable and interpretable strategy for data-driven covalent inhibitor discovery.

bioinformatics↗

bioRxiv2025

Cross-species phenotypic profiling uncovers functional determinants of bacterial cold shock adaptation

Temperature shifts impose broad physiological stress, requiring precise and dynamic regulatory programs to restore cellular homeostasis. While the heat shock response is well characterized, the mechanisms underlying cold shock response (CSR) remain less understood. To identify genes critical for cold adaptation, we applied transposon sequencing (Tn-seq) to monitor mutant fitness across the full course of CSR and sustained low-temperature growth in two mesophilic bacteria, Escherichia coli and Bacillus subtilis. In B. subtilis, phenotypic profiling revealed a temporally structured program: membrane fluidity and cell wall remodeling were most critical in the early stage of CSR, whereas post-transcriptional regulation became essential during late-stage recovery to reprogram gene expression and restore growth. Cross-species comparison uncovered both conserved and species-specific mechanisms, with RNA metabolism and ribosome/translation regulators playing broad roles. Specifically, we identified a conserved synergy between two ribosomal RNA methyltransferases, RsmA and RsmH, in promoting cold adaptation. In B. subtilis, mutants lacking these enzymes exhibited significant delay in translation recovery following cold-induced global inhibition. Together, these findings provide a comparative, systems-level view of bacterial cold adaptation and establish a framework for exploring stress responses in pathogens and extremophiles.

microbiology↗

bioRxiv2025

Distinct neural moderators of resilience and vulnerability confer heterogeneous outcomes following early-life adversity

Early-life adversity (ELA) increases risk for psychiatric disorders, but outcomes are highly variable. Using multimodal neuroimaging and computational moderation in large adolescent cohorts, we systematically identify brain features that buffer or amplify effects of three ELA subtypes--familial interpersonal, non-familial interpersonal, and non-interpersonal adversity--on transdiagnostic psychopathology. Multimodal neural moderators were subtype- and pathology dimension-specific, revealing distinct neurobiological mechanisms moderating heterogeneous outcomes. Protective features clustered in limbic, sensory integration, and regulatory circuits (amygdala, parietal cortex, anterior cingulate), while vulnerability features concentrated in frontotemporal circuits. Individual features and a new Relative Resilience Index (RRI)--reflecting the individual balance between protective and vulnerability features across the whole-brain--prospectively predicted psychopathological progression over two years, linking brain signatures to future mental health trajectories. Findings establish the brain as dynamic moderator of distinct adversity effects and introduce a system-level marker for risk stratification, advancing mechanistic precision in youth mental health and guiding early intervention.

neuroscience↗

bioRxiv2025

Discovery of A Small Molecule non-IMiD Degrader of ZBTB7A for the Treatment of β-hemoglobinopathies

Sickle cell disease and {beta}-thalassemia, two major {beta}-hemoglobinopathies, pose significant clinical challenges globally. Current treatments often face limitations in efficacy and tolerability. The transcription factor ZBTB7A has emerged as a promising therapeutic target for reactivating fetal hemoglobin expression. Here, we report the discovery and characterization of SH6, a small molecule non-IMiD degrader of ZBTB7A. SH6 induces fetal hemoglobin in erythroid cell lines in a CRBN and ZBTB7A-dependent manner, and it is capable of inducing fetal hemoglobin expression in healthy donor, SCD and {beta}-thalassemia patient CD34+ cell derived erythroid cells. The efficacy of SH6 is confirmed in a xenotransplantation humanized mouse model. SH6 outperforms currently available therapeutic agents in vitro, and shows synergy with hypomethylating agents. SH6 exhibits a favorable in vivo toxicity profile. Our findings establish SH6 as a promising therapeutic lead candidate for further optimization towards clinical development for treatment of sickle cell disease and {beta}-thalassemia.

cell biology↗

bioRxiv2025

Insights into the linker domain in ABCB1/P-glycoprotein

ABCB1/P-glycoprotein(P-gp) is one of the best-known ABC transporters and its involvement in the clearance of chemotherapy agents in cancer cells can lead to multidrug resistance. The N- and C-terminal halves of P-gp are joined by a flexible linker region. Linker regions in ABC transporters often play pivotal roles (i.e. CFTR), however, there is no consensus on the importance of the role of the linker, the complete 3D-structure of which has not yet been determined. Prior studies on linker length showed major effects on P-gp function. In this work, we combined microsecond simulations ({approx}50{micro}s) on mouse and human P-glycoprotein, cryo-EM and other computational methods to trace a profile of the linker region. Different experimentally verified conditions involving the linker region were simulated, analysed and compared. Attachment of the linker to the membrane was spontaneously and occasionally encountered via a recurrent series of amino-acids, despite random starting conformations, suggesting that the lipid bilayer might be involved in linker regulation. As carried out in previous experiments, shortening the linker could potentially disconnect the ATPase activity from the substrate transport by interfering with one ATP site while introducing a short partially-structured linker shows remarkable stability in accelerated MD. Finally, we investigated the linker region by positioning it in specific quadrants of the 3D space, with simulations suggesting 1) a possible influence on protein flexibility, 2) selective tightening and opening of the two halves of P-gp, and a 3) possible stabilization of the inward-facing/occluded-state. The interaction between the linker and ATPs was investigated using protein-protein docking, simulations and a re-refined cryo-EM map where medium-low resolution and weak Coulomb density was found between the nucleotide binding domains.

biochemistry↗

bioRxiv2025

CCAAT-enhancer binding protein delta functions as a tumor suppressor gene in acute myeloid leukemia

There is a continued need for identification of novel disease drivers of acute myeloid leukemia as many patients experience relapse and have poor clinical outcomes. Analyses from our study and publicly available datasets predicted CEBPD as a novel tumor suppressor gene in acute myeloid leukemia. Consistent with the analyses, CEBPD knockdown experiments showed activation of MAPK signaling with concomitant increase in cell growth rate, while upregulation experiments suggested induction of myeloid differentiation marker CD14 expression in AML cell lines OCI-AML2 and OCI-AML5. Consistent with a previous report, our genomics analyses and azacytidine treatment experiments suggested a role for DNA methylation in downregulation of CEBPD expression during AML pathogenesis. Altogether, our results provide experimental evidence for a tumor suppressor function of CEBPD in AML.

cancer biology↗

bioRxiv2025

Methyl gallate Attenuates Post-Stroke Emotional and Cognitive Symptoms by Promoting Hippocampal Neurogenesis via PI3K/GSK3 and AMPK Signaling

Restoring hippocampal neurogenesis is an effective strategy for post-stroke recovery. Methyl gallate (MET) exhibits neuroprotective properties. However, the effect of MET in improving brain functional recovery in the post-stroke depression (PSD) model and its underlying mechanism remains unknown. Single-cell data analysis showed that the cell types and molecular characteristics of PSD are similar to those of primary depression but exhibit weaker synaptic plasticity and stronger inflammatory signals. In addition, molecular docking studies revealed that MET exhibits a significant binding capacity with AMPK/GSK3, suggesting that MET mediates the neuroprotective effects of both. In this study, we created a post-stroke depression (PSD) model by performing physical restraint after ischemia and tested the treatment effects of MET. We observed that MET significantly attenuated PSD-induced depressive-/anxiety-behaviors associated with a reduction of stress hormone corticosterone and ACTH levels. Morris water maze and recognition task results indicate that MET can also alleviate cognitive impairments in the PSD model. In the hippocampus of the PSD model, MET improved the proliferation and differentiation of neural stem/progenitor cells (NSPCs). MET treatment significantly enhanced the activity of AMPK and decreased the activity of GSK3{beta}. Furthermore, in primary neural progenitors under hypoxia, both the PI3K inhibitor LY294002 and the AMPK inhibitor compound C blocked the effects of MET to promote neural development. Animal experiments also confirmed that LY294002/compound C treatment could reduce the effects of MET in antidepressant behaviours. Taken together, our results indicate that PI3K, as well as AMPK-mediated adult neurogenesis, is restored by MET to improve brain functions in the PSD model.

neuroscience↗

bioRxiv2025

An orally available PfPKG inhibitor blocks sporozoite infection of the liver

Malaria remains a global health threat exacerbated by emerging resistance to antimalarial therapies and insecticides, climate-driven outbreaks, and limited chemoprotective options. Here, we report the characterization of RUPB-61, the first orally bioavailable inhibitor of Plasmodium falciparum cGMP-dependent protein kinase (PfPKG). RUPB-61 prevents infection by P. falciparum and P. cynomolgi sporozoites, including the formation of hypnozoites by the latter. A single oral dose blocks liver infection by P. berghei sporozoites in vivo, demonstrating efficacy consistent with further development as a once-weekly prophylaxis based on pharmacokinetic modeling. The compound retains activity against field isolates resistant to chloroquine, mefloquine, cycloguanil, sulfadoxine and pyrimethamine, suggesting low likelihood of cross-resistance to existing antimalarials. Structural studies and free energy-based modeling guided-compound design prospectively validated the predictive accuracy of an in silico model of PfPKG interactions with this chemotype. While selectivity profiling identified off-target activity against human kinases, structural modeling provides a clear path for optimization. These results establish PfPKG inhibitors as promising candidates for chemoprevention and support further preclinical development of the RUPB-61 chemotype. Author SummaryMalaria remains a serious global health threat, made worse by growing resistance to existing drugs and the spread of insecticide-resistant mosquitoes. A critical gap in our prevention toolkit is the lack of safe, long-acting oral drugs that stop malaria parasites from infecting the liver - the first and obligatory step of every new infection. Here, we report the characterization of RUPB-61, a compound that blocks an enzyme that the malaria parasite needs to invade and survive in the liver. We show that a single oral dose completely prevents liver infection in mice, and that the compound remains active against parasites that are resistant to several currently used antimalarial drugs. Using X-ray crystallography and computer-based modeling, we determined how RUPB-61 binds to its target in atomic detail, providing a roadmap for designing improved versions. While the compound shows some unwanted interactions with human proteins, our structural data offer clear strategies to solve this challenge. Together, these findings provide a solid foundation for developing a new class of once-weekly oral malaria prevention drugs.

microbiology↗

bioRxiv2025

Evaluating Molecular Docking Programs for RNA-Targeted Ligand Screening: Influence of Binding Modes and Ligand Types

Structured RNAs are critical regulators of gene expression and represent promising targets for drug discovery. Despite this potential, structure-based virtual screening approaches--in particular, molecular docking--have been underutilized for RNA targets, largely due to the intrinsic conformational flexibility of RNA and the limited docking methods specifically optimized for RNA. In our study, we evaluated the efficacy of three widely used docking programs for RNA-ligand docking screens. The performance of these programs -- Glide, Gold, and rDock, were evaluated with the dataset of 25 diverse RNA targets with 432 small molecule RNA binders. We found that the performance was similar across docking methods, but consistent differences emerged among RNA classes. We further explored consensus scoring across both receptor conformations and docking methods, finding that selecting the average scores across docking programs and RNA structures yielded stable performance when compared to individual methods. Finally, clustering analysis of RNA binders revealed distinct scoring function preferences for different chemotypes of RNA binders, underscoring the potential for tailored scoring strategies in RNA-targeted drug discovery. Together, this work provides a comprehensive evaluation of the performance of available docking methods in different cases of RNA-ligand docking and offers practical guidance for improving virtual screening against structured RNAs.

bioinformatics↗

bioRxiv2025

Structure and iron-transporting mechanism of brain organic cation transporter 1

Brain organic cation transporter 1 (BOCT1), also known as the solute carrier family 22 member 17 (SLC22A17) or the receptor for lipocalin-2 (LCN2), plays critical roles in health and disease. Its deficiency in mice results in early postnatal mortality and severe neurogenesis impairments. Despite its importance in physiology and pathophysiology, BOCT1s structure and transport mechanism remain elusive. Here, we integrate cryo-electron microscopy (cryo-EM), functional assays, biochemical experiments, and molecular dynamics simulations to elucidate the structure, substrate recognition, and transport mechanism of mouse BOCT1 (mBOCT1). The high-resolution cryo-EM structure reveals a distinctive N-terminal domain with a unique folding pattern dominated by a transmembrane loop atop TM6 (TML6), diverging from both known structures of SLC22 transporters and AlphaFold predictions. Notably, mBOCT1 functions as a high-capacity, low-affinity iron transporter independent of LCN2 binding. Iron transport is facilitated by a substrate gating mechanism involving TML6. These findings establish a structural basis for BOCT1s role as an independent iron transporter, enhancing our understanding of the transport mechanisms within major facilitator superfamily (MFS) transporters and providing new insights into brain iron homeostasis.

biophysics↗

bioRxiv2025

Nucleotide Asymmetry and Flexible Linker Dynamics Modulate Drug Efflux Cycle of P-glycoprotein, a Computational Study

Despite advancements in oncology, multidrug resistance (MDR) mediated by P-glycoprotein (P-gp/ABCB1) remains a major barrier to chemotherapy. P-gp is an ATP-binding cassette transporter that undergoes nucleotide-driven structural rearrangements to efflux chemotherapeutics, but the mechanistic details of the substrate transport remain poorly resolved. Here, we performed high-throughput molecular dynamics to simulate P-gp in a lipid bilayer (totaling [~]110 {micro}s) to dissect nucleotide-dependent conformational changes across the transport cycle. Our adaptive sampling strategy reveals asymmetric nucleotide coordination at nucleotide-binding sites (NBS), which correlates with transmembrane domain (TMD) restructuring for substrate efflux. The experimentally unresolved flexible linker transiently forms up to five turn -helix that affects nucleotide binding domain (NBD) dimerization process. We identified conformation-dependent substrate/allocrite pathways including nucleotide-specific access routes, while TMD-linker interaction facilitates substrate access tunnel formation. Together, these pathways reveal that the concerted interplay of nucleotide occupancy, linker dynamics, and overall protein conformation governs the structural plasticity and broad substrate promiscuity of the substrate binding cavity in P-gp. By integrating these findings, this work bridges static structural data with dynamic functional insights to further our understanding of the P-gp substrate translocation cycle.

biochemistry↗

bioRxiv2025

Dendritic cell-intrinsic TLR/MyD88 signaling promotes the clearance of a live-attenuated oral vaccine

A genital tract pathogenicity-attenuated Chlamydia muridarum mutant, named intrOv, is being developed into an oral vaccine against C. trachomatis infection in the genital tract. Although wild-type C. muridarum persists in the mouse large intestine for long periods, intrOv is cleared by the group 3 innate lymphoid cells that produce IFN{gamma} (IFN{gamma}+ILC3s). The current study aims to reveal the mechanism by which intrOv induces IFN{gamma}+ILC3s for its own clearance from the large intestine. IntrOv-induced IL-23 and IL-23 signaling were required for the clearance of intrOv from the large intestine. The intrOv clearance depended on dendritic cells, as depletion of CD11c+ cells reduced both IL-23 and IFN-{gamma}, resulting in the growth of intrOv. Deletion of MyD88 from dendritic cells, but not phagocytes or epithelial cells, rescued the growth of intrOv, indicating a critical role of MyD88 signaling in dendritic cells. Furthermore, TLR2/4 signaling is also essential for inhibiting intrOv, as the deficiency in TLR2/4 fully rescues the growth of intrOv. Both the TLR and MyD88 signaling must be in the same dendritic cells to inhibit intrOv, as the growth of intrOv in the MyD88- or TLR2/4-deficient mice was blocked by only wild-type bone marrow-derived dendritic cells but not dendritic cells deficient in either MyD88 or TLR2/4. Thus, we have demonstrated a dendritic cell-intrinsic TLR/MyD88/IL-23 pathway for recruiting effectors to clear intrOv from the large intestine. The information may help further improve the efficacy and safety of intrOv and guide the design of future mucosal vaccines.

immunology↗

bioRxiv2025

Enhancing CYP450-Ligand Binding Predictions: A Comparative Analysis of Ligand-Based and Hybrid Machine Learning Models

Predicting cytochrome P450 (CYP450) ligand binding is critical in early-stage drug discovery, as CYP450-mediated metabolism profoundly influences drug efficacy, safety, and adverse reaction risks. However, experimental determination of CYP450-ligand interactions remains resource- and time-intensive, underscoring the need for robust computational alternatives. While ligand-based methods are commonly employed, they often fail to fully account for structural intricacies governing protein-ligand interactions. To address this gap, we developed a hybrid machine learning framework integrating ligand descriptors, protein descriptors, and protein-ligand interaction descriptors, that include molecular docking-derived parameters, rescoring function components from multiple algorithms and structural interaction fingerprints (SIFt). Evaluated on CYP1A2 and CYP17A1 isoforms, our model demonstrated superior predictive accuracy in cross-validation compared to stand-alone molecular docking and ligand-based approaches. Furthermore, benchmarking against state-of-the-art tools --SwissADME and ADMETlab 3.0 -- revealed enhanced performance in binding prediction. This work establishes a versatile framework for advancing computational tools to prioritize CYP450 binding assessments during drug discovery.

bioinformatics↗

bioRxiv2025

Integrating Multimodal Data for a Comprehensive Knowledge Graph to Advance Infectious Disease Research

Infectious diseases remain a formidable threat to global public health, with their escalating morbidity and mortality rates compounded by recurrent epidemics and the alarming rise of antimicrobial resistance (AMR). These challenges have intensified the urgent demand for innovative therapeutic strategies that can accelerate drug development cycles and overcome traditional research bottlenecks. To address these critical needs, we present IDKG (Infectious Disease Knowledge Graph), a specialized large-scale biomedical knowledge network designed to bridge data fragmentation through multimodal data integration. The IDKG constructs comprehensive associations from 345 infectious diseases and 708 pathogens across heterogeneous biomedical sources systematically. The graph architecture comprises nearly 50,000 nodes (8 types, including Pathogen, Protein, etc.) and over 1.2 million edges (11 types, including treats, contains, etc.), establishing an interconnected framework that enables systematic interrogation of cross-disciplinary knowledge. The integrative approach effectively dismantles conventional data silos while preserving biological contextuality. We validated the IDKGs potential by applying graph neural network-based approaches for drug repurposing prediction in human metapneumovirus (hMPV) infection, a common acute respiratory infection for which effective specific antiviral drugs are currently absent. The successfully identification of established antiviral agents, such as ribavirin and emetine, by our M1 model demonstrated its predictive accuracy and biological relevance. IDKG unifies multimodal biomedical data into a network to accelerate drug discovery and bolster outbreak response. This establishes a data-driven, knowledge-based paradigm for infectious disease research. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/657361v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@f5dc24org.highwire.dtl.DTLVardef@147d584org.highwire.dtl.DTLVardef@113083corg.highwire.dtl.DTLVardef@81d523_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

A lineage-specific heat-induced feedback loop controls HrcA to promote chlamydial fitness under stress

Bacterial stress responses rely on transcriptional regulation by sigma factors and repressors. In Chlamydia, which lacks a dedicated heat shock sigma factor, repressor HrcA limits chaperone gene expression under non-stressed conditions. While HrcA function may be enhanced by the chaperone GroESL in a positive feedback loop, here we identify a heat-induced negative feedback loop mediated by HagF, a protein unique to Chlamydiota and conserved across Chlamydia species. We show that HrcA represses hagF, but heat shock induces hagF expression, leading to HagF accumulation and binding to HrcA. Structural modeling and pulldown assays indicate that HagF blocks HrcA dimerization, impairing DNA binding. This relieves repression of the hrcA-grpE-dnaK operon and promotes secondary differentiation in the developmental cycle, enabling infectious elementary bodies to form under heat stress. Our findings reveal dual feedback regulation that tunes chaperone gene expression and illustrate how transcriptional repression can be modulated in a minimal-genome pathogen.

microbiology↗