Biology subjects

Chen, J.

Publications and source records attributed to Chen, J..

At least 145 records · Page 8Linked to original sources

bioRxiv2026

A human intracranial map of consciousness returning from anesthesia

How consciousness arises from the brain remains a central yet unsolved question. Although substantial effort has been devoted to characterizing the neural correlates of conscious perception during wakefulness, how consciousness re-emerges from unconscious states remains poorly understood. Here, we took advantage of the rare opportunity to record human intracranial local field potentials from propofol-induced general anesthesia through the transition to behavioral engagement and subsequent full wakefulness, capturing both the stable states of unconsciousness and consciousness and the reconstituting neural dynamics that bridge them. Anesthesia cannot be defined by any single electrophysiological signature; rather, it is an organized low-frequency regime characterized by a constellation of coordinated neural phenomena, including aperiodic slow waves, alpha/beta periodicity, global alpha synchronization, and slow-wave-alpha/beta phase-amplitude coupling. Following anesthetic cessation, this regime progressively dissolved as neural excitability and dynamical complexity climbed. The appearance of conscious behavior coincided with a fast and dramatic transformation in high-gamma activity, from stochastic and unpredictable bursts to structured responses that were distributed, task-selective, and event-locked. These findings suggest that the recovery of consciousness is a multiscale reorganization in which distinct neural underpinnings rise and fall. Together, this work charts an electrophysiological map of how conscious cognition is extinguished, reconfigured, and restored in the human brain.

neuroscience↗

bioRxiv2026

Upregulation of ATP-purinergic P2x2 receptors in the cochlea over-amplifies hearing sensitivity leading to hyperacusis and attenuation by antagonists

Hearing hypersensitivity (hyperacusis) is a common hearing stress and can cause many psychological diseases, e.g., anxiety, learning disabilities, and attention-deficit/hyperactivity disorder (ADHD). Here, we report an unexpected finding that the upregulation of P2x2 ATP-purinergic receptors in the cochlea links to hyperacusis generation. We found that P2x2 expression in the cochlea but not in auditory centers was upregulated in the hyperacusis generated by Cx26 deficiency. Overexpression of P2x2 in the cochlea also caused hyperacusis. Conversely, downregulation of P2x2 expression or administration of P2x2 antagonists attenuated hyperacusis. We further found that upregulation of P2x2 receptors in the cochlea increased outer hair cell (OHC) electromotility through the post-transcription functional modulation to potentiate active cochlear amplification leading to hearing hypersensitivity. Such enhancements in OHC electromotility and active cochlear amplification were also suppressed by P2x2 receptor antagonists. Overall, these findings demonstrate that P2x2-mediated ATP-purinergic signaling in the cochlea plays a critical role in hyperacusis generation; targeting P2x2 receptors can attenuate hyperacusis stress, which may also offer a therapeutic strategy for other related psychological comorbidities. Significance statementHearing hypersensitivity is a common hearing stress and can cause many other psychological disorders. However, little is known about the underlying genetic and cellular mechanisms. Also, it lacks efficient drugs for their treatments in the clinic. In this study, we found that upregulation of P2x2 ATP-purinergic receptors in the cochlea can potentiate outer hair cell electromotility, which is an active cochlear amplifier in mammals and can increase hearing sensitivity and frequency selectivity, through post-transcription functional modulation to enhance active cochlear amplification leading to hearing hypersensitivity. These enhancements can be inhibited by administrations of P2x2 receptor antagonists both in vitro and in vivo. These findings revealed a new genetic and cellular mechanism underlying hyperacusis generation and opened a new avenue to develop an efficient therapy for this common hearing stress and other associated psychological comorbidities.

physiology↗

bioRxiv2026

A Transformer-based Multi-omics Model for Translation Efficiency in S. cerevisiae

Precise regulation of protein synthesis is fundamental to cellular homeostasis and remains a primary target for synthetic biology applications. However, the non-linear relationship between mRNA abundance and protein levels presents complexities that poses challenges for predictive engineering. Here, we present TRIM, a Transformer-based RNA Inference Model that leverages full-length mRNA sequences and multi-omics data to predict translation efficiency. By employing a Parallel Expert Mixer, TRIM achieves robust prediction accuracy (R2 [≥] 0.8,Pearson r [≥] 0.9). Trained on multimodal data from massive Saccharomyces cerevisiae isolates, TRIM demonstrates outstanding biological interpretability, helping to decipher complex translational patterns such as synergistic effects between bases, sequence-dependent codon preference in different stages, and distinct attention on key secondary structures. These results indicate that the integration of multi-omics data with holistic sequence modeling can effectively decode the cis-regulatory grammar of translation as well as providing a scalable and interpretable generative framework for future synthetic biology engineering. Availability and ImplementationThe source code and data used to produce the results and analyses presented in the manuscript are available from Github (https://github.com/ZeusLiu666/TRIM).

Molecular Biology↗

bioRxiv2026

EMAlign: accurate alignment of cryo-EM maps through main-chain probability using deep learning

Accurate alignment of cryo-EM density maps is essential for comparing conformational states, searching map libraries, and guiding atomic model building, but remains challenging for noisy ex-perimental maps and partially overlapping structures. Existing alignment methods are often based on raw maps, which may result in reduced accuracy due to the density noise, or require manual intervention for local alignment, which suffers from limited general applicability. Addressing the limitations, we present EMAlign, an automatic global and local cryo-EM map alignment with predicted main-chain probability using deep learning. First, EMAlign predicts main-chain prob-ability maps from raw cryo-EM density maps using a BiMCUNet network. Then, a fast Fourier transform (FFT)-based search strategy is used to globally search the accurate alignment between cryo-EM maps based on predicted main-chain probability maps. As such, the main-chain prob-ability map overcomes the noisy raw map problem, and the FFT-based exhaustive global search ensures the general applicability of alignment. EMAlign is evaluated on 64 global map pairs, 195 local map pairs, and 60 structure-to-map pairs at 3-10 [A] resolution and compared with gm-fit, fitmap, VESPER, and CryoAlign. It is shown that EMAlign outperforms the other methods in both global and local alignment, achieving mean RMSDs of 1.03 [A] (global), 2.56 [A] (lo-cal), and 0.82 [A] (structure-to-map), with success rates of 100.0%, 100.0%, and 98.3% under the criterion of RMSD < 10 [A] . The EMAlign package is freely available at https://github.com/huang-laboratory/EMAlign/.

bioinformatics↗

bioRxiv2026

Cortical adaptation to muscle fatigue does not alter early proprioceptive processing in primary sensorimotor cortex

Muscle fatigue potentially interferes with proprioceptive afference from peripheral "movement sensors"-- the proprioceptors, which may hinder the crucial sensorimotor integration and thus locomotor performance. However, little is known about how muscle fatigue affects cortical processing of proprioceptive afference. Twenty-four healthy volunteers (30.7 {+/-} 6.5 yrs, 13 females) participated in the experiment, which included magnetoencephalography (MEG) recordings during ankle proprioceptive stimulation (2-Hz passive movements), and fatigue tasks comprised of isometric ankle plantar flexion. Corticokinematic coherence (CKC) between foot acceleration and MEG signals was examined before (PRE) and [~]3 min after (POST) the fatigue tasks to quantify the cortical proprioceptive processing. CKC peaked in the gradiometer pairs above the foot region of the primary sensorimotor (SM1) cortex in each participant. CKC strength did not show significant difference between PRE and POST at 2 Hz (0.30 {+/-} 0.12 vs. 0.30 {+/-} 0.14, p = 0.981) or its first harmonic at 4 Hz (0.38 {+/-} 0.14 vs. 0.37 {+/-} 0.13, p = 0.724). However, 4-Hz MEG power was [~]30% lower in POST than in PRE. Surprisingly, fatigue-induced bilateral increase of alpha and beta power was observed in SM1 hand regions during the movement stimulation. Our results indicated that the early processing of proprioceptive afference from the ankle joint was negligibly affected by muscle fatigue, or it recovered rapidly. The effects of muscle fatigue on the proprioceptive processing appear to extend beyond the primary somatotopic regions to bilateral SM1 neuronal networks. This cortical adaptation to muscle fatigue potentially preserves proprioceptive processing by modulating SM1 inhibitory neurons, offering a novel perspective for future research on proprioception.

neuroscience↗

bioRxiv2026

Multitrophic interaction networks mediate biodiversity effects on ecosystem multifunctionality

Biodiversity loss threatens the multifunctionality of ecosystems on which human well-being ultimately depends. Changes in multitrophic species interactions may be key to explaining the ecological consequences of biodiversity loss, but research explicitly linking species interactions and ecosystem multifunctionality remains rare. To assess interaction-mediated biodiversity effects and underlying mechanisms, characterizing the structure of species interaction networks is invaluable. Using comprehensive species interaction and ecosystem functioning data from a large-scale tree biodiversity experiment, we find consistent effects of the structure of species interaction networks on ecosystem multifunctionality across multiple types of antagonistic and mutualistic interactions. While positive effects of network size align with expected positive effects of multitrophic species diversity, positive effects of niche overlap among interacting species and negative effects of highly connected species (i.e. high linkage density) reveal additional, interaction-mediated drivers of multifunctionality. Specifically, the effects of niche overlap suggest benefits of functionally similar species, and the effects of linkage density underscore the importance of specialized interactions in promoting ecosystem multifunctionality. These findings emphasize that to effectively safeguard ecosystem service provisioning, ecosystem management and biodiversity conservation not only need to account for biodiversity changes at multiple trophic levels, but also explicitly for how species interact among each other.

ecology↗

bioRxiv2026

Antagonism of stress granules key for SARS-CoV-2 infection and pathogenesis.

Viruses must subvert host responses to facilitate successful infection. While most antiviral responses are associated with interferons, stress granules (SG) are another barrier to viral infection by inducing translation arrest. To combat SG activity, viruses have evolved mechanisms to disrupt formation and disassemble these complexes. Our prior studies identified residues in SARS-CoV-2 NSP3 (Y138/F145) and nucleocapsid (F17) that independently antagonize SG activity. Disrupting these key residues in NSP3 or nucleocapsid attenuated viral replication, but only modestly impacted in vivo pathogenesis suggesting overlap in SG antagonism partially compensate for the individual losses. In this study, we evaluated a SARS-CoV-2 mutant (YF/F17A) that combines the NSP3 and N mutations. We find that loss of both SG antagonizing functions attenuates SARS-CoV-2 replication in vitro. While no changes are seen in type I IFN sensitivity, attenuation corresponds to increased induction of SGs. Importantly, the SARS-CoV-2 YF/F17A mutant has significant attenuation in vivo with reduced viral replication, less weight loss, and limited immune pathology. Notably, infection with the YF/F17A mutant stimulated less interferon and inflammation. Despite these muted host responses, the YF/F17A mutant stimulated robust protection against subsequent challenge with WT SARS-CoV-2. Overall, the study highlights the importance of SG control for SARS-CoV-2 infection and offers a novel, interferon independent target for vaccination and therapeutic treatment going forward. ImportanceThis study demonstrates that SARS-CoV-2 uses multiple mechanisms to block host stress granules during infection. Knocking out both N and NSP3 mediated antagonism of stress granules attenuates viral replication and disease caused by SARS-CoV-2. Importantly, while most therapeutics target key viral processes or induce interferon pathways, this study shows stress granule activation as a novel approach to attenuate and treat coronavirus infection.

microbiology↗

bioRxiv2026

Stability and Compressibility of Tear Film Lipid Layer: Impact of Benzalkonium Chloride Presence

The tear film lipid layer (TFLL) prevents excessive evaporation, thereby maintaining normal ocular surface function. One characteristic of a healthy TFLL is a gel-like structure that resists disruptive mechanical forces; however, this has not been clearly demonstrated. Herein, the compressibility of TFLL was investigated via surface chemistry experiments of meibomian gland secretions (meibum), the source of TFLL. Meibum was collected post-mortem from bovine eyelids, and purity was verified by mass spectrometry. Meibum films on a water subphase in a Langmuir-Blodgett trough were studied. The changes in surface pressure ({pi}) versus area (A) during compression were recorded, and the corresponding compressive modulus (Cs-1) versus{pi} isotherms were determined. The meibum film was stable at a surface pressure as high as 32 mN/m and maintained a near-constant Cs-1 of 24-32 mN/m across a{pi} range of 8-30 mN/m, demonstrating gel-like behavior. Comparison of the maximum Cs-1 with those of representative individual meibum lipids supports the presence of a monolayer predominantly composed of low-polarity lipids, including wax esters, cholesteryl esters, and diesters. The average molecular areas determined for the film and reported for representative lipid species suggest that the monolayer is predominantly composed of saturated, ultralong-chain, low-polarity lipids and that the TFLL includes a dense monolayer and a loose overlying sublayer. This structural model is further supported by the lower Cs-1 (10 mN/m) and larger average molecular area (68 [A]2) observed for films containing a mixture of meibum and benzalkonium chloride (BAK), a preservative with surfactant properties.

biophysics↗

bioRxiv2026

mRNA concentration-dependent translation enables rapid and sharp patterning in resource constraint Drosophila embryos

One of the fundamental challenges in protein expression during embryogenesis is the establishment of dynamic protein patterns under the resource constraint. This constraint is particularly stringent in enclosed Drosophila early embryogenesis, where protein synthesis relies exclusively on maternally supplied resources, yet its zygotic protein patterns still exhibit sharp boundaries and dynamic abundance changes for body plan development. Here, by integrating single-molecule imaging with mathematical modeling, we reveal that an mRNA concentration-dependent translation enables sharp and dynamics patterning even under resource constraint in embryos. Firstly, we reveal pronounced spatial heterogeneity in the fraction of hunchback (hb) mRNAs engaged in translation, challenging the conventional assumption of uniform translation rates. We further demonstrate that hb mRNA concentration is a dominant predictor of this heterogeneity, showing an increasing-saturation relationship between this translating fraction and mRNA abundance. This regulatory strategy enables combination of sharp Hb protein boundaries and close tracking of protein level to mRNA concentration decline under slow protein turnover rates, correlated to the resource efficiency in embryos. Together, our findings identify a translational control strategy that links molecular-scale regulation to embryonic pattern formation under resource constraints and highlight mRNA concentration-dependent translation as an effective way simultaneously enabling dynamic and economical spatial gene expression in biological systems.

biophysics↗

bioRxiv2026

Genetic manipulation of a giant virus-associated virophage

Virophages are double-stranded DNA viruses that hyperparasitize giant viruses infecting unicellular eukaryotes. Parasitization by virophages often reduces the replication of giant viruses, thereby modulating microbial communities in the environment. However, the molecular mechanisms underlying the tripartite relationship are largely unknown due to methodological limitations. In the present study, we developed a reverse-genetics system for a Sputnik virophage that parasitizes the amoeba-infecting giant virus, mimivirus. We demonstrated that transfection of genomic DNA could recover infectious virophage particles. Transfection of genomic DNA synthesized by circular polymerase extension reaction (CPER) also resulted in the recovery of infectious viruses. As a proof of concept, we successfully modified two Sputnik genes by transfecting CPER-assembled mutant genomic DNA. Collectively, our reverse-genetics system provides a framework for assessing the functional importance of Sputnik genes and should facilitate future genetic studies of virophages. Significance statementVirophages are viruses that hyperparasitize giant viruses, which infect unicellular eukaryotes and have extremely large particles and genomes. Giant viruses modulate microbial communities not only by killing their hosts but also by altering host cellular functions. Virophages modulate the replication of giant viruses, thereby driving ecosystem dynamics. Previous studies have demonstrated their widespread distribution through isolation and metagenomic analyses. However, the functions of most virophage genes remain unknown. Due to the lack of genetic tools, the molecular mechanisms underlying the interactions between virophages and giant viruses remain largely elusive. Here, we established a virophage reverse-genetics system based on circular polymerase extension reaction. Our results demonstrate that the system can dissect virophage gene functions and will accelerate virophage genetics.

microbiology↗

bioRxiv2026

Trans-kingdom delivery of aphid-derived small RNAs into Arabidopsis thaliana modulates plant immunity

Herbivore insects are on an evolutionary tug-of-war with plants. An important part of the plant-herbivore insect interaction is the exchange of molecules, in particular proteins (in the form of effectors) and RNA. Among RNAs, small RNAs have been identified as important molecules shaping the communication between different pests/parasites and their host, but the role of these molecules in the interaction between aphids and plants is not well understood. Here, we explored the role of aphid-derived sRNAs in the interaction between Arabidopsis thaliana and the green peach aphid, Myzus persicae. Using sRNA sequencing, we identified a significant amount of bona-fide aphid-derived sRNAs within Arabidopsis tissues. Using immunoprecipitation followed by sRNA sequencing and degradome sequencing we determined that these sRNAs are incorporated into endogenous AGO proteins, in particular AGO1, and induce the cleavage of transcripts involved in the modulation of the immune response against the aphid. Our results indicate that aphid sRNAs attenuate the immune response of Arabidopsis thaliana and can improve aphid performance. In addition, we identified that aphid-derived sRNAs are commonly injected into other aphid-host combinations. Accordingly, our work indicates that aphid-derived sRNAs are active players in aphid-host interactions.

Plant Biology↗

bioRxiv2026

AI-Accelerated Structure Elucidation of Boavistamides A-C, Cyclic Depsipeptides from a Marine Filamentous Cyanobacterium Collected in Cabo Verde

Boavistamide A (1), a new alkyne-containing cyclic depsipeptide featuring the rare 3-amino-2-methyl-7-octynoic acid (AMOYA) moiety, was discovered along with two structurally related analogs, boavistamides B and C (2 and 3), from a filamentous marine cyanobacterium collected on Boa Vista Island, Cabo Verde. Their isolation was guided by antiplasmodial activity, GNPS MS/MS molecular networking, LC-MS profiling, and dereplication using the MarinLit database. The planar structures of boavistamides A-C (1-3) were elucidated through comprehensive HRMS and 1D/2D NMR analyses, with annotation support from AI-based tools SMART-NMR 2.1 and DeepSAT. The absolute configurations were established using Marfeys analysis and L-Phe-OMe coupling, complemented by NMR-based conformational studies. Boavistamides A and B exhibited moderate antiplasmodial activity with no mammalian cell cytotoxicity. Microscopic observations and metagenomic binning identified the producer strain as belonging to the genus Okeania (Microcoleaceae). These results expand the chemical diversity of AMOYA-containing cyanobacterial metabolites and highlight the utility of integrated metabolomics and AI-assisted workflows for natural product discovery from environmental samples. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/732064v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@6577feorg.highwire.dtl.DTLVardef@1a8d656org.highwire.dtl.DTLVardef@18fc299org.highwire.dtl.DTLVardef@130d3d0_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Zfp719 is a transcription factor important for maintenance of hearing in mice

Zfp719 is a zinc finger transcription factor which, when mutated, results in hearing impairment in mice. Its closest human orthologue, OTK18, has been linked to tinnitus in large human cohorts. Here we present our investigation of the electrophysiological, structural and transcriptional phenotypes in Zfp719tm1a mutant mice. Homozygotes have near-normal hearing at two weeks old, but lose sensitivity rapidly between two and three weeks, suggesting that while Zfp719 is not required for development, it is important for maintaining hearing. Heterozygous mice exhibit progressive hearing impairment for high frequencies at older ages. We observed damaged and degenerating outer hair cells from as early as three weeks old in homozygotes. We carried out bulk RNAseq at three ages and found one gene consistently misregulated, a long non-coding RNA specific to mice, Gm15083. A better understanding of the genes regulated by Zfp719 may shed light on genes and proteins important for maintaining hearing in humans.

neuroscience↗

bioRxiv2026

Unlocking Your Programmable and Creative RNA Sequence Designer with RDiffusion

RNA, a pillar of the central dogma, has shaped three billion years of evolution. Despite cataloging tens of millions of non-coding RNAs and annotating millions, we have barely scratched the surface of the vast, unexplored RNA sequence space. Here, we introduce RDiffusion, a discrete-diffusion-based generative transformer model for RNA sequence design. Conditioned on diverse biological features, such as desired function, family type, secondary and tertiary structure, or binding protein partners, it can guide the generation of novel RNA sequences tailored to specific design specifications. We evaluate RDiffusion across a broad spectrum of RNA design tasks and find that it not only surpasses all baseline methods in design success rate and sequence diversity but also achieves advanced performance on downstream tasks. To demonstrate its translational potential, we applied RDiffusion with a customized seed-screening pipeline to de novo design therapeutic MicroRNA(miRNA) mimics in osteoarthritis (OA). This strategy identified mimic 0-4 as a lead candidate targeting SDC4 to preserve ECM homeostasis and cartilage integrity, with robust efficacy validated in clinical OA samples. Altogether, RDiffusion holds strong potential to serve as a cornerstone for RNA generation and representation learning, establishing a generalizable AI-driven paradigm for RNA therapeutic discovery.

bioengineering↗

bioRxiv2026

Continuous Strategy Adaptation and Discrete Switching Driven by Environment and Internal State in Meta-Learning

AO_SCPLOWBSTRACTC_SCPLOWBehavioral strategies can change in response to environmental and internal states, either gradually or abruptly, enabling flexible adaptation. Such strategy regulation is central to meta-learning, the ability to learn to learn. Previous studies analyzed temporal or condition-dependent strategy change using models and theories that assume continuous or discrete changes. Here, we analyze the mices behavior in a two-step decision task using four different approaches: stay-switch choice probability analysis; generalized linear mixed model (GLMM) of choice and reaction time (RT) given preceding task events; fitting a reinforcement learning (RL) model with time-varying meta-parameter by a novel multiple-step particle filtering method; and fitting a finite internal state (FIS) model that produces choice and RT depending on discrete state transition. Together, the stay probability and GLMM analyses reveal that learning progress encourages a shift toward a model-based, value-based learning strategy, accompanied by elevated choice perseveration. More uncertain reward settings or changes in them lead to random, exploratory behavior. Meta-parameter dynamics show faster learning, greater involvement of a model-based strategy, higher choice stochasticity, and more rapid development of choice perseveration with less contribution to the final decision as learning progresses. Exploratory behavior in the face of uncertain reward settings or changes in those settings is underpinned by slower forgetting and greater model-based contribution. FIS modeling discovered a trial-level switch between an optimal value-based learning state and a suboptimal self-repeating state. Meta-parameter dynamics reflect continuous strategy changes, while state transitions capture abrupt, discrete strategy switches. At an intermediate timescale, when reward settings change, two processes interact: mice persist in a self-repeating state, leading to attempts at model-based strategy with incomplete adaptation.

animal behavior and cognition↗

bioRxiv2026

GEOAgent: An AI-driven Autonomous Framework for Intelligent GEO Data Retrieval and Standardized Preprocessing

Datasets in the Gene Expression Omnibus (GEO) remain difficult to reuse at scale because sample annotations are heterogeneous and raw sequencing data require assay-specific preprocessing. We present GEOAgent, an AI-driven autonomous framework designed for intelligent dataset retrieval and standardized preprocessing by coupling autonomous semantic governance with an automated Nextflow pipeline named bioStream. Metadata from 181,760 sequencing series and 84,756 associated PubMed records were organized in a relational database and semantic index to support natural-language dataset retrieval. The framework automatically determines assay modalities, resolves experimental design pairings, and standardizes sample naming to minimize manual curation overhead. Based on these parsed attributes, the framework generates deployment-ready manifests to automatically execute containerized workflows across bulk and single-cell omics modalities. In expert-curated benchmarks, the workflow achieved 96% retrieval precision alongside 100% accuracy in assay classification and sample relationship resolution. The web platform is publicly accessible, while the source code and associated databases are openly available via GitHub and Zenodo.

bioinformatics↗

bioRxiv2026

Enhanced Target Binding by Leritrelvir Restores Dimerization of Mpro Mutants and Mitigates Drug Resistance

The SARS-CoV-2 main protease (Mpro) has been a major target of antiviral drug development, leading to the development of inhibitors such as nirmatrelvir, the antiviral component of the COVID-19 drug Paxlovid. However, resistance-associated mutations that reduce the efficacy of current Mpro inhibitors, particularly nirmatrelvir, have emerged. Here, we evaluated the inhibitory activity of leritrelvir (RAY1216), an Mpro inhibitor approved in China for COVID-19 monotherapy, against a panel of Mpro variants carrying mutations at 12 resistance-associated residues distributed across four catalytic subsites. Using integrated biochemical, biophysical, structural, and cellular analyses, we demonstrate that leritrelvir retains stronger inhibitory activity against most tested resistant mutants compared with nirmatrelvir. Most of the tested mutations promote Mpro dimer dissociation, with E166V showing a particularly pronounced effect and markedly compromising nirmatrelvir binding. In contrast, thermal shift and size-exclusion chromatography assays demonstrate that leritrelvir binding restores dimerization of these Mpro mutants. Sixteen high-resolution crystal structures reveal that leritrelvir binding re-instates key dimer-interface interactions disrupted by resistance mutations. Mini-replicon assays further confirm leritrelvir to possess enhanced cellular antiviral efficacy compared with nirmatrelvir. Our findings indicate that tighter leritrelvir binding enables more effective inhibition of dissociation-prone Mpro mutants than nirmatrelvir, supporting its use as a more resilient antiviral agent for SARS-CoV-2 treatment.

molecular biology↗

bioRxiv2026

Most inhibitors with defined yeast targets have limited activity against the microsporidian Nematocida parisii

Microsporidia are obligate intracellular parasites that infect diverse animals. Budding yeast has long been used to define core molecular pathways and inhibitors that target them. To test whether these compounds can target conserved pathways in the microsporidian Nematocida parisii, we assessed 15 inhibitors with defined yeast targets that had not previously been tested for effects on infection of Caenorhabditis elegans. Most showed little activity against N. parisii, except tunicamycin. These results identify tunicamycin as a potential tool for studying endoplasmic reticulum stress in microsporidia, while indicating that most yeast-targeted inhibitors are largely ineffective in this system.

microbiology↗