Biology subjects

Song, L.

Publications and source records attributed to Song, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Liverwort MpSDR4 regulates abscisic acid sensitivity and gemma cup growth

Complex traits often evolve by co-opting pre-existing genetic components. Orthologs of the transcriptional co-factor SEED DORMANCY 4 (SDR4) are found across seed-bearing and seed-free land plants. In flowering plants, loss-of-function mutants of sdr4 orthologs in rice and Arabidopsis exhibit opposite phenotypes in seed germination, a trait regulated by the phytohormone abscisic acid (ABA). We uncovered a major gene duplication event that closely preceded the origin of seed plants, by using a structure-informed molecular phylogenetic analysis. This duplication gave rise to the paralogous SDR4 and DIG/DIL clades, which are broadly retained across the seed plants. Investigating the role of SDR4 homologs in the common liverwort Marchantia polymorpha, a seed-free model organism with only a single SDR4-like homolog (MpSDR4), may provide insights into how SDR4 evolved to regulate dormancy and germination in other land plants. Loss-of-function mutants of Mpsdr4 and transcriptome profiling showed that MpSDR4 modulates ABA sensitivity, consistent with the idea that SDR4 subsequently evolved to regulate hormone responses related to seed germination, with additional functional divergence between monocots and eudicots. Furthermore, Mpsdr4 mutants exhibit elevated growth of gemma cups, contrasting the roles of SDR4 orthologs in asexual reproduction in liverwort with the regulation of seed traits in flowering plants.

plant biology↗

bioRxiv2026

Common viral infections seed regionally distinct resident memory T cells in the human CNS

T cells persist in the central nervous system (CNS) and can drive both protection and neurological disease. How these cells are organized in humans and what they recognize is largely unknown. Here, we profiled CD8 T cells across anatomically distinct CNS regions, obtained through on-site autopsies and temporal lobe resection surgeries, using single-cell RNA sequencing, paired T cell receptor sequencing, and DNA-barcoded tetramers. Resident memory T cells (TRM) specific for Epstein-Barr virus, cytomegalovirus, influenza A, and SARS-CoV-2 were identified across CNS compartments. Anatomical location was the strongest correlate of TRM cell state, with leptomeningeal cells adopting a cytokine-poised TRM program, whereas brain TRM cells were transcriptionally restrained. Cells of the same clonotype spanned tissues yet adopted local transcriptional states. Viral specificity added another layer of TRM heterogeneity with GZMK/GZMA-expressing EBV-specific populations and interferon-stimulated gene signatures in SARS-CoV-2 and Influenza A-specific cells. The human CNS thus harbors regionally distinct CD8+ TRM shaped by common viral exposures.

immunology↗

bioRxiv2026

Lossless compression of protein databases for efficient and accurate metagenomic sequence classification with Centrifuger

We present a lossless compression algorithm for indexing a protein database while supporting fast taxonomic classification in the method Centrifuger. The algorithm is a new scheme of the previously proposed run-block compression algorithm to reduce the size of the Ferragina-Manzini (FM) index, and it scales better with alphabet size than the original. On the RefSeq prokaryotic and viral protein sequences, Centrifuger reduces the memory footprint by over a third compared to the method Kaiju that builds on a plain FM-index, while having comparable running time. Furthermore, the compressed FM-index is lossless and can locate matches of arbitrary length, which helps Centrifuger achieve greater accuracy than Kraken2, a k-mer-based taxonomic classification method. We leverage the computational efficiency of Centrifuger to create an index of size 182 GB for classifying the reads against the full nr database that contains about 250 billion amino acid characters. Using this index, Centrifuger reveals different SARS-CoV-2 infection states and viral transcriptome profiles across human cell types from single-cell RNA-seq data.

bioinformatics↗

bioRxiv2026

ABSCISIC ACID INSENSITIVE 5 fine-tunes expression of lipid body genes through modulating ABSCISIC ACID INSENSITIVE 3 binding strength

Seed development and germination are two important transitions in a plant's life cycle. During such transitions, extensive transcriptional regulation reprogramming is performed to support major changes in cellular, tissue, and physiological levels. Transcription factors contain diverse interacting partners for precise transcriptional regulations. Different combinations of interactors would affect temporal and spatial transcriptional regulations. While a large number of transcription factors (TFs) are involved in these transcriptional networks, in vivo investigation on how TF interaction dynamics affect transcriptional regulation in seed-to-seedling transition is lacking. ABSCISIC ACID INSENSITIVE 3 (ABI3) has played a major role serving as the center hub of these transcriptional networks during seed development. ABI3 has diverse interacting partners, including ABI5. The presence of these interacting partners allows ABI3 to bind to diverse cis-regulatory elements (CRE) in a precise manner. One of the processes collectively governed by ABI3 and ABI5 is nutrient deposition, including lipid storage. ABI3 and ABI5 regulate lipid body (LB) related genes such as oleosins for controlling LB dynamics. Notwithstanding, not much is known on ABI5's significance on ABI3's binding towards CREs. Here, we showed that ABI5 impacts ABI3's binding strength towards G-Box motifs. The interaction of ABI3 and ABI5 strengthens ABI3's binding towards ABI3 induced genes. We further demonstrated that ABI3 and ABI5 regulates far more LB related genes during seed development and germination, suggesting that ABI3 and ABI5's have a more precise role in regulating LB dynamics. Our results had further consolidated ABI5's role in ABI3's binding preferences and strength and its significance in controlling LB during seed development and germination.

plant biology↗

bioRxiv2026

A mycovirus identified from an outbreak fungal species complex reveals a parallel antiviral system

Mycoviruses are prevalent across major fungal lineages, yet none have been reported in the Cryptococcus gattii species complex (CGSC), the causative agent of the largest known fungal outbreak in immunocompetent hosts. Consequently, the occurrence of mycoviruses and the host determinants governing their infection in this important pathogenic clade remain unexplored. Through screening of 386 Cryptococcus isolates, we identified a mycovirus, designated CgTV1, in an environmental isolate of the Cryptococcus gattii species complex (CGSC). CgTV1 is a double-stranded RNA (dsRNA) mycovirus of the genus Totivirus, with a genome encoding a capsid protein and an RNA-dependent RNA polymerase. We showed that CgTV1 establishes a cryptic infection, because neither viral presence nor its clearance significantly alters host transcriptomic profiles, suggesting the existence of mechanisms that maintain virus-host homeostasis. Population genomic analyses reveal that an intact RNAi pathway constitutes a critical genetic barrier, and CgTV1 persistence strictly requires loss of function mutations in both AGO1 and AGO2. By pan-transcriptomics across 43 CGSC strains, we further uncovered an RNase III gene, CAI1, which exhibits high expression in the mycovirus positive isolate. Biochemical analysis indicates that Cai1 directly recognizes and degrades CgTV1 dsRNA, thereby constraining excessive mycoviral proliferation. We further demonstrate that Dicer and Cai1 act in parallel to maintain virus-host homeostasis: their combined ablation results in higher viral loads and more pronounced changes in host gene expression than ablation of either factor alone. Collectively, our findings provide the evidence of the occurrence of a mycovirus in the CGSC and reveal parallel mechanisms that enable cryptic mycoviral infections.

genetics↗

bioRxiv2026

Tumor γδ T-cell abundance is associated with favorable cancer treatment outcomes

Purpose: Clinical response to immune checkpoint blockade (ICB) remains variable. We asked whether immune-cell populations in the tumor microenvironment (TME) are associated with benefit across treatments and tumor types. Experimental Design: We analyzed pretreatment bulk tumor RNA-seq from ICB cohorts and TCGA. Gene-level effects associated with ICB response or TCGA survival were projected onto Human Primary Cell Atlas profiles of 157 cell types. Cox and mixed-effects models accounted for cancer type, cohort, and therapy, as appropriate. After {gamma}{delta} T cells emerged as a leading population, we adjusted their associations for eight CD8 estimators and evaluated them using TRUST4-based TRG/TRD reconstruction and single-cell RNA-seq. Results: {gamma}{delta} T-cell programs were among the signatures consistently associated with ICB response and favorable TCGA survival. Across ICB cohorts, {gamma}{delta} T-cell abundance was associated with response (n=1,356; OR, 1.38; 95% CI, 1.23-1.56) and overall survival (n=1,074; HR, 0.82; 95% CI, 0.76-0.88), with associations persisting after CD8 adjustment. ICB-response-associated cell-type profiles were strongly concordant with chemotherapy response (r=0.92) and moderately concordant with radiation response (r=0.58); targeted and hormone therapy analyses were underpowered. TRUST4 reconstruction and single-cell RNA-seq provided orthogonal support for the {gamma}{delta} signal. Conclusions: Pretreatment {gamma}{delta} T-cell abundance was associated with favorable ICB outcomes and survival across cancers, while related cell-type programs extended to selected non-immunotherapy response settings. Although associative and context dependent, these findings support prospective evaluation of {gamma}{delta} T-cell abundance as a candidate tumor-immune biomarker.

immunology↗

bioRxiv2026

Pretraining Enhances Megabase-Scale Gene Expression Prediction with GeneUnet

Predicting gene expression from DNA sequence across diverse genomic tracks is essential for understanding gene regulation and interpreting non-coding variants. Existing supervised methods are limited to few species and fail to exploit conserved regulatory mechanisms, while DNA foundation models capture cross-species information but remain constrained to kilobase-scale contexts insufficient for this task. Here we introduce GB.GeneUnet, an 837M-parameter transformer-based U-Net pretrained on 6 trillion tokens from multi-species genomes in OpenGenome2, extending genomic context to 1 Mb with up to 100x inference speedup over GeneMoE, a preliminary MoE transformer baseline of similar model size pretrained on the same data. Fine-tuned for gene expression prediction, GB.GeneUnet achieves state-of-the-art performance on the Borzoi benchmark at 524 kb context, and attains performance comparable to AlphaGenome at 1 Mb context while requiring a lighter fine-tuning procedure. Together, these results establish a scalable framework linking multi-species pretraining to ultra-long-context gene expression modeling.

genomics↗

bioRxiv2026

mBaoJin-labeled pangolin coronavirus for evaluating population cross-neutralizing antibodies and the entry-inhibitory activity of cepharanthine

Replication-competent coronaviruses carrying fluorescent protein-tagged structural proteins remain scarce. Using the highly attenuated pangolin coronavirus GX_P2V(short_3UTR) as a backbone, we generated GX_P2V-mBJ-N, a recombinant coronavirus in which the bright green fluorescent protein mBaoJin is fused to the nucleocapsid (N) protein. The reporter virus is attenuated and genetically unstable in normal Vero cells but can be amplified to high titers in cells expressing wild-type N, and its fluorescence directly reports N protein expression. Using this authentic-virus platform, we show that high-titer GX_P2V cross-neutralizing antibodies persist in most healthy individuals and that cepharanthine potently blocks viral entry. GX_P2V-mBJ-N thus provides a simple and reliable tool for coronavirus tracing, immune surveillance, and antiviral drug evaluation.

microbiology↗

bioRxiv2026

Quantitative profiling of intrinsic dCas9-DNA recognition reveals key determinants of guide RNA performance

CRISPR technologies based on nuclease-deactivated Cas9 (dCas9) rely on programmable DNA binding rather than DNA cleavage, yet the intrinsic DNA-recognition properties that govern optimal guide RNA (gRNA) performance remain poorly understood. Existing approaches either measure genomic occupancy in cells or infer dCas9 behavior from cleavage-based Cas9 datasets, despite DNA binding being substantially more permissive than DNA cleavage. Here we introduce TANGO (Targeted Array-based Nucleic acid-Guided Occupancy), a high-density DNA-array platform that quantitatively profiles intrinsic dCas9:gRNA binding across tens of thousands of DNA targets in a cell-free system. TANGO captures established features of dCas9 target recognition, while providing substantially greater sensitivity than prior assays. Comparison with ChIP-seq data demonstrates that intrinsic DNA-binding specificity is a major driver of genomic occupancy and reveals that chromatin accessibility modulates the intrinsic binding affinity required for dCas9 recruitment. Across CRISPRi/a guides, TANGO identifies multiple independent biochemical determinants of guide performance--including on-target affinity, mismatch tolerance, and ribonucleoprotein assembly--and flags problematic and highly promiscuous guides overlooked by current specificity metrics. Unexpectedly, some guides retain substantial guide-directed DNA binding even in the absence of a protospacer-adjacent motif (PAM), revealing an additional dimension of dCas9 specificity. Together, these results establish intrinsic DNA recognition as a quantitative and experimentally accessible determinant of dCas9 function, providing a framework for improving guide selection and enhancing the precision of CRISPR technologies.

genomics↗

bioRxiv2026

A thalamostriatal brake counteracts cortical recruitment of striatal ensembles in levodopa-induced dyskinesia

Levodopa-induced dyskinesia (LID) is a disabling complication of Parkinsons disease therapy, yet how upstream circuits recruit and restrain dyskinesia-linked striatal ensembles remains unclear. Using FosTRAP-based ensemble access in a unilateral 6-hydroxydopamine mouse model, we identified secondary motor cortex (M2) and parafascicular thalamus (PF) as dominant afferents with opposing functions. Projection-wide M2 activation promoted dyskinesia, whereas PF activation suppressed ongoing dyskinesia and shifted behavior toward non-dyskinetic states. Chronic levodopa reduced overall presynaptic terminal abundance while preserving putative contacts onto ensemble neurons, thereby increasing effective pathway-to-ensemble coupling. This remodeling followed distinct pathway rules: M2 contacts became spatially dispersed and biased toward NMDAR-mediated excitation, whereas PF inputs recruited stronger polysynaptic inhibition. Dyskinesia preferentially re-engaged ensemble-projecting M2 neurons, but reactivated PF neurons were topographically segregated from PF neurons directly innervating the ensemble. Accordingly, selective M2-to-ensemble stimulation promoted dyskinesia, whereas selective PF-to-ensemble stimulation was ineffective. Finally, ensemble-restricted Grin1 knockdown reduced peak dyskinesia and weakened M2-driven dyskinesia. These findings define LID as a targetable imbalance between cortical ensemble recruitment and thalamostriatal restraint.

neuroscience↗

bioRxiv2026

cf-Cabernet: Nick Repair Prior to End Repair Preserves Endogenous DNA Methylation Information in Cell-Free DNA Methylation Sequencing

Cell-free DNA (cfDNA) methylation profiling holds great promise for non-invasive cancer detection, yet accurate methylome analysis is compromised by DNA damage inherent to cfDNA. Standard library preparation workflows involve an end-repair step during which DNA polymerases can initiate synthesis from single-strand breaks (nicks), replacing endogenous methylated nucleotides with unmethylated nucleotides in the 3' direction and systematically erasing methylation information. This artifact is distinct from the terminal jagged-end effect and disproportionately affects cfDNA and FFPE DNA, which harbor abundant nicks. Here, we developed cf-Cabernet, which builds upon the Cabernet framework (Cao et al., 2023) -- an enzymatic methylation sequencing method featuring carrier DNA-assisted sample recovery and amplification-friendly post-conversion processing -- with the addition of a Taq DNA ligase-mediated nick repair step prior to end repair. Using matched cfDNA samples, we compared cf-Cabernet against standard EM-seq and WGBS. cf-Cabernet and EM-seq both substantially outperformed WGBS in alignment rate. Critically, while standard EM-seq exhibited globally reduced methylation levels compared to WGBS, cf-Cabernet yielded methylation levels concordant with WGBS. M-bias analysis revealed that EM-seq libraries showed persistently depressed methylation across the entire read length, whereas cf-Cabernet methylation recovered to the WGBS baseline beyond the terminal [~]40 bp jagged-end region. Nick-induced methylation erasure during end repair is a significant but previously underappreciated source of error in cfDNA methylation sequencing. cf-Cabernet effectively mitigates this artifact through pre-emptive nick ligation, enabling accurate methylome profiling from damaged DNA templates. This method is broadly applicable to cfDNA, FFPE DNA, and other clinical specimens where DNA integrity is compromised, providing a robust foundation for methylation-based liquid biopsy applications.

genetics↗

bioRxiv2026

Adeno-Associated Virus (AAV) Synthetic Inverted Terminal Repeats Enhance Tissue-Specific Transduction and Alter the Vector Induced Stress Response

While adeno-associated virus (AAV) vectors have shown therapeutic benefit in clinical applications, noted challenges include low transduction efficiencies, poor cellular targeting, and vector related adverse events. Recently, it was demonstrated that a rationally designed synthetic inverted terminal repeat (SynITR) altered the AAV vector-induced DNA damage response and abrogated apoptosis in human embryonic stem cells. To explore the utility of AAV-SynITR for diverse gene therapy applications, vector production, transduction, and the cellular response were evaluated in various contexts. Regarding production, SynITR preparations exhibited comparable titers to wtITR in a serotype/transgene-independent manner. Despite slightly decreased transduction efficiency in various cell lines, intravenous administration of AAV8 vectors showed SynITR enhanced transduction in a tissue-specific manner in liver (>7-fold) and kidney and pancreas (>2-fold) at equivalent vector copy numbers; however, no differences were observed in muscle/heart/spleen tissues. Interestingly, persistent {gamma}H2AX, a marker of aging/chronic inflammation, was abundant in the liver and spleen following wtITR (but not SynITR) transduction. In human corneas, SynITR enhanced transduction up to 16-fold over wtITRs. These data demonstrate that SynITRs elicit tissue-specific transduction enhancement and alter the cellular stress response. Importantly, the SynITRs offer an alternative context to elucidate wtITR biology for targeted, enhanced, and potentially safer human gene therapy.

molecular biology↗

bioRxiv2026

EpiBinder: a multimodal framework for cell-type-specific prediction and interpretation of transcription factor binding

Transcription factor (TF) occupancy in vivo depends not only on the underlying DNA sequence but also on the local epigenetic environment, which varies across cell types and strongly influences whether sequence-encoded binding potential becomes functional. Here we present EpiBinder, a multimodal deep-learning framework for cell-type-specific prediction of TF binding that jointly models DNA sequence with base-resolution epigenetic information, including cytosine methylation from whole-genome bisulfite sequencing and chromatin accessibility from DNase I hypersensitivity data. Across multiple human cell lines, EpiBinder consistently outperforms strong sequence-only baselines, improving TF-binding prediction by up to 10% in area under the precision-recall curve. Beyond predictive performance, EpiBinder provides base-level attribution maps that enable systematic interrogation of regulatory context, including candidate methylation-sensitive loci, contextual motif dependencies, and putative TF-TF interactions. These results position EpiBinder as a practical framework for modeling and exploring the local regulatory grammar underlying cell-type-specific TF occupancy.

genomics↗

bioRxiv2026

A GPX4 phosphorylation switch by FGFR1 guards against ferroptosis

Ferroptosis is driven by lipid peroxidation, yet the mechanisms by which cells rapidly adjust their sensitivity to ferroptosis in response to extracellular cues remain elusive. We identify a direct phosphorylation switch controlling the activity of glutathione peroxidase 4 (GPX4), the core ferroptosis regulator. The receptor tyrosine kinase FGFR1 directly binds and phosphorylates GPX4 at Tyr180/Tyr196 in a kinase-dependent manner, requiring its Tyr730 as a docking site. This phosphorylation enhances GPX4s catalytic activity and suppresses ferroptosis. In cardiac ischemia/reperfusion injury, the FGFR1-GPX4 axis is suppressed, and a selective FGFR1 agonist (FGF-1{Delta}NT) reactivates it to protect against ferroptosis-mediated damage. Critically, a phosphorylation-deficient GPX4 knock-in mouse exhibits hypersensitivity to injury and non-responsive to this agonist, proving that GPX4 phosphorylation is essential. Our findings reveal a rapid mechanism for regulating ferroptosis via GPX4 tyrosine phosphorylation, directly linking receptor tyrosine kinase signaling to ferroptosis, and offering new strategies for treating ischemic-and other ferroptosis-associated diseases.

Cell Biology↗

bioRxiv2026

RAD: A Read-structure Agnostic Demultiplexer for Single-Cell Long-Read Sequencing and Analysis

Single-cell long-read sequencing (LRS) techniques enable the analysis of full transcript sequences within a cell. However, the high error rate inherent to LRS introduces computational challenges for parsing information like cell barcode, and custom workflows are often required to handle complex read layouts, such as split combinatorial barcodes. We introduce an error-robust, read-structure agnostic demultiplexer (RAD). In RAD, users can easily specify read structure, such as adapter sequence and barcode relative position, and can rapidly extract these elements for each read. In addition to finding the barcode, RAD implements efficient barcode correction strategies for scenarios of knowing or not knowing the full barcode whitelist or having paired short-read single-cell sequencing data for a short whitelist. In synthetic and real-world benchmarks, RAD is faster and achieves significantly higher sensitivity than existing pipelines while having comparable precision. We show RAD can be applied to high-definition long-read spatial transcriptomic data and demonstrate single cell and spatial analysis of B cell isotype and secretion states.

bioinformatics↗

bioRxiv2026

Differential Transcript Usage Reveals Isoform-Level Remodeling of Tumor Biology in Clear Cell Renal Cell Carcinoma

Clear cell renal cell carcinoma (ccRCC) is characterized by transcriptional reprogramming driven by hypoxia signaling, metabolic rewiring, and immune modulation. While gene-level analyses have defined key features of ccRCC biology, they do not capture isoform-level variation arising from alternative splicing. Differential transcript usage (DTU) represents an additional regulatory layer that may influence protein function, pathway activity, and clinical outcomes, yet its role in ccRCC biology and prognosis remains incompletely understood. We assessed differential expression in 127 ccRCC tumors and 33 normal-adjacent tissues from the Dartmouth Cancer Center cohort, with external validation in 94 CPTAC tumors, adjusting for cell-type proportions. DTU was identified using DRIMSeq/stageR, followed by limmavoom modeling with clinical and tumor microenvironment covariates. Transcript-based consensus clustering defined tumor subgroups, and Cox proportional hazards modeling integrated transcript-level features with clinical variables. In tumor versus normal comparisons, 1,170 transcripts exhibited significant differential usage, mapping to canonical ccRCC pathways with distinct patterns across functional and non-functional transcript classes. Consensus clustering based on transcript us-age identified two subgroups with distinct angiogenic profiles and significant survival differences. Cluster-level analysis revealed DTU in genes involved in cytoskeletal organization (ACTB), immune processes (B2M), extracellular matrix organization (FN1, APLP2), and iron metabolism (FTH1) with protein domain alterations, including the loss of actin-associated domains in ACTB and immunoglobulin-like domains in B2M. Prognostic modeling identified twelve transcripts consistently retained across bootstraps, improving risk stratification over clinical variables alone. External validation confirmed overlapping prognostic transcripts, including FGFR1 and NUCB1. Isoform-level features may serve as biomarkers and therapeutic targets in ccRCC. Statement of significanceTranscript-level analysis uncovers potential regulatory pathways in ccRCC missed by gene-level approaches, revealing isoform-specific alterations that define survival sub-groups and offer potential biomarkers and therapeutic targets.

cancer biology↗

bioRxiv2026

Distinct defense strategies against interbacterial antagonism underpin Acinetobacter persistence in polymicrobial environments

Despite intense interbacterial antagonism mediated by mechanisms such as the type VI secretion system (T6SS), pathogenic Acinetobacter frequently persist within highly competitive polymicrobial infections. How these pathogens navigate such hostile environments to achieve co-existence remains poorly understood. Here, we show that pathogenic Acinetobacter employ distinct, multifaceted strategies to resist elimination by both distantly related competitors and closely related kin. T6SS-active strains outcompete heterologous bacteria by deploying a large and diverse repertoire of antibacterial effectors. In contrast, some naturally T6SS-deficient strains resist exogenous T6SS attacks by elaborating a unique, high-density polysaccharide capsule (KL34) that functions as an effective physical shield. Most intriguingly, we uncover a mechanism that prevents lethal competition among kins. A conjugative multidrug-resistant plasmid encoding T6SS repressors is transferred into aggressive strains upon T6SS-mediated attack, leading to suppression of their antibacterial activity. We also found that conjugation is induced by T6SS attack, which effectively suppresses attacking kin and promotes co-infection in vivo. Together, these findings reveal a dynamic and multilayer defense program that enables Acinetobacter to withstand interbacterial warfare while facilitating co-existence. Our study establishes a paradigm in which damage-triggered plasmid transfer enforces targeted suppression, reshaping microbial interactions in polymicrobial communities.

microbiology↗

bioRxiv2026

Orally Bioavailable SARS-CoV-2 Protease Inhibitors Bearing a Hydroxymethyl Ketone Warhead

The use of covalent warheads targeting the catalytic cysteine has been a cornerstone in coronavirus main protease (Mpro) inhibitor development, where various electrophilic motifs have been used including aldehydes, nitriles, ketoamides, and hydroxymethyl ketones (HMKs). Recent efforts have been mostly centered around nitrile warheads, given the success of compounds like Nirmatrelvir and Ensitrelvir in the clinic. However, finding and advancing alternative chemotypes with differentiating chemical and pharmacological profiles is essential for future pandemic preparedness. Among such alternatives, HMKs hold special interest because they balance reduced intrinsic electrophilicity with an excellent selectivity profile. Nevertheless, early HMK-based compounds, such as the clinical-stage Mpro inhibitor PF-00835231, suffered from poor oral bioavailability and therefore required intravenous administration, with or without prodrug derivatization of the hydroxyl group. Here, we describe our efforts in advancing the HMK field via the discovery of mCMX110, a lead that has superior potency, increased unbound exposure in vivo, and favorable oral bioavailability in preclinical studies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/725542v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@40222aorg.highwire.dtl.DTLVardef@831b88org.highwire.dtl.DTLVardef@184a910org.highwire.dtl.DTLVardef@779095_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗