Biology subjects

Natarajan, K.

Publications and source records attributed to Natarajan, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Chronic lower limb pain is not associated with a loss of inhibitory neurons in the human lumbar spinal dorsal horn

The spinal dorsal horn is the primary processing site of nociceptive sensory input from the periphery. Excitatory spinal interneurons releasing glutamate can amplify this information before it is sent to the brain, whereas inhibitory neurons releasing GABA and/or glycine can suppress the outflow of nociceptive signals. An imbalance favoring excitation is thought to underlie certain aspects of chronic pain. Although rodent studies have identified spinal mechanisms underlying hyperalgesia and allodynia, little is known about the anatomical changes associated with chronic pain in the human spinal cord, a gap in knowledge we sought to address in this study. Using immunohistochemistry and in situ hybridization on lumbar spinal cord tissue recovered from organ donors, we characterized neuronal size and density across the human dorsal horn and confirmed the presence of the human equivalent of the lateral spinal nucleus in many individuals. Chronic lower limb pain was not associated with changes in neuronal density in the dorsal horn. Likewise, the ratio of excitatory (SLC17A6+) to inhibitory (PAX2+) neurons remained consistent across laminae for age, sex and chronic pain state, providing no evidence for selective loss of inhibitory neurons with chronic pain in humans. We found no differences in the size or density of the postsynaptic markers Homer1 and gephyrin between groups, suggesting glutamatergic and GABAergic postsynaptic sites remain structurally stable. These findings provide a thorough evaluation of cellular anatomy of the human dorsal horn and form a foundation for future studies investigating neuronal changes that may contribute to chronic pain in humans.

neuroscience↗

bioRxiv2026

Cryo-EM and X-ray structures of an anti-MHC-I monoclonal antibody/H2-Kb complex reveal the basis of conformational dependence and allelic specificity

Monoclonal antibodies (mAbs) directed against MHC class I molecules (MHC-I) have been invaluable for a host of functions including tissue typing for transplantation, exploration of immune activation, and probing molecular structure and dynamics. We previously studied a set of murine mAbs directed against MHC-I to characterize their domain and allele specificity and demonstrated the consistency of structural identification of epitopes with prior mapping studies. Here, we report cryo-EM and X-ray crystal structures of a novel mAb (AF6-88.5) in complex with the mouse MHC-I molecule H2-Kb. We characterize the conformational epitope that is sensitive to polymorphic amino acid residues in the MHC-I extracellular domains. The structure of the mAb/MHC-I complex reveals contacts of the mAb to residues of the 2, 3, and {beta}2m domains and comparison to the unliganded mAb shows slight adjustments of the mAb CDRH3 and CDRL3 loops to accommodate the epitope surface. The structurally identified site overlaps with that seen by some coreceptors and immunoevasins. Amino acid sequence alignments and site-directed mutagenesis of H2-Kb, H2-Db, and {beta}2m explain the allelic specificity. These results emphasize the remarkable ability of antibodies to bind conformationally defined epitopes with exquisite discrimination and the contribution of MHC-I polymorphisms to antigenicity.

immunology↗

bioRxiv2026

Synthetic Cannabidiol Attenuates Heart Failure Progression with Concomitant and Post Injury Administration Through Modulation of Immune and Endothelial to Mesenchymal Transition Related Remodeling Programs

BackgroundCardiac fibrosis is a central driver of adverse remodeling in heart failure with reduced ejection fraction (HFrEF), yet therapies directly targeting these pathways remain less established. We investigated the role of a pharmaceutical-grade synthetic (s) cannabidiol in HFrEF using an invitro and in vivo strategy. MethodsHFrEF was induced in 12-week-old C57BL/6J mice using angiotensin II, L-NAME, and salt exposure. A 5-week (w) s-cannabidiol course was administered either concomitantly (beginning at week 0) during disease induction or after disease induction (beginning at week 4). Echocardiography, cardiac morphological characterization was performed at 5 and 9 weeks of the experiment. Cardiac tissue was processed for RNA extraction. Standard statistical and informatics methodology was used to compare groups. ResultsAt 5 weeks, mice in the concomitant s-cannabidiol group had reduced cardiomyocyte hypertrophy and fibrosis area with better isovolumetric relaxation time, ejection fraction, and fractional shortening compared to HFrEF mice. In the treatment after disease induction model, at 9 weeks, s-cannabidiol treated mice maintained therapeutic effect compared to 5w HFrEF mice but also had enhanced structural and functional recovery compared to mice that recovered naturally. Bulk RNA-sequencing analysis demonstrated a significant transcriptional change in HFrEF compared to controls, with s-cannabidiol partially shifting the cardiac transcriptome away from the failing state and attenuates the HF-enriched transcriptional programs of oxidative stress, inflammatory signaling, hypoxia, apoptosis, p53/MYC/mTORC1/E2F remodeling, and EMT/fibrotic remodeling, while enriching lipid/peroxisomal metabolic pathways. In an invitro HUVEC model of Endothelial to Mesenchymal Transition (EndMT), s-cannabidiol inhibited the transition and also reversed established EndMT, with these effects attenuated by pharmacologic inhibition of CB2 and PPAR{gamma}, but not CB1 receptors. Conclusionss-cannabidiol attenuates adverse remodeling in experimental HFrEF, promotes recovery after injury, and is associated with suppression of EndMT-related programs mediated through CB2/PPAR{gamma}-linked endothelial signaling.

bioinformatics↗

bioRxiv2026

Targeting Autophagy Accelerates Intestinal Repair after Acute Ionizing Radiation

Radiation exposure induces systemic and cellular damage, contributing to acute radiation syndrome and long-term effects such as premature aging and carcinogenesis. At the cellular level, radiation triggers apoptosis, mutation, and transformation through oxidative damage and activation of pathways including ER stress-mediated autophagy. Autophagy plays a context-dependent dual role in stressed cells, but its contribution to intestinal recovery after acute radiation remains unclear. Here, we evaluated combinatorial radiomodification using gamma radiation (8 Gy) and autophagy modulators in whole-body irradiated C57BL/6 mice (8-10 weeks old, n = 10). Mice were treated with autophagy inducers or inhibitors and euthanized at 3-, 8-, and 30-day post-irradiation. The jejunal-ileal region was analyzed via antioxidant assays, immunoblotting, H&E staining, and immunohistochemistry. Radiation significantly altered oxidative stress and autophagy markers, including increased LC3-II and decreased SQSTM1/p62. Autophagy induction enhanced intestinal proliferation (as measured by Ki-67), whereas inhibition impaired regeneration. Rapamycin pretreatment improved survival and reduced markers of intestinal injury following 8 Gy total body irradiation (TBI), whereas chloroquine exacerbated several injury-associated parameters. Overall, our findings suggest that targeted modulation of autophagy is a promising strategy for alleviating radiation-induced gastrointestinal injury and provide mechanistic insights relevant to therapeutic development.

molecular biology↗

bioRxiv2026

Antibody Blockade of Ly49/MHC-I interactions enhances Innate and Adaptive Immunity Against Cancer Metastasis

BackgroundAntibody-mediated blockade of innate receptor-MHC-I interactions represents a promising strategy to enhance anti-tumor immunity, particularly against metastatic cancers resistant to conventional checkpoint inhibitors. In this study, we investigated the effects of the pan anti-MHC-I monoclonal antibody M1/42, which targets MHC-I interactions with Ly49, selectively expressed on murine NK cell subsets. MethodsWe administered M1/42 to mice and assayed the proliferation and activation immune cells. Anti-tumor activity of growth and metastasis of checkpoint inhibitor-resistant pancreatic ductal adenocarcoma (PDAC) and B16F10 melanoma were assessed, complemented by extensive cellular phenotypic and RNA expression analysis. Binding and cryo-electron microscopic (cryo-EM) and X-ray crystallographic structural studies of M1/42 complexed with the mouse MHC-I molecule, H2-Dd, examined the Ab interaction site in comparison with those of Ly49 inhibitory receptors. ResultsM1/42 administration in mice robustly unleashed the proliferation and activation of natural killer (NK) cells, memory CD4+ and CD8+ T cells, dendritic cells, and macrophages in both lymphoid and non-lymphoid tissues, independent of Fc{gamma} receptors. M1/42 significantly restricted the growth and metastasis of checkpoint inhibitor-resistant pancreatic ductal adenocarcinoma (PDAC) and B16F10 melanoma in the liver and lungs, accompanied by increased tumor infiltration of effector CD8+ T cells, reduction of T regulatory cells, and a pro-inflammatory cytokine milieu. The anti-tumor effects of M1/42 depend on NK cells and are associated with upregulation of genes involved in antigen processing, interferon gamma responsiveness, and Th1 cytokine production, while downregulating inhibitory PD1/11 signaling. Structural analysis indicated that the effect of M1/42 on Ly49/MHC-I interactions was not due to direct steric competition. ConclusionsCollectively, these findings demonstrate that M1/42 unleashes coordinated innate and adaptive immune responses, overcoming tumor-induced immunosuppression and resistance to checkpoint blockade. This approach represents a paradigm shift in cancer immunotherapy, offering potential for more effective treatment of metastatic cancers that evade immune surveillance through MHC-I modulation. KEY MESSAGESO_ST_ABSWhat is already known on this topicC_ST_ABSA pan anti-mouse MHC-I mAb (M1/42) blocks interaction with several NK inhibitory receptors (Ly49A or Ly49C) resulting in NK cell activation and anti-viral and anti-tumor responses in vitro and in vivo. Other pan anti-human MHC-I mAbs (DX17 and W6/32) function similarly, blocking LILRB inhibitory receptor interaction of myeloid cells and NK cells. These stimulate human immune cells in humanized mouse models. What this study addsThis study analyzes the effects of the pan anti-mouse MHC-I mAb on NK and myeloid cell activation in detail, in the absence of T or B cells, and independent of FcR interaction. Additionally we analyze several mouse models of metastatic tumor progression, indicative of the progressive activation not only of the innate immune response, but also adaptive responses. The molecular mechanism of the mAb blocking of inhibitory receptors is revealed by cryo-EM and X-ray structures of M1/42 Fab/MHC-I (H2-Dd) complexes. How this study might affect research, practice, or policyElucidation of the details of the inhibitory effects of the mouse pan anti-mouse MHC-I mAb provides not only a more advanced understanding of the murine model system, but suggests additional functional avenues to be explored using the parallel an anti-human MHC-I mAbs.

cancer biology↗

bioRxiv2026

Histone Fold mediated heterodimerization specifies the selective association of TAF12 paralogs with TFIID and SAGA complexes in Candida albicans.

Transcription initiation in eukaryotes is coordinated by the multisubunit coactivator complexes TFIID and SAGA, which share five core TBP-associated factors (TAFs) that assemble through histone fold (HF) mediated heterodimerization. While, in most organisms, a single TAF12 incorporates in both complexes; however, Candida albicans uniquely encodes two TAF12 paralogs, TAF12 and TAF12L, which associate preferentially with TFIID and SAGA, respectively. The molecular basis and functional consequences of this specialization remain unclear. Here, we demonstrate that Taf12 and Taf12L are functionally non-redundant and show strict complex specificity in vivo, even under conditions where the alternate paralog is depleted. Taf12 associates exclusively with TFIID through Taf4, whereas Taf12L incorporates specifically into SAGA through Ada1. Ectopic expression experiments reveal limited and asymmetric cross-complementation, wherein Taf12L led to partial growth rescue and incorporation into TFIID in absence of Taf12 but not vice versa. Biochemical and genetic analyses further show that the conserved histone fold domains (HFDs) of both paralogs are sufficient for biological function and complex incorporation. In vitro interaction assays uncover intrinsic differences in binding selectivity of Histone fold domains, with HFD-Taf12L displaying strong preference for Ada1, while HFD-Taf12 exhibits more promiscuous binding. Structure-guided mutational analysis identifies the 2-L2 region of the HFD as a major determinant of paralog-specific partner selection. Together, our findings establish that subtle divergence within a conserved histone fold domain underlies the non-redundant integration of Taf12 paralogs into distinct coactivator complexes, revealing a mechanism by which transcriptional machinery can evolve functional specialization through gene duplication.

molecular biology↗

bioRxiv2026

Modular Architecture of the SAGA Complex Governs Stress Adaptation, Morphogenesis, and Histone Acetylation in Candida albicans

The SAGA complex is a conserved, multifunctional transcriptional co-activator known for its roles in chromatin modification and transcriptional regulation. While SAGA has been extensively characterized in Saccharomyces cerevisiae and metazoans, its modular organization and functional significance in the major human fungal pathogen Candida albicans remain poorly understood. Through bioinformatic analyses, we found that SAGA subunits are conserved in C. albicans. Genetic disruption of the histone acetyltransferase (HAT; GCN5, ADA2), structural (SPT; SPT7, SPT20, TAF12L), and TATA-binding protein interaction (TBP-interaction; SPT3, SPT8) modules leads to impaired growth under oxidative, metal, and antifungal stress conditions and causes severe defects in filamentation. In contrast, deletion of the deubiquitination (DUB) module components UBP8 and SUS1 results in minimal phenotypic consequences. Strikingly, loss of SGF73, a structural component linking the DUB module to the SAGA core, produces pronounced defects in stress conditions and filamentation, phenocopying SPT3 and SPT8 mutants. Consistent with these observations, filamentation-associated genes are significantly upregulated in SGF73, SPT3 and SPT8 mutants. Notably, these mutants also exhibit elevated global levels of histone H3 lysine-9 acetylation (H3K9ac), suggesting a critical role for SGF73-mediated SAGA integrity in coordinating chromatin acetylation with transcriptional programs governing stress responses and filamentation in C. albicans.

molecular biology↗

bioRxiv2026

TDP-43 dysfunction leads to the accumulation of cryptic transposable element-derived exons, crypTEs, in iPSC derived neurons and ALS/FTD patient tissues

TDP-43 is an RNA and DNA binding protein that plays major roles in regulating RNA processing. In particular, TDP-43 dysfunction leads to the accumulation of cryptic splice isoforms that result from improperly spliced mRNAs. In addition to its role in regulating splicing, TDP-43 is also known to regulate the expression of transposable elements (TEs). TEs are mobile genetic elements which comprise a significant proportion of the human genome, but are normally silenced in healthy somatic cells. TEs are interspersed throughout the genome, both in gene-depleted regions and within gene introns and gene regulatory sequences. We used optimized long-read RNA sequencing assays to generate catalogs of mis-spliced and mis-expressed genes and TEs in human neurons depleted for TDP-43. In addition to known TDP-43 driven cryptic isoforms, we identified hundreds of TDP-43 dependent spliced RNAs that form cryptic gene-TE fusion events as a result of mis-splicing of TE sequences into gene transcripts. Among these TDP-43 dependent cryptic gene-TE transcripts (crypTEs), we found: TEs that provide alternate gene promoters/5UTRs, TEs that act as cassette exons inside host gene mRNAs, as well as TEs that provide alternate transcript 3 ends. These cryptic gene-TE fusions are predicted to induce aberrant expression of ALS relevant genes, nonsense mediated decay (NMD) products, as well as novel peptides from gene-TE fusions within the gene coding sequence. Using coupled long-read RNA (Iso-seq) and single-nucleus (snRNA-seq) profiles from postmortem ALS tissues, we further verified that many of these crypTE transcripts are enriched in frontal cortex samples from ALS donors with cognitive involvement (ALSci) and associated with altered expression of those genes in deep layer cortical excitatory neurons. In short, TDP-43 dependent crypTEs greatly expand the catalogs of TDP-43 dependent cryptic splice isoforms and represent a novel mechanism by which TE dysregulation impacts ALS.

genomics↗

bioRxiv2025

Enabling wider access to human molecular neuroscience research in pain: A simple preservation method for human dorsal root ganglion neurons in Hibernate A media

The use of human dorsal root ganglion (DRG) from organ donors opens the door for research into the molecular biology and physiology of human nociceptors; however, there are barriers to working with this tissue including logistical difficulties and limited access. We present an approach using Hibernate media to temporarily store either whole DRGs or dissociated DRG neurons prior to culturing and functional testing. Dissociation of DRGs following temporary storage (4-16hrs) in Hibernate media resulted in similar neuronal and immune cell yield as acutely dissociated DRGs. Neurons derived from DRGs stored in Hibernate media prior to dissociation exhibited similar electrophysiological properties and capsaicin responses as acutely dissociated DRG neurons. Similarly, neurons from acutely dissociated DRGs stored in Hibernate media (>24hrs) and shipped to geographically distant laboratories produced neuronal cultures displaying comparable electrophysiological properties as acutely cultured neurons. This approach overcomes insurmountable logistical burdens and increases access to freshly recovered human DRGs.

neuroscience↗

bioRxiv2025

Histone acetylation by SAGA Complex but not by NuA4 Complex is Required for filamentation programme in Candida albicans

Candida albicans, a major human fungal pathogen undergoes filamentation from yeast to hyphal state under filamentation-inducing conditions. Gcn5 and Esa1 are key histone H3 and H4 acetyltransferases, respectively, encoded by the budding yeast and other eukaryotes. While Gcn5, a subunit of the SAGA complex, and Esa1, a subunit of the NuA4 complex are critical for C. albicans virulence and hyphal induction, how the relative HAT activities impinge on hyphal gene expression during filamentation is less understood. We found that hyphal gene promoters are hyperacetylated at H3K9 and H4 upon filamentation. By creating point mutations in the HAT domain of Gcn5 and Esa1, we investigated the relative requirement of the SAGA and NuA4 HAT activities for filamentation response. We show that Gcn5 HAT activity is essential for hyperacetylation of H3K9 and H4 at promoters and across hyphal gene ORFs. Surprisingly, the Esa1 HAT domain mutation did not impair H4 acetylation at hyphal genes suggesting that Gcn5 HAT activity is sufficient for H4 (and H3K9) acetylation. Paradoxically, the Esa1 HAT mutant formed filaments constitutively and showed elevated H3K9ac and H4ac at promoters under inducing conditions. Furthermore, we show that the basic helix-loop-helix transcriptional regulator Efg1 is essential for Gcn5-mediated hyperacetylation and RNA pol II recruitment to promoters. Thus, our results indicate that the SAGA-mediated H3K9 and H4 acetylation is sufficient and essential for induction of C. albicans filamentation.

molecular biology↗

bioRxiv2025

Cotranslational assembly confers specificity for in vivo target heterodimerization of paralogous H2B-like TAF12 proteins in the human fungal pathogen Candida albicans

The fidelity of assembly of multiprotein complexes is essential for the formation of stable and functional protein complexes that are critical for cell growth and survival. In this context, TBP-associated factor (TAF) subunits maintain tight specificity for their integration into TFIID and SAGA complexes. In this work, using affinity purification-coupled mass spectrometry of epitope-tagged TFIID subunits TBP and TAF11, and the SAGA subunit TAF12L we identified components of the C. albicans TFIID and SAGA complexes. Whereas TAF12 is a subunit of TFIID, the paralogous TAF12L is a subunit of the SAGA complex, and we further identified each of the TFIID and SAGA complex subunits with high confidence. We found that the steady-state levels of the H2B-H2A-like histone fold domain containing pairs, TAF12-TAF4 and TAF12L-Ada1 proteins, are mutually dependent on the stable expression of each other. Using RNA coimmunoprecipitation from polysome-containing extracts, we found that nascent TAF4 and Ada1 proteins interact with TAF12 and TAF12L, respectively, by a cotranslational mechanism in an ordered, sequential mode of assembly. Thus, our results indicate that heterodimerization of the TAF12 paralogs with cognate partners occur by sequential cotranslational assembly thereby ensuring both selectivity and stability of the H2A-H2B heterodimers in fungal pathogen C. albicans.

genetics↗

bioRxiv2025

Type I interferons enhance human dorsal root ganglion nociceptor excitability and induce TRPV1 sensitization

Type I interferons (IFNs) are critical cytokines for antiviral defense and are linked to painful inflammatory diseases like rheumatoid arthritis and neuropathic pain in humans. Studies in rodent models demonstrate a direct action on sensory neurons in the dorsal root ganglion (DRG) to promote hyperexcitability but rodent behavioral results are conflicting with some reports of pro-nociceptive actions and others of anti-nociception. Given the role of type I IFNs in human disease, we sought to clarify the action of action of IFN- and IFN-{beta} on human DRG (hDRG) nociceptors. We found that IFN receptor subunits IFNAR1 and IFNAR2 are functionally expressed by these neurons and their engagement induces canonical STAT1 signaling and non-canonical MAPK activation as measured by increased phosphorylation of the cap-binding protein eIF4E by MNK1/2 kinases. Using patch clamp electrophysiology, Ca2+-imaging, and multi-electrode arrays we demonstrate that IFN- and -{beta} increase the excitability of hDRG neurons with short (30 min) and long-term (24-48 h) exposure and prolong the duration of capsaicin responses, an effect that is blocked by inhibition of MNK1/2 with eFT508, a specific inhibitor of these kinases. Our studies support the conclusion that type I IFNs are pronociceptive when they interact with hDRG nociceptors in the periphery.

neuroscience↗

bioRxiv2024

Epigenomic landscape of the human dorsal root ganglion: sex differences and transcriptional regulation of nociceptive genes

Gene expression is influenced by chromatin architecture via controlled access of regulatory factors to DNA. To better understand gene regulation in the human dorsal root ganglion (hDRG) we used bulk and spatial transposase-accessible chromatin technology followed by sequencing (ATAC-seq). Using bulk ATAC-seq, we detected that in females diverse differentially accessible chromatin regions (DARs) mapped to the X chromosome and in males to autosomal genes. EGR1/3 and SP1/4 transcription factor binding motifs were abundant within DARs in females, and JUN, FOS and other AP-1 factors in males. To dissect the open chromatin profile in hDRG neurons, we used spatial ATAC-seq. The neuron cluster showed higher chromatin accessibility in GABAergic, glutamatergic, and interferon-related genes in females, and in Ca2+-signaling-related genes in males. Sex differences in transcription factor binding sites in neuron-proximal barcodes were consistent with the trends observed in bulk ATAC-seq data. We validated that EGR1 expression is biased to female hDRG compared to male. Strikingly, XIST, the long-noncoding RNA responsible for X inactivation, hybridization signal was found to be highly dispersed in the female neuronal but not non-neuronal nuclei suggesting weak X inactivation in female hDRG neurons. Our findings point to baseline epigenomic sex differences in the hDRG that likely underlie divergent transcriptional responses that determine mechanistic sex differences in pain.

neuroscience↗

bioRxiv2024

Kinase activity of histone chaperone APLF maintains steady state of centrosomes in mouse embryonic stem cells

Our recent studies revealed the role of mouse Aprataxin PNK-like Factor (APLF) in development. Nevertheless, the comprehensive characterization of mouse APLF remains entirely unexplored. Based on domain deletion studies, here we report that mouse APLFs Acidic Domain and Fork Head Associated (FHA) domain can chaperone histones and repair DNA like the respective human orthologs. Immunofluorescence studies in mouse embryonic stem cells showed APLF co-localized with {gamma}-tubulin within and around the centrosomes and govern the number and integrity of centrosomes via PLK4 phosphorylation. Enzymatic analysis established mouse APLF as a kinase. Docking studies identified three putative ATP binding sites within the FHA domain. Site-directed mutagenesis showed that R37 residue is indispensable for the kinase activity of APLF thereby regulating the centrosome number. These findings might assist us comprehend APLF in different pathological and developmental conditions and reveal non-canonical kinase activity of proteins harbouring FHA domains that might impact multiple cellular processes.

biochemistry↗

bioRxiv2023

Experimental structures of antibody/MHC-I complexes reveal details of epitopes overlooked by computational prediction

Monoclonal antibodies (mAb) to major histocompatibility complex class I (MHC-I) molecules have proved to be crucial reagents for tissue typing and fundamental studies of immune recognition. To augment our understanding of epitopic sites seen by a set of anti-MHC-I mAb, we determined X-ray crystal structures of four complexes of anti-MHC-I antigen-binding fragments (Fab) bound to peptide/MHC-I/{beta}2m (pMHC-I). An anti-H2-Dd mAb, two anti-MHC-I 3 domain mAb, and an anti-{beta}2-microglobulin ({beta}2m) mAb bind pMHC-I at sites consistent with earlier mutational and functional experiments, and the structures explain allelomorph specificity. Comparison of the experimentally determined structures with computationally derived models using AlphaFold Multimer (AF-M) showed that although predictions of the individual pMHC-I heterodimers were quite acceptable, the computational models failed to properly identify the docking sites of the mAb on pMHC-I. The experimental and predicted structures provide insight into strengths and weaknesses of purely computational approaches and suggest areas that merit additional attention. ONE SENTENCE SUMMARYX-ray structures of anti-MHC-I/MHC-I complexes define epitopes overlooked by computational prediction.

immunology↗

bioRxiv2023

Structure-based virtual screening and Molecular Dynamic Simulations identified FDA-approved molecules as potential inhibitors against the surface proteins of H1N1

H1N1, a subtype of influenza A virus, remains a global concern due to its ability to cause highly contagious, and fatal infections of the respiratory tract that can lead to seasonal pandemics. Factors such as genetic reassortment and antigenic shift due to the segmented nature of its RNA genome, lead to its rapid evolution that impacts drug and vaccine interactions. Thus, there is growing interest in identifying small-molecules against H1N1 to address the challenges posed by its ever-changing nature and enhance ability to combat the virus. By targeting the surface proteins crucial in the viral life cycle and interactions with host cells, we conducted structure-based virtual screening of 2,471 FDA-approved small molecules against H1N1s hemagglutinin (HA) and neuraminidase (NA) using molecular docking, and molecular dynamic simulations. A binding pocket for HA was identified at the interface of the three protomers, close to the fusion peptide, while in the case of NA the co-crystal ligand binding site was targeted. We identified 5 molecules, namely Econazole, Butoconazole, Miconazole, Isoconazole, and Tioconazole with higher binding affinity to HA and 4 molecules, namely Acarbose, Rutin, Paromomycin, and Idarubicin showing superior binding affinity to NA. Further molecular dynamic simulation of these molecules bound with HA and NA reaffirm the stability of the complexes. These molecules are known to have antifungal and antiviral properties. Thus, this study elucidates the importance of targeting HA and NA and paves the way for repurposing existing antivirals, antibacterials, and antifungals as inhibitors of the H1N1 viral entry into host cells.

bioinformatics↗

bioRxiv2023

Vinorelbine causes a neuropathic pain-like state in mice via STING and MNK1 signaling associated with type I interferon induction.

Type I interferons (IFNs) increase the excitability of dorsal root ganglion (DRG) neurons via activation of MNK-eIF4E translation signaling to promote pain sensitization in mice. Activation of STING signaling is a key component of type I IFN induction. Manipulation of STING signaling is an active area of investigation in cancer and other therapeutic areas. Vinorelbine is a chemotherapeutic that activates STING and has been shown to cause pain and neuropathy in oncology clinical trials in patients. There are conflicting reports on whether STING signaling promotes or inhibits pain in mice. We hypothesized that vinorelbine would cause a neuropathic pain-like state in mice via STING and signaling pathways in DRG neurons associated with type I IFN induction. Vinorelbine (10 mg/kg, i.v.) induced tactile allodynia and grimacing in WT male and female mice and increased p-IRF3 and type I IFN protein in peripheral nerves. In support of our hypothesis, vinorelbine-mediated pain was absent in male and female StingGt/Gt mice. Vinorelbine also failed to induce IRF3 and type I IFN signaling in these mice. Since type I IFNs engage translational control via MNK1-eIF4E in DRG nociceptors, we assessed vinorelbine-mediated p-eIF4E changes. Vinorelbine increased p-eIF4E in DRG in WT animals but not in StingGt/Gtor Mknk1-/- (MNK1 KO) mice. Consistent with these biochemical findings, vinorelbine had an attenuated pro-nociceptive effect in male and female MNK1 KO mice. Our findings support the conclusion that activation of STING signaling in the peripheral nervous system causes a neuropathic pain-like state that is mediated by type I IFN signaling to DRG nociceptors.

neuroscience↗

bioRxiv2021

Dynamic Expedition of Leading Mutations in SARS-CoV-2 Spike Glycoproteins

Throughout the coronavirus disease 2019 (COVID-19) pandemic, the continuous genomic evolution of its etiological agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has generated many new variants with enhanced transmissibility and immune escape capabilities. Being an essential mediator of infections and a key target of antibodies, mutations of its spike glycoprotein play a vital role in modulating its evolutionary trajectory. Here, we present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike. Together with analysis of its single amino acid polymorphism (SAP), we propose the use of L-index in quantifying the mutation strength of each amino acid site, such that the evolutionary mutation pattern of the spike glycoprotein can be unravelled.

evolutionary biology↗