Biology subjects

Kumar, J.

Publications and source records attributed to Kumar, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Immunoinformatics-Guided Design and In Silico Evaluation of a Multi-Epitope Vaccine Against Influenza A H10N5 and H3N2 Strains Based on Hemagglutinin and Neuraminidase Proteins

Influenza A viruses H3N2 and H10N5 represent, respectively, a persistently dominant seasonal pathogen and a newly documented zoonotic threat with the latter strain variants responsible for the first confirmed human fatality in January 2024, yet no vaccine platform currently addresses co-protection against both subtypes within a unified immunogen. We report here the immunoinformatics based vaccine design and multi-layered computational validation of a 419-amino-acid multi-epitope subunit vaccine construct targeting conserved hemagglutinin (HA) and neuraminidase (NA) antigens identified through multiple sequence alignment of the avian H10N5 (A/swine/Hubei/10/2008) and H3N2 human reference strain sequences to identify viral agents undergoing mammalian adaptations. Linear B-cell, cytotoxic T lymphocyte (CTL), and helper T lymphocyte (HTL) epitopes were predicted using ABCpred, BCEpred, BepiPred 2.0, NetMHCpan 2.1, and NetMHCpan 4.0, then filtered through VaxiJen 3.0, AllerTOP v2.1, and ToxinPred to retain only antigenic, non-allergenic, non-toxic candidates. The final construct, incorporating an avian {beta}-defensin N-terminal adjuvant with GPGPG, AAY, and EAAAK linkers, exhibited a molecular weight of 43.9 kDa, instability index of 31.15, and SOLPro solubility probability of 0.763. Tertiary structure modeling via I-TASSER and GalaxyRefine achieved 84.4% Ramachandran-favored residues. Molecular docking against TLR3 and TLR7 yielded binding free energies of -16.1 and -16.8 kcal/mol with picomolar dissociation constants. Molecular dynamics simulations confirmed complex stability over extended trajectories. Furthermore, codon optimization produced a Codon Adaptation Index of 1.0 for E. coli K12 expression. In silico immune simulation demonstrated robust activation of humoral and cellular immunity including elevated IgG1, IgM, IFN-{gamma}, IL-2, rapid NK cell expansion, and broad B-cell clonal diversity. These findings establish a computationally validated candidate capable of providing protection against influenza in multiple host organisms, warranting experimental advancement.

bioinformatics↗

bioRxiv2026

AgroGem: A Rapid and Scalable Transient Transformation System for Functional Genetics in Multiple Plant Species

Plant genetic transformation technologies are essential for functional genomics and genome engineering in plants. While transient expression systems offer a rapid alternative to stable transformation, existing platforms are often constrained by low efficiency, technical complexity, and limited scalability. Here, we developed AgroGem, an efficient Agrobacterium-mediated transient transformation system utilizing a geminiviral replicon-based T-DNA vector for Arabidopsis and Brassicaceae species. AgroGem significantly outperformed existing transient approaches, including AGROBEST and protoplast-based assays, in CRISPR-mediated editing efficiency. Moreover, AgroGem recapitulated the mutation spectra and chromatin accessibility-dependent editing patterns observed in stable transformation across both Cas9 and Cas12a systems, indicating that it captures genome editing outcomes in native chromatin contexts. Leveraging this capability, we performed high-resolution profiling of CRISPR-induced mutation outcomes across a panel of DNA repair mutants and identified distinct repair signatures, including unexpected roles for KU80 and XRCC4 in regulating non-homologous end joining (NHEJ). AgroGem also supported bimolecular fluorescence complementation assays for protein-protein interaction studies in Arabidopsis and was readily adapted to plate-based formats for high-throughput applications. Together, these results establish AgroGem as a robust, scalable, and versatile platform for genome editing, DNA repair analysis, and functional genetics in plants.

plant biology↗

bioRxiv2026

A Paracrine Dietary Lipid Axis Constrains Antitumor Immunity in Liver Cancer

Overnutrition-related liver dysfunction and cancer are increasingly prevalent and highly resistant to immunotherapy. While metabolic dysregulation is a hallmark of hepatocellular carcinoma (HCC), how nutrient overload impairs antitumor immunity remains unclear. Here, we show that short-term Western diet (WD) exposure drives near-complete loss of CD8 T cell infiltration and antitumor function in HCC. We identify dietary linoleic acid (LA), the most abundant {omega}-6 fatty acid, as the dominant immunosuppressive driver. Cancer cell-restricted FADS2-mediated desaturation of LA to longer-chain {omega}-6 PUFAs drives their accumulation in the tumor interstitial fluid, suppressing infiltrating CD8 T cells via lipid peroxidation. FADS2 inhibition restores CD8 T cell function and sensitizes WD-driven HCC to PD-1-based immunotherapy. Further, the Parkinsons disease-associated deglycase DJ-1 protects LA-handling proteins from methylglyoxal-mediated glycation, sustaining tumoral immunosuppressive PUFA production. Across multiple independent human MASLD-HCC cohorts, LA metabolic activity correlates with CD8 T cell impairment, immune exclusion, and immunotherapy resistance. Overall, these studies identify a dietary lipid axis as a therapeutically actionable vulnerability in WD-associated HCC.

Cancer Biology↗

bioRxiv2026

A Tissue Culture Free Genome Editing Strategy in Plants Using Broad-Host-Range Viral Vectors Derived from Geminiviruses

The use of viral vectors offers a promising alternative to traditional transformation methods for creating gene-edited plants. In this study, we developed a novel plant genome editing system by delivering Cas9, Cas12f, and Cas12j nucleases along with their guide RNAs using a broad-host-range geminivirus, Wheat dwarf India virus (WDIV), in combination with Ageratum yellow leaf curl betasatellite (AYLCB). Cas9, Cas12f, and Cas12j nucleases were efficiently expressed along with corresponding guide RNAs under viral promoters. By leveraging tRNA spacers in place of external promoters and terminators, we significantly reduced the overall cargo size, streamlining vector design. Additionally, we compared the traditional AtU6-driven gRNA delivery with a novel spacer:gRNA:spacer format in Cas9-expressing lines and observed comparable editing efficiencies. The broad host range of WDIV and AYLCB, combined with this tissue culture-free genome editing platform, opens up possibilities for editing across a wide range of plant species.

plant biology↗

bioRxiv2026

Bro1-Mediated Trafficking Couples TOR Signalling to Cellular Metabolism and Longevity

Adaptation to nutrient availability requires coordination between growth control, metabolism, and intracellular trafficking. In eukaryotes, inhibition of Target of Rapamycin (TOR) signalling robustly promotes stress resistance and longevity, yet how reduced growth signalling is coupled to organelle dynamics and proteome remodelling remains unclear. Here, we identify the conserved ESCRT-associated protein Bro1 as a central integrator of TOR signalling, vacuolar trafficking, and metabolic adaptation. Using fission yeast, we show that Bro1 is required for normal lifespan and for the global proteomic reprogramming that accompanies TOR inhibition. In Bro1 mutant cells, repression of ribosome biogenesis is uncoupled from activation of catabolic, vacuolar, and metabolic pathways, resulting in an altered metabolic state characterised by elevated lipid metabolism and increased abundance of nutrient transporters. Mechanistically, Bro1 promotes TOR-dependent cargo deubiquitination, vacuolar trafficking, and turnover of plasma membrane hexose transporters and enables appropriate nuclear relocalisation of the transcriptional repressor Scr1. In the absence of Bro1, nutrient transporters persist at the cell surface despite TOR inhibition, conferring resistance to TOR inhibitors while impairing stress responses and reducing lifespan. Together, our findings establish Bro1 as a key coordinator linking ESCRT-mediated endosomal-vacuolar trafficking to TOR-dependent metabolic control. By coupling growth suppression to enhanced recycling and cellular maintenance, Bro1 enables the transition from growth to longevity-promoting states, revealing a mechanism connecting intracellular trafficking, metabolism, and ageing.

genetics↗

bioRxiv2025

A painless nerve growth factor variant uncouples nociceptive and neurotrophic TrkA signaling

Nerve growth factor (NGF) binding to the receptor tyrosine kinase, TrkA, drives neurotrophic signaling essential for neuronal development and survival. This interaction simultaneously drives peripheral pain, making this pathway an attractive but complicated therapeutic target for chronic pain. By integrating single-molecule microscopy, structural and electrophysiology analyses, with a human NGF variant, NGFpainless, which retains neurotrophic effects but abolishes pain, we delineate the molecular mechanisms that bias TrkA signaling towards neurotrophic functions without triggering nociception. We show that, unlike wild-type NGF, NGFpainless fails to sensitize TRPV1 channels to capsaicin, thus disengaging TrkA from the nociceptive pathway. We further show that this selective loss of nociceptive TrkA signaling by NGFpainless results from its reduced ability to activate PLC{gamma}1 and trigger calcium release compared to NGF, while still preserving the ERK and AKT signaling essential for neurotrophic functions. This biased signaling arises from reduced electrostatic complementarity at the TrkA:NGFpainless complex interface, which shortens the lifetime of this functional complex on native membranes. Mutations in TrkA that restore the electrostatic complementarity at the TrkA:NGFpainless interface eliminate biased signaling. This mechanistic understanding of TrkA binding by NGFpainless, and how it differs from NGF, will spur the development of two therapeutic classes of molecules - one that selectively suppresses nociceptive signaling while preserving neurotrophic functions in chronic pain, and another that enhances neurotrophic activity without evoking peripheral pain in neurodegenerative conditions.

neuroscience↗

bioRxiv2025

A Wnt-induced conformational phospho-switch in DVL3 controls interaction with Frizzled receptors and Wnt/β-catenin signaling

When Wnt ligands bind to Frizzled (FZD) receptors, Dishevelled protein (DVL) gets multiphosphorylated by Casein kinase 1 (CK1). Although, it is well known that DVL phosphorylation relays Wnt signals from receptors to downstream effectors, any mechanistic aspects of DVL function related to phosphorylation remain unresolved. Here, we uncovered a Wnt-induced DVL phospho-switch which is mutually exclusive with FZD engagement. CK1 multiphosphorylation changes dramatically the bulk electrostatics to promote DVL intramolecular coupling between the DEP domain and the adjacent disordered region. A panel of phospho-switch mutants demonstrated a switch-like coupling at the molecular level when a charge threshold is reached. Charge accumulation proximal to DEP proved to be a key functional event required, but not sufficient, for Wnt/{beta}-catenin signaling. Interestingly, the charge-dependent switch-like character of DVL controlled its association with FZD. By integrating findings at different levels, we propose a universal mechanism in which Wnt-induced DVL conformational phospho-switch outcompetes FZD binding and triggers DVL detachment from FZD.

molecular biology↗

bioRxiv2025

Angiogenic CD8 T cells from PWH induce Granzymes-dependent PAR1 activation promoting endothelial inflammation

In people with HIV (PWH), T cell immune activation and endothelial inflammation are contributors of the increased cardiovascular risk, however the mechanisms remain poorly understood. PAR1 connects the coagulation cascade, endothelial cells and CD8 T cells at the site of endothelial inflammation and we hypothesized that HIV driven CD8 T cell immune activation alters endothelial repair mechanisms. Endothelial repair is partially mediated by angiogenic T (Tang) cells that facilitate proliferation of endothelial cells, and differentiation of endothelial progenitor cells at site of vascular injury. During LCMV infection, we identified a subset of CD31highCD8 T cells that exhibited a long-lived memory precursor phenotype (CD127+KLRG1-) and secreted the proangiogenic cytokine vascular endothelial growth factor (VEGF) after viral control. Furthermore, in PWH, the frequencies of CD8 Tang cells were reduced and showed an activated phenotype and expression of granzymes. GZMA+GZMB+CD8 Tang cells correlated with atherosclerotic cardiovascular disease (ASCVD) risk. In vitro, granzyme dependent PAR1 activation led to calcium mobilization and secretion of proinflammatory cytokines IL-6, IL-8 and angiopoietin-2 by primary human endothelial cells. Altogether, these findings suggest that CD8 T cells are involved in immunity against viruses and endothelial homeostasis and HIV driven immune activation alters these functions.

immunology↗

bioRxiv2025

Macrophage Cholesterol Homeostasis Underpins the role of Sertraline as an Adjunctive Agent in Tuberculosis Therapy.

Cellular metabolism plays a deterministic role in the macrophage responses to intracellular pathogens such as Mycobacterium tuberculosis (Mtb) and infection control. Here, we demonstrate that the significant rewiring of the macrophage cholesterol metabolism by sertraline (SRT), an FDA-approved antidepressant, effectively enhances bacterial control. SRT, by virtue of its potent cationic amphiphilicity leads to the accumulation of lysosomal cholesterol in macrophages and activating the transcription factor SREBP2 and enhancing cholesterol biosynthesis. By specific gene silencing and biochemical inhibition assays, we further demonstrate that this metabolic reprogramming promotes lysosomal membrane permeabilization, mitochondrial reactive oxygen species (ROS) generation, heightened IL-1{beta} release, collectively enhancing macrophage bactericidal activity. Our results thus highlight a previously underappreciated link between cholesterol homeostasis and inflammasome activation, which contributes to improved Mtb clearance in the presence of adjunctive sertraline therapy. Statement of significanceTuberculosis remains a leading cause of global mortality, and treatment success is limited due to a long treatment regimen. This study identifies macrophage cholesterol homeostasis as a central pathway to enhance anti-tubercular therapy. We show that Sertraline, an FDA-approved antidepressant, a cationic amphiphilic drug (CAD), reprograms cholesterol trafficking through NPC1 inhibition. This drives the consequential processing of the master regulator SREBP2, accompanied by lysosomal membrane permeabilization. Collectively, these lead to mitochondrial ROS production and activation of NLRP3 signalling, boosting inflammasome-mediated bacterial clearance. By establishing cholesterol sequestration as the mechanistic basis of host-directed activity of sertraline and distinguishing it from ineffective CADs, our work provides a mechanistic framework for developing cholesterol-modulating host-directed adjuncts to improve TB treatment outcomes. Graphical abstract: SRT induced lysosomal cholesterol accumulation results in enhanced bacterial control via inflammasome activation O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/665474v3_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1019b4dorg.highwire.dtl.DTLVardef@7b0ae8org.highwire.dtl.DTLVardef@9297eorg.highwire.dtl.DTLVardef@1832bef_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Edible Bird's Nest Enhances Memory and Learning in a Rat Model of Sporadic Alzheimer's Disease

Alzheimers disease (AD) has emerged as a major global health concern, with the glutamate hyperexcitability hypothesis suggesting that synaptic dysfunction and neuronal death are key contributors to cognitive impairments. Despite decades of research, current AD treatments only manage symptoms without offering a cure. This study investigates the potential of edible birds nest (EBN) as a therapeutic intervention for mitigating cognitive decline in a streptozotocin (STZ)-induced model of sporadic AD. Male Sprague-Dawley rats were randomly assigned to seven groups: control, sham, STZ, low EBN (LEBN, 300 mg/kg), medium EBN (MEBN, 600 mg/kg), high EBN (HEBN, 1200 mg/kg), and memantine (MEM, 10 mg/kg). On day 1, rats received a 3 mg/kg intracerebroventricular (ICV) injection of STZ and were allowed a 7-day recovery period. Following recovery, the rats were treated with their respective interventions daily via oral gavage for 21 days. Behavioral performance was assessed using the Open Field (OF), Novel Object Recognition Test (NORT), and Morris Water Maze (MWM). After behavioral testing, animals were euthanized, and hippocampal tissues were processed for Congo red staining, Bielschowsky staining, and immunohistochemistry to evaluate the expression of NR1, NR2A, NR2B, Glial fibrillary acidic protein (GFAP), and excitatory amino acid transporter 2 (EAAT2). STZ-treated rats exhibited significant declines in recognition memory, spatial learning, and increased anxiety in the open field, along with elevated Congo red and Bielschowsky staining, and higher expression of N-Methyl-D-aspartate receptor (NMDAR) subunits (NR1, NR2A, NR2B), GFAP, and EAAT2, indicative of astrogliosis and glutamate excitotoxicity. Treatment with MEBN (600 mg/kg) significantly improved exploratory behavior, memory, and cognition in the ICV-STZ rats. MEBN effectively attenuated cognitive decline and modulated hippocampal markers, yielding results comparable to the positive control, memantine. These findings underscore the potential of EBN as a promising therapeutic approach for AD and highlight the increasing relevance of traditional medicine in the treatment of neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Saddle Curvature Association of nsP1 Facilitates the Replication Complex Assembly of Chikungunya Virus in Cells

The replication of positive-sense RNA viruses, including the pathogenic SARS-CoV-1 and -2, DENV, and ZIKV, often takes place in curved cellular membrane compartments of tens to hundreds of nanometers in diameter within host cells. The non-structural proteins (nsPs) of viruses are found to critically control the formation and maintenance of such unique nanoscale membrane structures. However, the molecular mechanism underlying the association and assembly of nsPs around curved membranes has remained elusive, due to the technical difficulties of imaging the nanoscale interaction in live cells. In this study, we leveraged vertically aligned nanostructures to define membrane curvatures in live cells and investigated the assembly of viral nsPs on these curved membranes. Using Chikungunya virus as a model system, we found that its nsP1 was preferentially bound to and stabilized around positively curved membrane sites and the preference became more apparent as the radius of curvature decreased to 150 nm or smaller. This preferential accumulation was mainly attributed to the hydrophobic residues on recently identified membrane association loops (MA loops) of each nsP1 monomer. Molecular dynamics simulations further confirmed the improved binding kinetics and stability of nsP1 on positively curved membranes, especially when a 12-mer ring was formed by the nsP1 dodecamer. More interestingly, a saddle curvature association was enabled by the 3D coordination of nsP1 monomers along the dodecamer ring, where the MA loops of individual nsP1 monomers sensed a wide range of the positively curved membrane in the x-z plane while the rigid nsP1 dodecamer ring stabilized the negative curvature in the x-y plane. Its strong coupling to the saddle curvature fulfilled the need to constrain the neck of the membrane spherule for viral replication. Strikingly, productive CHIKV replication exhibited strong enrichment on patterned nanostructure array, proving the effectiveness of membrane curvature-guided assembly of the functional replication complex. Our findings revealed that the cell membrane facilitated the local enrichment of viral nsPs in a curvature- dependent manner. It opens up membrane curvature modulation as a new dimension to dissect the formation and regulation of membrane compartments for viral replication.

biophysics↗

bioRxiv2025

Comparative Computational Docking Analysis of MPP+ and Dopamine Binding to Dopamine Transporter in Human and Zebrafish: Mechanistic Insights into MPTP Neurotoxicity

1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) induces parkinsonism via its toxic metabolite, 1-methyl-4-phenylpyridinium (MPP+), which structurally mimics dopamine and enters dopaminergic neurons via the dopamine transporter (DAT). To visually depict this mimicry, we performed ligand-protein docking analysis on two species: humans and zebrafish. Human DAT (PDB ID: Q01959) and zebrafish DAT (UniProt ID: Q90ZV1) proteins were prepared with AutoDock Tools. Meanwhile, MPP+ (PubChem ID: CID_39484) and dopamine (PubChem ID: CID_681) ligands were prepared and optimized using the General AMBER Force Field (GAFF) tool. Docking with AutoDock Vina used identical grid parameters of 40 x 40 x 40 [A], which allows blind docking. Binding affinities and interactions were analyzed and visualized using PyMol and LigPlot+. MPP+ exhibited comparable binding affinities to dopamine in both species (human: -7.2 vs -6.1 kcal/mol; zebrafish: -7.6 vs -6.4 kcal/mol), sharing seven out of nine binding residues in humans and nine out of twelve in zebrafish. Spatial overlap with dopamine binding site suggests MPP+ exploits DAT for neuronal entry. However, static docking limitations warrant dynamic validation. This study provides computational evidence for the dopamine-mimetic mechanism of MPP+ but underscores the need for molecular dynamics (MD) simulation and experimental confirmation.

bioinformatics↗

bioRxiv2024

Discovery of Natural MCL1 Inhibitors using Pharmacophore modelling, QSAR, Docking, ADMET, Molecular Dynamics, and DFT Analysis

Mcl-1, a Bcl-2 family protein, is a key regulator of apoptosis and is often overexpressed in cancers such as lung, breast, pancreatic, cervical, ovarian cancers, leukemia, and lymphoma. Its role in inhibiting apoptosis enables tumor cells to evade cell death and contributes to drug resistance. Targeting Mcl-1 is crucial in inducing apoptosis and overcoming resistance to therapies that target other anti-apoptotic proteins, making it a prominent target for anticancer drug development across multiple malignancies. So, our study aimed to discover potent antileukemic compounds targeting MCL1. We began by selecting a diverse set of molecules from the BindingDB database to construct a structure-based pharmacophore model, which was subsequently used to virtually screen a library of 407,270 compounds from the COCONUT database. Subsequently, we developed an e-pharmacophore model using the co- crystallized inhibitor AMG-176, for further screening. A QSAR model was then implemented to estimate the IC50 values of these compounds, filtering those with predicted IC50 values below the median. The top hits were subjected to molecular docking and MMGBSA binding energy calculations against MCL1, leading to the selection of two promising candidates for further ADMET analysis. To assess their electronic properties, density functional theory (DFT) calculations were conducted, which included geometry optimization, frontier molecular orbital (FMO) analysis, HOMO-LUMO gaps, and global reactivity descriptors. These analyses confirmed favourable profiles and reactivity for the chosen compounds. In addition, predictions for physicochemical and ADMET properties aligned well with the expected bioactivity and safety profiles of the candidates. Molecular dynamics (MD) simulations further validated their strong binding affinity and stability, positioning them as potential MCL1 inhibitors. Our comprehensive computational approach highlights these compounds as promising and safe antileukemic agents, with future in vivo and in vitro validation recommended for further confirmation.

bioinformatics↗

bioRxiv2024

DNA methylation and demethylation driven regulation of sepsis

During dysregulated inflammation and sepsis, there is a sudden surge of cytokines, such as TNF alpha, IL6, and IL10, which disrupts the body homeostasis. This sudden and rapid increase in cytokine gene expression cannot be explained by the conventional central dogma mechanism. DNA methylation is one of the most significant epigenetic modifications. DNA methylation is mostly associated with the suppression of gene activity, and DNA demethylation is associated with the activation of gene activity. There are numerous transcription factors, such as CREB1, c-FOS, AP-1, IRF1, and EGR1, that play pivotal roles in regulating inflammation. Thus, it was hypothesized that changes in the DNA methylation patterns of cytokine promoter regions or in the promoter regions of these specific transcription factors might be the potential reasons for the increase in cytokine levels during sepsis. During endotoxin stimulation, DNA methyltransferases were suppressed, and DNA methylation levels were altered at the global level. Bisulfite sequencing revealed no change in the DNA methylation patterns of the TNF-alpha, IL6 and IL10 cytokine promoters. The CREB1 and c-FOS transcription factor promoters were demethylated after LPS stimulation and in clinical sepsis samples. Overall, this study highlights the importance of the role of DNA methylation in sepsis.

molecular biology↗

bioRxiv2024

Discovery of natural compounds as novel FMS-like tyrosine kinase 3 (FLT3) therapeutic inhibitors for the treatment of acute myeloid leukemia: an in silico approach

FLT3 mutations, observed in approximately 30-35% of Acute Myeloid Leukemia (AML) cases, drive leukemic proliferation and survival pathways, presenting a significant challenge in clinical management. To address this therapeutic need, we employed a comprehensive computational approach integrating pharmacophore screening, molecular docking, ADMET analysis, and molecular dynamics simulations to identify potent inhibitors targeting FLT3. Utilizing ligand-based pharmacophore models generated from experimentally proven FLT3 inhibitors from BindingDB, we screened over 400,000 natural compounds from the COCONUT database. Hits identified through pharmacophore screening underwent further evaluation via Lipinski and Golden triangle criteria to ensure drug-like properties. Molecular docking against the FLT3 receptor, combined with ADMET analyses, facilitated the prioritization of lead compounds. Subsequently, three promising candidates were subjected to molecular dynamics simulations to assess binding stability. Our findings reveal three top- performing compounds, demonstrating robust and stable binding affinity and favorable ADMET characteristics. These compounds hold promise as potential scaffolds or leads for developing novel FLT3 inhibitors in AML therapy.

bioinformatics↗

bioRxiv2024

In silico Exploration Natural Compounds for the Discovery of Novel DNMT3A Inhibitors as Potential Therapeutic Agents for Acute Myeloid Leukemia

Aberrant DNA methylation, a hallmark of acute myeloid leukemia (AML), is catalyzed by DNA methyltransferase 3A (DNMT3A). Approximately 20-30% of AML patients harbor DNMT3A mutations, leading to disrupted DNA methylation patterns and leukemogenesis. To identify potential therapeutic interventions, this study employed computational drug discovery. A pharmacophore model was constructed and utilized to screen a natural product database, yielding a set of promising compounds. Subsequent molecular docking, MM-GBSA calculations, and ADMET profiling identified two compounds, CNP0375130 and CNP0256178, as potential DNMT3A inhibitors. These compounds exhibited favorable binding affinities and demonstrated desirable drug-like properties. Molecular dynamics simulations confirmed stable protein-ligand interactions. These findings suggest that CNP0375130 and CNP0256178 may serve as promising lead compounds for the development of novel anti-leukemic therapies targeting DNMT3A, and contribute to the ongoing efforts to develop targeted therapies for leukemia.

bioinformatics↗

bioRxiv2024

Exploration of Natural Products for Targeting IDH1 and IDH2 Mutations in Acute Myeloid Leukemia Through Ligand-Based Pharmacophore Screening and Molecular Dynamic Simulation Approaches

BackgroundMutations in isocitrate dehydrogenase 1 (IDH1) and 2 (IDH2) are prevalent drivers of acute myeloid leukemia (AML). While targeted therapies exist, resistance can emerge. This study explored the potential of natural products to identify novel dual IDH inhibitors. MethodsIn-silico screening of the COCONUT database was performed using Lipinskis Rule of Five. Pharmacophore modelling identified crucial features for IDH binding. Docking simulations with Glide (Schrodinger) assessed binding affinity, followed by MM-GBSA calculations for free energy estimation. The most promising candidate underwent ADME/T and toxicity analysis. Finally, molecular dynamics (MD) simulations evaluated the stability of protein-ligand complexes and binding interactions, followed by trajectory analysis using DCCM and PCA. ResultsThe study identified Ternstroside D (CNP0166496) as a potential dual inhibitor for IDH1 and IDH2 mutations. Docking simulations and MM-GBSA calculations predicted favourable binding affinities. MD simulations revealed stable protein-ligand complexes, and in-silico ADME/T analysis suggested good drug-like properties and a favorable safety profile for CNP0166496. ConclusionThis in-silico study provides compelling evidence for Ternstroside D (CNP0166496) as a promising dual inhibitor for IDH1 and IDH2 mutations in AML. Further in-vitro and in-vivo studies are warranted to validate these findings.

bioinformatics↗

bioRxiv2024

Rapalink-1 reveals novel mTOR-dependent genes and the role of agmatinases in cellular growth and chronological lifespan

The mechanistic Target of Rapamycin, mTOR, is a conserved pro-ageing pathway with characterised inhibitors such as rapamycin, rapalogues and torins. Bi-steric third-generation inhibitors, such as rapalink-1 have been developed, however, their effects on organismal gene expression and lifespan have not been characterised. Here, we demonstrate that rapalink-1 affects fission yeast spatial and temporal growth and prolongs chronological lifespan with a distinct TORC1 selectivity profile. Endosome and vesicle-mediated transport and homeostasis processes related to autophagy and Pik3, the orthologue of human PI3K, render cells resistant to rapalink-1. Our study reveals mTOR-regulated genes with unknown roles in ageing including all fission yeast agmatinases, the enzymes that convert agmatine to putrescine and urea. Through genome-wide screens, we identify sensitive and resistant mutants to agmatine and putrescine. Genetic interactome assays for the agmatinase agm1 and further cell and molecular analyses, demonstrate that impairing the agmatinergic branch of arginine catabolism results in mTOR activity levels that are beneficial for growth but detrimental for chronological ageing. Our study reveals the anti-ageing action of agmatinases within a metabolic feedback circuit regulating mTOR activity levels and ageing and with possible implications to other systems, including human cells.

cell biology↗