Biology subjects

Mahajan, D.

Publications and source records attributed to Mahajan, D..

6 recordsLinked to original sources

bioRxiv2026

Target-Specific Discovery of BMM_1567 Restores Aminoglycoside Activity Against Multidrug-Resistant Gram-Negative ESKAPE Pathogens

The global emergence of multidrug-resistant (MDR) ESKAPE pathogens has significantly reduced the effectiveness of existing antibiotics, highlighting the urgent need for new strategies to restore antimicrobial susceptibility. Here, we report the discovery and mechanism of BMM_1567, a peptide potentiator that enhances aminoglycoside efficacy against MDR pathogens. A genetically defined reporter-based screen identified BMM_1567 as a potent inhibitor of aminoglycoside resistance, potentiating spectinomycin activity against MDR Gram-negative ESKAPE isolates at low micromolar concentrations. Structural modeling and molecular dynamics simulations indicated that BMM_1567 interacts with residues lining the antibiotic-binding groove of aminoglycoside-modifying enzymes (ANT, APH, AAC), with highest affinity for ANT ({Delta}G_bind = -62.25 kcal/mol), suggesting competitive inhibition of substrate binding. Site-directed mutagenesis of key ANT residues identified critical amino acids involved in BMM_1567 binding, confirming their role in mediating spectinomycin potentiation. In murine abscess model using XDR E. coli, BMM_1567 in combination with spectinomycin significantly reduced bacterial burden and pro-inflammatory cytokine levels, comparable to colistin. Collectively, these findings establish BMM_1567 as a promising aminoglycoside potentiator that restores antibiotic activity against MDR pathogens through direct inhibition of resistance enzymes, while exhibiting in vivo efficacy and a remarkably low propensity for resistance development.

microbiology↗

bioRxiv2026

NanoLabel: A fast and accurate real-time nanopore signal classifier

Oxford Nanopore Technologies adaptive sampling capability promises to reduce sequencing cost and turnaround time. At its core, adaptive sampling is a real-time classification problem that distinguishes reads originating from regions of interest. Direct signal-based classification approaches bypass the computational bottleneck of basecalling and can eliminate the need for powerful GPUs. However, operating directly on noisy raw signals remains challenging in real-time settings, where classification decisions must be made quickly. In this work, we propose NanoLabel, a new method for real-time classification of nanopore signals. We build NanoLabel on top of signal-based read mapping tool, RawHash2. We accelerate the classification workflow by mapping reads using only the target regions as the reference. To further improve accuracy, we train a lightweight classifier on mapping-derived features and introduce a data augmentation strategy to construct sufficiently large and class-balanced training datasets. We evaluate NanoLabel using publicly available real sequencing datasets from three human genomes (HG001, HG002, and HG005), while assuming a cancer gene panel as the target. Compared to directly mapping reads with RawHash2, we demonstrate 80 x improvement in the classification time and 0.10 - 0.25 units improvement in the F1 score.

genomics↗

bioRxiv2025

Billi: Provably Accurate and Scalable Bubble Detection in Pangenome Graphs

A key application of pangenome graphs is the characterization of small and large genomic variants represented as bubbles within the graph. Although bubbles have been extensively studied in directed graphs in the context of genome assembly, there remains a need for a rigorous definition and systematic analysis of bubbles in bidirected graphs, which is the predominant data structure used to represent pangenomes. We show that existing bubble definitions for bidirected graphs do not fully meet the requirements for representing genetic sites and alleles; in particular, overlapping bubbles may not exhibit strict nesting. To address this, we introduce a new sub-graph abstraction called panbubble and prove that it satisfies the desired structural properties for variant characterization. We then present an exact algorithm with runtime [O] (|V |2(|V | + |E|)) for detecting all panbubbles in a bidirected graph G = (V, E). In addition, we propose a heuristic algorithm that produces identical output as the exact algorithm in practice and scales to large graphs, including both the first and second releases of the Human Pangenome Reference Consortium (HPRC). We implemented our algorithms in the tool Billi (github.com/at-cg/billi). On our largest dataset, Billi is more than 15x faster and uses over 5x less memory than VG.

bioinformatics↗

bioRxiv2024

Withaferin A downregulates NDRG1 to overcome hypoxia mediated EMT and chemoresistance in lung adenocarcinoma and glioma cells

One of the important hurdles to be overcome in the management of cancers is the acquired resistance to therapy. There is a crucial need to not only understand molecular pathways underpinning resistance to therapy but to find better and more effective therapeutic avenues to overcome such acquired resistance. Tumor microenvironmental conditions such as hypoxia have long been known to result in chemoresistance in various cancers that become unresponsive to standard-of-care drugs such as cisplatin. Although many new compounds are screened for their anticancer properties, the recalcitrant tumor microenviroenment has not been given due importance in many potential drugs. In this study, we examine the efficacy of Withaferin A (WA), a bioactive compound isolated from Withania somnifera, in overcoming hypoxia-induced metabolic adaptation, chemoresistance, and epithelial-to-mesenchymal transition (EMT) in both lung adenocarcinoma and glioma cells. Our results reveal that WA significantly inhibits hypoxia-induced increased migration, EMT, and metabolic reprogramming, leading to enhanced cytotoxicity in otherwise chemoresistant cancer cells. WA treatment suppressed the expression of markers of EMT, glucose metabolism, and bonafide hypoxia markers, particularly NDRG1 thereby inducing cell death in these cancer cells. WA showed significant cytotoxic effects in chemoresistant lung adenocarcinoma and glioma cells, both alone or in combination with cisplatin, highlighting its potential as a therapeutic agent for overcoming chemoresistance in these cancers. Our results provide new insights into the anti-cancer mechanisms of WA especially under hypoxic conditions, and support its further investigation as a promising adjunctive therapy for the treatment against hypoxia-induced chemoresistance in cancers.

cancer biology↗

bioRxiv2023

Methotrimeprazine exerts antiviral and neuroprotective effects in Japanese encephalitis virus infection through activation of adaptive ER stress and autophagy

Japanese encephalitis virus (JEV) is the leading global cause of virus-induced encephalitis. Its pathogenesis is driven by a combination of neuronal cell death and neuroinflammation. We hypothesized that pharmacological upregulation of autophagy could exert a neuroprotective antiviral effect, and tested a panel of forty-two FDA-approved drugs that were shown to induce autophagy. Four drugs were tested in the JE mouse model based on in vitro protective effects on neuronal cell death, inhibition of viral replication, and anti-inflammatory effects in microglial cells. The antipsychotic phenothiazines Methotrimeprazine (MTP) and Trifluoperazine (TFP) showed a significant survival benefit with reduced virus titers in the brain, prevention of blood-brain barrier (BBB) breach, and inhibition of neuroinflammation. Both drugs were potent mTOR-independent autophagy flux inducers. Mechanistically MTP inhibited SERCA channel functioning, thereby resulting in rise in cytosolic calcium levels, and induction of a unique adaptive ER stress response. In virus infected drug treated cells, there was a strong transcriptional downregulation of type I interferon and interferon-stimulated genes and upregulation of cholesterol metabolic pathway genes. The drugs exerted an autophagy-dependent antiviral effect at the level of JEV protein translation/replication complex formation in diverse cell types. Inhibition of inflammatory cytokine/chemokine release from mouse microglial cells was partly autophagy-dependent. Our study suggests that MTP exerts a combined antiviral and anti-inflammatory effect in JEV infection, and has therapeutic potential to be repurposed for JE treatment.

microbiology↗

bioRxiv2021

Arl15 upregulates the TGFβ family signaling by promoting the assembly of the Smad-complex

The hallmark event of the canonical transforming growth factor {beta} (TGF{beta}) family signaling is the assembly of the Smad-complex, consisting of the common Smad, Smad4, and phosphorylated receptor-regulated Smads. How the Smad-complex is assembled and regulated is still unclear. Here, we report that active Arl15, an Arf-like small G protein, specifically binds to the MH2 domain of Smad4 and colocalizes with Smad4 at the endolysosome. The binding relieves the autoinhibition of Smad4, which is imposed by the intramolecular interaction between its MH1 and MH2 domains. Activated Smad4 subsequently interacts with phosphorylated receptor-regulated Smads, forming the Smad-complex. Our observations suggest that Smad4 functions as an effector and a GTPase activating protein (GAP) of Arl15. Assembly of the Smad-complex enhances the GAP activity of Smad4 toward Arl15, therefore dissociating Arl15 before the nuclear translocation of the Smad-complex. Our data further demonstrate that Arl15 positively regulates the TGF{beta} family signaling.

cell biology↗