Biology subjects

Kaur, B.

Publications and source records attributed to Kaur, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Discovery of a brain-penetrant CHI3L1 inhibitor as an oral modulator of neuroinflammation in Alzheimers disease

Chitinase-3-like protein 1 (CHI3L1) is elevated in Alzheimers disease (AD), but its role in glial dysfunction and therapeutic tractability remain unclear. Here, screening a 4.2-billion-compound DNA-encoded library identified DELC2, a brain-penetrant CHI3L1 modulator. Biophysical and crystallographic studies showed that DELC2 binds the CHI3L1 glycan-recognition groove within an aromatic-hydrophobic pocket centered on Trp99 and Trp352. DELC2 inhibited CHI3L1-RAGE association, suppressed CHI3L1-induced inflammatory signaling, reduced Gal-3-positive microglia, and restored amyloid-{beta} uptake in glial cultures. In human cerebrospinal fluid, CHI3L1 was elevated in AD and correlated with astrocytic NF-{kappa}B activation. DELC2 phenocopied CHI3L1 immunodepletion, whereas CHI3L1 add-back restored inflammatory and amyloid-{beta}-handling defects. Oral DELC2 achieved sustained unbound brain exposure in 5xFAD mice, improved cognitive performance, reduced multiple amyloid-{beta} species, and attenuated astrocytic and microglial inflammatory programs. These findings establish the CHI3L1 glycan-recognition groove as a druggable regulator of RAGE-associated glial dysfunction and identify DELC2 as a chemical scaffold for CHI3L1-directed therapy in AD.

pharmacology and toxicology↗

bioRxiv2026

DNA-Encoded Library-Guided Discovery of a First-in-Class Molecular Glue of the NOS1AP-SCRIB Complex in Alzheimer's Disease Patient-Derived Neurons

NOS1AP is an adaptor for neuronal nitric oxide synthase that engages several partner proteins and is implicated in Alzheimer's disease. Efforts to drug NOS1AP have sought to disrupt these; we instead report pharmacological stabilization of one interaction. Affinity selection of a 1.4-billion-member DNA-encoded library identified a benzimidazole-5-carboxamide chemotype, optimized by fragment-directed SAR to NOSTRA with submicromolar NOS1AP binding affinity. Of six interactions, NOSTRA enhanced only SCRIB binding, with a cooperativity factor of 30, predominantly through a 14-fold slowing of dissociation; native mass spectrometry resolved a NOS1AP:NOSTRA:SCRIB ternary complex. In healthy human iPSC-derived cortical neurons, NOSTRA engaged the endogenous complex and activated Rac1 without cytotoxicity; in Alzheimer's patient-derived neurons, it lowered the A{beta}42/A{beta}40 ratio and p-tau217, reduced neurofilament light and improved network activity. With an in vitro ADME profile consistent with CNS exposure, NOSTRA is the first molecular glue for a NOS1AP complex, establishing interaction stabilization as a viable NOS1AP pharmacology.

pharmacology and toxicology↗

bioRxiv2026

Microbial bioprospecting for benzoxazolinate-like molecules: unleashing the potential of genome mining

The benzoxazolinate moiety is a key functional group found in a few natural products (NPs), exhibiting diverse bioactivities, including antitumor, antibacterial, and cytotoxic activities. Despite their clinical importance, only a few bacterial strains and NPs have been reported harboring this rare bis-heterocyclic moiety, underscoring a largely unexplored chemical space. Here, we performed large-scale genome mining and identified 277 putative biosynthetic gene clusters (BGCs) across diverse bacterial hosts, including previously unreported bacterial genera and strains. The BGCs were grouped into three compound classes: benzoxazolinate, benzobactin, and ashimides based on sequence similarity network clustering. Bioactivity predictions of the identified BGCs revealed the predominance of antibacterial and cytotoxic potential, highlighting promising candidates for future experimental validation and functional studies. This study also presents a neural network-based bioprospecting model that efficiently detects rare BGCs encoding benzoxazolinate-containing molecules from genomic sequences. Overall, our findings expand the known repertoire of bacterial hosts with the potential to produce benzoxazolinate-containing NPs and provide a comprehensive framework for the discovery and identification of candidate BGCs.

bioinformatics↗

bioRxiv2026

A distribution-aware and functionally relevant novel framework for generation and discovery of bioactive peptides

Recent advances in artificial intelligence have accelerated the discovery of bioactive peptides by enabling computational exploration of the vast peptide sequence space. However, existing peptide generation approaches generally rely on either distribution-learning models, which generate biologically realistic sequences but do not consistently optimize functional activity, or optimization-based methods, which maximize prediction confidence while often deviating from the underlying distribution of experimentally validated peptides. To address this limitation, a two-phase generative-evolutionary framework is proposed that integrates distribution learning with evolutionary optimization. In the first phase, Variational Autoencoders (VAE), Autoregressive Transformers (ART), and Token Diffusion Transformers (TDT) are used to generate biologically plausible seed peptides. In the second phase, these peptides were used as initial seed for Hill Climbing optimization procedure that iteratively improves fitness function score. The proposed two-phase framework was evaluated using a dataset of experimentally validated IL-2-inducing peptides. Evaluation using independent IL-2 prediction models showed that Autoregressive Transformer combined with Hill Climbing achieved the best overall performance, achieving the mean IL-2 induction confidence score of 0.96 while reducing KL divergence from 2.26 for standalone Hill Climbing to 0.75. A case study on an independent IL-13 inducing peptide dataset showed similar trends, with ART initialized Hill Climbing achieving the mean IL-13 induction score of 0.99 while reducing KL divergence from 1.76 to 0.59. Overall, the framework provides a generalizable approach for balancing functional optimization and distributional realism and can be applied to peptide discovery and data augmentation in imbalanced biological datasets thereby generating high confidence peptides for wet lab validation. HighlightsO_LIProposed a two-phase framework for bioactive peptide generation with potential to address class imbalance in peptide classification tasks. C_LIO_LIPerformed a systematic comparison of distribution-learning and optimization-based approaches for peptide generation. C_LIO_LICombined distribution-learning models for sequence generation with optimization algorithms for improving peptide functional properties. C_LIO_LIDemonstrated the applicability of the proposed framework across multiple bioactive peptide datasets. C_LI

bioinformatics↗

bioRxiv2026

BGX: A Comprehensive Pipeline for Genomic Insight into Bioactivity Prediction, Genomic Surveillance, and Novel Biosynthetic Gene Cluster Assessment

The increasing availability of genomic and metagenomic data has created significant opportunities to explore microbial diversity, biosynthetic potential and functional traits. However, comprehensive and comparative genome analysis often requires integrating multiple independent tools, making large-scale studies challenging to implement and manage. Here, we present Bacterial Genome eXplorer (BGX), an integrated and scalable pipeline that streamlines large-scale genome analysis and exploration of biosynthetic potential. BGX integrates different analytical tools into six major stages: (i) genome retrieval and assembly, (ii) genome quality assessment, (iii) antimicrobial resistance (AMR) gene profiling, (iv) annotating Biosynthetic gene clusters (BGCs) and novelty assessment, (v) bioactivity predictions, and (vi) clustering and networking analysis. In addition, BGX provides a user-friendly interactive interface to facilitate data exploration and interpretation. We demonstrated the versatility and scalability of BGX through large-scale analysis of two independent datasets: 248 genomes from the One Day One Genome (ODOG) initiative and 153 publicly available genomes from NCBI. This analysis enabled the comprehensive characterisation of genome quality, AMR determinants, biosynthetic potential and candidate bioactive metabolites across two datasets. BGX is distributed as a Docker container that simplifies installation, enables reproducible data processing, and supports pipeline execution across different computational environments. The modular and reproducible architecture of the BGX pipeline provides an effective framework for large-scale genome mining, genomic surveillance, and accelerates the discovery and prioritisation of novel secondary metabolites. BGX is now accessible at https://bgx.nabi.res.in

bioinformatics↗

bioRxiv2026

Tyrosine hydroxylase–mediated neuroimmune crosstalk regulates antitumor immunity in glioblastoma during oncolytic herpes virotherapy

Neuroimmune crosstalk is increasingly recognized as a key regulator of tumor progression and therapeutic response, yet its role in central nervous system (CNS) tumors remains poorly understood. Here, we investigate tyrosine hydroxylase (TH)-mediated neuronal signaling in glioblastoma (GBM) and its impact on antitumor immunity and response to oncolytic virotherapy (OV). We show that TH cells are widely distributed within the GBM microenvironment, including neurons, astrocytes, and immune cells, and are enriched at the tumor margin. In addition, TH cells are present in the tumor-draining lymph nodes (TDLNs) of GBM, where they localize near lymphatic vessels and are associated with lymphangiogenesis. Notably, a subset of CD3TH T cells is detected within lymphatic structures of TDLNs, suggesting immune-intrinsic catecholamine signaling. Single-cell RNA sequencing reveals that noradrenergic signaling, particularly via {beta}2-adrenergic receptors (ADRB2), predominates in tumor-infiltrating myeloid cells and is dynamically regulated by therapy. Intratumoral administration of oncolytic herpes simplex virus (oHSV) upregulates ADRB2 expression in macrophages, whereas systemic chemo-immunotherapy induces distinct receptor modulation patterns in tumors and TDLNs. Functionally, pharmacologic {beta}-adrenergic blockade significantly enhances the efficacy of oHSV therapy in orthotopic GBM and subcutaneous melanoma models, resulting in reduced tumor growth, increased tumor cell death, and enhanced CD8 T cell infiltration. Similarly, direct inhibition of TH enzymatic activity suppresses tumor progression and further potentiates OV. Mechanistically, TH inhibition not only promotes tumor-infiltrated cytotoxic immune cells CD8, NK and {gamma}{delta} T cells, but also suppresses the activity of immunosuppressive myeloid cells, including transcriptional (Fos), and metabolism (Arg) modification in M2 macrophages and other immune cells. Collectively, these findings identify TH-mediated neuroimmune signaling as a critical regulator of tumor immunity in GBM and demonstrate that targeting catecholaminergic pathways or downstream neuroimmune crosstalk pathways can enhance the efficacy of OV. This study provides a rationale for integrating neural modulation into immunotherapeutic strategies for CNS malignancies.

Cancer Biology↗

bioRxiv2026

BTK inhibition enhances immunovirotherapy in glioblastoma via tertiary lymphoid structure modulation

Glioblastoma (GBM) is a highly aggressive type of glioma that is resistant to immunotherapy and is associated with poor prognosis, largely due to its immunosuppressive tumor microenvironment. Brutons tyrosine kinase (BTK) is a non-receptor kinase that not only plays an important role in oncogenic signaling, particularly in tumor growth, but also regulates the activity of tumor-infiltrating myeloid cells, including dendritic cells, macrophages, and microglia in brain tumors. High BTK expression is associated with poor survival in patients with glioma. Oncolytic herpes simplex virus type 1 (oHSV)-derived virotherapy, a novel treatment strategy, has demonstrated effectiveness against GBM; however, its efficacy is limited by the tumor microenvironment. In this study, we found that BTK is predominantly expressed in GBM-infiltrating myeloid cells. Intratumoral injection of oHSV not only promotes infiltration of myeloid cells and T cells but also activates BTK in these myeloid cells, thereby limiting oHSV infection and replication in tumor cells. Combination treatment with BTK inhibitor ibrutinib improves anti-tumor efficacy of oHSV in both human GBM12 xenograft and syngeneic murine GSC005 models. Mechanistically, BTK inhibition increases oHSV-mediated tumor cell death (cleaved caspase-3) and cytotoxic CD8 T cell infiltration, while decreasing tumor cell proliferation (Ki-67). BTK inhibition not only suppresses oHSV clearance by tumor-infiltrating microglia and macrophages but also reduces their pro-invasive effects on tumor cells. Addition of IDO inhibitor, an immune modulator, further prolongs survival in tumor-bearing mice in a syngeneic GBM model. Single-cell mRNA sequencing (scRNA-seq) analysis indicates that combination treatment modifies key signaling pathways in both tumor-infiltrating myeloid cells (macrophages and microglia) and CD8 T cells. Further analysis shows that BTK inhibition, with or without IDO inhibition, promotes the formation of tumor-infiltrating tertiary lymphoid structures (TLS) during intratumoral oHSV treatment, subsequently remodeling T cell, NKT cell, and monocyte-macrophage populations. These results indicate that BTK inhibition exerts multifaceted effects in enhancing the anti-tumor efficacy of oHSV therapy.

cancer biology↗

bioRxiv2026

Structural Optimization of CHI3L1 Inhibitors with Improved Pharmacokinetics and Functional Activity in 3D Glioblastoma Models

Chitinase-3-like protein 1 (CHI3L1) is a key driver of glioblastoma (GBM) progression and an emerging therapeutic target. Building on the CHI3L1 inhibitor 11g, we optimized the scaffold through medicinal chemistry to assess structure-property relationships and improve pharmacokinetics. Using microscale thermophoresis (MST) and computational studies, we validated 10p, which exhibits a CHI31 binding affinity (Kd) of 13.22 {micro}M. Notably, 10p overcomes previous developability hurdles by achieving a kinetic solubility of 758 {micro}M, a five-fold improvement over 11g. It further demonstrates high metabolic stability across species and no hERG inhibition. In 3D GBM spheroid models, 10p significantly reduced tumor viability, mass, and migration, exceeding the efficacy of prior analogues. Collectively, these findings establish 10p as a potent CHI3L1 inhibitor with a superior pharmacokinetic profile and robust functional activity, marking it as a promising candidate for further GBM drug development. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/702243v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@dff733org.highwire.dtl.DTLVardef@1de4e56org.highwire.dtl.DTLVardef@1e910dcorg.highwire.dtl.DTLVardef@51e9d4_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

Targeting CHI3L1 in Alzheimers Disease: Optimization of G721-0282 and Functional Evaluation in Astrocyte Models

Alzheimers disease (AD) involves astrocytic dysfunction characterized by impaired lysosomal activity, defective amyloid clearance, and neuroinflammation, processes strongly regulated by the inflammatory effector CHI3L1. G721-0282, a reported CHI3L1-binding small molecule with demonstrated modulation of downstream signaling pathways including MAPK and STAT3, provides a validated chemical starting point for targeting CHI3L1-driven astrocytic pathology in AD, but exhibits suboptimal potency and drug-like properties that limit its translational potential. We therefore performed a virtual screening of commercially available analogues of G721-0282 to enable structure-guided optimization, generating a detailed structure-activity map and prioritizing 24 derivatives. Biophysical analyses identified compound G721-0377 as the most promising candidate, with optimized substitutions improving CHI3L1 binding affinity. Compound G721-0377 also exhibited favorable pharmacokinetic properties, including improved solubility, balanced permeability, reduced microsomal clearance, and an enhanced cardiac safety margin. Functionally, G721-0377 uniquely reversed CHI3L1-induced astrocytic dysfunction, restoring amyloid uptake, lysosomal proteolysis and acidification, suppressing CHI3L1 and IL-6 secretion, and inhibiting NF-{kappa}B activation to levels comparable to a neutralizing anti-CHI3L1 antibody. In contrast, compounds G721-0179 and G857-1069 showed minimal activity. Collectively, these findings establish G721-0377 as a next-generation CHI3L1 inhibitor with improved affinity, safety, and robust functional efficacy, supporting its further development as a disease-modifying therapeutic for AD.

pharmacology and toxicology↗

bioRxiv2025

Restoring Amyloid Clearance via Astrocytes: Z17 Is a Selective Inhibitor of CHI3L1 in Alzheimers Disease

Alzheimers disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline, accumulation of hallmark protein aggregates and substantial neuroinflammation. Chitinase-3-like protein 1 (CHI3L1) which is predominantly produced by activated astrocytes in the central nervous system (CNS). Overexpression of CHI3L1 has been implicated with AD progression and worsening of symptoms. Herein, we report the identification of Z17 as a novel and selective CHI3L1 inhibitor which directly bind to CHI3L1 an equilibrium dissociation constant (KD) of 6.0 {micro}M. In human iPSC-derived astrocytes, Z17 acted as a dual-action regulator by reinstating astrocytic function and suppressing inflammation. Additionally, Z17 rescued CHI3L1-induced impairment by dose-dependently restoring A{beta} uptake and normalizing lysosomal proteolytic activity and pH. Furthermore, Z17 effectively blocked CHI3L1-driven activation of the NF-{kappa}B pathway in human astrocytes, providing a mechanistic explanation for the functional rescue. The in vitro pharmacokinetic (PK) profiling of Z17 demonstrated favorable drug-like properties for CNS development. These findings support the advancement of Z17 as a selective CHI3L1 inhibitor capable of simultaneously mitigating neuroinflammation and restoring astrocytic clearance mechanisms, making it a highly promising therapeutic candidate for Alzheimers disease. Abstract Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/692801v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@5cfc38org.highwire.dtl.DTLVardef@b2e291org.highwire.dtl.DTLVardef@38d243org.highwire.dtl.DTLVardef@746330_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

HTS-Oracle: Experimentally validated AI-enabled prioritization for generalizable small molecule hit discovery

High-throughput screening (HTS) remains a central pillar of small molecule discovery yet routinely fails for immune receptors and protein-protein interaction-driven targets. Here, we introduce HTS-Oracle, an experimentally validated AI system for prospective hit discovery that integrates molecular language modeling with cheminformatics to prioritize bioactive compounds at scale. We deploy HTS-Oracle across three clinically validated yet historically intractable immune targets, TREM2, CHI3L1, and CD28, representing cryptic binding pockets, intrinsically disordered proteins, and protein-protein interaction-driven immune checkpoint, respectively. Across the tested targets, HTS-Oracle reduces experimental screening requirements by up to >99% while increasing hit rates by up to 176-fold relative to traditional HTS. Notably, the platform remains predictive under extreme data sparsity, achieving an eightfold improvement for CD28 despite fewer than 2% actives in training. By consistently enriching for experimentally validated hits, HTS-Oracle establishes a new performance benchmark for hit discovery and unlocks small molecule access to immune targets long regarded as chemically inaccessible.

bioinformatics↗

bioRxiv2025

Discovery of a CHI3L1-Targeted Small Molecule Modulating Neuroinflammation in Alzheimers Disease via DNA-Encoded Library (DEL) Screening

Chitinase-3-like protein 1 (CHI3L1, also known as YKL-40) has emerged as a central effector of astrocyte-mediated neuroinflammation and a promising biomarker for Alzheimers disease (AD). However, small molecule CHI3L1 inhibitors that modulate neuroinflammation are limited. Here, we report the discovery of a CHI3L1-targeted small molecule, DEL-C1, identified through DNA-encoded library (DEL) screening and validated using orthogonal biophysical, computational, and cellular approaches. DEL-C1 demonstrated direct CHI3L1 binding in microscale thermophoresis (MST) and surface plasmon resonance (SPR) assays, with reversible and concentration-dependent association. Molecular docking and 100-ns molecular dynamics simulations revealed a stable binding mode within the CHI3L1 substrate groove, anchored by Tyr206 and flanked by Trp99 and Trp352, supporting a thermodynamically favorable interaction. In vitro ADME profiling indicated a balanced physicochemical profile, permeability, and metabolic stability, consistent with CNS drug-like properties. Functionally, DEL-C1 reversed CHI3L1-induced astrocyte dysfunction by restoring A{beta} uptake, lysosomal acidification, and proteolytic activity, while reducing CHI3L1 and IL-6 secretion. DEL-C1 also suppressed CHI3L1-driven NF-{kappa}B transcriptional activation, highlighting its anti-inflammatory potential. Collectively, this study establishes DEL-C1 as a promising small molecule modulator of CHI3L1 and a chemical tool to interrogate astrocyte-driven neuroinflammation in AD.

biophysics↗

bioRxiv2025

Affinity Selection-Mass Spectrometry Coupled with Biophysical Validation Enables Proof-of-Concept Discovery of CHI3L1 Binders

Chitinase-3-like protein 1 (CHI3L1) is a multifunctional extracellular glycoprotein implicated in tumor progression, immune suppression, and fibrosis, making it an attractive but challenging therapeutic target. To explore its chemical tractability, we applied an affinity selection-mass spectrometry (AS-MS) workflow to screen 10,000 small molecules for CHI3L1 binding. The screen yielded 124 initial hits with a hit rate of 1.24%, which were prioritized based on chemical suitability, and six candidates were advanced for validation using microscale thermophoresis (MST). Among these, compound A9 exhibited a clear, dose-dependent binding response in MST with a Kd of 182 {+/-} 18 {micro}M. Molecular docking supported these findings, revealing that A9 forms hydrophobic and hydrogen-bonding interactions within a defined pocket of the CHI3L1 structure. Although modest in affinity, A9 represents the first small molecule binder of CHI3L1 identified through AS-MS. This study provides a proof-of-concept demonstration that CHI3L1 can be chemically engaged using AS-MS, establishing a foundation for future medicinal chemistry optimization and the development of chemical probes targeting this previously undruggable extracellular protein. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/681114v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@12959c2org.highwire.dtl.DTLVardef@1c3e3a4org.highwire.dtl.DTLVardef@1962a04org.highwire.dtl.DTLVardef@1a0a2c4_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Structure-Based Virtual Screening Identifies TREM2-Targeted Small Molecules that Enhance Microglial Phagocytosis

Triggering receptor expressed on myeloid cells 2 (TREM2) is a microglia-specific receptor whose activation promotes phagocytosis and neuroprotection in Alzheimers disease (AD) and related neurodegenerative disorders. While therapeutic efforts have largely focused on antibodies, small molecule TREM2 modulators remain limited. Here, we applied a structure- based virtual screening workflow targeting a putative allosteric site on TREM2, guided by PyRod-derived pharmacophores from molecular dynamics simulations. Screening of the Enamine Collection yielded 20 candidate compounds, three of which demonstrated binding in TRIC assays. The top hit, EN020, exhibited a KD of 14.2 {micro}M (MST) and 35.9 {micro}M (SPR), and significantly enhanced microglial phagocytosis in BV2 cells outperforming the known TREM2 agonist VG-3927. A preliminary structure-activity relationship (SAR) study, including synthetic and catalog-derived analogs, highlighted a narrow tolerance for scaffold modifications, with only T2V002 retaining partial TREM2 binding affinity. This work identifies EN020 as a novel small molecule TREM2 modulator with functional activity, providing a framework for rational optimization toward potential AD therapeutics.

pharmacology and toxicology↗

bioRxiv2025

Structure-Guided Discovery of CHI3L1 Inhibitors from Ultralarge Chemical Spaces for Glioblastoma Therapy

Glioblastoma (GBM) is the most aggressive primary brain tumor, with a median survival of approximately one year and limited therapeutic options. Chitinase 3-like 1 (CHI3L1) is increasingly recognized as a promising target in GBM due to its role in tumor progression and immune modulation. In this study, we employed an in-house structure-based screening strategy (SpaceDock) to explore a virtual chemical space of 377 billion compounds for potential CHI3L1 inhibitors. Using a reaction-aware ligand design approach, 60 top-scoring virtual hits were synthesized, and 45 were obtained with sufficient purity for experimental testing. Primary screening by microscale thermophoresis (MST) identified nine hits. Compounds showing dose-dependent binding were subsequently analyzed using surface plasmon resonance (SPR), leading to the identification of compound 9e with a dissociation constant (Kd) of 19.11 {micro}M. Importantly, 9e demonstrated robust, dose-dependent efficacy in a multicellular 3D GBM spheroid model, significantly reducing spheroid viability and downstream STAT3 signaling. These results highlight 9e as a promising drug candidate for modulating the CHI3L1-STAT3 axis and underscore the potential of structure-guided, reactivity-aware virtual screening of ultralarge chemical spaces to target non-enzymatic, conformationally dynamic proteins in complex cancer models.

pharmacology and toxicology↗

bioRxiv2025

Virtual Screening-Guided Discovery of Small Molecule CHI3L1 Inhibitors with Functional Activity in Glioblastoma Spheroids

Chitinase-3-like protein 1 (CHI3L1), a glycoprotein implicated in inflammation, fibrosis, and cancer, has emerged as a potential therapeutic target for glioblastoma (GBM). CHI3L1 contributes to tumor progression and immune evasion by promoting STAT3 signaling and mesenchymal transition. To identify small molecule CHI3L1 inhibitors, a structure-based 3D pharmacophore model was developed and applied to virtually screen over 4.4 million compounds from the Enamine collection. Following multi-tiered filtering, 35 candidates were selected for experimental evaluation. Binding validation via microscale thermophoresis (MST) confirmed dose-dependent CHI3L1 interactions for two compounds, 8 and 39, with dissociation constants (Kd) of 6.8 {micro}M and 22 {micro}M, respectively. These affinities were further supported by surface plasmon resonance (SPR), which yielded Kd values of 5.69 {micro}M for compound 8 and 17.09 {micro}M for compound 39. In 3D GBM spheroid models, compound 8 significantly reduced spheroid viability and attenuated phospho-STAT3 levels, consistent with CHI3L1 pathway disruption. These findings identify two promising scaffolds and support the utility of pharmacophore-guided virtual screening for discovering functionally active ligands targeting CHI3L1 in GBM. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/667816v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@291464org.highwire.dtl.DTLVardef@f9d224org.highwire.dtl.DTLVardef@1535eeaorg.highwire.dtl.DTLVardef@7c596e_HPS_FORMAT_FIGEXP M_FIG Table of Contents artwork C_FIG

pharmacology and toxicology↗

bioRxiv2025

CHI3L1-Targeted Small Molecules as Glioblastoma Therapies: Virtual Screening-Based Discovery, Biophysical Validation, Pharmacokinetic Profiling, and Evaluation in Glioblastoma Spheroids

Glioblastoma (GBM) remains the most aggressive primary brain malignancy with a 10% three- year survival rate. Chitinase-3-like protein 1 (CHI3L1) has emerged as a critical factor in the progression of GBM progression, invasion, and treatment resistance. However, small molecule inhibitors targeting CHI3L1 are largely unexplored. Microscale thermophoresis (MST) investigation of the direct binding potential of reported CHI3L1 modulators (K284, G721-0282, CHI3L1-IN-1) revealed modest to undetectable direct CHI3L1 binding affinity. Herein, pharmacophore-based virtual screening of in-house library resulted in the discovery of G28 as the most potent small molecule CHI3L1 binder reported to date. The CHI3L1 binding affinity of G28 was validated using MST and surface plasmon resonance (SPR). To evaluate the GBM-modulatory potential of G28, we conducted comprehensive pharmacokinetic and 3D spheroid studies alongside established CHI3L1 modulators. G28 demonstrated outstanding bioavailability and low toxicity, addressing key limitations faced by previous CHI3L1-targeted strategies. Notably, in 3D GBM spheroid models, G28 significantly outperformed reported CHI3L1 small molecule modulators, showing the most pronounced dose-dependent reductions in spheroid weight, migration, and viability. These findings position G28 as the most promising CHI3L1-targeted small molecule to date and a compelling candidate for GBM therapeutic development.

pharmacology and toxicology↗

bioRxiv2024

Synovial fluid transcriptome dynamics in osteoarthritis progression: Implications in pathogenesis

BackgroundOsteoarthritis, a degenerative joint disease associated with various pathological manifestations in the joint including cartilage loss, alterations in subchondral bone and synovial inflammation. ObjectiveThis study aimed to elucidate the transcriptional and molecular changes in synovial fluid associated with OA progression, focusing on differential gene expression and pathway enrichment across OA grades. MethodologyPatients with different OA grades were recruited from PGIMER, Chandigarh, following the KL classification. Microarray analysis was conducted to study the transcriptional profiles in different OA grades using a fold-change (FC) cutoff of 2 and a p-value cutoff of 0.05, followed by pathway analysis performed using GSEA and STRING database. Selected genes from microarray and pathway analysis were validated using qRT-PCR. ResultsMicroarray analysis reveals distinct gene expression patterns corresponding to different OA stages (KL grade 2 to KL grade 4). Notably, the upregulation of AMTN and DKK2, alongside the downregulation of MSLN, highlighted their roles in pathological mineralization and disrupted bone remodeling in OA. Pathway enrichment analysis revealed significant changes in immune response, inflammation related pathways and cellular processes such as autophagy and programmed cell death, indicating their involvement in disease progression. Furthermore, mitochondrial dysfunction and impaired autophagy were linked to increased inflammation in advanced OA. ConclusionThese findings suggest that targeting mineralization and inflammatory pathways could offer novel therapeutic avenues for OA management.

pathology↗